%PDF-1.3 1 0 obj << /Type /Catalog /Outlines 2 0 R /Pages 3 0 R >> endobj 2 0 obj << /Type /Outlines /Count 0 >> endobj 3 0 obj << /Type /Pages /Kids [6 0 R 117 0 R 223 0 R 251 0 R 277 0 R ] /Count 5 /Resources << /ProcSet 4 0 R /Font << /F1 8 0 R /F2 9 0 R /F3 10 0 R /F4 11 0 R /F5 12 0 R >> /XObject << /I1 13 0 R /I2 14 0 R /I3 151 0 R /I4 152 0 R /I5 185 0 R /I6 186 0 R /I7 219 0 R /I8 220 0 R /I9 221 0 R /I10 222 0 R /I11 231 0 R /I12 232 0 R /I13 239 0 R /I14 240 0 R /I15 247 0 R /I16 248 0 R /I17 249 0 R /I18 250 0 R >> >> /MediaBox [0.000 0.000 612.000 792.000] >> endobj 4 0 obj [/PDF /Text /ImageC ] endobj 5 0 obj << /Creator (DOMPDF) /CreationDate (D:20180721211317+00'00') /ModDate (D:20180721211317+00'00') /Title (Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a Member of the Zare Lineage PLOS Currents Outbreaks) >> endobj 6 0 obj << /Type /Page /Parent 3 0 R /Annots [ 15 0 R 17 0 R 19 0 R 21 0 R 23 0 R 25 0 R 27 0 R 29 0 R 31 0 R 33 0 R 35 0 R 37 0 R 39 0 R 41 0 R 43 0 R 45 0 R 47 0 R 49 0 R 51 0 R 53 0 R 55 0 R 57 0 R 59 0 R 61 0 R 63 0 R 65 0 R 67 0 R 69 0 R 71 0 R 73 0 R 75 0 R 77 0 R 79 0 R 81 0 R 83 0 R 85 0 R 87 0 R 89 0 R 91 0 R 93 0 R 95 0 R 97 0 R 99 0 R 101 0 R 103 0 R 105 0 R 107 0 R 109 0 R 111 0 R 113 0 R 115 0 R ] /Contents 7 0 R >> endobj 7 0 obj << /Length 25103 >> stream q 375.000 0 0 39.000 222.000 738.000 cm /I2 Do Q q 15.000 684.354 577.500 53.646 re W n 0.267 0.267 0.267 rg BT 15.000 718.042 Td /F2 21.0 Tf [(Clock Rooting Further Demonstrates that Guinea 2014 EBOV )] TJ ET BT 15.000 693.094 Td /F2 21.0 Tf [(is a Member of the Zare Lineage)] TJ ET Q 0.271 0.267 0.267 rg BT 15.000 675.088 Td /F3 9.8 Tf [(June 16, 2014)] TJ ET BT 74.846 675.088 Td /F3 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 79.721 675.088 Td /F3 9.8 Tf [(Research Article)] TJ ET BT 26.250 663.247 Td /F1 9.8 Tf [(Sbastien Calvignac-Spencer)] TJ ET 0.271 0.267 0.267 rg BT 154.677 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 160.098 663.247 Td /F1 9.8 Tf [(Jakob M. Schulze)] TJ ET 0.271 0.267 0.267 rg BT 237.045 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 242.466 663.247 Td /F1 9.8 Tf [(Franziska Zickmann)] TJ ET 0.271 0.267 0.267 rg BT 329.689 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 335.110 663.247 Td /F1 9.8 Tf [(Bernhard Y. Renard)] TJ ET 0.271 0.267 0.267 rg BT 26.250 651.342 Td /F1 9.8 Tf [(Calvignac-Spencer S, Schulze JM, Zickmann F, Renard BY. Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a )] TJ ET BT 26.250 639.438 Td /F1 9.8 Tf [(Member of the Zare Lineage. PLOS Currents Outbreaks. 2014 Jun 16 . Edition 1. doi: )] TJ ET BT 26.250 627.533 Td /F1 9.8 Tf [(10.1371/currents.outbreaks.c0e035c86d721668a6ad7353f7f6fe86.)] TJ ET q 15.000 22.378 577.500 602.774 re W n 0.271 0.267 0.267 rg BT 26.250 598.430 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 578.476 Td /F1 9.8 Tf [(While initial phylogenetic analyses concluded to Guinea 2014 EBOV falling outside the Zare lineage \(ZEBOV\), a recent re-)] TJ ET BT 26.250 566.571 Td /F1 9.8 Tf [(analysis of the same dataset by Dudas and Rambaut \(2014\) suggested that Guinea 2014 EBOV actually is ZEBOV. Under the )] TJ ET BT 26.250 554.667 Td /F1 9.8 Tf [(same hypothesis as used by these authors \(the molecular clock hypothesis\), we reinforce their conclusion by providing a )] TJ ET BT 26.250 542.762 Td /F1 9.8 Tf [(statistical assessment of the location of the root of the Zare lineage. Our analysis unambiguously supports Guinea 2014 EBOV )] TJ ET BT 26.250 530.857 Td /F1 9.8 Tf [(as a member of the Zare lineage. In addition, we also show that some uncertainty exists so as to the location of the root of the )] TJ ET BT 26.250 518.952 Td /F1 9.8 Tf [(genus Ebolavirus. We release the software we used for these re-analyses. RootAnnotator allows for the easy determination of )] TJ ET BT 26.250 507.048 Td /F1 9.8 Tf [(branch root posterior probability from any posterior sample of clocked trees and is freely available at )] TJ ET BT 26.250 495.143 Td /F1 9.8 Tf [(http://sourceforge.net/projects/rootannotator/.)] TJ ET BT 26.250 458.540 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 438.586 Td /F1 9.8 Tf [(This work was entirely funded by the Robert Koch-Institute.)] TJ ET BT 26.250 409.484 Td /F4 12.0 Tf [(Introduction)] TJ ET BT 26.250 389.529 