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Andrs Lpez)] TJ ET 0.271 0.267 0.267 rg BT 457.901 692.083 Td /F1 8.7 Tf [(5)] TJ ET BT 462.720 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 468.141 688.195 Td /F1 9.8 Tf [(Chenhong Li)] TJ ET 0.271 0.267 0.267 rg BT 523.423 692.083 Td /F1 8.7 Tf [(6)] TJ ET BT 528.242 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 533.663 688.195 Td /F1 9.8 Tf [(Nancy I. )] TJ ET BT 26.250 676.290 Td /F1 9.8 Tf [(Holcroft)] TJ ET 0.271 0.267 0.267 rg BT 59.839 680.179 Td /F1 8.7 Tf [(7)] TJ ET BT 64.657 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 70.078 676.290 Td /F1 9.8 Tf [(Dahiana Arcila)] TJ ET 0.271 0.267 0.267 rg BT 133.473 680.179 Td /F1 8.7 Tf [(1)] TJ ET BT 138.292 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 143.713 676.290 Td /F1 9.8 Tf [(Millicent Sanciangco)] TJ ET 0.271 0.267 0.267 rg BT 232.574 680.179 Td /F1 8.7 Tf [(4)] TJ ET BT 237.393 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 242.814 676.290 Td /F1 9.8 Tf [(James C Cureton II)] TJ ET 0.271 0.267 0.267 rg BT 326.800 680.179 Td /F1 8.7 Tf [(2)] TJ ET BT 331.619 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 337.040 676.290 Td /F1 9.8 Tf [(Feifei Zhang)] TJ ET 0.271 0.267 0.267 rg BT 391.230 680.179 Td /F1 8.7 Tf [(2)] TJ ET BT 396.049 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 401.470 676.290 Td /F1 9.8 Tf [(Thaddaeus Buser)] TJ ET 0.271 0.267 0.267 rg BT 478.427 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 483.848 676.290 Td /F1 9.8 Tf [(Matthew A. Campbell)] TJ ET 0.271 0.267 0.267 rg BT 26.250 668.274 Td /F1 8.7 Tf [(5)] TJ ET BT 31.069 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 36.490 664.386 Td /F1 9.8 Tf [(Jesus A Ballesteros)] TJ ET 0.271 0.267 0.267 rg BT 122.104 668.274 Td /F1 8.7 Tf [(1)] TJ ET BT 126.923 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 132.344 664.386 Td /F1 9.8 Tf [(Adela Roa-Varon)] TJ ET 0.271 0.267 0.267 rg BT 207.127 668.274 Td /F1 8.7 Tf [(8)] TJ ET BT 211.945 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 217.366 664.386 Td /F1 9.8 Tf [(Stuart Willis)] TJ ET 0.271 0.267 0.267 rg BT 268.827 668.274 Td /F1 8.7 Tf [(9)] TJ ET BT 273.645 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 279.066 664.386 Td /F1 9.8 Tf [(W. Calvin Borden)] TJ ET 0.271 0.267 0.267 rg BT 354.921 668.274 Td /F1 8.7 Tf [(10)] TJ ET BT 364.559 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 369.980 664.386 Td /F1 9.8 Tf [(Thaine Rowley)] TJ ET 0.271 0.267 0.267 rg BT 434.457 668.274 Td /F1 8.7 Tf [(11)] TJ ET BT 444.094 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 449.515 664.386 Td /F1 9.8 Tf [(Paulette C. Reneau)] TJ ET 0.271 0.267 0.267 rg BT 534.603 668.274 Td /F1 8.7 Tf [(12)] TJ ET BT 544.240 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 549.661 664.386 Td /F1 9.8 Tf [(Daniel )] TJ ET BT 26.250 652.481 Td /F1 9.8 Tf [(J. Hough)] TJ ET 0.271 0.267 0.267 rg BT 65.269 656.369 Td /F1 8.7 Tf [(2)] TJ ET BT 70.088 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 75.509 652.481 Td /F1 9.8 Tf [(Guoqing Lu)] TJ ET 0.271 0.267 0.267 rg BT 125.917 656.369 Td /F1 8.7 Tf [(13)] TJ ET BT 135.554 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 140.975 652.481 Td /F1 9.8 Tf [(Terry Grande)] TJ ET 0.271 0.267 0.267 rg BT 198.949 656.369 Td /F1 8.7 Tf [(10)] TJ ET BT 208.586 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 214.007 652.481 Td /F1 9.8 Tf [(Gloria Arratia)] TJ ET 0.271 0.267 0.267 rg BT 271.434 656.369 Td /F1 8.7 Tf [(3)] TJ ET BT 276.253 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 281.674 652.481 Td /F1 9.8 Tf [(Guillermo Ort)] TJ ET 0.271 0.267 0.267 rg BT 342.348 656.369 Td /F1 8.7 Tf [(1)] TJ ET BT 26.250 641.309 Td /F4 9.0 Tf [(1)] TJ ET BT 31.254 641.309 Td /F1 9.0 Tf [( The George Washington University, )] TJ ET BT 178.809 641.309 Td /F4 9.0 Tf [(2)] TJ ET BT 183.813 641.309 Td /F1 9.0 Tf [( University of Oklahoma, )] TJ ET BT 284.343 641.309 Td /F4 9.0 Tf [(3)] TJ ET BT 289.347 641.309 Td /F1 9.0 Tf [( University of Kansas, )] TJ ET BT 378.879 641.309 Td /F4 9.0 Tf [(4)] TJ ET BT 383.883 641.309 Td /F1 9.0 Tf [( Old Dominion University, )] TJ ET BT 487.905 641.309 Td /F4 9.0 Tf [(5)] TJ ET BT 492.909 641.309 Td /F1 9.0 Tf [( University of Alaska )] TJ ET BT 26.250 630.320 Td /F1 9.0 Tf [(Fairbanks, )] TJ ET BT 70.764 630.320 Td /F4 9.0 Tf [(6)] TJ ET BT 75.768 630.320 Td /F1 9.0 Tf [( Shanghai Ocean University, )] TJ ET BT 192.318 630.320 Td /F4 9.0 Tf [(7)] TJ ET BT 197.322 630.320 Td /F1 9.0 Tf [( Johnson County Community College, )] TJ ET BT 350.880 630.320 Td /F4 9.0 Tf [(8)] TJ ET BT 355.884 630.320 Td /F1 9.0 Tf [( George Washington University, )] TJ ET BT 485.430 630.320 Td /F4 9.0 Tf [(9)] TJ ET BT 490.434 630.320 Td /F1 9.0 Tf [( University of )] TJ ET BT 26.250 619.331 Td /F1 9.0 Tf [(Nebraska-Lincoln, )] TJ ET BT 101.274 619.331 Td /F4 9.0 Tf [(10)] TJ ET BT 111.282 619.331 Td /F1 9.0 Tf [( Loyola University Chicago, )] TJ ET BT 222.819 619.331 Td /F4 9.0 Tf [(11)] TJ ET BT 232.827 619.331 Td /F1 9.0 Tf [( University of Nebraska-Omaha, )] TJ ET BT 363.363 619.331 Td /F4 9.0 Tf [(12)] TJ ET BT 373.371 619.331 Td /F1 9.0 Tf [( Florida A&M University, )] TJ ET BT 472.389 619.331 Td /F4 9.0 Tf [(13)] TJ ET BT 482.397 619.331 Td /F1 9.0 Tf [( University of Nebraska )] TJ ET BT 26.250 608.342 Td /F1 9.0 Tf [(at Omaha)] TJ ET BT 26.250 596.620 Td /F1 9.8 Tf [(Betancur-R. R, Broughton RE, Wiley EO, Carpenter K, Lpez JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton II JC, )] TJ ET BT 26.250 584.715 Td /F1 9.8 Tf [(Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, )] TJ ET BT 26.250 572.811 Td /F1 9.8 Tf [(Grande T, Arratia G, Ort G. The Tree of Life and a New Classification of Bony Fishes. PLOS Currents Tree of Life. 2013 Apr 18 )] TJ ET BT 26.250 560.906 Td /F1 9.8 Tf [(. Edition 1. doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288.)] TJ ET q 15.000 22.409 577.500 536.116 re W n 0.271 0.267 0.267 rg BT 26.250 531.803 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 511.849 Td /F1 9.8 Tf [(The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The )] TJ ET BT 26.250 499.944 Td /F1 9.8 Tf [(situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain )] TJ ET BT 26.250 488.040 Td /F1 9.8 Tf [(relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among )] TJ ET BT 26.250 476.135 Td /F1 9.8 Tf [(fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic )] TJ ET BT 26.250 464.230 Td /F1 9.8 Tf [(concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. )] TJ ET BT 26.250 452.325 Td /F1 9.8 Tf [(DNA sequence data for 21 molecular markers \(one mitochondrial and 20 nuclear genes\) were collected for 1410 bony fish taxa, )] TJ ET BT 26.250 440.421 Td /F1 9.8 Tf [(plus four tetrapod species and two chondrichthyan outgroups \(total 1416 terminals\). Bony fish diversity is represented by 1093 )] TJ ET BT 26.250 428.516 Td /F1 9.8 Tf [(genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution )] TJ ET BT 26.250 416.611 Td /F1 9.8 Tf [(and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general )] TJ ET BT 26.250 404.706 Td /F1 9.8 Tf [(structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new )] TJ ET BT 26.250 392.802 Td /F1 9.8 Tf [(clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported )] TJ ET BT 26.250 380.897 Td /F1 9.8 Tf [(supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first )] TJ ET BT 26.250 368.992 Td /F1 9.8 Tf [(time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed )] TJ ET BT 26.250 357.087 Td /F1 9.8 Tf [(to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is )] TJ ET BT 26.250 345.183 Td /F1 9.8 Tf [(calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the )] TJ ET BT 26.250 333.278 Td /F1 9.8 Tf [(basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.)] TJ ET BT 26.250 296.675 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 276.721 Td /F1 9.8 Tf [(This work was supported by NSF awards DEB-0732988 \(to REB\), DEB-0732838, DEB-1019308 \(to GO and CL\), DEB-)] TJ ET BT 538.866 276.721 Td /F1 9.8 Tf [(0732819 )] TJ ET BT 26.250 264.816 Td /F1 9.8 Tf [(\(EOW\), DEB 0732589 \(TG\), DEB-0732894 \(KC\), DEB 0963767 \(JAL\), and DEB-0732969 \(GL\); GWU Selective Excellence in )] TJ ET BT 26.250 252.912 Td /F1 9.8 Tf [(Diversity of Life program \(to RBR\); Leading Academic Discipline Project of Shanghai Municipal Education Commission, project )] TJ ET BT 26.250 241.007 Td /F1 9.8 Tf [(number S30701 \(CL\). The Biodiversity Institute, University of Kansas, provided financial support for the collection used in this )] TJ ET BT 26.250 229.102 Td /F1 9.8 Tf [(study.)] TJ ET BT 26.250 200.000 Td /F4 12.0 Tf [(Introduction)] TJ ET 0.965 0.965 0.965 rg 26.250 105.742 555.000 83.827 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 189.569 m 581.250 189.569 l 581.250 188.819 l 26.250 188.819 l f 26.250 105.742 m 581.250 105.742 l 581.250 106.492 l 26.250 106.492 l f 0.271 0.267 0.267 rg BT 35.250 169.840 Td /F3 10.5 Tf [(With the variety of both primitive and advanced teleosts living today, we are most emphatically of the opinion that )] TJ ET BT 35.250 157.366 Td /F3 10.5 Tf [(approaches other than morphological ones would be exceedingly fruitful in the investigation of teleostean )] TJ ET BT 35.250 144.892 Td /F3 10.5 Tf [(interrelationships)] TJ ET BT 35.250 117.873 Td /F1 9.8 Tf [()] TJ ET BT 45.000 117.873 Td /F1 9.8 Tf [( Greenwood et al. \(1966\))] TJ ET BT 152.845 121.762 Td /F1 8.7 Tf [(1)] TJ ET BT 26.250 96.219 Td /F1 9.8 Tf [(Our view of the phylogeny and classification of bony fishes is rapidly changing under the influence of molecular phylogenetic )] TJ ET BT 26.250 84.314 Td /F1 9.8 Tf [(studies based on larger and more taxonomically comprehensive datasets. Classification schemes displayed in widely used text )] TJ ET BT 26.250 72.409 Td /F1 9.8 Tf [(books on fish biodiversity \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 160.098 73.916 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 164.917 76.297 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 167.326 73.916 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 172.145 72.409 Td /F1 9.8 Tf [(\) have been based on loosely formulated syntheses \(supertrees\) and community consensus )] TJ ET BT 26.250 60.504 Td /F1 9.8 Tf [(views of largely disconnected studies. The phylogenetic structure underpinning such classifications has many areas that are )] TJ ET BT 26.250 48.600 Td /F1 9.8 Tf [(notably unresolved and poorly known, providing weak or no justification for many groups that, although formally recognized, are )] TJ ET BT 26.250 36.695 Td /F1 9.8 Tf [(implicitly known to be polyphyletic \(e.g. percoids, perciforms, scorpaeniforms\). A comprehensive phylogenetic tree for all major )] TJ ET Q q 15.000 709.302 577.500 28.698 re W n 0.267 0.267 0.267 rg BT 15.000 718.042 Td /F2 21.0 Tf [(The Tree of Life and a New Classification of Bony Fishes)] TJ ET Q 0.271 0.267 0.267 rg BT 15.000 700.036 Td /F3 9.8 Tf [(April 18, 2013)] TJ ET BT 76.483 700.036 Td /F3 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 81.358 700.036 Td /F3 9.8 Tf [(Tree of Life)] TJ ET BT 26.250 688.195 Td /F1 9.8 Tf [(Ricardo Betancur-R.)] TJ ET 0.271 0.267 0.267 rg BT 114.566 692.083 Td /F1 8.7 Tf [(1)] TJ ET BT 119.384 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 124.805 688.195 Td /F1 9.8 Tf [(Richard E. Broughton)] TJ ET 0.271 0.267 0.267 rg BT 218.015 692.083 Td /F1 8.7 Tf [(2)] TJ ET BT 222.834 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 228.255 688.195 Td /F1 9.8 Tf [(Edward O. Wiley)] TJ ET 0.271 0.267 0.267 rg BT 300.853 692.083 Td /F1 8.7 Tf [(3)] TJ ET BT 305.672 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 311.093 688.195 Td /F1 9.8 Tf [(Kent Carpenter)] TJ ET 0.271 0.267 0.267 rg BT 377.208 692.083 Td /F1 8.7 Tf [(4)] TJ ET BT 382.026 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 387.447 688.195 Td /F1 9.8 Tf [(J. Andrs Lpez)] TJ ET 0.271 0.267 0.267 rg BT 457.901 692.083 Td /F1 8.7 Tf [(5)] TJ ET BT 462.720 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 468.141 688.195 Td /F1 9.8 Tf [(Chenhong Li)] TJ ET 0.271 0.267 0.267 rg BT 523.423 692.083 Td /F1 8.7 Tf [(6)] TJ ET BT 528.242 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 533.663 688.195 Td /F1 9.8 Tf [(Nancy I. )] TJ ET BT 26.250 676.290 Td /F1 9.8 Tf [(Holcroft)] TJ ET 0.271 0.267 0.267 rg BT 59.839 680.179 Td /F1 8.7 Tf [(7)] TJ ET BT 64.657 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 70.078 676.290 Td /F1 9.8 Tf [(Dahiana Arcila)] TJ ET 0.271 0.267 0.267 rg BT 133.473 680.179 Td /F1 8.7 Tf [(1)] TJ ET BT 138.292 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 143.713 676.290 Td /F1 9.8 Tf [(Millicent Sanciangco)] TJ ET 0.271 0.267 0.267 rg BT 232.574 680.179 Td /F1 8.7 Tf [(4)] TJ ET BT 237.393 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 242.814 676.290 Td /F1 9.8 Tf [(James C Cureton II)] TJ ET 0.271 0.267 0.267 rg BT 326.800 680.179 Td /F1 8.7 Tf [(2)] TJ ET BT 331.619 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 337.040 676.290 Td /F1 9.8 Tf [(Feifei Zhang)] TJ ET 0.271 0.267 0.267 rg BT 391.230 680.179 Td /F1 8.7 Tf [(2)] TJ ET BT 396.049 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 401.470 676.290 Td /F1 9.8 Tf [(Thaddaeus Buser)] TJ ET 0.271 0.267 0.267 rg BT 478.427 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 483.848 676.290 Td /F1 9.8 Tf [(Matthew A. Campbell)] TJ ET 0.271 0.267 0.267 rg BT 26.250 668.274 Td /F1 8.7 Tf [(5)] TJ ET BT 31.069 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 36.490 664.386 Td /F1 9.8 Tf [(Jesus A Ballesteros)] TJ ET 0.271 0.267 0.267 rg BT 122.104 668.274 Td /F1 8.7 Tf [(1)] TJ ET BT 126.923 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 132.344 664.386 Td /F1 9.8 Tf [(Adela Roa-Varon)] TJ ET 0.271 0.267 0.267 rg BT 207.127 668.274 Td /F1 8.7 Tf [(8)] TJ ET BT 211.945 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 217.366 664.386 Td /F1 9.8 Tf [(Stuart Willis)] TJ ET 0.271 0.267 0.267 rg BT 268.827 668.274 Td /F1 8.7 Tf [(9)] TJ ET BT 273.645 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 279.066 664.386 Td /F1 9.8 Tf [(W. Calvin Borden)] TJ ET 0.271 0.267 0.267 rg BT 354.921 668.274 Td /F1 8.7 Tf [(10)] TJ ET BT 364.559 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 369.980 664.386 Td /F1 9.8 Tf [(Thaine Rowley)] TJ ET 0.271 0.267 0.267 rg BT 434.457 668.274 Td /F1 8.7 Tf [(11)] TJ ET BT 444.094 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 449.515 664.386 Td /F1 9.8 Tf [(Paulette C. Reneau)] TJ ET 0.271 0.267 0.267 rg BT 534.603 668.274 Td /F1 8.7 Tf [(12)] TJ ET BT 544.240 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 549.661 664.386 Td /F1 9.8 Tf [(Daniel )] TJ ET BT 26.250 652.481 Td /F1 9.8 Tf [(J. Hough)] TJ ET 0.271 0.267 0.267 rg BT 65.269 656.369 Td /F1 8.7 Tf [(2)] TJ ET BT 70.088 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 75.509 652.481 Td /F1 9.8 Tf [(Guoqing Lu)] TJ ET 0.271 0.267 0.267 rg BT 125.917 656.369 Td /F1 8.7 Tf [(13)] TJ ET BT 135.554 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 140.975 652.481 Td /F1 9.8 Tf [(Terry Grande)] TJ ET 0.271 0.267 0.267 rg BT 198.949 656.369 Td /F1 8.7 Tf [(10)] TJ ET BT 208.586 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 214.007 652.481 Td /F1 9.8 Tf [(Gloria Arratia)] TJ ET 0.271 0.267 0.267 rg BT 271.434 656.369 Td /F1 8.7 Tf [(3)] TJ ET BT 276.253 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 281.674 652.481 Td /F1 9.8 Tf [(Guillermo Ort)] TJ ET 0.271 0.267 0.267 rg BT 342.348 656.369 Td /F1 8.7 Tf [(1)] TJ ET BT 26.250 641.309 Td /F4 9.0 Tf [(1)] TJ ET BT 31.254 641.309 Td /F1 9.0 Tf [( The George Washington University, )] TJ ET BT 178.809 641.309 Td /F4 9.0 Tf [(2)] TJ ET BT 183.813 641.309 Td /F1 9.0 Tf [( University of Oklahoma, )] TJ ET BT 284.343 641.309 Td /F4 9.0 Tf [(3)] TJ ET BT 289.347 641.309 Td /F1 9.0 Tf [( University of Kansas, )] TJ ET BT 378.879 641.309 Td /F4 9.0 Tf [(4)] TJ ET BT 383.883 641.309 Td /F1 9.0 Tf [( Old Dominion University, )] TJ ET BT 487.905 641.309 Td /F4 9.0 Tf [(5)] TJ ET BT 492.909 641.309 Td /F1 9.0 Tf [( University of Alaska )] TJ ET BT 26.250 630.320 Td /F1 9.0 Tf [(Fairbanks, )] TJ ET BT 70.764 630.320 Td /F4 9.0 Tf [(6)] TJ ET BT 75.768 630.320 Td /F1 9.0 Tf [( Shanghai Ocean University, )] TJ ET BT 192.318 630.320 Td /F4 9.0 Tf [(7)] TJ ET BT 197.322 630.320 Td /F1 9.0 Tf [( Johnson County Community College, )] TJ ET BT 350.880 630.320 Td /F4 9.0 Tf [(8)] TJ ET BT 355.884 630.320 Td /F1 9.0 Tf [( George Washington University, )] TJ ET BT 485.430 630.320 Td /F4 9.0 Tf [(9)] TJ ET BT 490.434 630.320 Td /F1 9.0 Tf [( University of )] TJ ET BT 26.250 619.331 Td /F1 9.0 Tf [(Nebraska-Lincoln, )] TJ ET BT 101.274 619.331 Td /F4 9.0 Tf [(10)] TJ ET BT 111.282 619.331 Td /F1 9.0 Tf [( Loyola University Chicago, )] TJ ET BT 222.819 619.331 Td /F4 9.0 Tf [(11)] TJ ET BT 232.827 619.331 Td /F1 9.0 Tf [( University of Nebraska-Omaha, )] TJ ET BT 363.363 619.331 Td /F4 9.0 Tf [(12)] TJ ET BT 373.371 619.331 Td /F1 9.0 Tf [( Florida A&M University, )] TJ ET BT 472.389 619.331 Td /F4 9.0 Tf [(13)] TJ ET BT 482.397 619.331 Td /F1 9.0 Tf [( University of Nebraska )] TJ ET BT 26.250 608.342 Td /F1 9.0 Tf [(at Omaha)] TJ ET BT 26.250 596.620 Td /F1 9.8 Tf [(Betancur-R. R, Broughton RE, Wiley EO, Carpenter K, Lpez JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton II JC, )] TJ ET BT 26.250 584.715 Td /F1 9.8 Tf [(Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, )] TJ ET BT 26.250 572.811 Td /F1 9.8 Tf [(Grande T, Arratia G, Ort G. The Tree of Life and a New Classification of Bony Fishes. PLOS Currents Tree of Life. 2013 Apr 18 )] TJ ET BT 26.250 560.906 Td /F1 9.8 Tf [(. Edition 1. doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288.)] TJ ET q 15.000 22.409 577.500 536.116 re W n 0.271 0.267 0.267 rg BT 26.250 531.803 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 511.849 Td /F1 9.8 Tf [(The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The )] TJ ET BT 26.250 499.944 Td /F1 9.8 Tf [(situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain )] TJ ET BT 26.250 488.040 Td /F1 9.8 Tf [(relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among )] TJ ET BT 26.250 476.135 Td /F1 9.8 Tf [(fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic )] TJ ET BT 26.250 464.230 Td /F1 9.8 Tf [(concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. )] TJ ET BT 26.250 452.325 Td /F1 9.8 Tf [(DNA sequence data for 21 molecular markers \(one mitochondrial and 20 nuclear genes\) were collected for 1410 bony fish taxa, )] TJ ET BT 26.250 440.421 Td /F1 9.8 Tf [(plus four tetrapod species and two chondrichthyan outgroups \(total 1416 terminals\). Bony fish diversity is represented by 1093 )] TJ ET BT 26.250 428.516 Td /F1 9.8 Tf [(genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution )] TJ ET BT 26.250 416.611 Td /F1 9.8 Tf [(and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general )] TJ ET BT 26.250 404.706 Td /F1 9.8 Tf [(structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new )] TJ ET BT 26.250 392.802 Td /F1 9.8 Tf [(clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported )] TJ ET BT 26.250 380.897 Td /F1 9.8 Tf [(supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first )] TJ ET BT 26.250 368.992 Td /F1 9.8 Tf [(time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed )] TJ ET BT 26.250 357.087 Td /F1 9.8 Tf [(to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is )] TJ ET BT 26.250 345.183 Td /F1 9.8 Tf [(calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the )] TJ ET BT 26.250 333.278 Td /F1 9.8 Tf [(basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.)] TJ ET BT 26.250 296.675 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 276.721 Td /F1 9.8 Tf [(This work was supported by NSF awards DEB-0732988 \(to REB\), DEB-0732838, DEB-1019308 \(to GO and CL\), DEB-)] TJ ET BT 538.866 276.721 Td /F1 9.8 Tf [(0732819 )] TJ ET BT 26.250 264.816 Td /F1 9.8 Tf [(\(EOW\), DEB 0732589 \(TG\), DEB-0732894 \(KC\), DEB 0963767 \(JAL\), and DEB-0732969 \(GL\); GWU Selective Excellence in )] TJ ET BT 26.250 252.912 Td /F1 9.8 Tf [(Diversity of Life program \(to RBR\); Leading Academic Discipline Project of Shanghai Municipal Education Commission, project )] TJ ET BT 26.250 241.007 Td /F1 9.8 Tf [(number S30701 \(CL\). The Biodiversity Institute, University of Kansas, provided financial support for the collection used in this )] TJ ET BT 26.250 229.102 Td /F1 9.8 Tf [(study.)] TJ ET BT 26.250 200.000 Td /F4 12.0 Tf [(Introduction)] TJ ET 0.965 0.965 0.965 rg 26.250 105.742 555.000 83.827 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 189.569 m 581.250 189.569 l 581.250 188.819 l 26.250 188.819 l f 26.250 105.742 m 581.250 105.742 l 581.250 106.492 l 26.250 106.492 l f 0.271 0.267 0.267 rg BT 35.250 169.840 Td /F3 10.5 Tf [(With the variety of both primitive and advanced teleosts living today, we are most emphatically of the opinion that )] TJ ET BT 35.250 157.366 Td /F3 10.5 Tf [(approaches other than morphological ones would be exceedingly fruitful in the investigation of teleostean )] TJ ET BT 35.250 144.892 Td /F3 10.5 Tf [(interrelationships)] TJ ET BT 35.250 117.873 Td /F1 9.8 Tf [()] TJ ET BT 45.000 117.873 Td /F1 9.8 Tf [( Greenwood et al. \(1966\))] TJ ET BT 152.845 121.762 Td /F1 8.7 Tf [(1)] TJ ET BT 26.250 96.219 Td /F1 9.8 Tf [(Our view of the phylogeny and classification of bony fishes is rapidly changing under the influence of molecular phylogenetic )] TJ ET BT 26.250 84.314 Td /F1 9.8 Tf [(studies based on larger and more taxonomically comprehensive datasets. Classification schemes displayed in widely used text )] TJ ET BT 26.250 72.409 Td /F1 9.8 Tf [(books on fish biodiversity \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 160.098 73.916 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 164.917 76.297 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 167.326 73.916 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 172.145 72.409 Td /F1 9.8 Tf [(\) have been based on loosely formulated syntheses \(supertrees\) and community consensus )] TJ ET BT 26.250 60.504 Td /F1 9.8 Tf [(views of largely disconnected studies. The phylogenetic structure underpinning such classifications has many areas that are )] TJ ET BT 26.250 48.600 Td /F1 9.8 Tf [(notably unresolved and poorly known, providing weak or no justification for many groups that, although formally recognized, are )] TJ ET BT 26.250 36.695 Td /F1 9.8 Tf [(implicitly known to be polyphyletic \(e.g. percoids, perciforms, scorpaeniforms\). A comprehensive phylogenetic tree for all major )] TJ ET Q q 15.000 709.302 577.500 28.698 re W n 0.267 0.267 0.267 rg BT 15.000 718.042 Td /F2 21.0 Tf [(The Tree of Life and a New Classification of Bony Fishes)] TJ ET Q 0.271 0.267 0.267 rg BT 15.000 700.036 Td /F3 9.8 Tf [(April 18, 2013)] TJ ET BT 76.483 700.036 Td /F3 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 81.358 700.036 Td /F3 9.8 Tf [(Tree of Life)] TJ ET BT 26.250 688.195 Td /F1 9.8 Tf [(Ricardo Betancur-R.)] TJ ET 0.271 0.267 0.267 rg BT 114.566 692.083 Td /F1 8.7 Tf [(1)] TJ ET BT 119.384 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 124.805 688.195 Td /F1 9.8 Tf [(Richard E. Broughton)] TJ ET 0.271 0.267 0.267 rg BT 218.015 692.083 Td /F1 8.7 Tf [(2)] TJ ET BT 222.834 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 228.255 688.195 Td /F1 9.8 Tf [(Edward O. Wiley)] TJ ET 0.271 0.267 0.267 rg BT 300.853 692.083 Td /F1 8.7 Tf [(3)] TJ ET BT 305.672 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 311.093 688.195 Td /F1 9.8 Tf [(Kent Carpenter)] TJ ET 0.271 0.267 0.267 rg BT 377.208 692.083 Td /F1 8.7 Tf [(4)] TJ ET BT 382.026 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 387.447 688.195 Td /F1 9.8 Tf [(J. Andrs Lpez)] TJ ET 0.271 0.267 0.267 rg BT 457.901 692.083 Td /F1 8.7 Tf [(5)] TJ ET BT 462.720 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 468.141 688.195 Td /F1 9.8 Tf [(Chenhong Li)] TJ ET 0.271 0.267 0.267 rg BT 523.423 692.083 Td /F1 8.7 Tf [(6)] TJ ET BT 528.242 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 533.663 688.195 Td /F1 9.8 Tf [(Nancy I. )] TJ ET BT 26.250 676.290 Td /F1 9.8 Tf [(Holcroft)] TJ ET 0.271 0.267 0.267 rg BT 59.839 680.179 Td /F1 8.7 Tf [(7)] TJ ET BT 64.657 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 70.078 676.290 Td /F1 9.8 Tf [(Dahiana Arcila)] TJ ET 0.271 0.267 0.267 rg BT 133.473 680.179 Td /F1 8.7 Tf [(1)] TJ ET BT 138.292 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 143.713 676.290 Td /F1 9.8 Tf [(Millicent Sanciangco)] TJ ET 0.271 0.267 0.267 rg BT 232.574 680.179 Td /F1 8.7 Tf [(4)] TJ ET BT 237.393 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 242.814 676.290 Td /F1 9.8 Tf [(James C Cureton II)] TJ ET 0.271 0.267 0.267 rg BT 326.800 680.179 Td /F1 8.7 Tf [(2)] TJ ET BT 331.619 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 337.040 676.290 Td /F1 9.8 Tf [(Feifei Zhang)] TJ ET 0.271 0.267 0.267 rg BT 391.230 680.179 Td /F1 8.7 Tf [(2)] TJ ET BT 396.049 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 401.470 676.290 Td /F1 9.8 Tf [(Thaddaeus Buser)] TJ ET 0.271 0.267 0.267 rg BT 478.427 676.290 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 483.848 676.290 Td /F1 9.8 Tf [(Matthew A. Campbell)] TJ ET 0.271 0.267 0.267 rg BT 26.250 668.274 Td /F1 8.7 Tf [(5)] TJ ET BT 31.069 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 36.490 664.386 Td /F1 9.8 Tf [(Jesus A Ballesteros)] TJ ET 0.271 0.267 0.267 rg BT 122.104 668.274 Td /F1 8.7 Tf [(1)] TJ ET BT 126.923 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 132.344 664.386 Td /F1 9.8 Tf [(Adela Roa-Varon)] TJ ET 0.271 0.267 0.267 rg BT 207.127 668.274 Td /F1 8.7 Tf [(8)] TJ ET BT 211.945 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 217.366 664.386 Td /F1 9.8 Tf [(Stuart Willis)] TJ ET 0.271 0.267 0.267 rg BT 268.827 668.274 Td /F1 8.7 Tf [(9)] TJ ET BT 273.645 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 279.066 664.386 Td /F1 9.8 Tf [(W. Calvin Borden)] TJ ET 0.271 0.267 0.267 rg BT 354.921 668.274 Td /F1 8.7 Tf [(10)] TJ ET BT 364.559 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 369.980 664.386 Td /F1 9.8 Tf [(Thaine Rowley)] TJ ET 0.271 0.267 0.267 rg BT 434.457 668.274 Td /F1 8.7 Tf [(11)] TJ ET BT 444.094 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 449.515 664.386 Td /F1 9.8 Tf [(Paulette C. Reneau)] TJ ET 0.271 0.267 0.267 rg BT 534.603 668.274 Td /F1 8.7 Tf [(12)] TJ ET BT 544.240 664.386 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 549.661 664.386 Td /F1 9.8 Tf [(Daniel )] TJ ET BT 26.250 652.481 Td /F1 9.8 Tf [(J. Hough)] TJ ET 0.271 0.267 0.267 rg BT 65.269 656.369 Td /F1 8.7 Tf [(2)] TJ ET BT 70.088 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 75.509 652.481 Td /F1 9.8 Tf [(Guoqing Lu)] TJ ET 0.271 0.267 0.267 rg BT 125.917 656.369 Td /F1 8.7 Tf [(13)] TJ ET BT 135.554 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 140.975 652.481 Td /F1 9.8 Tf [(Terry Grande)] TJ ET 0.271 0.267 0.267 rg BT 198.949 656.369 Td /F1 8.7 Tf [(10)] TJ ET BT 208.586 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 214.007 652.481 Td /F1 9.8 Tf [(Gloria Arratia)] TJ ET 0.271 0.267 0.267 rg BT 271.434 656.369 Td /F1 8.7 Tf [(3)] TJ ET BT 276.253 652.481 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 281.674 652.481 Td /F1 9.8 Tf [(Guillermo Ort)] TJ ET 0.271 0.267 0.267 rg BT 342.348 656.369 Td /F1 8.7 Tf [(1)] TJ ET BT 26.250 641.309 Td /F4 9.0 Tf [(1)] TJ ET BT 31.254 641.309 Td /F1 9.0 Tf [( The George Washington University, )] TJ ET BT 178.809 641.309 Td /F4 9.0 Tf [(2)] TJ ET BT 183.813 641.309 Td /F1 9.0 Tf [( University of Oklahoma, )] TJ ET BT 284.343 641.309 Td /F4 9.0 Tf [(3)] TJ ET BT 289.347 641.309 Td /F1 9.0 Tf [( University of Kansas, )] TJ ET BT 378.879 641.309 Td /F4 9.0 Tf [(4)] TJ ET BT 383.883 641.309 Td /F1 9.0 Tf [( Old Dominion University, )] TJ ET BT 487.905 641.309 Td /F4 9.0 Tf [(5)] TJ ET BT 492.909 641.309 Td /F1 9.0 Tf [( University of Alaska )] TJ ET BT 26.250 630.320 Td /F1 9.0 Tf [(Fairbanks, )] TJ ET BT 70.764 630.320 Td /F4 9.0 Tf [(6)] TJ ET BT 75.768 630.320 Td /F1 9.0 Tf [( Shanghai Ocean University, )] TJ ET BT 192.318 630.320 Td /F4 9.0 Tf [(7)] TJ ET BT 197.322 630.320 Td /F1 9.0 Tf [( Johnson County Community College, )] TJ ET BT 350.880 630.320 Td /F4 9.0 Tf [(8)] TJ ET BT 355.884 630.320 Td /F1 9.0 Tf [( George Washington University, )] TJ ET BT 485.430 630.320 Td /F4 9.0 Tf [(9)] TJ ET BT 490.434 630.320 Td /F1 9.0 Tf [( University of )] TJ ET BT 26.250 619.331 Td /F1 9.0 Tf [(Nebraska-Lincoln, )] TJ ET BT 101.274 619.331 Td /F4 9.0 Tf [(10)] TJ ET BT 111.282 619.331 Td /F1 9.0 Tf [( Loyola University Chicago, )] TJ ET BT 222.819 619.331 Td /F4 9.0 Tf [(11)] TJ ET BT 232.827 619.331 Td /F1 9.0 Tf [( University of Nebraska-Omaha, )] TJ ET BT 363.363 619.331 Td /F4 9.0 Tf [(12)] TJ ET BT 373.371 619.331 Td /F1 9.0 Tf [( Florida A&M University, )] TJ ET BT 472.389 619.331 Td /F4 9.0 Tf [(13)] TJ ET BT 482.397 619.331 Td /F1 9.0 Tf [( University of Nebraska )] TJ ET BT 26.250 608.342 Td /F1 9.0 Tf [(at Omaha)] TJ ET BT 26.250 596.620 Td /F1 9.8 Tf [(Betancur-R. R, Broughton RE, Wiley EO, Carpenter K, Lpez JA, Li C, Holcroft NI, Arcila D, Sanciangco M, Cureton II JC, )] TJ ET BT 26.250 584.715 Td /F1 9.8 Tf [(Zhang F, Buser T, Campbell MA, Ballesteros JA, Roa-Varon A, Willis S, Borden WC, Rowley T, Reneau PC, Hough DJ, Lu G, )] TJ ET BT 26.250 572.811 Td /F1 9.8 Tf [(Grande T, Arratia G, Ort G. The Tree of Life and a New Classification of Bony Fishes. PLOS Currents Tree of Life. 2013 Apr 18 )] TJ ET BT 26.250 560.906 Td /F1 9.8 Tf [(. Edition 1. doi: 10.1371/currents.tol.53ba26640df0ccaee75bb165c8c26288.)] TJ ET q 15.000 22.409 577.500 536.116 re W n 0.271 0.267 0.267 rg BT 26.250 531.803 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 511.849 Td /F1 9.8 Tf [(The tree of life of fishes is in a state of flux because we still lack a comprehensive phylogeny that includes all major groups. The )] TJ ET BT 26.250 499.944 Td /F1 9.8 Tf [(situation is most critical for a large clade of spiny-finned fishes, traditionally referred to as percomorphs, whose uncertain )] TJ ET BT 26.250 488.040 Td /F1 9.8 Tf [(relationships have plagued ichthyologists for over a century. Most of what we know about the higher-level relationships among )] TJ ET BT 26.250 476.135 Td /F1 9.8 Tf [(fish lineages has been based on morphology, but rapid influx of molecular studies is changing many established systematic )] TJ ET BT 26.250 464.230 Td /F1 9.8 Tf [(concepts. We report a comprehensive molecular phylogeny for bony fishes that includes representatives of all major lineages. )] TJ ET BT 26.250 452.325 Td /F1 9.8 Tf [(DNA sequence data for 21 molecular markers \(one mitochondrial and 20 nuclear genes\) were collected for 1410 bony fish taxa, )] TJ ET BT 26.250 440.421 Td /F1 9.8 Tf [(plus four tetrapod species and two chondrichthyan outgroups \(total 1416 terminals\). Bony fish diversity is represented by 1093 )] TJ ET BT 26.250 428.516 Td /F1 9.8 Tf [(genera, 369 families, and all traditionally recognized orders. The maximum likelihood tree provides unprecedented resolution )] TJ ET BT 26.250 416.611 Td /F1 9.8 Tf [(and high bootstrap support for most backbone nodes, defining for the first time a global phylogeny of fishes. The general )] TJ ET BT 26.250 404.706 Td /F1 9.8 Tf [(structure of the tree is in agreement with expectations from previous morphological and molecular studies, but significant new )] TJ ET BT 26.250 392.802 Td /F1 9.8 Tf [(clades arise. Most interestingly, the high degree of uncertainty among percomorphs is now resolved into nine well-supported )] TJ ET BT 26.250 380.897 Td /F1 9.8 Tf [(supraordinal groups. The order Perciformes, considered by many a polyphyletic taxonomic waste basket, is defined for the first )] TJ ET BT 26.250 368.992 Td /F1 9.8 Tf [(time as a monophyletic group in the global phylogeny. A new classification that reflects our phylogenetic hypothesis is proposed )] TJ ET BT 26.250 357.087 Td /F1 9.8 Tf [(to facilitate communication about the newly found structure of the tree of life of fishes. Finally, the molecular phylogeny is )] TJ ET BT 26.250 345.183 Td /F1 9.8 Tf [(calibrated using 60 fossil constraints to produce a comprehensive time tree. The new time-calibrated phylogeny will provide the )] TJ ET BT 26.250 333.278 Td /F1 9.8 Tf [(basis for and stimulate new comparative studies to better understand the evolution of the amazing diversity of fishes.)] TJ ET BT 26.250 296.675 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 276.721 Td /F1 9.8 Tf [(This work was supported by NSF awards DEB-0732988 \(to REB\), DEB-0732838, DEB-1019308 \(to GO and CL\), DEB-)] TJ ET BT 538.866 276.721 Td /F1 9.8 Tf [(0732819 )] TJ ET BT 26.250 264.816 Td /F1 9.8 Tf [(\(EOW\), DEB 0732589 \(TG\), DEB-0732894 \(KC\), DEB 0963767 \(JAL\), and DEB-0732969 \(GL\); GWU Selective Excellence in )] TJ ET BT 26.250 252.912 Td /F1 9.8 Tf [(Diversity of Life program \(to RBR\); Leading Academic Discipline Project of Shanghai Municipal Education Commission, project )] TJ ET BT 26.250 241.007 Td /F1 9.8 Tf [(number S30701 \(CL\). The Biodiversity Institute, University of Kansas, provided financial support for the collection used in this )] TJ ET BT 26.250 229.102 Td /F1 9.8 Tf [(study.)] TJ ET BT 26.250 200.000 Td /F4 12.0 Tf [(Introduction)] TJ ET 0.965 0.965 0.965 rg 26.250 105.742 555.000 83.827 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 189.569 m 581.250 189.569 l 581.250 188.819 l 26.250 188.819 l f 26.250 105.742 m 581.250 105.742 l 581.250 106.492 l 26.250 106.492 l f 0.271 0.267 0.267 rg BT 35.250 169.840 Td /F3 10.5 Tf [(With the variety of both primitive and advanced teleosts living today, we are most emphatically of the opinion that )] TJ ET BT 35.250 157.366 Td /F3 10.5 Tf [(approaches other than morphological ones would be exceedingly fruitful in the investigation of teleostean )] TJ ET BT 35.250 144.892 Td /F3 10.5 Tf [(interrelationships)] TJ ET BT 35.250 117.873 Td /F1 9.8 Tf [()] TJ ET BT 45.000 117.873 Td /F1 9.8 Tf [( Greenwood et al. \(1966\))] TJ ET BT 152.845 121.762 Td /F1 8.7 Tf [(1)] TJ ET BT 26.250 96.219 Td /F1 9.8 Tf [(Our view of the phylogeny and classification of bony fishes is rapidly changing under the influence of molecular phylogenetic )] TJ ET BT 26.250 84.314 Td /F1 9.8 Tf [(studies based on larger and more taxonomically comprehensive datasets. Classification schemes displayed in widely used text )] TJ ET BT 26.250 72.409 Td /F1 9.8 Tf [(books on fish biodiversity \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 160.098 73.916 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 164.917 76.297 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 167.326 73.916 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 172.145 72.409 Td /F1 9.8 Tf [(\) have been based on loosely formulated syntheses \(supertrees\) and community consensus )] TJ ET BT 26.250 60.504 Td /F1 9.8 Tf [(views of largely disconnected studies. The phylogenetic structure underpinning such classifications has many areas that are )] TJ ET BT 26.250 48.600 Td /F1 9.8 Tf [(notably unresolved and poorly known, providing weak or no justification for many groups that, although formally recognized, are )] TJ ET BT 26.250 36.695 Td /F1 9.8 Tf [(implicitly known to be polyphyletic \(e.g. percoids, perciforms, scorpaeniforms\). 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Detailed morphological cladistic investigations of fish relationships have typically focused on lower taxonomic )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(scales and few attempts to synthesize morphology at higher taxonomic levels proved to be challenging and met limited success )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(\(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 48.470 733.269 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 53.289 731.762 Td /F1 9.8 Tf [(\). A recent effort to systematically collect morphological synapomorphies from published records for all currently )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(recognized groups resulted in the first teleost classification based on monophyletic groups)] TJ ET 0.267 0.267 0.267 rg BT 413.715 721.364 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 418.534 719.857 Td /F1 9.8 Tf [(. This effort, however, did not )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(produce a global phylogenetic hypothesis. 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Studies based on mitogenomic data proliferated to methodically )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(probe conflicting hypotheses of relationship for several groups at diverse taxonomic levels, many times proposing alternative )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(arrangements supporting new clades unsuspected by previous classifications)] TJ ET 0.267 0.267 0.267 rg BT 359.515 630.531 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 369.152 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 371.561 630.531 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 381.199 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 383.608 630.531 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 393.245 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 395.655 630.531 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 405.292 629.024 Td /F1 9.8 Tf [(. In spite of their new powerful insights, )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(mitogenomic hypotheses were not universally embraced because they represent information from a single locus, prompting )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(corroboration from additional genomic regions. Several nuclear DNA markers were subsequently developed and applied to infer )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(bony fish relationships. The most popular ones include 28S ribosomal subunit)] TJ ET 0.267 0.267 0.267 rg BT 360.607 594.817 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 370.244 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 372.653 594.817 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 382.291 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 384.700 594.817 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 394.337 593.310 Td /F1 9.8 Tf [(, )] TJ ET BT 399.758 593.310 Td /F5 9.8 Tf [(tmo4c4 )] TJ ET 0.267 0.267 0.267 rg BT 434.439 594.817 Td /F4 8.7 Tf [(17)] TJ ET 0.271 0.267 0.267 rg BT 444.077 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 446.486 594.817 Td /F4 8.7 Tf [(18)] TJ ET 0.271 0.267 0.267 rg BT 456.123 593.310 Td /F1 9.8 Tf [(, rhodopsin)] TJ ET 0.267 0.267 0.267 rg BT 504.356 594.817 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 513.994 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 516.403 594.817 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 526.040 593.310 Td /F1 9.8 Tf [(, )] TJ ET BT 531.461 593.310 Td /F5 9.8 Tf [(rag1)] TJ ET BT 550.971 593.310 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 581.405 Td /F5 9.8 Tf [(rag2)] TJ ET 0.267 0.267 0.267 rg BT 45.760 582.912 Td /F4 8.7 Tf [(21)] TJ ET 0.271 0.267 0.267 rg BT 55.397 585.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 57.806 582.912 Td /F4 8.7 Tf [(22)] TJ ET 0.271 0.267 0.267 rg BT 67.444 581.405 Td /F5 9.8 Tf [(, mll)] TJ ET 0.267 0.267 0.267 rg BT 85.316 582.912 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 94.953 581.405 Td /F1 9.8 Tf [(, )] TJ ET BT 100.374 581.405 Td /F5 9.8 Tf [(irbp)] TJ ET 0.267 0.267 0.267 rg BT 116.627 582.912 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 126.264 581.405 Td /F1 9.8 Tf [(, and )] TJ ET BT 150.659 581.405 Td /F5 9.8 Tf [(rnf213)] TJ ET 0.267 0.267 0.267 rg BT 178.300 582.912 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 187.938 581.405 Td /F1 9.8 Tf [(. Using a systematic approach to scan genomic databases, a larger set of nuclear markers )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(became available in 2007 )] TJ ET 0.267 0.267 0.267 rg BT 139.516 571.007 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 149.153 569.500 Td /F1 9.8 Tf [(, opening a new window to obtaining large multilocus datasets)] TJ ET 0.267 0.267 0.267 rg BT 416.323 571.007 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 425.960 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 428.369 571.007 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 438.007 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 440.416 571.007 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 450.053 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 452.463 571.007 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 462.100 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 464.509 571.007 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 474.147 569.500 Td /F1 9.8 Tf [(. Recent studies using )] TJ ET BT 26.250 557.595 Td /F1 9.8 Tf [(between 10 and 20 of these nuclear markers for a few hundred taxa)] TJ ET 0.267 0.267 0.267 rg BT 318.906 559.103 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 328.543 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 330.953 559.103 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 340.590 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 342.999 559.103 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 352.637 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 355.046 559.103 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 364.683 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 367.093 559.103 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 376.730 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 379.139 559.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 388.777 557.595 Td /F1 9.8 Tf [(, have shown improved resolution of )] TJ ET BT 26.250 545.691 Td /F1 9.8 Tf [(phylogenetic relationship at higher and lower taxonomic levels. Many but not all of the mitogenomic hypotheses received )] TJ ET BT 26.250 533.786 Td /F1 9.8 Tf [(support from nuclear gene data, but the discovery of new clades continued with increasing taxonomic sampling. Initially )] TJ ET BT 26.250 521.881 Td /F1 9.8 Tf [(identified by letters \(e.g., clades A, B, C, etc.)] TJ ET 0.267 0.267 0.267 rg BT 218.091 523.388 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 227.728 525.769 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 230.138 523.388 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 239.775 525.769 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 242.184 523.388 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 251.822 521.881 Td /F1 9.8 Tf [(\), new names were recently proposed for many groupings supported by )] TJ ET BT 26.250 509.976 Td /F1 9.8 Tf [(molecular evidence, such as Stiassnyiformes, Zeiogadiformes, Carangimorpha, Cottimorpha, Ovalentaria, Gobiiformes etc.)] TJ ET 0.267 0.267 0.267 rg BT 556.182 511.484 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 565.819 513.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 568.229 511.484 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 577.866 513.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 26.250 499.579 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 35.887 498.072 Td /F1 9.8 Tf [(. Validation of these groups \(and their proposed names\) is pending until a comprehensive study including all taxa is produced. )] TJ ET BT 26.250 486.167 Td /F1 9.8 Tf [(Proliferation of new names is useful for identification of the newly discovered groups, but may create confusion if not )] TJ ET BT 26.250 474.262 Td /F1 9.8 Tf [(systematically organized into a global classification.)] TJ ET BT 26.250 454.857 Td /F1 9.8 Tf [(Molecular phylogenetic methods \(e.g., BEAST)] TJ ET 0.267 0.267 0.267 rg BT 225.667 456.365 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 235.304 454.857 Td /F1 9.8 Tf [(\) in combination with fossil evidence also opened a new temporal window to )] TJ ET BT 26.250 442.953 Td /F1 9.8 Tf [(understand bony fish diversification. Attempts to estimate divergence dates among crow-group lineages using this approach )] TJ ET BT 26.250 431.048 Td /F1 9.8 Tf [(\(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 51.181 432.555 Td /F4 8.7 Tf [(35)] TJ ET 0.271 0.267 0.267 rg BT 60.818 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 63.227 432.555 Td /F4 8.7 Tf [(36)] TJ ET 0.271 0.267 0.267 rg BT 72.865 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 75.274 432.555 Td /F4 8.7 Tf [(37)] TJ ET 0.271 0.267 0.267 rg BT 84.911 431.048 Td /F1 9.8 Tf [(\) frequently produced conflicting views with the paleontological literature)] TJ ET 0.267 0.267 0.267 rg BT 394.874 432.555 Td /F4 8.7 Tf [(38)] TJ ET 0.271 0.267 0.267 rg BT 404.511 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 406.920 432.555 Td /F4 8.7 Tf [(39)] TJ ET 0.271 0.267 0.267 rg BT 416.558 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 418.967 432.555 Td /F4 8.7 Tf [(40)] TJ ET 0.271 0.267 0.267 rg BT 428.604 431.048 Td /F1 9.8 Tf [(, sometimes implying large gaps in )] TJ ET BT 26.250 419.143 Td /F1 9.8 Tf [(the fossil record. The discrepancy is larger when divergence estimates for crown teleost lineages have been based on )] TJ ET BT 26.250 407.238 Td /F1 9.8 Tf [(mitogenomic data \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 128.128 408.746 Td /F4 8.7 Tf [(37)] TJ ET 0.271 0.267 0.267 rg BT 137.765 411.127 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 140.174 408.746 Td /F4 8.7 Tf [(41)] TJ ET 0.271 0.267 0.267 rg BT 149.812 411.127 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 152.221 408.746 Td /F4 8.7 Tf [(115)] TJ ET 0.271 0.267 0.267 rg BT 166.677 407.238 Td /F1 9.8 Tf [(\). Nucleotide saturation, compressing basal branch lengths for mtDNA, and the specific )] TJ ET BT 26.250 395.334 Td /F1 9.8 Tf [(approaches used to apply fossils constraints to calibrate the molecular phylogeny may explain this discordance)] TJ ET 0.267 0.267 0.267 rg BT 504.205 396.841 Td /F4 8.7 Tf [(43)] TJ ET 0.271 0.267 0.267 rg BT 513.842 395.334 Td /F1 9.8 Tf [(. Other studies )] TJ ET BT 26.250 383.429 Td /F1 9.8 Tf [(based on several nuclear genes and larger sets of fossil calibration points produced divergence dates more consistent with the )] TJ ET BT 26.250 371.524 Td /F1 9.8 Tf [(fossil record)] TJ ET 0.267 0.267 0.267 rg BT 78.803 373.031 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 88.440 375.412 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 90.849 373.031 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 100.487 371.524 Td /F1 9.8 Tf [(, but a comprehensive time-tree for osteichthyan diversification is not yet available.)] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(The shape of the bony fish tree of life is currently better resolved for the early-branching lineages than for the more apical )] TJ ET BT 26.250 340.215 Td /F1 9.8 Tf [(acanthomorph groups, in particular the percomorphs, a large and diverse group of spiny-finned fishes with uncertain affinities )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(that came to be known as )] TJ ET BT 140.062 328.310 Td /F4 9.8 Tf [()] TJ ET BT 144.937 328.310 Td /F1 9.8 Tf [(bush at the top)] TJ ET BT 209.443 328.310 Td /F4 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 214.318 329.817 Td /F4 8.7 Tf [(44)] TJ ET 0.271 0.267 0.267 rg BT 223.955 328.310 Td /F1 9.8 Tf [(. Few basal branching events among osteichthyans remain problematic, for )] TJ ET BT 26.250 316.405 Td /F1 9.8 Tf [(example, the relationships among lungfishes, coelacanths, and tetrapods)] TJ ET 0.267 0.267 0.267 rg BT 341.116 317.912 Td /F4 8.7 Tf [(45)] TJ ET 0.271 0.267 0.267 rg BT 350.754 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 353.163 317.912 Td /F4 8.7 Tf [(46)] TJ ET 0.271 0.267 0.267 rg BT 362.800 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 365.210 317.912 Td /F4 8.7 Tf [(47)] TJ ET 0.271 0.267 0.267 rg BT 374.847 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 377.257 317.912 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 386.894 316.405 Td /F1 9.8 Tf [(. In contrast, the basal branching pattern for )] TJ ET BT 26.250 304.500 Td /F1 9.8 Tf [(early extant actinopterygians \(involving polypteriforms, chondrosteans, lepisosteids, )] TJ ET BT 389.311 304.500 Td /F5 9.8 Tf [(Amia)] TJ ET BT 411.521 304.500 Td /F1 9.8 Tf [( and teleosts\) have been resolved with )] TJ ET BT 26.250 292.596 Td /F1 9.8 Tf [(confidence based on morphological and DNA sequence evidence)] TJ ET 0.267 0.267 0.267 rg BT 308.600 294.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 318.238 292.596 Td /F1 9.8 Tf [(. Similarly, recent molecular studies based on several )] TJ ET BT 26.250 280.691 Td /F1 9.8 Tf [(nuclear genes)] TJ ET 0.267 0.267 0.267 rg BT 87.490 282.198 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 97.127 280.691 Td /F1 9.8 Tf [( consistently support relationships among major teleost groups: Elopomorpha, Osteoglossomorpha and )] TJ ET BT 26.250 268.786 Td /F1 9.8 Tf [(Euteleostei)] TJ ET 0.267 0.267 0.267 rg BT 74.483 270.293 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 84.121 272.674 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 86.530 270.293 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 96.167 268.786 Td /F1 9.8 Tf [(. The deeper nodes among euteleosts and percomorphs also could be resolved with confidence with this new )] TJ ET BT 26.250 256.881 Td /F1 9.8 Tf [(set of nuclear markers, but a comprehensive phylogeny including all groups is lacking. In this study we report phylogenetic )] TJ ET BT 26.250 244.977 Td /F1 9.8 Tf [(results based on a taxonomically comprehensive dataset with DNA sequences for 21 nuclear genes. A dataset with 1416 taxa )] TJ ET BT 26.250 233.072 Td /F1 9.8 Tf [(was assembled, including four tetrapod and two chondrichthyan outgroups. Bony fish diversity is represented by 1093 genera )] TJ ET BT 26.250 221.167 Td /F1 9.8 Tf [(\(of ca. 4300\), 369 families \(of 502\), and all traditionally recognized orders)] TJ ET 0.267 0.267 0.267 rg BT 341.633 222.674 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 346.452 221.167 Td /F1 9.8 Tf [(, making this the most comprehensive dataset ever )] TJ ET BT 26.250 209.262 Td /F1 9.8 Tf [(compiled in systematic ichthyology. Phylogenetic results corroborate many previously established hypotheses, but also provide )] TJ ET BT 26.250 197.358 Td /F1 9.8 Tf [(unprecedented resolution among percomorphs. The uncertain relationships involving most of the extant diversity of )] TJ ET BT 26.250 185.453 Td /F1 9.8 Tf [(percomorphs is resolved into several well-supported groups and, for the first time, we offer a monophyletic definition for )] TJ ET BT 26.250 173.548 Td /F1 9.8 Tf [(Perciformes. Using a set of 60 calibrations, we also provide the most comprehensive hypothesis to date about the tempo of )] TJ ET BT 26.250 161.643 Td /F1 9.8 Tf [(osteichthyan diversification. Considering the new clades obtained in this study and previously published well-supported clades, )] TJ ET BT 26.250 149.739 Td /F1 9.8 Tf [(we propose a new classification for bony fishes based on the nomenclatural scheme recently proposed by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 567.619 151.246 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 572.437 149.739 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 137.834 Td /F1 9.8 Tf [(Our hope is that this explicit proposal will facilitate communication among ichthyologists attempting to chart the rapidly changing )] TJ ET BT 26.250 125.929 Td /F1 9.8 Tf [(landscape of phylogeny and classification of fishes.)] TJ ET BT 26.250 89.327 Td /F4 12.0 Tf [(Materials and Methods)] TJ ET BT 26.250 69.372 Td /F4 9.8 Tf [(Molecular data and taxonomic sampling)] TJ ET BT 26.250 49.968 Td /F1 9.8 Tf [(This study is the main product of the Euteleost Tree of Life Project \()] TJ ET 0.267 0.267 0.267 rg BT 317.258 49.968 Td /F1 9.8 Tf [(EToL)] TJ ET 0.271 0.267 0.267 rg BT 340.561 49.968 Td /F1 9.8 Tf [(\). A total of 21 molecular markers with a genome-wide )] TJ ET BT 26.250 38.063 Td /F1 9.8 Tf [(distribution were examined, the majority of which were developed by EToL using a genomic screen pipeline)] TJ ET 0.267 0.267 0.267 rg BT 489.024 39.570 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 498.661 38.063 Td /F1 9.8 Tf [(. This pipeline )] TJ ET Q q 15.000 23.777 577.500 753.223 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(groups of fishes has been elusive because explicit analyses including representatives across their diversity have never been )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(accomplished. Detailed morphological cladistic investigations of fish relationships have typically focused on lower taxonomic )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(scales and few attempts to synthesize morphology at higher taxonomic levels proved to be challenging and met limited success )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(\(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 48.470 733.269 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 53.289 731.762 Td /F1 9.8 Tf [(\). A recent effort to systematically collect morphological synapomorphies from published records for all currently )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(recognized groups resulted in the first teleost classification based on monophyletic groups)] TJ ET 0.267 0.267 0.267 rg BT 413.715 721.364 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 418.534 719.857 Td /F1 9.8 Tf [(. This effort, however, did not )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(produce a global phylogenetic hypothesis. Similarly, molecular analyses have been limited and many times conflicting in terms )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(of genetic coverage and taxonomic sampling.)] TJ ET BT 26.250 676.643 Td /F1 9.8 Tf [(As predicted by Greenwood et al.)] TJ ET 0.267 0.267 0.267 rg BT 170.404 678.150 Td /F4 8.7 Tf [(1)] TJ ET 0.271 0.267 0.267 rg BT 175.222 676.643 Td /F1 9.8 Tf [(, development of molecular markers, especially sequences of mitochondrial DNA \(mtDNA\) )] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(genes or complete mitochondrial genomes, catalyzed new views of bony fish relationships by providing a common yardstick of )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(phylogenetic information across vast taxonomic scales)] TJ ET 0.267 0.267 0.267 rg BT 261.420 654.341 Td /F4 8.7 Tf [(6)] TJ ET 0.271 0.267 0.267 rg BT 266.239 656.722 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 268.648 654.341 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 273.467 656.722 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 275.876 654.341 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 280.695 652.833 Td /F1 9.8 Tf [(. Studies based on mitogenomic data proliferated to methodically )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(probe conflicting hypotheses of relationship for several groups at diverse taxonomic levels, many times proposing alternative )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(arrangements supporting new clades unsuspected by previous classifications)] TJ ET 0.267 0.267 0.267 rg BT 359.515 630.531 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 369.152 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 371.561 630.531 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 381.199 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 383.608 630.531 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 393.245 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 395.655 630.531 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 405.292 629.024 Td /F1 9.8 Tf [(. In spite of their new powerful insights, )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(mitogenomic hypotheses were not universally embraced because they represent information from a single locus, prompting )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(corroboration from additional genomic regions. Several nuclear DNA markers were subsequently developed and applied to infer )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(bony fish relationships. The most popular ones include 28S ribosomal subunit)] TJ ET 0.267 0.267 0.267 rg BT 360.607 594.817 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 370.244 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 372.653 594.817 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 382.291 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 384.700 594.817 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 394.337 593.310 Td /F1 9.8 Tf [(, )] TJ ET BT 399.758 593.310 Td /F5 9.8 Tf [(tmo4c4 )] TJ ET 0.267 0.267 0.267 rg BT 434.439 594.817 Td /F4 8.7 Tf [(17)] TJ ET 0.271 0.267 0.267 rg BT 444.077 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 446.486 594.817 Td /F4 8.7 Tf [(18)] TJ ET 0.271 0.267 0.267 rg BT 456.123 593.310 Td /F1 9.8 Tf [(, rhodopsin)] TJ ET 0.267 0.267 0.267 rg BT 504.356 594.817 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 513.994 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 516.403 594.817 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 526.040 593.310 Td /F1 9.8 Tf [(, )] TJ ET BT 531.461 593.310 Td /F5 9.8 Tf [(rag1)] TJ ET BT 550.971 593.310 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 581.405 Td /F5 9.8 Tf [(rag2)] TJ ET 0.267 0.267 0.267 rg BT 45.760 582.912 Td /F4 8.7 Tf [(21)] TJ ET 0.271 0.267 0.267 rg BT 55.397 585.