Td /F1 9.8 Tf [(Phylogenetic analyses are a very popular and powerful way to extract information from sequences. The end product is a tree-)] TJ ET BT 26.250 377.625 Td /F1 9.8 Tf [(like graph intended to summarize the course of evolution. Sequence relatedness can be discussed on the basis of this graph )] TJ ET BT 26.250 365.720 Td /F1 9.8 Tf [(but only on condition that it is assigned a direction for time. This is achieved by a process known as rooting, that turns a tree-like )] TJ ET BT 26.250 353.815 Td /F1 9.8 Tf [(graph into a proper phylogenetic tree)] TJ ET 0.267 0.267 0.267 rg BT 185.584 355.322 Td /F4 8.7 Tf [(1)] TJ ET 0.271 0.267 0.267 rg BT 190.403 353.815 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 334.410 Td /F1 9.8 Tf [(Dudas and Rambaut \(2014\) recently demonstrated that improper rooting can end up in supporting strikingly erroneous )] TJ ET BT 26.250 322.506 Td /F1 9.8 Tf [(evolutionary scenarios, which can in turn mislead the formulation of important epidemiological hypotheses)] TJ ET 0.267 0.267 0.267 rg BT 481.975 324.013 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 486.793 322.506 Td /F1 9.8 Tf [( . These authors )] TJ ET BT 26.250 310.601 Td /F1 9.8 Tf [(contradicted a preliminary report that identified Guinea 2014 Ebolavirus \(EBOV\) as a divergent lineage falling outside the Zare )] TJ ET BT 26.250 298.696 Td /F1 9.8 Tf [(lineage \(ZEBOV\))] TJ ET 0.267 0.267 0.267 rg BT 99.941 300.203 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 104.759 298.696 Td /F1 9.8 Tf [( , and suggested that Guinea 2014 EBOV instead nests within this lineage, i.e. is ZEBOV. Accordingly, )] TJ ET BT 26.250 286.791 Td /F1 9.8 Tf [(Guinea 2014 EBOV is more likely to be the result of a fairly recent introduction of ZEBOV from Central Africa than a long-term )] TJ ET BT 26.250 274.887 Td /F1 9.8 Tf [(endemic in West Africa.)] TJ ET BT 26.250 255.482 Td /F1 9.8 Tf [(The initial misplacement of Guinea 2014 EBOV was due to unnoticed long-branch attraction to the outgroup)] TJ ET 0.267 0.267 0.267 rg BT 490.155 256.989 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 494.974 255.482 Td /F1 9.8 Tf [( . As pointed out by )] TJ ET BT 26.250 243.577 Td /F1 9.8 Tf [(Dudas and Rambaut \(2014\), this phenomenon made the long branch of Guinea 2014 EBOV drift towards the basis of the Zare )] TJ ET BT 26.250 231.672 Td /F1 9.8 Tf [(clade as it was attracted to the other \(very divergent\) EBOV lineages included in the analyses \(Bundibugyo, Ta Forest, Reston )] TJ ET BT 26.250 219.768 Td /F1 9.8 Tf [(and Sudan\))] TJ ET 0.267 0.267 0.267 rg BT 76.657 221.275 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 81.476 219.768 Td /F1 9.8 Tf [( . To identify the location of the root within the Zare clade, Dudas and Rambaut \(2014\) excluded any outgroup and )] TJ ET BT 26.250 207.863 Td /F1 9.8 Tf [(rooted the ingroup tree by minimizing the variance of root-to-tip distances \(using Path-O-Gen, available at )] TJ ET 0.267 0.267 0.267 rg BT 26.250 195.958 Td /F1 9.8 Tf [(http://tree.bio.ed.ac.uk/software/pathogen/)] TJ ET 0.271 0.267 0.267 rg BT 208.361 195.958 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg BT 211.607 197.465 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 216.426 195.958 Td /F1 9.8 Tf [( . By doing so, they made the reasonable hypothesis that ZEBOV sequences evolve )] TJ ET BT 26.250 184.053 Td /F1 9.8 Tf [(according to some kind of molecular clock and that the most likely root location minimizes rate variation across lineages.)] TJ ET BT 26.250 164.649 Td /F1 9.8 Tf [(This approach is very sensible. However, here we introduce an alternative method which is built under the same hypothesis but )] TJ ET BT 26.250 152.744 Td /F1 9.8 Tf [(additionally allows for a quantitative assessment of the support for any root location. As an illustration, we apply this method to )] TJ ET BT 26.250 140.839 Td /F1 9.8 Tf [(localize the root within the Zare clade. Using this same tool, we also investigate the position of the root within the genus )] TJ ET BT 26.250 128.934 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 71.763 128.934 Td /F1 9.8 Tf [(, whose deep branching order is controversial)] TJ ET 0.267 0.267 0.267 rg BT 268.469 130.442 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 278.107 132.823 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 280.516 130.442 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 290.153 128.934 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 92.332 Td /F4 12.0 Tf [(Rationale)] TJ ET BT 26.250 72.378 Td /F1 9.8 Tf [(Over the last decade, one of the most fundamental developments in the field of phylogenetics was the introduction of models )] TJ ET BT 26.250 60.473 Td /F1 9.8 Tf [(employing relaxed molecular clocks)] TJ ET 0.267 0.267 0.267 rg BT 180.125 61.980 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 184.943 60.473 Td /F1 9.8 Tf [( . These are clock models that recognize some degree of clocklikeness to the substitution )] TJ ET BT 26.250 48.568 Td /F1 9.8 Tf [(process without going to the extreme of a single constant rate of evolution applied to the entire tree. This methodological leap )] TJ ET BT 26.250 36.663 Td /F1 9.8 Tf [(considerably popularized phylogenetic analyses under clock models, which are commonly performed on one of the two leading )] TJ ET Q q 15.000 684.354 577.500 53.646 re W n 0.267 0.267 0.267 rg BT 15.000 718.042 Td /F2 21.0 Tf [(Clock Rooting Further Demonstrates that Guinea 2014 EBOV )] TJ ET BT 15.000 693.094 Td /F2 21.0 Tf [(is a Member of the Zare Lineage)] TJ ET Q 0.271 0.267 0.267 rg BT 15.000 675.088 Td /F3 9.8 Tf [(June 16, 2014)] TJ ET BT 74.846 675.088 Td /F3 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 79.721 675.088 Td /F3 9.8 Tf [(Research Article)] TJ ET BT 26.250 663.247 Td /F1 9.8 Tf [(Sbastien Calvignac-Spencer)] TJ ET 0.271 0.267 0.267 rg BT 154.677 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 160.098 663.247 Td /F1 9.8 Tf [(Jakob M. Schulze)] TJ ET 0.271 0.267 0.267 rg BT 237.045 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 242.466 663.247 Td /F1 9.8 Tf [(Franziska Zickmann)] TJ ET 0.271 0.267 0.267 rg BT 329.689 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 335.110 663.247 Td /F1 9.8 Tf [(Bernhard Y. Renard)] TJ ET 0.271 0.267 0.267 rg BT 26.250 651.342 Td /F1 9.8 Tf [(Calvignac-Spencer S, Schulze JM, Zickmann F, Renard BY. Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a )] TJ ET BT 26.250 639.438 Td /F1 9.8 Tf [(Member of the Zare Lineage. PLOS Currents Outbreaks. 2014 Jun 16 . Edition 1. doi: )] TJ ET BT 26.250 627.533 Td /F1 9.8 Tf [(10.1371/currents.outbreaks.c0e035c86d721668a6ad7353f7f6fe86.)] TJ ET q 15.000 22.378 577.500 602.774 re W n 0.271 0.267 0.267 rg BT 26.250 598.430 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 578.476 Td /F1 9.8 Tf [(While initial phylogenetic analyses concluded to Guinea 2014 EBOV falling outside the Zare lineage \(ZEBOV\), a recent re-)] TJ ET BT 26.250 566.571 Td /F1 9.8 Tf [(analysis of the same dataset by Dudas and Rambaut \(2014\) suggested that Guinea 2014 EBOV actually is ZEBOV. Under the )] TJ ET BT 26.250 554.667 Td /F1 9.8 Tf [(same hypothesis as used by these authors \(the molecular clock hypothesis\), we reinforce their conclusion by providing a )] TJ ET BT 26.250 542.762 Td /F1 9.8 Tf [(statistical assessment of the location of the root of the Zare lineage. Our analysis unambiguously supports Guinea 2014 EBOV )] TJ ET BT 26.250 530.857 Td /F1 9.8 Tf [(as a member of the Zare lineage. In addition, we also show that some uncertainty exists so as to the location of the root of the )] TJ ET BT 26.250 518.952 Td /F1 9.8 Tf [(genus Ebolavirus. We release the software we used for these re-analyses. RootAnnotator allows for the easy determination of )] TJ ET BT 26.250 507.048 Td /F1 9.8 Tf [(branch root posterior probability from any posterior sample of clocked trees and is freely available at )] TJ ET BT 26.250 495.143 Td /F1 9.8 Tf [(http://sourceforge.net/projects/rootannotator/.)] TJ ET BT 26.250 458.540 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 438.586 Td /F1 9.8 Tf [(This work was entirely funded by the Robert Koch-Institute.)] TJ ET BT 26.250 409.484 Td /F4 12.0 Tf [(Introduction)] TJ ET BT 26.250 389.529 Td /F1 9.8 Tf [(Phylogenetic analyses are a very popular and powerful way to extract information from sequences. The end product is a tree-)] TJ ET BT 26.250 377.625 Td /F1 9.8 Tf [(like graph intended to summarize the course of evolution. Sequence relatedness can be discussed on the basis of this graph )] TJ ET BT 26.250 365.720 Td /F1 