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 57.806 582.912 Td /F4 8.7 Tf [(22)] TJ ET 0.271 0.267 0.267 rg BT 67.444 581.405 Td /F5 9.8 Tf [(, mll)] TJ ET 0.267 0.267 0.267 rg BT 85.316 582.912 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 94.953 581.405 Td /F1 9.8 Tf [(, )] TJ ET BT 100.374 581.405 Td /F5 9.8 Tf [(irbp)] TJ ET 0.267 0.267 0.267 rg BT 116.627 582.912 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 126.264 581.405 Td /F1 9.8 Tf [(, and )] TJ ET BT 150.659 581.405 Td /F5 9.8 Tf [(rnf213)] TJ ET 0.267 0.267 0.267 rg BT 178.300 582.912 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 187.938 581.405 Td /F1 9.8 Tf [(. Using a systematic approach to scan genomic databases, a larger set of nuclear markers )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(became available in 2007 )] TJ ET 0.267 0.267 0.267 rg BT 139.516 571.007 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 149.153 569.500 Td /F1 9.8 Tf [(, opening a new window to obtaining large multilocus datasets)] TJ ET 0.267 0.267 0.267 rg BT 416.323 571.007 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 425.960 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 428.369 571.007 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 438.007 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 440.416 571.007 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 450.053 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 452.463 571.007 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 462.100 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 464.509 571.007 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 474.147 569.500 Td /F1 9.8 Tf [(. Recent studies using )] TJ ET BT 26.250 557.595 Td /F1 9.8 Tf [(between 10 and 20 of these nuclear markers for a few hundred taxa)] TJ ET 0.267 0.267 0.267 rg BT 318.906 559.103 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 328.543 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 330.953 559.103 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 340.590 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 342.999 559.103 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 352.637 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 355.046 559.103 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 364.683 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 367.093 559.103 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 376.730 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 379.139 559.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 388.777 557.595 Td /F1 9.8 Tf [(, have shown improved resolution of )] TJ ET BT 26.250 545.691 Td /F1 9.8 Tf [(phylogenetic relationship at higher and lower taxonomic levels. Many but not all of the mitogenomic hypotheses received )] TJ ET BT 26.250 533.786 Td /F1 9.8 Tf [(support from nuclear gene data, but the discovery of new clades continued with increasing taxonomic sampling. Initially )] TJ ET BT 26.250 521.881 Td /F1 9.8 Tf [(identified by letters \(e.g., clades A, B, C, etc.)] TJ ET 0.267 0.267 0.267 rg BT 218.091 523.388 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 227.728 525.769 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 230.138 523.388 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 239.775 525.769 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 242.184 523.388 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 251.822 521.881 Td /F1 9.8 Tf [(\), new names were recently proposed for many groupings supported by )] TJ ET BT 26.250 509.976 Td /F1 9.8 Tf [(molecular evidence, such as Stiassnyiformes, Zeiogadiformes, Carangimorpha, Cottimorpha, Ovalentaria, Gobiiformes etc.)] TJ ET 0.267 0.267 0.267 rg BT 556.182 511.484 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 565.819 513.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 568.229 511.484 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 577.866 513.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 26.250 499.579 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 35.887 498.072 Td /F1 9.8 Tf [(. Validation of these groups \(and their proposed names\) is pending until a comprehensive study including all taxa is produced. )] TJ ET BT 26.250 486.167 Td /F1 9.8 Tf [(Proliferation of new names is useful for identification of the newly discovered groups, but may create confusion if not )] TJ ET BT 26.250 474.262 Td /F1 9.8 Tf [(systematically organized into a global classification.)] TJ ET BT 26.250 454.857 Td /F1 9.8 Tf [(Molecular phylogenetic methods \(e.g., BEAST)] TJ ET 0.267 0.267 0.267 rg BT 225.667 456.365 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 235.304 454.857 Td /F1 9.8 Tf [(\) in combination with fossil evidence also opened a new temporal window to )] TJ ET BT 26.250 442.953 Td /F1 9.8 Tf [(understand bony fish diversification. Attempts to estimate divergence dates among crow-group lineages using this approach )] TJ ET BT 26.250 431.048 Td /F1 9.8 Tf [(\(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 51.181 432.555 Td /F4 8.7 Tf [(35)] TJ ET 0.271 0.267 0.267 rg BT 60.818 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 63.227 432.555 Td /F4 8.7 Tf [(36)] TJ ET 0.271 0.267 0.267 rg BT 72.865 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 75.274 432.555 Td /F4 8.7 Tf [(37)] TJ ET 0.271 0.267 0.267 rg BT 84.911 431.048 Td /F1 9.8 Tf [(\) frequently produced conflicting views with the paleontological literature)] TJ ET 0.267 0.267 0.267 rg BT 394.874 432.555 Td /F4 8.7 Tf [(38)] TJ ET 0.271 0.267 0.267 rg BT 404.511 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 406.920 432.555 Td /F4 8.7 Tf [(39)] TJ ET 0.271 0.267 0.267 rg BT 416.558 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 418.967 432.555 Td /F4 8.7 Tf [(40)] TJ ET 0.271 0.267 0.267 rg BT 428.604 431.048 Td /F1 9.8 Tf [(, sometimes implying large gaps in )] TJ ET BT 26.250 419.143 Td /F1 9.8 Tf [(the fossil record. The discrepancy is larger when divergence estimates for crown teleost lineages have been based on )] TJ ET BT 26.250 407.238 Td /F1 9.8 Tf [(mitogenomic data \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 128.128 408.746 Td /F4 8.7 Tf [(37)] TJ ET 0.271 0.267 0.267 rg BT 137.765 411.127 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 140.174 408.746 Td /F4 8.7 Tf [(41)] TJ ET 0.271 0.267 0.267 rg BT 149.812 411.127 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 152.221 408.746 Td /F4 8.7 Tf [(115)] TJ ET 0.271 0.267 0.267 rg BT 166.677 407.238 Td /F1 9.8 Tf [(\). Nucleotide saturation, compressing basal branch lengths for mtDNA, and the specific )] TJ ET BT 26.250 395.334 Td /F1 9.8 Tf [(approaches used to apply fossils constraints to calibrate the molecular phylogeny may explain this discordance)] TJ ET 0.267 0.267 0.267 rg BT 504.205 396.841 Td /F4 8.7 Tf [(43)] TJ ET 0.271 0.267 0.267 rg BT 513.842 395.334 Td /F1 9.8 Tf [(. Other studies )] TJ ET BT 26.250 383.429 Td /F1 9.8 Tf [(based on several nuclear genes and larger sets of fossil calibration points produced divergence dates more consistent with the )] TJ ET BT 26.250 371.524 Td /F1 9.8 Tf [(fossil record)] TJ ET 0.267 0.267 0.267 rg BT 78.803 373.031 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 88.440 375.412 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 90.849 373.031 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 100.487 371.524 Td /F1 9.8 Tf [(, but a comprehensive time-tree for osteichthyan diversification is not yet available.)] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(The shape of the bony fish tree of life is currently better resolved for the early-branching lineages than for the more apical )] TJ ET BT 26.250 340.215 Td /F1 9.8 Tf [(acanthomorph groups, in particular the percomorphs, a large and diverse group of spiny-finned fishes with uncertain affinities )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(that came to be known as )] TJ ET BT 140.062 328.310 Td /F4 9.8 Tf [()] TJ ET BT 144.937 328.310 Td /F1 9.8 Tf [(bush at the top)] TJ ET BT 209.443 328.310 Td /F4 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 214.318 329.817 Td /F4 8.7 Tf [(44)] TJ ET 0.271 0.267 0.267 rg BT 223.955 328.310 Td /F1 9.8 Tf [(. Few basal branching events among osteichthyans remain problematic, for )] TJ ET BT 26.250 316.405 Td /F1 9.8 Tf [(example, the relationships among lungfishes, coelacanths, and tetrapods)] TJ ET 0.267 0.267 0.267 rg BT 341.116 317.912 Td /F4 8.7 Tf [(45)] TJ ET 0.271 0.267 0.267 rg BT 350.754 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 353.163 317.912 Td /F4 8.7 Tf [(46)] TJ ET 0.271 0.267 0.267 rg BT 362.800 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 365.210 317.912 Td /F4 8.7 Tf [(47)] TJ ET 0.271 0.267 0.267 rg BT 374.847 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 377.257 317.912 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 386.894 316.405 Td /F1 9.8 Tf [(. In contrast, the basal branching pattern for )] TJ ET BT 26.250 304.500 Td /F1 9.8 Tf [(early extant actinopterygians \(involving polypteriforms, chondrosteans, lepisosteids, )] TJ ET BT 389.311 304.500 Td /F5 9.8 Tf [(Amia)] TJ ET BT 411.521 304.500 Td /F1 9.8 Tf [( and teleosts\) have been resolved with )] TJ ET BT 26.250 292.596 Td /F1 9.8 Tf [(confidence based on morphological and DNA sequence evidence)] TJ ET 0.267 0.267 0.267 rg BT 308.600 294.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 318.238 292.596 Td /F1 9.8 Tf [(. Similarly, recent molecular studies based on several )] TJ ET BT 26.250 280.691 Td /F1 9.8 Tf [(nuclear genes)] TJ ET 0.267 0.267 0.267 rg BT 87.490 282.198 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 97.127 280.691 Td /F1 9.8 Tf [( consistently support relationships among major teleost groups: Elopomorpha, Osteoglossomorpha and )] TJ ET BT 26.250 268.786 Td /F1 9.8 Tf [(Euteleostei)] TJ ET 0.267 0.267 0.267 rg BT 74.483 270.293 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 84.121 272.674 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 86.530 270.293 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 96.167 268.786 Td /F1 9.8 Tf [(. The deeper nodes among euteleosts and percomorphs also could be resolved with confidence with this new )] TJ ET BT 26.250 256.881 Td /F1 9.8 Tf [(set of nuclear markers, but a comprehensive phylogeny including all groups is lacking. In this study we report phylogenetic )] TJ ET BT 26.250 244.977 Td /F1 9.8 Tf [(results based on a taxonomically comprehensive dataset with DNA sequences for 21 nuclear genes. A dataset with 1416 taxa )] TJ ET BT 26.250 233.072 Td /F1 9.8 Tf [(was assembled, including four tetrapod and two chondrichthyan outgroups. Bony fish diversity is represented by 1093 genera )] TJ ET BT 26.250 221.167 Td /F1 9.8 Tf [(\(of ca. 4300\), 369 families \(of 502\), and all traditionally recognized orders)] TJ ET 0.267 0.267 0.267 rg BT 341.633 222.674 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 346.452 221.167 Td /F1 9.8 Tf [(, making this the most comprehensive dataset ever )] TJ ET BT 26.250 209.262 Td /F1 9.8 Tf [(compiled in systematic ichthyology. Phylogenetic results corroborate many previously established hypotheses, but also provide )] TJ ET BT 26.250 197.358 Td /F1 9.8 Tf [(unprecedented resolution among percomorphs. The uncertain relationships involving most of the extant diversity of )] TJ ET BT 26.250 185.453 Td /F1 9.8 Tf [(percomorphs is resolved into several well-supported groups and, for the first time, we offer a monophyletic definition for )] TJ ET BT 26.250 173.548 Td /F1 9.8 Tf [(Perciformes. Using a set of 60 calibrations, we also provide the most comprehensive hypothesis to date about the tempo of )] TJ ET BT 26.250 161.643 Td /F1 9.8 Tf [(osteichthyan diversification. Considering the new clades obtained in this study and previously published well-supported clades, )] TJ ET BT 26.250 149.739 Td /F1 9.8 Tf [(we propose a new classification for bony fishes based on the nomenclatural scheme recently proposed by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 567.619 151.246 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 572.437 149.739 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 137.834 Td /F1 9.8 Tf [(Our hope is that this explicit proposal will facilitate communication among ichthyologists attempting to chart the rapidly changing )] TJ ET BT 26.250 125.929 Td /F1 9.8 Tf [(landscape of phylogeny and classification of fishes.)] TJ ET BT 26.250 89.327 Td /F4 12.0 Tf [(Materials and Methods)] TJ ET BT 26.250 69.372 Td /F4 9.8 Tf [(Molecular data and taxonomic sampling)] TJ ET BT 26.250 49.968 Td /F1 9.8 Tf [(This study is the main product of the Euteleost Tree of Life Project \()] TJ ET 0.267 0.267 0.267 rg BT 317.258 49.968 Td /F1 9.8 Tf [(EToL)] TJ ET 0.271 0.267 0.267 rg BT 340.561 49.968 Td /F1 9.8 Tf [(\). A total of 21 molecular markers with a genome-wide )] TJ ET BT 26.250 38.063 Td /F1 9.8 Tf [(distribution were examined, the majority of which were developed by EToL using a genomic screen pipeline)] TJ ET 0.267 0.267 0.267 rg BT 489.024 39.570 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 498.661 38.063 Td /F1 9.8 Tf [(. This pipeline )] TJ ET Q q 15.000 23.777 577.500 753.223 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(groups of fishes has been elusive because explicit analyses including representatives across their diversity have never been )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(accomplished. Detailed morphological cladistic investigations of fish relationships have typically focused on lower taxonomic )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(scales and few attempts to synthesize morphology at higher taxonomic levels proved to be challenging and met limited success )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(\(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 48.470 733.269 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 53.289 731.762 Td /F1 9.8 Tf [(\). A recent effort to systematically collect morphological synapomorphies from published records for all currently )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(recognized groups resulted in the first teleost classification based on monophyletic groups)] TJ ET 0.267 0.267 0.267 rg BT 413.715 721.364 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 418.534 719.857 Td /F1 9.8 Tf [(. This effort, however, did not )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(produce a global phylogenetic hypothesis. Similarly, molecular analyses have been limited and many times conflicting in terms )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(of genetic coverage and taxonomic sampling.)] TJ ET BT 26.250 676.643 Td /F1 9.8 Tf [(As predicted by Greenwood et al.)] TJ ET 0.267 0.267 0.267 rg BT 170.404 678.150 Td /F4 8.7 Tf [(1)] TJ ET 0.271 0.267 0.267 rg BT 175.222 676.643 Td /F1 9.8 Tf [(, development of molecular markers, especially sequences of mitochondrial DNA \(mtDNA\) )] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(genes or complete mitochondrial genomes, catalyzed new views of bony fish relationships by providing a common yardstick of )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(phylogenetic information across vast taxonomic scales)] TJ ET 0.267 0.267 0.267 rg BT 261.420 654.341 Td /F4 8.7 Tf [(6)] TJ ET 0.271 0.267 0.267 rg BT 266.239 656.722 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 268.648 654.341 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 273.467 656.722 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 275.876 654.341 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 280.695 652.833 Td /F1 9.8 Tf [(. Studies based on mitogenomic data proliferated to methodically )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(probe conflicting hypotheses of relationship for several groups at diverse taxonomic levels, many times proposing alternative )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(arrangements supporting new clades unsuspected by previous classifications)] TJ ET 0.267 0.267 0.267 rg BT 359.515 630.531 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 369.152 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 371.561 630.531 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 381.199 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 383.608 630.531 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 393.245 632.912 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 395.655 630.531 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 405.292 629.024 Td /F1 9.8 Tf [(. In spite of their new powerful insights, )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(mitogenomic hypotheses were not universally embraced because they represent information from a single locus, prompting )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(corroboration from additional genomic regions. Several nuclear DNA markers were subsequently developed and applied to infer )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(bony fish relationships. The most popular ones include 28S ribosomal subunit)] TJ ET 0.267 0.267 0.267 rg BT 360.607 594.817 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 370.244 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 372.653 594.817 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 382.291 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 384.700 594.817 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 394.337 593.310 Td /F1 9.8 Tf [(, )] TJ ET BT 399.758 593.310 Td /F5 9.8 Tf [(tmo4c4 )] TJ ET 0.267 0.267 0.267 rg BT 434.439 594.817 Td /F4 8.7 Tf [(17)] TJ ET 0.271 0.267 0.267 rg BT 444.077 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 446.486 594.817 Td /F4 8.7 Tf [(18)] TJ ET 0.271 0.267 0.267 rg BT 456.123 593.310 Td /F1 9.8 Tf [(, rhodopsin)] TJ ET 0.267 0.267 0.267 rg BT 504.356 594.817 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 513.994 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 516.403 594.817 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 526.040 593.310 Td /F1 9.8 Tf [(, )] TJ ET BT 531.461 593.310 Td /F5 9.8 Tf [(rag1)] TJ ET BT 550.971 593.310 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 581.405 Td /F5 9.8 Tf [(rag2)] TJ ET 0.267 0.267 0.267 rg BT 45.760 582.912 Td /F4 8.7 Tf [(21)] TJ ET 0.271 0.267 0.267 rg BT 55.397 585.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 57.806 582.912 Td /F4 8.7 Tf [(22)] TJ ET 0.271 0.267 0.267 rg BT 67.444 581.405 Td /F5 9.8 Tf [(, mll)] TJ ET 0.267 0.267 0.267 rg BT 85.316 582.912 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 94.953 581.405 Td /F1 9.8 Tf [(, )] TJ ET BT 100.374 581.405 Td /F5 9.8 Tf [(irbp)] TJ ET 0.267 0.267 0.267 rg BT 116.627 582.912 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 126.264 581.405 Td /F1 9.8 Tf [(, and )] TJ ET BT 150.659 581.405 Td /F5 9.8 Tf [(rnf213)] TJ ET 0.267 0.267 0.267 rg BT 178.300 582.912 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 187.938 581.405 Td /F1 9.8 Tf [(. Using a systematic approach to scan genomic databases, a larger set of nuclear markers )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(became available in 2007 )] TJ ET 0.267 0.267 0.267 rg BT 139.516 571.007 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 149.153 569.500 Td /F1 9.8 Tf [(, opening a new window to obtaining large multilocus datasets)] TJ ET 0.267 0.267 0.267 rg BT 416.323 571.007 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 425.960 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 428.369 571.007 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 438.007 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 440.416 571.007 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 450.053 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 452.463 571.007 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 462.100 573.388 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 464.509 571.007 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 474.147 569.500 Td /F1 9.8 Tf [(. Recent studies using )] TJ ET BT 26.250 557.595 Td /F1 9.8 Tf [(between 10 and 20 of these nuclear markers for a few hundred taxa)] TJ ET 0.267 0.267 0.267 rg BT 318.906 559.103 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 328.543 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 330.953 559.103 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 340.590 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 342.999 559.103 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 352.637 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 355.046 559.103 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 364.683 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 367.093 559.103 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 376.730 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 379.139 559.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 388.777 557.595 Td /F1 9.8 Tf [(, have shown improved resolution of )] TJ ET BT 26.250 545.691 Td /F1 9.8 Tf [(phylogenetic relationship at higher and lower taxonomic levels. Many but not all of the mitogenomic hypotheses received )] TJ ET BT 26.250 533.786 Td /F1 9.8 Tf [(support from nuclear gene data, but the discovery of new clades continued with increasing taxonomic sampling. Initially )] TJ ET BT 26.250 521.881 Td /F1 9.8 Tf [(identified by letters \(e.g., clades A, B, C, etc.)] TJ ET 0.267 0.267 0.267 rg BT 218.091 523.388 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 227.728 525.769 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 230.138 523.388 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 239.775 525.769 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 242.184 523.388 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 251.822 521.881 Td /F1 9.8 Tf [(\), new names were recently proposed for many groupings supported by )] TJ ET BT 26.250 509.976 Td /F1 9.8 Tf [(molecular evidence, such as Stiassnyiformes, Zeiogadiformes, Carangimorpha, Cottimorpha, Ovalentaria, Gobiiformes etc.)] TJ ET 0.267 0.267 0.267 rg BT 556.182 511.484 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 565.819 513.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 568.229 511.484 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 577.866 513.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 26.250 499.579 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 35.887 498.072 Td /F1 9.8 Tf [(. Validation of these groups \(and their proposed names\) is pending until a comprehensive study including all taxa is produced. )] TJ ET BT 26.250 486.167 Td /F1 9.8 Tf [(Proliferation of new names is useful for identification of the newly discovered groups, but may create confusion if not )] TJ ET BT 26.250 474.262 Td /F1 9.8 Tf [(systematically organized into a global classification.)] TJ ET BT 26.250 454.857 Td /F1 9.8 Tf [(Molecular phylogenetic methods \(e.g., BEAST)] TJ ET 0.267 0.267 0.267 rg BT 225.667 456.365 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 235.304 454.857 Td /F1 9.8 Tf [(\) in combination with fossil evidence also opened a new temporal window to )] TJ ET BT 26.250 442.953 Td /F1 9.8 Tf [(understand bony fish diversification. Attempts to estimate divergence dates among crow-group lineages using this approach )] TJ ET BT 26.250 431.048 Td /F1 9.8 Tf [(\(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 51.181 432.555 Td /F4 8.7 Tf [(35)] TJ ET 0.271 0.267 0.267 rg BT 60.818 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 63.227 432.555 Td /F4 8.7 Tf [(36)] TJ ET 0.271 0.267 0.267 rg BT 72.865 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 75.274 432.555 Td /F4 8.7 Tf [(37)] TJ ET 0.271 0.267 0.267 rg BT 84.911 431.048 Td /F1 9.8 Tf [(\) frequently produced conflicting views with the paleontological literature)] TJ ET 0.267 0.267 0.267 rg BT 394.874 432.555 Td /F4 8.7 Tf [(38)] TJ ET 0.271 0.267 0.267 rg BT 404.511 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 406.920 432.555 Td /F4 8.7 Tf [(39)] TJ ET 0.271 0.267 0.267 rg BT 416.558 434.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 418.967 432.555 Td /F4 8.7 Tf [(40)] TJ ET 0.271 0.267 0.267 rg BT 428.604 431.048 Td /F1 9.8 Tf [(, sometimes implying large gaps in )] TJ ET BT 26.250 419.143 Td /F1 9.8 Tf [(the fossil record. The discrepancy is larger when divergence estimates for crown teleost lineages have been based on )] TJ ET BT 26.250 407.238 Td /F1 9.8 Tf [(mitogenomic data \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 128.128 408.746 Td /F4 8.7 Tf [(37)] TJ ET 0.271 0.267 0.267 rg BT 137.765 411.127 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 140.174 408.746 Td /F4 8.7 Tf [(41)] TJ ET 0.271 0.267 0.267 rg BT 149.812 411.127 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 152.221 408.746 Td /F4 8.7 Tf [(115)] TJ ET 0.271 0.267 0.267 rg BT 166.677 407.238 Td /F1 9.8 Tf [(\). Nucleotide saturation, compressing basal branch lengths for mtDNA, and the specific )] TJ ET BT 26.250 395.334 Td /F1 9.8 Tf [(approaches used to apply fossils constraints to calibrate the molecular phylogeny may explain this discordance)] TJ ET 0.267 0.267 0.267 rg BT 504.205 396.841 Td /F4 8.7 Tf [(43)] TJ ET 0.271 0.267 0.267 rg BT 513.842 395.334 Td /F1 9.8 Tf [(. Other studies )] TJ ET BT 26.250 383.429 Td /F1 9.8 Tf [(based on several nuclear genes and larger sets of fossil calibration points produced divergence dates more consistent with the )] TJ ET BT 26.250 371.524 Td /F1 9.8 Tf [(fossil record)] TJ ET 0.267 0.267 0.267 rg BT 78.803 373.031 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 88.440 375.412 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 90.849 373.031 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 100.487 371.524 Td /F1 9.8 Tf [(, but a comprehensive time-tree for osteichthyan diversification is not yet available.)] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(The shape of the bony fish tree of life is currently better resolved for the early-branching lineages than for the more apical )] TJ ET BT 26.250 340.215 Td /F1 9.8 Tf [(acanthomorph groups, in particular the percomorphs, a large and diverse group of spiny-finned fishes with uncertain affinities )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(that came to be known as )] TJ ET BT 140.062 328.310 Td /F4 9.8 Tf [()] TJ ET BT 144.937 328.310 Td /F1 9.8 Tf [(bush at the top)] TJ ET BT 209.443 328.310 Td /F4 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 214.318 329.817 Td /F4 8.7 Tf [(44)] TJ ET 0.271 0.267 0.267 rg BT 223.955 328.310 Td /F1 9.8 Tf [(. Few basal branching events among osteichthyans remain problematic, for )] TJ ET BT 26.250 316.405 Td /F1 9.8 Tf [(example, the relationships among lungfishes, coelacanths, and tetrapods)] TJ ET 0.267 0.267 0.267 rg BT 341.116 317.912 Td /F4 8.7 Tf [(45)] TJ ET 0.271 0.267 0.267 rg BT 350.754 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 353.163 317.912 Td /F4 8.7 Tf [(46)] TJ ET 0.271 0.267 0.267 rg BT 362.800 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 365.210 317.912 Td /F4 8.7 Tf [(47)] TJ ET 0.271 0.267 0.267 rg BT 374.847 320.293 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 377.257 317.912 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 386.894 316.405 Td /F1 9.8 Tf [(. In contrast, the basal branching pattern for )] TJ ET BT 26.250 304.500 Td /F1 9.8 Tf [(early extant actinopterygians \(involving polypteriforms, chondrosteans, lepisosteids, )] TJ ET BT 389.311 304.500 Td /F5 9.8 Tf [(Amia)] TJ ET BT 411.521 304.500 Td /F1 9.8 Tf [( and teleosts\) have been resolved with )] TJ ET BT 26.250 292.596 Td /F1 9.8 Tf [(confidence based on morphological and DNA sequence evidence)] TJ ET 0.267 0.267 0.267 rg BT 308.600 294.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 318.238 292.596 Td /F1 9.8 Tf [(. Similarly, recent molecular studies based on several )] TJ ET BT 26.250 280.691 Td /F1 9.8 Tf [(nuclear genes)] TJ ET 0.267 0.267 0.267 rg BT 87.490 282.198 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 97.127 280.691 Td /F1 9.8 Tf [( consistently support relationships among major teleost groups: Elopomorpha, Osteoglossomorpha and )] TJ ET BT 26.250 268.786 Td /F1 9.8 Tf [(Euteleostei)] TJ ET 0.267 0.267 0.267 rg BT 74.483 270.293 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 84.121 272.674 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 86.530 270.293 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 96.167 268.786 Td /F1 9.8 Tf [(. The deeper nodes among euteleosts and percomorphs also could be resolved with confidence with this new )] TJ ET BT 26.250 256.881 Td /F1 9.8 Tf [(set of nuclear markers, but a comprehensive phylogeny including all groups is lacking. In this study we report phylogenetic )] TJ ET BT 26.250 244.977 Td /F1 9.8 Tf [(results based on a taxonomically comprehensive dataset with DNA sequences for 21 nuclear genes. A dataset with 1416 taxa )] TJ ET BT 26.250 233.072 Td /F1 9.8 Tf [(was assembled, including four tetrapod and two chondrichthyan outgroups. Bony fish diversity is represented by 1093 genera )] TJ ET BT 26.250 221.167 Td /F1 9.8 Tf [(\(of ca. 4300\), 369 families \(of 502\), and all traditionally recognized orders)] TJ ET 0.267 0.267 0.267 rg BT 341.633 222.674 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 346.452 221.167 Td /F1 9.8 Tf [(, making this the most comprehensive dataset ever )] TJ ET BT 26.250 209.262 Td /F1 9.8 Tf [(compiled in systematic ichthyology. Phylogenetic results corroborate many previously established hypotheses, but also provide )] TJ ET BT 26.250 197.358 Td /F1 9.8 Tf [(unprecedented resolution among percomorphs. The uncertain relationships involving most of the extant diversity of )] TJ ET BT 26.250 185.453 Td /F1 9.8 Tf [(percomorphs is resolved into several well-supported groups and, for the first time, we offer a monophyletic definition for )] TJ ET BT 26.250 173.548 Td /F1 9.8 Tf [(Perciformes. Using a set of 60 calibrations, we also provide the most comprehensive hypothesis to date about the tempo of )] TJ ET BT 26.250 161.643 Td /F1 9.8 Tf [(osteichthyan diversification. Considering the new clades obtained in this study and previously published well-supported clades, )] TJ ET BT 26.250 149.739 Td /F1 9.8 Tf [(we propose a new classification for bony fishes based on the nomenclatural scheme recently proposed by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 567.619 151.246 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 572.437 149.739 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 137.834 Td /F1 9.8 Tf [(Our hope is that this explicit proposal will facilitate communication among ichthyologists attempting to chart the rapidly changing )] TJ ET BT 26.250 125.929 Td /F1 9.8 Tf [(landscape of phylogeny and classification of fishes.)] TJ ET BT 26.250 89.327 Td /F4 12.0 Tf [(Materials and Methods)] TJ ET BT 26.250 69.372 Td /F4 9.8 Tf [(Molecular data and taxonomic sampling)] TJ ET BT 26.250 49.968 Td /F1 9.8 Tf [(This study is the main product of the Euteleost Tree of Life Project \()] TJ ET 0.267 0.267 0.267 rg BT 317.258 49.968 Td /F1 9.8 Tf [(EToL)] TJ ET 0.271 0.267 0.267 rg BT 340.561 49.968 Td /F1 9.8 Tf [(\). A total of 21 molecular markers with a genome-wide )] TJ ET BT 26.250 38.063 Td /F1 9.8 Tf [(distribution were examined, the majority of which were developed by EToL using a genomic screen pipeline)] TJ ET 0.267 0.267 0.267 rg BT 489.024 39.570 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 498.661 38.063 Td /F1 9.8 Tf [(. This pipeline )] TJ ET Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(2)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 196 0 obj << /Type /Font /Subtype /Type1 /Name /F5 /BaseFont /Helvetica-Oblique /Encoding /WinAnsiEncoding >> endobj 197 0 obj << /Type /Annot /Subtype /Link /A 198 0 R /Border [0 0 0] /H /I /Rect [ 48.4703 732.4674 53.2889 741.2858 ] >> endobj 198 0 obj << /Type /Action >> endobj 199 0 obj << /Type /Annot /Subtype /Link /A 200 0 R /Border [0 0 0] /H /I /Rect [ 413.7150 720.5627 418.5337 729.3810 ] >> endobj 200 0 obj << /Type /Action >> endobj 201 0 obj << /Type /Annot /Subtype /Link /A 202 0 R /Border [0 0 0] /H /I /Rect [ 170.4038 677.3484 175.2224 686.1667 ] >> endobj 202 0 obj << /Type /Action >> endobj 203 0 obj << /Type /Annot /Subtype /Link /A 204 0 R /Border [0 0 0] /H /I /Rect [ 261.4200 653.5389 266.2387 662.3573 ] >> endobj 204 0 obj << /Type /Action >> endobj 205 0 obj << /Type /Annot /Subtype 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Exons )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(markers were sequenced from 11 nuclear genes previously published by our group \()] TJ ET BT 389.857 743.667 Td /F5 9.8 Tf [(kiaa1239)] TJ ET BT 429.422 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 434.843 743.667 Td /F5 9.8 Tf [(ficd)] TJ ET BT 450.014 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 455.435 743.667 Td /F5 9.8 Tf [(myh6)] TJ ET BT 479.274 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 484.695 743.667 Td /F5 9.8 Tf [(panx2)] TJ ET BT 511.254 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 516.675 743.667 Td /F5 9.8 Tf [(plagl2)] TJ ET BT 542.688 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 548.109 743.667 Td /F5 9.8 Tf [(ptchd4)] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(\(=)] TJ ET BT 35.191 731.762 Td /F5 9.8 Tf [(ptr)] TJ ET BT 46.569 731.762 Td /F1 9.8 Tf [(\), )] TJ ET BT 55.237 731.762 Td /F5 9.8 Tf [(ripk4)] TJ ET BT 76.365 731.762 Td /F1 9.8 Tf [(, )] TJ ET BT 81.786 731.762 Td /F5 9.8 Tf [(sidkey)] TJ ET BT 109.418 731.762 Td /F1 9.8 Tf [(, )] TJ ET BT 114.839 731.762 Td /F5 9.8 Tf [(snx33)] TJ ET BT 140.852 731.762 Td /F1 9.8 Tf [( \(=)] TJ ET BT 152.503 731.762 Td /F5 9.8 Tf [(sh3px3)] TJ ET BT 183.937 731.762 Td /F1 9.8 Tf [(\), )] TJ ET BT 192.605 731.762 Td /F5 9.8 Tf [(tbr1b)] TJ ET BT 214.825 731.762 Td /F1 9.8 Tf [( \(=)] TJ ET BT 226.476 731.762 Td /F5 9.8 Tf [(tbr1)] TJ ET BT 243.275 731.762 Td /F1 9.8 Tf [(\), and )] TJ ET BT 270.917 731.762 Td /F5 9.8 Tf [(zic1)] TJ ET BT 288.252 731.762 Td /F1 9.8 Tf [(\) and three additional markers, including one intron \()] TJ ET BT 513.682 731.762 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 545.116 731.762 Td /F1 9.8 Tf [(\) and )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(two exons \()] TJ ET BT 76.102 719.857 Td /F5 9.8 Tf [(svep1)] TJ ET BT 102.115 719.857 Td /F1 9.8 Tf [(, and )] TJ ET BT 126.509 719.857 Td /F5 9.8 Tf [(vcpip)] TJ ET BT 149.266 719.857 Td /F1 9.8 Tf [(\), were newly developed for this study using the same approach. Sequence data from seven )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(additional markers, including EToL markers \()] TJ ET BT 219.680 707.952 Td /F5 9.8 Tf [(enc1)] TJ ET BT 240.818 707.952 Td /F1 9.8 Tf [(, )] TJ ET BT 246.239 707.952 Td /F5 9.8 Tf [(gtdc2)] TJ ET BT 270.088 707.952 Td /F1 9.8 Tf [( \(=)] TJ ET BT 281.739 707.952 Td /F5 9.8 Tf [(glyt)] TJ ET BT 296.910 707.952 Td /F1 9.8 Tf [(\), and )] TJ ET BT 324.551 707.952 Td /F5 9.8 Tf [(gpr85)] TJ ET BT 349.482 707.952 Td /F1 9.8 Tf [( \(=)] TJ ET BT 361.133 707.952 Td /F5 9.8 Tf [(sreb2)] TJ ET BT 385.518 707.952 Td /F1 9.8 Tf [(\)\) or markers developed by others \(16S )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(mtDNA, )] TJ ET BT 63.086 696.048 Td /F5 9.8 Tf [(rag1)] TJ ET BT 82.595 696.048 Td /F1 9.8 Tf [(, )] TJ ET BT 88.016 696.048 Td /F5 9.8 Tf [(rag2)] TJ ET BT 107.526 696.048 Td /F1 9.8 Tf [(, and )] TJ ET BT 131.921 696.048 Td /F5 9.8 Tf [(rh)] TJ ET BT 140.588 696.048 Td /F1 9.8 Tf [(\), were generated for our previous studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 348.683 697.555 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 358.320 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 360.729 697.555 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 370.367 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 372.776 697.555 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 382.413 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 384.823 697.555 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 394.460 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 396.869 697.555 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 406.507 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 408.916 697.555 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 418.553 696.048 Td /F1 9.8 Tf [(\) or obtained from NCBI, Ensembl, )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(or other genomic databases.)] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(A total of 1184 bony fish taxa were initially targeted for this study and samples were primarily obtained from the tissue repository )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(of the Ichthyology Collection at University of Kansas \(1129 samples\) or other collections. Of the initial list, samples for 18 taxa )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(either failed to amplify or belonged to duplicate species that were ultimately combined or discarded. Sixty taxa that produced )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(sequence data for one or two genes only were also discarded. Twenty-five additional taxa were excluded from the final matrix )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(because they had low genetic coverage and highly variable phylogenetic placement in preliminary analyses, as identified using )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(bootstrap trees obtained with RAxML v7.3)] TJ ET 0.267 0.267 0.267 rg BT 207.249 606.722 Td /F4 8.7 Tf [(49)] TJ ET 0.271 0.267 0.267 rg BT 216.886 605.214 Td /F1 9.8 Tf [( and the )] TJ ET 0.267 0.267 0.267 rg BT 254.833 605.214 Td /F1 9.8 Tf [(RogueNaRok server)] TJ ET BT 343.149 606.722 Td /F4 8.7 Tf [(50)] TJ ET 0.271 0.267 0.267 rg BT 352.786 605.214 Td /F1 9.8 Tf [(. Our final sampling thus included 1081 taxa and )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(sequence data from 335 additional taxa were obtained from previous EToL studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 409.942 594.817 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 419.579 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 421.988 594.817 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 431.626 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 434.035 594.817 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 443.672 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 446.082 594.817 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 455.719 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 458.128 594.817 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 467.766 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 470.175 594.817 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 479.812 593.310 Td /F1 9.8 Tf [(\) or public databases )] TJ ET BT 26.250 581.405 Td /F1 9.8 Tf [(\(Table S1\). In order to minimize missing data, some sequences retrieved from public databases were combined as genus-level )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(composite taxa \(52 taxa\). DNA extraction, amplification protocols via nested PCR, and primers followed previous studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 26.250 559.103 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 35.887 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 38.297 559.103 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 47.934 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 50.343 559.103 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 59.981 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 62.390 559.103 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 72.027 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 74.437 559.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 84.074 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 86.483 559.103 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 96.121 557.595 Td /F1 9.8 Tf [(\). Primer sequences and optimized PCR conditions used for the three new markers is presented in Table 1. The )] TJ ET BT 26.250 545.691 Td /F1 9.8 Tf [(PCR amplicons obtained were submitted for purification and sequencing in both directions to High Throughput Sequencing )] TJ ET BT 26.250 533.786 Td /F1 9.8 Tf [(Solutions \(HTSeq.org\) or other core facilities.)] TJ ET BT 26.250 514.381 Td /F1 9.8 Tf [(Fish diversity is represented in the phylogenetic data matrix by a sample of 1410 bony fish species \(of ca. 31000)] TJ ET 0.267 0.267 0.267 rg BT 510.182 515.888 Td /F4 8.7 Tf [(51)] TJ ET 0.271 0.267 0.267 rg BT 519.819 514.381 Td /F1 9.8 Tf [(\) plus four )] TJ ET BT 26.250 502.476 Td /F1 9.8 Tf [(tetrapod species and two chondrichthyan outgroups \(total 1416 terminals\). The taxonomic sampling of bony fishes consists of )] TJ ET BT 26.250 490.572 Td /F1 9.8 Tf [(1093 genera \(of ca. 4300\), 369 families \(of 502; see below\), and all traditionally recognized orders \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 473.336 492.079 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 478.155 490.572 Td /F1 9.8 Tf [(\). Our taxonomic )] TJ ET BT 26.250 478.667 Td /F1 9.8 Tf [(sampling emphasizes representation of percomorph groups, with 1037 \(of >15000\) species in 201 families. All scientific names )] TJ ET BT 26.250 466.762 Td /F1 9.8 Tf [(were checked against the )] TJ ET 0.267 0.267 0.267 rg BT 139.516 466.762 Td /F1 9.8 Tf [(Catalog of Fishes)] TJ ET BT 215.380 468.269 Td /F4 8.7 Tf [(51)] TJ ET 0.271 0.267 0.267 rg BT 225.018 466.762 Td /F1 9.8 Tf [(. A complete list of material examined is given in Table S1.)] TJ ET q 26.250 443.145 555.000 13.736 re W n 0.271 0.267 0.267 rg BT 26.250 445.892 Td /F1 9.8 Tf [(Table 1. Primers used for new markers developed and optimized PCR conditions.)] TJ ET Q 0.965 0.965 0.965 rg 26.250 412.237 555.000 23.408 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 435.645 m 581.250 435.645 l 580.500 434.895 l 27.000 434.895 l f 581.250 435.645 m 581.250 412.237 l 580.500 412.237 l 580.500 434.895 l f 26.250 435.645 m 26.250 412.237 l 27.000 412.237 l 27.000 434.895 l f 0.271 0.267 0.267 rg BT 33.000 421.569 Td /F1 9.0 Tf [(*1st and 2nd are primers for the first and nested/seminested \(optional\) rounds of PCR, respectively.)] TJ ET 1.000 1.000 1.000 rg 26.250 255.526 555.000 156.711 re f 0.965 0.965 0.965 rg 27.000 399.208 119.339 12.280 re f 0.267 0.267 0.267 rg 26.625 411.112 119.714 0.750 re f 26.625 398.833 0.750 13.030 re f 0.271 0.267 0.267 rg BT 31.500 401.964 Td /F4 9.8 Tf [(Marker_primer name)] TJ ET 0.965 0.965 0.965 rg 146.339 399.208 284.895 12.280 re f 0.267 0.267 0.267 rg 146.339 411.112 284.895 0.750 re f 0.271 0.267 0.267 rg BT 150.839 401.964 Td /F4 9.8 Tf [(Primer sequence)] TJ ET 0.965 0.965 0.965 rg 431.234 399.208 90.588 12.280 re f 0.267 0.267 0.267 rg 431.234 411.112 90.588 0.750 re f 0.271 0.267 0.267 rg BT 435.734 401.964 Td /F4 9.8 Tf [(Optimized temp.)] TJ ET 0.965 0.965 0.965 rg 521.823 399.208 58.677 12.280 re f 0.267 0.267 0.267 rg 521.823 411.112 59.052 0.750 re f 580.125 398.833 0.750 13.030 re f 0.271 0.267 0.267 rg BT 526.323 401.964 Td /F4 9.8 Tf [(PCR*)] TJ ET 0.267 0.267 0.267 rg 26.625 398.833 120.089 0.750 re f 26.625 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 388.978 Td /F1 9.8 Tf [(hoxc6a_F215)] TJ ET 0.267 0.267 0.267 rg 145.964 398.833 285.645 0.750 re f 145.964 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 388.978 Td /F1 9.8 Tf [(5?-ATGGATCAAACGTGTTTCTTCA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 398.833 91.338 0.750 re f 430.859 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 388.978 Td /F1 9.8 Tf [(60-56)] TJ ET 0.267 0.267 0.267 rg 521.448 398.833 59.427 0.750 re f 521.448 382.951 0.750 16.631 re f 580.125 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 388.978 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 382.951 120.089 0.750 re f 26.625 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 373.096 Td /F1 9.8 Tf [(hoxc6a_R1129)] TJ ET 0.267 0.267 0.267 rg 145.964 382.951 285.645 0.750 re f 145.964 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 373.096 Td /F1 9.8 Tf [(5?-GCGATYTCGATGCGTCTGCG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 382.951 91.338 0.750 re f 430.859 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 373.096 Td /F1 9.8 Tf [(60-56/62-58)] TJ ET 0.267 0.267 0.267 rg 521.448 382.951 59.427 0.750 re f 521.448 367.070 0.750 16.631 re f 580.125 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 373.096 Td /F1 9.8 Tf [(1st/2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 367.070 120.089 0.750 re f 26.625 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 357.215 Td /F1 9.8 Tf [(hoxc6a_F386)] TJ ET 0.267 0.267 0.267 rg 145.964 367.070 285.645 0.750 re f 145.964 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 357.215 Td /F1 9.8 Tf [(5?-GATCTACCCGTGGATGCAGCG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 367.070 91.338 0.750 re f 430.859 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 357.215 Td /F1 9.8 Tf [(62-58)] TJ ET 0.267 0.267 0.267 rg 521.448 367.070 59.427 0.750 re f 521.448 351.189 0.750 16.631 re f 580.125 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 357.215 Td /F1 9.8 Tf [(2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 351.189 120.089 0.750 re f 26.625 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 341.334 Td /F1 9.8 Tf [(svep1_F7960)] TJ ET 0.267 0.267 0.267 rg 145.964 351.189 285.645 0.750 re f 145.964 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 341.334 Td /F1 9.8 Tf [(5?-CCTCCNCAYATYGAYTTTGGDGAMTA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 351.189 91.338 0.750 re f 430.859 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 341.334 Td /F1 9.8 Tf [(50)] TJ ET 0.267 0.267 0.267 rg 521.448 351.189 59.427 0.750 re f 521.448 335.308 0.750 16.631 re f 580.125 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 341.334 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 335.308 120.089 0.750 re f 26.625 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 325.453 Td /F1 9.8 Tf [(svep1_R8889)] TJ ET 0.267 0.267 0.267 rg 145.964 335.308 285.645 0.750 re f 145.964 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 325.453 Td /F1 9.8 Tf [(5?-TTCAGGWARCCRTGRCTRATRTCCTC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 335.308 91.338 0.750 re f 430.859 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 325.453 Td /F1 9.8 Tf [(50)] TJ ET 0.267 0.267 0.267 rg 521.448 335.308 59.427 0.750 re f 521.448 319.426 0.750 16.631 re f 580.125 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 325.453 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 319.426 120.089 0.750 re f 26.625 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 309.571 Td /F1 9.8 Tf [(vcpip_F84)] TJ ET 0.267 0.267 0.267 rg 145.964 319.426 285.645 0.750 re f 145.964 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 309.571 Td /F1 9.8 Tf [(5?-CCGGACCCGMARTGYCAGGC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 319.426 91.338 0.750 re f 430.859 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 309.571 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 319.426 59.427 0.750 re f 521.448 303.545 0.750 16.631 re f 580.125 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 309.571 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 303.545 120.089 0.750 re f 26.625 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 293.690 Td /F1 9.8 Tf [(vcpip_R946)] TJ ET 0.267 0.267 0.267 rg 145.964 303.545 285.645 0.750 re f 145.964 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 293.690 Td /F1 9.8 Tf [(5?-GTGRTTBCKGCYVGAGCTGCTCCABGC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 303.545 91.338 0.750 re f 430.859 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 293.690 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 303.545 59.427 0.750 re f 521.448 287.664 0.750 16.631 re f 580.125 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 293.690 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 287.664 120.089 0.750 re f 26.625 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 277.809 Td /F1 9.8 Tf [(vcpip_F134)] TJ ET 0.267 0.267 0.267 rg 145.964 287.664 285.645 0.750 re f 145.964 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 277.809 Td /F1 9.8 Tf [(5?-AGCATYGAGTGCACSGASTGCGGMCA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 287.664 91.338 0.750 re f 430.859 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 277.809 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 287.664 59.427 0.750 re f 521.448 271.783 0.750 16.631 re f 580.125 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 277.809 Td /F1 9.8 Tf [(2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 271.783 120.089 0.750 re f 26.625 255.901 120.089 0.750 re f 26.625 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 261.928 Td /F1 9.8 Tf [(vcpip_R930)] TJ ET 0.267 0.267 0.267 rg 145.964 271.783 285.645 0.750 re f 145.964 255.901 285.645 0.750 re f 145.964 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 261.928 Td /F1 9.8 Tf [(5?-CTGCTCCASGCRATGCAKATGGGYTTG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 271.783 91.338 0.750 re f 430.859 255.901 91.338 0.750 re f 430.859 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 261.928 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 271.783 59.427 0.750 re f 521.448 255.901 59.427 0.750 re f 521.448 255.901 0.750 16.631 re f 580.125 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 261.928 Td /F1 9.8 Tf [(2nd)] TJ ET BT 26.250 201.003 Td /F4 9.8 Tf [(Sequence alignment and phylogenetic analyses)] TJ ET BT 26.250 181.598 Td /F1 9.8 Tf [(Contigs were assembled from forward and reverse sequences using CodonCode Aligner v3.5.4 \(CodonCode Corporation\), )] TJ ET BT 26.250 169.693 Td /F1 9.8 Tf [(Sequencher v4 \(Gene Codes Corporation\), or Geneious Pro v4.5 \(Biomatters Ltd.\). Exon markers were aligned individually )] TJ ET BT 26.250 157.788 Td /F1 9.8 Tf [(based on their underlying reading frame in TranslatorX)] TJ ET 0.267 0.267 0.267 rg BT 261.976 159.296 Td /F4 8.7 Tf [(52)] TJ ET 0.271 0.267 0.267 rg BT 271.613 157.788 Td /F1 9.8 Tf [( using the MAFFT aligner)] TJ ET 0.267 0.267 0.267 rg BT 381.067 159.296 Td /F4 8.7 Tf [(53)] TJ ET 0.271 0.267 0.267 rg BT 390.704 157.788 Td /F1 9.8 Tf [(. The )] TJ ET BT 415.635 157.788 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 447.069 157.788 Td /F1 9.8 Tf [( and 16S sequences were )] TJ ET BT 26.250 145.884 Td /F1 9.8 Tf [(aligned with MAFFT v6.9)] TJ ET 0.267 0.267 0.267 rg BT 134.075 147.391 Td /F4 8.7 Tf [(53)] TJ ET 0.271 0.267 0.267 rg BT 143.713 145.884 Td /F1 9.8 Tf [( using 1000 iterations and the genafpair algorithm. Because nested PCR is highly prone to cross-)] TJ ET BT 26.250 133.979 Td /F1 9.8 Tf [(contamination, we vetted the data by visually inspecting individual gene trees estimated with the Geneious Tree Builder )] TJ ET BT 26.250 122.074 Td /F1 9.8 Tf [(algorithm in Geneious. To qualitatively assess gene-tree congruence, the final gene alignments were analyzed under maximum )] TJ ET BT 26.250 110.169 Td /F1 9.8 Tf [(likelihood \(ML\) in RAxML using ten independent runs for each; exon alignments were partitioned by codon position. Alternative )] TJ ET BT 26.250 98.265 Td /F1 9.8 Tf [(approaches to analyze combined data based on species-tree methods that account for gene-tree heterogeneity due to lineage )] TJ ET BT 26.250 86.360 Td /F1 9.8 Tf [(sorting \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 80.441 87.867 Td /F4 8.7 Tf [(54)] TJ ET 0.271 0.267 0.267 rg BT 90.078 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 92.487 87.867 Td /F4 8.7 Tf [(55)] TJ ET 0.271 0.267 0.267 rg BT 102.125 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 104.534 87.867 Td /F4 8.7 Tf [(56)] TJ ET 0.271 0.267 0.267 rg BT 114.171 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 116.581 87.867 Td /F4 8.7 Tf [(57)] TJ ET 0.271 0.267 0.267 rg BT 126.218 86.360 Td /F1 9.8 Tf [(\) could not be applied to this dataset due to high proportion of missing data \(see Results\).)] TJ ET BT 26.250 66.955 Td /F1 9.8 Tf [(Individual genes were concatenated using SequenceMatrix v1.7.8)] TJ ET 0.267 0.267 0.267 rg BT 310.228 68.462 Td /F4 8.7 Tf [(58)] TJ ET 0.271 0.267 0.267 rg BT 319.866 66.955 Td /F1 9.8 Tf [( or Geneious. Two datasets were assembled and analyzed )] TJ ET BT 26.250 55.050 Td /F1 9.8 Tf [(separately, one including all 1416 taxa with sequence data from three genes or more \(3+ dataset\) and a subset including 1020 )] TJ ET BT 26.250 43.146 Td /F1 9.8 Tf [(taxa with sequence data from seven genes or more \(7+ dataset\). Analyses of the 3+ dataset were performed under maximum )] TJ ET Q q 15.000 28.860 577.500 748.140 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(compared the )] TJ ET BT 88.572 767.476 Td /F5 9.8 Tf [(Danio rerio)] TJ ET BT 136.250 767.476 Td /F1 9.8 Tf [( and )] TJ ET BT 157.934 767.476 Td /F5 9.8 Tf [(Takifugu rubripes)] TJ ET BT 233.252 767.476 Td /F1 9.8 Tf [( genomes to identify single-copy genes with long exons \(>800 bp\) and )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(divergence levels suggesting they evolve at rates appropriate for phylogenetic resolution among distantly related taxa. Exons )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(markers were sequenced from 11 nuclear genes previously published by our group \()] TJ ET BT 389.857 743.667 Td /F5 9.8 Tf [(kiaa1239)] TJ ET BT 429.422 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 434.843 743.667 Td /F5 9.8 Tf [(ficd)] TJ ET BT 450.014 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 455.435 743.667 Td /F5 9.8 Tf [(myh6)] TJ ET BT 479.274 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 484.695 743.667 Td /F5 9.8 Tf [(panx2)] TJ ET BT 511.254 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 516.675 743.667 Td /F5 9.8 Tf [(plagl2)] TJ ET BT 542.688 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 548.109 743.667 Td /F5 9.8 Tf [(ptchd4)] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(\(=)] TJ ET BT 35.191 731.762 Td /F5 9.8 Tf [(ptr)] TJ ET BT 46.569 731.762 Td /F1 9.8 Tf [(\), )] TJ ET BT 55.237 731.762 Td /F5 9.8 Tf [(ripk4)] TJ ET BT 76.365 731.762 Td /F1 9.8 Tf [(, )] TJ ET BT 81.786 731.762 Td /F5 9.8 Tf [(sidkey)] TJ ET BT 109.418 731.762 Td /F1 9.8 Tf [(, )] TJ ET BT 114.839 731.762 Td /F5 9.8 Tf [(snx33)] TJ ET BT 140.852 731.762 Td /F1 9.8 Tf [( \(=)] TJ ET BT 152.503 731.762 Td /F5 9.8 Tf [(sh3px3)] TJ ET BT 183.937 731.762 Td /F1 9.8 Tf [(\), )] TJ ET BT 192.605 731.762 Td /F5 9.8 Tf [(tbr1b)] TJ ET BT 214.825 731.762 Td /F1 9.8 Tf [( \(=)] TJ ET BT 226.476 731.762 Td /F5 9.8 Tf [(tbr1)] TJ ET BT 243.275 731.762 Td /F1 9.8 Tf [(\), and )] TJ ET BT 270.917 731.762 Td /F5 9.8 Tf [(zic1)] TJ ET BT 288.252 731.762 Td /F1 9.8 Tf [(\) and three additional markers, including one intron \()] TJ ET BT 513.682 731.762 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 545.116 731.762 Td /F1 9.8 Tf [(\) and )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(two exons \()] TJ ET BT 76.102 719.857 Td /F5 9.8 Tf [(svep1)] TJ ET BT 102.115 719.857 Td /F1 9.8 Tf [(, and )] TJ ET BT 126.509 719.857 Td /F5 9.8 Tf [(vcpip)] TJ ET BT 149.266 719.857 Td /F1 9.8 Tf [(\), were newly developed for this study using the same approach. Sequence data from seven )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(additional markers, including EToL markers \()] TJ ET BT 219.680 707.952 Td /F5 9.8 Tf [(enc1)] TJ ET BT 240.818 707.952 Td /F1 9.8 Tf [(, )] TJ ET BT 246.239 707.952 Td /F5 9.8 Tf [(gtdc2)] TJ ET BT 270.088 707.952 Td /F1 9.8 Tf [( \(=)] TJ ET BT 281.739 707.952 Td /F5 9.8 Tf [(glyt)] TJ ET BT 296.910 707.952 Td /F1 9.8 Tf [(\), and )] TJ ET BT 324.551 707.952 Td /F5 9.8 Tf [(gpr85)] TJ ET BT 349.482 707.952 Td /F1 9.8 Tf [( \(=)] TJ ET BT 361.133 707.952 Td /F5 9.8 Tf [(sreb2)] TJ ET BT 385.518 707.952 Td /F1 9.8 Tf [(\)\) or markers developed by others \(16S )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(mtDNA, )] TJ ET BT 63.086 696.048 Td /F5 9.8 Tf [(rag1)] TJ ET BT 82.595 696.048 Td /F1 9.8 Tf [(, )] TJ ET BT 88.016 696.048 Td /F5 9.8 Tf [(rag2)] TJ ET BT 107.526 696.048 Td /F1 9.8 Tf [(, and )] TJ ET BT 131.921 696.048 Td /F5 9.8 Tf [(rh)] TJ ET BT 140.588 696.048 Td /F1 9.8 Tf [(\), were generated for our previous studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 348.683 697.555 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 358.320 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 360.729 697.555 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 370.367 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 372.776 697.555 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 382.413 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 384.823 697.555 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 394.460 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 396.869 697.555 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 406.507 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 408.916 697.555 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 418.553 696.048 Td /F1 9.8 Tf [(\) or obtained from NCBI, Ensembl, )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(or other genomic databases.)] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(A total of 1184 bony fish taxa were initially targeted for this study and samples were primarily obtained from the tissue repository )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(of the Ichthyology Collection at University of Kansas \(1129 samples\) or other collections. Of the initial list, samples for 18 taxa )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(either failed to amplify or belonged to duplicate species that were ultimately combined or discarded. Sixty taxa that produced )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(sequence data for one or two genes only were also discarded. Twenty-five additional taxa were excluded from the final matrix )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(because they had low genetic coverage and highly variable phylogenetic placement in preliminary analyses, as identified using )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(bootstrap trees obtained with RAxML v7.3)] TJ ET 0.267 0.267 0.267 rg BT 207.249 606.722 Td /F4 8.7 Tf [(49)] TJ ET 0.271 0.267 0.267 rg BT 216.886 605.214 Td /F1 9.8 Tf [( and the )] TJ ET 0.267 0.267 0.267 rg BT 254.833 605.214 Td /F1 9.8 Tf [(RogueNaRok server)] TJ ET BT 343.149 606.722 Td /F4 8.7 Tf [(50)] TJ ET 0.271 0.267 0.267 rg BT 352.786 605.214 Td /F1 9.8 Tf [(. Our final sampling thus included 1081 taxa and )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(sequence data from 335 additional taxa were obtained from previous EToL studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 409.942 594.817 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 419.579 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 421.988 594.817 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 431.626 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 434.035 594.817 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 443.672 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 446.082 594.817 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 455.719 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 458.128 594.817 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 467.766 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 470.175 594.817 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 479.812 593.310 Td /F1 9.8 Tf [(\) or public databases )] TJ ET BT 26.250 581.405 Td /F1 9.8 Tf [(\(Table S1\). In order to minimize missing data, some sequences retrieved from public databases were combined as genus-level )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(composite taxa \(52 taxa\). DNA extraction, amplification protocols via nested PCR, and primers followed previous studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 26.250 559.103 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 35.887 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 38.297 559.103 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 47.934 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 50.343 559.103 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 59.981 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 62.390 559.103 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 72.027 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 74.437 559.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 84.074 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 86.483 559.103 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 96.121 557.595 Td /F1 9.8 Tf [(\). Primer sequences and optimized PCR conditions used for the three new markers is presented in Table 1. The )] TJ ET BT 26.250 545.691 Td /F1 9.8 Tf [(PCR amplicons obtained were submitted for purification and sequencing in both directions to High Throughput Sequencing )] TJ ET BT 26.250 533.786 Td /F1 9.8 Tf [(Solutions \(HTSeq.org\) or other core facilities.)] TJ ET BT 26.250 514.381 Td /F1 9.8 Tf [(Fish diversity is represented in the phylogenetic data matrix by a sample of 1410 bony fish species \(of ca. 31000)] TJ ET 0.267 0.267 0.267 rg BT 510.182 515.888 Td /F4 8.7 Tf [(51)] TJ ET 0.271 0.267 0.267 rg BT 519.819 514.381 Td /F1 9.8 Tf [(\) plus four )] TJ ET BT 26.250 502.476 Td /F1 9.8 Tf [(tetrapod species and two chondrichthyan outgroups \(total 1416 terminals\). The taxonomic sampling of bony fishes consists of )] TJ ET BT 26.250 490.572 Td /F1 9.8 Tf [(1093 genera \(of ca. 4300\), 369 families \(of 502; see below\), and all traditionally recognized orders \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 473.336 492.079 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 478.155 490.572 Td /F1 9.8 Tf [(\). Our taxonomic )] TJ ET BT 26.250 478.667 Td /F1 9.8 Tf [(sampling emphasizes representation of percomorph groups, with 1037 \(of >15000\) species in 201 families. All scientific names )] TJ ET BT 26.250 466.762 Td /F1 9.8 Tf [(were checked against the )] TJ ET 0.267 0.267 0.267 rg BT 139.516 466.762 Td /F1 9.8 Tf [(Catalog of Fishes)] TJ ET BT 215.380 468.269 Td /F4 8.7 Tf [(51)] TJ ET 0.271 0.267 0.267 rg BT 225.018 466.762 Td /F1 9.8 Tf [(. A complete list of material examined is given in Table S1.)] TJ ET q 26.250 443.145 555.000 13.736 re W n 0.271 0.267 0.267 rg BT 26.250 445.892 Td /F1 9.8 Tf [(Table 1. Primers used for new markers developed and optimized PCR conditions.)] TJ ET Q 0.965 0.965 0.965 rg 26.250 412.237 555.000 23.408 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 435.645 m 581.250 435.645 l 580.500 434.895 l 27.000 434.895 l f 581.250 435.645 m 581.250 412.237 l 580.500 412.237 l 580.500 434.895 l f 26.250 435.645 m 26.250 412.237 l 27.000 412.237 l 27.000 434.895 l f 0.271 0.267 0.267 rg BT 33.000 421.569 Td /F1 9.0 Tf [(*1st and 2nd are primers for the first and nested/seminested \(optional\) rounds of PCR, respectively.)] TJ ET 1.000 1.000 1.000 rg 26.250 255.526 555.000 156.711 re f 0.965 0.965 0.965 rg 27.000 399.208 119.339 12.280 re f 0.267 0.267 0.267 rg 26.625 411.112 119.714 0.750 re f 26.625 398.833 0.750 13.030 re f 0.271 0.267 0.267 rg BT 31.500 401.964 Td /F4 9.8 Tf [(Marker_primer name)] TJ ET 0.965 0.965 0.965 rg 146.339 399.208 284.895 12.280 re f 0.267 0.267 0.267 rg 146.339 411.112 284.895 0.750 re f 0.271 0.267 0.267 rg BT 150.839 401.964 Td /F4 9.8 Tf [(Primer sequence)] TJ ET 0.965 0.965 0.965 rg 431.234 399.208 90.588 12.280 re f 0.267 0.267 0.267 rg 431.234 411.112 90.588 0.750 re f 0.271 0.267 0.267 rg BT 435.734 401.964 Td /F4 9.8 Tf [(Optimized temp.)] TJ ET 0.965 0.965 0.965 rg 521.823 399.208 58.677 12.280 re f 0.267 0.267 0.267 rg 521.823 411.112 59.052 0.750 re f 580.125 398.833 0.750 13.030 re f 0.271 0.267 0.267 rg BT 526.323 401.964 Td /F4 9.8 Tf [(PCR*)] TJ ET 0.267 0.267 0.267 rg 26.625 398.833 120.089 0.750 re f 26.625 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 388.978 Td /F1 9.8 Tf [(hoxc6a_F215)] TJ ET 0.267 0.267 0.267 rg 145.964 398.833 285.645 0.750 re f 145.964 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 388.978 Td /F1 9.8 Tf [(5?-ATGGATCAAACGTGTTTCTTCA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 398.833 91.338 0.750 re f 430.859 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 388.978 Td /F1 9.8 Tf [(60-56)] TJ ET 0.267 0.267 0.267 rg 521.448 398.833 59.427 0.750 re f 521.448 382.951 0.750 16.631 re f 580.125 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 388.978 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 382.951 120.089 0.750 re f 26.625 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 373.096 Td /F1 9.8 Tf [(hoxc6a_R1129)] TJ ET 0.267 0.267 0.267 rg 145.964 382.951 285.645 0.750 re f 145.964 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 373.096 Td /F1 9.8 Tf [(5?-GCGATYTCGATGCGTCTGCG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 382.951 91.338 0.750 re f 430.859 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 373.096 Td /F1 9.8 Tf [(60-56/62-58)] TJ ET 0.267 0.267 0.267 rg 521.448 382.951 59.427 0.750 re f 521.448 367.070 0.750 16.631 re f 580.125 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 373.096 Td /F1 9.8 Tf [(1st/2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 367.070 120.089 0.750 re f 26.625 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 357.215 Td /F1 9.8 Tf [(hoxc6a_F386)] TJ ET 0.267 0.267 0.267 rg 145.964 367.070 285.645 0.750 re f 145.964 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 357.215 Td /F1 9.8 Tf [(5?-GATCTACCCGTGGATGCAGCG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 367.070 91.338 0.750 re f 430.859 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 357.215 Td /F1 9.8 Tf [(62-58)] TJ ET 0.267 0.267 0.267 rg 521.448 367.070 59.427 0.750 re f 521.448 351.189 0.750 16.631 re f 580.125 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 357.215 Td /F1 9.8 Tf [(2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 351.189 120.089 0.750 re f 26.625 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 341.334 Td /F1 9.8 Tf [(svep1_F7960)] TJ ET 0.267 0.267 0.267 rg 145.964 351.189 285.645 0.750 re f 145.964 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 341.334 Td /F1 9.8 Tf [(5?-CCTCCNCAYATYGAYTTTGGDGAMTA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 351.189 91.338 0.750 re f 430.859 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 341.334 Td /F1 9.8 Tf [(50)] TJ ET 0.267 0.267 0.267 rg 521.448 351.189 59.427 0.750 re f 521.448 335.308 0.750 16.631 re f 580.125 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 341.334 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 335.308 120.089 0.750 re f 26.625 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 325.453 Td /F1 9.8 Tf [(svep1_R8889)] TJ ET 0.267 0.267 0.267 rg 145.964 335.308 285.645 0.750 re f 145.964 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 325.453 Td /F1 9.8 Tf [(5?-TTCAGGWARCCRTGRCTRATRTCCTC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 335.308 91.338 0.750 re f 430.859 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 325.453 Td /F1 9.8 Tf [(50)] TJ ET 0.267 0.267 0.267 rg 521.448 335.308 59.427 0.750 re f 521.448 319.426 0.750 16.631 re f 580.125 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 325.453 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 319.426 120.089 0.750 re f 26.625 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 309.571 Td /F1 9.8 Tf [(vcpip_F84)] TJ ET 0.267 0.267 0.267 rg 145.964 319.426 285.645 0.750 re f 145.964 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 309.571 Td /F1 9.8 Tf [(5?-CCGGACCCGMARTGYCAGGC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 319.426 91.338 0.750 re f 430.859 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 309.571 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 319.426 59.427 0.750 re f 521.448 303.545 0.750 16.631 re f 580.125 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 309.571 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 303.545 120.089 0.750 re f 26.625 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 293.690 Td /F1 9.8 Tf [(vcpip_R946)] TJ ET 0.267 0.267 0.267 rg 145.964 303.545 285.645 0.750 re f 145.964 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 293.690 Td /F1 9.8 Tf [(5?-GTGRTTBCKGCYVGAGCTGCTCCABGC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 303.545 91.338 0.750 re f 430.859 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 293.690 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 303.545 59.427 0.750 re f 521.448 287.664 0.750 16.631 re f 580.125 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 293.690 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 287.664 120.089 0.750 re f 26.625 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 277.809 Td /F1 9.8 Tf [(vcpip_F134)] TJ ET 0.267 0.267 0.267 rg 145.964 287.664 285.645 0.750 re f 145.964 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 277.809 Td /F1 9.8 Tf [(5?-AGCATYGAGTGCACSGASTGCGGMCA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 287.664 91.338 0.750 re f 430.859 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 277.809 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 287.664 59.427 0.750 re f 521.448 271.783 0.750 16.631 re f 580.125 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 277.809 Td /F1 9.8 Tf [(2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 271.783 120.089 0.750 re f 26.625 255.901 120.089 0.750 re f 26.625 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 261.928 Td /F1 9.8 Tf [(vcpip_R930)] TJ ET 0.267 0.267 0.267 rg 145.964 271.783 285.645 0.750 re f 145.964 255.901 285.645 0.750 re f 145.964 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 261.928 Td /F1 9.8 Tf [(5?-CTGCTCCASGCRATGCAKATGGGYTTG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 271.783 91.338 0.750 re f 430.859 255.901 91.338 0.750 re f 430.859 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 261.928 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 271.783 59.427 0.750 re f 521.448 255.901 59.427 0.750 re f 521.448 255.901 0.750 16.631 re f 580.125 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 261.928 Td /F1 9.8 Tf [(2nd)] TJ ET BT 26.250 201.003 Td /F4 9.8 Tf [(Sequence alignment and phylogenetic analyses)] TJ ET BT 26.250 181.598 Td /F1 9.8 Tf [(Contigs were assembled from forward and reverse sequences using CodonCode Aligner v3.5.4 \(CodonCode Corporation\), )] TJ ET BT 26.250 169.693 Td /F1 9.8 Tf [(Sequencher v4 \(Gene Codes Corporation\), or Geneious Pro v4.5 \(Biomatters Ltd.\). Exon markers were aligned individually )] TJ ET BT 26.250 157.788 Td /F1 9.8 Tf [(based on their underlying reading frame in TranslatorX)] TJ ET 0.267 0.267 0.267 rg BT 261.976 159.296 Td /F4 8.7 Tf [(52)] TJ ET 0.271 0.267 0.267 rg BT 271.613 157.788 Td /F1 9.8 Tf [( using the MAFFT aligner)] TJ ET 0.267 0.267 0.267 rg BT 381.067 159.296 Td /F4 8.7 Tf [(53)] TJ ET 0.271 0.267 0.267 rg BT 390.704 157.788 Td /F1 9.8 Tf [(. The )] TJ ET BT 415.635 157.788 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 447.069 157.788 Td /F1 9.8 Tf [( and 16S sequences were )] TJ ET BT 26.250 145.884 Td /F1 9.8 Tf [(aligned with MAFFT v6.9)] TJ ET 0.267 0.267 0.267 rg BT 134.075 147.391 Td /F4 8.7 Tf [(53)] TJ ET 0.271 0.267 0.267 rg BT 143.713 145.884 Td /F1 9.8 Tf [( using 1000 iterations and the genafpair algorithm. Because nested PCR is highly prone to cross-)] TJ ET BT 26.250 133.979 Td /F1 9.8 Tf [(contamination, we vetted the data by visually inspecting individual gene trees estimated with the Geneious Tree Builder )] TJ ET BT 26.250 122.074 Td /F1 9.8 Tf [(algorithm in Geneious. To qualitatively assess gene-tree congruence, the final gene alignments were analyzed under maximum )] TJ ET BT 26.250 110.169 Td /F1 9.8 Tf [(likelihood \(ML\) in RAxML using ten independent runs for each; exon alignments were partitioned by codon position. Alternative )] TJ ET BT 26.250 98.265 Td /F1 9.8 Tf [(approaches to analyze combined data based on species-tree methods that account for gene-tree heterogeneity due to lineage )] TJ ET BT 26.250 86.360 Td /F1 9.8 Tf [(sorting \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 80.441 87.867 Td /F4 8.7 Tf [(54)] TJ ET 0.271 0.267 0.267 rg BT 90.078 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 92.487 87.867 Td /F4 8.7 Tf [(55)] TJ ET 0.271 0.267 0.267 rg BT 102.125 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 104.534 87.867 Td /F4 8.7 Tf [(56)] TJ ET 0.271 0.267 0.267 rg BT 114.171 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 116.581 87.867 Td /F4 8.7 Tf [(57)] TJ ET 0.271 0.267 0.267 rg BT 126.218 86.360 Td /F1 9.8 Tf [(\) could not be applied to this dataset due to high proportion of missing data \(see Results\).)] TJ ET BT 26.250 66.955 Td /F1 9.8 Tf [(Individual genes were concatenated using SequenceMatrix v1.7.8)] TJ ET 0.267 0.267 0.267 rg BT 310.228 68.462 Td /F4 8.7 Tf [(58)] TJ ET 0.271 0.267 0.267 rg BT 319.866 66.955 Td /F1 9.8 Tf [( or Geneious. Two datasets were assembled and analyzed )] TJ ET BT 26.250 55.050 Td /F1 9.8 Tf [(separately, one including all 1416 taxa with sequence data from three genes or more \(3+ dataset\) and a subset including 1020 )] TJ ET BT 26.250 43.146 Td /F1 9.8 Tf [(taxa with sequence data from seven genes or more \(7+ dataset\). Analyses of the 3+ dataset were performed under maximum )] TJ ET Q q 15.000 28.860 577.500 748.140 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(compared the )] TJ ET BT 88.572 767.476 Td /F5 9.8 Tf [(Danio rerio)] TJ ET BT 136.250 767.476 Td /F1 9.8 Tf [( and )] TJ ET BT 157.934 767.476 Td /F5 9.8 Tf [(Takifugu rubripes)] TJ ET BT 233.252 767.476 Td /F1 9.8 Tf [( genomes to identify single-copy genes with long exons \(>800 bp\) and )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(divergence levels suggesting they evolve at rates appropriate for phylogenetic resolution among distantly related taxa. Exons )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(markers were sequenced from 11 nuclear genes previously published by our group \()] TJ ET BT 389.857 743.667 Td /F5 9.8 Tf [(kiaa1239)] TJ ET BT 429.422 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 434.843 743.667 Td /F5 9.8 Tf [(ficd)] TJ ET BT 450.014 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 455.435 743.667 Td /F5 9.8 Tf [(myh6)] TJ ET BT 479.274 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 484.695 743.667 Td /F5 9.8 Tf [(panx2)] TJ ET BT 511.254 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 516.675 743.667 Td /F5 9.8 Tf [(plagl2)] TJ ET BT 542.688 743.667 Td /F1 9.8 Tf [(, )] TJ ET BT 548.109 743.667 Td /F5 9.8 Tf [(ptchd4)] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(\(=)] TJ ET BT 35.191 731.762 Td /F5 9.8 Tf [(ptr)] TJ ET BT 46.569 731.762 Td /F1 9.8 Tf [(\), )] TJ ET BT 55.237 731.762 Td /F5 9.8 Tf [(ripk4)] TJ ET BT 76.365 731.762 Td /F1 9.8 Tf [(, )] TJ ET BT 81.786 731.762 Td /F5 9.8 Tf [(sidkey)] TJ ET BT 109.418 731.762 Td /F1 9.8 Tf [(, )] TJ ET BT 114.839 731.762 Td /F5 9.8 Tf [(snx33)] TJ ET BT 140.852 731.762 Td /F1 9.8 Tf [( \(=)] TJ ET BT 152.503 731.762 Td /F5 9.8 Tf [(sh3px3)] TJ ET BT 183.937 731.762 Td /F1 9.8 Tf [(\), )] TJ ET BT 192.605 731.762 Td /F5 9.8 Tf [(tbr1b)] TJ ET BT 214.825 731.762 Td /F1 9.8 Tf [( \(=)] TJ ET BT 226.476 731.762 Td /F5 9.8 Tf [(tbr1)] TJ ET BT 243.275 731.762 Td /F1 9.8 Tf [(\), and )] TJ ET BT 270.917 731.762 Td /F5 9.8 Tf [(zic1)] TJ ET BT 288.252 731.762 Td /F1 9.8 Tf [(\) and three additional markers, including one intron \()] TJ ET BT 513.682 731.762 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 545.116 731.762 Td /F1 9.8 Tf [(\) and )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(two exons \()] TJ ET BT 76.102 719.857 Td /F5 9.8 Tf [(svep1)] TJ ET BT 102.115 719.857 Td /F1 9.8 Tf [(, and )] TJ ET BT 126.509 719.857 Td /F5 9.8 Tf [(vcpip)] TJ ET BT 149.266 719.857 Td /F1 9.8 Tf [(\), were newly developed for this study using the same approach. Sequence data from seven )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(additional markers, including EToL markers \()] TJ ET BT 219.680 707.952 Td /F5 9.8 Tf [(enc1)] TJ ET BT 240.818 707.952 Td /F1 9.8 Tf [(, )] TJ ET BT 246.239 707.952 Td /F5 9.8 Tf [(gtdc2)] TJ ET BT 270.088 707.952 Td /F1 9.8 Tf [( \(=)] TJ ET BT 281.739 707.952 Td /F5 9.8 Tf [(glyt)] TJ ET BT 296.910 707.952 Td /F1 9.8 Tf [(\), and )] TJ ET BT 324.551 707.952 Td /F5 9.8 Tf [(gpr85)] TJ ET BT 349.482 707.952 Td /F1 9.8 Tf [( \(=)] TJ ET BT 361.133 707.952 Td /F5 9.8 Tf [(sreb2)] TJ ET BT 385.518 707.952 Td /F1 9.8 Tf [(\)\) or markers developed by others \(16S )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(mtDNA, )] TJ ET BT 63.086 696.048 Td /F5 9.8 Tf [(rag1)] TJ ET BT 82.595 696.048 Td /F1 9.8 Tf [(, )] TJ ET BT 88.016 696.048 Td /F5 9.8 Tf [(rag2)] TJ ET BT 107.526 696.048 Td /F1 9.8 Tf [(, and )] TJ ET BT 131.921 696.048 Td /F5 9.8 Tf [(rh)] TJ ET BT 140.588 696.048 Td /F1 9.8 Tf [(\), were generated for our previous studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 348.683 697.555 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 358.320 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 360.729 697.555 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 370.367 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 372.776 697.555 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 382.413 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 384.823 697.555 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 394.460 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 396.869 697.555 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 406.507 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 408.916 697.555 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 418.553 696.048 Td /F1 9.8 Tf [(\) or obtained from NCBI, Ensembl, )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(or other genomic databases.)] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(A total of 1184 bony fish taxa were initially targeted for this study and samples were primarily obtained from the tissue repository )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(of the Ichthyology Collection at University of Kansas \(1129 samples\) or other collections. Of the initial list, samples for 18 taxa )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(either failed to amplify or belonged to duplicate species that were ultimately combined or discarded. Sixty taxa that produced )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(sequence data for one or two genes only were also discarded. Twenty-five additional taxa were excluded from the final matrix )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(because they had low genetic coverage and highly variable phylogenetic placement in preliminary analyses, as identified using )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(bootstrap trees obtained with RAxML v7.3)] TJ ET 0.267 0.267 0.267 rg BT 207.249 606.722 Td /F4 8.7 Tf [(49)] TJ ET 0.271 0.267 0.267 rg BT 216.886 605.214 Td /F1 9.8 Tf [( and the )] TJ ET 0.267 0.267 0.267 rg BT 254.833 605.214 Td /F1 9.8 Tf [(RogueNaRok server)] TJ ET BT 343.149 606.722 Td /F4 8.7 Tf [(50)] TJ ET 0.271 0.267 0.267 rg BT 352.786 605.214 Td /F1 9.8 Tf [(. Our final sampling thus included 1081 taxa and )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(sequence data from 335 additional taxa were obtained from previous EToL studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 409.942 594.817 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 419.579 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 421.988 594.817 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 431.626 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 434.035 594.817 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 443.672 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 446.082 594.817 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 455.719 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 458.128 594.817 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 467.766 597.198 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 470.175 594.817 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 479.812 593.310 Td /F1 9.8 Tf [(\) or public databases )] TJ ET BT 26.250 581.405 Td /F1 9.8 Tf [(\(Table S1\). In order to minimize missing data, some sequences retrieved from public databases were combined as genus-level )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(composite taxa \(52 taxa\). DNA extraction, amplification protocols via nested PCR, and primers followed previous studies \(e.g., )] TJ ET 0.267 0.267 0.267 rg BT 26.250 559.103 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 35.887 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 38.297 559.103 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 47.934 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 50.343 559.103 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 59.981 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 62.390 559.103 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 72.027 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 74.437 559.103 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 84.074 561.484 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 86.483 559.103 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 96.121 557.595 Td /F1 9.8 Tf [(\). Primer sequences and optimized PCR conditions used for the three new markers is presented in Table 1. The )] TJ ET BT 26.250 545.691 Td /F1 9.8 Tf [(PCR amplicons obtained were submitted for purification and sequencing in both directions to High Throughput Sequencing )] TJ ET BT 26.250 533.786 Td /F1 9.8 Tf [(Solutions \(HTSeq.org\) or other core facilities.)] TJ ET BT 26.250 514.381 Td /F1 9.8 Tf [(Fish diversity is represented in the phylogenetic data matrix by a sample of 1410 bony fish species \(of ca. 31000)] TJ ET 0.267 0.267 0.267 rg BT 510.182 515.888 Td /F4 8.7 Tf [(51)] TJ ET 0.271 0.267 0.267 rg BT 519.819 514.381 Td /F1 9.8 Tf [(\) plus four )] TJ ET BT 26.250 502.476 Td /F1 9.8 Tf [(tetrapod species and two chondrichthyan outgroups \(total 1416 terminals\). The taxonomic sampling of bony fishes consists of )] TJ ET BT 26.250 490.572 Td /F1 9.8 Tf [(1093 genera \(of ca. 4300\), 369 families \(of 502; see below\), and all traditionally recognized orders \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 473.336 492.079 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 478.155 490.572 Td /F1 9.8 Tf [(\). Our taxonomic )] TJ ET BT 26.250 478.667 Td /F1 9.8 Tf [(sampling emphasizes representation of percomorph groups, with 1037 \(of >15000\) species in 201 families. All scientific names )] TJ ET BT 26.250 466.762 Td /F1 9.8 Tf [(were checked against the )] TJ ET 0.267 0.267 0.267 rg BT 139.516 466.762 Td /F1 9.8 Tf [(Catalog of Fishes)] TJ ET BT 215.380 468.269 Td /F4 8.7 Tf [(51)] TJ ET 0.271 0.267 0.267 rg BT 225.018 466.762 Td /F1 9.8 Tf [(. A complete list of material examined is given in Table S1.)] TJ ET q 26.250 443.145 555.000 13.736 re W n 0.271 0.267 0.267 rg BT 26.250 445.892 Td /F1 9.8 Tf [(Table 1. Primers used for new markers developed and optimized PCR conditions.)] TJ ET Q 0.965 0.965 0.965 rg 26.250 412.237 555.000 23.408 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 435.645 m 581.250 435.645 l 580.500 434.895 l 27.000 434.895 l f 581.250 435.645 m 581.250 412.237 l 580.500 412.237 l 580.500 434.895 l f 26.250 435.645 m 26.250 412.237 l 27.000 412.237 l 27.000 434.895 l f 0.271 0.267 0.267 rg BT 33.000 421.569 Td /F1 9.0 Tf [(*1st and 2nd are primers for the first and nested/seminested \(optional\) rounds of PCR, respectively.)] TJ ET 1.000 1.000 1.000 rg 26.250 255.526 555.000 156.711 re f 0.965 0.965 0.965 rg 27.000 399.208 119.339 12.280 re f 0.267 0.267 0.267 rg 26.625 411.112 119.714 0.750 re f 26.625 398.833 0.750 13.030 re f 0.271 0.267 0.267 rg BT 31.500 401.964 Td /F4 9.8 Tf [(Marker_primer name)] TJ ET 0.965 0.965 0.965 rg 146.339 399.208 284.895 12.280 re f 0.267 0.267 0.267 rg 146.339 411.112 284.895 0.750 re f 0.271 0.267 0.267 rg BT 150.839 401.964 Td /F4 9.8 Tf [(Primer sequence)] TJ ET 0.965 0.965 0.965 rg 431.234 399.208 90.588 12.280 re f 0.267 0.267 0.267 rg 431.234 411.112 90.588 0.750 re f 0.271 0.267 0.267 rg BT 435.734 401.964 Td /F4 9.8 Tf [(Optimized temp.)] TJ ET 0.965 0.965 0.965 rg 521.823 399.208 58.677 12.280 re f 0.267 0.267 0.267 rg 521.823 411.112 59.052 0.750 re f 580.125 398.833 0.750 13.030 re f 0.271 0.267 0.267 rg BT 526.323 401.964 Td /F4 9.8 Tf [(PCR*)] TJ ET 0.267 0.267 0.267 rg 26.625 398.833 120.089 0.750 re f 26.625 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 388.978 Td /F1 9.8 Tf [(hoxc6a_F215)] TJ ET 0.267 0.267 0.267 rg 145.964 398.833 285.645 0.750 re f 145.964 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 388.978 Td /F1 9.8 Tf [(5?-ATGGATCAAACGTGTTTCTTCA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 398.833 91.338 0.750 re f 430.859 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 388.978 Td /F1 9.8 Tf [(60-56)] TJ ET 0.267 0.267 0.267 rg 521.448 398.833 59.427 0.750 re f 521.448 382.951 0.750 16.631 re f 580.125 382.951 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 388.978 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 382.951 120.089 0.750 re f 26.625 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 373.096 Td /F1 9.8 Tf [(hoxc6a_R1129)] TJ ET 0.267 0.267 0.267 rg 145.964 382.951 285.645 0.750 re f 145.964 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 373.096 Td /F1 9.8 Tf [(5?-GCGATYTCGATGCGTCTGCG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 382.951 91.338 0.750 re f 430.859 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 373.096 Td /F1 9.8 Tf [(60-56/62-58)] TJ ET 0.267 0.267 0.267 rg 521.448 382.951 59.427 0.750 re f 521.448 367.070 0.750 16.631 re f 580.125 367.070 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 373.096 Td /F1 9.8 Tf [(1st/2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 367.070 120.089 0.750 re f 26.625 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 357.215 Td /F1 9.8 Tf [(hoxc6a_F386)] TJ ET 0.267 0.267 0.267 rg 145.964 367.070 285.645 0.750 re f 145.964 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 357.215 Td /F1 9.8 Tf [(5?-GATCTACCCGTGGATGCAGCG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 367.070 91.338 0.750 re f 430.859 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 357.215 Td /F1 9.8 Tf [(62-58)] TJ ET 0.267 0.267 0.267 rg 521.448 367.070 59.427 0.750 re f 521.448 351.189 0.750 16.631 re f 580.125 351.189 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 357.215 Td /F1 9.8 Tf [(2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 351.189 120.089 0.750 re f 26.625 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 341.334 Td /F1 9.8 Tf [(svep1_F7960)] TJ ET 0.267 0.267 0.267 rg 145.964 351.189 285.645 0.750 re f 145.964 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 341.334 Td /F1 9.8 Tf [(5?-CCTCCNCAYATYGAYTTTGGDGAMTA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 351.189 91.338 0.750 re f 430.859 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 341.334 Td /F1 9.8 Tf [(50)] TJ ET 0.267 0.267 0.267 rg 521.448 351.189 59.427 0.750 re f 521.448 335.308 0.750 16.631 re f 580.125 335.308 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 341.334 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 335.308 120.089 0.750 re f 26.625 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 325.453 Td /F1 9.8 Tf [(svep1_R8889)] TJ ET 0.267 0.267 0.267 rg 145.964 335.308 285.645 0.750 re f 145.964 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 325.453 Td /F1 9.8 Tf [(5?-TTCAGGWARCCRTGRCTRATRTCCTC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 335.308 91.338 0.750 re f 430.859 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 325.453 Td /F1 9.8 Tf [(50)] TJ ET 0.267 0.267 0.267 rg 521.448 335.308 59.427 0.750 re f 521.448 319.426 0.750 16.631 re f 580.125 319.426 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 325.453 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 319.426 120.089 0.750 re f 26.625 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 309.571 Td /F1 9.8 Tf [(vcpip_F84)] TJ ET 0.267 0.267 0.267 rg 145.964 319.426 285.645 0.750 re f 145.964 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 309.571 Td /F1 9.8 Tf [(5?-CCGGACCCGMARTGYCAGGC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 319.426 91.338 0.750 re f 430.859 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 309.571 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 319.426 59.427 0.750 re f 521.448 303.545 0.750 16.631 re f 580.125 303.545 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 309.571 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 303.545 120.089 0.750 re f 26.625 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 293.690 Td /F1 9.8 Tf [(vcpip_R946)] TJ ET 0.267 0.267 0.267 rg 145.964 303.545 285.645 0.750 re f 145.964 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 293.690 Td /F1 9.8 Tf [(5?-GTGRTTBCKGCYVGAGCTGCTCCABGC-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 303.545 91.338 0.750 re f 430.859 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 293.690 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 303.545 59.427 0.750 re f 521.448 287.664 0.750 16.631 re f 580.125 287.664 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 293.690 Td /F1 9.8 Tf [(1st)] TJ ET 0.267 0.267 0.267 rg 26.625 287.664 120.089 0.750 re f 26.625 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 277.809 Td /F1 9.8 Tf [(vcpip_F134)] TJ ET 0.267 0.267 0.267 rg 145.964 287.664 285.645 0.750 re f 145.964 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 277.809 Td /F1 9.8 Tf [(5?-AGCATYGAGTGCACSGASTGCGGMCA-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 287.664 91.338 0.750 re f 430.859 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 277.809 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 287.664 59.427 0.750 re f 521.448 271.783 0.750 16.631 re f 580.125 271.783 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 277.809 Td /F1 9.8 Tf [(2nd)] TJ ET 0.267 0.267 0.267 rg 26.625 271.783 120.089 0.750 re f 26.625 255.901 120.089 0.750 re f 26.625 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 261.928 Td /F1 9.8 Tf [(vcpip_R930)] TJ ET 0.267 0.267 0.267 rg 145.964 271.783 285.645 0.750 re f 145.964 255.901 285.645 0.750 re f 145.964 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 151.214 261.928 Td /F1 9.8 Tf [(5?-CTGCTCCASGCRATGCAKATGGGYTTG-3?)] TJ ET 0.267 0.267 0.267 rg 430.859 271.783 91.338 0.750 re f 430.859 255.901 91.338 0.750 re f 430.859 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 436.109 261.928 Td /F1 9.8 Tf [(52)] TJ ET 0.267 0.267 0.267 rg 521.448 271.783 59.427 0.750 re f 521.448 255.901 59.427 0.750 re f 521.448 255.901 0.750 16.631 re f 580.125 255.901 0.750 16.631 re f 0.271 0.267 0.267 rg BT 526.698 261.928 Td /F1 9.8 Tf [(2nd)] TJ ET BT 26.250 201.003 Td /F4 9.8 Tf [(Sequence alignment and phylogenetic analyses)] TJ ET BT 26.250 181.598 Td /F1 9.8 Tf [(Contigs were assembled from forward and reverse sequences using CodonCode Aligner v3.5.4 \(CodonCode Corporation\), )] TJ ET BT 26.250 169.693 Td /F1 9.8 Tf [(Sequencher v4 \(Gene Codes Corporation\), or Geneious Pro v4.5 \(Biomatters Ltd.\). Exon markers were aligned individually )] TJ ET BT 26.250 157.788 Td /F1 9.8 Tf [(based on their underlying reading frame in TranslatorX)] TJ ET 0.267 0.267 0.267 rg BT 261.976 159.296 Td /F4 8.7 Tf [(52)] TJ ET 0.271 0.267 0.267 rg BT 271.613 157.788 Td /F1 9.8 Tf [( using the MAFFT aligner)] TJ ET 0.267 0.267 0.267 rg BT 381.067 159.296 Td /F4 8.7 Tf [(53)] TJ ET 0.271 0.267 0.267 rg BT 390.704 157.788 Td /F1 9.8 Tf [(. The )] TJ ET BT 415.635 157.788 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 447.069 157.788 Td /F1 9.8 Tf [( and 16S sequences were )] TJ ET BT 26.250 145.884 Td /F1 9.8 Tf [(aligned with MAFFT v6.9)] TJ ET 0.267 0.267 0.267 rg BT 134.075 147.391 Td /F4 8.7 Tf [(53)] TJ ET 0.271 0.267 0.267 rg BT 143.713 145.884 Td /F1 9.8 Tf [( using 1000 iterations and the genafpair algorithm. Because nested PCR is highly prone to cross-)] TJ ET BT 26.250 133.979 Td /F1 9.8 Tf [(contamination, we vetted the data by visually inspecting individual gene trees estimated with the Geneious Tree Builder )] TJ ET BT 26.250 122.074 Td /F1 9.8 Tf [(algorithm in Geneious. To qualitatively assess gene-tree congruence, the final gene alignments were analyzed under maximum )] TJ ET BT 26.250 110.169 Td /F1 9.8 Tf [(likelihood \(ML\) in RAxML using ten independent runs for each; exon alignments were partitioned by codon position. Alternative )] TJ ET BT 26.250 98.265 Td /F1 9.8 Tf [(approaches to analyze combined data based on species-tree methods that account for gene-tree heterogeneity due to lineage )] TJ ET BT 26.250 86.360 Td /F1 9.8 Tf [(sorting \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 80.441 87.867 Td /F4 8.7 Tf [(54)] TJ ET 0.271 0.267 0.267 rg BT 90.078 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 92.487 87.867 Td /F4 8.7 Tf [(55)] TJ ET 0.271 0.267 0.267 rg BT 102.125 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 104.534 87.867 Td /F4 8.7 Tf [(56)] TJ ET 0.271 0.267 0.267 rg BT 114.171 90.248 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 116.581 87.867 Td /F4 8.7 Tf [(57)] TJ ET 0.271 0.267 0.267 rg BT 126.218 86.360 Td /F1 9.8 Tf [(\) could not be applied to this dataset due to high proportion of missing data \(see Results\).)] TJ ET BT 26.250 66.955 Td /F1 9.8 Tf [(Individual genes were concatenated using SequenceMatrix v1.7.8)] TJ ET 0.267 0.267 0.267 rg BT 310.228 68.462 Td /F4 8.7 Tf [(58)] TJ ET 0.271 0.267 0.267 rg BT 319.866 66.955 Td /F1 9.8 Tf [( or Geneious. Two datasets were assembled and analyzed )] TJ ET BT 26.250 55.050 Td /F1 9.8 Tf [(separately, one including all 1416 taxa with sequence data from three genes or more \(3+ dataset\) and a subset including 1020 )] TJ ET BT 26.250 43.146 Td /F1 9.8 Tf [(taxa with sequence data from seven genes or more \(7+ dataset\). Analyses of the 3+ dataset were performed under maximum )] TJ ET Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(3)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 595 0 obj << /Type /Annot /Subtype /Link /A 596 0 R /Border [0 0 0] /H /I /Rect [ 348.6825 696.7532 358.3198 705.5715 ] >> endobj 596 0 obj << /Type /Action >> endobj 597 0 obj << /Type /Annot /Subtype /Link /A 598 0 R /Border [0 0 0] /H /I /Rect [ 360.7292 696.7532 370.3665 705.5715 ] >> endobj 598 0 obj << /Type /Action >> endobj 599 0 obj << /Type /Annot /Subtype /Link /A 600 0 R /Border [0 0 0] /H /I /Rect [ 372.7758 696.7532 382.4132 705.5715 ] >> endobj 600 0 obj << /Type /Action >> endobj 601 0 obj << /Type /Annot /Subtype /Link /A 602 0 R /Border [0 0 0] /H /I /Rect [ 384.8225 696.7532 394.4598 705.5715 ] >> endobj 602 0 obj << /Type /Action >> endobj 603 0 obj << /Type /Annot /Subtype /Link /A 604 0 R /Border [0 0 0] /H /I /Rect [ 396.8692 696.7532 406.5065 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/F1 9.8 Tf [(likelihood \(ML\) using two partitioning schemes, a simple one determined arbitrarily with 5 data partitions \(3 codon positions )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(across all exons plus 16S and )] TJ ET BT 158.480 755.571 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 189.913 755.571 Td /F1 9.8 Tf [(\), and a more complex scheme with 24 partitions \(a combination of codon positions and )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(individual genes plus 16S and )] TJ ET BT 158.489 743.667 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 189.923 743.667 Td /F1 9.8 Tf [(\) indicated by PartitionFinder)] TJ ET 0.267 0.267 0.267 rg BT 314.012 745.174 Td /F4 8.7 Tf [(59)] TJ ET 0.271 0.267 0.267 rg BT 323.649 743.667 Td /F1 9.8 Tf [(. To make the PartitionFinder analysis scalable, a )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(representative subset of 201 taxa was run under the Bayesian Information Criterion)] TJ ET 0.267 0.267 0.267 rg BT 385.001 733.269 Td /F4 8.7 Tf [(59)] TJ ET 0.271 0.267 0.267 rg BT 394.639 731.762 Td /F1 9.8 Tf [(. The 7+ dataset was analyzed with the 24-)] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(partition scheme only. Analyses for both datasets and partition schemes were conducted in RAxML using 30 independent )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(replicates under the GTRGAMMA model. Nodal support was assessed using the rapid bootstrapping algorithm of RAxML with )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(1000 replicates estimated under the GTRCAT model)] TJ ET 0.267 0.267 0.267 rg BT 253.298 697.555 Td /F4 8.7 Tf [(60)] TJ ET 0.271 0.267 0.267 rg BT 262.936 696.048 Td /F1 9.8 Tf [(, and the collection of sample trees was used to draw the bibartition )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(frequencies on the optimal tree. All RAxML analyses were conducted in the )] TJ ET 0.267 0.267 0.267 rg BT 353.021 684.143 Td /F1 9.8 Tf [(CIPRES portal v3.1)] TJ ET 0.271 0.267 0.267 rg BT 437.554 684.143 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(For comparison purposes, the 3+ dataset was also analyzed under implied-weighted parsimony)] TJ ET 0.267 0.267 0.267 rg BT 437.817 666.245 Td /F4 8.7 Tf [(61)] TJ ET 0.271 0.267 0.267 rg BT 447.454 664.738 Td /F1 9.8 Tf [(. The optimal tree search and )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(bootstrap trees were set to run independently. Gaps were treated as missing characters and all parsimony uninformative )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(characters were ignored. A relatively mild value of )] TJ ET BT 244.075 640.929 Td /F5 9.8 Tf [(k)] TJ ET BT 248.950 640.929 Td /F1 9.8 Tf [( \(20\) was chosen arbitrarily due to computational limitations to explore )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(sensitivity of the nodes to other weighting functions. Tree searches were performed in TNT 1.1)] TJ ET 0.267 0.267 0.267 rg BT 433.215 630.531 Td /F4 8.7 Tf [(63)] TJ ET 0.271 0.267 0.267 rg BT 442.852 629.024 Td /F1 9.8 Tf [( using a driven-search strategy )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(combining the following tree-search algorithms: ratchet, drift, sectorial searches and tree fusion. The exhaustiveness of the )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(search parameters was self-adjusted every 2 hits of the current best score. To maximize tree-space exploration, the final )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(searches implemented tree-bisection-reconnection \(TBR\). A strict consensus of nine equally optimal trees \(length 407187 steps; )] TJ ET BT 26.250 581.405 Td /F1 9.8 Tf [(fit 7309.19\) was computed. Bootstrap search strategies were relaxed to ten random addition sequences and TBR, saving only )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(one tree per replicate \(1000 replicates\); bootstrap bipartition frequencies were drawn on the consensus tree.)] TJ ET BT 26.250 550.095 Td /F4 9.8 Tf [(Divergence time estimates)] TJ ET BT 26.250 530.691 Td /F1 9.8 Tf [(Time-tree estimation in a Bayesian framework using the complete dataset was computationally infeasible. Thus, we selected a )] TJ ET BT 26.250 518.786 Td /F1 9.8 Tf [(subset of 202 taxa for 18 genes that had representation of: \(i\) all major bony fish lineages, \(ii\) lineages encompassing the nodes )] TJ ET BT 26.250 506.881 Td /F1 9.8 Tf [(in which the assignment of fossil calibrations is most informative, \(iii\) taxa with the highest genetic coverage to minimize missing )] TJ ET BT 26.250 494.976 Td /F1 9.8 Tf [(data in the data matrix \(the markers )] TJ ET BT 182.855 494.976 Td /F5 9.8 Tf [(vcpip)] TJ ET BT 205.611 494.976 Td /F1 9.8 Tf [(, )] TJ ET BT 211.032 494.976 Td /F5 9.8 Tf [(svep1)] TJ ET BT 237.045 494.976 Td /F1 9.8 Tf [(, )] TJ ET BT 242.466 494.976 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 273.900 494.976 Td /F1 9.8 Tf [(, including a high proportion of missing data, were also excluded\). )] TJ ET BT 26.250 483.072 Td /F1 9.8 Tf [(Divergence times were estimated in BEAST v1.7 using the uncorrelated log-normal \(UCLN\) clock-model)] TJ ET 0.267 0.267 0.267 rg BT 474.887 484.579 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 484.524 483.072 Td /F1 9.8 Tf [(. Sixty calibration )] TJ ET BT 26.250 471.167 Td /F1 9.8 Tf [(points were selected as priors for divergence time estimates, of which 58 are based on previous studies)] TJ ET 0.267 0.267 0.267 rg BT 472.771 472.674 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 482.408 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 484.817 472.674 Td /F4 8.7 Tf [(64)] TJ ET 0.271 0.267 0.267 rg BT 494.455 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 496.864 472.674 Td /F4 8.7 Tf [(65)] TJ ET 0.271 0.267 0.267 rg BT 506.501 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 508.911 472.674 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 518.548 471.167 Td /F1 9.8 Tf [( and two )] TJ ET BT 26.250 459.262 Td /F1 9.8 Tf [(\(calibrations 45 and 60\) are proposed here \(Appendix 1\). However, the actual BEAST analysis conducted for this study included )] TJ ET BT 26.250 447.357 Td /F1 9.8 Tf [(59 calibrations only \(see details under calibration 60, Appendix 1\). A starting chronogram that satisfied all priors \(e.g., )] TJ ET BT 26.250 435.453 Td /F1 9.8 Tf [(monophyly and initial divergence times\) was generated under penalized likelihood in r8s v1.71)] TJ ET 0.267 0.267 0.267 rg BT 432.133 436.960 Td /F4 8.7 Tf [(67)] TJ ET 0.271 0.267 0.267 rg BT 441.770 435.453 Td /F1 9.8 Tf [( using the RAxML tree. To )] TJ ET BT 26.250 423.548 Td /F1 9.8 Tf [(model branching rates on the tree, a birth-death process was used for the tree prior with initial birth rate = 1.0 and death rate = )] TJ ET BT 26.250 411.643 Td /F1 9.8 Tf [(0.5. The substitution model was GTR+G with 4 rate classes and the data were partitioned into 4 categories with independent )] TJ ET BT 26.250 399.738 Td /F1 9.8 Tf [(parameter estimation: three codon positions across exons of protein-coding genes plus 16S. Clock and tree priors were linked )] TJ ET BT 26.250 387.834 Td /F1 9.8 Tf [(across partitions. Five replicates of the Markov chain Monte Carlo \(MCMC\) analyses were each run for 200 million generations, )] TJ ET BT 26.250 375.929 Td /F1 9.8 Tf [(with the topology constrained to that recovered in the phylogenetic analyses of the 3+ dataset \(pruned for taxa not included in )] TJ ET BT 26.250 364.024 Td /F1 9.8 Tf [(the subset\). Post-run analysis of MCMC log files was assessed using Tracer v. 1.5)] TJ ET 0.267 0.267 0.267 rg BT 381.706 365.531 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 391.343 364.024 Td /F1 9.8 Tf [( and mixing was considered complete if the )] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(effective sample size of each parameter was >200)] TJ ET 0.267 0.267 0.267 rg BT 243.285 353.627 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 252.922 356.008 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 255.332 353.627 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 264.969 352.119 Td /F1 9.8 Tf [(. Tree files from the five runs were combined in LogCombiner v1.7.4)] TJ ET 0.267 0.267 0.267 rg BT 558.122 353.627 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 26.250 340.215 Td /F1 9.8 Tf [(with the first 10% of trees from each run discarded as burn-in. The maximum clade credibility tree, with means and 95% highest )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(posterior density of divergence times, was estimated with TreeAnnotator v1.6.1)] TJ ET 0.267 0.267 0.267 rg BT 367.100 329.817 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 376.738 328.310 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 308.905 Td /F1 9.8 Tf [(The complete tree with 1416 taxa was time-calibrated under penalized likelihood \(PL)] TJ ET 0.267 0.267 0.267 rg BT 390.403 310.412 Td /F4 8.7 Tf [(67)] TJ ET 0.271 0.267 0.267 rg BT 400.040 308.905 Td /F1 9.8 Tf [(\) with treePL)] TJ ET 0.267 0.267 0.267 rg BT 454.767 310.412 Td /F4 8.7 Tf [(69)] TJ ET 0.271 0.267 0.267 rg BT 464.404 308.905 Td /F1 9.8 Tf [(. The PL model, which )] TJ ET BT 26.250 297.000 Td /F1 9.8 Tf [(assumes rate autocorrelation, has been shown to perform poorly in simulation studies resulting in high stochastic error of )] TJ ET BT 26.250 285.096 Td /F1 9.8 Tf [(divergence time estimates)] TJ ET 0.267 0.267 0.267 rg BT 139.496 286.603 Td /F4 8.7 Tf [(70)] TJ ET 0.271 0.267 0.267 rg BT 149.134 285.096 Td /F1 9.8 Tf [(. To ameliorate this problem, mean highest posterior density estimates of clade ages obtained with )] TJ ET BT 26.250 273.191 Td /F1 9.8 Tf [(the subset in BEAST were imposed as fixed secondary calibrations for the PL analysis, rather than using primary calibrations )] TJ ET BT 26.250 261.286 Td /F1 9.8 Tf [(with minimum and maximum age constrains. A total of 126 secondary calibrations were used for this analysis, including the )] TJ ET BT 26.250 249.381 Td /F1 9.8 Tf [(ages obtained for all major groups in the tree as well as the nodes near which primary calibrations were defined. The rate )] TJ ET BT 26.250 237.477 Td /F1 9.8 Tf [(smoothing parameter was set to 10 based on the cross-validation procedure and the )] TJ ET BT 392.596 237.477 Td /F4 9.8 Tf [(?)] TJ ET BT 398.554 241.365 Td /F4 8.7 Tf [(2)] TJ ET BT 403.372 237.477 Td /F1 9.8 Tf [( test in treePL \(four smoothing values )] TJ ET BT 26.250 225.572 Td /F1 9.8 Tf [(between 1 and 1000 were compared\).)] TJ ET BT 26.250 188.969 Td /F4 12.0 Tf [(Results and Discussion)] TJ ET BT 26.250 169.015 Td /F1 9.8 Tf [(The final concatenated alignments included 21 markers with 20853 sites for 1416 taxa in the 3+ dataset and 1020 taxa in the 7+ )] TJ ET BT 26.250 157.110 Td /F1 9.8 Tf [(dataset. The average presence of data \(number of sequences per taxon\) across the alignments was 41.0% for the 3+ dataset )] TJ ET BT 26.250 145.206 Td /F1 9.8 Tf [(and 48.2% for the 7+ dataset. A summary of dataset features, including data presence, alignment length, and sequence )] TJ ET BT 26.250 133.301 Td /F1 9.8 Tf [(variation for each marker is given in Table 2 \(see also Table S1\). The new sequences have been deposited in GenBank under )] TJ ET BT 26.250 121.396 Td /F1 9.8 Tf [(accession numbers KC825360-KC831391. The sequence alignment \(nexus format\), ML tree \(newick format\), and Table S1 are )] TJ ET BT 26.250 109.491 Td /F1 9.8 Tf [(available from the Dryad repository \()] TJ ET 0.267 0.267 0.267 rg BT 183.381 109.491 Td /F1 9.8 Tf [(DOI:10.5061/dryad.c4d3j)] TJ ET 0.271 0.267 0.267 rg BT 291.772 109.491 Td /F1 9.8 Tf [(\). The main phylogenetic hypothesis is summarized in Fig. 1 \(24-)] TJ ET BT 26.250 97.587 Td /F1 9.8 Tf [(partition RAxML tree, 3+ dataset, time-calibrated under PL\). Fig. 2 provides measures of congruence among alternative )] TJ ET BT 26.250 85.682 Td /F1 9.8 Tf [(analyses \(concatenation and gene trees\) for all major clades and provides discrete tests for traditional hypotheses in )] TJ ET BT 26.250 73.777 Td /F1 9.8 Tf [(ichthyology. Figs. 310 provide more detail on the relationships within selected percomorph clades based on the tree in Fig. 1. )] TJ ET BT 26.250 61.872 Td /F1 9.8 Tf [(The time-calibrated \(BEAST\) tree for the subset \(202 taxa and 18 genes\) and 59 calibration points are shown in Fig. 11 \(see )] TJ ET BT 26.250 49.968 Td /F1 9.8 Tf [(also Appendix 1\); Fig. 12 compares the results of divergence times estimated for major groups with those obtained by other )] TJ ET BT 26.250 38.063 Td /F1 9.8 Tf [(recent multi-locus studies. The complete phylogeny with bootstrap values and taxonomic annotations is depicted in )] TJ ET 0.267 0.267 0.267 rg BT 523.724 38.063 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 554.612 38.063 Td /F1 9.8 Tf [( as a )] TJ ET Q q 15.000 23.777 577.500 753.223 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(likelihood \(ML\) using two partitioning schemes, a simple one determined arbitrarily with 5 data partitions \(3 codon positions )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(across all exons plus 16S and )] TJ ET BT 158.480 755.571 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 189.913 755.571 Td /F1 9.8 Tf [(\), and a more complex scheme with 24 partitions \(a combination of codon positions and )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(individual genes plus 16S and )] TJ ET BT 158.489 743.667 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 189.923 743.667 Td /F1 9.8 Tf [(\) indicated by PartitionFinder)] TJ ET 0.267 0.267 0.267 rg BT 314.012 745.174 Td /F4 8.7 Tf [(59)] TJ ET 0.271 0.267 0.267 rg BT 323.649 743.667 Td /F1 9.8 Tf [(. To make the PartitionFinder analysis scalable, a )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(representative subset of 201 taxa was run under the Bayesian Information Criterion)] TJ ET 0.267 0.267 0.267 rg BT 385.001 733.269 Td /F4 8.7 Tf [(59)] TJ ET 0.271 0.267 0.267 rg BT 394.639 731.762 Td /F1 9.8 Tf [(. The 7+ dataset was analyzed with the 24-)] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(partition scheme only. Analyses for both datasets and partition schemes were conducted in RAxML using 30 independent )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(replicates under the GTRGAMMA model. Nodal support was assessed using the rapid bootstrapping algorithm of RAxML with )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(1000 replicates estimated under the GTRCAT model)] TJ ET 0.267 0.267 0.267 rg BT 253.298 697.555 Td /F4 8.7 Tf [(60)] TJ ET 0.271 0.267 0.267 rg BT 262.936 696.048 Td /F1 9.8 Tf [(, and the collection of sample trees was used to draw the bibartition )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(frequencies on the optimal tree. All RAxML analyses were conducted in the )] TJ ET 0.267 0.267 0.267 rg BT 353.021 684.143 Td /F1 9.8 Tf [(CIPRES portal v3.1)] TJ ET 0.271 0.267 0.267 rg BT 437.554 684.143 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(For comparison purposes, the 3+ dataset was also analyzed under implied-weighted parsimony)] TJ ET 0.267 0.267 0.267 rg BT 437.817 666.245 Td /F4 8.7 Tf [(61)] TJ ET 0.271 0.267 0.267 rg BT 447.454 664.738 Td /F1 9.8 Tf [(. The optimal tree search and )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(bootstrap trees were set to run independently. Gaps were treated as missing characters and all parsimony uninformative )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(characters were ignored. A relatively mild value of )] TJ ET BT 244.075 640.929 Td /F5 9.8 Tf [(k)] TJ ET BT 248.950 640.929 Td /F1 9.8 Tf [( \(20\) was chosen arbitrarily due to computational limitations to explore )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(sensitivity of the nodes to other weighting functions. Tree searches were performed in TNT 1.1)] TJ ET 0.267 0.267 0.267 rg BT 433.215 630.531 Td /F4 8.7 Tf [(63)] TJ ET 0.271 0.267 0.267 rg BT 442.852 629.024 Td /F1 9.8 Tf [( using a driven-search strategy )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(combining the following tree-search algorithms: ratchet, drift, sectorial searches and tree fusion. The exhaustiveness of the )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(search parameters was self-adjusted every 2 hits of the current best score. To maximize tree-space exploration, the final )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(searches implemented tree-bisection-reconnection \(TBR\). A strict consensus of nine equally optimal trees \(length 407187 steps; )] TJ ET BT 26.250 581.405 Td /F1 9.8 Tf [(fit 7309.19\) was computed. Bootstrap search strategies were relaxed to ten random addition sequences and TBR, saving only )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(one tree per replicate \(1000 replicates\); bootstrap bipartition frequencies were drawn on the consensus tree.)] TJ ET BT 26.250 550.095 Td /F4 9.8 Tf [(Divergence time estimates)] TJ ET BT 26.250 530.691 Td /F1 9.8 Tf [(Time-tree estimation in a Bayesian framework using the complete dataset was computationally infeasible. Thus, we selected a )] TJ ET BT 26.250 518.786 Td /F1 9.8 Tf [(subset of 202 taxa for 18 genes that had representation of: \(i\) all major bony fish lineages, \(ii\) lineages encompassing the nodes )] TJ ET BT 26.250 506.881 Td /F1 9.8 Tf [(in which the assignment of fossil calibrations is most informative, \(iii\) taxa with the highest genetic coverage to minimize missing )] TJ ET BT 26.250 494.976 Td /F1 9.8 Tf [(data in the data matrix \(the markers )] TJ ET BT 182.855 494.976 Td /F5 9.8 Tf [(vcpip)] TJ ET BT 205.611 494.976 Td /F1 9.8 Tf [(, )] TJ ET BT 211.032 494.976 Td /F5 9.8 Tf [(svep1)] TJ ET BT 237.045 494.976 Td /F1 9.8 Tf [(, )] TJ ET BT 242.466 494.976 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 273.900 494.976 Td /F1 9.8 Tf [(, including a high proportion of missing data, were also excluded\). )] TJ ET BT 26.250 483.072 Td /F1 9.8 Tf [(Divergence times were estimated in BEAST v1.7 using the uncorrelated log-normal \(UCLN\) clock-model)] TJ ET 0.267 0.267 0.267 rg BT 474.887 484.579 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 484.524 483.072 Td /F1 9.8 Tf [(. Sixty calibration )] TJ ET BT 26.250 471.167 Td /F1 9.8 Tf [(points were selected as priors for divergence time estimates, of which 58 are based on previous studies)] TJ ET 0.267 0.267 0.267 rg BT 472.771 472.674 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 482.408 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 484.817 472.674 Td /F4 8.7 Tf [(64)] TJ ET 0.271 0.267 0.267 rg BT 494.455 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 496.864 472.674 Td /F4 8.7 Tf [(65)] TJ ET 0.271 0.267 0.267 rg BT 506.501 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 508.911 472.674 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 518.548 471.167 Td /F1 9.8 Tf [( and two )] TJ ET BT 26.250 459.262 Td /F1 9.8 Tf [(\(calibrations 45 and 60\) are proposed here \(Appendix 1\). However, the actual BEAST analysis conducted for this study included )] TJ ET BT 26.250 447.357 Td /F1 9.8 Tf [(59 calibrations only \(see details under calibration 60, Appendix 1\). A starting chronogram that satisfied all priors \(e.g., )] TJ ET BT 26.250 435.453 Td /F1 9.8 Tf [(monophyly and initial divergence times\) was generated under penalized likelihood in r8s v1.71)] TJ ET 0.267 0.267 0.267 rg BT 432.133 436.960 Td /F4 8.7 Tf [(67)] TJ ET 0.271 0.267 0.267 rg BT 441.770 435.453 Td /F1 9.8 Tf [( using the RAxML tree. To )] TJ ET BT 26.250 423.548 Td /F1 9.8 Tf [(model branching rates on the tree, a birth-death process was used for the tree prior with initial birth rate = 1.0 and death rate = )] TJ ET BT 26.250 411.643 Td /F1 9.8 Tf [(0.5. The substitution model was GTR+G with 4 rate classes and the data were partitioned into 4 categories with independent )] TJ ET BT 26.250 399.738 Td /F1 9.8 Tf [(parameter estimation: three codon positions across exons of protein-coding genes plus 16S. Clock and tree priors were linked )] TJ ET BT 26.250 387.834 Td /F1 9.8 Tf [(across partitions. Five replicates of the Markov chain Monte Carlo \(MCMC\) analyses were each run for 200 million generations, )] TJ ET BT 26.250 375.929 Td /F1 9.8 Tf [(with the topology constrained to that recovered in the phylogenetic analyses of the 3+ dataset \(pruned for taxa not included in )] TJ ET BT 26.250 364.024 Td /F1 9.8 Tf [(the subset\). Post-run analysis of MCMC log files was assessed using Tracer v. 1.5)] TJ ET 0.267 0.267 0.267 rg BT 381.706 365.531 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 391.343 364.024 Td /F1 9.8 Tf [( and mixing was considered complete if the )] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(effective sample size of each parameter was >200)] TJ ET 0.267 0.267 0.267 rg BT 243.285 353.627 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 252.922 356.008 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 255.332 353.627 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 264.969 352.119 Td /F1 9.8 Tf [(. Tree files from the five runs were combined in LogCombiner v1.7.4)] TJ ET 0.267 0.267 0.267 rg BT 558.122 353.627 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 26.250 340.215 Td /F1 9.8 Tf [(with the first 10% of trees from each run discarded as burn-in. The maximum clade credibility tree, with means and 95% highest )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(posterior density of divergence times, was estimated with TreeAnnotator v1.6.1)] TJ ET 0.267 0.267 0.267 rg BT 367.100 329.817 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 376.738 328.310 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 308.905 Td /F1 9.8 Tf [(The complete tree with 1416 taxa was time-calibrated under penalized likelihood \(PL)] TJ ET 0.267 0.267 0.267 rg BT 390.403 310.412 Td /F4 8.7 Tf [(67)] TJ ET 0.271 0.267 0.267 rg BT 400.040 308.905 Td /F1 9.8 Tf [(\) with treePL)] TJ ET 0.267 0.267 0.267 rg BT 454.767 310.412 Td /F4 8.7 Tf [(69)] TJ ET 0.271 0.267 0.267 rg BT 464.404 308.905 Td /F1 9.8 Tf [(. The PL model, which )] TJ ET BT 26.250 297.000 Td /F1 9.8 Tf [(assumes rate autocorrelation, has been shown to perform poorly in simulation studies resulting in high stochastic error of )] TJ ET BT 26.250 285.096 Td /F1 9.8 Tf [(divergence time estimates)] TJ ET 0.267 0.267 0.267 rg BT 139.496 286.603 Td /F4 8.7 Tf [(70)] TJ ET 0.271 0.267 0.267 rg BT 149.134 285.096 Td /F1 9.8 Tf [(. To ameliorate this problem, mean highest posterior density estimates of clade ages obtained with )] TJ ET BT 26.250 273.191 Td /F1 9.8 Tf [(the subset in BEAST were imposed as fixed secondary calibrations for the PL analysis, rather than using primary calibrations )] TJ ET BT 26.250 261.286 Td /F1 9.8 Tf [(with minimum and maximum age constrains. A total of 126 secondary calibrations were used for this analysis, including the )] TJ ET BT 26.250 249.381 Td /F1 9.8 Tf [(ages obtained for all major groups in the tree as well as the nodes near which primary calibrations were defined. The rate )] TJ ET BT 26.250 237.477 Td /F1 9.8 Tf [(smoothing parameter was set to 10 based on the cross-validation procedure and the )] TJ ET BT 392.596 237.477 Td /F4 9.8 Tf [(?)] TJ ET BT 398.554 241.365 Td /F4 8.7 Tf [(2)] TJ ET BT 403.372 237.477 Td /F1 9.8 Tf [( test in treePL \(four smoothing values )] TJ ET BT 26.250 225.572 Td /F1 9.8 Tf [(between 1 and 1000 were compared\).)] TJ ET BT 26.250 188.969 Td /F4 12.0 Tf [(Results and Discussion)] TJ ET BT 26.250 169.015 Td /F1 9.8 Tf [(The final concatenated alignments included 21 markers with 20853 sites for 1416 taxa in the 3+ dataset and 1020 taxa in the 7+ )] TJ ET BT 26.250 157.110 Td /F1 9.8 Tf [(dataset. The average presence of data \(number of sequences per taxon\) across the alignments was 41.0% for the 3+ dataset )] TJ ET BT 26.250 145.206 Td /F1 9.8 Tf [(and 48.2% for the 7+ dataset. A summary of dataset features, including data presence, alignment length, and sequence )] TJ ET BT 26.250 133.301 Td /F1 9.8 Tf [(variation for each marker is given in Table 2 \(see also Table S1\). The new sequences have been deposited in GenBank under )] TJ ET BT 26.250 121.396 Td /F1 9.8 Tf [(accession numbers KC825360-KC831391. The sequence alignment \(nexus format\), ML tree \(newick format\), and Table S1 are )] TJ ET BT 26.250 109.491 Td /F1 9.8 Tf [(available from the Dryad repository \()] TJ ET 0.267 0.267 0.267 rg BT 183.381 109.491 Td /F1 9.8 Tf [(DOI:10.5061/dryad.c4d3j)] TJ ET 0.271 0.267 0.267 rg BT 291.772 109.491 Td /F1 9.8 Tf [(\). The main phylogenetic hypothesis is summarized in Fig. 1 \(24-)] TJ ET BT 26.250 97.587 Td /F1 9.8 Tf [(partition RAxML tree, 3+ dataset, time-calibrated under PL\). Fig. 2 provides measures of congruence among alternative )] TJ ET BT 26.250 85.682 Td /F1 9.8 Tf [(analyses \(concatenation and gene trees\) for all major clades and provides discrete tests for traditional hypotheses in )] TJ ET BT 26.250 73.777 Td /F1 9.8 Tf [(ichthyology. Figs. 310 provide more detail on the relationships within selected percomorph clades based on the tree in Fig. 1. )] TJ ET BT 26.250 61.872 Td /F1 9.8 Tf [(The time-calibrated \(BEAST\) tree for the subset \(202 taxa and 18 genes\) and 59 calibration points are shown in Fig. 11 \(see )] TJ ET BT 26.250 49.968 Td /F1 9.8 Tf [(also Appendix 1\); Fig. 12 compares the results of divergence times estimated for major groups with those obtained by other )] TJ ET BT 26.250 38.063 Td /F1 9.8 Tf [(recent multi-locus studies. The complete phylogeny with bootstrap values and taxonomic annotations is depicted in )] TJ ET 0.267 0.267 0.267 rg BT 523.724 38.063 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 554.612 38.063 Td /F1 9.8 Tf [( as a )] TJ ET Q q 15.000 23.777 577.500 753.223 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(likelihood \(ML\) using two partitioning schemes, a simple one determined arbitrarily with 5 data partitions \(3 codon positions )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(across all exons plus 16S and )] TJ ET BT 158.480 755.571 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 189.913 755.571 Td /F1 9.8 Tf [(\), and a more complex scheme with 24 partitions \(a combination of codon positions and )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(individual genes plus 16S and )] TJ ET BT 158.489 743.667 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 189.923 743.667 Td /F1 9.8 Tf [(\) indicated by PartitionFinder)] TJ ET 0.267 0.267 0.267 rg BT 314.012 745.174 Td /F4 8.7 Tf [(59)] TJ ET 0.271 0.267 0.267 rg BT 323.649 743.667 Td /F1 9.8 Tf [(. To make the PartitionFinder analysis scalable, a )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(representative subset of 201 taxa was run under the Bayesian Information Criterion)] TJ ET 0.267 0.267 0.267 rg BT 385.001 733.269 Td /F4 8.7 Tf [(59)] TJ ET 0.271 0.267 0.267 rg BT 394.639 731.762 Td /F1 9.8 Tf [(. The 7+ dataset was analyzed with the 24-)] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(partition scheme only. Analyses for both datasets and partition schemes were conducted in RAxML using 30 independent )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(replicates under the GTRGAMMA model. Nodal support was assessed using the rapid bootstrapping algorithm of RAxML with )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(1000 replicates estimated under the GTRCAT model)] TJ ET 0.267 0.267 0.267 rg BT 253.298 697.555 Td /F4 8.7 Tf [(60)] TJ ET 0.271 0.267 0.267 rg BT 262.936 696.048 Td /F1 9.8 Tf [(, and the collection of sample trees was used to draw the bibartition )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(frequencies on the optimal tree. All RAxML analyses were conducted in the )] TJ ET 0.267 0.267 0.267 rg BT 353.021 684.143 Td /F1 9.8 Tf [(CIPRES portal v3.1)] TJ ET 0.271 0.267 0.267 rg BT 437.554 684.143 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(For comparison purposes, the 3+ dataset was also analyzed under implied-weighted parsimony)] TJ ET 0.267 0.267 0.267 rg BT 437.817 666.245 Td /F4 8.7 Tf [(61)] TJ ET 0.271 0.267 0.267 rg BT 447.454 664.738 Td /F1 9.8 Tf [(. The optimal tree search and )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(bootstrap trees were set to run independently. Gaps were treated as missing characters and all parsimony uninformative )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(characters were ignored. A relatively mild value of )] TJ ET BT 244.075 640.929 Td /F5 9.8 Tf [(k)] TJ ET BT 248.950 640.929 Td /F1 9.8 Tf [( \(20\) was chosen arbitrarily due to computational limitations to explore )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(sensitivity of the nodes to other weighting functions. Tree searches were performed in TNT 1.1)] TJ ET 0.267 0.267 0.267 rg BT 433.215 630.531 Td /F4 8.7 Tf [(63)] TJ ET 0.271 0.267 0.267 rg BT 442.852 629.024 Td /F1 9.8 Tf [( using a driven-search strategy )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(combining the following tree-search algorithms: ratchet, drift, sectorial searches and tree fusion. The exhaustiveness of the )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(search parameters was self-adjusted every 2 hits of the current best score. To maximize tree-space exploration, the final )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(searches implemented tree-bisection-reconnection \(TBR\). A strict consensus of nine equally optimal trees \(length 407187 steps; )] TJ ET BT 26.250 581.405 Td /F1 9.8 Tf [(fit 7309.19\) was computed. Bootstrap search strategies were relaxed to ten random addition sequences and TBR, saving only )] TJ ET BT 26.250 569.500 Td /F1 9.8 Tf [(one tree per replicate \(1000 replicates\); bootstrap bipartition frequencies were drawn on the consensus tree.)] TJ ET BT 26.250 550.095 Td /F4 9.8 Tf [(Divergence time estimates)] TJ ET BT 26.250 530.691 Td /F1 9.8 Tf [(Time-tree estimation in a Bayesian framework using the complete dataset was computationally infeasible. Thus, we selected a )] TJ ET BT 26.250 518.786 Td /F1 9.8 Tf [(subset of 202 taxa for 18 genes that had representation of: \(i\) all major bony fish lineages, \(ii\) lineages encompassing the nodes )] TJ ET BT 26.250 506.881 Td /F1 9.8 Tf [(in which the assignment of fossil calibrations is most informative, \(iii\) taxa with the highest genetic coverage to minimize missing )] TJ ET BT 26.250 494.976 Td /F1 9.8 Tf [(data in the data matrix \(the markers )] TJ ET BT 182.855 494.976 Td /F5 9.8 Tf [(vcpip)] TJ ET BT 205.611 494.976 Td /F1 9.8 Tf [(, )] TJ ET BT 211.032 494.976 Td /F5 9.8 Tf [(svep1)] TJ ET BT 237.045 494.976 Td /F1 9.8 Tf [(, )] TJ ET BT 242.466 494.976 Td /F5 9.8 Tf [(hoxc6a)] TJ ET BT 273.900 494.976 Td /F1 9.8 Tf [(, including a high proportion of missing data, were also excluded\). )] TJ ET BT 26.250 483.072 Td /F1 9.8 Tf [(Divergence times were estimated in BEAST v1.7 using the uncorrelated log-normal \(UCLN\) clock-model)] TJ ET 0.267 0.267 0.267 rg BT 474.887 484.579 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 484.524 483.072 Td /F1 9.8 Tf [(. Sixty calibration )] TJ ET BT 26.250 471.167 Td /F1 9.8 Tf [(points were selected as priors for divergence time estimates, of which 58 are based on previous studies)] TJ ET 0.267 0.267 0.267 rg BT 472.771 472.674 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 482.408 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 484.817 472.674 Td /F4 8.7 Tf [(64)] TJ ET 0.271 0.267 0.267 rg BT 494.455 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 496.864 472.674 Td /F4 8.7 Tf [(65)] TJ ET 0.271 0.267 0.267 rg BT 506.501 475.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 508.911 472.674 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 518.548 471.167 Td /F1 9.8 Tf [( and two )] TJ ET BT 26.250 459.262 Td /F1 9.8 Tf [(\(calibrations 45 and 60\) are proposed here \(Appendix 1\). However, the actual BEAST analysis conducted for this study included )] TJ ET BT 26.250 447.357 Td /F1 9.8 Tf [(59 calibrations only \(see details under calibration 60, Appendix 1\). A starting chronogram that satisfied all priors \(e.g., )] TJ ET BT 26.250 435.453 Td /F1 9.8 Tf [(monophyly and initial divergence times\) was generated under penalized likelihood in r8s v1.71)] TJ ET 0.267 0.267 0.267 rg BT 432.133 436.960 Td /F4 8.7 Tf [(67)] TJ ET 0.271 0.267 0.267 rg BT 441.770 435.453 Td /F1 9.8 Tf [( using the RAxML tree. To )] TJ ET BT 26.250 423.548 Td /F1 9.8 Tf [(model branching rates on the tree, a birth-death process was used for the tree prior with initial birth rate = 1.0 and death rate = )] TJ ET BT 26.250 411.643 Td /F1 9.8 Tf [(0.5. The substitution model was GTR+G with 4 rate classes and the data were partitioned into 4 categories with independent )] TJ ET BT 26.250 399.738 Td /F1 9.8 Tf [(parameter estimation: three codon positions across exons of protein-coding genes plus 16S. Clock and tree priors were linked )] TJ ET BT 26.250 387.834 Td /F1 9.8 Tf [(across partitions. Five replicates of the Markov chain Monte Carlo \(MCMC\) analyses were each run for 200 million generations, )] TJ ET BT 26.250 375.929 Td /F1 9.8 Tf [(with the topology constrained to that recovered in the phylogenetic analyses of the 3+ dataset \(pruned for taxa not included in )] TJ ET BT 26.250 364.024 Td /F1 9.8 Tf [(the subset\). Post-run analysis of MCMC log files was assessed using Tracer v. 1.5)] TJ ET 0.267 0.267 0.267 rg BT 381.706 365.531 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 391.343 364.024 Td /F1 9.8 Tf [( and mixing was considered complete if the )] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(effective sample size of each parameter was >200)] TJ ET 0.267 0.267 0.267 rg BT 243.285 353.627 Td /F4 8.7 Tf [(34)] TJ ET 0.271 0.267 0.267 rg BT 252.922 356.008 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 255.332 353.627 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 264.969 352.119 Td /F1 9.8 Tf [(. Tree files from the five runs were combined in LogCombiner v1.7.4)] TJ ET 0.267 0.267 0.267 rg BT 558.122 353.627 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 26.250 340.215 Td /F1 9.8 Tf [(with the first 10% of trees from each run discarded as burn-in. The maximum clade credibility tree, with means and 95% highest )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(posterior density of divergence times, was estimated with TreeAnnotator v1.6.1)] TJ ET 0.267 0.267 0.267 rg BT 367.100 329.817 Td /F4 8.7 Tf [(68)] TJ ET 0.271 0.267 0.267 rg BT 376.738 328.310 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 308.905 Td /F1 9.8 Tf [(The complete tree with 1416 taxa was time-calibrated under penalized likelihood \(PL)] TJ ET 0.267 0.267 0.267 rg BT 390.403 310.412 Td /F4 8.7 Tf [(67)] TJ ET 0.271 0.267 0.267 rg BT 400.040 308.905 Td /F1 9.8 Tf [(\) with treePL)] TJ ET 0.267 0.267 0.267 rg BT 454.767 310.412 Td /F4 8.7 Tf [(69)] TJ ET 0.271 0.267 0.267 rg BT 464.404 308.905 Td /F1 9.8 Tf [(. The PL model, which )] TJ ET BT 26.250 297.000 Td /F1 9.8 Tf [(assumes rate autocorrelation, has been shown to perform poorly in simulation studies resulting in high stochastic error of )] TJ ET BT 26.250 285.096 Td /F1 9.8 Tf [(divergence time estimates)] TJ ET 0.267 0.267 0.267 rg BT 139.496 286.603 Td /F4 8.7 Tf [(70)] TJ ET 0.271 0.267 0.267 rg BT 149.134 285.096 Td /F1 9.8 Tf [(. To ameliorate this problem, mean highest posterior density estimates of clade ages obtained with )] TJ ET BT 26.250 273.191 Td /F1 9.8 Tf [(the subset in BEAST were imposed as fixed secondary calibrations for the PL analysis, rather than using primary calibrations )] TJ ET BT 26.250 261.286 Td /F1 9.8 Tf [(with minimum and maximum age constrains. A total of 126 secondary calibrations were used for this analysis, including the )] TJ ET BT 26.250 249.381 Td /F1 9.8 Tf [(ages obtained for all major groups in the tree as well as the nodes near which primary calibrations were defined. The rate )] TJ ET BT 26.250 237.477 Td /F1 9.8 Tf [(smoothing parameter was set to 10 based on the cross-validation procedure and the )] TJ ET BT 392.596 237.477 Td /F4 9.8 Tf [(?)] TJ ET BT 398.554 241.365 Td /F4 8.7 Tf [(2)] TJ ET BT 403.372 237.477 Td /F1 9.8 Tf [( test in treePL \(four smoothing values )] TJ ET BT 26.250 225.572 Td /F1 9.8 Tf [(between 1 and 1000 were compared\).)] TJ ET BT 26.250 188.969 Td /F4 12.0 Tf [(Results and Discussion)] TJ ET BT 26.250 169.015 Td /F1 9.8 Tf [(The final concatenated alignments included 21 markers with 20853 sites for 1416 taxa in the 3+ dataset and 1020 taxa in the 7+ )] TJ ET BT 26.250 157.110 Td /F1 9.8 Tf [(dataset. The average presence of data \(number of sequences per taxon\) across the alignments was 41.0% for the 3+ dataset )] TJ ET BT 26.250 145.206 Td /F1 9.8 Tf [(and 48.2% for the 7+ dataset. A summary of dataset features, including data presence, alignment length, and sequence )] TJ ET BT 26.250 133.301 Td /F1 9.8 Tf [(variation for each marker is given in Table 2 \(see also Table S1\). The new sequences have been deposited in GenBank under )] TJ ET BT 26.250 121.396 Td /F1 9.8 Tf [(accession numbers KC825360-KC831391. The sequence alignment \(nexus format\), ML tree \(newick format\), and Table S1 are )] TJ ET BT 26.250 109.491 Td /F1 9.8 Tf [(available from the Dryad repository \()] TJ ET 0.267 0.267 0.267 rg BT 183.381 109.491 Td /F1 9.8 Tf [(DOI:10.5061/dryad.c4d3j)] TJ ET 0.271 0.267 0.267 rg BT 291.772 109.491 Td /F1 9.8 Tf [(\). The main phylogenetic hypothesis is summarized in Fig. 1 \(24-)] TJ ET BT 26.250 97.587 Td /F1 9.8 Tf [(partition RAxML tree, 3+ dataset, time-calibrated under PL\). Fig. 2 provides measures of congruence among alternative )] TJ ET BT 26.250 85.682 Td /F1 9.8 Tf [(analyses \(concatenation and gene trees\) for all major clades and provides discrete tests for traditional hypotheses in )] TJ ET BT 26.250 73.777 Td /F1 9.8 Tf [(ichthyology. Figs. 310 provide more detail on the relationships within selected percomorph clades based on the tree in Fig. 1. )] TJ ET BT 26.250 61.872 Td /F1 9.8 Tf [(The time-calibrated \(BEAST\) tree for the subset \(202 taxa and 18 genes\) and 59 calibration points are shown in Fig. 11 \(see )] TJ ET BT 26.250 49.968 Td /F1 9.8 Tf [(also Appendix 1\); Fig. 12 compares the results of divergence times estimated for major groups with those obtained by other )] TJ ET BT 26.250 38.063 Td /F1 9.8 Tf [(recent multi-locus studies. The complete phylogeny with bootstrap values and taxonomic annotations is depicted in )] TJ ET 0.267 0.267 0.267 rg BT 523.724 38.063 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 554.612 38.063 Td /F1 9.8 Tf [( as a )] TJ ET Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(4)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 795 0 obj << /Type /Annot /Subtype /Link /A 796 0 R /Border [0 0 0] /H /I /Rect [ 314.0115 744.3722 323.6488 753.1905 ] >> endobj 796 0 obj << /Type /Action >> endobj 797 0 obj << /Type /Annot /Subtype /Link /A 798 0 R /Border [0 0 0] /H /I /Rect [ 385.0013 732.4674 394.6386 741.2858 ] >> endobj 798 0 obj << /Type /Action >> endobj 799 0 obj << /Type /Annot /Subtype /Link /A 800 0 R /Border [0 0 0] /H /I /Rect [ 253.2982 696.7532 262.9356 705.5715 ] >> endobj 800 0 obj << /Type /Action >> endobj 801 0 obj << /Type /Annot /Subtype /Link /A 802 0 R /Border [0 0 0] /H /I /Rect [ 353.0213 683.2411 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We also provide for the first time a monophyletic definition of )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(Perciformes, sinking into this clade components of Scorpaeniformes, Gasterosteiformes, and Cottiformes \(Fig. 10; see also)] TJ ET 0.267 0.267 0.267 rg BT 556.202 642.436 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 565.839 644.817 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 568.248 642.436 Td /F4 8.7 Tf [(74)] TJ ET 0.271 0.267 0.267 rg BT 26.250 629.024 Td /F1 9.8 Tf [(\). Among the euacanthomorphs, we find the non-monophyly of Beryciformes \(including Stephanoberyciformes\) and a sister-)] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(group relationship between holocentrids and percomorphs, first recognized by Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 450.560 618.626 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 460.198 617.119 Td /F1 9.8 Tf [( and Moore)] TJ ET 0.267 0.267 0.267 rg BT 509.513 618.626 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 519.150 617.119 Td /F1 9.8 Tf [(, but )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(challenged by Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 189.387 606.722 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 194.206 605.214 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 585.810 Td /F1 9.8 Tf [(Based on the topology obtained \(Figs. 1-10, )] TJ ET 0.267 0.267 0.267 rg BT 218.111 585.810 Td /F1 9.8 Tf [(S1)] TJ ET 0.271 0.267 0.267 rg BT 230.035 585.810 Td /F1 9.8 Tf [(\) we propose a new classification for ordinal and subordinal groups of bony )] TJ ET BT 26.250 573.905 Td /F1 9.8 Tf [(fishes and subsequently discuss some of the most significant findings.)] TJ ET 0.965 0.965 0.965 rg 26.250 78.119 555.000 485.905 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 564.024 m 581.250 564.024 l 581.250 563.274 l 26.250 563.274 l f q 355.500 0 0 452.250 35.250 102.024 cm /I3 Do Q q 35.250 78.119 537.000 17.905 re W n Q Q q 15.000 78.119 577.500 698.881 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(cladogram and can also be visualized online as a time-tree using a fractal explorer and zooming interface at )] TJ ET 0.267 0.267 0.267 rg BT 493.373 767.476 Td /F1 9.8 Tf [(OneZoom)] TJ ET BT 536.721 768.983 Td /F4 8.7 Tf [(73)] TJ ET 0.271 0.267 0.267 rg BT 546.358 767.476 Td /F1 9.8 Tf [( \(also )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(posted at )] TJ ET 0.267 0.267 0.267 rg BT 69.072 755.571 Td /F1 9.8 Tf [(DeepFin)] TJ ET 0.271 0.267 0.267 rg BT 105.917 755.571 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 736.167 Td /F1 9.8 Tf [(The basal nodes of the tree and relationships among early branching groups of bony fishes have been well established and )] TJ ET BT 26.250 724.262 Td /F1 9.8 Tf [(thoroughly discussed by recent molecular systematic studies based on similar sets of genes)] TJ ET 0.267 0.267 0.267 rg BT 422.363 725.769 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 432.001 728.150 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 434.410 725.769 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 444.047 724.262 Td /F1 9.8 Tf [(, albeit with reduced taxonomic )] TJ ET BT 26.250 712.357 Td /F1 9.8 Tf [(sampling. 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We also provide for the first time a monophyletic definition of )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(Perciformes, sinking into this clade components of Scorpaeniformes, Gasterosteiformes, and Cottiformes \(Fig. 10; see also)] TJ ET 0.267 0.267 0.267 rg BT 556.202 642.436 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 565.839 644.817 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 568.248 642.436 Td /F4 8.7 Tf [(74)] TJ ET 0.271 0.267 0.267 rg BT 26.250 629.024 Td /F1 9.8 Tf [(\). Among the euacanthomorphs, we find the non-monophyly of Beryciformes \(including Stephanoberyciformes\) and a sister-)] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(group relationship between holocentrids and percomorphs, first recognized by Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 450.560 618.626 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 460.198 617.119 Td /F1 9.8 Tf [( and Moore)] TJ ET 0.267 0.267 0.267 rg BT 509.513 618.626 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 519.150 617.119 Td /F1 9.8 Tf [(, but )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(challenged by Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 189.387 606.722 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 194.206 605.214 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 585.810 Td /F1 9.8 Tf [(Based on the topology obtained \(Figs. 1-10, )] TJ ET 0.267 0.267 0.267 rg BT 218.111 585.810 Td /F1 9.8 Tf [(S1)] TJ ET 0.271 0.267 0.267 rg BT 230.035 585.810 Td /F1 9.8 Tf [(\) we propose a new classification for ordinal and subordinal groups of bony )] TJ ET BT 26.250 573.905 Td /F1 9.8 Tf [(fishes and subsequently discuss some of the most significant findings.)] TJ ET 0.965 0.965 0.965 rg 26.250 78.119 555.000 485.905 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 564.024 m 581.250 564.024 l 581.250 563.274 l 26.250 563.274 l f q 355.500 0 0 452.250 35.250 102.024 cm /I3 Do Q q 35.250 78.119 537.000 17.905 re W n Q Q q 15.000 78.119 577.500 698.881 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(cladogram and can also be visualized online as a time-tree using a fractal explorer and zooming interface at )] TJ ET 0.267 0.267 0.267 rg BT 493.373 767.476 Td /F1 9.8 Tf [(OneZoom)] TJ ET BT 536.721 768.983 Td /F4 8.7 Tf [(73)] TJ ET 0.271 0.267 0.267 rg BT 546.358 767.476 Td /F1 9.8 Tf [( \(also )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(posted at )] TJ ET 0.267 0.267 0.267 rg BT 69.072 755.571 Td /F1 9.8 Tf [(DeepFin)] TJ ET 0.271 0.267 0.267 rg BT 105.917 755.571 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 736.167 Td /F1 9.8 Tf [(The basal nodes of the tree and relationships among early branching groups of bony fishes have been well established and )] TJ ET BT 26.250 724.262 Td /F1 9.8 Tf [(thoroughly discussed by recent molecular systematic studies based on similar sets of genes)] TJ ET 0.267 0.267 0.267 rg BT 422.363 725.769 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 432.001 728.150 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 434.410 725.769 Td /F4 8.7 Tf [(66)] TJ ET 0.271 0.267 0.267 rg BT 444.047 724.262 Td /F1 9.8 Tf [(, albeit with reduced taxonomic )] TJ ET BT 26.250 712.357 Td /F1 9.8 Tf [(sampling. 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We also provide for the first time a monophyletic definition of )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(Perciformes, sinking into this clade components of Scorpaeniformes, Gasterosteiformes, and Cottiformes \(Fig. 10; see also)] TJ ET 0.267 0.267 0.267 rg BT 556.202 642.436 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 565.839 644.817 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 568.248 642.436 Td /F4 8.7 Tf [(74)] TJ ET 0.271 0.267 0.267 rg BT 26.250 629.024 Td /F1 9.8 Tf [(\). Among the euacanthomorphs, we find the non-monophyly of Beryciformes \(including Stephanoberyciformes\) and a sister-)] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(group relationship between holocentrids and percomorphs, first recognized by Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 450.560 618.626 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 460.198 617.119 Td /F1 9.8 Tf [( and Moore)] TJ ET 0.267 0.267 0.267 rg BT 509.513 618.626 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 519.150 617.119 Td /F1 9.8 Tf [(, but )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(challenged by Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 189.387 606.722 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 194.206 605.214 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 585.810 Td /F1 9.8 Tf [(Based on the topology obtained \(Figs. 1-10, )] TJ ET 0.267 0.267 0.267 rg BT 218.111 585.810 Td /F1 9.8 Tf [(S1)] TJ ET 0.271 0.267 0.267 rg BT 230.035 585.810 Td /F1 9.8 Tf [(\) we propose a new classification for ordinal and subordinal groups of bony )] TJ ET BT 26.250 573.905 Td /F1 9.8 Tf [(fishes and subsequently discuss some of the most significant findings.)] TJ ET 0.965 0.965 0.965 rg 26.250 78.119 555.000 485.905 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 564.024 m 581.250 564.024 l 581.250 563.274 l 26.250 563.274 l f q 355.500 0 0 452.250 35.250 102.024 cm /I3 Do Q q 35.250 78.119 537.000 17.905 re W n Q Q q 355.500 0 0 452.250 35.250 102.024 cm /I3 Do Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(5)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 929 0 obj << /Type /Annot /Subtype /Link /A 930 0 R /Border [0 0 0] /H /I /Rect [ 493.3725 766.5743 536.7210 776.4950 ] >> endobj 930 0 obj << /Type /Action /S /URI /URI (http://www.deepfin.org/OneZoomFish/fish.htm) >> endobj 931 0 obj << /Type /Annot /Subtype /Link /A 932 0 R /Border [0 0 0] /H /I /Rect [ 536.7210 768.1817 546.3583 777.0000 ] >> endobj 932 0 obj << /Type /Action >> endobj 933 0 obj << /Type /Annot /Subtype /Link /A 934 0 R /Border [0 0 0] /H /I /Rect [ 69.0720 754.6696 105.9172 764.5902 ] >> endobj 934 0 obj << /Type /Action /S /URI /URI (http://www.deepfin.org) >> endobj 935 0 obj << /Type /Annot /Subtype /Link /A 936 0 R /Border [0 0 0] /H /I /Rect [ 422.3632 724.9674 432.0006 733.7858 ] >> endobj 936 0 obj << /Type /Action >> endobj 937 0 obj << /Type /Annot /Subtype /Link /A 938 0 R /Border [0 0 0] /H /I /Rect [ 434.4099 724.9674 444.0473 733.7858 ] >> endobj 938 0 obj << /Type /Action >> endobj 939 0 obj << /Type /Annot /Subtype /Link /A 940 0 R /Border [0 0 0] /H /I /Rect [ 556.2015 641.6342 565.8388 650.4525 ] >> endobj 940 0 obj << /Type /Action >> endobj 941 0 obj << /Type /Annot /Subtype /Link /A 942 0 R /Border [0 0 0] /H /I /Rect [ 568.2482 641.6342 577.8855 650.4525 ] >> endobj 942 0 obj << /Type /Action >> endobj 943 0 obj << /Type /Annot /Subtype /Link /A 944 0 R /Border [0 0 0] /H /I /Rect [ 450.5602 617.8247 460.1976 626.6430 ] >> endobj 944 0 obj << /Type /Action >> endobj 945 0 obj << /Type /Annot /Subtype /Link /A 946 0 R /Border [0 0 0] /H /I /Rect [ 509.5131 617.8247 519.1504 626.6430 ] >> endobj 946 0 obj << /Type /Action >> endobj 947 0 obj << /Type /Annot /Subtype /Link /A 948 0 R /Border [0 0 0] /H /I /Rect [ 189.3870 605.9199 194.2057 614.7382 ] >> endobj 948 0 obj << /Type /Action >> endobj 949 0 obj << /Type /Annot /Subtype /Link /A 950 0 R /Border [0 0 0] /H /I /Rect [ 218.1105 584.9078 230.0348 594.8284 ] >> endobj 950 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/04/Fig_S1_Complete_tree_classification3.pdf) >> endobj 951 0 obj << /Type /Annot /Subtype /Link /A 952 0 R /Border [0 0 0] /H /I /Rect [ 35.2500 102.0240 390.7500 554.2740 ] >> endobj 952 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/04/Betancur-Figure-1.jpg) >> endobj 953 0 obj << /Type /XObject /Subtype /Image /Width 474 /Height 603 /ColorSpace /DeviceRGB /Filter /DCTDecode /BitsPerComponent 8 /Length 91782>> stream JFIF;CREATOR: gd-jpeg v1.0 (using IJG JPEG v62), quality = 90 C     C   [" }!1AQa"q2#BR$3br %&'()*456789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz w!1AQaq"2B #3Rbr $4%&'()*56789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz ?RZ_4xzClԴ qi6vJm`# dt#k_~14q]Vio˨o XzZqc?Xm9z/Qi |<|Y4xu;XYy[ ݶv#?xog6Mˬ|4ϫ萵[ZXFќRW WgojxuEӅ3ıXblj0PofTC\4~75 KKa~̝jWVG!Lޤ^?f/:Nigo&c }W# 1$Utv/G|<^x7ZKXki$#f)vmg5_#>x5cK-ⴰA<` ?niP2יQPZhIq O y'>no!#lB@ 8Q +3~Ҁ>zᇇ Y|! 7JzJV&C3 ̤r tx@AnM'NR] 8$Q(^# Tlg/Լy fo^ IjF{UdGw~~Me8vnɵ m26XOqsZ)%|^ |-fúcHTX]̼d1=v j>ѵi߆s<6| 4]#'٧.eO }15Ft,ē׷¹Ia_1_ :FᣮE=Gҁ81yTAcakwzƧ;MGwmn)k$@F +Xd<} j:4kILѭKyn0;|eA~Ο UK> rI-8uiC[P@|#`wu;mNRM.=&( B8"$%'g<[ +7v{utpj}&k+K̖kYf 7 ēhҗ?Jo~̟we%>#oct6|eA?4mzޮ?B2hu t QS{i%t+PguRU? 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(http://currents.plos.org/treeoflife/files/2013/04/Fig_S1_Complete_tree_classification3.pdf) >> endobj 1000 0 obj << /Type /Annot /Subtype /Link /A 1001 0 R /Border [0 0 0] /H /I /Rect [ 35.2500 102.0240 390.7500 554.2740 ] >> endobj 1001 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/04/Betancur-Figure-1.jpg) >> endobj 1002 0 obj << /Type /Page /Parent 3 0 R /Annots [ 1004 0 R 1006 0 R 1009 0 R 1011 0 R 1013 0 R 1015 0 R ] /Contents 1003 0 R >> endobj 1003 0 obj << /Length 79648 >> stream q 15.000 -380.567 577.500 1157.567 re W n 0.965 0.965 0.965 rg 26.250 620.080 555.000 156.920 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 620.080 m 581.250 620.080 l 581.250 620.830 l 26.250 620.830 l f q 35.250 631.330 537.000 145.670 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 1: Main phylogenetic hypothesis of bony fish groups collapsed to depict higher-level clades.)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(The phylogenetic tree was estimated in RAxML using the 3+ dataset \(1416 taxa\) and 24 partitions with divergence times )] TJ ET BT 35.250 734.370 Td /F1 9.8 Tf [(estimated under PL using 126 fixed secondary calibrations from the BEAST analysis \(see Fig. 11\). Terminal clades are )] TJ ET BT 35.250 720.634 Td /F1 9.8 Tf [(either orders or supraordinal taxa with multiple orders included. Values in parentheses indicate number of families )] TJ ET BT 35.250 706.897 Td /F1 9.8 Tf [(examined. See also Figs. 3-10 for relationship details on selected percomorph clades. The complete phylogeny with )] TJ ET BT 35.250 693.161 Td /F1 9.8 Tf [(bootstrap support values and names for supraordinal taxa is in )] TJ ET 0.267 0.267 0.267 rg BT 307.295 693.161 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 338.183 693.161 Td /F1 9.8 Tf [(\).)] TJ ET BT 35.250 639.866 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc..)] TJ ET Q q 26.250 598.843 555.000 13.736 re W n 0.271 0.267 0.267 rg BT 26.250 601.591 Td /F1 9.8 Tf [(Table 2. Characterization of molecular markers examined.)] TJ ET Q 0.965 0.965 0.965 rg 26.250 567.936 555.000 23.407 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 591.343 m 581.250 591.343 l 580.500 590.593 l 27.000 590.593 l f 581.250 591.343 m 581.250 567.936 l 580.500 567.936 l 580.500 590.593 l f 26.250 591.343 m 26.250 567.936 l 27.000 567.936 l 27.000 590.593 l f 0.271 0.267 0.267 rg BT 33.000 577.267 Td /F1 9.0 Tf [(*New markers developed here)] TJ ET 1.000 1.000 1.000 rg 26.250 132.433 555.000 435.503 re f 0.965 0.965 0.965 rg 27.000 543.001 67.459 24.185 re f 0.267 0.267 0.267 rg 26.625 566.811 67.834 0.750 re f 26.625 542.626 0.750 24.935 re f 0.271 0.267 0.267 rg BT 31.500 557.662 Td /F4 9.8 Tf [(Locus)] TJ ET 0.965 0.965 0.965 rg 94.459 543.001 172.449 24.185 re f 0.267 0.267 0.267 rg 94.459 566.811 172.449 0.750 re f 0.271 0.267 0.267 rg BT 98.959 557.662 Td /F4 9.8 Tf [(Description)] TJ ET 0.965 0.965 0.965 rg 266.908 543.001 82.793 24.185 re f 0.267 0.267 0.267 rg 266.908 566.811 82.793 0.750 re f 0.271 0.267 0.267 rg BT 271.408 557.662 Td /F4 9.8 Tf [(Type)] TJ ET 0.965 0.965 0.965 rg 349.701 543.001 77.669 24.185 re f 0.267 0.267 0.267 rg 349.701 566.811 77.669 0.750 re f 0.271 0.267 0.267 rg BT 354.201 557.662 Td /F4 9.8 Tf [(Total )] TJ ET BT 354.201 545.757 Td /F4 9.8 Tf [(sequences)] TJ ET 0.965 0.965 0.965 rg 427.370 543.001 82.353 24.185 re f 0.267 0.267 0.267 rg 427.370 566.811 82.353 0.750 re f 0.271 0.267 0.267 rg BT 431.870 557.662 Td /F4 9.8 Tf [(Alignment )] TJ ET BT 431.870 545.757 Td /F4 9.8 Tf [(length \(sites\))] TJ ET 0.965 0.965 0.965 rg 509.723 543.001 70.777 24.185 re f 0.267 0.267 0.267 rg 509.723 566.811 71.152 0.750 re f 580.125 542.626 0.750 24.935 re f 0.271 0.267 0.267 rg BT 514.223 557.662 Td /F4 9.8 Tf [(Pairwise )] TJ ET BT 514.223 545.757 Td /F4 9.8 Tf [(identity \(%\))] TJ ET 0.267 0.267 0.267 rg 26.625 542.626 68.209 0.750 re f 26.625 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 532.771 Td /F5 9.8 Tf [(16S)] TJ ET 0.267 0.267 0.267 rg 94.084 542.626 173.199 0.750 re f 94.084 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 532.771 Td /F1 9.8 Tf [(16S rRNA)] TJ ET 0.267 0.267 0.267 rg 266.533 542.626 83.543 0.750 re f 266.533 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 532.771 Td /F1 9.8 Tf [(Mitochondrial)] TJ ET 0.267 0.267 0.267 rg 349.326 542.626 78.419 0.750 re f 349.326 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 532.771 Td /F1 9.8 Tf [(983)] TJ ET 0.267 0.267 0.267 rg 426.995 542.626 83.103 0.750 re f 426.995 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 532.771 Td /F1 9.8 Tf [(2326)] TJ ET 0.267 0.267 0.267 rg 509.348 542.626 71.527 0.750 re f 509.348 526.745 0.750 16.631 re f 580.125 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 532.771 Td /F1 9.8 Tf [(70.0)] TJ ET 0.267 0.267 0.267 rg 26.625 526.745 68.209 0.750 re f 26.625 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 31.875 516.890 Td /F5 9.8 Tf [(enc1)] TJ ET 0.267 0.267 0.267 rg 94.084 526.745 173.199 0.750 re f 94.084 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 99.334 516.890 Td /F1 9.8 Tf [(Gene for peroxisomal enoyl-CoA )] TJ ET BT 99.334 509.259 Td /F1 9.8 Tf [(hydratase/L-3-hydroxyacyl-CoA )] TJ ET BT 99.334 501.628 Td /F1 9.8 Tf [(dehydrogenase)] TJ ET 0.267 0.267 0.267 rg 266.533 526.745 83.543 0.750 re f 266.533 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 271.783 516.890 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 526.745 78.419 0.750 re f 349.326 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 354.576 516.890 Td /F1 9.8 Tf [(360)] TJ ET 0.267 0.267 0.267 rg 426.995 526.745 83.103 0.750 re f 426.995 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 432.245 516.890 Td /F1 9.8 Tf [(657)] TJ ET 0.267 0.267 0.267 rg 509.348 526.745 71.527 0.750 re f 509.348 495.601 0.750 31.894 re f 580.125 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 514.598 516.890 Td /F1 9.8 Tf [(84.6)] TJ ET 0.267 0.267 0.267 rg 26.625 495.601 68.209 0.750 re f 26.625 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 485.746 Td /F5 9.8 Tf [(ficd)] TJ ET 0.267 0.267 0.267 rg 94.084 495.601 173.199 0.750 re f 94.084 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 485.746 Td /F1 9.8 Tf [(FIC domain)] TJ ET 0.267 0.267 0.267 rg 266.533 495.601 83.543 0.750 re f 266.533 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 485.746 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 495.601 78.419 0.750 re f 349.326 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 485.746 Td /F1 9.8 Tf [(602)] TJ ET 0.267 0.267 0.267 rg 426.995 495.601 83.103 0.750 re f 426.995 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 485.746 Td /F1 9.8 Tf [(732)] TJ ET 0.267 0.267 0.267 rg 509.348 495.601 71.527 0.750 re f 509.348 479.720 0.750 16.631 re f 580.125 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 485.746 Td /F1 9.8 Tf [(86.0)] TJ ET 0.267 0.267 0.267 rg 26.625 479.720 68.209 0.750 re f 26.625 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 469.865 Td /F5 9.8 Tf [(gtdc2 )] TJ ET BT 58.434 469.865 Td /F1 9.8 Tf [(\()] TJ ET BT 61.681 469.865 Td /F5 9.8 Tf [(= glyt)] TJ ET BT 85.256 469.865 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 479.720 173.199 0.750 re f 94.084 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 469.865 Td /F1 9.8 Tf [(Glycosyltransferase-like domain )] TJ ET BT 99.334 462.234 Td /F1 9.8 Tf [(containing 2)] TJ ET 0.267 0.267 0.267 rg 266.533 479.720 83.543 0.750 re f 266.533 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 469.865 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 479.720 78.419 0.750 re f 349.326 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 469.865 Td /F1 9.8 Tf [(343)] TJ ET 0.267 0.267 0.267 rg 426.995 479.720 83.103 0.750 re f 426.995 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 469.865 Td /F1 9.8 Tf [(891)] TJ ET 0.267 0.267 0.267 rg 509.348 479.720 71.527 0.750 re f 509.348 456.208 0.750 24.263 re f 580.125 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 469.865 Td /F1 9.8 Tf [(78.3)] TJ ET 0.267 0.267 0.267 rg 26.625 456.208 68.209 0.750 re f 26.625 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 446.353 Td /F5 9.8 Tf [(hoxc6a*)] TJ ET 0.267 0.267 0.267 rg 94.084 456.208 173.199 0.750 re f 94.084 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 446.353 Td /F1 9.8 Tf [(Homeo box C6a)] TJ ET 0.267 0.267 0.267 rg 266.533 456.208 83.543 0.750 re f 266.533 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 446.353 Td /F1 9.8 Tf [(Nuclear intron)] TJ ET 0.267 0.267 0.267 rg 349.326 456.208 78.419 0.750 re f 349.326 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 446.353 Td /F1 9.8 Tf [(362)] TJ ET 0.267 0.267 0.267 rg 426.995 456.208 83.103 0.750 re f 426.995 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 446.353 Td /F1 9.8 Tf [(1184)] TJ ET 0.267 0.267 0.267 rg 509.348 456.208 71.527 0.750 re f 509.348 440.326 0.750 16.631 re f 580.125 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 446.353 Td /F1 9.8 Tf [(61.0)] TJ ET 0.267 0.267 0.267 rg 26.625 440.326 68.209 0.750 re f 26.625 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 430.471 Td /F5 9.8 Tf [(kiaa1239)] TJ ET 0.267 0.267 0.267 rg 94.084 440.326 173.199 0.750 re f 94.084 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 430.471 Td /F1 9.8 Tf [(Leucine-rich repeat and WD repeat-)] TJ ET BT 99.334 422.840 Td /F1 9.8 Tf [(containing protein, KIAA1239-like)] TJ ET 0.267 0.267 0.267 rg 266.533 440.326 83.543 0.750 re f 266.533 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 430.471 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 440.326 78.419 0.750 re f 349.326 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 430.471 Td /F1 9.8 Tf [(749)] TJ ET 0.267 0.267 0.267 rg 426.995 440.326 83.103 0.750 re f 426.995 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 430.471 Td /F1 9.8 Tf [(963)] TJ ET 0.267 0.267 0.267 rg 509.348 440.326 71.527 0.750 re f 509.348 416.814 0.750 24.263 re f 580.125 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 430.471 Td /F1 9.8 Tf [(86.3)] TJ ET 0.267 0.267 0.267 rg 26.625 416.814 68.209 0.750 re f 26.625 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 406.959 Td /F5 9.8 Tf [(myh6)] TJ ET 0.267 0.267 0.267 rg 94.084 416.814 173.199 0.750 re f 94.084 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 406.959 Td /F1 9.8 Tf [(Myosin, heavy polypeptide 6)] TJ ET 0.267 0.267 0.267 rg 266.533 416.814 83.543 0.750 re f 266.533 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 406.959 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 416.814 78.419 0.750 re f 349.326 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 406.959 Td /F1 9.8 Tf [(874)] TJ ET 0.267 0.267 0.267 rg 426.995 416.814 83.103 0.750 re f 426.995 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 406.959 Td /F1 9.8 Tf [(789)] TJ ET 0.267 0.267 0.267 rg 509.348 416.814 71.527 0.750 re f 509.348 400.933 0.750 16.631 re f 580.125 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 406.959 Td /F1 9.8 Tf [(84.5)] TJ ET 0.267 0.267 0.267 rg 26.625 400.933 68.209 0.750 re f 26.625 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 391.078 Td /F5 9.8 Tf [(panx2)] TJ ET 0.267 0.267 0.267 rg 94.084 400.933 173.199 0.750 re f 94.084 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 391.078 Td /F1 9.8 Tf [(Pannexin 2)] TJ ET 0.267 0.267 0.267 rg 266.533 400.933 83.543 0.750 re f 266.533 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 391.078 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 400.933 78.419 0.750 re f 349.326 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 391.078 Td /F1 9.8 Tf [(656)] TJ ET 0.267 0.267 0.267 rg 426.995 400.933 83.103 0.750 re f 426.995 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 391.078 Td /F1 9.8 Tf [(984)] TJ ET 0.267 0.267 0.267 rg 509.348 400.933 71.527 0.750 re f 509.348 385.051 0.750 16.631 re f 580.125 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 391.078 Td /F1 9.8 Tf [(86.2)] TJ ET 0.267 0.267 0.267 rg 26.625 385.051 68.209 0.750 re f 26.625 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 375.196 Td /F5 9.8 Tf [(plagl2)] TJ ET 0.267 0.267 0.267 rg 94.084 385.051 173.199 0.750 re f 94.084 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 375.196 Td /F1 9.8 Tf [(Pleiomorphic adenoma gene-like 2)] TJ ET 0.267 0.267 0.267 rg 266.533 385.051 83.543 0.750 re f 266.533 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 375.196 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 385.051 78.419 0.750 re f 349.326 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 375.196 Td /F1 9.8 Tf [(854)] TJ ET 0.267 0.267 0.267 rg 426.995 385.051 83.103 0.750 re f 426.995 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 375.196 Td /F1 9.8 Tf [(819)] TJ ET 0.267 0.267 0.267 rg 509.348 385.051 71.527 0.750 re f 509.348 369.170 0.750 16.631 re f 580.125 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 375.196 Td /F1 9.8 Tf [(87.9)] TJ ET 0.267 0.267 0.267 rg 26.625 369.170 68.209 0.750 re f 26.625 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 359.315 Td /F5 9.8 Tf [(ptchd1)] TJ ET BT 61.145 359.315 Td /F1 9.8 Tf [( \(=)] TJ ET BT 72.796 359.315 Td /F5 9.8 Tf [(ptr)] TJ ET BT 84.174 359.315 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 369.170 173.199 0.750 re f 94.084 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 359.315 Td /F1 9.8 Tf [(Patched domain containing 4)] TJ ET 0.267 0.267 0.267 rg 266.533 369.170 83.543 0.750 re f 266.533 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 359.315 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 369.170 78.419 0.750 re f 349.326 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 359.315 Td /F1 9.8 Tf [(736)] TJ ET 0.267 0.267 0.267 rg 426.995 369.170 83.103 0.750 re f 426.995 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 359.315 Td /F1 9.8 Tf [(756)] TJ ET 0.267 0.267 0.267 rg 509.348 369.170 71.527 0.750 re f 509.348 353.289 0.750 16.631 re f 580.125 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 359.315 Td /F1 9.8 Tf [(86.0)] TJ ET 0.267 0.267 0.267 rg 26.625 353.289 68.209 0.750 re f 26.625 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 343.434 Td /F5 9.8 Tf [(rag1)] TJ ET 0.267 0.267 0.267 rg 94.084 353.289 173.199 0.750 re f 94.084 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 343.434 Td /F1 9.8 Tf [(Recombination activating gene 1)] TJ ET 0.267 0.267 0.267 rg 266.533 353.289 83.543 0.750 re f 266.533 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 343.434 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 353.289 78.419 0.750 re f 349.326 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 343.434 Td /F1 9.8 Tf [(784)] TJ ET 0.267 0.267 0.267 rg 426.995 353.289 83.103 0.750 re f 426.995 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 343.434 Td /F1 9.8 Tf [(1575)] TJ ET 0.267 0.267 0.267 rg 509.348 353.289 71.527 0.750 re f 509.348 337.408 0.750 16.631 re f 580.125 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 343.434 Td /F1 9.8 Tf [(80.6)] TJ ET 0.267 0.267 0.267 rg 26.625 337.408 68.209 0.750 re f 26.625 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 327.553 Td /F5 9.8 Tf [(rag2)] TJ ET 0.267 0.267 0.267 rg 94.084 337.408 173.199 0.750 re f 94.084 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 327.553 Td /F1 9.8 Tf [(Recombination activating gene 2)] TJ ET 0.267 0.267 0.267 rg 266.533 337.408 83.543 0.750 re f 266.533 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 327.553 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 337.408 78.419 0.750 re f 349.326 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 327.553 Td /F1 9.8 Tf [(276)] TJ ET 0.267 0.267 0.267 rg 426.995 337.408 83.103 0.750 re f 426.995 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 327.553 Td /F1 9.8 Tf [(1206)] TJ ET 0.267 0.267 0.267 rg 509.348 337.408 71.527 0.750 re f 509.348 321.526 0.750 16.631 re f 580.125 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 327.553 Td /F1 9.8 Tf [(71.2)] TJ ET 0.267 0.267 0.267 rg 26.625 321.526 68.209 0.750 re f 26.625 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 311.671 Td /F5 9.8 Tf [(rh)] TJ ET 0.267 0.267 0.267 rg 94.084 321.526 173.199 0.750 re f 94.084 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 311.671 Td /F1 9.8 Tf [(Rhodopsin)] TJ ET 0.267 0.267 0.267 rg 266.533 321.526 83.543 0.750 re f 266.533 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 311.671 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 321.526 78.419 0.750 re f 349.326 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 311.671 Td /F1 9.8 Tf [(417)] TJ ET 0.267 0.267 0.267 rg 426.995 321.526 83.103 0.750 re f 426.995 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 311.671 Td /F1 9.8 Tf [(927)] TJ ET 0.267 0.267 0.267 rg 509.348 321.526 71.527 0.750 re f 509.348 305.645 0.750 16.631 re f 580.125 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 311.671 Td /F1 9.8 Tf [(84.2)] TJ ET 0.267 0.267 0.267 rg 26.625 305.645 68.209 0.750 re f 26.625 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 295.790 Td /F5 9.8 Tf [(ripk4)] TJ ET 0.267 0.267 0.267 rg 94.084 305.645 173.199 0.750 re f 94.084 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 295.790 Td /F1 9.8 Tf [(Receptor-interacting serine-)] TJ ET BT 99.334 288.159 Td /F1 9.8 Tf [(threonine kinase 4)] TJ ET 0.267 0.267 0.267 rg 266.533 305.645 83.543 0.750 re f 266.533 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 295.790 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 305.645 78.419 0.750 re f 349.326 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 295.790 Td /F1 9.8 Tf [(662)] TJ ET 0.267 0.267 0.267 rg 426.995 305.645 83.103 0.750 re f 426.995 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 295.790 Td /F1 9.8 Tf [(645)] TJ ET 0.267 0.267 0.267 rg 509.348 305.645 71.527 0.750 re f 509.348 282.133 0.750 24.263 re f 580.125 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 295.790 Td /F1 9.8 Tf [(83.2)] TJ ET 0.267 0.267 0.267 rg 26.625 282.133 68.209 0.750 re f 26.625 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 272.278 Td /F5 9.8 Tf [(snx33)] TJ ET BT 57.888 272.278 Td /F1 9.8 Tf [( \(=)] TJ ET BT 31.875 264.646 Td /F5 9.8 Tf [(sh3px3)] TJ ET BT 63.309 264.646 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 282.133 173.199 0.750 re f 94.084 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 272.278 Td /F1 9.8 Tf [(Sorting nexin 3; similar to SH3 and )] TJ ET BT 99.334 264.646 Td /F1 9.8 Tf [(PX domain containing 3 gene)] TJ ET 0.267 0.267 0.267 rg 266.533 282.133 83.543 0.750 re f 266.533 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 272.278 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 282.133 78.419 0.750 re f 349.326 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 272.278 Td /F1 9.8 Tf [(742)] TJ ET 0.267 0.267 0.267 rg 426.995 282.133 83.103 0.750 re f 426.995 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 272.278 Td /F1 9.8 Tf [(705)] TJ ET 0.267 0.267 0.267 rg 509.348 282.133 71.527 0.750 re f 509.348 258.620 0.750 24.263 re f 580.125 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 272.278 Td /F1 9.8 Tf [(85.6)] TJ ET 0.267 0.267 0.267 rg 26.625 258.620 68.209 0.750 re f 26.625 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 248.765 Td /F5 9.8 Tf [(sidkey)] TJ ET 0.267 0.267 0.267 rg 94.084 258.620 173.199 0.750 re f 94.084 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 248.765 Td /F1 9.8 Tf [(si:dkey-174m14.3)] TJ ET 0.267 0.267 0.267 rg 266.533 258.620 83.543 0.750 re f 266.533 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 248.765 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 258.620 78.419 0.750 re f 349.326 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 248.765 Td /F1 9.8 Tf [(547)] TJ ET 0.267 0.267 0.267 rg 426.995 258.620 83.103 0.750 re f 426.995 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 248.765 Td /F1 9.8 Tf [(1299)] TJ ET 0.267 0.267 0.267 rg 509.348 258.620 71.527 0.750 re f 509.348 242.739 0.750 16.631 re f 580.125 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 248.765 Td /F1 9.8 Tf [(85.4)] TJ ET 0.267 0.267 0.267 rg 26.625 242.739 68.209 0.750 re f 26.625 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 232.884 Td /F5 9.8 Tf [(gpr85 )] TJ ET BT 59.516 232.884 Td /F1 9.8 Tf [(\()] TJ ET BT 31.875 225.253 Td /F5 9.8 Tf [(=sreb2)] TJ ET BT 61.954 225.253 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 242.739 173.199 0.750 re f 94.084 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 232.884 Td /F1 9.8 Tf [(G protein-coupled receptor 85)] TJ ET 0.267 0.267 0.267 rg 266.533 242.739 83.543 0.750 re f 266.533 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 232.884 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 242.739 78.419 0.750 re f 349.326 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 232.884 Td /F1 9.8 Tf [(320)] TJ ET 0.267 0.267 0.267 rg 426.995 242.739 83.103 0.750 re f 426.995 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 232.884 Td /F1 9.8 Tf [(990)] TJ ET 0.267 0.267 0.267 rg 509.348 242.739 71.527 0.750 re f 509.348 219.226 0.750 24.263 re f 580.125 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 232.884 Td /F1 9.8 Tf [(87.7)] TJ ET 0.267 0.267 0.267 rg 26.625 219.226 68.209 0.750 re f 26.625 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 31.875 209.371 Td /F5 9.8 Tf [(svep1)] TJ ET BT 57.888 209.371 Td /F1 9.8 Tf [(*)] TJ ET 0.267 0.267 0.267 rg 94.084 219.226 173.199 0.750 re f 94.084 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 99.334 209.371 Td /F1 9.8 Tf [(Sushi, von Willebrand factor type A, )] TJ ET BT 99.334 201.740 Td /F1 9.8 Tf [(EGF and pentraxin domain )] TJ ET BT 99.334 194.109 Td /F1 9.8 Tf [(containing 1)] TJ ET 0.267 0.267 0.267 rg 266.533 219.226 83.543 0.750 re f 266.533 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 271.783 209.371 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 219.226 78.419 0.750 re f 349.326 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 354.576 209.371 Td /F1 9.8 Tf [(226)] TJ ET 0.267 0.267 0.267 rg 426.995 219.226 83.103 0.750 re f 426.995 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 432.245 209.371 Td /F1 9.8 Tf [(825)] TJ ET 0.267 0.267 0.267 rg 509.348 219.226 71.527 0.750 re f 509.348 188.083 0.750 31.894 re f 580.125 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 514.598 209.371 Td /F1 9.8 Tf [(77.6)] TJ ET 0.267 0.267 0.267 rg 26.625 188.083 68.209 0.750 re f 26.625 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 178.228 Td /F5 9.8 Tf [(tbr1b)] TJ ET BT 54.095 178.228 Td /F1 9.8 Tf [( \(=)] TJ ET BT 65.746 178.228 Td /F5 9.8 Tf [(tbr1)] TJ ET BT 82.546 178.228 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 188.083 173.199 0.750 re f 94.084 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 178.228 Td /F1 9.8 Tf [(T-box, brain, 1b)] TJ ET 0.267 0.267 0.267 rg 266.533 188.083 83.543 0.750 re f 266.533 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 178.228 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 188.083 78.419 0.750 re f 349.326 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 178.228 Td /F1 9.8 Tf [(601)] TJ ET 0.267 0.267 0.267 rg 426.995 188.083 83.103 0.750 re f 426.995 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 178.228 Td /F1 9.8 Tf [(831)] TJ ET 0.267 0.267 0.267 rg 509.348 188.083 71.527 0.750 re f 509.348 172.201 0.750 16.631 re f 580.125 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 178.228 Td /F1 9.8 Tf [(86.4)] TJ ET 0.267 0.267 0.267 rg 26.625 172.201 68.209 0.750 re f 26.625 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 162.346 Td /F5 9.8 Tf [(vcpip*)] TJ ET 0.267 0.267 0.267 rg 94.084 172.201 173.199 0.750 re f 94.084 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 162.346 Td /F1 9.8 Tf [(Valosin-containing protein p97/p47 )] TJ ET BT 99.334 154.715 Td /F1 9.8 Tf [(complete interacting protein 1)] TJ ET 0.267 0.267 0.267 rg 266.533 172.201 83.543 0.750 re f 266.533 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 162.346 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 172.201 78.419 0.750 re f 349.326 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 162.346 Td /F1 9.8 Tf [(236)] TJ ET 0.267 0.267 0.267 rg 426.995 172.201 83.103 0.750 re f 426.995 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 162.346 Td /F1 9.8 Tf [(765)] TJ ET 0.267 0.267 0.267 rg 509.348 172.201 71.527 0.750 re f 509.348 148.689 0.750 24.263 re f 580.125 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 162.346 Td /F1 9.8 Tf [(87.5)] TJ ET 0.267 0.267 0.267 rg 26.625 148.689 68.209 0.750 re f 26.625 132.808 68.209 0.750 re f 26.625 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 138.834 Td /F5 9.8 Tf [(zic1)] TJ ET 0.267 0.267 0.267 rg 94.084 148.689 173.199 0.750 re f 94.084 132.808 173.199 0.750 re f 94.084 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 138.834 Td /F1 9.8 Tf [(Zic family member 1)] TJ ET 0.267 0.267 0.267 rg 266.533 148.689 83.543 0.750 re f 266.533 132.808 83.543 0.750 re f 266.533 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 138.834 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 148.689 78.419 0.750 re f 349.326 132.808 78.419 0.750 re f 349.326 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 138.834 Td /F1 9.8 Tf [(983)] TJ ET 0.267 0.267 0.267 rg 426.995 148.689 83.103 0.750 re f 426.995 132.808 83.103 0.750 re f 426.995 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 138.834 Td /F1 9.8 Tf [(984)] TJ ET 0.267 0.267 0.267 rg 509.348 148.689 71.527 0.750 re f 509.348 132.808 71.527 0.750 re f 509.348 132.808 0.750 16.631 re f 580.125 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 138.834 Td /F1 9.8 Tf [(89.9)] TJ ET 0.965 0.965 0.965 rg 26.250 -380.567 555.000 468.000 re f 0.267 0.267 0.267 rg 26.250 87.433 m 581.250 87.433 l 581.250 86.683 l 26.250 86.683 l f q 357.750 0 0 452.250 35.250 -374.567 cm /I4 Do Q q 35.250 -380.567 537.000 0.000 re W n Q Q q 15.000 -380.567 577.500 1157.567 re W n 0.965 0.965 0.965 rg 26.250 620.080 555.000 156.920 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 620.080 m 581.250 620.080 l 581.250 620.830 l 26.250 620.830 l f q 35.250 631.330 537.000 145.670 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 1: Main phylogenetic hypothesis of bony fish groups collapsed to depict higher-level clades.)