9.8 Tf [(but only on condition that it is assigned a direction for time. This is achieved by a process known as rooting, that turns a tree-like )] TJ ET BT 26.250 353.815 Td /F1 9.8 Tf [(graph into a proper phylogenetic tree)] TJ ET 0.267 0.267 0.267 rg BT 185.584 355.322 Td /F4 8.7 Tf [(1)] TJ ET 0.271 0.267 0.267 rg BT 190.403 353.815 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 334.410 Td /F1 9.8 Tf [(Dudas and Rambaut \(2014\) recently demonstrated that improper rooting can end up in supporting strikingly erroneous )] TJ ET BT 26.250 322.506 Td /F1 9.8 Tf [(evolutionary scenarios, which can in turn mislead the formulation of important epidemiological hypotheses)] TJ ET 0.267 0.267 0.267 rg BT 481.975 324.013 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 486.793 322.506 Td /F1 9.8 Tf [( . These authors )] TJ ET BT 26.250 310.601 Td /F1 9.8 Tf [(contradicted a preliminary report that identified Guinea 2014 Ebolavirus \(EBOV\) as a divergent lineage falling outside the Zare )] TJ ET BT 26.250 298.696 Td /F1 9.8 Tf [(lineage \(ZEBOV\))] TJ ET 0.267 0.267 0.267 rg BT 99.941 300.203 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 104.759 298.696 Td /F1 9.8 Tf [( , and suggested that Guinea 2014 EBOV instead nests within this lineage, i.e. is ZEBOV. Accordingly, )] TJ ET BT 26.250 286.791 Td /F1 9.8 Tf [(Guinea 2014 EBOV is more likely to be the result of a fairly recent introduction of ZEBOV from Central Africa than a long-term )] TJ ET BT 26.250 274.887 Td /F1 9.8 Tf [(endemic in West Africa.)] TJ ET BT 26.250 255.482 Td /F1 9.8 Tf [(The initial misplacement of Guinea 2014 EBOV was due to unnoticed long-branch attraction to the outgroup)] TJ ET 0.267 0.267 0.267 rg BT 490.155 256.989 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 494.974 255.482 Td /F1 9.8 Tf [( . As pointed out by )] TJ ET BT 26.250 243.577 Td /F1 9.8 Tf [(Dudas and Rambaut \(2014\), this phenomenon made the long branch of Guinea 2014 EBOV drift towards the basis of the Zare )] TJ ET BT 26.250 231.672 Td /F1 9.8 Tf [(clade as it was attracted to the other \(very divergent\) EBOV lineages included in the analyses \(Bundibugyo, Ta Forest, Reston )] TJ ET BT 26.250 219.768 Td /F1 9.8 Tf [(and Sudan\))] TJ ET 0.267 0.267 0.267 rg BT 76.657 221.275 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 81.476 219.768 Td /F1 9.8 Tf [( . To identify the location of the root within the Zare clade, Dudas and Rambaut \(2014\) excluded any outgroup and )] TJ ET BT 26.250 207.863 Td /F1 9.8 Tf [(rooted the ingroup tree by minimizing the variance of root-to-tip distances \(using Path-O-Gen, available at )] TJ ET 0.267 0.267 0.267 rg BT 26.250 195.958 Td /F1 9.8 Tf [(http://tree.bio.ed.ac.uk/software/pathogen/)] TJ ET 0.271 0.267 0.267 rg BT 208.361 195.958 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg BT 211.607 197.465 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 216.426 195.958 Td /F1 9.8 Tf [( . By doing so, they made the reasonable hypothesis that ZEBOV sequences evolve )] TJ ET BT 26.250 184.053 Td /F1 9.8 Tf [(according to some kind of molecular clock and that the most likely root location minimizes rate variation across lineages.)] TJ ET BT 26.250 164.649 Td /F1 9.8 Tf [(This approach is very sensible. However, here we introduce an alternative method which is built under the same hypothesis but )] TJ ET BT 26.250 152.744 Td /F1 9.8 Tf [(additionally allows for a quantitative assessment of the support for any root location. As an illustration, we apply this method to )] TJ ET BT 26.250 140.839 Td /F1 9.8 Tf [(localize the root within the Zare clade. Using this same tool, we also investigate the position of the root within the genus )] TJ ET BT 26.250 128.934 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 71.763 128.934 Td /F1 9.8 Tf [(, whose deep branching order is controversial)] TJ ET 0.267 0.267 0.267 rg BT 268.469 130.442 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 278.107 132.823 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 280.516 130.442 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 290.153 128.934 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 92.332 Td /F4 12.0 Tf [(Rationale)] TJ ET BT 26.250 72.378 Td /F1 9.8 Tf [(Over the last decade, one of the most fundamental developments in the field of phylogenetics was the introduction of models )] TJ ET BT 26.250 60.473 Td /F1 9.8 Tf [(employing relaxed molecular clocks)] TJ ET 0.267 0.267 0.267 rg BT 180.125 61.980 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 184.943 60.473 Td /F1 9.8 Tf [( . These are clock models that recognize some degree of clocklikeness to the substitution )] TJ ET BT 26.250 48.568 Td /F1 9.8 Tf [(process without going to the extreme of a single constant rate of evolution applied to the entire tree. This methodological leap )] TJ ET BT 26.250 36.663 Td /F1 9.8 Tf [(considerably popularized phylogenetic analyses under clock models, which are commonly performed on one of the two leading )] TJ ET Q q 15.000 684.354 577.500 53.646 re W n 0.267 0.267 0.267 rg BT 15.000 718.042 Td /F2 21.0 Tf [(Clock Rooting Further Demonstrates that Guinea 2014 EBOV )] TJ ET BT 15.000 693.094 Td /F2 21.0 Tf [(is a Member of the Zare Lineage)] TJ ET Q 0.271 0.267 0.267 rg BT 15.000 675.088 Td /F3 9.8 Tf [(June 16, 2014)] TJ ET BT 74.846 675.088 Td /F3 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 79.721 675.088 Td /F3 9.8 Tf [(Research Article)] TJ ET BT 26.250 663.247 Td /F1 9.8 Tf [(Sbastien Calvignac-Spencer)] TJ ET 0.271 0.267 0.267 rg BT 154.677 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 160.098 663.247 Td /F1 9.8 Tf [(Jakob M. Schulze)] TJ ET 0.271 0.267 0.267 rg BT 237.045 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 242.466 663.247 Td /F1 9.8 Tf [(Franziska Zickmann)] TJ ET 0.271 0.267 0.267 rg BT 329.689 663.247 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 335.110 663.247 Td /F1 9.8 Tf [(Bernhard Y. Renard)] TJ ET 0.271 0.267 0.267 rg BT 26.250 651.342 Td /F1 9.8 Tf [(Calvignac-Spencer S, Schulze JM, Zickmann F, Renard BY. Clock Rooting Further Demonstrates that Guinea 2014 EBOV is a )] TJ ET BT 26.250 639.438 Td /F1 9.8 Tf [(Member of the Zare Lineage. PLOS Currents Outbreaks. 2014 Jun 16 . Edition 1. doi: )] TJ ET BT 26.250 627.533 Td /F1 9.8 Tf [(10.1371/currents.outbreaks.c0e035c86d721668a6ad7353f7f6fe86.)] TJ ET q 15.000 22.378 577.500 602.774 re W n 0.271 0.267 0.267 rg BT 26.250 598.430 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 578.476 Td /F1 9.8 Tf [(While initial phylogenetic analyses concluded to Guinea 2014 EBOV falling outside the Zare lineage \(ZEBOV\), a recent re-)] TJ ET BT 26.250 566.571 Td /F1 9.8 Tf [(analysis of the same dataset by Dudas and Rambaut \(2014\) suggested that Guinea 2014 EBOV actually is ZEBOV. Under the )] TJ ET BT 26.250 554.667 Td /F1 9.8 Tf [(same hypothesis as used by these authors \(the molecular clock hypothesis\), we reinforce their conclusion by providing a )] TJ ET BT 26.250 542.762 Td /F1 9.8 Tf [(statistical assessment of the location of the root of the Zare lineage. Our analysis unambiguously supports Guinea 2014 EBOV )] TJ ET BT 26.250 530.857 Td /F1 9.8 Tf [(as a member of the Zare lineage. In addition, we also show that some uncertainty exists so as to the location of the root of the )] TJ ET BT 26.250 518.952 Td /F1 9.8 Tf [(genus Ebolavirus. We release the software we used for these re-analyses. RootAnnotator allows for the easy determination of )] TJ ET BT 26.250 507.048 Td /F1 9.8 Tf [(branch root posterior probability from any posterior sample of clocked trees and is freely available at )] TJ ET BT 26.250 495.143 Td /F1 9.8 Tf [(http://sourceforge.net/projects/rootannotator/.)] TJ ET BT 26.250 458.540 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 438.586 Td /F1 9.8 Tf [(This work was entirely funded by the Robert Koch-Institute.)] TJ ET BT 26.250 409.484 Td /F4 12.0 Tf [(Introduction)] TJ ET BT 26.250 389.529 Td /F1 9.8 Tf [(Phylogenetic analyses are a very popular and powerful way to extract information from sequences. The end product is a tree-)] TJ ET BT 26.250 377.625 Td /F1 9.8 Tf [(like graph intended to summarize the course of evolution. Sequence relatedness can be discussed on the basis of this graph )] TJ ET BT 26.250 365.720 Td /F1 9.8 Tf [(but only on condition that it is assigned a direction for time. This is achieved by a process known as rooting, that turns a tree-like )] TJ ET BT 26.250 353.815 Td /F1 9.8 Tf [(graph into a proper phylogenetic tree)] TJ ET 0.267 0.267 0.267 rg BT 185.584 355.322 Td /F4 8.7 Tf [(1)] TJ ET 0.271 0.267 0.267 rg BT 