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(The phylogenetic tree was estimated in RAxML using the 3+ dataset \(1416 taxa\) and 24 partitions with divergence times )] TJ ET BT 35.250 734.370 Td /F1 9.8 Tf [(estimated under PL using 126 fixed secondary calibrations from the BEAST analysis \(see Fig. 11\). Terminal clades are )] TJ ET BT 35.250 720.634 Td /F1 9.8 Tf [(either orders or supraordinal taxa with multiple orders included. Values in parentheses indicate number of families )] TJ ET BT 35.250 706.897 Td /F1 9.8 Tf [(examined. See also Figs. 3-10 for relationship details on selected percomorph clades. The complete phylogeny with )] TJ ET BT 35.250 693.161 Td /F1 9.8 Tf [(bootstrap support values and names for supraordinal taxa is in )] TJ ET 0.267 0.267 0.267 rg BT 307.295 693.161 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 338.183 693.161 Td /F1 9.8 Tf [(\).)] TJ ET BT 35.250 639.866 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc..)] TJ ET Q q 26.250 598.843 555.000 13.736 re W n 0.271 0.267 0.267 rg BT 26.250 601.591 Td /F1 9.8 Tf [(Table 2. Characterization of molecular markers examined.)] TJ ET Q 0.965 0.965 0.965 rg 26.250 567.936 555.000 23.407 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 591.343 m 581.250 591.343 l 580.500 590.593 l 27.000 590.593 l f 581.250 591.343 m 581.250 567.936 l 580.500 567.936 l 580.500 590.593 l f 26.250 591.343 m 26.250 567.936 l 27.000 567.936 l 27.000 590.593 l f 0.271 0.267 0.267 rg BT 33.000 577.267 Td /F1 9.0 Tf [(*New markers developed here)] TJ ET 1.000 1.000 1.000 rg 26.250 132.433 555.000 435.503 re f 0.965 0.965 0.965 rg 27.000 543.001 67.459 24.185 re f 0.267 0.267 0.267 rg 26.625 566.811 67.834 0.750 re f 26.625 542.626 0.750 24.935 re f 0.271 0.267 0.267 rg BT 31.500 557.662 Td /F4 9.8 Tf [(Locus)] TJ ET 0.965 0.965 0.965 rg 94.459 543.001 172.449 24.185 re f 0.267 0.267 0.267 rg 94.459 566.811 172.449 0.750 re f 0.271 0.267 0.267 rg BT 98.959 557.662 Td /F4 9.8 Tf [(Description)] TJ ET 0.965 0.965 0.965 rg 266.908 543.001 82.793 24.185 re f 0.267 0.267 0.267 rg 266.908 566.811 82.793 0.750 re f 0.271 0.267 0.267 rg BT 271.408 557.662 Td /F4 9.8 Tf [(Type)] TJ ET 0.965 0.965 0.965 rg 349.701 543.001 77.669 24.185 re f 0.267 0.267 0.267 rg 349.701 566.811 77.669 0.750 re f 0.271 0.267 0.267 rg BT 354.201 557.662 Td /F4 9.8 Tf [(Total )] TJ ET BT 354.201 545.757 Td /F4 9.8 Tf [(sequences)] TJ ET 0.965 0.965 0.965 rg 427.370 543.001 82.353 24.185 re f 0.267 0.267 0.267 rg 427.370 566.811 82.353 0.750 re f 0.271 0.267 0.267 rg BT 431.870 557.662 Td /F4 9.8 Tf [(Alignment )] TJ ET BT 431.870 545.757 Td /F4 9.8 Tf [(length \(sites\))] TJ ET 0.965 0.965 0.965 rg 509.723 543.001 70.777 24.185 re f 0.267 0.267 0.267 rg 509.723 566.811 71.152 0.750 re f 580.125 542.626 0.750 24.935 re f 0.271 0.267 0.267 rg BT 514.223 557.662 Td /F4 9.8 Tf [(Pairwise )] TJ ET BT 514.223 545.757 Td /F4 9.8 Tf [(identity \(%\))] TJ ET 0.267 0.267 0.267 rg 26.625 542.626 68.209 0.750 re f 26.625 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 532.771 Td /F5 9.8 Tf [(16S)] TJ ET 0.267 0.267 0.267 rg 94.084 542.626 173.199 0.750 re f 94.084 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 532.771 Td /F1 9.8 Tf [(16S rRNA)] TJ ET 0.267 0.267 0.267 rg 266.533 542.626 83.543 0.750 re f 266.533 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 532.771 Td /F1 9.8 Tf [(Mitochondrial)] TJ ET 0.267 0.267 0.267 rg 349.326 542.626 78.419 0.750 re f 349.326 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 532.771 Td /F1 9.8 Tf [(983)] TJ ET 0.267 0.267 0.267 rg 426.995 542.626 83.103 0.750 re f 426.995 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 532.771 Td /F1 9.8 Tf [(2326)] TJ ET 0.267 0.267 0.267 rg 509.348 542.626 71.527 0.750 re f 509.348 526.745 0.750 16.631 re f 580.125 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 532.771 Td /F1 9.8 Tf [(70.0)] TJ ET 0.267 0.267 0.267 rg 26.625 526.745 68.209 0.750 re f 26.625 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 31.875 516.890 Td /F5 9.8 Tf [(enc1)] TJ ET 0.267 0.267 0.267 rg 94.084 526.745 173.199 0.750 re f 94.084 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 99.334 516.890 Td /F1 9.8 Tf [(Gene for peroxisomal enoyl-CoA )] TJ ET BT 99.334 509.259 Td /F1 9.8 Tf [(hydratase/L-3-hydroxyacyl-CoA )] TJ ET BT 99.334 501.628 Td /F1 9.8 Tf [(dehydrogenase)] TJ ET 0.267 0.267 0.267 rg 266.533 526.745 83.543 0.750 re f 266.533 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 271.783 516.890 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 526.745 78.419 0.750 re f 349.326 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 354.576 516.890 Td /F1 9.8 Tf [(360)] TJ ET 0.267 0.267 0.267 rg 426.995 526.745 83.103 0.750 re f 426.995 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 432.245 516.890 Td /F1 9.8 Tf [(657)] TJ ET 0.267 0.267 0.267 rg 509.348 526.745 71.527 0.750 re f 509.348 495.601 0.750 31.894 re f 580.125 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 514.598 516.890 Td /F1 9.8 Tf [(84.6)] TJ ET 0.267 0.267 0.267 rg 26.625 495.601 68.209 0.750 re f 26.625 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 485.746 Td /F5 9.8 Tf [(ficd)] TJ ET 0.267 0.267 0.267 rg 94.084 495.601 173.199 0.750 re f 94.084 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 485.746 Td /F1 9.8 Tf [(FIC domain)] TJ ET 0.267 0.267 0.267 rg 266.533 495.601 83.543 0.750 re f 266.533 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 485.746 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 495.601 78.419 0.750 re f 349.326 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 485.746 Td /F1 9.8 Tf [(602)] TJ ET 0.267 0.267 0.267 rg 426.995 495.601 83.103 0.750 re f 426.995 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 485.746 Td /F1 9.8 Tf [(732)] TJ ET 0.267 0.267 0.267 rg 509.348 495.601 71.527 0.750 re f 509.348 479.720 0.750 16.631 re f 580.125 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 485.746 Td /F1 9.8 Tf [(86.0)] TJ ET 0.267 0.267 0.267 rg 26.625 479.720 68.209 0.750 re f 26.625 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 469.865 Td /F5 9.8 Tf [(gtdc2 )] TJ ET BT 58.434 469.865 Td /F1 9.8 Tf [(\()] TJ ET BT 61.681 469.865 Td /F5 9.8 Tf [(= glyt)] TJ ET BT 85.256 469.865 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 479.720 173.199 0.750 re f 94.084 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 469.865 Td /F1 9.8 Tf [(Glycosyltransferase-like domain )] TJ ET BT 99.334 462.234 Td /F1 9.8 Tf [(containing 2)] TJ ET 0.267 0.267 0.267 rg 266.533 479.720 83.543 0.750 re f 266.533 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 469.865 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 479.720 78.419 0.750 re f 349.326 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 469.865 Td /F1 9.8 Tf [(343)] TJ ET 0.267 0.267 0.267 rg 426.995 479.720 83.103 0.750 re f 426.995 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 469.865 Td /F1 9.8 Tf [(891)] TJ ET 0.267 0.267 0.267 rg 509.348 479.720 71.527 0.750 re f 509.348 456.208 0.750 24.263 re f 580.125 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 469.865 Td /F1 9.8 Tf [(78.3)] TJ ET 0.267 0.267 0.267 rg 26.625 456.208 68.209 0.750 re f 26.625 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 446.353 Td /F5 9.8 Tf [(hoxc6a*)] TJ ET 0.267 0.267 0.267 rg 94.084 456.208 173.199 0.750 re f 94.084 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 446.353 Td /F1 9.8 Tf [(Homeo box C6a)] TJ ET 0.267 0.267 0.267 rg 266.533 456.208 83.543 0.750 re f 266.533 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 446.353 Td /F1 9.8 Tf [(Nuclear intron)] TJ ET 0.267 0.267 0.267 rg 349.326 456.208 78.419 0.750 re f 349.326 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 446.353 Td /F1 9.8 Tf [(362)] TJ ET 0.267 0.267 0.267 rg 426.995 456.208 83.103 0.750 re f 426.995 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 446.353 Td /F1 9.8 Tf [(1184)] TJ ET 0.267 0.267 0.267 rg 509.348 456.208 71.527 0.750 re f 509.348 440.326 0.750 16.631 re f 580.125 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 446.353 Td /F1 9.8 Tf [(61.0)] TJ ET 0.267 0.267 0.267 rg 26.625 440.326 68.209 0.750 re f 26.625 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 430.471 Td /F5 9.8 Tf [(kiaa1239)] TJ ET 0.267 0.267 0.267 rg 94.084 440.326 173.199 0.750 re f 94.084 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 430.471 Td /F1 9.8 Tf [(Leucine-rich repeat and WD repeat-)] TJ ET BT 99.334 422.840 Td /F1 9.8 Tf [(containing protein, KIAA1239-like)] TJ ET 0.267 0.267 0.267 rg 266.533 440.326 83.543 0.750 re f 266.533 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 430.471 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 440.326 78.419 0.750 re f 349.326 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 430.471 Td /F1 9.8 Tf [(749)] TJ ET 0.267 0.267 0.267 rg 426.995 440.326 83.103 0.750 re f 426.995 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 430.471 Td /F1 9.8 Tf [(963)] TJ ET 0.267 0.267 0.267 rg 509.348 440.326 71.527 0.750 re f 509.348 416.814 0.750 24.263 re f 580.125 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 430.471 Td /F1 9.8 Tf [(86.3)] TJ ET 0.267 0.267 0.267 rg 26.625 416.814 68.209 0.750 re f 26.625 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 406.959 Td /F5 9.8 Tf [(myh6)] TJ ET 0.267 0.267 0.267 rg 94.084 416.814 173.199 0.750 re f 94.084 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 406.959 Td /F1 9.8 Tf [(Myosin, heavy polypeptide 6)] TJ ET 0.267 0.267 0.267 rg 266.533 416.814 83.543 0.750 re f 266.533 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 406.959 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 416.814 78.419 0.750 re f 349.326 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 406.959 Td /F1 9.8 Tf [(874)] TJ ET 0.267 0.267 0.267 rg 426.995 416.814 83.103 0.750 re f 426.995 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 406.959 Td /F1 9.8 Tf [(789)] TJ ET 0.267 0.267 0.267 rg 509.348 416.814 71.527 0.750 re f 509.348 400.933 0.750 16.631 re f 580.125 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 406.959 Td /F1 9.8 Tf [(84.5)] TJ ET 0.267 0.267 0.267 rg 26.625 400.933 68.209 0.750 re f 26.625 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 391.078 Td /F5 9.8 Tf [(panx2)] TJ ET 0.267 0.267 0.267 rg 94.084 400.933 173.199 0.750 re f 94.084 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 391.078 Td /F1 9.8 Tf [(Pannexin 2)] TJ ET 0.267 0.267 0.267 rg 266.533 400.933 83.543 0.750 re f 266.533 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 391.078 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 400.933 78.419 0.750 re f 349.326 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 391.078 Td /F1 9.8 Tf [(656)] TJ ET 0.267 0.267 0.267 rg 426.995 400.933 83.103 0.750 re f 426.995 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 391.078 Td /F1 9.8 Tf [(984)] TJ ET 0.267 0.267 0.267 rg 509.348 400.933 71.527 0.750 re f 509.348 385.051 0.750 16.631 re f 580.125 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 391.078 Td /F1 9.8 Tf [(86.2)] TJ ET 0.267 0.267 0.267 rg 26.625 385.051 68.209 0.750 re f 26.625 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 375.196 Td /F5 9.8 Tf [(plagl2)] TJ ET 0.267 0.267 0.267 rg 94.084 385.051 173.199 0.750 re f 94.084 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 375.196 Td /F1 9.8 Tf [(Pleiomorphic adenoma gene-like 2)] TJ ET 0.267 0.267 0.267 rg 266.533 385.051 83.543 0.750 re f 266.533 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 375.196 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 385.051 78.419 0.750 re f 349.326 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 375.196 Td /F1 9.8 Tf [(854)] TJ ET 0.267 0.267 0.267 rg 426.995 385.051 83.103 0.750 re f 426.995 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 375.196 Td /F1 9.8 Tf [(819)] TJ ET 0.267 0.267 0.267 rg 509.348 385.051 71.527 0.750 re f 509.348 369.170 0.750 16.631 re f 580.125 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 375.196 Td /F1 9.8 Tf [(87.9)] TJ ET 0.267 0.267 0.267 rg 26.625 369.170 68.209 0.750 re f 26.625 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 359.315 Td /F5 9.8 Tf [(ptchd1)] TJ ET BT 61.145 359.315 Td /F1 9.8 Tf [( \(=)] TJ ET BT 72.796 359.315 Td /F5 9.8 Tf [(ptr)] TJ ET BT 84.174 359.315 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 369.170 173.199 0.750 re f 94.084 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 359.315 Td /F1 9.8 Tf [(Patched domain containing 4)] TJ ET 0.267 0.267 0.267 rg 266.533 369.170 83.543 0.750 re f 266.533 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 359.315 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 369.170 78.419 0.750 re f 349.326 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 359.315 Td /F1 9.8 Tf [(736)] TJ ET 0.267 0.267 0.267 rg 426.995 369.170 83.103 0.750 re f 426.995 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 359.315 Td /F1 9.8 Tf [(756)] TJ ET 0.267 0.267 0.267 rg 509.348 369.170 71.527 0.750 re f 509.348 353.289 0.750 16.631 re f 580.125 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 359.315 Td /F1 9.8 Tf [(86.0)] TJ ET 0.267 0.267 0.267 rg 26.625 353.289 68.209 0.750 re f 26.625 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 343.434 Td /F5 9.8 Tf [(rag1)] TJ ET 0.267 0.267 0.267 rg 94.084 353.289 173.199 0.750 re f 94.084 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 343.434 Td /F1 9.8 Tf [(Recombination activating gene 1)] TJ ET 0.267 0.267 0.267 rg 266.533 353.289 83.543 0.750 re f 266.533 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 343.434 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 353.289 78.419 0.750 re f 349.326 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 343.434 Td /F1 9.8 Tf [(784)] TJ ET 0.267 0.267 0.267 rg 426.995 353.289 83.103 0.750 re f 426.995 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 343.434 Td /F1 9.8 Tf [(1575)] TJ ET 0.267 0.267 0.267 rg 509.348 353.289 71.527 0.750 re f 509.348 337.408 0.750 16.631 re f 580.125 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 343.434 Td /F1 9.8 Tf [(80.6)] TJ ET 0.267 0.267 0.267 rg 26.625 337.408 68.209 0.750 re f 26.625 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 327.553 Td /F5 9.8 Tf [(rag2)] TJ ET 0.267 0.267 0.267 rg 94.084 337.408 173.199 0.750 re f 94.084 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 327.553 Td /F1 9.8 Tf [(Recombination activating gene 2)] TJ ET 0.267 0.267 0.267 rg 266.533 337.408 83.543 0.750 re f 266.533 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 327.553 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 337.408 78.419 0.750 re f 349.326 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 327.553 Td /F1 9.8 Tf [(276)] TJ ET 0.267 0.267 0.267 rg 426.995 337.408 83.103 0.750 re f 426.995 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 327.553 Td /F1 9.8 Tf [(1206)] TJ ET 0.267 0.267 0.267 rg 509.348 337.408 71.527 0.750 re f 509.348 321.526 0.750 16.631 re f 580.125 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 327.553 Td /F1 9.8 Tf [(71.2)] TJ ET 0.267 0.267 0.267 rg 26.625 321.526 68.209 0.750 re f 26.625 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 311.671 Td /F5 9.8 Tf [(rh)] TJ ET 0.267 0.267 0.267 rg 94.084 321.526 173.199 0.750 re f 94.084 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 311.671 Td /F1 9.8 Tf [(Rhodopsin)] TJ ET 0.267 0.267 0.267 rg 266.533 321.526 83.543 0.750 re f 266.533 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 311.671 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 321.526 78.419 0.750 re f 349.326 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 311.671 Td /F1 9.8 Tf [(417)] TJ ET 0.267 0.267 0.267 rg 426.995 321.526 83.103 0.750 re f 426.995 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 311.671 Td /F1 9.8 Tf [(927)] TJ ET 0.267 0.267 0.267 rg 509.348 321.526 71.527 0.750 re f 509.348 305.645 0.750 16.631 re f 580.125 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 311.671 Td /F1 9.8 Tf [(84.2)] TJ ET 0.267 0.267 0.267 rg 26.625 305.645 68.209 0.750 re f 26.625 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 295.790 Td /F5 9.8 Tf [(ripk4)] TJ ET 0.267 0.267 0.267 rg 94.084 305.645 173.199 0.750 re f 94.084 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 295.790 Td /F1 9.8 Tf [(Receptor-interacting serine-)] TJ ET BT 99.334 288.159 Td /F1 9.8 Tf [(threonine kinase 4)] TJ ET 0.267 0.267 0.267 rg 266.533 305.645 83.543 0.750 re f 266.533 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 295.790 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 305.645 78.419 0.750 re f 349.326 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 295.790 Td /F1 9.8 Tf [(662)] TJ ET 0.267 0.267 0.267 rg 426.995 305.645 83.103 0.750 re f 426.995 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 295.790 Td /F1 9.8 Tf [(645)] TJ ET 0.267 0.267 0.267 rg 509.348 305.645 71.527 0.750 re f 509.348 282.133 0.750 24.263 re f 580.125 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 295.790 Td /F1 9.8 Tf [(83.2)] TJ ET 0.267 0.267 0.267 rg 26.625 282.133 68.209 0.750 re f 26.625 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 272.278 Td /F5 9.8 Tf [(snx33)] TJ ET BT 57.888 272.278 Td /F1 9.8 Tf [( \(=)] TJ ET BT 31.875 264.646 Td /F5 9.8 Tf [(sh3px3)] TJ ET BT 63.309 264.646 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 282.133 173.199 0.750 re f 94.084 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 272.278 Td /F1 9.8 Tf [(Sorting nexin 3; similar to SH3 and )] TJ ET BT 99.334 264.646 Td /F1 9.8 Tf [(PX domain containing 3 gene)] TJ ET 0.267 0.267 0.267 rg 266.533 282.133 83.543 0.750 re f 266.533 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 272.278 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 282.133 78.419 0.750 re f 349.326 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 272.278 Td /F1 9.8 Tf [(742)] TJ ET 0.267 0.267 0.267 rg 426.995 282.133 83.103 0.750 re f 426.995 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 272.278 Td /F1 9.8 Tf [(705)] TJ ET 0.267 0.267 0.267 rg 509.348 282.133 71.527 0.750 re f 509.348 258.620 0.750 24.263 re f 580.125 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 272.278 Td /F1 9.8 Tf [(85.6)] TJ ET 0.267 0.267 0.267 rg 26.625 258.620 68.209 0.750 re f 26.625 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 248.765 Td /F5 9.8 Tf [(sidkey)] TJ ET 0.267 0.267 0.267 rg 94.084 258.620 173.199 0.750 re f 94.084 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 248.765 Td /F1 9.8 Tf [(si:dkey-174m14.3)] TJ ET 0.267 0.267 0.267 rg 266.533 258.620 83.543 0.750 re f 266.533 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 248.765 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 258.620 78.419 0.750 re f 349.326 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 248.765 Td /F1 9.8 Tf [(547)] TJ ET 0.267 0.267 0.267 rg 426.995 258.620 83.103 0.750 re f 426.995 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 248.765 Td /F1 9.8 Tf [(1299)] TJ ET 0.267 0.267 0.267 rg 509.348 258.620 71.527 0.750 re f 509.348 242.739 0.750 16.631 re f 580.125 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 248.765 Td /F1 9.8 Tf [(85.4)] TJ ET 0.267 0.267 0.267 rg 26.625 242.739 68.209 0.750 re f 26.625 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 232.884 Td /F5 9.8 Tf [(gpr85 )] TJ ET BT 59.516 232.884 Td /F1 9.8 Tf [(\()] TJ ET BT 31.875 225.253 Td /F5 9.8 Tf [(=sreb2)] TJ ET BT 61.954 225.253 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 242.739 173.199 0.750 re f 94.084 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 232.884 Td /F1 9.8 Tf [(G protein-coupled receptor 85)] TJ ET 0.267 0.267 0.267 rg 266.533 242.739 83.543 0.750 re f 266.533 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 232.884 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 242.739 78.419 0.750 re f 349.326 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 232.884 Td /F1 9.8 Tf [(320)] TJ ET 0.267 0.267 0.267 rg 426.995 242.739 83.103 0.750 re f 426.995 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 232.884 Td /F1 9.8 Tf [(990)] TJ ET 0.267 0.267 0.267 rg 509.348 242.739 71.527 0.750 re f 509.348 219.226 0.750 24.263 re f 580.125 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 232.884 Td /F1 9.8 Tf [(87.7)] TJ ET 0.267 0.267 0.267 rg 26.625 219.226 68.209 0.750 re f 26.625 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 31.875 209.371 Td /F5 9.8 Tf [(svep1)] TJ ET BT 57.888 209.371 Td /F1 9.8 Tf [(*)] TJ ET 0.267 0.267 0.267 rg 94.084 219.226 173.199 0.750 re f 94.084 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 99.334 209.371 Td /F1 9.8 Tf [(Sushi, von Willebrand factor type A, )] TJ ET BT 99.334 201.740 Td /F1 9.8 Tf [(EGF and pentraxin domain )] TJ ET BT 99.334 194.109 Td /F1 9.8 Tf [(containing 1)] TJ ET 0.267 0.267 0.267 rg 266.533 219.226 83.543 0.750 re f 266.533 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 271.783 209.371 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 219.226 78.419 0.750 re f 349.326 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 354.576 209.371 Td /F1 9.8 Tf [(226)] TJ ET 0.267 0.267 0.267 rg 426.995 219.226 83.103 0.750 re f 426.995 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 432.245 209.371 Td /F1 9.8 Tf [(825)] TJ ET 0.267 0.267 0.267 rg 509.348 219.226 71.527 0.750 re f 509.348 188.083 0.750 31.894 re f 580.125 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 514.598 209.371 Td /F1 9.8 Tf [(77.6)] TJ ET 0.267 0.267 0.267 rg 26.625 188.083 68.209 0.750 re f 26.625 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 178.228 Td /F5 9.8 Tf [(tbr1b)] TJ ET BT 54.095 178.228 Td /F1 9.8 Tf [( \(=)] TJ ET BT 65.746 178.228 Td /F5 9.8 Tf [(tbr1)] TJ ET BT 82.546 178.228 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 188.083 173.199 0.750 re f 94.084 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 178.228 Td /F1 9.8 Tf [(T-box, brain, 1b)] TJ ET 0.267 0.267 0.267 rg 266.533 188.083 83.543 0.750 re f 266.533 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 178.228 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 188.083 78.419 0.750 re f 349.326 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 178.228 Td /F1 9.8 Tf [(601)] TJ ET 0.267 0.267 0.267 rg 426.995 188.083 83.103 0.750 re f 426.995 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 178.228 Td /F1 9.8 Tf [(831)] TJ ET 0.267 0.267 0.267 rg 509.348 188.083 71.527 0.750 re f 509.348 172.201 0.750 16.631 re f 580.125 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 178.228 Td /F1 9.8 Tf [(86.4)] TJ ET 0.267 0.267 0.267 rg 26.625 172.201 68.209 0.750 re f 26.625 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 162.346 Td /F5 9.8 Tf [(vcpip*)] TJ ET 0.267 0.267 0.267 rg 94.084 172.201 173.199 0.750 re f 94.084 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 162.346 Td /F1 9.8 Tf [(Valosin-containing protein p97/p47 )] TJ ET BT 99.334 154.715 Td /F1 9.8 Tf [(complete interacting protein 1)] TJ ET 0.267 0.267 0.267 rg 266.533 172.201 83.543 0.750 re f 266.533 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 162.346 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 172.201 78.419 0.750 re f 349.326 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 162.346 Td /F1 9.8 Tf [(236)] TJ ET 0.267 0.267 0.267 rg 426.995 172.201 83.103 0.750 re f 426.995 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 162.346 Td /F1 9.8 Tf [(765)] TJ ET 0.267 0.267 0.267 rg 509.348 172.201 71.527 0.750 re f 509.348 148.689 0.750 24.263 re f 580.125 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 162.346 Td /F1 9.8 Tf [(87.5)] TJ ET 0.267 0.267 0.267 rg 26.625 148.689 68.209 0.750 re f 26.625 132.808 68.209 0.750 re f 26.625 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 138.834 Td /F5 9.8 Tf [(zic1)] TJ ET 0.267 0.267 0.267 rg 94.084 148.689 173.199 0.750 re f 94.084 132.808 173.199 0.750 re f 94.084 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 138.834 Td /F1 9.8 Tf [(Zic family member 1)] TJ ET 0.267 0.267 0.267 rg 266.533 148.689 83.543 0.750 re f 266.533 132.808 83.543 0.750 re f 266.533 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 138.834 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 148.689 78.419 0.750 re f 349.326 132.808 78.419 0.750 re f 349.326 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 138.834 Td /F1 9.8 Tf [(983)] TJ ET 0.267 0.267 0.267 rg 426.995 148.689 83.103 0.750 re f 426.995 132.808 83.103 0.750 re f 426.995 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 138.834 Td /F1 9.8 Tf [(984)] TJ ET 0.267 0.267 0.267 rg 509.348 148.689 71.527 0.750 re f 509.348 132.808 71.527 0.750 re f 509.348 132.808 0.750 16.631 re f 580.125 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 138.834 Td /F1 9.8 Tf [(89.9)] TJ ET 0.965 0.965 0.965 rg 26.250 -380.567 555.000 468.000 re f 0.267 0.267 0.267 rg 26.250 87.433 m 581.250 87.433 l 581.250 86.683 l 26.250 86.683 l f q 357.750 0 0 452.250 35.250 -374.567 cm /I4 Do Q q 35.250 -380.567 537.000 0.000 re W n Q Q q 15.000 -380.567 577.500 1157.567 re W n 0.965 0.965 0.965 rg 26.250 620.080 555.000 156.920 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 620.080 m 581.250 620.080 l 581.250 620.830 l 26.250 620.830 l f q 35.250 631.330 537.000 145.670 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 1: Main phylogenetic hypothesis of bony fish groups collapsed to depict higher-level clades.)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(The phylogenetic tree was estimated in RAxML using the 3+ dataset \(1416 taxa\) and 24 partitions with divergence times )] TJ ET BT 35.250 734.370 Td /F1 9.8 Tf [(estimated under PL using 126 fixed secondary calibrations from the BEAST analysis \(see Fig. 11\). Terminal clades are )] TJ ET BT 35.250 720.634 Td /F1 9.8 Tf [(either orders or supraordinal taxa with multiple orders included. Values in parentheses indicate number of families )] TJ ET BT 35.250 706.897 Td /F1 9.8 Tf [(examined. See also Figs. 3-10 for relationship details on selected percomorph clades. The complete phylogeny with )] TJ ET BT 35.250 693.161 Td /F1 9.8 Tf [(bootstrap support values and names for supraordinal taxa is in )] TJ ET 0.267 0.267 0.267 rg BT 307.295 693.161 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 338.183 693.161 Td /F1 9.8 Tf [(\).)] TJ ET BT 35.250 639.866 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc..)] TJ ET Q q 26.250 598.843 555.000 13.736 re W n 0.271 0.267 0.267 rg BT 26.250 601.591 Td /F1 9.8 Tf [(Table 2. Characterization of molecular markers examined.)] TJ ET Q 0.965 0.965 0.965 rg 26.250 567.936 555.000 23.407 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 591.343 m 581.250 591.343 l 580.500 590.593 l 27.000 590.593 l f 581.250 591.343 m 581.250 567.936 l 580.500 567.936 l 580.500 590.593 l f 26.250 591.343 m 26.250 567.936 l 27.000 567.936 l 27.000 590.593 l f 0.271 0.267 0.267 rg BT 33.000 577.267 Td /F1 9.0 Tf [(*New markers developed here)] TJ ET 1.000 1.000 1.000 rg 26.250 132.433 555.000 435.503 re f 0.965 0.965 0.965 rg 27.000 543.001 67.459 24.185 re f 0.267 0.267 0.267 rg 26.625 566.811 67.834 0.750 re f 26.625 542.626 0.750 24.935 re f 0.271 0.267 0.267 rg BT 31.500 557.662 Td /F4 9.8 Tf [(Locus)] TJ ET 0.965 0.965 0.965 rg 94.459 543.001 172.449 24.185 re f 0.267 0.267 0.267 rg 94.459 566.811 172.449 0.750 re f 0.271 0.267 0.267 rg BT 98.959 557.662 Td /F4 9.8 Tf [(Description)] TJ ET 0.965 0.965 0.965 rg 266.908 543.001 82.793 24.185 re f 0.267 0.267 0.267 rg 266.908 566.811 82.793 0.750 re f 0.271 0.267 0.267 rg BT 271.408 557.662 Td /F4 9.8 Tf [(Type)] TJ ET 0.965 0.965 0.965 rg 349.701 543.001 77.669 24.185 re f 0.267 0.267 0.267 rg 349.701 566.811 77.669 0.750 re f 0.271 0.267 0.267 rg BT 354.201 557.662 Td /F4 9.8 Tf [(Total )] TJ ET BT 354.201 545.757 Td /F4 9.8 Tf [(sequences)] TJ ET 0.965 0.965 0.965 rg 427.370 543.001 82.353 24.185 re f 0.267 0.267 0.267 rg 427.370 566.811 82.353 0.750 re f 0.271 0.267 0.267 rg BT 431.870 557.662 Td /F4 9.8 Tf [(Alignment )] TJ ET BT 431.870 545.757 Td /F4 9.8 Tf [(length \(sites\))] TJ ET 0.965 0.965 0.965 rg 509.723 543.001 70.777 24.185 re f 0.267 0.267 0.267 rg 509.723 566.811 71.152 0.750 re f 580.125 542.626 0.750 24.935 re f 0.271 0.267 0.267 rg BT 514.223 557.662 Td /F4 9.8 Tf [(Pairwise )] TJ ET BT 514.223 545.757 Td /F4 9.8 Tf [(identity \(%\))] TJ ET 0.267 0.267 0.267 rg 26.625 542.626 68.209 0.750 re f 26.625 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 532.771 Td /F5 9.8 Tf [(16S)] TJ ET 0.267 0.267 0.267 rg 94.084 542.626 173.199 0.750 re f 94.084 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 532.771 Td /F1 9.8 Tf [(16S rRNA)] TJ ET 0.267 0.267 0.267 rg 266.533 542.626 83.543 0.750 re f 266.533 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 532.771 Td /F1 9.8 Tf [(Mitochondrial)] TJ ET 0.267 0.267 0.267 rg 349.326 542.626 78.419 0.750 re f 349.326 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 532.771 Td /F1 9.8 Tf [(983)] TJ ET 0.267 0.267 0.267 rg 426.995 542.626 83.103 0.750 re f 426.995 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 532.771 Td /F1 9.8 Tf [(2326)] TJ ET 0.267 0.267 0.267 rg 509.348 542.626 71.527 0.750 re f 509.348 526.745 0.750 16.631 re f 580.125 526.745 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 532.771 Td /F1 9.8 Tf [(70.0)] TJ ET 0.267 0.267 0.267 rg 26.625 526.745 68.209 0.750 re f 26.625 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 31.875 516.890 Td /F5 9.8 Tf [(enc1)] TJ ET 0.267 0.267 0.267 rg 94.084 526.745 173.199 0.750 re f 94.084 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 99.334 516.890 Td /F1 9.8 Tf [(Gene for peroxisomal enoyl-CoA )] TJ ET BT 99.334 509.259 Td /F1 9.8 Tf [(hydratase/L-3-hydroxyacyl-CoA )] TJ ET BT 99.334 501.628 Td /F1 9.8 Tf [(dehydrogenase)] TJ ET 0.267 0.267 0.267 rg 266.533 526.745 83.543 0.750 re f 266.533 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 271.783 516.890 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 526.745 78.419 0.750 re f 349.326 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 354.576 516.890 Td /F1 9.8 Tf [(360)] TJ ET 0.267 0.267 0.267 rg 426.995 526.745 83.103 0.750 re f 426.995 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 432.245 516.890 Td /F1 9.8 Tf [(657)] TJ ET 0.267 0.267 0.267 rg 509.348 526.745 71.527 0.750 re f 509.348 495.601 0.750 31.894 re f 580.125 495.601 0.750 31.894 re f 0.271 0.267 0.267 rg BT 514.598 516.890 Td /F1 9.8 Tf [(84.6)] TJ ET 0.267 0.267 0.267 rg 26.625 495.601 68.209 0.750 re f 26.625 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 485.746 Td /F5 9.8 Tf [(ficd)] TJ ET 0.267 0.267 0.267 rg 94.084 495.601 173.199 0.750 re f 94.084 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 485.746 Td /F1 9.8 Tf [(FIC domain)] TJ ET 0.267 0.267 0.267 rg 266.533 495.601 83.543 0.750 re f 266.533 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 485.746 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 495.601 78.419 0.750 re f 349.326 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 485.746 Td /F1 9.8 Tf [(602)] TJ ET 0.267 0.267 0.267 rg 426.995 495.601 83.103 0.750 re f 426.995 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 485.746 Td /F1 9.8 Tf [(732)] TJ ET 0.267 0.267 0.267 rg 509.348 495.601 71.527 0.750 re f 509.348 479.720 0.750 16.631 re f 580.125 479.720 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 485.746 Td /F1 9.8 Tf [(86.0)] TJ ET 0.267 0.267 0.267 rg 26.625 479.720 68.209 0.750 re f 26.625 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 469.865 Td /F5 9.8 Tf [(gtdc2 )] TJ ET BT 58.434 469.865 Td /F1 9.8 Tf [(\()] TJ ET BT 61.681 469.865 Td /F5 9.8 Tf [(= glyt)] TJ ET BT 85.256 469.865 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 479.720 173.199 0.750 re f 94.084 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 469.865 Td /F1 9.8 Tf [(Glycosyltransferase-like domain )] TJ ET BT 99.334 462.234 Td /F1 9.8 Tf [(containing 2)] TJ ET 0.267 0.267 0.267 rg 266.533 479.720 83.543 0.750 re f 266.533 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 469.865 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 479.720 78.419 0.750 re f 349.326 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 469.865 Td /F1 9.8 Tf [(343)] TJ ET 0.267 0.267 0.267 rg 426.995 479.720 83.103 0.750 re f 426.995 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 469.865 Td /F1 9.8 Tf [(891)] TJ ET 0.267 0.267 0.267 rg 509.348 479.720 71.527 0.750 re f 509.348 456.208 0.750 24.263 re f 580.125 456.208 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 469.865 Td /F1 9.8 Tf [(78.3)] TJ ET 0.267 0.267 0.267 rg 26.625 456.208 68.209 0.750 re f 26.625 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 446.353 Td /F5 9.8 Tf [(hoxc6a*)] TJ ET 0.267 0.267 0.267 rg 94.084 456.208 173.199 0.750 re f 94.084 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 446.353 Td /F1 9.8 Tf [(Homeo box C6a)] TJ ET 0.267 0.267 0.267 rg 266.533 456.208 83.543 0.750 re f 266.533 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 446.353 Td /F1 9.8 Tf [(Nuclear intron)] TJ ET 0.267 0.267 0.267 rg 349.326 456.208 78.419 0.750 re f 349.326 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 446.353 Td /F1 9.8 Tf [(362)] TJ ET 0.267 0.267 0.267 rg 426.995 456.208 83.103 0.750 re f 426.995 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 446.353 Td /F1 9.8 Tf [(1184)] TJ ET 0.267 0.267 0.267 rg 509.348 456.208 71.527 0.750 re f 509.348 440.326 0.750 16.631 re f 580.125 440.326 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 446.353 Td /F1 9.8 Tf [(61.0)] TJ ET 0.267 0.267 0.267 rg 26.625 440.326 68.209 0.750 re f 26.625 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 430.471 Td /F5 9.8 Tf [(kiaa1239)] TJ ET 0.267 0.267 0.267 rg 94.084 440.326 173.199 0.750 re f 94.084 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 430.471 Td /F1 9.8 Tf [(Leucine-rich repeat and WD repeat-)] TJ ET BT 99.334 422.840 Td /F1 9.8 Tf [(containing protein, KIAA1239-like)] TJ ET 0.267 0.267 0.267 rg 266.533 440.326 83.543 0.750 re f 266.533 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 430.471 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 440.326 78.419 0.750 re f 349.326 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 430.471 Td /F1 9.8 Tf [(749)] TJ ET 0.267 0.267 0.267 rg 426.995 440.326 83.103 0.750 re f 426.995 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 430.471 Td /F1 9.8 Tf [(963)] TJ ET 0.267 0.267 0.267 rg 509.348 440.326 71.527 0.750 re f 509.348 416.814 0.750 24.263 re f 580.125 416.814 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 430.471 Td /F1 9.8 Tf [(86.3)] TJ ET 0.267 0.267 0.267 rg 26.625 416.814 68.209 0.750 re f 26.625 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 406.959 Td /F5 9.8 Tf [(myh6)] TJ ET 0.267 0.267 0.267 rg 94.084 416.814 173.199 0.750 re f 94.084 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 406.959 Td /F1 9.8 Tf [(Myosin, heavy polypeptide 6)] TJ ET 0.267 0.267 0.267 rg 266.533 416.814 83.543 0.750 re f 266.533 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 406.959 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 416.814 78.419 0.750 re f 349.326 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 406.959 Td /F1 9.8 Tf [(874)] TJ ET 0.267 0.267 0.267 rg 426.995 416.814 83.103 0.750 re f 426.995 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 406.959 Td /F1 9.8 Tf [(789)] TJ ET 0.267 0.267 0.267 rg 509.348 416.814 71.527 0.750 re f 509.348 400.933 0.750 16.631 re f 580.125 400.933 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 406.959 Td /F1 9.8 Tf [(84.5)] TJ ET 0.267 0.267 0.267 rg 26.625 400.933 68.209 0.750 re f 26.625 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 391.078 Td /F5 9.8 Tf [(panx2)] TJ ET 0.267 0.267 0.267 rg 94.084 400.933 173.199 0.750 re f 94.084 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 391.078 Td /F1 9.8 Tf [(Pannexin 2)] TJ ET 0.267 0.267 0.267 rg 266.533 400.933 83.543 0.750 re f 266.533 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 391.078 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 400.933 78.419 0.750 re f 349.326 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 391.078 Td /F1 9.8 Tf [(656)] TJ ET 0.267 0.267 0.267 rg 426.995 400.933 83.103 0.750 re f 426.995 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 391.078 Td /F1 9.8 Tf [(984)] TJ ET 0.267 0.267 0.267 rg 509.348 400.933 71.527 0.750 re f 509.348 385.051 0.750 16.631 re f 580.125 385.051 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 391.078 Td /F1 9.8 Tf [(86.2)] TJ ET 0.267 0.267 0.267 rg 26.625 385.051 68.209 0.750 re f 26.625 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 375.196 Td /F5 9.8 Tf [(plagl2)] TJ ET 0.267 0.267 0.267 rg 94.084 385.051 173.199 0.750 re f 94.084 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 375.196 Td /F1 9.8 Tf [(Pleiomorphic adenoma gene-like 2)] TJ ET 0.267 0.267 0.267 rg 266.533 385.051 83.543 0.750 re f 266.533 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 375.196 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 385.051 78.419 0.750 re f 349.326 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 375.196 Td /F1 9.8 Tf [(854)] TJ ET 0.267 0.267 0.267 rg 426.995 385.051 83.103 0.750 re f 426.995 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 375.196 Td /F1 9.8 Tf [(819)] TJ ET 0.267 0.267 0.267 rg 509.348 385.051 71.527 0.750 re f 509.348 369.170 0.750 16.631 re f 580.125 369.170 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 375.196 Td /F1 9.8 Tf [(87.9)] TJ ET 0.267 0.267 0.267 rg 26.625 369.170 68.209 0.750 re f 26.625 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 359.315 Td /F5 9.8 Tf [(ptchd1)] TJ ET BT 61.145 359.315 Td /F1 9.8 Tf [( \(=)] TJ ET BT 72.796 359.315 Td /F5 9.8 Tf [(ptr)] TJ ET BT 84.174 359.315 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 369.170 173.199 0.750 re f 94.084 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 359.315 Td /F1 9.8 Tf [(Patched domain containing 4)] TJ ET 0.267 0.267 0.267 rg 266.533 369.170 83.543 0.750 re f 266.533 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 359.315 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 369.170 78.419 0.750 re f 349.326 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 359.315 Td /F1 9.8 Tf [(736)] TJ ET 0.267 0.267 0.267 rg 426.995 369.170 83.103 0.750 re f 426.995 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 359.315 Td /F1 9.8 Tf [(756)] TJ ET 0.267 0.267 0.267 rg 509.348 369.170 71.527 0.750 re f 509.348 353.289 0.750 16.631 re f 580.125 353.289 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 359.315 Td /F1 9.8 Tf [(86.0)] TJ ET 0.267 0.267 0.267 rg 26.625 353.289 68.209 0.750 re f 26.625 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 343.434 Td /F5 9.8 Tf [(rag1)] TJ ET 0.267 0.267 0.267 rg 94.084 353.289 173.199 0.750 re f 94.084 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 343.434 Td /F1 9.8 Tf [(Recombination activating gene 1)] TJ ET 0.267 0.267 0.267 rg 266.533 353.289 83.543 0.750 re f 266.533 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 343.434 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 353.289 78.419 0.750 re f 349.326 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 343.434 Td /F1 9.8 Tf [(784)] TJ ET 0.267 0.267 0.267 rg 426.995 353.289 83.103 0.750 re f 426.995 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 343.434 Td /F1 9.8 Tf [(1575)] TJ ET 0.267 0.267 0.267 rg 509.348 353.289 71.527 0.750 re f 509.348 337.408 0.750 16.631 re f 580.125 337.408 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 343.434 Td /F1 9.8 Tf [(80.6)] TJ ET 0.267 0.267 0.267 rg 26.625 337.408 68.209 0.750 re f 26.625 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 327.553 Td /F5 9.8 Tf [(rag2)] TJ ET 0.267 0.267 0.267 rg 94.084 337.408 173.199 0.750 re f 94.084 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 327.553 Td /F1 9.8 Tf [(Recombination activating gene 2)] TJ ET 0.267 0.267 0.267 rg 266.533 337.408 83.543 0.750 re f 266.533 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 327.553 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 337.408 78.419 0.750 re f 349.326 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 327.553 Td /F1 9.8 Tf [(276)] TJ ET 0.267 0.267 0.267 rg 426.995 337.408 83.103 0.750 re f 426.995 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 327.553 Td /F1 9.8 Tf [(1206)] TJ ET 0.267 0.267 0.267 rg 509.348 337.408 71.527 0.750 re f 509.348 321.526 0.750 16.631 re f 580.125 321.526 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 327.553 Td /F1 9.8 Tf [(71.2)] TJ ET 0.267 0.267 0.267 rg 26.625 321.526 68.209 0.750 re f 26.625 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 311.671 Td /F5 9.8 Tf [(rh)] TJ ET 0.267 0.267 0.267 rg 94.084 321.526 173.199 0.750 re f 94.084 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 311.671 Td /F1 9.8 Tf [(Rhodopsin)] TJ ET 0.267 0.267 0.267 rg 266.533 321.526 83.543 0.750 re f 266.533 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 311.671 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 321.526 78.419 0.750 re f 349.326 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 311.671 Td /F1 9.8 Tf [(417)] TJ ET 0.267 0.267 0.267 rg 426.995 321.526 83.103 0.750 re f 426.995 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 311.671 Td /F1 9.8 Tf [(927)] TJ ET 0.267 0.267 0.267 rg 509.348 321.526 71.527 0.750 re f 509.348 305.645 0.750 16.631 re f 580.125 305.645 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 311.671 Td /F1 9.8 Tf [(84.2)] TJ ET 0.267 0.267 0.267 rg 26.625 305.645 68.209 0.750 re f 26.625 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 295.790 Td /F5 9.8 Tf [(ripk4)] TJ ET 0.267 0.267 0.267 rg 94.084 305.645 173.199 0.750 re f 94.084 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 295.790 Td /F1 9.8 Tf [(Receptor-interacting serine-)] TJ ET BT 99.334 288.159 Td /F1 9.8 Tf [(threonine kinase 4)] TJ ET 0.267 0.267 0.267 rg 266.533 305.645 83.543 0.750 re f 266.533 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 295.790 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 305.645 78.419 0.750 re f 349.326 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 295.790 Td /F1 9.8 Tf [(662)] TJ ET 0.267 0.267 0.267 rg 426.995 305.645 83.103 0.750 re f 426.995 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 295.790 Td /F1 9.8 Tf [(645)] TJ ET 0.267 0.267 0.267 rg 509.348 305.645 71.527 0.750 re f 509.348 282.133 0.750 24.263 re f 580.125 282.133 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 295.790 Td /F1 9.8 Tf [(83.2)] TJ ET 0.267 0.267 0.267 rg 26.625 282.133 68.209 0.750 re f 26.625 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 272.278 Td /F5 9.8 Tf [(snx33)] TJ ET BT 57.888 272.278 Td /F1 9.8 Tf [( \(=)] TJ ET BT 31.875 264.646 Td /F5 9.8 Tf [(sh3px3)] TJ ET BT 63.309 264.646 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 282.133 173.199 0.750 re f 94.084 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 272.278 Td /F1 9.8 Tf [(Sorting nexin 3; similar to SH3 and )] TJ ET BT 99.334 264.646 Td /F1 9.8 Tf [(PX domain containing 3 gene)] TJ ET 0.267 0.267 0.267 rg 266.533 282.133 83.543 0.750 re f 266.533 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 272.278 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 282.133 78.419 0.750 re f 349.326 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 272.278 Td /F1 9.8 Tf [(742)] TJ ET 0.267 0.267 0.267 rg 426.995 282.133 83.103 0.750 re f 426.995 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 272.278 Td /F1 9.8 Tf [(705)] TJ ET 0.267 0.267 0.267 rg 509.348 282.133 71.527 0.750 re f 509.348 258.620 0.750 24.263 re f 580.125 258.620 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 272.278 Td /F1 9.8 Tf [(85.6)] TJ ET 0.267 0.267 0.267 rg 26.625 258.620 68.209 0.750 re f 26.625 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 248.765 Td /F5 9.8 Tf [(sidkey)] TJ ET 0.267 0.267 0.267 rg 94.084 258.620 173.199 0.750 re f 94.084 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 248.765 Td /F1 9.8 Tf [(si:dkey-174m14.3)] TJ ET 0.267 0.267 0.267 rg 266.533 258.620 83.543 0.750 re f 266.533 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 248.765 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 258.620 78.419 0.750 re f 349.326 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 248.765 Td /F1 9.8 Tf [(547)] TJ ET 0.267 0.267 0.267 rg 426.995 258.620 83.103 0.750 re f 426.995 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 248.765 Td /F1 9.8 Tf [(1299)] TJ ET 0.267 0.267 0.267 rg 509.348 258.620 71.527 0.750 re f 509.348 242.739 0.750 16.631 re f 580.125 242.739 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 248.765 Td /F1 9.8 Tf [(85.4)] TJ ET 0.267 0.267 0.267 rg 26.625 242.739 68.209 0.750 re f 26.625 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 232.884 Td /F5 9.8 Tf [(gpr85 )] TJ ET BT 59.516 232.884 Td /F1 9.8 Tf [(\()] TJ ET BT 31.875 225.253 Td /F5 9.8 Tf [(=sreb2)] TJ ET BT 61.954 225.253 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 242.739 173.199 0.750 re f 94.084 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 232.884 Td /F1 9.8 Tf [(G protein-coupled receptor 85)] TJ ET 0.267 0.267 0.267 rg 266.533 242.739 83.543 0.750 re f 266.533 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 232.884 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 242.739 78.419 0.750 re f 349.326 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 232.884 Td /F1 9.8 Tf [(320)] TJ ET 0.267 0.267 0.267 rg 426.995 242.739 83.103 0.750 re f 426.995 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 232.884 Td /F1 9.8 Tf [(990)] TJ ET 0.267 0.267 0.267 rg 509.348 242.739 71.527 0.750 re f 509.348 219.226 0.750 24.263 re f 580.125 219.226 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 232.884 Td /F1 9.8 Tf [(87.7)] TJ ET 0.267 0.267 0.267 rg 26.625 219.226 68.209 0.750 re f 26.625 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 31.875 209.371 Td /F5 9.8 Tf [(svep1)] TJ ET BT 57.888 209.371 Td /F1 9.8 Tf [(*)] TJ ET 0.267 0.267 0.267 rg 94.084 219.226 173.199 0.750 re f 94.084 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 99.334 209.371 Td /F1 9.8 Tf [(Sushi, von Willebrand factor type A, )] TJ ET BT 99.334 201.740 Td /F1 9.8 Tf [(EGF and pentraxin domain )] TJ ET BT 99.334 194.109 Td /F1 9.8 Tf [(containing 1)] TJ ET 0.267 0.267 0.267 rg 266.533 219.226 83.543 0.750 re f 266.533 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 271.783 209.371 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 219.226 78.419 0.750 re f 349.326 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 354.576 209.371 Td /F1 9.8 Tf [(226)] TJ ET 0.267 0.267 0.267 rg 426.995 219.226 83.103 0.750 re f 426.995 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 432.245 209.371 Td /F1 9.8 Tf [(825)] TJ ET 0.267 0.267 0.267 rg 509.348 219.226 71.527 0.750 re f 509.348 188.083 0.750 31.894 re f 580.125 188.083 0.750 31.894 re f 0.271 0.267 0.267 rg BT 514.598 209.371 Td /F1 9.8 Tf [(77.6)] TJ ET 0.267 0.267 0.267 rg 26.625 188.083 68.209 0.750 re f 26.625 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 178.228 Td /F5 9.8 Tf [(tbr1b)] TJ ET BT 54.095 178.228 Td /F1 9.8 Tf [( \(=)] TJ ET BT 65.746 178.228 Td /F5 9.8 Tf [(tbr1)] TJ ET BT 82.546 178.228 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg 94.084 188.083 173.199 0.750 re f 94.084 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 178.228 Td /F1 9.8 Tf [(T-box, brain, 1b)] TJ ET 0.267 0.267 0.267 rg 266.533 188.083 83.543 0.750 re f 266.533 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 178.228 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 188.083 78.419 0.750 re f 349.326 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 178.228 Td /F1 9.8 Tf [(601)] TJ ET 0.267 0.267 0.267 rg 426.995 188.083 83.103 0.750 re f 426.995 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 178.228 Td /F1 9.8 Tf [(831)] TJ ET 0.267 0.267 0.267 rg 509.348 188.083 71.527 0.750 re f 509.348 172.201 0.750 16.631 re f 580.125 172.201 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 178.228 Td /F1 9.8 Tf [(86.4)] TJ ET 0.267 0.267 0.267 rg 26.625 172.201 68.209 0.750 re f 26.625 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 31.875 162.346 Td /F5 9.8 Tf [(vcpip*)] TJ ET 0.267 0.267 0.267 rg 94.084 172.201 173.199 0.750 re f 94.084 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 99.334 162.346 Td /F1 9.8 Tf [(Valosin-containing protein p97/p47 )] TJ ET BT 99.334 154.715 Td /F1 9.8 Tf [(complete interacting protein 1)] TJ ET 0.267 0.267 0.267 rg 266.533 172.201 83.543 0.750 re f 266.533 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 271.783 162.346 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 172.201 78.419 0.750 re f 349.326 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 354.576 162.346 Td /F1 9.8 Tf [(236)] TJ ET 0.267 0.267 0.267 rg 426.995 172.201 83.103 0.750 re f 426.995 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 432.245 162.346 Td /F1 9.8 Tf [(765)] TJ ET 0.267 0.267 0.267 rg 509.348 172.201 71.527 0.750 re f 509.348 148.689 0.750 24.263 re f 580.125 148.689 0.750 24.263 re f 0.271 0.267 0.267 rg BT 514.598 162.346 Td /F1 9.8 Tf [(87.5)] TJ ET 0.267 0.267 0.267 rg 26.625 148.689 68.209 0.750 re f 26.625 132.808 68.209 0.750 re f 26.625 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 31.875 138.834 Td /F5 9.8 Tf [(zic1)] TJ ET 0.267 0.267 0.267 rg 94.084 148.689 173.199 0.750 re f 94.084 132.808 173.199 0.750 re f 94.084 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 99.334 138.834 Td /F1 9.8 Tf [(Zic family member 1)] TJ ET 0.267 0.267 0.267 rg 266.533 148.689 83.543 0.750 re f 266.533 132.808 83.543 0.750 re f 266.533 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 271.783 138.834 Td /F1 9.8 Tf [(Nuclear exon)] TJ ET 0.267 0.267 0.267 rg 349.326 148.689 78.419 0.750 re f 349.326 132.808 78.419 0.750 re f 349.326 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 354.576 138.834 Td /F1 9.8 Tf [(983)] TJ ET 0.267 0.267 0.267 rg 426.995 148.689 83.103 0.750 re f 426.995 132.808 83.103 0.750 re f 426.995 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 432.245 138.834 Td /F1 9.8 Tf [(984)] TJ ET 0.267 0.267 0.267 rg 509.348 148.689 71.527 0.750 re f 509.348 132.808 71.527 0.750 re f 509.348 132.808 0.750 16.631 re f 580.125 132.808 0.750 16.631 re f 0.271 0.267 0.267 rg BT 514.598 138.834 Td /F1 9.8 Tf [(89.9)] TJ ET 0.965 0.965 0.965 rg 26.250 -380.567 555.000 468.000 re f 0.267 0.267 0.267 rg 26.250 87.433 m 581.250 87.433 l 581.250 86.683 l 26.250 86.683 l f q 357.750 0 0 452.250 35.250 -374.567 cm /I4 Do Q q 35.250 -380.567 537.000 0.000 re W n Q Q q 357.750 0 0 452.250 35.250 -374.567 cm /I4 Do Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(6)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 1004 0 obj << /Type /Annot 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JcnZ0( (vӒOo0'LͶFA=_O=6;eg [6#E nIsPXEhm7WKoob7rc1=\[־P}ɗ陈]Cr0nj'׿x__:Wg&ɦ FȰ_*`n dqLZ?o[[Nz,?[g:P}r6N\@*f2I&Caǟ[/I#!X2@:ٲ۵v0˶Iq( /& 4:;[X?E $2I4[Ehk_k|Cu/m`ay%`mk@8,?_51|-<_vĺa&M3 [SPm;^c@l-{{W𶖚v lIeX $#ǯ~8Ehc!Qk/c߿n#o8Ͻ v n⇋_i} zT߽+kQ_:[ڧ7y"ǰ\r,r"ߴ.X.~ax_Yx(x/C+ܩsȝF2N5:||}3.Lzg[(_-[p'   +Cxj{m7#A=`ۦWV@~6: 0( +C\]gk=d3(x8 kk<@VdEw+>5zW ࢿ7|?h7y-.:=y:uܰ2 ~Rw#`ᆷq|FTc^6h3)۬`aG+O_~<_+4b'n,>د# +ChSXCx$Ԯc71D0|I +CjZ\Cy/)y~b~9^9ڋُ? u~.*xHc {$;N,pA{ |!VJGmQ6${_?f^{+xVFAIc)4+{KQ6vosnoQ~(xYV8Y͑@QrI7Ꮇoh<_pxXI#7Buޘv÷oW5ZwΗ7c6E"V  3ԓF"q'ʘ,% yW#2x[gƇ<O#' ngë(x9|9:A d"f2I䞵SOUԩ];ꇇ?01l$_⇋N >Be! -ࢿ5kPCt{G Ƹ0``' ws WY +=3p{=E +>5zW ᆷyGCh. =3bnc5#6? tGEho hV l-C`Abǖ=M ? u[//ld7!41ݣ I~8|0<e$<_vZ ysǦm{E$0QFA +CE)U;).?,>hQvsg 5( {?ul6 `'6:` X.~§׿_\߂o⇋x_CI]^KD,yX?$ߴ.Eho XIg|C{[i.o?3O33e'Glt ,?_/{3.Lzg]X nӸNT`O u?