190.403 353.815 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 334.410 Td /F1 9.8 Tf [(Dudas and Rambaut \(2014\) recently demonstrated that improper rooting can end up in supporting strikingly erroneous )] TJ ET BT 26.250 322.506 Td /F1 9.8 Tf [(evolutionary scenarios, which can in turn mislead the formulation of important epidemiological hypotheses)] TJ ET 0.267 0.267 0.267 rg BT 481.975 324.013 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 486.793 322.506 Td /F1 9.8 Tf [( . These authors )] TJ ET BT 26.250 310.601 Td /F1 9.8 Tf [(contradicted a preliminary report that identified Guinea 2014 Ebolavirus \(EBOV\) as a divergent lineage falling outside the Zare )] TJ ET BT 26.250 298.696 Td /F1 9.8 Tf [(lineage \(ZEBOV\))] TJ ET 0.267 0.267 0.267 rg BT 99.941 300.203 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 104.759 298.696 Td /F1 9.8 Tf [( , and suggested that Guinea 2014 EBOV instead nests within this lineage, i.e. is ZEBOV. Accordingly, )] TJ ET BT 26.250 286.791 Td /F1 9.8 Tf [(Guinea 2014 EBOV is more likely to be the result of a fairly recent introduction of ZEBOV from Central Africa than a long-term )] TJ ET BT 26.250 274.887 Td /F1 9.8 Tf [(endemic in West Africa.)] TJ ET BT 26.250 255.482 Td /F1 9.8 Tf [(The initial misplacement of Guinea 2014 EBOV was due to unnoticed long-branch attraction to the outgroup)] TJ ET 0.267 0.267 0.267 rg BT 490.155 256.989 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 494.974 255.482 Td /F1 9.8 Tf [( . As pointed out by )] TJ ET BT 26.250 243.577 Td /F1 9.8 Tf [(Dudas and Rambaut \(2014\), this phenomenon made the long branch of Guinea 2014 EBOV drift towards the basis of the Zare )] TJ ET BT 26.250 231.672 Td /F1 9.8 Tf [(clade as it was attracted to the other \(very divergent\) EBOV lineages included in the analyses \(Bundibugyo, Ta Forest, Reston )] TJ ET BT 26.250 219.768 Td /F1 9.8 Tf [(and Sudan\))] TJ ET 0.267 0.267 0.267 rg BT 76.657 221.275 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 81.476 219.768 Td /F1 9.8 Tf [( . To identify the location of the root within the Zare clade, Dudas and Rambaut \(2014\) excluded any outgroup and )] TJ ET BT 26.250 207.863 Td /F1 9.8 Tf [(rooted the ingroup tree by minimizing the variance of root-to-tip distances \(using Path-O-Gen, available at )] TJ ET 0.267 0.267 0.267 rg BT 26.250 195.958 Td /F1 9.8 Tf [(http://tree.bio.ed.ac.uk/software/pathogen/)] TJ ET 0.271 0.267 0.267 rg BT 208.361 195.958 Td /F1 9.8 Tf [(\))] TJ ET 0.267 0.267 0.267 rg BT 211.607 197.465 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 216.426 195.958 Td /F1 9.8 Tf [( . By doing so, they made the reasonable hypothesis that ZEBOV sequences evolve )] TJ ET BT 26.250 184.053 Td /F1 9.8 Tf [(according to some kind of molecular clock and that the most likely root location minimizes rate variation across lineages.)] TJ ET BT 26.250 164.649 Td /F1 9.8 Tf [(This approach is very sensible. However, here we introduce an alternative method which is built under the same hypothesis but )] TJ ET BT 26.250 152.744 Td /F1 9.8 Tf [(additionally allows for a quantitative assessment of the support for any root location. As an illustration, we apply this method to )] TJ ET BT 26.250 140.839 Td /F1 9.8 Tf [(localize the root within the Zare clade. Using this same tool, we also investigate the position of the root within the genus )] TJ ET BT 26.250 128.934 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 71.763 128.934 Td /F1 9.8 Tf [(, whose deep branching order is controversial)] TJ ET 0.267 0.267 0.267 rg BT 268.469 130.442 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 278.107 132.823 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 280.516 130.442 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 290.153 128.934 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 92.332 Td /F4 12.0 Tf [(Rationale)] TJ ET BT 26.250 72.378 Td /F1 9.8 Tf [(Over the last decade, one of the most fundamental developments in the field of phylogenetics was the introduction of models )] TJ ET BT 26.250 60.473 Td /F1 9.8 Tf [(employing relaxed molecular clocks)] TJ ET 0.267 0.267 0.267 rg BT 180.125 61.980 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 184.943 60.473 Td /F1 9.8 Tf [( . These are clock models that recognize some degree of clocklikeness to the substitution )] TJ ET BT 26.250 48.568 Td /F1 9.8 Tf [(process without going to the extreme of a single constant rate of evolution applied to the entire tree. 