~,O/DbmL%l} ࢿ4"_mk-W,2> endobj 1010 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/04/Fig_S1_Complete_tree_classification3.pdf) >> endobj 1011 0 obj << /Type /Annot /Subtype /Link /A 1012 0 R /Border [0 0 0] /H /I /Rect [ 35.2500 -374.5674 393.0000 77.6826 ] >> endobj 1012 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/04/Fig2_Sensitivity.jpg) >> endobj 1013 0 obj << /Type /Annot /Subtype /Link /A 1014 0 R /Border [0 0 0] /H /I /Rect [ 307.2945 692.2594 338.1825 702.1800 ] >> endobj 1014 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/04/Fig_S1_Complete_tree_classification3.pdf) >> endobj 1015 0 obj << /Type /Annot /Subtype /Link /A 1016 0 R /Border [0 0 0] /H /I /Rect [ 35.2500 -374.5674 393.0000 77.6826 ] >> endobj 1016 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/04/Fig2_Sensitivity.jpg) >> endobj 1017 0 obj << /Type /Page /Parent 3 0 R /Annots [ 1019 0 R 1021 0 R 1023 0 R 1025 0 R 1027 0 R 1029 0 R 1031 0 R 1033 0 R 1035 0 R 1037 0 R 1039 0 R 1041 0 R 1043 0 R 1045 0 R 1047 0 R 1049 0 R 1051 0 R 1053 0 R 1055 0 R 1057 0 R 1059 0 R 1061 0 R 1063 0 R 1065 0 R 1067 0 R 1069 0 R 1071 0 R 1073 0 R 1075 0 R 1077 0 R 1079 0 R 1081 0 R 1083 0 R 1085 0 R 1087 0 R 1089 0 R 1091 0 R 1093 0 R 1095 0 R 1097 0 R 1099 0 R 1101 0 R 1103 0 R 1105 0 R 1107 0 R 1109 0 R 1111 0 R 1113 0 R 1115 0 R 1117 0 R 1119 0 R 1121 0 R 1123 0 R 1125 0 R 1127 0 R 1129 0 R 1131 0 R 1133 0 R 1135 0 R 1137 0 R 1139 0 R 1141 0 R 1143 0 R 1145 0 R 1147 0 R 1149 0 R 1151 0 R 1153 0 R 1155 0 R 1157 0 R 1159 0 R 1161 0 R 1163 0 R 1165 0 R 1167 0 R 1169 0 R 1171 0 R 1173 0 R 1175 0 R 1177 0 R 1179 0 R 1181 0 R 1183 0 R 1185 0 R 1187 0 R 1189 0 R 1191 0 R 1193 0 R 1195 0 R 1197 0 R 1199 0 R 1201 0 R 1203 0 R 1205 0 R 1207 0 R 1209 0 R 1211 0 R 1213 0 R 1215 0 R 1217 0 R 1219 0 R 1221 0 R 1223 0 R 1225 0 R 1227 0 R 1229 0 R 1231 0 R 1233 0 R 1235 0 R 1237 0 R 1239 0 R 1241 0 R 1243 0 R 1245 0 R 1247 0 R 1249 0 R 1251 0 R 1253 0 R 1255 0 R 1257 0 R 1259 0 R 1261 0 R 1263 0 R 1265 0 R 1267 0 R 1269 0 R 1271 0 R 1273 0 R 1275 0 R 1277 0 R 1279 0 R 1281 0 R 1283 0 R 1285 0 R 1287 0 R 1289 0 R 1291 0 R 1293 0 R 1295 0 R 1297 0 R 1299 0 R 1301 0 R 1303 0 R 1305 0 R 1307 0 R 1309 0 R 1311 0 R ] /Contents 1018 0 R >> endobj 1018 0 obj << /Length 51193 >> stream q 15.000 27.763 577.500 749.237 re W n 0.965 0.965 0.965 rg 26.250 632.287 555.000 144.713 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 632.287 m 581.250 632.287 l 581.250 633.037 l 26.250 633.037 l f q 35.250 643.537 537.000 133.463 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 2: Sensitivity analyses for selected clades obtained in this study \(shown in Figs. 1, 3-10\) and for selected )] TJ ET BT 35.250 755.571 Td /F4 9.8 Tf [(alternative hypotheses.)] TJ ET BT 35.250 736.201 Td /F1 9.8 Tf [(For each case, we assess support from individual gene trees \(indicating whether the group was obtained\) or from the )] TJ ET BT 35.250 722.465 Td /F1 9.8 Tf [(concatenated data sets \(indicating whether the group was obtained and showing boostrap support\). For some gene trees, )] TJ ET BT 35.250 708.729 Td /F1 9.8 Tf [(monophyletic groups ignore a few rogue taxa falling outside. N/A: insufficient taxonomic sampling to test hypothesis. )] TJ ET BT 538.145 714.449 Td /F1 8.7 Tf [(1)] TJ ET BT 35.250 694.993 Td /F1 9.8 Tf [(Excluding Gymnotiformes \(e.g., Saitoh et al.)] TJ ET 0.267 0.267 0.267 rg BT 225.453 697.965 Td /F4 8.7 Tf [(77)] TJ ET 0.271 0.267 0.267 rg BT 235.090 694.993 Td /F1 9.8 Tf [(\); )] TJ ET BT 243.758 700.712 Td /F1 8.7 Tf [(2)] TJ ET BT 248.577 694.993 Td /F1 9.8 Tf [(Stomiatii; )] TJ ET BT 291.379 700.712 Td /F1 8.7 Tf [(3)] TJ ET BT 296.198 694.993 Td /F1 9.8 Tf [(Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 382.359 697.965 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 391.996 694.993 Td /F1 9.8 Tf [(; )] TJ ET BT 397.417 700.712 Td /F1 8.7 Tf [(4)] TJ ET BT 402.236 694.993 Td /F1 9.8 Tf [(Nelson)] TJ ET 0.267 0.267 0.267 rg BT 432.578 697.965 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 437.396 694.993 Td /F1 9.8 Tf [( and Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 541.448 697.965 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 546.267 694.993 Td /F1 9.8 Tf [(; )] TJ ET BT 551.688 700.712 Td /F1 8.7 Tf [(5)] TJ ET BT 35.250 681.256 Td /F1 9.8 Tf [(Shan and Gras)] TJ ET 0.267 0.267 0.267 rg BT 100.829 684.229 Td /F4 8.7 Tf [(47)] TJ ET 0.271 0.267 0.267 rg BT 110.466 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 115.887 686.976 Td /F1 8.7 Tf [(6)] TJ ET BT 120.706 681.256 Td /F1 9.8 Tf [(Patterson and Rosen)] TJ ET 0.267 0.267 0.267 rg BT 212.297 684.229 Td /F4 8.7 Tf [(78)] TJ ET 0.271 0.267 0.267 rg BT 221.934 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 227.355 686.976 Td /F1 8.7 Tf [(7)] TJ ET BT 232.174 681.256 Td /F1 9.8 Tf [(Arratia)] TJ ET 0.267 0.267 0.267 rg BT 260.888 684.229 Td /F4 8.7 Tf [(79)] TJ ET 0.271 0.267 0.267 rg BT 270.525 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 275.946 686.976 Td /F1 8.7 Tf [(8)] TJ ET BT 280.765 681.256 Td /F1 9.8 Tf [(Fink and Fink)] TJ ET 0.267 0.267 0.267 rg BT 339.284 684.229 Td /F4 8.7 Tf [(80)] TJ ET 0.271 0.267 0.267 rg BT 348.922 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 354.343 686.976 Td /F1 8.7 Tf [(9)] TJ ET BT 359.161 681.256 Td /F1 9.8 Tf [(Nelson)] TJ ET 0.267 0.267 0.267 rg BT 389.503 684.229 Td /F4 8.7 Tf [(81)] TJ ET 0.271 0.267 0.267 rg BT 399.141 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 404.562 686.976 Td /F1 8.7 Tf [(10)] TJ ET BT 414.199 681.256 Td /F1 9.8 Tf [(Olney et al.)] TJ ET 0.267 0.267 0.267 rg BT 463.514 684.229 Td /F4 8.7 Tf [(82)] TJ ET 0.271 0.267 0.267 rg BT 473.152 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 478.573 686.976 Td /F1 8.7 Tf [(11)] TJ ET BT 488.210 681.256 Td /F1 9.8 Tf [(Johnson and )] TJ ET BT 35.250 667.520 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 76.980 670.493 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 81.799 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 87.220 673.240 Td /F1 8.7 Tf [(12)] TJ ET BT 96.857 667.520 Td /F1 9.8 Tf [(Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 141.288 670.493 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 146.106 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 151.527 673.240 Td /F1 8.7 Tf [(13)] TJ ET BT 161.165 667.520 Td /F1 9.8 Tf [(Johnson)] TJ ET 0.267 0.267 0.267 rg BT 198.020 670.493 Td /F4 8.7 Tf [(83)] TJ ET 0.271 0.267 0.267 rg BT 207.657 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 213.078 673.240 Td /F1 8.7 Tf [(14)] TJ ET BT 222.715 667.520 Td /F1 9.8 Tf [(Kaufman and Liem)] TJ ET 0.267 0.267 0.267 rg BT 304.547 670.493 Td /F4 8.7 Tf [(84)] TJ ET 0.271 0.267 0.267 rg BT 314.185 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 319.606 673.240 Td /F1 8.7 Tf [(15)] TJ ET BT 329.243 667.520 Td /F1 9.8 Tf [(Gill)] TJ ET 0.267 0.267 0.267 rg BT 343.322 670.493 Td /F4 8.7 Tf [(85)] TJ ET 0.271 0.267 0.267 rg BT 352.959 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 358.380 673.240 Td /F1 8.7 Tf [(16)] TJ ET BT 368.018 667.520 Td /F1 9.8 Tf [(Acanthuriformes sensu Tyler et al.)] TJ ET 0.267 0.267 0.267 rg BT 515.945 670.493 Td /F4 8.7 Tf [(86)] TJ ET 0.271 0.267 0.267 rg BT 525.582 667.520 Td /F1 9.8 Tf [( \(i.e., )] TJ ET BT 35.250 653.784 Td /F1 9.8 Tf [(Acanthuriformes sensu stricto)] TJ ET 0.267 0.267 0.267 rg BT 163.667 656.756 Td /F4 8.7 Tf [(87)] TJ ET 0.271 0.267 0.267 rg BT 173.305 653.784 Td /F1 9.8 Tf [( plus Scatophagidae and Siganidae\); )] TJ ET BT 335.359 659.504 Td /F1 8.7 Tf [(17)] TJ ET BT 344.997 653.784 Td /F1 9.8 Tf [(Jordan)] TJ ET 0.267 0.267 0.267 rg BT 374.802 656.756 Td /F4 8.7 Tf [(88)] TJ ET Q 0.271 0.267 0.267 rg BT 26.250 615.263 Td /F4 9.8 Tf [(Revised Classification for Bony Fishes)] TJ ET BT 26.250 595.858 Td /F1 9.8 Tf [(The nomenclatural arrangement presented in )] TJ ET 0.267 0.267 0.267 rg BT 224.048 595.858 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 272.827 595.858 Td /F1 9.8 Tf [( builds on the existing classification by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 522.642 597.365 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 527.461 595.858 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 583.953 Td /F1 9.8 Tf [(intends to preserve names and taxonomic composition of groups whenever possible. However, adjustments are made to )] TJ ET BT 26.250 572.049 Td /F1 9.8 Tf [(recognize new well-supported molecular clades, many of which also have been obtained by previous molecular studies \(several )] TJ ET BT 26.250 560.144 Td /F1 9.8 Tf [(examples discussed below\). Order-level or supraordinal taxa are erected \(new\) or resurrected on the basis of well-supported )] TJ ET BT 26.250 548.239 Td /F1 9.8 Tf [(clades only \(>90% bootstrap values\). Current taxon names supported by previous molecular or morphological studies are )] TJ ET BT 26.250 536.334 Td /F1 9.8 Tf [(retained if congruent with our results, even if bootstrap support is low \(e.g., Osteoglossocephalai )] TJ ET BT 444.067 536.334 Td /F5 9.8 Tf [(sensu )] TJ ET BT 472.790 536.334 Td /F1 9.8 Tf [(Arratia)] TJ ET 0.267 0.267 0.267 rg BT 501.504 537.842 Td /F4 8.7 Tf [(79)] TJ ET 0.271 0.267 0.267 rg BT 511.141 536.334 Td /F1 9.8 Tf [( with only 38% )] TJ ET BT 26.250 524.430 Td /F1 9.8 Tf [(bootstrap\). In some cases, ordinal or subordinal taxa that were not monophyletic in our analysis are also validated, as long as )] TJ ET BT 26.250 512.525 Td /F1 9.8 Tf [(the incongruence is not supported by strong bootstrap values. Examples include the suborder Blennioidei \(not monophyletic )] TJ ET BT 26.250 500.620 Td /F1 9.8 Tf [(here but monophyletic in Wainwright et al.)] TJ ET 0.267 0.267 0.267 rg BT 207.239 502.127 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 216.877 500.620 Td /F1 9.8 Tf [(\) and the order Pleuronectiformes \(not monophyletic here but monophyletic in )] TJ ET BT 26.250 488.715 Td /F1 9.8 Tf [(Betancur-R. et al.)] TJ ET 0.267 0.267 0.267 rg BT 102.115 490.223 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 111.752 488.715 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 469.311 Td /F1 9.8 Tf [(Family names for bony fishes are based on Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 308.035 470.818 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 317.672 469.311 Td /F1 9.8 Tf [( and van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 420.115 470.818 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 429.753 469.311 Td /F1 9.8 Tf [(, with minor modifications. Consult )] TJ ET BT 26.250 457.406 Td /F1 9.8 Tf [(van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 107.009 458.913 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 116.647 457.406 Td /F1 9.8 Tf [( for authorship of family names and Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 354.001 458.913 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 358.819 457.406 Td /F1 9.8 Tf [( for authorship of ordinal and subordinal names. )] TJ ET BT 26.250 445.501 Td /F1 9.8 Tf [(Our list is not intended as a comprehensive revision of valid family names; instead, it is simply an adaptation of their list based )] TJ ET BT 26.250 433.596 Td /F1 9.8 Tf [(on published studies that we know validate or synonymize family groups using explicit phylogenetic evidence. Unlike )] TJ ET BT 26.250 421.692 Td /F1 9.8 Tf [(Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 118.914 423.199 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 128.551 421.692 Td /F1 9.8 Tf [( and van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 230.995 423.199 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 240.632 421.692 Td /F1 9.8 Tf [(, we do not recognize the family status of Anotopteridae, Omosudidae )] TJ ET BT 26.250 409.787 Td /F1 9.8 Tf [(\(synonyms of Alepisauridae)] TJ ET 0.267 0.267 0.267 rg BT 146.000 411.294 Td /F4 8.7 Tf [(91)] TJ ET 0.271 0.267 0.267 rg BT 155.637 409.787 Td /F1 9.8 Tf [(\) or Latidae \(synonym of Centropomidae)] TJ ET 0.267 0.267 0.267 rg BT 330.123 411.294 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 339.760 413.675 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 342.170 411.294 Td /F4 8.7 Tf [(92)] TJ ET 0.271 0.267 0.267 rg BT 351.807 409.787 Td /F1 9.8 Tf [(\). Also, we recognize the following families, listed in )] TJ ET BT 26.250 397.882 Td /F1 9.8 Tf [(Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 118.914 399.389 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 128.551 397.882 Td /F1 9.8 Tf [( and van der Laan et al. )] TJ ET 0.267 0.267 0.267 rg BT 233.705 399.389 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 243.342 397.882 Td /F1 9.8 Tf [( as synonyms or subfamilies of other families: Botiidae \(following Chen et al.)] TJ ET 0.267 0.267 0.267 rg BT 26.250 387.485 Td /F4 8.7 Tf [(93)] TJ ET 0.271 0.267 0.267 rg BT 35.887 385.977 Td /F1 9.8 Tf [(\), Diplophidae \(following Nelson)] TJ ET 0.267 0.267 0.267 rg BT 172.972 387.485 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 177.791 385.977 Td /F1 9.8 Tf [(; apparently omitted by Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 371.797 387.485 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 381.434 385.977 Td /F1 9.8 Tf [(\), Horabagridae \(following Sullivan et al.)] TJ ET 0.267 0.267 0.267 rg BT 553.746 387.485 Td /F4 8.7 Tf [(94)] TJ ET 0.271 0.267 0.267 rg BT 563.383 385.977 Td /F1 9.8 Tf [(\), )] TJ ET BT 26.250 374.073 Td /F1 9.8 Tf [(Sinipercidae \(following Li et al.)] TJ ET 0.267 0.267 0.267 rg BT 157.924 375.580 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 167.561 374.073 Td /F1 9.8 Tf [(\), Steindachneriidae \(following Roa-Varon and Ort)] TJ ET 0.267 0.267 0.267 rg BT 385.942 375.580 Td /F4 8.7 Tf [(98)] TJ ET 0.271 0.267 0.267 rg BT 395.579 374.073 Td /F1 9.8 Tf [(\), Zanclorhynchidae, the aulopiform )] TJ ET BT 26.250 362.168 Td /F1 9.8 Tf [(Bathysauropsidae and Sudidae \(following Davis)] TJ ET 0.267 0.267 0.267 rg BT 232.716 363.675 Td /F4 8.7 Tf [(91)] TJ ET 0.271 0.267 0.267 rg BT 242.353 362.168 Td /F1 9.8 Tf [(\), and the pleuronectiform Paralichthodidae, Poecilopsettidae, and )] TJ ET BT 26.250 350.263 Td /F1 9.8 Tf [(Rhombosoleidae \(following Chapleau)] TJ ET 0.267 0.267 0.267 rg BT 187.730 351.770 Td /F4 8.7 Tf [(97)] TJ ET 0.271 0.267 0.267 rg BT 197.367 350.263 Td /F1 9.8 Tf [(, Munroe)] TJ ET 0.267 0.267 0.267 rg BT 235.840 351.770 Td /F4 8.7 Tf [(99)] TJ ET 0.271 0.267 0.267 rg BT 245.478 350.263 Td /F1 9.8 Tf [(, Betancur-R. et al.)] TJ ET 0.267 0.267 0.267 rg BT 326.763 351.770 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 336.401 350.263 Td /F1 9.8 Tf [(\). A total of 502 families are recognized here, of which )] TJ ET BT 26.250 338.358 Td /F1 9.8 Tf [(369 \(73.5%\) were examined. Of these, 146 families included only one representative \(39.6%\) and 40 \(17.9%\) of the remaining )] TJ ET BT 26.250 326.454 Td /F1 9.8 Tf [(223 were rendered non-monophyletic in our analysis \(non-monophyletic families are indicated below\). For each order/suborder )] TJ ET BT 26.250 314.549 Td /F1 9.8 Tf [(we list all families examined as well as the unexamined families whose taxonomic affinity is expected on the basis of traditional )] TJ ET BT 26.250 302.644 Td /F1 9.8 Tf [(taxonomy or phylogenetic evidence. The list of unexamined families is also intended as a resource that may help fish )] TJ ET BT 26.250 290.739 Td /F1 9.8 Tf [(systematists to direct future sequencing efforts.)] TJ ET BT 26.250 271.335 Td /F1 9.8 Tf [(A total of 66 orders are classified, three of which are new \(Holocentriformes, Istiophoriformes, and Pempheriformes\), and 15 are )] TJ ET BT 26.250 259.430 Td /F1 9.8 Tf [(resurrected or validated under a new circumscription. Some ordinal or subordinal names may appear to be new, but most can )] TJ ET BT 26.250 247.525 Td /F1 9.8 Tf [(be found in the literature at various hierarchical levels. As examples, Spariformes is a Bleeker name and Centrarchiformes is a )] TJ ET BT 26.250 235.620 Td /F1 9.8 Tf [(Webber and de Beaufort name. Because priority is not applied to names above the family level, we have not made a thorough )] TJ ET BT 26.250 223.716 Td /F1 9.8 Tf [(attempt to establish first use. Only those three for which no reference could be found are listed as new. New infraorders are )] TJ ET BT 26.250 211.811 Td /F1 9.8 Tf [(named in Suborder Cottioidei to circumscribe well-corroborated clades and may conserve the rank of superfamily in subsequent )] TJ ET BT 26.250 199.906 Td /F1 9.8 Tf [(revisions. The ordinal status of 50 percomorph families examined \(as well as many others unexamined\) belonging to )] TJ ET BT 26.250 188.001 Td /F1 9.8 Tf [(Carangimorphariae, Ovalentariae, and Percomorpharia remains uncertain \(i.e.,)] TJ ET BT 365.998 188.001 Td /F5 9.8 Tf [(incertae sedis)] TJ ET BT 426.146 188.001 Td /F1 9.8 Tf [(\) due to poor phylogenetic )] TJ ET BT 26.250 176.097 Td /F1 9.8 Tf [(resolution. Percentages in parentheses following names indicate bootstrap support \(no bootstrap values shown for redundant )] TJ ET BT 26.250 164.192 Td /F1 9.8 Tf [(groups or monotypic taxa\). The complete phylogenetic tree with annotated classification is illustrated in )] TJ ET 0.267 0.267 0.267 rg BT 471.688 164.192 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 502.576 164.192 Td /F1 9.8 Tf [(. The new )] TJ ET BT 26.250 152.287 Td /F1 9.8 Tf [(classification scheme presented here should be considered a work in progress \(version 1; )] TJ ET 0.267 0.267 0.267 rg BT 415.324 152.287 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 464.103 152.287 Td /F1 9.8 Tf [(\), as any other hypothesis. )] TJ ET BT 26.250 140.382 Td /F1 9.8 Tf [(It is likely to include involuntary errors and omissions in addition to the many unexamined, )] TJ ET BT 415.324 140.382 Td /F5 9.8 Tf [(sedis mutabilis,)] TJ ET BT 481.965 140.382 Td /F1 9.8 Tf [( and )] TJ ET BT 503.649 140.382 Td /F5 9.8 Tf [(incertae sedis)] TJ ET BT 26.250 128.478 Td /F1 9.8 Tf [(taxa. Updates should be forthcoming as new evidence become available and feedback from experts help refine it. For the most )] TJ ET BT 26.250 116.573 Td /F1 9.8 Tf [(updated version visit )] TJ ET 0.267 0.267 0.267 rg BT 117.832 116.573 Td /F1 9.8 Tf [(DeepFin)] TJ ET 0.271 0.267 0.267 rg BT 154.677 116.573 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 97.168 Td /F4 9.8 Tf [(Comparison of classifications)] TJ ET BT 26.250 77.763 Td /F1 9.8 Tf [(Our results \()] TJ ET 0.267 0.267 0.267 rg BT 79.885 77.763 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 128.664 77.763 Td /F1 9.8 Tf [(\) invite comparison to the recent classification of Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 421.281 79.271 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 426.100 77.763 Td /F1 9.8 Tf [( based on morphological evidence )] TJ ET BT 26.250 65.859 Td /F1 9.8 Tf [(gleamed from many investigators. Of 123 clades recognized by them, 70 \(56.9%\) are congruent with bootstrap values >95% )] TJ ET BT 26.250 53.954 Td /F1 9.8 Tf [(obtained in this study. Five of these 70 clades are included in our sample by only one family and thus their monophyly is not )] TJ ET BT 26.250 42.049 Td /F1 9.8 Tf [(critically tested. Another six clades \(4.9%\) are congruent but are supported by lower bootstrap values; seven additional clades )] TJ ET Q q 15.000 27.763 577.500 749.237 re W n 0.965 0.965 0.965 rg 26.250 632.287 555.000 144.713 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 632.287 m 581.250 632.287 l 581.250 633.037 l 26.250 633.037 l f q 35.250 643.537 537.000 133.463 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 2: Sensitivity analyses for selected clades obtained in this study \(shown in Figs. 1, 3-10\) and for selected )] TJ ET BT 35.250 755.571 Td /F4 9.8 Tf [(alternative hypotheses.)] TJ ET BT 35.250 736.201 Td /F1 9.8 Tf [(For each case, we assess support from individual gene trees \(indicating whether the group was obtained\) or from the )] TJ ET BT 35.250 722.465 Td /F1 9.8 Tf [(concatenated data sets \(indicating whether the group was obtained and showing boostrap support\). For some gene trees, )] TJ ET BT 35.250 708.729 Td /F1 9.8 Tf [(monophyletic groups ignore a few rogue taxa falling outside. N/A: insufficient taxonomic sampling to test hypothesis. )] TJ ET BT 538.145 714.449 Td /F1 8.7 Tf [(1)] TJ ET BT 35.250 694.993 Td /F1 9.8 Tf [(Excluding Gymnotiformes \(e.g., Saitoh et al.)] TJ ET 0.267 0.267 0.267 rg BT 225.453 697.965 Td /F4 8.7 Tf [(77)] TJ ET 0.271 0.267 0.267 rg BT 235.090 694.993 Td /F1 9.8 Tf [(\); )] TJ ET BT 243.758 700.712 Td /F1 8.7 Tf [(2)] TJ ET BT 248.577 694.993 Td /F1 9.8 Tf [(Stomiatii; )] TJ ET BT 291.379 700.712 Td /F1 8.7 Tf [(3)] TJ ET BT 296.198 694.993 Td /F1 9.8 Tf [(Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 382.359 697.965 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 391.996 694.993 Td /F1 9.8 Tf [(; )] TJ ET BT 397.417 700.712 Td /F1 8.7 Tf [(4)] TJ ET BT 402.236 694.993 Td /F1 9.8 Tf [(Nelson)] TJ ET 0.267 0.267 0.267 rg BT 432.578 697.965 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 437.396 694.993 Td /F1 9.8 Tf [( and Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 541.448 697.965 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 546.267 694.993 Td /F1 9.8 Tf [(; )] TJ ET BT 551.688 700.712 Td /F1 8.7 Tf [(5)] TJ ET BT 35.250 681.256 Td /F1 9.8 Tf [(Shan and Gras)] TJ ET 0.267 0.267 0.267 rg BT 100.829 684.229 Td /F4 8.7 Tf [(47)] TJ ET 0.271 0.267 0.267 rg BT 110.466 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 115.887 686.976 Td /F1 8.7 Tf [(6)] TJ ET BT 120.706 681.256 Td /F1 9.8 Tf [(Patterson and Rosen)] TJ ET 0.267 0.267 0.267 rg BT 212.297 684.229 Td /F4 8.7 Tf [(78)] TJ ET 0.271 0.267 0.267 rg BT 221.934 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 227.355 686.976 Td /F1 8.7 Tf [(7)] TJ ET BT 232.174 681.256 Td /F1 9.8 Tf [(Arratia)] TJ ET 0.267 0.267 0.267 rg BT 260.888 684.229 Td /F4 8.7 Tf [(79)] TJ ET 0.271 0.267 0.267 rg BT 270.525 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 275.946 686.976 Td /F1 8.7 Tf [(8)] TJ ET BT 280.765 681.256 Td /F1 9.8 Tf [(Fink and Fink)] TJ ET 0.267 0.267 0.267 rg BT 339.284 684.229 Td /F4 8.7 Tf [(80)] TJ ET 0.271 0.267 0.267 rg BT 348.922 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 354.343 686.976 Td /F1 8.7 Tf [(9)] TJ ET BT 359.161 681.256 Td /F1 9.8 Tf [(Nelson)] TJ ET 0.267 0.267 0.267 rg BT 389.503 684.229 Td /F4 8.7 Tf [(81)] TJ ET 0.271 0.267 0.267 rg BT 399.141 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 404.562 686.976 Td /F1 8.7 Tf [(10)] TJ ET BT 414.199 681.256 Td /F1 9.8 Tf [(Olney et al.)] TJ ET 0.267 0.267 0.267 rg BT 463.514 684.229 Td /F4 8.7 Tf [(82)] TJ ET 0.271 0.267 0.267 rg BT 473.152 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 478.573 686.976 Td /F1 8.7 Tf [(11)] TJ ET BT 488.210 681.256 Td /F1 9.8 Tf [(Johnson and )] TJ ET BT 35.250 667.520 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 76.980 670.493 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 81.799 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 87.220 673.240 Td /F1 8.7 Tf [(12)] TJ ET BT 96.857 667.520 Td /F1 9.8 Tf [(Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 141.288 670.493 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 146.106 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 151.527 673.240 Td /F1 8.7 Tf [(13)] TJ ET BT 161.165 667.520 Td /F1 9.8 Tf [(Johnson)] TJ ET 0.267 0.267 0.267 rg BT 198.020 670.493 Td /F4 8.7 Tf [(83)] TJ ET 0.271 0.267 0.267 rg BT 207.657 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 213.078 673.240 Td /F1 8.7 Tf [(14)] TJ ET BT 222.715 667.520 Td /F1 9.8 Tf [(Kaufman and Liem)] TJ ET 0.267 0.267 0.267 rg BT 304.547 670.493 Td /F4 8.7 Tf [(84)] TJ ET 0.271 0.267 0.267 rg BT 314.185 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 319.606 673.240 Td /F1 8.7 Tf [(15)] TJ ET BT 329.243 667.520 Td /F1 9.8 Tf [(Gill)] TJ ET 0.267 0.267 0.267 rg BT 343.322 670.493 Td /F4 8.7 Tf [(85)] TJ ET 0.271 0.267 0.267 rg BT 352.959 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 358.380 673.240 Td /F1 8.7 Tf [(16)] TJ ET BT 368.018 667.520 Td /F1 9.8 Tf [(Acanthuriformes sensu Tyler et al.)] TJ ET 0.267 0.267 0.267 rg BT 515.945 670.493 Td /F4 8.7 Tf [(86)] TJ ET 0.271 0.267 0.267 rg BT 525.582 667.520 Td /F1 9.8 Tf [( \(i.e., )] TJ ET BT 35.250 653.784 Td /F1 9.8 Tf [(Acanthuriformes sensu stricto)] TJ ET 0.267 0.267 0.267 rg BT 163.667 656.756 Td /F4 8.7 Tf [(87)] TJ ET 0.271 0.267 0.267 rg BT 173.305 653.784 Td /F1 9.8 Tf [( plus Scatophagidae and Siganidae\); )] TJ ET BT 335.359 659.504 Td /F1 8.7 Tf [(17)] TJ ET BT 344.997 653.784 Td /F1 9.8 Tf [(Jordan)] TJ ET 0.267 0.267 0.267 rg BT 374.802 656.756 Td /F4 8.7 Tf [(88)] TJ ET Q 0.271 0.267 0.267 rg BT 26.250 615.263 Td /F4 9.8 Tf [(Revised Classification for Bony Fishes)] TJ ET BT 26.250 595.858 Td /F1 9.8 Tf [(The nomenclatural arrangement presented in )] TJ ET 0.267 0.267 0.267 rg BT 224.048 595.858 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 272.827 595.858 Td /F1 9.8 Tf [( builds on the existing classification by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 522.642 597.365 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 527.461 595.858 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 583.953 Td /F1 9.8 Tf [(intends to preserve names and taxonomic composition of groups whenever possible. However, adjustments are made to )] TJ ET BT 26.250 572.049 Td /F1 9.8 Tf [(recognize new well-supported molecular clades, many of which also have been obtained by previous molecular studies \(several )] TJ ET BT 26.250 560.144 Td /F1 9.8 Tf [(examples discussed below\). Order-level or supraordinal taxa are erected \(new\) or resurrected on the basis of well-supported )] TJ ET BT 26.250 548.239 Td /F1 9.8 Tf [(clades only \(>90% bootstrap values\). Current taxon names supported by previous molecular or morphological studies are )] TJ ET BT 26.250 536.334 Td /F1 9.8 Tf [(retained if congruent with our results, even if bootstrap support is low \(e.g., Osteoglossocephalai )] TJ ET BT 444.067 536.334 Td /F5 9.8 Tf [(sensu )] TJ ET BT 472.790 536.334 Td /F1 9.8 Tf [(Arratia)] TJ ET 0.267 0.267 0.267 rg BT 501.504 537.842 Td /F4 8.7 Tf [(79)] TJ ET 0.271 0.267 0.267 rg BT 511.141 536.334 Td /F1 9.8 Tf [( with only 38% )] TJ ET BT 26.250 524.430 Td /F1 9.8 Tf [(bootstrap\). In some cases, ordinal or subordinal taxa that were not monophyletic in our analysis are also validated, as long as )] TJ ET BT 26.250 512.525 Td /F1 9.8 Tf [(the incongruence is not supported by strong bootstrap values. Examples include the suborder Blennioidei \(not monophyletic )] TJ ET BT 26.250 500.620 Td /F1 9.8 Tf [(here but monophyletic in Wainwright et al.)] TJ ET 0.267 0.267 0.267 rg BT 207.239 502.127 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 216.877 500.620 Td /F1 9.8 Tf [(\) and the order Pleuronectiformes \(not monophyletic here but monophyletic in )] TJ ET BT 26.250 488.715 Td /F1 9.8 Tf [(Betancur-R. et al.)] TJ ET 0.267 0.267 0.267 rg BT 102.115 490.223 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 111.752 488.715 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 469.311 Td /F1 9.8 Tf [(Family names for bony fishes are based on Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 308.035 470.818 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 317.672 469.311 Td /F1 9.8 Tf [( and van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 420.115 470.818 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 429.753 469.311 Td /F1 9.8 Tf [(, with minor modifications. Consult )] TJ ET BT 26.250 457.406 Td /F1 9.8 Tf [(van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 107.009 458.913 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 116.647 457.406 Td /F1 9.8 Tf [( for authorship of family names and Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 354.001 458.913 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 358.819 457.406 Td /F1 9.8 Tf [( for authorship of ordinal and subordinal names. )] TJ ET BT 26.250 445.501 Td /F1 9.8 Tf [(Our list is not intended as a comprehensive revision of valid family names; instead, it is simply an adaptation of their list based )] TJ ET BT 26.250 433.596 Td /F1 9.8 Tf [(on published studies that we know validate or synonymize family groups using explicit phylogenetic evidence. Unlike )] TJ ET BT 26.250 421.692 Td /F1 9.8 Tf [(Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 118.914 423.199 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 128.551 421.692 Td /F1 9.8 Tf [( and van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 230.995 423.199 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 240.632 421.692 Td /F1 9.8 Tf [(, we do not recognize the family status of Anotopteridae, Omosudidae )] TJ ET BT 26.250 409.787 Td /F1 9.8 Tf [(\(synonyms of Alepisauridae)] TJ ET 0.267 0.267 0.267 rg BT 146.000 411.294 Td /F4 8.7 Tf [(91)] TJ ET 0.271 0.267 0.267 rg BT 155.637 409.787 Td /F1 9.8 Tf [(\) or Latidae \(synonym of Centropomidae)] TJ ET 0.267 0.267 0.267 rg BT 330.123 411.294 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 339.760 413.675 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 342.170 411.294 Td /F4 8.7 Tf [(92)] TJ ET 0.271 0.267 0.267 rg BT 351.807 409.787 Td /F1 9.8 Tf [(\). Also, we recognize the following families, listed in )] TJ ET BT 26.250 397.882 Td /F1 9.8 Tf [(Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 118.914 399.389 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 128.551 397.882 Td /F1 9.8 Tf [( and van der Laan et al. )] TJ ET 0.267 0.267 0.267 rg BT 233.705 399.389 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 243.342 397.882 Td /F1 9.8 Tf [( as synonyms or subfamilies of other families: Botiidae \(following Chen et al.)] TJ ET 0.267 0.267 0.267 rg BT 26.250 387.485 Td /F4 8.7 Tf [(93)] TJ ET 0.271 0.267 0.267 rg BT 35.887 385.977 Td /F1 9.8 Tf [(\), Diplophidae \(following Nelson)] TJ ET 0.267 0.267 0.267 rg BT 172.972 387.485 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 177.791 385.977 Td /F1 9.8 Tf [(; apparently omitted by Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 371.797 387.485 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 381.434 385.977 Td /F1 9.8 Tf [(\), Horabagridae \(following Sullivan et al.)] TJ ET 0.267 0.267 0.267 rg BT 553.746 387.485 Td /F4 8.7 Tf [(94)] TJ ET 0.271 0.267 0.267 rg BT 563.383 385.977 Td /F1 9.8 Tf [(\), )] TJ ET BT 26.250 374.073 Td /F1 9.8 Tf [(Sinipercidae \(following Li et al.)] TJ ET 0.267 0.267 0.267 rg BT 157.924 375.580 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 167.561 374.073 Td /F1 9.8 Tf [(\), Steindachneriidae \(following Roa-Varon and Ort)] TJ ET 0.267 0.267 0.267 rg BT 385.942 375.580 Td /F4 8.7 Tf [(98)] TJ ET 0.271 0.267 0.267 rg BT 395.579 374.073 Td /F1 9.8 Tf [(\), Zanclorhynchidae, the aulopiform )] TJ ET BT 26.250 362.168 Td /F1 9.8 Tf [(Bathysauropsidae and Sudidae \(following Davis)] TJ ET 0.267 0.267 0.267 rg BT 232.716 363.675 Td /F4 8.7 Tf [(91)] TJ ET 0.271 0.267 0.267 rg BT 242.353 362.168 Td /F1 9.8 Tf [(\), and the pleuronectiform Paralichthodidae, Poecilopsettidae, and )] TJ ET BT 26.250 350.263 Td /F1 9.8 Tf [(Rhombosoleidae \(following Chapleau)] TJ ET 0.267 0.267 0.267 rg BT 187.730 351.770 Td /F4 8.7 Tf [(97)] TJ ET 0.271 0.267 0.267 rg BT 197.367 350.263 Td /F1 9.8 Tf [(, Munroe)] TJ ET 0.267 0.267 0.267 rg BT 235.840 351.770 Td /F4 8.7 Tf [(99)] TJ ET 0.271 0.267 0.267 rg BT 245.478 350.263 Td /F1 9.8 Tf [(, Betancur-R. et al.)] TJ ET 0.267 0.267 0.267 rg BT 326.763 351.770 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 336.401 350.263 Td /F1 9.8 Tf [(\). A total of 502 families are recognized here, of which )] TJ ET BT 26.250 338.358 Td /F1 9.8 Tf [(369 \(73.5%\) were examined. Of these, 146 families included only one representative \(39.6%\) and 40 \(17.9%\) of the remaining )] TJ ET BT 26.250 326.454 Td /F1 9.8 Tf [(223 were rendered non-monophyletic in our analysis \(non-monophyletic families are indicated below\). For each order/suborder )] TJ ET BT 26.250 314.549 Td /F1 9.8 Tf [(we list all families examined as well as the unexamined families whose taxonomic affinity is expected on the basis of traditional )] TJ ET BT 26.250 302.644 Td /F1 9.8 Tf [(taxonomy or phylogenetic evidence. The list of unexamined families is also intended as a resource that may help fish )] TJ ET BT 26.250 290.739 Td /F1 9.8 Tf [(systematists to direct future sequencing efforts.)] TJ ET BT 26.250 271.335 Td /F1 9.8 Tf [(A total of 66 orders are classified, three of which are new \(Holocentriformes, Istiophoriformes, and Pempheriformes\), and 15 are )] TJ ET BT 26.250 259.430 Td /F1 9.8 Tf [(resurrected or validated under a new circumscription. Some ordinal or subordinal names may appear to be new, but most can )] TJ ET BT 26.250 247.525 Td /F1 9.8 Tf [(be found in the literature at various hierarchical levels. As examples, Spariformes is a Bleeker name and Centrarchiformes is a )] TJ ET BT 26.250 235.620 Td /F1 9.8 Tf [(Webber and de Beaufort name. Because priority is not applied to names above the family level, we have not made a thorough )] TJ ET BT 26.250 223.716 Td /F1 9.8 Tf [(attempt to establish first use. Only those three for which no reference could be found are listed as new. New infraorders are )] TJ ET BT 26.250 211.811 Td /F1 9.8 Tf [(named in Suborder Cottioidei to circumscribe well-corroborated clades and may conserve the rank of superfamily in subsequent )] TJ ET BT 26.250 199.906 Td /F1 9.8 Tf [(revisions. The ordinal status of 50 percomorph families examined \(as well as many others unexamined\) belonging to )] TJ ET BT 26.250 188.001 Td /F1 9.8 Tf [(Carangimorphariae, Ovalentariae, and Percomorpharia remains uncertain \(i.e.,)] TJ ET BT 365.998 188.001 Td /F5 9.8 Tf [(incertae sedis)] TJ ET BT 426.146 188.001 Td /F1 9.8 Tf [(\) due to poor phylogenetic )] TJ ET BT 26.250 176.097 Td /F1 9.8 Tf [(resolution. Percentages in parentheses following names indicate bootstrap support \(no bootstrap values shown for redundant )] TJ ET BT 26.250 164.192 Td /F1 9.8 Tf [(groups or monotypic taxa\). The complete phylogenetic tree with annotated classification is illustrated in )] TJ ET 0.267 0.267 0.267 rg BT 471.688 164.192 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 502.576 164.192 Td /F1 9.8 Tf [(. The new )] TJ ET BT 26.250 152.287 Td /F1 9.8 Tf [(classification scheme presented here should be considered a work in progress \(version 1; )] TJ ET 0.267 0.267 0.267 rg BT 415.324 152.287 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 464.103 152.287 Td /F1 9.8 Tf [(\), as any other hypothesis. )] TJ ET BT 26.250 140.382 Td /F1 9.8 Tf [(It is likely to include involuntary errors and omissions in addition to the many unexamined, )] TJ ET BT 415.324 140.382 Td /F5 9.8 Tf [(sedis mutabilis,)] TJ ET BT 481.965 140.382 Td /F1 9.8 Tf [( and )] TJ ET BT 503.649 140.382 Td /F5 9.8 Tf [(incertae sedis)] TJ ET BT 26.250 128.478 Td /F1 9.8 Tf [(taxa. Updates should be forthcoming as new evidence become available and feedback from experts help refine it. For the most )] TJ ET BT 26.250 116.573 Td /F1 9.8 Tf [(updated version visit )] TJ ET 0.267 0.267 0.267 rg BT 117.832 116.573 Td /F1 9.8 Tf [(DeepFin)] TJ ET 0.271 0.267 0.267 rg BT 154.677 116.573 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 97.168 Td /F4 9.8 Tf [(Comparison of classifications)] TJ ET BT 26.250 77.763 Td /F1 9.8 Tf [(Our results \()] TJ ET 0.267 0.267 0.267 rg BT 79.885 77.763 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 128.664 77.763 Td /F1 9.8 Tf [(\) invite comparison to the recent classification of Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 421.281 79.271 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 426.100 77.763 Td /F1 9.8 Tf [( based on morphological evidence )] TJ ET BT 26.250 65.859 Td /F1 9.8 Tf [(gleamed from many investigators. Of 123 clades recognized by them, 70 \(56.9%\) are congruent with bootstrap values >95% )] TJ ET BT 26.250 53.954 Td /F1 9.8 Tf [(obtained in this study. Five of these 70 clades are included in our sample by only one family and thus their monophyly is not )] TJ ET BT 26.250 42.049 Td /F1 9.8 Tf [(critically tested. Another six clades \(4.9%\) are congruent but are supported by lower bootstrap values; seven additional clades )] TJ ET Q q 15.000 27.763 577.500 749.237 re W n 0.965 0.965 0.965 rg 26.250 632.287 555.000 144.713 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 632.287 m 581.250 632.287 l 581.250 633.037 l 26.250 633.037 l f q 35.250 643.537 537.000 133.463 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 2: Sensitivity analyses for selected clades obtained in this study \(shown in Figs. 1, 3-10\) and for selected )] TJ ET BT 35.250 755.571 Td /F4 9.8 Tf [(alternative hypotheses.)] TJ ET BT 35.250 736.201 Td /F1 9.8 Tf [(For each case, we assess support from individual gene trees \(indicating whether the group was obtained\) or from the )] TJ ET BT 35.250 722.465 Td /F1 9.8 Tf [(concatenated data sets \(indicating whether the group was obtained and showing boostrap support\). For some gene trees, )] TJ ET BT 35.250 708.729 Td /F1 9.8 Tf [(monophyletic groups ignore a few rogue taxa falling outside. N/A: insufficient taxonomic sampling to test hypothesis. )] TJ ET BT 538.145 714.449 Td /F1 8.7 Tf [(1)] TJ ET BT 35.250 694.993 Td /F1 9.8 Tf [(Excluding Gymnotiformes \(e.g., Saitoh et al.)] TJ ET 0.267 0.267 0.267 rg BT 225.453 697.965 Td /F4 8.7 Tf [(77)] TJ ET 0.271 0.267 0.267 rg BT 235.090 694.993 Td /F1 9.8 Tf [(\); )] TJ ET BT 243.758 700.712 Td /F1 8.7 Tf [(2)] TJ ET BT 248.577 694.993 Td /F1 9.8 Tf [(Stomiatii; )] TJ ET BT 291.379 700.712 Td /F1 8.7 Tf [(3)] TJ ET BT 296.198 694.993 Td /F1 9.8 Tf [(Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 382.359 697.965 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 391.996 694.993 Td /F1 9.8 Tf [(; )] TJ ET BT 397.417 700.712 Td /F1 8.7 Tf [(4)] TJ ET BT 402.236 694.993 Td /F1 9.8 Tf [(Nelson)] TJ ET 0.267 0.267 0.267 rg BT 432.578 697.965 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 437.396 694.993 Td /F1 9.8 Tf [( and Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 541.448 697.965 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 546.267 694.993 Td /F1 9.8 Tf [(; )] TJ ET BT 551.688 700.712 Td /F1 8.7 Tf [(5)] TJ ET BT 35.250 681.256 Td /F1 9.8 Tf [(Shan and Gras)] TJ ET 0.267 0.267 0.267 rg BT 100.829 684.229 Td /F4 8.7 Tf [(47)] TJ ET 0.271 0.267 0.267 rg BT 110.466 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 115.887 686.976 Td /F1 8.7 Tf [(6)] TJ ET BT 120.706 681.256 Td /F1 9.8 Tf [(Patterson and Rosen)] TJ ET 0.267 0.267 0.267 rg BT 212.297 684.229 Td /F4 8.7 Tf [(78)] TJ ET 0.271 0.267 0.267 rg BT 221.934 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 227.355 686.976 Td /F1 8.7 Tf [(7)] TJ ET BT 232.174 681.256 Td /F1 9.8 Tf [(Arratia)] TJ ET 0.267 0.267 0.267 rg BT 260.888 684.229 Td /F4 8.7 Tf [(79)] TJ ET 0.271 0.267 0.267 rg BT 270.525 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 275.946 686.976 Td /F1 8.7 Tf [(8)] TJ ET BT 280.765 681.256 Td /F1 9.8 Tf [(Fink and Fink)] TJ ET 0.267 0.267 0.267 rg BT 339.284 684.229 Td /F4 8.7 Tf [(80)] TJ ET 0.271 0.267 0.267 rg BT 348.922 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 354.343 686.976 Td /F1 8.7 Tf [(9)] TJ ET BT 359.161 681.256 Td /F1 9.8 Tf [(Nelson)] TJ ET 0.267 0.267 0.267 rg BT 389.503 684.229 Td /F4 8.7 Tf [(81)] TJ ET 0.271 0.267 0.267 rg BT 399.141 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 404.562 686.976 Td /F1 8.7 Tf [(10)] TJ ET BT 414.199 681.256 Td /F1 9.8 Tf [(Olney et al.)] TJ ET 0.267 0.267 0.267 rg BT 463.514 684.229 Td /F4 8.7 Tf [(82)] TJ ET 0.271 0.267 0.267 rg BT 473.152 681.256 Td /F1 9.8 Tf [(; )] TJ ET BT 478.573 686.976 Td /F1 8.7 Tf [(11)] TJ ET BT 488.210 681.256 Td /F1 9.8 Tf [(Johnson and )] TJ ET BT 35.250 667.520 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 76.980 670.493 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 81.799 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 87.220 673.240 Td /F1 8.7 Tf [(12)] TJ ET BT 96.857 667.520 Td /F1 9.8 Tf [(Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 141.288 670.493 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 146.106 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 151.527 673.240 Td /F1 8.7 Tf [(13)] TJ ET BT 161.165 667.520 Td /F1 9.8 Tf [(Johnson)] TJ ET 0.267 0.267 0.267 rg BT 198.020 670.493 Td /F4 8.7 Tf [(83)] TJ ET 0.271 0.267 0.267 rg BT 207.657 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 213.078 673.240 Td /F1 8.7 Tf [(14)] TJ ET BT 222.715 667.520 Td /F1 9.8 Tf [(Kaufman and Liem)] TJ ET 0.267 0.267 0.267 rg BT 304.547 670.493 Td /F4 8.7 Tf [(84)] TJ ET 0.271 0.267 0.267 rg BT 314.185 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 319.606 673.240 Td /F1 8.7 Tf [(15)] TJ ET BT 329.243 667.520 Td /F1 9.8 Tf [(Gill)] TJ ET 0.267 0.267 0.267 rg BT 343.322 670.493 Td /F4 8.7 Tf [(85)] TJ ET 0.271 0.267 0.267 rg BT 352.959 667.520 Td /F1 9.8 Tf [(; )] TJ ET BT 358.380 673.240 Td /F1 8.7 Tf [(16)] TJ ET BT 368.018 667.520 Td /F1 9.8 Tf [(Acanthuriformes sensu Tyler et al.)] TJ ET 0.267 0.267 0.267 rg BT 515.945 670.493 Td /F4 8.7 Tf [(86)] TJ ET 0.271 0.267 0.267 rg BT 525.582 667.520 Td /F1 9.8 Tf [( \(i.e., )] TJ ET BT 35.250 653.784 Td /F1 9.8 Tf [(Acanthuriformes sensu stricto)] TJ ET 0.267 0.267 0.267 rg BT 163.667 656.756 Td /F4 8.7 Tf [(87)] TJ ET 0.271 0.267 0.267 rg BT 173.305 653.784 Td /F1 9.8 Tf [( plus Scatophagidae and Siganidae\); )] TJ ET BT 335.359 659.504 Td /F1 8.7 Tf [(17)] TJ ET BT 344.997 653.784 Td /F1 9.8 Tf [(Jordan)] TJ ET 0.267 0.267 0.267 rg BT 374.802 656.756 Td /F4 8.7 Tf [(88)] TJ ET Q 0.271 0.267 0.267 rg BT 26.250 615.263 Td /F4 9.8 Tf [(Revised Classification for Bony Fishes)] TJ ET BT 26.250 595.858 Td /F1 9.8 Tf [(The nomenclatural arrangement presented in )] TJ ET 0.267 0.267 0.267 rg BT 224.048 595.858 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 272.827 595.858 Td /F1 9.8 Tf [( builds on the existing classification by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 522.642 597.365 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 527.461 595.858 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 583.953 Td /F1 9.8 Tf [(intends to preserve names and taxonomic composition of groups whenever possible. However, adjustments are made to )] TJ ET BT 26.250 572.049 Td /F1 9.8 Tf [(recognize new well-supported molecular clades, many of which also have been obtained by previous molecular studies \(several )] TJ ET BT 26.250 560.144 Td /F1 9.8 Tf [(examples discussed below\). Order-level or supraordinal taxa are erected \(new\) or resurrected on the basis of well-supported )] TJ ET BT 26.250 548.239 Td /F1 9.8 Tf [(clades only \(>90% bootstrap values\). Current taxon names supported by previous molecular or morphological studies are )] TJ ET BT 26.250 536.334 Td /F1 9.8 Tf [(retained if congruent with our results, even if bootstrap support is low \(e.g., Osteoglossocephalai )] TJ ET BT 444.067 536.334 Td /F5 9.8 Tf [(sensu )] TJ ET BT 472.790 536.334 Td /F1 9.8 Tf [(Arratia)] TJ ET 0.267 0.267 0.267 rg BT 501.504 537.842 Td /F4 8.7 Tf [(79)] TJ ET 0.271 0.267 0.267 rg BT 511.141 536.334 Td /F1 9.8 Tf [( with only 38% )] TJ ET BT 26.250 524.430 Td /F1 9.8 Tf [(bootstrap\). In some cases, ordinal or subordinal taxa that were not monophyletic in our analysis are also validated, as long as )] TJ ET BT 26.250 512.525 Td /F1 9.8 Tf [(the incongruence is not supported by strong bootstrap values. Examples include the suborder Blennioidei \(not monophyletic )] TJ ET BT 26.250 500.620 Td /F1 9.8 Tf [(here but monophyletic in Wainwright et al.)] TJ ET 0.267 0.267 0.267 rg BT 207.239 502.127 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 216.877 500.620 Td /F1 9.8 Tf [(\) and the order Pleuronectiformes \(not monophyletic here but monophyletic in )] TJ ET BT 26.250 488.715 Td /F1 9.8 Tf [(Betancur-R. et al.)] TJ ET 0.267 0.267 0.267 rg BT 102.115 490.223 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 111.752 488.715 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 469.311 Td /F1 9.8 Tf [(Family names for bony fishes are based on Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 308.035 470.818 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 317.672 469.311 Td /F1 9.8 Tf [( and van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 420.115 470.818 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 429.753 469.311 Td /F1 9.8 Tf [(, with minor modifications. Consult )] TJ ET BT 26.250 457.406 Td /F1 9.8 Tf [(van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 107.009 458.913 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 116.647 457.406 Td /F1 9.8 Tf [( for authorship of family names and Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 354.001 458.913 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 358.819 457.406 Td /F1 9.8 Tf [( for authorship of ordinal and subordinal names. )] TJ ET BT 26.250 445.501 Td /F1 9.8 Tf [(Our list is not intended as a comprehensive revision of valid family names; instead, it is simply an adaptation of their list based )] TJ ET BT 26.250 433.596 Td /F1 9.8 Tf [(on published studies that we know validate or synonymize family groups using explicit phylogenetic evidence. Unlike )] TJ ET BT 26.250 421.692 Td /F1 9.8 Tf [(Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 118.914 423.199 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 128.551 421.692 Td /F1 9.8 Tf [( and van der Laan et al.)] TJ ET 0.267 0.267 0.267 rg BT 230.995 423.199 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 240.632 421.692 Td /F1 9.8 Tf [(, we do not recognize the family status of Anotopteridae, Omosudidae )] TJ ET BT 26.250 409.787 Td /F1 9.8 Tf [(\(synonyms of Alepisauridae)] TJ ET 0.267 0.267 0.267 rg BT 146.000 411.294 Td /F4 8.7 Tf [(91)] TJ ET 0.271 0.267 0.267 rg BT 155.637 409.787 Td /F1 9.8 Tf [(\) or Latidae \(synonym of Centropomidae)] TJ ET 0.267 0.267 0.267 rg BT 330.123 411.294 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 339.760 413.675 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 342.170 411.294 Td /F4 8.7 Tf [(92)] TJ ET 0.271 0.267 0.267 rg BT 351.807 409.787 Td /F1 9.8 Tf [(\). Also, we recognize the following families, listed in )] TJ ET BT 26.250 397.882 Td /F1 9.8 Tf [(Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 118.914 399.389 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 128.551 397.882 Td /F1 9.8 Tf [( and van der Laan et al. )] TJ ET 0.267 0.267 0.267 rg BT 233.705 399.389 Td /F4 8.7 Tf [(90)] TJ ET 0.271 0.267 0.267 rg BT 243.342 397.882 Td /F1 9.8 Tf [( as synonyms or subfamilies of other families: Botiidae \(following Chen et al.)] TJ ET 0.267 0.267 0.267 rg BT 26.250 387.485 Td /F4 8.7 Tf [(93)] TJ ET 0.271 0.267 0.267 rg BT 35.887 385.977 Td /F1 9.8 Tf [(\), Diplophidae \(following Nelson)] TJ ET 0.267 0.267 0.267 rg BT 172.972 387.485 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 177.791 385.977 Td /F1 9.8 Tf [(; apparently omitted by Eschmeyer and Fong)] TJ ET 0.267 0.267 0.267 rg BT 371.797 387.485 Td /F4 8.7 Tf [(89)] TJ ET 0.271 0.267 0.267 rg BT 381.434 385.977 Td /F1 9.8 Tf [(\), Horabagridae \(following Sullivan et al.)] TJ ET 0.267 0.267 0.267 rg BT 553.746 387.485 Td /F4 8.7 Tf [(94)] TJ ET 0.271 0.267 0.267 rg BT 563.383 385.977 Td /F1 9.8 Tf [(\), )] TJ ET BT 26.250 374.073 Td /F1 9.8 Tf [(Sinipercidae \(following Li et al.)] TJ ET 0.267 0.267 0.267 rg BT 157.924 375.580 Td /F4 8.7 Tf [(96)] TJ ET 0.271 0.267 0.267 rg BT 167.561 374.073 Td /F1 9.8 Tf [(\), Steindachneriidae \(following Roa-Varon and Ort)] TJ ET 0.267 0.267 0.267 rg BT 385.942 375.580 Td /F4 8.7 Tf [(98)] TJ ET 0.271 0.267 0.267 rg BT 395.579 374.073 Td /F1 9.8 Tf [(\), Zanclorhynchidae, the aulopiform )] TJ ET BT 26.250 362.168 Td /F1 9.8 Tf [(Bathysauropsidae and Sudidae \(following Davis)] TJ ET 0.267 0.267 0.267 rg BT 232.716 363.675 Td /F4 8.7 Tf [(91)] TJ ET 0.271 0.267 0.267 rg BT 242.353 362.168 Td /F1 9.8 Tf [(\), and the pleuronectiform Paralichthodidae, Poecilopsettidae, and )] TJ ET BT 26.250 350.263 Td /F1 9.8 Tf [(Rhombosoleidae \(following Chapleau)] TJ ET 0.267 0.267 0.267 rg BT 187.730 351.770 Td /F4 8.7 Tf [(97)] TJ ET 0.271 0.267 0.267 rg BT 197.367 350.263 Td /F1 9.8 Tf [(, Munroe)] TJ ET 0.267 0.267 0.267 rg BT 235.840 351.770 Td /F4 8.7 Tf [(99)] TJ ET 0.271 0.267 0.267 rg BT 245.478 350.263 Td /F1 9.8 Tf [(, Betancur-R. et al.)] TJ ET 0.267 0.267 0.267 rg BT 326.763 351.770 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 336.401 350.263 Td /F1 9.8 Tf [(\). A total of 502 families are recognized here, of which )] TJ ET BT 26.250 338.358 Td /F1 9.8 Tf [(369 \(73.5%\) were examined. Of these, 146 families included only one representative \(39.6%\) and 40 \(17.9%\) of the remaining )] TJ ET BT 26.250 326.454 Td /F1 9.8 Tf [(223 were rendered non-monophyletic in our analysis \(non-monophyletic families are indicated below\). For each order/suborder )] TJ ET BT 26.250 314.549 Td /F1 9.8 Tf [(we list all families examined as well as the unexamined families whose taxonomic affinity is expected on the basis of traditional )] TJ ET BT 26.250 302.644 Td /F1 9.8 Tf [(taxonomy or phylogenetic evidence. The list of unexamined families is also intended as a resource that may help fish )] TJ ET BT 26.250 290.739 Td /F1 9.8 Tf [(systematists to direct future sequencing efforts.)] TJ ET BT 26.250 271.335 Td /F1 9.8 Tf [(A total of 66 orders are classified, three of which are new \(Holocentriformes, Istiophoriformes, and Pempheriformes\), and 15 are )] TJ ET BT 26.250 259.430 Td /F1 9.8 Tf [(resurrected or validated under a new circumscription. Some ordinal or subordinal names may appear to be new, but most can )] TJ ET BT 26.250 247.525 Td /F1 9.8 Tf [(be found in the literature at various hierarchical levels. As examples, Spariformes is a Bleeker name and Centrarchiformes is a )] TJ ET BT 26.250 235.620 Td /F1 9.8 Tf [(Webber and de Beaufort name. Because priority is not applied to names above the family level, we have not made a thorough )] TJ ET BT 26.250 223.716 Td /F1 9.8 Tf [(attempt to establish first use. Only those three for which no reference could be found are listed as new. New infraorders are )] TJ ET BT 26.250 211.811 Td /F1 9.8 Tf [(named in Suborder Cottioidei to circumscribe well-corroborated clades and may conserve the rank of superfamily in subsequent )] TJ ET BT 26.250 199.906 Td /F1 9.8 Tf [(revisions. The ordinal status of 50 percomorph families examined \(as well as many others unexamined\) belonging to )] TJ ET BT 26.250 188.001 Td /F1 9.8 Tf [(Carangimorphariae, Ovalentariae, and Percomorpharia remains uncertain \(i.e.,)] TJ ET BT 365.998 188.001 Td /F5 9.8 Tf [(incertae sedis)] TJ ET BT 426.146 188.001 Td /F1 9.8 Tf [(\) due to poor phylogenetic )] TJ ET BT 26.250 176.097 Td /F1 9.8 Tf [(resolution. Percentages in parentheses following names indicate bootstrap support \(no bootstrap values shown for redundant )] TJ ET BT 26.250 164.192 Td /F1 9.8 Tf [(groups or monotypic taxa\). The complete phylogenetic tree with annotated classification is illustrated in )] TJ ET 0.267 0.267 0.267 rg BT 471.688 164.192 Td /F1 9.8 Tf [(Fig. S1)] TJ ET 0.271 0.267 0.267 rg BT 502.576 164.192 Td /F1 9.8 Tf [(. The new )] TJ ET BT 26.250 152.287 Td /F1 9.8 Tf [(classification scheme presented here should be considered a work in progress \(version 1; )] TJ ET 0.267 0.267 0.267 rg BT 415.324 152.287 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 464.103 152.287 Td /F1 9.8 Tf [(\), as any other hypothesis. )] TJ ET BT 26.250 140.382 Td /F1 9.8 Tf [(It is likely to include involuntary errors and omissions in addition to the many unexamined, )] TJ ET BT 415.324 140.382 Td /F5 9.8 Tf [(sedis mutabilis,)] TJ ET BT 481.965 140.382 Td /F1 9.8 Tf [( and )] TJ ET BT 503.649 140.382 Td /F5 9.8 Tf [(incertae sedis)] TJ ET BT 26.250 128.478 Td /F1 9.8 Tf [(taxa. Updates should be forthcoming as new evidence become available and feedback from experts help refine it. For the most )] TJ ET BT 26.250 116.573 Td /F1 9.8 Tf [(updated version visit )] TJ ET 0.267 0.267 0.267 rg BT 117.832 116.573 Td /F1 9.8 Tf [(DeepFin)] TJ ET 0.271 0.267 0.267 rg BT 154.677 116.573 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 97.168 Td /F4 9.8 Tf [(Comparison of classifications)] TJ ET BT 26.250 77.763 Td /F1 9.8 Tf [(Our results \()] TJ ET 0.267 0.267 0.267 rg BT 79.885 77.763 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 128.664 77.763 Td /F1 9.8 Tf [(\) invite comparison to the recent classification of Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 421.281 79.271 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 426.100 77.763 Td /F1 9.8 Tf [( based on morphological evidence )] TJ ET BT 26.250 65.859 Td /F1 9.8 Tf [(gleamed from many investigators. Of 123 clades recognized by them, 70 \(56.9%\) are congruent with bootstrap values >95% )] TJ ET BT 26.250 53.954 Td /F1 9.8 Tf [(obtained in this study. Five of these 70 clades are included in our sample by only one family and thus their monophyly is not )] TJ ET BT 26.250 42.049 Td /F1 9.8 Tf [(critically tested. Another six clades \(4.9%\) are congruent but are supported by lower bootstrap values; seven additional clades )] TJ ET Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(7)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 1019 0 obj << /Type /Annot /Subtype /Link /A 1020 0 R /Border [0 0 0] /H /I /Rect [ 225.4530 697.1634 235.0903 705.9817 ] >> endobj 1020 0 obj << /Type /Action >> endobj 1021 0 obj << /Type /Annot /Subtype /Link /A 1022 0 R /Border [0 0 0] /H /I /Rect [ 382.3587 697.1634 391.9960 705.9817 ] >> endobj 1022 0 obj << /Type /Action >> endobj 1023 0 obj << /Type /Annot /Subtype /Link /A 1024 0 R /Border [0 0 0] /H /I /Rect [ 432.5777 697.1634 437.3963 705.9817 ] >> endobj 1024 0 obj << /Type /Action >> endobj 1025 0 obj << /Type /Annot /Subtype /Link /A 1026 0 R /Border [0 0 0] /H /I /Rect [ 541.4483 697.1634 546.2670 705.9817 ] >> endobj 1026 0 obj << /Type /Action >> endobj 1027 0 obj << /Type /Annot /Subtype /Link 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Forty clades \(32.5%\) are incongruent, with some being grossly polyphyletic in our tree. Notable examples )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(are Protacanthopterygii, Smegmamorpharia, and Labriformes. Others are incongruent based on exclusion of subclades and are )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(rendered monophyletic in our classification by the addition or removal of smaller clades. Examples include Stomiatii \(inclusion of )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(Osmeriformes )] TJ ET BT 90.171 731.762 Td /F5 9.8 Tf [(sensu stricto)] TJ ET BT 144.898 731.762 Td /F1 9.8 Tf [(\), Otomorpha \(inclusion of Alepocephaliformes\), Neoteleostei \(removal of Stomiatiformes\), and )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(Lampridiformes \(removal of )] TJ ET BT 147.608 719.857 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 199.088 719.857 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 700.452 Td /F1 9.8 Tf [(There is considerable consensus between morphology and the interrelationships of major clades. For example, the major )] TJ ET BT 26.250 688.548 Td /F1 9.8 Tf [(cohorts of living teleosts and their interrelationships are congruent with the listing convention employed by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 567.073 690.055 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 571.891 688.548 Td /F1 9.8 Tf [(; )] TJ ET BT 26.250 676.643 Td /F1 9.8 Tf [(this is also true within many of the major clades \(e.g. relationships within Elopomorpha\). But there is also incongruence. For )] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(example, relationships among early-branching acanthomorph groups differ considerably from previous morphological )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(hypotheses \(e.g., Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 204.022 654.341 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 208.840 652.833 Td /F1 9.8 Tf [(\) with lampridiforms, percopsiforms, zeiforms and gadiforms branching off basally )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(relative to polymixiiforms. More explicit tests of new and alternative phylogenetic hypotheses based on multiple analyses of our )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(dataset are presented in Fig. 2.)] TJ ET BT 26.250 609.619 Td /F4 9.8 Tf [(Novel Clades of Teleost Fishes)] TJ ET BT 26.250 590.214 Td /F1 9.8 Tf [(The following sections highlight some of the salient features of this global phylogeny and classification of bony fishes, especially )] TJ ET BT 26.250 578.310 Td /F1 9.8 Tf [(in reference to well-established relationships and newly found clades among the euteleosts. We do not attempt to provide a )] TJ ET BT 26.250 566.405 Td /F1 9.8 Tf [(complete account of all taxonomic issues, but to give some perspective and contrast to discuss the evidence supporting novel )] TJ ET BT 26.250 554.500 Td /F1 9.8 Tf [(and established taxa.)] TJ ET BT 26.250 535.095 Td /F5 9.8 Tf [(Early euteleost lineages: tenuous relationships \(Fig. 1\))] TJ ET BT 26.250 515.691 Td /F1 9.8 Tf [(Our analyses support several recent hypotheses based on molecular data that contradict the consensus based on morphology)] TJ ET 0.267 0.267 0.267 rg BT 570.895 517.198 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 575.713 519.579 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 26.250 505.293 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 31.069 503.786 Td /F1 9.8 Tf [( relative to the composition of protacanthopterygians. Although our results fall short of resolving with confidence )] TJ ET BT 26.250 491.881 Td /F1 9.8 Tf [(circumscription and relationships among taxa in this group \(hence Protacathopterygii is a )] TJ ET BT 411.531 491.881 Td /F5 9.8 Tf [(sedis mutabilis)] TJ ET BT 475.462 491.881 Td /F1 9.8 Tf [( taxon in our proposed )] TJ ET BT 26.250 479.976 Td /F1 9.8 Tf [(classification\), some relationships are well supported and consistent with previous studies \(Fig. 1\). First, is the hypothesis that )] TJ ET BT 26.250 468.072 Td /F1 9.8 Tf [(alepocephalid fishes \(slickheads\) have affinities within Otomorpha, instead of Argentiformes, as proposed by Johnson and )] TJ ET BT 26.250 456.167 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 67.980 457.674 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 72.799 456.167 Td /F1 9.8 Tf [(. This result was first proposed on the basis of mitogenomic data)] TJ ET 0.267 0.267 0.267 rg BT 350.791 457.674 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 360.428 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 362.837 457.674 Td /F4 8.7 Tf [(41)] TJ ET 0.271 0.267 0.267 rg BT 372.475 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 374.884 457.674 Td /F4 8.7 Tf [(100)] TJ ET 0.271 0.267 0.267 rg BT 389.340 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 391.749 457.674 Td /F4 8.7 Tf [(101)] TJ ET 0.271 0.267 0.267 rg BT 406.205 456.167 Td /F1 9.8 Tf [( and recently corroborated with a )] TJ ET BT 26.250 444.262 Td /F1 9.8 Tf [(subset of the nuclear markers used in this study)] TJ ET 0.267 0.267 0.267 rg BT 232.716 445.769 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 242.353 444.262 Td /F1 9.8 Tf [(. Second, is the sister group relationship of Osmeriformes and Stomiatiformes )] TJ ET BT 26.250 432.357 Td /F1 9.8 Tf [(\(=Stomiiformes\), first proposed by Lpez et al.)] TJ ET 0.267 0.267 0.267 rg BT 225.930 433.865 Td /F4 8.7 Tf [(21)] TJ ET 0.271 0.267 0.267 rg BT 235.567 432.357 Td /F1 9.8 Tf [( based on mtDNA and )] TJ ET BT 334.198 432.357 Td /F5 9.8 Tf [(rag1)] TJ ET BT 353.708 432.357 Td /F1 9.8 Tf [( sequence data. Finally, the position of )] TJ ET BT 26.250 420.453 Td /F5 9.8 Tf [(Lepidogalaxias)] TJ ET BT 91.282 420.453 Td /F1 9.8 Tf [( at the base of the euteleosts rendering Galaxiidae non-monophyletic also was proposed previously)] TJ ET 0.267 0.267 0.267 rg BT 519.405 421.960 Td /F4 8.7 Tf [(102)] TJ ET 0.271 0.267 0.267 rg BT 533.861 424.341 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 536.270 421.960 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 545.908 420.453 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 408.548 Td /F1 9.8 Tf [(supported by our data \(see also Fig. 2\).)] TJ ET BT 26.250 389.143 Td /F5 9.8 Tf [(Paracanthomorphacea: mitogenomics dixit \(Fig. 1\))] TJ ET BT 26.250 369.738 Td /F1 9.8 Tf [(This name was first introduced as superorder Paracanthopterygii \()] TJ ET BT 311.272 369.738 Td /F5 9.8 Tf [(sensu)] TJ ET BT 337.285 369.738 Td /F1 9.8 Tf [( Greenwood et al.)] TJ ET 0.267 0.267 0.267 rg BT 414.241 371.246 Td /F4 8.7 Tf [(1)] TJ ET 0.271 0.267 0.267 rg BT 419.060 369.738 Td /F1 9.8 Tf [(\) to refer to a large group of spiny-)] TJ ET BT 26.250 357.834 Td /F1 9.8 Tf [(finned fishes that included Batrachoidiformes, Gadiformes \(with Ophioidei and Zoarcoidei\), Gobiesociformes, Lophiiformes, and )] TJ ET BT 26.250 345.929 Td /F1 9.8 Tf [(Percopsiformes. Many other taxa were added and also removed on the basis of conflicting evidence ever since )] TJ ET BT 26.250 334.024 Td /F1 9.8 Tf [(Paracanthopterygii was conceived, but a conservative stance persisted in classifications supporting the original circumscription, )] TJ ET BT 26.250 322.119 Td /F1 9.8 Tf [(with the exclusion of Gobiesociformes)] TJ ET 0.267 0.267 0.267 rg BT 189.894 323.627 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 194.713 322.119 Td /F1 9.8 Tf [(. More recently, mitogenomic data)] TJ ET 0.267 0.267 0.267 rg BT 341.557 323.627 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 346.376 326.008 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 348.785 323.627 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 353.604 322.119 Td /F1 9.8 Tf [( discovered a sister-group relationship between )] TJ ET BT 26.250 310.215 Td /F1 9.8 Tf [(Zeiformes and Gadiformes, a result also obtained with nuclear genes )] TJ ET 0.267 0.267 0.267 rg BT 326.462 311.722 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 336.100 314.103 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 338.509 311.722 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 348.146 314.103 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 350.556 311.722 Td /F4 8.7 Tf [(103)] TJ ET 0.271 0.267 0.267 rg BT 365.012 310.215 Td /F1 9.8 Tf [(; the name Zeioigadiformes)] TJ ET 0.267 0.267 0.267 rg BT 483.143 311.722 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 492.780 310.215 Td /F1 9.8 Tf [( was coined for this )] TJ ET BT 26.250 298.310 Td /F1 9.8 Tf [(new grouping. Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 134.631 299.817 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 144.268 298.310 Td /F1 9.8 Tf [( redefined the Paracanthopterygii to include Polymixiidae, Percopsiformes, Gadiformes, and Zeioidei )] TJ ET BT 26.250 286.405 Td /F1 9.8 Tf [(and subsequently Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 149.812 287.912 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 159.449 286.405 Td /F1 9.8 Tf [( added to this group the lampridiform genus )] TJ ET BT 350.208 286.405 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 401.688 286.405 Td /F1 9.8 Tf [(, which was unexpectedly found to form )] TJ ET BT 26.250 274.500 Td /F1 9.8 Tf [(the sister group of Gadiformes. Analysis of four nuclear markers in addition to mtDNA confirmed this result)] TJ ET 0.267 0.267 0.267 rg BT 484.120 276.008 Td /F4 8.7 Tf [(103)] TJ ET 0.271 0.267 0.267 rg BT 498.576 274.500 Td /F1 9.8 Tf [(, supporting a )] TJ ET BT 26.250 262.596 Td /F1 9.8 Tf [(monophyletic taxon Paracanthopterygii that includes percopsiforms, gadiforms, )] TJ ET BT 369.265 262.596 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 420.745 262.596 Td /F1 9.8 Tf [( \(placed in its own order )] TJ ET BT 26.250 250.691 Td /F1 9.8 Tf [(Stylephoriformes\) and zeiforms, in agreement with our results \(Fig. 1, 2\). A review of published morphological characters by )] TJ ET BT 26.250 238.786 Td /F1 9.8 Tf [(Borden et al.)] TJ ET 0.267 0.267 0.267 rg BT 81.532 240.293 Td /F4 8.7 Tf [(105)] TJ ET 0.271 0.267 0.267 rg BT 95.989 238.786 Td /F1 9.8 Tf [( also found significant congruence between this arrangement and morphological character-state distributions for )] TJ ET BT 26.250 226.881 Td /F1 9.8 Tf [(many of the proposed relationships.)] TJ ET BT 26.250 207.477 Td /F5 9.8 Tf [(Euacanthomorphacea: holocentrids sister to percomorphs \(Fig. 1\))] TJ ET Q q 15.000 35.334 577.500 741.666 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(\(5.7%\) are monotypic. Forty clades \(32.5%\) are incongruent, with some being grossly polyphyletic in our tree. Notable examples )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(are Protacanthopterygii, Smegmamorpharia, and Labriformes. Others are incongruent based on exclusion of subclades and are )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(rendered monophyletic in our classification by the addition or removal of smaller clades. Examples include Stomiatii \(inclusion of )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(Osmeriformes )] TJ ET BT 90.171 731.762 Td /F5 9.8 Tf [(sensu stricto)] TJ ET BT 144.898 731.762 Td /F1 9.8 Tf [(\), Otomorpha \(inclusion of Alepocephaliformes\), Neoteleostei \(removal of Stomiatiformes\), and )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(Lampridiformes \(removal of )] TJ ET BT 147.608 719.857 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 199.088 719.857 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 700.452 Td /F1 9.8 Tf [(There is considerable consensus between morphology and the interrelationships of major clades. For example, the major )] TJ ET BT 26.250 688.548 Td /F1 9.8 Tf [(cohorts of living teleosts and their interrelationships are congruent with the listing convention employed by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 567.073 690.055 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 571.891 688.548 Td /F1 9.8 Tf [(; )] TJ ET BT 26.250 676.643 Td /F1 9.8 Tf [(this is also true within many of the major clades \(e.g. relationships within Elopomorpha\). But there is also incongruence. For )] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(example, relationships among early-branching acanthomorph groups differ considerably from previous morphological )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(hypotheses \(e.g., Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 204.022 654.341 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 208.840 652.833 Td /F1 9.8 Tf [(\) with lampridiforms, percopsiforms, zeiforms and gadiforms branching off basally )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(relative to polymixiiforms. More explicit tests of new and alternative phylogenetic hypotheses based on multiple analyses of our )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(dataset are presented in Fig. 2.)] TJ ET BT 26.250 609.619 Td /F4 9.8 Tf [(Novel Clades of Teleost Fishes)] TJ ET BT 26.250 590.214 Td /F1 9.8 Tf [(The following sections highlight some of the salient features of this global phylogeny and classification of bony fishes, especially )] TJ ET BT 26.250 578.310 Td /F1 9.8 Tf [(in reference to well-established relationships and newly found clades among the euteleosts. We do not attempt to provide a )] TJ ET BT 26.250 566.405 Td /F1 9.8 Tf [(complete account of all taxonomic issues, but to give some perspective and contrast to discuss the evidence supporting novel )] TJ ET BT 26.250 554.500 Td /F1 9.8 Tf [(and established taxa.)] TJ ET BT 26.250 535.095 Td /F5 9.8 Tf [(Early euteleost lineages: tenuous relationships \(Fig. 1\))] TJ ET BT 26.250 515.691 Td /F1 9.8 Tf [(Our analyses support several recent hypotheses based on molecular data that contradict the consensus based on morphology)] TJ ET 0.267 0.267 0.267 rg BT 570.895 517.198 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 575.713 519.579 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 26.250 505.293 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 31.069 503.786 Td /F1 9.8 Tf [( relative to the composition of protacanthopterygians. Although our results fall short of resolving with confidence )] TJ ET BT 26.250 491.881 Td /F1 9.8 Tf [(circumscription and relationships among taxa in this group \(hence Protacathopterygii is a )] TJ ET BT 411.531 491.881 Td /F5 9.8 Tf [(sedis mutabilis)] TJ ET BT 475.462 491.881 Td /F1 9.8 Tf [( taxon in our proposed )] TJ ET BT 26.250 479.976 Td /F1 9.8 Tf [(classification\), some relationships are well supported and consistent with previous studies \(Fig. 1\). First, is the hypothesis that )] TJ ET BT 26.250 468.072 Td /F1 9.8 Tf [(alepocephalid fishes \(slickheads\) have affinities within Otomorpha, instead of Argentiformes, as proposed by Johnson and )] TJ ET BT 26.250 456.167 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 67.980 457.674 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 72.799 456.167 Td /F1 9.8 Tf [(. This result was first proposed on the basis of mitogenomic data)] TJ ET 0.267 0.267 0.267 rg BT 350.791 457.674 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 360.428 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 362.837 457.674 Td /F4 8.7 Tf [(41)] TJ ET 0.271 0.267 0.267 rg BT 372.475 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 374.884 457.674 Td /F4 8.7 Tf [(100)] TJ ET 0.271 0.267 0.267 rg BT 389.340 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 391.749 457.674 Td /F4 8.7 Tf [(101)] TJ ET 0.271 0.267 0.267 rg BT 406.205 456.167 Td /F1 9.8 Tf [( and recently corroborated with a )] TJ ET BT 26.250 444.262 Td /F1 9.8 Tf [(subset of the nuclear markers used in this study)] TJ ET 0.267 0.267 0.267 rg BT 232.716 445.769 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 242.353 444.262 Td /F1 9.8 Tf [(. Second, is the sister group relationship of Osmeriformes and Stomiatiformes )] TJ ET BT 26.250 432.357 Td /F1 9.8 Tf [(\(=Stomiiformes\), first proposed by Lpez et al.)] TJ ET 0.267 0.267 0.267 rg BT 225.930 433.865 Td /F4 8.7 Tf [(21)] TJ ET 0.271 0.267 0.267 rg BT 235.567 432.357 Td /F1 9.8 Tf [( based on mtDNA and )] TJ ET BT 334.198 432.357 Td /F5 9.8 Tf [(rag1)] TJ ET BT 353.708 432.357 Td /F1 9.8 Tf [( sequence data. Finally, the position of )] TJ ET BT 26.250 420.453 Td /F5 9.8 Tf [(Lepidogalaxias)] TJ ET BT 91.282 420.453 Td /F1 9.8 Tf [( at the base of the euteleosts rendering Galaxiidae non-monophyletic also was proposed previously)] TJ ET 0.267 0.267 0.267 rg BT 519.405 421.960 Td /F4 8.7 Tf [(102)] TJ ET 0.271 0.267 0.267 rg BT 533.861 424.341 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 536.270 421.960 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 545.908 420.453 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 408.548 Td /F1 9.8 Tf [(supported by our data \(see also Fig. 2\).)] TJ ET BT 26.250 389.143 Td /F5 9.8 Tf [(Paracanthomorphacea: mitogenomics dixit \(Fig. 1\))] TJ ET BT 26.250 369.738 Td /F1 9.8 Tf [(This name was first introduced as superorder Paracanthopterygii \()] TJ ET BT 311.272 369.738 Td /F5 9.8 Tf [(sensu)] TJ ET BT 337.285 369.738 Td /F1 9.8 Tf [( Greenwood et al.)] TJ ET 0.267 0.267 0.267 rg BT 414.241 371.246 Td /F4 8.7 Tf [(1)] TJ ET 0.271 0.267 0.267 rg BT 419.060 369.738 Td /F1 9.8 Tf [(\) to refer to a large group of spiny-)] TJ ET BT 26.250 357.834 Td /F1 9.8 Tf [(finned fishes that included Batrachoidiformes, Gadiformes \(with Ophioidei and Zoarcoidei\), Gobiesociformes, Lophiiformes, and )] TJ ET BT 26.250 345.929 Td /F1 9.8 Tf [(Percopsiformes. Many other taxa were added and also removed on the basis of conflicting evidence ever since )] TJ ET BT 26.250 334.024 Td /F1 9.8 Tf [(Paracanthopterygii was conceived, but a conservative stance persisted in classifications supporting the original circumscription, )] TJ ET BT 26.250 322.119 Td /F1 9.8 Tf [(with the exclusion of Gobiesociformes)] TJ ET 0.267 0.267 0.267 rg BT 189.894 323.627 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 194.713 322.119 Td /F1 9.8 Tf [(. More recently, mitogenomic data)] TJ ET 0.267 0.267 0.267 rg BT 341.557 323.627 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 346.376 326.008 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 348.785 323.627 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 353.604 322.119 Td /F1 9.8 Tf [( discovered a sister-group relationship between )] TJ ET BT 26.250 310.215 Td /F1 9.8 Tf [(Zeiformes and Gadiformes, a result also obtained with nuclear genes )] TJ ET 0.267 0.267 0.267 rg BT 326.462 311.722 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 336.100 314.103 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 338.509 311.722 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 348.146 314.103 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 350.556 311.722 Td /F4 8.7 Tf [(103)] TJ ET 0.271 0.267 0.267 rg BT 365.012 310.215 Td /F1 9.8 Tf [(; the name Zeioigadiformes)] TJ ET 0.267 0.267 0.267 rg BT 483.143 311.722 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 492.780 310.215 Td /F1 9.8 Tf [( was coined for this )] TJ ET BT 26.250 298.310 Td /F1 9.8 Tf [(new grouping. Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 134.631 299.817 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 144.268 298.310 Td /F1 9.8 Tf [( redefined the Paracanthopterygii to include Polymixiidae, Percopsiformes, Gadiformes, and Zeioidei )] TJ ET BT 26.250 286.405 Td /F1 9.8 Tf [(and subsequently Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 149.812 287.912 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 159.449 286.405 Td /F1 9.8 Tf [( added to this group the lampridiform genus )] TJ ET BT 350.208 286.405 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 401.688 286.405 Td /F1 9.8 Tf [(, which was unexpectedly found to form )] TJ ET BT 26.250 274.500 Td /F1 9.8 Tf [(the sister group of Gadiformes. Analysis of four nuclear markers in addition to mtDNA confirmed this result)] TJ ET 0.267 0.267 0.267 rg BT 484.120 276.008 Td /F4 8.7 Tf [(103)] TJ ET 0.271 0.267 0.267 rg BT 498.576 274.500 Td /F1 9.8 Tf [(, supporting a )] TJ ET BT 26.250 262.596 Td /F1 9.8 Tf [(monophyletic taxon Paracanthopterygii that includes percopsiforms, gadiforms, )] TJ ET BT 369.265 262.596 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 420.745 262.596 Td /F1 9.8 Tf [( \(placed in its own order )] TJ ET BT 26.250 250.691 Td /F1 9.8 Tf [(Stylephoriformes\) and zeiforms, in agreement with our results \(Fig. 1, 2\). A review of published morphological characters by )] TJ ET BT 26.250 238.786 Td /F1 9.8 Tf [(Borden et al.)] TJ ET 0.267 0.267 0.267 rg BT 81.532 240.293 Td /F4 8.7 Tf [(105)] TJ ET 0.271 0.267 0.267 rg BT 95.989 238.786 Td /F1 9.8 Tf [( also found significant congruence between this arrangement and morphological character-state distributions for )] TJ ET BT 26.250 226.881 Td /F1 9.8 Tf [(many of the proposed relationships.)] TJ ET BT 26.250 207.477 Td /F5 9.8 Tf [(Euacanthomorphacea: holocentrids sister to percomorphs \(Fig. 1\))] TJ ET Q q 15.000 35.334 577.500 741.666 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(\(5.7%\) are monotypic. Forty clades \(32.5%\) are incongruent, with some being grossly polyphyletic in our tree. Notable examples )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(are Protacanthopterygii, Smegmamorpharia, and Labriformes. Others are incongruent based on exclusion of subclades and are )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(rendered monophyletic in our classification by the addition or removal of smaller clades. Examples include Stomiatii \(inclusion of )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(Osmeriformes )] TJ ET BT 90.171 731.762 Td /F5 9.8 Tf [(sensu stricto)] TJ ET BT 144.898 731.762 Td /F1 9.8 Tf [(\), Otomorpha \(inclusion of Alepocephaliformes\), Neoteleostei \(removal of Stomiatiformes\), and )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(Lampridiformes \(removal of )] TJ ET BT 147.608 719.857 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 199.088 719.857 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 700.452 Td /F1 9.8 Tf [(There is considerable consensus between morphology and the interrelationships of major clades. For example, the major )] TJ ET BT 26.250 688.548 Td /F1 9.8 Tf [(cohorts of living teleosts and their interrelationships are congruent with the listing convention employed by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 567.073 690.055 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 571.891 688.548 Td /F1 9.8 Tf [(; )] TJ ET BT 26.250 676.643 Td /F1 9.8 Tf [(this is also true within many of the major clades \(e.g. relationships within Elopomorpha\). But there is also incongruence. For )] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(example, relationships among early-branching acanthomorph groups differ considerably from previous morphological )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(hypotheses \(e.g., Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 204.022 654.341 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 208.840 652.833 Td /F1 9.8 Tf [(\) with lampridiforms, percopsiforms, zeiforms and gadiforms branching off basally )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(relative to polymixiiforms. More explicit tests of new and alternative phylogenetic hypotheses based on multiple analyses of our )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(dataset are presented in Fig. 2.)] TJ ET BT 26.250 609.619 Td /F4 9.8 Tf [(Novel Clades of Teleost Fishes)] TJ ET BT 26.250 590.214 Td /F1 9.8 Tf [(The following sections highlight some of the salient features of this global phylogeny and classification of bony fishes, especially )] TJ ET BT 26.250 578.310 Td /F1 9.8 Tf [(in reference to well-established relationships and newly found clades among the euteleosts. We do not attempt to provide a )] TJ ET BT 26.250 566.405 Td /F1 9.8 Tf [(complete account of all taxonomic issues, but to give some perspective and contrast to discuss the evidence supporting novel )] TJ ET BT 26.250 554.500 Td /F1 9.8 Tf [(and established taxa.)] TJ ET BT 26.250 535.095 Td /F5 9.8 Tf [(Early euteleost lineages: tenuous relationships \(Fig. 1\))] TJ ET BT 26.250 515.691 Td /F1 9.8 Tf [(Our analyses support several recent hypotheses based on molecular data that contradict the consensus based on morphology)] TJ ET 0.267 0.267 0.267 rg BT 570.895 517.198 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 575.713 519.579 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 26.250 505.293 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 31.069 503.786 Td /F1 9.8 Tf [( relative to the composition of protacanthopterygians. Although our results fall short of resolving with confidence )] TJ ET BT 26.250 491.881 Td /F1 9.8 Tf [(circumscription and relationships among taxa in this group \(hence Protacathopterygii is a )] TJ ET BT 411.531 491.881 Td /F5 9.8 Tf [(sedis mutabilis)] TJ ET BT 475.462 491.881 Td /F1 9.8 Tf [( taxon in our proposed )] TJ ET BT 26.250 479.976 Td /F1 9.8 Tf [(classification\), some relationships are well supported and consistent with previous studies \(Fig. 1\). First, is the hypothesis that )] TJ ET BT 26.250 468.072 Td /F1 9.8 Tf [(alepocephalid fishes \(slickheads\) have affinities within Otomorpha, instead of Argentiformes, as proposed by Johnson and )] TJ ET BT 26.250 456.167 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 67.980 457.674 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 72.799 456.167 Td /F1 9.8 Tf [(. This result was first proposed on the basis of mitogenomic data)] TJ ET 0.267 0.267 0.267 rg BT 350.791 457.674 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 360.428 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 362.837 457.674 Td /F4 8.7 Tf [(41)] TJ ET 0.271 0.267 0.267 rg BT 372.475 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 374.884 457.674 Td /F4 8.7 Tf [(100)] TJ ET 0.271 0.267 0.267 rg BT 389.340 460.055 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 391.749 457.674 Td /F4 8.7 Tf [(101)] TJ ET 0.271 0.267 0.267 rg BT 406.205 456.167 Td /F1 9.8 Tf [( and recently corroborated with a )] TJ ET BT 26.250 444.262 Td /F1 9.8 Tf [(subset of the nuclear markers used in this study)] TJ ET 0.267 0.267 0.267 rg BT 232.716 445.769 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 242.353 444.262 Td /F1 9.8 Tf [(. Second, is the sister group relationship of Osmeriformes and Stomiatiformes )] TJ ET BT 26.250 432.357 Td /F1 9.8 Tf [(\(=Stomiiformes\), first proposed by Lpez et al.)] TJ ET 0.267 0.267 0.267 rg BT 225.930 433.865 Td /F4 8.7 Tf [(21)] TJ ET 0.271 0.267 0.267 rg BT 235.567 432.357 Td /F1 9.8 Tf [( based on mtDNA and )] TJ ET BT 334.198 432.357 Td /F5 9.8 Tf [(rag1)] TJ ET BT 353.708 432.357 Td /F1 9.8 Tf [( sequence data. Finally, the position of )] TJ ET BT 26.250 420.453 Td /F5 9.8 Tf [(Lepidogalaxias)] TJ ET BT 91.282 420.453 Td /F1 9.8 Tf [( at the base of the euteleosts rendering Galaxiidae non-monophyletic also was proposed previously)] TJ ET 0.267 0.267 0.267 rg BT 519.405 421.960 Td /F4 8.7 Tf [(102)] TJ ET 0.271 0.267 0.267 rg BT 533.861 424.341 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 536.270 421.960 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 545.908 420.453 Td /F1 9.8 Tf [( and )] TJ ET BT 26.250 408.548 Td /F1 9.8 Tf [(supported by our data \(see also Fig. 2\).)] TJ ET BT 26.250 389.143 Td /F5 9.8 Tf [(Paracanthomorphacea: mitogenomics dixit \(Fig. 1\))] TJ ET BT 26.250 369.738 Td /F1 9.8 Tf [(This name was first introduced as superorder Paracanthopterygii \()] TJ ET BT 311.272 369.738 Td /F5 9.8 Tf [(sensu)] TJ ET BT 337.285 369.738 Td /F1 9.8 Tf [( Greenwood et al.)] TJ ET 0.267 0.267 0.267 rg BT 414.241 371.246 Td /F4 8.7 Tf [(1)] TJ ET 0.271 0.267 0.267 rg BT 419.060 369.738 Td /F1 9.8 Tf [(\) to refer to a large group of spiny-)] TJ ET BT 26.250 357.834 Td /F1 9.8 Tf [(finned fishes that included Batrachoidiformes, Gadiformes \(with Ophioidei and Zoarcoidei\), Gobiesociformes, Lophiiformes, and )] TJ ET BT 26.250 345.929 Td /F1 9.8 Tf [(Percopsiformes. Many other taxa were added and also removed on the basis of conflicting evidence ever since )] TJ ET BT 26.250 334.024 Td /F1 9.8 Tf [(Paracanthopterygii was conceived, but a conservative stance persisted in classifications supporting the original circumscription, )] TJ ET BT 26.250 322.119 Td /F1 9.8 Tf [(with the exclusion of Gobiesociformes)] TJ ET 0.267 0.267 0.267 rg BT 189.894 323.627 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 194.713 322.119 Td /F1 9.8 Tf [(. More recently, mitogenomic data)] TJ ET 0.267 0.267 0.267 rg BT 341.557 323.627 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 346.376 326.008 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 348.785 323.627 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 353.604 322.119 Td /F1 9.8 Tf [( discovered a sister-group relationship between )] TJ ET BT 26.250 310.215 Td /F1 9.8 Tf [(Zeiformes and Gadiformes, a result also obtained with nuclear genes )] TJ ET 0.267 0.267 0.267 rg BT 326.462 311.722 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 336.100 314.103 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 338.509 311.722 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 348.146 314.103 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 350.556 311.722 Td /F4 8.7 Tf [(103)] TJ ET 0.271 0.267 0.267 rg BT 365.012 310.215 Td /F1 9.8 Tf [(; the name Zeioigadiformes)] TJ ET 0.267 0.267 0.267 rg BT 483.143 311.722 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 492.780 310.215 Td /F1 9.8 Tf [( was coined for this )] TJ ET BT 26.250 298.310 Td /F1 9.8 Tf [(new grouping. Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 134.631 299.817 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 144.268 298.310 Td /F1 9.8 Tf [( redefined the Paracanthopterygii to include Polymixiidae, Percopsiformes, Gadiformes, and Zeioidei )] TJ ET BT 26.250 286.405 Td /F1 9.8 Tf [(and subsequently Miya et al.)] TJ ET 0.267 0.267 0.267 rg BT 149.812 287.912 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 159.449 286.405 Td /F1 9.8 Tf [( added to this group the lampridiform genus )] TJ ET BT 350.208 286.405 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 401.688 286.405 Td /F1 9.8 Tf [(, which was unexpectedly found to form )] TJ ET BT 26.250 274.500 Td /F1 9.8 Tf [(the sister group of Gadiformes. Analysis of four nuclear markers in addition to mtDNA confirmed this result)] TJ ET 0.267 0.267 0.267 rg BT 484.120 276.008 Td /F4 8.7 Tf [(103)] TJ ET 0.271 0.267 0.267 rg BT 498.576 274.500 Td /F1 9.8 Tf [(, supporting a )] TJ ET BT 26.250 262.596 Td /F1 9.8 Tf [(monophyletic taxon Paracanthopterygii that includes percopsiforms, gadiforms, )] TJ ET BT 369.265 262.596 Td /F5 9.8 Tf [(Stylephorus)] TJ ET BT 420.745 262.596 Td /F1 9.8 Tf [( \(placed in its own order )] TJ ET BT 26.250 250.691 Td /F1 9.8 Tf [(Stylephoriformes\) and zeiforms, in agreement with our results \(Fig. 1, 2\). A review of published morphological characters by )] TJ ET BT 26.250 238.786 Td /F1 9.8 Tf [(Borden et al.)] TJ ET 0.267 0.267 0.267 rg BT 81.532 240.293 Td /F4 8.7 Tf [(105)] TJ ET 0.271 0.267 0.267 rg BT 95.989 238.786 Td /F1 9.8 Tf [( also found significant congruence between this arrangement and morphological character-state distributions for )] TJ ET BT 26.250 226.881 Td /F1 9.8 Tf [(many of the proposed relationships.)] TJ ET BT 26.250 207.477 Td /F5 9.8 Tf [(Euacanthomorphacea: holocentrids sister to percomorphs \(Fig. 1\))] TJ ET Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(8)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 1315 0 obj << /Type /Annot /Subtype /Link /A 1316 0 R /Border [0 0 0] /H /I /Rect [ 567.0728 689.2532 571.8914 698.0715 ] >> endobj 1316 0 obj << /Type /Action >> endobj 1317 0 obj << /Type /Annot /Subtype /Link /A 1318 0 R /Border [0 0 0] /H /I /Rect [ 204.0217 653.5389 208.8404 662.3573 ] >> 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polymixiids, percopsids and crown acanthomorphs in their Euacanthopterygii, a taxon not )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(classified by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 164.427 757.079 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 169.246 755.571 Td /F1 9.8 Tf [(. We adopt the name but modify the circumscription to recognize a well-supported clade \(99% )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(bootstrap\) that includes beryciforms, holocentrids and percomorphs. The main issue at this level is delimitation of Beryciformes )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(and relationships of its proposed components to Percomorphaceae. Most classifications)] TJ ET 0.267 0.267 0.267 rg BT 405.038 733.269 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 409.856 735.650 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 412.266 733.269 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 417.084 731.762 Td /F1 9.8 Tf [( accept separate orders )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(Stephanoberyciformes and Beryciformes, each monophyletic and placed as successive sister-groups of the percomorphs. )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(Molecular data \(mitogenomic and smaller subsets of nuclear genes\), in contrast, have supported the inclusion of )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(Stephanoberyciformes in the same clade as Beryciformes)] TJ ET 0.267 0.267 0.267 rg BT 275.509 697.555 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 280.327 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 282.737 697.555 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 292.374 696.048 Td /F1 9.8 Tf [( and consistently include holocentrids within this clade. Our )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(results, however, reject this hypothesis in favor of recognizing a separate holocentrid clade \(proposed here as a new order, )] TJ ET BT 26.250 672.238 Td /F1 9.8 Tf [(Holocentriformes\) that is sister to percomorphs \(Fig. 1\), a result first obtained by Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 459.735 673.745 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 469.372 672.238 Td /F1 9.8 Tf [( and Moore )] TJ ET 0.267 0.267 0.267 rg BT 521.398 673.745 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 531.036 672.238 Td /F1 9.8 Tf [( but )] TJ ET BT 26.250 660.333 Td /F1 9.8 Tf [(subsequently challenged by Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 249.544 661.841 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 254.363 660.333 Td /F1 9.8 Tf [(. Despite relatively low support for our holocentrid-percomorph clade \(57-)] TJ ET BT 26.250 648.429 Td /F1 9.8 Tf [(69% bootstrap\), proportionally more individual gene trees support this relationship \(47%\) relative to the alternative molecular )] TJ ET BT 26.250 636.524 Td /F1 9.8 Tf [(hypothesis uniting holocentrids with the remaining beryciform groups \(20%; Fig. 2\). Our new circumscription of Beryciformes is )] TJ ET BT 26.250 624.619 Td /F1 9.8 Tf [(also most similar to that of the order Trachichthyiformes described by Moore)] TJ ET 0.267 0.267 0.267 rg BT 354.611 626.126 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 364.248 624.619 Td /F1 9.8 Tf [(, except that the latter excludes the berycids.)] TJ ET BT 26.250 605.214 Td /F5 9.8 Tf [(Percomorphaceae: no longer an unresolved bush \(Figs. 1-10\))] TJ ET BT 26.250 585.810 Td /F1 9.8 Tf [(A major contribution from our study has been the disambiguation of the percomorph bush into nine well-supported supraordinal )] TJ ET BT 26.250 573.905 Td /F1 9.8 Tf [(groups \(six Series and three Subseries; Fig. 1; )] TJ ET 0.267 0.267 0.267 rg BT 229.459 573.905 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 278.239 573.905 Td /F1 9.8 Tf [(\): Ophidiimorpharia, Batrachoidimorpharia, Gobiomorpharia \(Fig. 3\), )] TJ ET BT 26.250 562.000 Td /F1 9.8 Tf [(Scombrimorpharia \(Figs. 4 and 5\), Carangimorpharia \(with three Subseries: Anabantomorphariae, Fig. 6; Carangimorphariae, )] TJ ET BT 26.250 550.095 Td /F1 9.8 Tf [(Fig. 7; and Ovalentariae, Fig. 8\), and Percomorpharia \(Figs. 9\). Furthermore, increased phylogenetic resolution within )] TJ ET BT 26.250 538.191 Td /F1 9.8 Tf [(Percomorpharia allowed the definition of a monophyletic Perciformes \(Figs. 9 and 10\), for the first time recovered from a vast )] TJ ET BT 26.250 526.286 Td /F1 9.8 Tf [(taxonomic sample. With the exception of the cusk-eels \(Ophidiimorpharia\) and the toadfishes \(Batrachoidimorpharia\), whose )] TJ ET BT 26.250 514.381 Td /F1 9.8 Tf [(monophyly has been recognized in most classifications \(i.e., )] TJ ET 0.267 0.267 0.267 rg BT 287.979 515.888 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 292.798 518.269 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 295.207 515.888 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 300.026 514.381 Td /F1 9.8 Tf [(; but see )] TJ ET 0.267 0.267 0.267 rg BT 340.137 515.888 Td /F4 8.7 Tf [(106)] TJ ET 0.271 0.267 0.267 rg BT 354.593 518.269 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 357.003 515.888 Td /F4 8.7 Tf [(107)] TJ ET 0.271 0.267 0.267 rg BT 371.459 514.381 Td /F1 9.8 Tf [(\), the remaining seven supraordinal clades \(four )] TJ ET BT 26.250 502.476 Td /F1 9.8 Tf [(Series and three Subseries\) have never been discovered by examination of anatomical features. Under different combinations )] TJ ET BT 26.250 490.572 Td /F1 9.8 Tf [(of taxa, however, and based on diverse genetic markers, several of these clades have been obtained, in one form or another, )] TJ ET BT 26.250 478.667 Td /F1 9.8 Tf [(by previous molecular studies \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 179.598 480.174 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 184.417 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 186.826 480.174 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 191.645 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 194.054 480.174 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 203.691 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 206.101 480.174 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 215.738 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 218.147 480.174 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 227.785 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 230.194 480.174 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 239.831 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 242.241 480.174 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 251.878 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 254.287 480.174 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 263.925 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 266.334 480.174 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 275.971 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 278.381 480.174 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 288.018 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 290.427 480.174 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 300.065 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 302.474 480.174 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 312.111 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 314.521 480.174 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 324.158 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 326.567 480.174 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 336.205 478.667 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 459.262 Td /F1 9.8 Tf [(A corollary of the increased resolution of percomorph relationships is the demise of the Smegmamorpharia )] TJ ET BT 487.932 459.262 Td /F5 9.8 Tf [(sensu)] TJ ET BT 513.945 459.262 Td /F1 9.8 Tf [( Johnson and )] TJ ET BT 26.250 447.357 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 67.980 448.865 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 72.799 447.357 Td /F1 9.8 Tf [( \(see also Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 200.143 448.865 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 204.962 447.357 Td /F1 9.8 Tf [(; Fig. 2\). Elements included in this supraordinal taxon are now scattered throughout )] TJ ET BT 26.250 435.453 Td /F1 9.8 Tf [(the molecular phylogeny, placed within many of the newly found clades with high bootstrap support. For example, the pygmy )] TJ ET BT 26.250 423.548 Td /F1 9.8 Tf [(sunfishes \()] TJ ET BT 73.391 423.548 Td /F5 9.8 Tf [(Elassoma)] TJ ET BT 116.194 423.548 Td /F1 9.8 Tf [(\) are back with the other sunfishes \(centrarchids\), as suggested by earlier classifications and recently )] TJ ET BT 26.250 411.643 Td /F1 9.8 Tf [(confirmed by molecules)] TJ ET 0.267 0.267 0.267 rg BT 128.654 413.150 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 138.292 411.643 Td /F1 9.8 Tf [(. Centrarchids plus elassomatids are placed here in the resurrected order Centrarchiformes \(within )] TJ ET BT 26.250 399.738 Td /F1 9.8 Tf [(Percomorpharia, Fig. 9\). Mugiliforms \(mullets\) and atherinomorphs \(silversides, needlefishes, halfbeaks, guppies and allies\) are )] TJ ET BT 26.250 387.834 Td /F1 9.8 Tf [(placed within Ovalentariae \(Fig. 8\). The swamp eels and spiny eels \(order Synbranchiformes, suborders Synbranchoidei and )] TJ ET BT 26.250 375.929 Td /F1 9.8 Tf [(Mastacembeloidei\) are placed with confidence in Anabantomorphariae \(Fig. 5\), together with armored sticklebacks )] TJ ET BT 26.250 364.024 Td /F1 9.8 Tf [(\(Indostomidae\), one of the 11 families previously included in the order Gasterosteiformes. The polyphyly of Gasterosteiformes )] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(\(another large clade assigned to Smegmamorpha\) was first pointed out by mitogenomic evidence)] TJ ET 0.267 0.267 0.267 rg BT 445.675 353.627 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 455.313 352.119 Td /F1 9.8 Tf [(. Our results place the )] TJ ET BT 26.250 340.215 Td /F1 9.8 Tf [(sticklebacks, tubesnouts and sand eels \(previously assigned to Gasterosteoidei\) in our newly defined Perciformes \(suborder )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(Cottioidei; Fig. 10\) and the rest of the families previously assigned to the suborder Syngnathoidei were relocated to our newly )] TJ ET BT 26.250 316.405 Td /F1 9.8 Tf [(defined order Syngnathiformes within the Scombrimorpharia \(Fig. 4, see below\).)] TJ ET BT 26.250 297.000 Td /F1 9.8 Tf [(Phylogenetic resolution within five newly discovered clades, however, will require additional study. Relationships within )] TJ ET BT 26.250 285.096 Td /F1 9.8 Tf [(Syngnathiformes, Scombriformes, Carangimorphariae, Ovalentariae, and Percomorpharia may be challenging to recover given )] TJ ET BT 26.250 273.191 Td /F1 9.8 Tf [(the rapid radiation and diversification of these clades.)] TJ ET BT 26.250 253.786 Td /F5 9.8 Tf [(Gobiomorpharia: sweepers are out )] TJ ET BT 179.062 253.786 Td /F5 9.8 Tf [(\(Fig. 3\))] TJ ET BT 26.250 234.381 Td /F1 9.8 Tf [(Based on a phylogeny estimated with four mitochondrial markers, Thacker)] TJ ET 0.267 0.267 0.267 rg BT 346.498 235.889 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 356.136 234.381 Td /F1 9.8 Tf [( resurrected the order Gobiiformes, to )] TJ ET BT 26.250 222.477 Td /F1 9.8 Tf [(accommodate three suborders: Gobioidei \(gobies and sleepers\), Kurtidoidei \(nurseryfish\), and Apogonoidei \(including )] TJ ET BT 26.250 210.572 Td /F1 9.8 Tf [(apogonids and pempherids\). Previous molecular studies have shown affinities between gobioids, apogonids, kurtids and, to )] TJ ET BT 26.250 198.667 Td /F1 9.8 Tf [(some extent, pempherids and dactylopterids)] TJ ET 0.267 0.267 0.267 rg BT 217.545 200.174 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 222.364 202.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 224.773 200.174 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 234.410 202.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 236.820 200.174 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 246.457 198.667 Td /F1 9.8 Tf [(. There is also morphological evidence supporting a close relationship )] TJ ET BT 26.250 186.762 Td /F1 9.8 Tf [(between gobids and apogonids)] TJ ET 0.267 0.267 0.267 rg BT 161.209 188.270 Td /F4 8.7 Tf [(108)] TJ ET 0.271 0.267 0.267 rg BT 175.666 190.651 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 178.075 188.270 Td /F4 8.7 Tf [(109)] TJ ET 0.271 0.267 0.267 rg BT 192.531 186.762 Td /F1 9.8 Tf [( as well as between kurtids and apogonids)] TJ ET 0.267 0.267 0.267 rg BT 375.704 188.270 Td /F4 8.7 Tf [(110)] TJ ET 0.271 0.267 0.267 rg BT 390.160 186.762 Td /F1 9.8 Tf [(. Our results provide partial support for the )] TJ ET BT 26.250 174.858 Td /F1 9.8 Tf [(Gobiiformes )] TJ ET BT 81.513 174.858 Td /F5 9.8 Tf [(sensu )] TJ ET BT 110.237 174.858 Td /F1 9.8 Tf [(Thacker)] TJ ET 0.267 0.267 0.267 rg BT 145.454 176.365 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 155.091 174.858 Td /F1 9.8 Tf [( but we treat it here as a supraordinal group \(Gobiomorpharia\). A major difference is that our )] TJ ET BT 26.250 162.953 Td /F1 9.8 Tf [(hypothesis segregates the family Pempheridae \(sweepers\) to its own order \(Pempheriformes, together with Glaucosomatidae\), )] TJ ET BT 26.250 151.048 Td /F1 9.8 Tf [(within Percomorpharia \(Figs. 1, 3, 9\).)] TJ ET 0.965 0.965 0.965 rg 26.250 -73.333 555.000 214.500 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 141.167 m 581.250 141.167 l 581.250 140.417 l 26.250 140.417 l f q 452.250 0 0 198.750 35.250 -67.333 cm /I5 Do Q q 35.250 -73.333 537.000 0.000 re W n Q Q q 15.000 -73.333 577.500 850.333 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 126.519 768.983 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 131.338 767.476 Td /F1 9.8 Tf [( included polymixiids, percopsids and crown acanthomorphs in their Euacanthopterygii, a taxon not )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(classified by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 164.427 757.079 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 169.246 755.571 Td /F1 9.8 Tf [(. We adopt the name but modify the circumscription to recognize a well-supported clade \(99% )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(bootstrap\) that includes beryciforms, holocentrids and percomorphs. The main issue at this level is delimitation of Beryciformes )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(and relationships of its proposed components to Percomorphaceae. Most classifications)] TJ ET 0.267 0.267 0.267 rg BT 405.038 733.269 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 409.856 735.650 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 412.266 733.269 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 417.084 731.762 Td /F1 9.8 Tf [( accept separate orders )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(Stephanoberyciformes and Beryciformes, each monophyletic and placed as successive sister-groups of the percomorphs. )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(Molecular data \(mitogenomic and smaller subsets of nuclear genes\), in contrast, have supported the inclusion of )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(Stephanoberyciformes in the same clade as Beryciformes)] TJ ET 0.267 0.267 0.267 rg BT 275.509 697.555 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 280.327 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 282.737 697.555 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 292.374 696.048 Td /F1 9.8 Tf [( and consistently include holocentrids within this clade. Our )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(results, however, reject this hypothesis in favor of recognizing a separate holocentrid clade \(proposed here as a new order, )] TJ ET BT 26.250 672.238 Td /F1 9.8 Tf [(Holocentriformes\) that is sister to percomorphs \(Fig. 1\), a result first obtained by Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 459.735 673.745 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 469.372 672.238 Td /F1 9.8 Tf [( and Moore )] TJ ET 0.267 0.267 0.267 rg BT 521.398 673.745 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 531.036 672.238 Td /F1 9.8 Tf [( but )] TJ ET BT 26.250 660.333 Td /F1 9.8 Tf [(subsequently challenged by Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 249.544 661.841 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 254.363 660.333 Td /F1 9.8 Tf [(. Despite relatively low support for our holocentrid-percomorph clade \(57-)] TJ ET BT 26.250 648.429 Td /F1 9.8 Tf [(69% bootstrap\), proportionally more individual gene trees support this relationship \(47%\) relative to the alternative molecular )] TJ ET BT 26.250 636.524 Td /F1 9.8 Tf [(hypothesis uniting holocentrids with the remaining beryciform groups \(20%; Fig. 2\). Our new circumscription of Beryciformes is )] TJ ET BT 26.250 624.619 Td /F1 9.8 Tf [(also most similar to that of the order Trachichthyiformes described by Moore)] TJ ET 0.267 0.267 0.267 rg BT 354.611 626.126 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 364.248 624.619 Td /F1 9.8 Tf [(, except that the latter excludes the berycids.)] TJ ET BT 26.250 605.214 Td /F5 9.8 Tf [(Percomorphaceae: no longer an unresolved bush \(Figs. 1-10\))] TJ ET BT 26.250 585.810 Td /F1 9.8 Tf [(A major contribution from our study has been the disambiguation of the percomorph bush into nine well-supported supraordinal )] TJ ET BT 26.250 573.905 Td /F1 9.8 Tf [(groups \(six Series and three Subseries; Fig. 1; )] TJ ET 0.267 0.267 0.267 rg BT 229.459 573.905 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 278.239 573.905 Td /F1 9.8 Tf [(\): Ophidiimorpharia, Batrachoidimorpharia, Gobiomorpharia \(Fig. 3\), )] TJ ET BT 26.250 562.000 Td /F1 9.8 Tf [(Scombrimorpharia \(Figs. 4 and 5\), Carangimorpharia \(with three Subseries: Anabantomorphariae, Fig. 6; Carangimorphariae, )] TJ ET BT 26.250 550.095 Td /F1 9.8 Tf [(Fig. 7; and Ovalentariae, Fig. 8\), and Percomorpharia \(Figs. 9\). Furthermore, increased phylogenetic resolution within )] TJ ET BT 26.250 538.191 Td /F1 9.8 Tf [(Percomorpharia allowed the definition of a monophyletic Perciformes \(Figs. 9 and 10\), for the first time recovered from a vast )] TJ ET BT 26.250 526.286 Td /F1 9.8 Tf [(taxonomic sample. With the exception of the cusk-eels \(Ophidiimorpharia\) and the toadfishes \(Batrachoidimorpharia\), whose )] TJ ET BT 26.250 514.381 Td /F1 9.8 Tf [(monophyly has been recognized in most classifications \(i.e., )] TJ ET 0.267 0.267 0.267 rg BT 287.979 515.888 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 292.798 518.269 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 295.207 515.888 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 300.026 514.381 Td /F1 9.8 Tf [(; but see )] TJ ET 0.267 0.267 0.267 rg BT 340.137 515.888 Td /F4 8.7 Tf [(106)] TJ ET 0.271 0.267 0.267 rg BT 354.593 518.269 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 357.003 515.888 Td /F4 8.7 Tf [(107)] TJ ET 0.271 0.267 0.267 rg BT 371.459 514.381 Td /F1 9.8 Tf [(\), the remaining seven supraordinal clades \(four )] TJ ET BT 26.250 502.476 Td /F1 9.8 Tf [(Series and three Subseries\) have never been discovered by examination of anatomical features. Under different combinations )] TJ ET BT 26.250 490.572 Td /F1 9.8 Tf [(of taxa, however, and based on diverse genetic markers, several of these clades have been obtained, in one form or another, )] TJ ET BT 26.250 478.667 Td /F1 9.8 Tf [(by previous molecular studies \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 179.598 480.174 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 184.417 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 186.826 480.174 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 191.645 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 194.054 480.174 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 203.691 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 206.101 480.174 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 215.738 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 218.147 480.174 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 227.785 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 230.194 480.174 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 239.831 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 242.241 480.174 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 251.878 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 254.287 480.174 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 263.925 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 266.334 480.174 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 275.971 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 278.381 480.174 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 288.018 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 290.427 480.174 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 300.065 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 302.474 480.174 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 312.111 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 314.521 480.174 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 324.158 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 326.567 480.174 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 336.205 478.667 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 459.262 Td /F1 9.8 Tf [(A corollary of the increased resolution of percomorph relationships is the demise of the Smegmamorpharia )] TJ ET BT 487.932 459.262 Td /F5 9.8 Tf [(sensu)] TJ ET BT 513.945 459.262 Td /F1 9.8 Tf [( Johnson and )] TJ ET BT 26.250 447.357 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 67.980 448.865 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 72.799 447.357 Td /F1 9.8 Tf [( \(see also Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 200.143 448.865 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 204.962 447.357 Td /F1 9.8 Tf [(; Fig. 2\). Elements included in this supraordinal taxon are now scattered throughout )] TJ ET BT 26.250 435.453 Td /F1 9.8 Tf [(the molecular phylogeny, placed within many of the newly found clades with high bootstrap support. For example, the pygmy )] TJ ET BT 26.250 423.548 Td /F1 9.8 Tf [(sunfishes \()] TJ ET BT 73.391 423.548 Td /F5 9.8 Tf [(Elassoma)] TJ ET BT 116.194 423.548 Td /F1 9.8 Tf [(\) are back with the other sunfishes \(centrarchids\), as suggested by earlier classifications and recently )] TJ ET BT 26.250 411.643 Td /F1 9.8 Tf [(confirmed by molecules)] TJ ET 0.267 0.267 0.267 rg BT 128.654 413.150 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 138.292 411.643 Td /F1 9.8 Tf [(. Centrarchids plus elassomatids are placed here in the resurrected order Centrarchiformes \(within )] TJ ET BT 26.250 399.738 Td /F1 9.8 Tf [(Percomorpharia, Fig. 9\). Mugiliforms \(mullets\) and atherinomorphs \(silversides, needlefishes, halfbeaks, guppies and allies\) are )] TJ ET BT 26.250 387.834 Td /F1 9.8 Tf [(placed within Ovalentariae \(Fig. 8\). The swamp eels and spiny eels \(order Synbranchiformes, suborders Synbranchoidei and )] TJ ET BT 26.250 375.929 Td /F1 9.8 Tf [(Mastacembeloidei\) are placed with confidence in Anabantomorphariae \(Fig. 5\), together with armored sticklebacks )] TJ ET BT 26.250 364.024 Td /F1 9.8 Tf [(\(Indostomidae\), one of the 11 families previously included in the order Gasterosteiformes. The polyphyly of Gasterosteiformes )] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(\(another large clade assigned to Smegmamorpha\) was first pointed out by mitogenomic evidence)] TJ ET 0.267 0.267 0.267 rg BT 445.675 353.627 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 455.313 352.119 Td /F1 9.8 Tf [(. Our results place the )] TJ ET BT 26.250 340.215 Td /F1 9.8 Tf [(sticklebacks, tubesnouts and sand eels \(previously assigned to Gasterosteoidei\) in our newly defined Perciformes \(suborder )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(Cottioidei; Fig. 10\) and the rest of the families previously assigned to the suborder Syngnathoidei were relocated to our newly )] TJ ET BT 26.250 316.405 Td /F1 9.8 Tf [(defined order Syngnathiformes within the Scombrimorpharia \(Fig. 4, see below\).)] TJ ET BT 26.250 297.000 Td /F1 9.8 Tf [(Phylogenetic resolution within five newly discovered clades, however, will require additional study. Relationships within )] TJ ET BT 26.250 285.096 Td /F1 9.8 Tf [(Syngnathiformes, Scombriformes, Carangimorphariae, Ovalentariae, and Percomorpharia may be challenging to recover given )] TJ ET BT 26.250 273.191 Td /F1 9.8 Tf [(the rapid radiation and diversification of these clades.)] TJ ET BT 26.250 253.786 Td /F5 9.8 Tf [(Gobiomorpharia: sweepers are out )] TJ ET BT 179.062 253.786 Td /F5 9.8 Tf [(\(Fig. 3\))] TJ ET BT 26.250 234.381 Td /F1 9.8 Tf [(Based on a phylogeny estimated with four mitochondrial markers, Thacker)] TJ ET 0.267 0.267 0.267 rg BT 346.498 235.889 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 356.136 234.381 Td /F1 9.8 Tf [( resurrected the order Gobiiformes, to )] TJ ET BT 26.250 222.477 Td /F1 9.8 Tf [(accommodate three suborders: Gobioidei \(gobies and sleepers\), Kurtidoidei \(nurseryfish\), and Apogonoidei \(including )] TJ ET BT 26.250 210.572 Td /F1 9.8 Tf [(apogonids and pempherids\). Previous molecular studies have shown affinities between gobioids, apogonids, kurtids and, to )] TJ ET BT 26.250 198.667 Td /F1 9.8 Tf [(some extent, pempherids and dactylopterids)] TJ ET 0.267 0.267 0.267 rg BT 217.545 200.174 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 222.364 202.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 224.773 200.174 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 234.410 202.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 236.820 200.174 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 246.457 198.667 Td /F1 9.8 Tf [(. There is also morphological evidence supporting a close relationship )] TJ ET BT 26.250 186.762 Td /F1 9.8 Tf [(between gobids and apogonids)] TJ ET 0.267 0.267 0.267 rg BT 161.209 188.270 Td /F4 8.7 Tf [(108)] TJ ET 0.271 0.267 0.267 rg BT 175.666 190.651 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 178.075 188.270 Td /F4 8.7 Tf [(109)] TJ ET 0.271 0.267 0.267 rg BT 192.531 186.762 Td /F1 9.8 Tf [( as well as between kurtids and apogonids)] TJ ET 0.267 0.267 0.267 rg BT 375.704 188.270 Td /F4 8.7 Tf [(110)] TJ ET 0.271 0.267 0.267 rg BT 390.160 186.762 Td /F1 9.8 Tf [(. Our results provide partial support for the )] TJ ET BT 26.250 174.858 Td /F1 9.8 Tf [(Gobiiformes )] TJ ET BT 81.513 174.858 Td /F5 9.8 Tf [(sensu )] TJ ET BT 110.237 174.858 Td /F1 9.8 Tf [(Thacker)] TJ ET 0.267 0.267 0.267 rg BT 145.454 176.365 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 155.091 174.858 Td /F1 9.8 Tf [( but we treat it here as a supraordinal group \(Gobiomorpharia\). A major difference is that our )] TJ ET BT 26.250 162.953 Td /F1 9.8 Tf [(hypothesis segregates the family Pempheridae \(sweepers\) to its own order \(Pempheriformes, together with Glaucosomatidae\), )] TJ ET BT 26.250 151.048 Td /F1 9.8 Tf [(within Percomorpharia \(Figs. 1, 3, 9\).)] TJ ET 0.965 0.965 0.965 rg 26.250 -73.333 555.000 214.500 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 141.167 m 581.250 141.167 l 581.250 140.417 l 26.250 140.417 l f q 452.250 0 0 198.750 35.250 -67.333 cm /I5 Do Q q 35.250 -73.333 537.000 0.000 re W n Q Q q 15.000 -73.333 577.500 850.333 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 126.519 768.983 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 131.338 767.476 Td /F1 9.8 Tf [( included polymixiids, percopsids and crown acanthomorphs in their Euacanthopterygii, a taxon not )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(classified by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 164.427 757.079 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 169.246 755.571 Td /F1 9.8 Tf [(. We adopt the name but modify the circumscription to recognize a well-supported clade \(99% )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(bootstrap\) that includes beryciforms, holocentrids and percomorphs. The main issue at this level is delimitation of Beryciformes )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(and relationships of its proposed components to Percomorphaceae. Most classifications)] TJ ET 0.267 0.267 0.267 rg BT 405.038 733.269 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 409.856 735.650 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 412.266 733.269 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 417.084 731.762 Td /F1 9.8 Tf [( accept separate orders )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(Stephanoberyciformes and Beryciformes, each monophyletic and placed as successive sister-groups of the percomorphs. )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(Molecular data \(mitogenomic and smaller subsets of nuclear genes\), in contrast, have supported the inclusion of )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(Stephanoberyciformes in the same clade as Beryciformes)] TJ ET 0.267 0.267 0.267 rg BT 275.509 697.555 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 280.327 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 282.737 697.555 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 292.374 696.048 Td /F1 9.8 Tf [( and consistently include holocentrids within this clade. Our )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(results, however, reject this hypothesis in favor of recognizing a separate holocentrid clade \(proposed here as a new order, )] TJ ET BT 26.250 672.238 Td /F1 9.8 Tf [(Holocentriformes\) that is sister to percomorphs \(Fig. 1\), a result first obtained by Stiassny and Moore)] TJ ET 0.267 0.267 0.267 rg BT 459.735 673.745 Td /F4 8.7 Tf [(75)] TJ ET 0.271 0.267 0.267 rg BT 469.372 672.238 Td /F1 9.8 Tf [( and Moore )] TJ ET 0.267 0.267 0.267 rg BT 521.398 673.745 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 531.036 672.238 Td /F1 9.8 Tf [( but )] TJ ET BT 26.250 660.333 Td /F1 9.8 Tf [(subsequently challenged by Johnson and Patterson)] TJ ET 0.267 0.267 0.267 rg BT 249.544 661.841 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 254.363 660.333 Td /F1 9.8 Tf [(. Despite relatively low support for our holocentrid-percomorph clade \(57-)] TJ ET BT 26.250 648.429 Td /F1 9.8 Tf [(69% bootstrap\), proportionally more individual gene trees support this relationship \(47%\) relative to the alternative molecular )] TJ ET BT 26.250 636.524 Td /F1 9.8 Tf [(hypothesis uniting holocentrids with the remaining beryciform groups \(20%; Fig. 2\). Our new circumscription of Beryciformes is )] TJ ET BT 26.250 624.619 Td /F1 9.8 Tf [(also most similar to that of the order Trachichthyiformes described by Moore)] TJ ET 0.267 0.267 0.267 rg BT 354.611 626.126 Td /F4 8.7 Tf [(76)] TJ ET 0.271 0.267 0.267 rg BT 364.248 624.619 Td /F1 9.8 Tf [(, except that the latter excludes the berycids.)] TJ ET BT 26.250 605.214 Td /F5 9.8 Tf [(Percomorphaceae: no longer an unresolved bush \(Figs. 1-10\))] TJ ET BT 26.250 585.810 Td /F1 9.8 Tf [(A major contribution from our study has been the disambiguation of the percomorph bush into nine well-supported supraordinal )] TJ ET BT 26.250 573.905 Td /F1 9.8 Tf [(groups \(six Series and three Subseries; Fig. 1; )] TJ ET 0.267 0.267 0.267 rg BT 229.459 573.905 Td /F1 9.8 Tf [(Appendix 2)] TJ ET 0.271 0.267 0.267 rg BT 278.239 573.905 Td /F1 9.8 Tf [(\): Ophidiimorpharia, Batrachoidimorpharia, Gobiomorpharia \(Fig. 3\), )] TJ ET BT 26.250 562.000 Td /F1 9.8 Tf [(Scombrimorpharia \(Figs. 4 and 5\), Carangimorpharia \(with three Subseries: Anabantomorphariae, Fig. 6; Carangimorphariae, )] TJ ET BT 26.250 550.095 Td /F1 9.8 Tf [(Fig. 7; and Ovalentariae, Fig. 8\), and Percomorpharia \(Figs. 9\). Furthermore, increased phylogenetic resolution within )] TJ ET BT 26.250 538.191 Td /F1 9.8 Tf [(Percomorpharia allowed the definition of a monophyletic Perciformes \(Figs. 9 and 10\), for the first time recovered from a vast )] TJ ET BT 26.250 526.286 Td /F1 9.8 Tf [(taxonomic sample. With the exception of the cusk-eels \(Ophidiimorpharia\) and the toadfishes \(Batrachoidimorpharia\), whose )] TJ ET BT 26.250 514.381 Td /F1 9.8 Tf [(monophyly has been recognized in most classifications \(i.e., )] TJ ET 0.267 0.267 0.267 rg BT 287.979 515.888 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 292.798 518.269 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 295.207 515.888 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 300.026 514.381 Td /F1 9.8 Tf [(; but see )] TJ ET 0.267 0.267 0.267 rg BT 340.137 515.888 Td /F4 8.7 Tf [(106)] TJ ET 0.271 0.267 0.267 rg BT 354.593 518.269 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 357.003 515.888 Td /F4 8.7 Tf [(107)] TJ ET 0.271 0.267 0.267 rg BT 371.459 514.381 Td /F1 9.8 Tf [(\), the remaining seven supraordinal clades \(four )] TJ ET BT 26.250 502.476 Td /F1 9.8 Tf [(Series and three Subseries\) have never been discovered by examination of anatomical features. Under different combinations )] TJ ET BT 26.250 490.572 Td /F1 9.8 Tf [(of taxa, however, and based on diverse genetic markers, several of these clades have been obtained, in one form or another, )] TJ ET BT 26.250 478.667 Td /F1 9.8 Tf [(by previous molecular studies \(e.g.,)] TJ ET 0.267 0.267 0.267 rg BT 179.598 480.174 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 184.417 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 186.826 480.174 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 191.645 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 194.054 480.174 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 203.691 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 206.101 480.174 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 215.738 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 218.147 480.174 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 227.785 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 230.194 480.174 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 239.831 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 242.241 480.174 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 251.878 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 254.287 480.174 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 263.925 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 266.334 480.174 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 275.971 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 278.381 480.174 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 288.018 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 290.427 480.174 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 300.065 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 302.474 480.174 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 312.111 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 314.521 480.174 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 324.158 482.