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Following others)] TJ ET 0.267 0.267 0.267 rg BT 272.252 697.555 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 277.071 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 279.480 697.555 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 289.118 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 291.527 697.555 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 301.164 696.048 Td /F1 9.8 Tf [( , we propose to apply the same logic to derive root support. )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(Here, the proportion of posterior trees for which the branch of interest wears the root would be taken as this branch root )] TJ ET BT 26.250 672.238 Td /F1 9.8 Tf [(posterior probability \(RPP\).)] TJ ET BT 26.250 635.636 Td /F4 12.0 Tf [(Software)] TJ ET BT 26.250 615.681 Td /F1 9.8 Tf [(Assessing branch RPP only requires parsing the posterior sample of trees, recording the branches wearing the root and their )] TJ ET BT 26.250 603.777 Td /F1 9.8 Tf [(frequency. Due to the large number of trees, this cannot be done manually. As, to the best of our knowledge, no software is )] TJ ET BT 26.250 591.872 Td /F1 9.8 Tf [(available for this purpose, we developed RootAnnotator, a user-friendly, portable software that collects information on root )] TJ ET BT 26.250 579.967 Td /F1 9.8 Tf [(positions in posterior samples of trees and annotates a target tree with the according RPP \(available from )] TJ ET 0.267 0.267 0.267 rg BT 26.250 568.062 Td /F1 9.8 Tf [(www.sourceforge.net/projects/rootannotator/)] TJ ET 0.271 0.267 0.267 rg BT 218.081 568.062 Td /F1 9.8 Tf [(\). 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This dataset therefore comprised 23 ZEBOV sequences and the three )] TJ ET BT 26.250 463.887 Td /F1 9.8 Tf [(Guinea 2014 EBOV sequences. To assess the position of the root within the genus )] TJ ET BT 386.659 463.887 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 432.172 463.887 Td /F1 9.8 Tf [(, we also used an alignment of )] TJ ET BT 26.250 451.982 Td /F1 9.8 Tf [(concatenated coding sequences derived from Dudas and Rambaut \(2014\))] TJ ET 0.267 0.267 0.267 rg BT 345.991 453.489 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 350.810 451.982 Td /F1 9.8 Tf [( . This alignment included 5 sequences which were )] TJ ET BT 26.250 440.077 Td /F1 9.8 Tf [(selected to represent the five recognized species in the genus.)] TJ ET BT 26.250 420.672 Td /F1 9.8 Tf [(The first alignment was analyzed in BEAST using a GTR+? model of nucleotide substitution and assuming an uncorrelated )] TJ ET BT 26.250 408.768 Td /F1 9.8 Tf [(relaxed clock \(lognormal\) which was tip-calibrated. We performed these analyses under the same three distinct demographic )] TJ ET BT 26.250 396.863 Td /F1 9.8 Tf [(priors used by Dudas and Rambaut \(2014\) \(constant population size, exponential growth and Bayesian skyride\))] TJ ET 0.267 0.267 0.267 rg BT 506.925 398.370 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 511.744 396.863 Td /F1 9.8 Tf [( . The second )] TJ ET BT 26.250 384.958 Td /F1 9.8 Tf [(alignment was first analyzed in PhyML)] TJ ET 0.267 0.267 0.267 rg BT 192.059 386.465 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 201.696 384.958 Td /F1 9.8 Tf [( using a GTR+? model of nucleotide substitution. The resulting tree was analysed with )] TJ ET BT 26.250 373.053 Td /F1 9.8 Tf [(Path-O-Gen which did not evidence any strong clocklike signal \(a positive correlation of time and root-to-tip distances was only )] TJ ET BT 26.250 361.149 Td /F1 9.8 Tf [(marginally supported; R)] TJ ET BT 129.200 365.037 Td /F1 8.7 Tf [(2)] TJ ET BT 134.019 361.149 Td /F1 9.8 Tf [(: 0.43\). The second alignment was therefore analyzed in BEAST using a GTR+? model of nucleotide )] TJ ET BT 26.250 349.244 Td /F1 9.8 Tf [(substitution and assuming an uncorrelated relaxed clock \(lognormal\) which was not tip-calibrated. We performed these analyses )] TJ ET BT 26.250 337.339 Td /F1 9.8 Tf [(under two speciation priors \(Yule and Birth-Death process\).)] TJ ET BT 26.250 317.934 Td /F1 9.8 Tf [(Branch RPP were determined using