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 326.567 480.174 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 336.205 478.667 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 459.262 Td /F1 9.8 Tf [(A corollary of the increased resolution of percomorph relationships is the demise of the Smegmamorpharia )] TJ ET BT 487.932 459.262 Td /F5 9.8 Tf [(sensu)] TJ ET BT 513.945 459.262 Td /F1 9.8 Tf [( Johnson and )] TJ ET BT 26.250 447.357 Td /F1 9.8 Tf [(Patterson)] TJ ET 0.267 0.267 0.267 rg BT 67.980 448.865 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 72.799 447.357 Td /F1 9.8 Tf [( \(see also Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 200.143 448.865 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 204.962 447.357 Td /F1 9.8 Tf [(; Fig. 2\). Elements included in this supraordinal taxon are now scattered throughout )] TJ ET BT 26.250 435.453 Td /F1 9.8 Tf [(the molecular phylogeny, placed within many of the newly found clades with high bootstrap support. For example, the pygmy )] TJ ET BT 26.250 423.548 Td /F1 9.8 Tf [(sunfishes \()] TJ ET BT 73.391 423.548 Td /F5 9.8 Tf [(Elassoma)] TJ ET BT 116.194 423.548 Td /F1 9.8 Tf [(\) are back with the other sunfishes \(centrarchids\), as suggested by earlier classifications and recently )] TJ ET BT 26.250 411.643 Td /F1 9.8 Tf [(confirmed by molecules)] TJ ET 0.267 0.267 0.267 rg BT 128.654 413.150 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 138.292 411.643 Td /F1 9.8 Tf [(. Centrarchids plus elassomatids are placed here in the resurrected order Centrarchiformes \(within )] TJ ET BT 26.250 399.738 Td /F1 9.8 Tf [(Percomorpharia, Fig. 9\). Mugiliforms \(mullets\) and atherinomorphs \(silversides, needlefishes, halfbeaks, guppies and allies\) are )] TJ ET BT 26.250 387.834 Td /F1 9.8 Tf [(placed within Ovalentariae \(Fig. 8\). The swamp eels and spiny eels \(order Synbranchiformes, suborders Synbranchoidei and )] TJ ET BT 26.250 375.929 Td /F1 9.8 Tf [(Mastacembeloidei\) are placed with confidence in Anabantomorphariae \(Fig. 5\), together with armored sticklebacks )] TJ ET BT 26.250 364.024 Td /F1 9.8 Tf [(\(Indostomidae\), one of the 11 families previously included in the order Gasterosteiformes. The polyphyly of Gasterosteiformes )] TJ ET BT 26.250 352.119 Td /F1 9.8 Tf [(\(another large clade assigned to Smegmamorpha\) was first pointed out by mitogenomic evidence)] TJ ET 0.267 0.267 0.267 rg BT 445.675 353.627 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 455.313 352.119 Td /F1 9.8 Tf [(. Our results place the )] TJ ET BT 26.250 340.215 Td /F1 9.8 Tf [(sticklebacks, tubesnouts and sand eels \(previously assigned to Gasterosteoidei\) in our newly defined Perciformes \(suborder )] TJ ET BT 26.250 328.310 Td /F1 9.8 Tf [(Cottioidei; Fig. 10\) and the rest of the families previously assigned to the suborder Syngnathoidei were relocated to our newly )] TJ ET BT 26.250 316.405 Td /F1 9.8 Tf [(defined order Syngnathiformes within the Scombrimorpharia \(Fig. 4, see below\).)] TJ ET BT 26.250 297.000 Td /F1 9.8 Tf [(Phylogenetic resolution within five newly discovered clades, however, will require additional study. Relationships within )] TJ ET BT 26.250 285.096 Td /F1 9.8 Tf [(Syngnathiformes, Scombriformes, Carangimorphariae, Ovalentariae, and Percomorpharia may be challenging to recover given )] TJ ET BT 26.250 273.191 Td /F1 9.8 Tf [(the rapid radiation and diversification of these clades.)] TJ ET BT 26.250 253.786 Td /F5 9.8 Tf [(Gobiomorpharia: sweepers are out )] TJ ET BT 179.062 253.786 Td /F5 9.8 Tf [(\(Fig. 3\))] TJ ET BT 26.250 234.381 Td /F1 9.8 Tf [(Based on a phylogeny estimated with four mitochondrial markers, Thacker)] TJ ET 0.267 0.267 0.267 rg BT 346.498 235.889 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 356.136 234.381 Td /F1 9.8 Tf [( resurrected the order Gobiiformes, to )] TJ ET BT 26.250 222.477 Td /F1 9.8 Tf [(accommodate three suborders: Gobioidei \(gobies and sleepers\), Kurtidoidei \(nurseryfish\), and Apogonoidei \(including )] TJ ET BT 26.250 210.572 Td /F1 9.8 Tf [(apogonids and pempherids\). Previous molecular studies have shown affinities between gobioids, apogonids, kurtids and, to )] TJ ET BT 26.250 198.667 Td /F1 9.8 Tf [(some extent, pempherids and dactylopterids)] TJ ET 0.267 0.267 0.267 rg BT 217.545 200.174 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 222.364 202.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 224.773 200.174 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 234.410 202.555 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 236.820 200.174 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 246.457 198.667 Td /F1 9.8 Tf [(. There is also morphological evidence supporting a close relationship )] TJ ET BT 26.250 186.762 Td /F1 9.8 Tf [(between gobids and apogonids)] TJ ET 0.267 0.267 0.267 rg BT 161.209 188.270 Td /F4 8.7 Tf [(108)] TJ ET 0.271 0.267 0.267 rg BT 175.666 190.651 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 178.075 188.270 Td /F4 8.7 Tf [(109)] TJ ET 0.271 0.267 0.267 rg BT 192.531 186.762 Td /F1 9.8 Tf [( as well as between kurtids and apogonids)] TJ ET 0.267 0.267 0.267 rg BT 375.704 188.270 Td /F4 8.7 Tf [(110)] TJ ET 0.271 0.267 0.267 rg BT 390.160 186.762 Td /F1 9.8 Tf [(. Our results provide partial support for the )] TJ ET BT 26.250 174.858 Td /F1 9.8 Tf [(Gobiiformes )] TJ ET BT 81.513 174.858 Td /F5 9.8 Tf [(sensu )] TJ ET BT 110.237 174.858 Td /F1 9.8 Tf [(Thacker)] TJ ET 0.267 0.267 0.267 rg BT 145.454 176.365 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 155.091 174.858 Td /F1 9.8 Tf [( but we treat it here as a supraordinal group \(Gobiomorpharia\). A major difference is that our )] TJ ET BT 26.250 162.953 Td /F1 9.8 Tf [(hypothesis segregates the family Pempheridae \(sweepers\) to its own order \(Pempheriformes, together with Glaucosomatidae\), )] TJ ET BT 26.250 151.048 Td /F1 9.8 Tf [(within Percomorpharia \(Figs. 1, 3, 9\).)] TJ ET 0.965 0.965 0.965 rg 26.250 -73.333 555.000 214.500 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 141.167 m 581.250 141.167 l 581.250 140.417 l 26.250 140.417 l f q 452.250 0 0 198.750 35.250 -67.333 cm /I5 Do Q q 35.250 -73.333 537.000 0.000 re W n Q Q q 452.250 0 0 198.750 35.250 -67.333 cm /I5 Do Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(9)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 1467 0 obj << /Type /Annot /Subtype /Link /A 1468 0 R /Border [0 0 0] /H /I /Rect [ 126.5190 768.1817 131.3377 777.0000 ] >> endobj 1468 0 obj << /Type /Action >> endobj 1469 0 obj << /Type /Annot /Subtype /Link /A 1470 0 R /Border [0 0 0] 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John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 690.906 Td /F5 9.8 Tf [(Scombrimorpharia: sea horses and tunas are close relatives \(Figs. 1, 4 and 5\))] TJ ET BT 26.250 671.501 Td /F1 9.8 Tf [(One of the most unanticipated new percomorph clades is the Scombrimorpharia, grouping such disparate fishes as seahorses )] TJ ET BT 26.250 659.596 Td /F1 9.8 Tf [(and tunas. This clade includes the newly circumscribed orders Syngnathiformes \(Fig. 4\) and Scombriformes \(Fig. 5\). Not )] TJ ET BT 26.250 647.691 Td /F1 9.8 Tf [(surprisingly, a close relationship among taxa contained within this group, including syngnathids, mullids, callionymids, )] TJ ET BT 26.250 635.787 Td /F1 9.8 Tf [(dactylopterids, scombrids, stromateids, an others, has never been proposed on morphological grounds. The Syngnathiformes, )] TJ ET BT 26.250 623.882 Td /F1 9.8 Tf [(as defined here \(Fig. 4\), comprises mostly tropical marine reef-dwellers, traditionally placed in three distinct percomorph orders, )] TJ ET BT 26.250 611.977 Td /F1 9.8 Tf [(including Gasterosteiformes \(syngnathids\), Perciformes \(mullids and callionymids\) and Scorpaeniformes \(dactylopterids\). )] TJ ET BT 26.250 600.072 Td /F1 9.8 Tf [(Recent molecular studies have emphasized the non-monophyly of Scorpaeniformes)] TJ ET 0.267 0.267 0.267 rg BT 387.692 601.579 Td /F4 8.7 Tf [(74)] TJ ET 0.271 0.267 0.267 rg BT 397.330 600.072 Td /F1 9.8 Tf [(. We have noted above the dissolution of )] TJ ET BT 26.250 588.168 Td /F1 9.8 Tf [(Gasterosteiformes)] TJ ET 0.267 0.267 0.267 rg BT 105.898 589.675 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 115.535 588.168 Td /F1 9.8 Tf [( and, as discussed below, we provide a restricted definition for Perciformes that includes many )] TJ ET BT 26.250 576.263 Td /F1 9.8 Tf [(scorpaeniform taxa \(Fig. 10\).)] TJ ET 0.965 0.965 0.965 rg 26.250 237.811 555.000 328.571 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 566.382 m 581.250 566.382 l 581.250 565.632 l 26.250 565.632 l f 26.250 237.811 m 581.250 237.811 l 581.250 238.561 l 26.250 238.561 l f q 452.250 0 0 243.750 35.250 312.882 cm /I6 Do Q q 35.250 249.061 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 297.358 Td /F4 9.8 Tf [(Fig. 4: Detailed relationships among families of Syngnathiformes \(see also Fig. 1\).)] TJ ET BT 35.250 277.988 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined)] TJ ET BT 35.250 257.597 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 220.787 Td /F1 9.8 Tf [(Our new order Scombriformes \(Fig. 5\) includes most of the families previously grouped in the perciform suborder Scombroidei)] TJ ET 0.267 0.267 0.267 rg BT 568.633 222.295 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 26.250 208.883 Td /F1 9.8 Tf [(or the order Scombriformes)] TJ ET 0.267 0.267 0.267 rg BT 144.907 210.390 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 149.726 208.883 Td /F1 9.8 Tf [(, except for the barracudas \(Sphyraenidae\) and the billfishes and swordfishes \(here placed in their )] TJ ET BT 26.250 196.978 Td /F1 9.8 Tf [(own order, Istiophoriformes\). Sphyraenidae and Istiophoriformes are now firmly placed within Carangimorphariae \(Fig. 7\) )] TJ ET BT 26.250 185.073 Td /F1 9.8 Tf [(together with disparate taxa such as remoras \(Echeneidae\), archer fishes \(Toxotidae\), jacks \(Carangidae\), flatfishes )] TJ ET BT 26.250 173.168 Td /F1 9.8 Tf [(\(Pleuronectiformes\), and others \(see below\). Because billfishes and tunas are not closely related as previously suggested by )] TJ ET BT 26.250 161.264 Td /F1 9.8 Tf [(anatomical studies)] TJ ET 0.267 0.267 0.267 rg BT 106.990 162.771 Td /F4 8.7 Tf [(83)] TJ ET 0.271 0.267 0.267 rg BT 116.627 161.264 Td /F1 9.8 Tf [( \(Fig. 2\), the new hypothesis implies that endothermy has evolved at least twice independently in teleosts)] TJ ET 0.267 0.267 0.267 rg BT 26.250 150.866 Td /F4 8.7 Tf [(111)] TJ ET 0.271 0.267 0.267 rg BT 40.706 153.247 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 43.115 150.866 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 57.571 149.359 Td /F1 9.8 Tf [(. This new circumscription of Scombriformes also comprises families belonging to multiple orders in previous )] TJ ET BT 26.250 137.454 Td /F1 9.8 Tf [(classifications, such as Stromateiformes \(Centrolophidae, Nomeidae, Ariommatidae, Stromateidae\), Trachiniformes )] TJ ET BT 26.250 125.549 Td /F1 9.8 Tf [(\(Chiasmodontidae\), Icosteiformes \(Icosteidae\), and Perciformes \(Bramidae, Pomatomidae, and Caristiidae\). Despite the )] TJ ET BT 26.250 113.645 Td /F1 9.8 Tf [(disparate morphology among members of Scombriformes, most are offshore fishes that inhabit pelagic and/or deep-sea waters.)] TJ ET 0.965 0.965 0.965 rg 26.250 -319.236 555.000 423.000 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 103.764 m 581.250 103.764 l 581.250 103.014 l 26.250 103.014 l f q 452.250 0 0 407.250 35.250 -313.236 cm /I7 Do Q q 35.250 -319.236 537.000 0.000 re W n Q Q q 15.000 -319.236 577.500 1096.236 re W n 0.965 0.965 0.965 rg 26.250 707.929 555.000 69.071 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 707.929 m 581.250 707.929 l 581.250 708.679 l 26.250 708.679 l f q 35.250 719.179 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 3: Detailed relationships among orders and families of Gobiomorpharia \(see also Fig. 1\).)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined.)] TJ ET BT 35.250 727.715 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 690.906 Td /F5 9.8 Tf [(Scombrimorpharia: sea horses and tunas are close relatives \(Figs. 1, 4 and 5\))] TJ ET BT 26.250 671.501 Td /F1 9.8 Tf [(One of the most unanticipated new percomorph clades is the Scombrimorpharia, grouping such disparate fishes as seahorses )] TJ ET BT 26.250 659.596 Td /F1 9.8 Tf [(and tunas. This clade includes the newly circumscribed orders Syngnathiformes \(Fig. 4\) and Scombriformes \(Fig. 5\). Not )] TJ ET BT 26.250 647.691 Td /F1 9.8 Tf [(surprisingly, a close relationship among taxa contained within this group, including syngnathids, mullids, callionymids, )] TJ ET BT 26.250 635.787 Td /F1 9.8 Tf [(dactylopterids, scombrids, stromateids, an others, has never been proposed on morphological grounds. The Syngnathiformes, )] TJ ET BT 26.250 623.882 Td /F1 9.8 Tf [(as defined here \(Fig. 4\), comprises mostly tropical marine reef-dwellers, traditionally placed in three distinct percomorph orders, )] TJ ET BT 26.250 611.977 Td /F1 9.8 Tf [(including Gasterosteiformes \(syngnathids\), Perciformes \(mullids and callionymids\) and Scorpaeniformes \(dactylopterids\). )] TJ ET BT 26.250 600.072 Td /F1 9.8 Tf [(Recent molecular studies have emphasized the non-monophyly of Scorpaeniformes)] TJ ET 0.267 0.267 0.267 rg BT 387.692 601.579 Td /F4 8.7 Tf [(74)] TJ ET 0.271 0.267 0.267 rg BT 397.330 600.072 Td /F1 9.8 Tf [(. We have noted above the dissolution of )] TJ ET BT 26.250 588.168 Td /F1 9.8 Tf [(Gasterosteiformes)] TJ ET 0.267 0.267 0.267 rg BT 105.898 589.675 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 115.535 588.168 Td /F1 9.8 Tf [( and, as discussed below, we provide a restricted definition for Perciformes that includes many )] TJ ET BT 26.250 576.263 Td /F1 9.8 Tf [(scorpaeniform taxa \(Fig. 10\).)] TJ ET 0.965 0.965 0.965 rg 26.250 237.811 555.000 328.571 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 566.382 m 581.250 566.382 l 581.250 565.632 l 26.250 565.632 l f 26.250 237.811 m 581.250 237.811 l 581.250 238.561 l 26.250 238.561 l f q 452.250 0 0 243.750 35.250 312.882 cm /I6 Do Q q 35.250 249.061 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 297.358 Td /F4 9.8 Tf [(Fig. 4: Detailed relationships among families of Syngnathiformes \(see also Fig. 1\).)] TJ ET BT 35.250 277.988 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined)] TJ ET BT 35.250 257.597 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 220.787 Td /F1 9.8 Tf [(Our new order Scombriformes \(Fig. 5\) includes most of the families previously grouped in the perciform suborder Scombroidei)] TJ ET 0.267 0.267 0.267 rg BT 568.633 222.295 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 26.250 208.883 Td /F1 9.8 Tf [(or the order Scombriformes)] TJ ET 0.267 0.267 0.267 rg BT 144.907 210.390 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 149.726 208.883 Td /F1 9.8 Tf [(, except for the barracudas \(Sphyraenidae\) and the billfishes and swordfishes \(here placed in their )] TJ ET BT 26.250 196.978 Td /F1 9.8 Tf [(own order, Istiophoriformes\). Sphyraenidae and Istiophoriformes are now firmly placed within Carangimorphariae \(Fig. 7\) )] TJ ET BT 26.250 185.073 Td /F1 9.8 Tf [(together with disparate taxa such as remoras \(Echeneidae\), archer fishes \(Toxotidae\), jacks \(Carangidae\), flatfishes )] TJ ET BT 26.250 173.168 Td /F1 9.8 Tf [(\(Pleuronectiformes\), and others \(see below\). Because billfishes and tunas are not closely related as previously suggested by )] TJ ET BT 26.250 161.264 Td /F1 9.8 Tf [(anatomical studies)] TJ ET 0.267 0.267 0.267 rg BT 106.990 162.771 Td /F4 8.7 Tf [(83)] TJ ET 0.271 0.267 0.267 rg BT 116.627 161.264 Td /F1 9.8 Tf [( \(Fig. 2\), the new hypothesis implies that endothermy has evolved at least twice independently in teleosts)] TJ ET 0.267 0.267 0.267 rg BT 26.250 150.866 Td /F4 8.7 Tf [(111)] TJ ET 0.271 0.267 0.267 rg BT 40.706 153.247 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 43.115 150.866 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 57.571 149.359 Td /F1 9.8 Tf [(. This new circumscription of Scombriformes also comprises families belonging to multiple orders in previous )] TJ ET BT 26.250 137.454 Td /F1 9.8 Tf [(classifications, such as Stromateiformes \(Centrolophidae, Nomeidae, Ariommatidae, Stromateidae\), Trachiniformes )] TJ ET BT 26.250 125.549 Td /F1 9.8 Tf [(\(Chiasmodontidae\), Icosteiformes \(Icosteidae\), and Perciformes \(Bramidae, Pomatomidae, and Caristiidae\). Despite the )] TJ ET BT 26.250 113.645 Td /F1 9.8 Tf [(disparate morphology among members of Scombriformes, most are offshore fishes that inhabit pelagic and/or deep-sea waters.)] TJ ET 0.965 0.965 0.965 rg 26.250 -319.236 555.000 423.000 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 103.764 m 581.250 103.764 l 581.250 103.014 l 26.250 103.014 l f q 452.250 0 0 407.250 35.250 -313.236 cm /I7 Do Q q 35.250 -319.236 537.000 0.000 re W n Q Q q 15.000 -319.236 577.500 1096.236 re W n 0.965 0.965 0.965 rg 26.250 707.929 555.000 69.071 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 707.929 m 581.250 707.929 l 581.250 708.679 l 26.250 708.679 l f q 35.250 719.179 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 3: Detailed relationships among orders and families of Gobiomorpharia \(see also Fig. 1\).)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined.)] TJ ET BT 35.250 727.715 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 690.906 Td /F5 9.8 Tf [(Scombrimorpharia: sea horses and tunas are close relatives \(Figs. 1, 4 and 5\))] TJ ET BT 26.250 671.501 Td /F1 9.8 Tf [(One of the most unanticipated new percomorph clades is the Scombrimorpharia, grouping such disparate fishes as seahorses )] TJ ET BT 26.250 659.596 Td /F1 9.8 Tf [(and tunas. This clade includes the newly circumscribed orders Syngnathiformes \(Fig. 4\) and Scombriformes \(Fig. 5\). Not )] TJ ET BT 26.250 647.691 Td /F1 9.8 Tf [(surprisingly, a close relationship among taxa contained within this group, including syngnathids, mullids, callionymids, )] TJ ET BT 26.250 635.787 Td /F1 9.8 Tf [(dactylopterids, scombrids, stromateids, an others, has never been proposed on morphological grounds. The Syngnathiformes, )] TJ ET BT 26.250 623.882 Td /F1 9.8 Tf [(as defined here \(Fig. 4\), comprises mostly tropical marine reef-dwellers, traditionally placed in three distinct percomorph orders, )] TJ ET BT 26.250 611.977 Td /F1 9.8 Tf [(including Gasterosteiformes \(syngnathids\), Perciformes \(mullids and callionymids\) and Scorpaeniformes \(dactylopterids\). )] TJ ET BT 26.250 600.072 Td /F1 9.8 Tf [(Recent molecular studies have emphasized the non-monophyly of Scorpaeniformes)] TJ ET 0.267 0.267 0.267 rg BT 387.692 601.579 Td /F4 8.7 Tf [(74)] TJ ET 0.271 0.267 0.267 rg BT 397.330 600.072 Td /F1 9.8 Tf [(. We have noted above the dissolution of )] TJ ET BT 26.250 588.168 Td /F1 9.8 Tf [(Gasterosteiformes)] TJ ET 0.267 0.267 0.267 rg BT 105.898 589.675 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 115.535 588.168 Td /F1 9.8 Tf [( and, as discussed below, we provide a restricted definition for Perciformes that includes many )] TJ ET BT 26.250 576.263 Td /F1 9.8 Tf [(scorpaeniform taxa \(Fig. 10\).)] TJ ET 0.965 0.965 0.965 rg 26.250 237.811 555.000 328.571 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 566.382 m 581.250 566.382 l 581.250 565.632 l 26.250 565.632 l f 26.250 237.811 m 581.250 237.811 l 581.250 238.561 l 26.250 238.561 l f q 452.250 0 0 243.750 35.250 312.882 cm /I6 Do Q q 35.250 249.061 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 297.358 Td /F4 9.8 Tf [(Fig. 4: Detailed relationships among families of Syngnathiformes \(see also Fig. 1\).)] TJ ET BT 35.250 277.988 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined)] TJ ET BT 35.250 257.597 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 220.787 Td /F1 9.8 Tf [(Our new order Scombriformes \(Fig. 5\) includes most of the families previously grouped in the perciform suborder Scombroidei)] TJ ET 0.267 0.267 0.267 rg BT 568.633 222.295 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 26.250 208.883 Td /F1 9.8 Tf [(or the order Scombriformes)] TJ ET 0.267 0.267 0.267 rg BT 144.907 210.390 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 149.726 208.883 Td /F1 9.8 Tf [(, except for the barracudas \(Sphyraenidae\) and the billfishes and swordfishes \(here placed in their )] TJ ET BT 26.250 196.978 Td /F1 9.8 Tf [(own order, Istiophoriformes\). Sphyraenidae and Istiophoriformes are now firmly placed within Carangimorphariae \(Fig. 7\) )] TJ ET BT 26.250 185.073 Td /F1 9.8 Tf [(together with disparate taxa such as remoras \(Echeneidae\), archer fishes \(Toxotidae\), jacks \(Carangidae\), flatfishes )] TJ ET BT 26.250 173.168 Td /F1 9.8 Tf [(\(Pleuronectiformes\), and others \(see below\). Because billfishes and tunas are not closely related as previously suggested by )] TJ ET BT 26.250 161.264 Td /F1 9.8 Tf [(anatomical studies)] TJ ET 0.267 0.267 0.267 rg BT 106.990 162.771 Td /F4 8.7 Tf [(83)] TJ ET 0.271 0.267 0.267 rg BT 116.627 161.264 Td /F1 9.8 Tf [( \(Fig. 2\), the new hypothesis implies that endothermy has evolved at least twice independently in teleosts)] TJ ET 0.267 0.267 0.267 rg BT 26.250 150.866 Td /F4 8.7 Tf [(111)] TJ ET 0.271 0.267 0.267 rg BT 40.706 153.247 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 43.115 150.866 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 57.571 149.359 Td /F1 9.8 Tf [(. This new circumscription of Scombriformes also comprises families belonging to multiple orders in previous )] TJ ET BT 26.250 137.454 Td /F1 9.8 Tf [(classifications, such as Stromateiformes \(Centrolophidae, Nomeidae, Ariommatidae, Stromateidae\), Trachiniformes )] TJ ET BT 26.250 125.549 Td /F1 9.8 Tf [(\(Chiasmodontidae\), Icosteiformes \(Icosteidae\), and Perciformes \(Bramidae, Pomatomidae, and Caristiidae\). Despite the )] TJ ET BT 26.250 113.645 Td /F1 9.8 Tf [(disparate morphology among members of Scombriformes, most are offshore fishes that inhabit pelagic and/or deep-sea waters.)] TJ ET 0.965 0.965 0.965 rg 26.250 -319.236 555.000 423.000 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 103.764 m 581.250 103.764 l 581.250 103.014 l 26.250 103.014 l f q 452.250 0 0 407.250 35.250 -313.236 cm /I7 Do Q q 35.250 -319.236 537.000 0.000 re W n Q Q q 452.250 0 0 243.750 35.250 312.882 cm /I6 Do Q q 452.250 0 0 407.250 35.250 -313.236 cm /I7 Do Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(10)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 1722 0 obj << /Type /Annot /Subtype /Link /A 1723 0 R /Border [0 0 0] /H /I /Rect [ 387.6923 600.7778 397.3296 609.5961 ] >> endobj 1723 0 obj << /Type /Action >> endobj 1724 0 obj << /Type /Annot /Subtype /Link /A 1725 0 R /Border [0 0 0] /H /I /Rect [ 105.8978 588.8731 115.5351 597.6914 ] >> endobj 1725 0 obj << /Type /Action >> endobj 1726 0 obj << /Type /Annot /Subtype /Link /A 1727 0 R /Border [0 0 0] /H /I /Rect [ 35.2500 312.8819 487.5000 556.6319 ] >> endobj 1727 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/03/Fig3_Syngnathiformes1.jpg) >> endobj 1728 0 obj << /Type /XObject /Subtype /Image /Width 603 /Height 325 /ColorSpace /DeviceRGB /Filter /DCTDecode /BitsPerComponent 8 /Length 47847>> stream JFIF;CREATOR: gd-jpeg v1.0 (using IJG JPEG v62), quality = 90 C     C   E[" }!1AQa"q2#BR$3br %&'()*456789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz w!1AQaq"2B #3Rbr $4%&'()*56789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz ?Q(Ҁ \RgF~QF}QGF}QaF}QaF}(ϰ3?J(>Œ 1F(ϰg7=/ᇅ]⻞][YGl=1kDtp׵-'.ZYXt:- mA&Bh_'𘞡jw_ }sH*MYFU0=AErNk\ؼlYՠ{14\~]V';0Q7hx_PE"ڵ^y"]l|m{dۖvi[UL_NA=ͭ%cME `<U_.c_([V9G2[;r#1ڀyxI4̐URS;D9;H eGi?|Ft?I𭾤drj:ex'a> ϴ,d&x;]ɪ|f%n^O)$ż 1\ܜc4PZ\F K[;ܢ |x<7 S+ZmROV9HdoѰUD4d9A^CƟoJѯ.-<-og7Ś_4ԯRo-V]=Ϗ< yg}iqO]} < Y..2O"þIO=jV৽o*kW7-N?,+ܰJ`(KmwU5o xY.dIbuE+4$W׉?<;\:gŸ[OrKTkK*?&'[%y/4ULOG4ULO@A%  ֱEy/4ULOG4ULO@Ey/4ULOG4ULO@Ey/4ULOG4ULO@1^K kD kDQ^K kD kDQoѴk@< rSm[^ NI7 wW:`h[n\L3 w~|V Ou8. nS!2HGG 'З?5ϡ4k3/'#HÍI^@OSY㇊?hSyƁZHZM/ n*G,?j&q5r57*wt*+'<'./,cҦYu A'<ܤza=$:N=۽cyXF#%Og{5_隧#[SKm6hhH}*YT,ٔRESi&-6[Wkf .[)N6܆3R F|Q^1Mjwh~mo.,"X.n'ӣb|ۄaiCneUXeO17֫麞siz=Q^4]Ip|[%d1^ڂ/^TԶR[T97[²@gƪ]3rgÿSjFiͶG3'k +lDَ].Wr Pk*/4BJ/xnTx<ƒ LjƢ K8gkMY(/!w9(L:63F~g@?JI&x:}W7DWб*FIz㚿My]fyP03Pӭq4׼W vZՎ$@>9X\oث0Ҝn'(xxF}ImlOyF Kp#[ѿ!5}q_ w5;(]f͎e#^Xd }9jL{Rڌ{Pcڌ{Rڌ{Pcڌ{Rڌ{Pcڗcڌ{Pcڌ{Rڌ{PjL{Rڌ{Pcڌ{Rڌ{Pcڌ{Rڌ{Pcڗcڌ{Pcڌ{Rڌ{PjL{Rڌ{Pcڌ{Rڌ{PceBu5;AI$c&k_x[JЬImtYf )r1I5Qj1Ij\{QjL{Rڌ{W?C&7wO*pGvULdAjL{W: Mq|t0kUV W-FgNQPGj1\<- -:MslYq'FSFu ~~Eu${V}tE]vwMG?qI,={'S??#{|BҁMsf/xOIY5K?(;T'bd/N#卽gO?>!DǦ 3H>";6v/'X4F{v' b3'%~h냕`J'‘:wE fӼ?whX^ۥ[6H,P$3-OȮp[*s?gmS\n5nc]R=ru[H`,an@A%>?f]rR7)}nɄ5ͱuMW&`X 嘂 ${?ϊgqAjm㘪CI2 Iwk3^ |vk:=2m[UHԤl1Q$"+O) }tM?94fc]Z&74KYB)mz\Z^|޿CO67=ơ5_rn@e!lѓ_'O>kYryS_e?7 ױC&̱J0ӒIHVFM|Vm~Sz}XbI\ƣR~Dψ&?^.89տ;Ͱ0޲#w&kQ|bȲ<=HEccPx3ZӏWK$0?+ϲy4fuƫ?MR$?iioֹGm[?k6_s[LWK Y?3\IlCu{F[㷈uy\*.k9_u<~yqMssK͸lxO)Ng#\Q_ 9?k{ڞ<Λx}8;Qie|%9^UQƈt+|yVv* ixG/{,}?7PӲ?9E5 )s~uLt>4uEz&/fWs\S]4ાL;"?ҾhK_O(.tԥ^d"F۷/"ADZƊ/]ɿƫm_# 9R+iHǯfƼI$6}2k='\ѾB.,IoG jRip7ڻު1jO2vor+sdɠ{?#L[|?[\FŘKe n 鵾TFK`=IjK3񵦆qo 0۱! ؕ\܀ @=w4fTej0&:RMeŧfyZ hQy@,'~Ӻf:n4;(E>IF<ei2ͺS>@,Q=4dןK㧄mk W6dbdef aGUSrG9V]J =”sK#-ی ÆS0Em$3jnC[!0sA+~hzT"I0D,(#>2hL2hhɣ&L2hh2hɠ&Z)2hɠ&o/M-䟲a?? 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Tf [(Fig. 5: Detailed relationships among families of Scombriformes \(see also Fig. 1\).)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined.)] TJ ET BT 35.250 727.715 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 690.906 Td /F5 9.8 Tf [(Anabantomorphariae: freshwater and air breathing \(Fig. 6\))] TJ ET BT 26.250 671.501 Td /F1 9.8 Tf [(Another major percomorph group proposed here is the series Carangimorpharia, including three subseries: )] TJ ET BT 26.250 659.596 Td /F1 9.8 Tf [(Anabantomorphariae, Carangimorphariae, and Ovalentariae \(Fig. 1\). Species in Anabantomorphariae include representatives )] TJ ET BT 26.250 647.691 Td /F1 9.8 Tf [(placed in three separate orders by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 259.275 649.198 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 264.094 647.691 Td /F1 9.8 Tf [(: Synbranchiformes \(swamp eels\), Gasterosteiformes \()] TJ ET BT 499.780 647.691 Td /F5 9.8 Tf [(Indostomus, )] TJ ET BT 555.599 647.691 Td /F1 9.8 Tf [(the )] TJ ET BT 26.250 635.787 Td /F1 9.8 Tf [(armored stickleback\), and Anabantiformes \(gouramis\) \(Fig. 6\). While the first two orders belonged to the Smegmamorpharia)] TJ ET 0.267 0.267 0.267 rg BT 559.975 637.294 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 564.793 639.675 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 567.203 637.294 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 572.021 635.787 Td /F1 9.8 Tf [(, )] TJ ET BT 26.250 623.882 Td /F1 9.8 Tf [(the Anabantiformes were placed as )] TJ ET BT 181.782 623.882 Td /F5 9.8 Tf [(incertae sedis )] TJ ET BT 244.640 623.882 Td /F1 9.8 Tf [(in Percomorphacea)] TJ ET 0.267 0.267 0.267 rg BT 329.173 625.389 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 333.991 623.882 Td /F1 9.8 Tf [(. The monophyly of Anabantomorphariae has also been )] TJ ET BT 26.250 611.977 Td /F1 9.8 Tf [(supported on the basis of mitogenomics)] TJ ET 0.267 0.267 0.267 rg BT 198.581 613.484 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 203.400 615.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 205.809 613.484 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 215.447 615.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 217.856 613.484 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 227.493 611.977 Td /F1 9.8 Tf [( and nuclear markers)] TJ ET 0.267 0.267 0.267 rg BT 319.065 613.484 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 328.703 611.977 Td /F1 9.8 Tf [(. A remarkable condition shared by members of this novel )] TJ ET BT 26.250 600.072 Td /F1 9.8 Tf [(grouping is their mostly freshwater origin and restriction to Africa and South East Asia \(although some members in the family )] TJ ET BT 26.250 588.168 Td /F1 9.8 Tf [(Synbranchidae occur in Mexico, and Central and South America\). Most are able to occupy marginal, stagnant waters due to )] TJ ET BT 26.250 576.263 Td /F1 9.8 Tf [(their capacity to tolerate anoxia and to obtain oxygen directly from the air. Anabantiforms have a suprabranchial organ and )] TJ ET BT 26.250 564.358 Td /F1 9.8 Tf [(synbranchids have suprabranchial pouches with respiratory function.)] TJ ET 0.965 0.965 0.965 rg 26.250 258.157 555.000 296.321 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 554.477 m 581.250 554.477 l 581.250 553.727 l 26.250 553.727 l f 26.250 258.157 m 581.250 258.157 l 581.250 258.907 l 26.250 258.907 l f q 452.250 0 0 211.500 35.250 333.227 cm /I8 Do Q q 35.250 269.407 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 317.703 Td /F4 9.8 Tf [(Fig. 6: Detailed relationships among orders and families of Anabantomorphariae \(see also Fig. 1\).)] TJ ET BT 35.250 298.333 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined.)] TJ ET BT 35.250 277.942 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 241.133 Td /F5 9.8 Tf [(Carangimorphariae: flatfishes and unlikely relatives \(Fig. 7\))] TJ ET BT 26.250 221.728 Td /F1 9.8 Tf [(A close affinity between other seemingly disparate groups, including barracudas, swordfishes, jacks, flatfishes, and others, has )] TJ ET BT 26.250 209.823 Td /F1 9.8 Tf [(been well established by recent molecular studies)] TJ ET 0.267 0.267 0.267 rg BT 240.838 211.330 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 250.475 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 252.884 211.330 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 262.522 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 264.931 211.330 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 274.568 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 276.978 211.330 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 286.615 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 289.024 211.330 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 298.662 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 301.071 211.330 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 310.708 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 313.118 211.330 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 327.574 209.823 Td /F1 9.8 Tf [( \(Fig. 7\). This higher-level group has been referred to as )] TJ ET BT 26.250 197.918 Td /F1 9.8 Tf [(clade L sensu Chen et al.)] TJ ET 0.267 0.267 0.267 rg BT 144.927 199.426 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 154.564 197.918 Td /F1 9.8 Tf [( or Carangimorpha by Li et al.)] TJ ET 0.267 0.267 0.267 rg BT 282.991 199.426 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 292.629 197.918 Td /F1 9.8 Tf [( \(see also)] TJ ET 0.267 0.267 0.267 rg BT 334.895 199.426 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 344.532 201.807 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 346.942 199.426 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 356.579 197.918 Td /F1 9.8 Tf [(\). In looking for possible anatomical )] TJ ET BT 26.250 186.014 Td /F1 9.8 Tf [(synapomorphies uniting flatfishes, billfishes, and carangids, Little et al.)] TJ ET 0.267 0.267 0.267 rg BT 329.719 187.521 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 344.175 186.014 Td /F1 9.8 Tf [( found that most taxa share a relatively low number of )] TJ ET BT 26.250 174.109 Td /F1 9.8 Tf [(vertebrae, have multiple dorsal pterygiophores inserting before the second neural spine, and lack supraneurals, among others. )] TJ ET BT 26.250 162.204 Td /F1 9.8 Tf [(However, according to Friedman)] TJ ET 0.267 0.267 0.267 rg BT 167.128 163.711 Td /F4 8.7 Tf [(113)] TJ ET 0.271 0.267 0.267 rg BT 181.584 162.204 Td /F1 9.8 Tf [(, some of these characters are symplesiomorphies while others are absent in the remaining )] TJ ET BT 26.250 150.299 Td /F1 9.8 Tf [(carangimorph groups. It thus seems paradoxical that despite the apparent lack of morphological synapomorphies for )] TJ ET BT 26.250 138.395 Td /F1 9.8 Tf [(carangimorphs there is a strong molecular signal supporting their monophyly, whereas the opposite is true for pleuronectiforms)] TJ ET 0.267 0.267 0.267 rg BT 26.250 127.997 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 35.887 126.490 Td /F1 9.8 Tf [(. For additional insights and discussion on Carangimorphariae we refer the reader to recent studies)] TJ ET 0.267 0.267 0.267 rg BT 462.362 127.997 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 471.999 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 474.409 127.997 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 484.046 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 486.455 127.997 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 496.093 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 498.502 127.997 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 512.958 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 515.367 127.997 Td /F4 8.7 Tf [(113)] TJ ET 0.271 0.267 0.267 rg BT 529.823 126.490 Td /F1 9.8 Tf [(.)] TJ ET 0.965 0.965 0.965 rg 26.250 -351.391 555.000 468.000 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 116.609 m 581.250 116.609 l 581.250 115.859 l 26.250 115.859 l f q 372.750 0 0 452.250 35.250 -345.391 cm /I9 Do Q q 35.250 -351.391 537.000 0.000 re W n Q Q q 15.000 -351.391 577.500 1128.391 re W n 0.965 0.965 0.965 rg 26.250 707.929 555.000 69.071 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 707.929 m 581.250 707.929 l 581.250 708.679 l 26.250 708.679 l f q 35.250 719.179 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 5: Detailed relationships among families of Scombriformes \(see also Fig. 1\).)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined.)] TJ ET BT 35.250 727.715 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 690.906 Td /F5 9.8 Tf [(Anabantomorphariae: freshwater and air breathing \(Fig. 6\))] TJ ET BT 26.250 671.501 Td /F1 9.8 Tf [(Another major percomorph group proposed here is the series Carangimorpharia, including three subseries: )] TJ ET BT 26.250 659.596 Td /F1 9.8 Tf [(Anabantomorphariae, Carangimorphariae, and Ovalentariae \(Fig. 1\). Species in Anabantomorphariae include representatives )] TJ ET BT 26.250 647.691 Td /F1 9.8 Tf [(placed in three separate orders by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 259.275 649.198 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 264.094 647.691 Td /F1 9.8 Tf [(: Synbranchiformes \(swamp eels\), Gasterosteiformes \()] TJ ET BT 499.780 647.691 Td /F5 9.8 Tf [(Indostomus, )] TJ ET BT 555.599 647.691 Td /F1 9.8 Tf [(the )] TJ ET BT 26.250 635.787 Td /F1 9.8 Tf [(armored stickleback\), and Anabantiformes \(gouramis\) \(Fig. 6\). While the first two orders belonged to the Smegmamorpharia)] TJ ET 0.267 0.267 0.267 rg BT 559.975 637.294 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 564.793 639.675 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 567.203 637.294 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 572.021 635.787 Td /F1 9.8 Tf [(, )] TJ ET BT 26.250 623.882 Td /F1 9.8 Tf [(the Anabantiformes were placed as )] TJ ET BT 181.782 623.882 Td /F5 9.8 Tf [(incertae sedis )] TJ ET BT 244.640 623.882 Td /F1 9.8 Tf [(in Percomorphacea)] TJ ET 0.267 0.267 0.267 rg BT 329.173 625.389 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 333.991 623.882 Td /F1 9.8 Tf [(. The monophyly of Anabantomorphariae has also been )] TJ ET BT 26.250 611.977 Td /F1 9.8 Tf [(supported on the basis of mitogenomics)] TJ ET 0.267 0.267 0.267 rg BT 198.581 613.484 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 203.400 615.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 205.809 613.484 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 215.447 615.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 217.856 613.484 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 227.493 611.977 Td /F1 9.8 Tf [( and nuclear markers)] TJ ET 0.267 0.267 0.267 rg BT 319.065 613.484 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 328.703 611.977 Td /F1 9.8 Tf [(. A remarkable condition shared by members of this novel )] TJ ET BT 26.250 600.072 Td /F1 9.8 Tf [(grouping is their mostly freshwater origin and restriction to Africa and South East Asia \(although some members in the family )] TJ ET BT 26.250 588.168 Td /F1 9.8 Tf [(Synbranchidae occur in Mexico, and Central and South America\). Most are able to occupy marginal, stagnant waters due to )] TJ ET BT 26.250 576.263 Td /F1 9.8 Tf [(their capacity to tolerate anoxia and to obtain oxygen directly from the air. Anabantiforms have a suprabranchial organ and )] TJ ET BT 26.250 564.358 Td /F1 9.8 Tf [(synbranchids have suprabranchial pouches with respiratory function.)] TJ ET 0.965 0.965 0.965 rg 26.250 258.157 555.000 296.321 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 554.477 m 581.250 554.477 l 581.250 553.727 l 26.250 553.727 l f 26.250 258.157 m 581.250 258.157 l 581.250 258.907 l 26.250 258.907 l f q 452.250 0 0 211.500 35.250 333.227 cm /I8 Do Q q 35.250 269.407 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 317.703 Td /F4 9.8 Tf [(Fig. 6: Detailed relationships among orders and families of Anabantomorphariae \(see also Fig. 1\).)] TJ ET BT 35.250 298.333 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined.)] TJ ET BT 35.250 277.942 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 241.133 Td /F5 9.8 Tf [(Carangimorphariae: flatfishes and unlikely relatives \(Fig. 7\))] TJ ET BT 26.250 221.728 Td /F1 9.8 Tf [(A close affinity between other seemingly disparate groups, including barracudas, swordfishes, jacks, flatfishes, and others, has )] TJ ET BT 26.250 209.823 Td /F1 9.8 Tf [(been well established by recent molecular studies)] TJ ET 0.267 0.267 0.267 rg BT 240.838 211.330 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 250.475 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 252.884 211.330 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 262.522 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 264.931 211.330 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 274.568 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 276.978 211.330 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 286.615 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 289.024 211.330 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 298.662 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 301.071 211.330 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 310.708 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 313.118 211.330 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 327.574 209.823 Td /F1 9.8 Tf [( \(Fig. 7\). This higher-level group has been referred to as )] TJ ET BT 26.250 197.918 Td /F1 9.8 Tf [(clade L sensu Chen et al.)] TJ ET 0.267 0.267 0.267 rg BT 144.927 199.426 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 154.564 197.918 Td /F1 9.8 Tf [( or Carangimorpha by Li et al.)] TJ ET 0.267 0.267 0.267 rg BT 282.991 199.426 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 292.629 197.918 Td /F1 9.8 Tf [( \(see also)] TJ ET 0.267 0.267 0.267 rg BT 334.895 199.426 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 344.532 201.807 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 346.942 199.426 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 356.579 197.918 Td /F1 9.8 Tf [(\). In looking for possible anatomical )] TJ ET BT 26.250 186.014 Td /F1 9.8 Tf [(synapomorphies uniting flatfishes, billfishes, and carangids, Little et al.)] TJ ET 0.267 0.267 0.267 rg BT 329.719 187.521 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 344.175 186.014 Td /F1 9.8 Tf [( found that most taxa share a relatively low number of )] TJ ET BT 26.250 174.109 Td /F1 9.8 Tf [(vertebrae, have multiple dorsal pterygiophores inserting before the second neural spine, and lack supraneurals, among others. )] TJ ET BT 26.250 162.204 Td /F1 9.8 Tf [(However, according to Friedman)] TJ ET 0.267 0.267 0.267 rg BT 167.128 163.711 Td /F4 8.7 Tf [(113)] TJ ET 0.271 0.267 0.267 rg BT 181.584 162.204 Td /F1 9.8 Tf [(, some of these characters are symplesiomorphies while others are absent in the remaining )] TJ ET BT 26.250 150.299 Td /F1 9.8 Tf [(carangimorph groups. It thus seems paradoxical that despite the apparent lack of morphological synapomorphies for )] TJ ET BT 26.250 138.395 Td /F1 9.8 Tf [(carangimorphs there is a strong molecular signal supporting their monophyly, whereas the opposite is true for pleuronectiforms)] TJ ET 0.267 0.267 0.267 rg BT 26.250 127.997 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 35.887 126.490 Td /F1 9.8 Tf [(. For additional insights and discussion on Carangimorphariae we refer the reader to recent studies)] TJ ET 0.267 0.267 0.267 rg BT 462.362 127.997 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 471.999 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 474.409 127.997 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 484.046 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 486.455 127.997 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 496.093 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 498.502 127.997 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 512.958 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 515.367 127.997 Td /F4 8.7 Tf [(113)] TJ ET 0.271 0.267 0.267 rg BT 529.823 126.490 Td /F1 9.8 Tf [(.)] TJ ET 0.965 0.965 0.965 rg 26.250 -351.391 555.000 468.000 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 116.609 m 581.250 116.609 l 581.250 115.859 l 26.250 115.859 l f q 372.750 0 0 452.250 35.250 -345.391 cm /I9 Do Q q 35.250 -351.391 537.000 0.000 re W n Q Q q 15.000 -351.391 577.500 1128.391 re W n 0.965 0.965 0.965 rg 26.250 707.929 555.000 69.071 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 707.929 m 581.250 707.929 l 581.250 708.679 l 26.250 708.679 l f q 35.250 719.179 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 5: Detailed relationships among families of Scombriformes \(see also Fig. 1\).)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined.)] TJ ET BT 35.250 727.715 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 690.906 Td /F5 9.8 Tf [(Anabantomorphariae: freshwater and air breathing \(Fig. 6\))] TJ ET BT 26.250 671.501 Td /F1 9.8 Tf [(Another major percomorph group proposed here is the series Carangimorpharia, including three subseries: )] TJ ET BT 26.250 659.596 Td /F1 9.8 Tf [(Anabantomorphariae, Carangimorphariae, and Ovalentariae \(Fig. 1\). Species in Anabantomorphariae include representatives )] TJ ET BT 26.250 647.691 Td /F1 9.8 Tf [(placed in three separate orders by Wiley and Johnson)] TJ ET 0.267 0.267 0.267 rg BT 259.275 649.198 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 264.094 647.691 Td /F1 9.8 Tf [(: Synbranchiformes \(swamp eels\), Gasterosteiformes \()] TJ ET BT 499.780 647.691 Td /F5 9.8 Tf [(Indostomus, )] TJ ET BT 555.599 647.691 Td /F1 9.8 Tf [(the )] TJ ET BT 26.250 635.787 Td /F1 9.8 Tf [(armored stickleback\), and Anabantiformes \(gouramis\) \(Fig. 6\). While the first two orders belonged to the Smegmamorpharia)] TJ ET 0.267 0.267 0.267 rg BT 559.975 637.294 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 564.793 639.675 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 567.203 637.294 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 572.021 635.787 Td /F1 9.8 Tf [(, )] TJ ET BT 26.250 623.882 Td /F1 9.8 Tf [(the Anabantiformes were placed as )] TJ ET BT 181.782 623.882 Td /F5 9.8 Tf [(incertae sedis )] TJ ET BT 244.640 623.882 Td /F1 9.8 Tf [(in Percomorphacea)] TJ ET 0.267 0.267 0.267 rg BT 329.173 625.389 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 333.991 623.882 Td /F1 9.8 Tf [(. The monophyly of Anabantomorphariae has also been )] TJ ET BT 26.250 611.977 Td /F1 9.8 Tf [(supported on the basis of mitogenomics)] TJ ET 0.267 0.267 0.267 rg BT 198.581 613.484 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 203.400 615.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 205.809 613.484 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 215.447 615.865 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 217.856 613.484 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 227.493 611.977 Td /F1 9.8 Tf [( and nuclear markers)] TJ ET 0.267 0.267 0.267 rg BT 319.065 613.484 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 328.703 611.977 Td /F1 9.8 Tf [(. A remarkable condition shared by members of this novel )] TJ ET BT 26.250 600.072 Td /F1 9.8 Tf [(grouping is their mostly freshwater origin and restriction to Africa and South East Asia \(although some members in the family )] TJ ET BT 26.250 588.168 Td /F1 9.8 Tf [(Synbranchidae occur in Mexico, and Central and South America\). Most are able to occupy marginal, stagnant waters due to )] TJ ET BT 26.250 576.263 Td /F1 9.8 Tf [(their capacity to tolerate anoxia and to obtain oxygen directly from the air. Anabantiforms have a suprabranchial organ and )] TJ ET BT 26.250 564.358 Td /F1 9.8 Tf [(synbranchids have suprabranchial pouches with respiratory function.)] TJ ET 0.965 0.965 0.965 rg 26.250 258.157 555.000 296.321 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 554.477 m 581.250 554.477 l 581.250 553.727 l 26.250 553.727 l f 26.250 258.157 m 581.250 258.157 l 581.250 258.907 l 26.250 258.907 l f q 452.250 0 0 211.500 35.250 333.227 cm /I8 Do Q q 35.250 269.407 537.000 57.821 re W n 0.271 0.267 0.267 rg BT 35.250 317.703 Td /F4 9.8 Tf [(Fig. 6: Detailed relationships among orders and families of Anabantomorphariae \(see also Fig. 1\).)] TJ ET BT 35.250 298.333 Td /F1 9.8 Tf [(Values in parentheses indicate number of genera examined.)] TJ ET BT 35.250 277.942 Td /F1 9.0 Tf [(Fish illustrations were obtained from Fishes of the World \(Nelson [2]\) and are reproduced with permission of John Wiley & Sons, Inc.)] TJ ET Q BT 26.250 241.133 Td /F5 9.8 Tf [(Carangimorphariae: flatfishes and unlikely relatives \(Fig. 7\))] TJ ET BT 26.250 221.728 Td /F1 9.8 Tf [(A close affinity between other seemingly disparate groups, including barracudas, swordfishes, jacks, flatfishes, and others, has )] TJ ET BT 26.250 209.823 Td /F1 9.8 Tf [(been well established by recent molecular studies)] TJ ET 0.267 0.267 0.267 rg BT 240.838 211.330 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 250.475 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 252.884 211.330 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 262.522 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 264.931 211.330 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 274.568 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 276.978 211.330 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 286.615 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 289.024 211.330 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 298.662 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 301.071 211.330 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 310.708 213.711 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 313.118 211.330 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 327.574 209.823 Td /F1 9.8 Tf [( \(Fig. 7\). This higher-level group has been referred to as )] TJ ET BT 26.250 197.918 Td /F1 9.8 Tf [(clade L sensu Chen et al.)] TJ ET 0.267 0.267 0.267 rg BT 144.927 199.426 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 154.564 197.918 Td /F1 9.8 Tf [( or Carangimorpha by Li et al.)] TJ ET 0.267 0.267 0.267 rg BT 282.991 199.426 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 292.629 197.918 Td /F1 9.8 Tf [( \(see also)] TJ ET 0.267 0.267 0.267 rg BT 334.895 199.426 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 344.532 201.807 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 346.942 199.426 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 356.579 197.918 Td /F1 9.8 Tf [(\). In looking for possible anatomical )] TJ ET BT 26.250 186.014 Td /F1 9.8 Tf [(synapomorphies uniting flatfishes, billfishes, and carangids, Little et al.)] TJ ET 0.267 0.267 0.267 rg BT 329.719 187.521 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 344.175 186.014 Td /F1 9.8 Tf [( found that most taxa share a relatively low number of )] TJ ET BT 26.250 174.109 Td /F1 9.8 Tf [(vertebrae, have multiple dorsal pterygiophores inserting before the second neural spine, and lack supraneurals, among others. )] TJ ET BT 26.250 162.204 Td /F1 9.8 Tf [(However, according to Friedman)] TJ ET 0.267 0.267 0.267 rg BT 167.128 163.711 Td /F4 8.7 Tf [(113)] TJ ET 0.271 0.267 0.267 rg BT 181.584 162.204 Td /F1 9.8 Tf [(, some of these characters are symplesiomorphies while others are absent in the remaining )] TJ ET BT 26.250 150.299 Td /F1 9.8 Tf [(carangimorph groups. It thus seems paradoxical that despite the apparent lack of morphological synapomorphies for )] TJ ET BT 26.250 138.395 Td /F1 9.8 Tf [(carangimorphs there is a strong molecular signal supporting their monophyly, whereas the opposite is true for pleuronectiforms)] TJ ET 0.267 0.267 0.267 rg BT 26.250 127.997 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 35.887 126.490 Td /F1 9.8 Tf [(. For additional insights and discussion on Carangimorphariae we refer the reader to recent studies)] TJ ET 0.267 0.267 0.267 rg BT 462.362 127.997 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 471.999 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 474.409 127.997 Td /F4 8.7 Tf [(27)] TJ ET 0.271 0.267 0.267 rg BT 484.046 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 486.455 127.997 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 496.093 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 498.502 127.997 Td /F4 8.7 Tf [(112)] TJ ET 0.271 0.267 0.267 rg BT 512.958 130.378 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 515.367 127.997 Td /F4 8.7 Tf [(113)] TJ ET 0.271 0.267 0.267 rg BT 529.823 126.490 Td /F1 9.8 Tf [(.)] TJ ET 0.965 0.965 0.965 rg 26.250 -351.391 555.000 468.000 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 116.609 m 581.250 116.609 l 581.250 115.859 l 26.250 115.859 l f q 372.750 0 0 452.250 35.250 -345.391 cm /I9 Do Q q 35.250 -351.391 537.000 0.000 re W n Q Q q 452.250 0 0 211.500 35.250 333.227 cm /I8 Do Q q 372.750 0 0 452.250 35.250 -345.391 cm /I9 Do Q q 0.000 0.000 0.000 rg BT 291.710 19.825 Td /F1 11.0 Tf [(11)] TJ ET BT 25.000 19.825 Td /F1 11.0 Tf [(PLOS Currents Tree of Life)] TJ ET Q endstream endobj 1780 0 obj << /Type /Annot /Subtype /Link /A 1781 0 R /Border [0 0 0] /H /I /Rect [ 259.2750 648.3968 264.0937 657.2151 ] >> endobj 1781 0 obj << /Type /Action >> endobj 1782 0 obj << /Type /Annot /Subtype /Link /A 1783 0 R /Border [0 0 0] /H /I /Rect [ 559.9747 636.4921 564.7934 645.3104 ] >> endobj 1783 0 obj << /Type /Action >> endobj 1784 0 obj << /Type /Annot /Subtype /Link /A 1785 0 R /Border [0 0 0] /H /I /Rect [ 567.2028 636.4921 572.0214 645.3104 ] >> endobj 1785 0 obj << /Type /Action >> endobj 1786 0 obj << /Type /Annot /Subtype /Link /A 1787 0 R /Border [0 0 0] /H /I /Rect [ 329.1728 624.5873 333.9914 633.4056 ] >> endobj 1787 0 obj << /Type /Action >> endobj 1788 0 obj << /Type /Annot /Subtype /Link /A 1789 0 R /Border [0 0 0] /H /I /Rect [ 198.5813 612.6826 203.3999 621.5009 ] >> endobj 1789 0 obj << /Type /Action >> endobj 1790 0 obj << /Type /Annot /Subtype /Link /A 1791 0 R /Border [0 0 0] /H /I /Rect [ 205.8093 612.6826 215.4466 621.5009 ] >> endobj 1791 0 obj << /Type /Action >> endobj 1792 0 obj << /Type /Annot /Subtype /Link /A 1793 0 R /Border [0 0 0] /H /I /Rect [ 217.8559 612.6826 227.4933 621.5009 ] >> endobj 1793 0 obj << /Type /Action >> endobj 1794 0 obj << /Type /Annot /Subtype /Link /A 1795 0 R /Border [0 0 0] /H /I /Rect [ 319.0653 612.6826 328.7026 621.5009 ] >> endobj 1795 0 obj << /Type /Action >> endobj 1796 0 obj << /Type /Annot /Subtype /Link /A 1797 0 R /Border [0 0 0] /H /I /Rect [ 35.2500 333.2271 487.5000 544.7271 ] >> endobj 1797 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2013/03/Fig5_Anabantomorphariae1.jpg) >> endobj 1798 0 obj << /Type /XObject /Subtype /Image /Width 603 /Height 282 /ColorSpace /DeviceRGB /Filter /DCTDecode /BitsPerComponent 8 /Length 34025>> stream JFIF;CREATOR: gd-jpeg v1.0 (using IJG JPEG v62), quality = 90 C     C   [" }!1AQa"q2#BR$3br %&'()*456789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz w!1AQaq"2B #3Rbr $4%&'()*56789:CDEFGHIJSTUVWXYZcdefghijstuvwxyz ?R%.EQFERRQ@ E.EP9");RQ@ KFERQ@%.EcJ\2(4dPQ.ETq\C;̑ʒ<-EV`6)GK_6j veηh~ZaDDhZ̭ǝc&6+@>kuݮ$%pY$"`,~(xZ֭el[*46Dor 8Ϙ 8P뻿ik;8OR"T qXd A# *ʁ2%}_K_/i3C-񭶉yK{-݀o |+d6#ݕZĚL"ּAݛ& =H~rT 73C0>YPN@>Ky5V<#,183 u5Vqxfè?Yii1u[\6wm <¹ۏ|D<7hΟ5+M,vGsºc%}5VY K2OjXŝF_]^]>M?-i&"?(F;_v~ (ȣ")r(ȠQFE%.(ȣ"\2(fH"yd`YU5hpzuwVg @i+7m7oGNcoϵi,"exn P_>*5ڛUl\mB[N2&Hx$ܱI^OkiIy{}a+m%F#-&]v 3_ɧ D^4u7,zXb\3n[ldzF{KԵ+m4*(=:-[iMSvS嫱a0784G fөY&Ǚm2Ia|q]8ʜV+ȼ=Y[|AhjA.s{`H4G!X|LX]ͼy3cƊÇ(عqX1K ꉫ@O:RW; /?Uhu<՝7 ]%[xX\cM.#sѥ*aN=[2n6F!i M\P ? 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