RootAnnotator and plotted on the MCC tree)] TJ ET BT 371.995 317.934 Td /F4 9.8 Tf [(s)] TJ ET BT 377.416 317.934 Td /F1 9.8 Tf [(. When a branch appearing at least once as )] TJ ET BT 26.250 306.030 Td /F1 9.8 Tf [(wearing the root in the posterior sample did not appear in the MCC tree, RootAnnotator was used to select a tree containing that )] TJ ET BT 26.250 294.125 Td /F1 9.8 Tf [(branch so as to visualize their RPP \(note that the RootAnnotator output also comprises a csv file comprising a list of all )] TJ ET BT 26.250 282.220 Td /F1 9.8 Tf [(branches identified as wearing the root together with the associated RPP\).)] TJ ET 0.965 0.965 0.965 rg 26.250 -12.661 555.000 285.000 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 272.339 m 581.250 272.339 l 581.250 271.589 l 26.250 271.589 l f q 450.000 0 0 269.250 35.250 -6.661 cm /I6 Do Q q 35.250 -12.661 537.000 0.000 re W n Q Q q 15.000 -12.661 577.500 789.661 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(platforms for Bayesian phylogenetics, BEAST)] TJ ET 0.267 0.267 0.267 rg BT 222.956 768.983 Td /F4 8.7 Tf [(6)] TJ ET 0.271 0.267 0.267 rg BT 227.775 771.364 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 230.184 768.983 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 235.003 767.476 Td /F1 9.8 Tf [( and MrBayes)] TJ ET 0.267 0.267 0.267 rg BT 295.151 768.983 Td /F4 8.7 Tf [(8)] TJ ET 0.271 0.267 0.267 rg BT 299.969 771.364 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 302.379 768.983 Td /F4 8.7 Tf [(9)] TJ ET 0.271 0.267 0.267 rg BT 307.197 771.364 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 309.607 768.983 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 319.244 767.476 Td /F1 9.8 Tf [( . These platforms use Markov chain Monte Carlo \(MCMC\) )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(samplers to approximate the \(Bayesian\) posterior distribution of all model parameters. Trees \(i.e. topology and branch lengths\) )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(are among the parameters to estimate and MCMC samplers typically end up generating plausible sets of phylogenetic trees. )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(When the model of evolution incorporates a clock model, MCMC samplers actually generate plausible sets of rooted trees. This )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(can be viewed as generating a plausible set of tree-like graphs on the one hand and a plausible set of root locations on the )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(other. Branch support is typically derived from posterior tree samples by counting the proportion of trees comprising the branch )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(of interest \(branch posterior probability\). Following others)] TJ ET 0.267 0.267 0.267 rg BT 272.252 697.555 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 277.071 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 279.480 697.555 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 289.118 699.936 Td /F1 8.7 Tf [(,)] TJ ET 0.267 0.267 0.267 rg BT 291.527 697.555 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 301.164 696.048 Td /F1 9.8 Tf [( , we propose to apply the same logic to derive root support. )] TJ ET BT 26.250 684.143 Td /F1 9.8 Tf [(Here, the proportion of posterior trees for which the branch of interest wears the root would be taken as this branch root )] TJ ET BT 26.250 672.238 Td /F1 9.8 Tf [(posterior probability \(RPP\).)] TJ ET BT 26.250 635.636 Td /F4 12.0 Tf [(Software)] TJ ET BT 26.250 615.681 Td /F1 9.8 Tf [(Assessing branch RPP only requires parsing the posterior sample of trees, recording the branches wearing the root and their )] TJ ET BT 26.250 603.777 Td /F1 9.8 Tf [(frequency. Due to the large number of trees, this cannot be done manually. As, to the best of our knowledge, no software is )] TJ ET BT 26.250 591.872 Td /F1 9.8 Tf [(available for this purpose, we developed RootAnnotator, a user-friendly, portable software that collects information on root )] TJ ET BT 26.250 579.967 Td /F1 9.8 Tf [(positions in posterior samples of trees and annotates a target tree with the according RPP \(available from )] TJ ET 0.267 0.267 0.267 rg BT 26.250 568.062 Td /F1 9.8 Tf [(www.sourceforge.net/projects/rootannotator/)] TJ ET 0.271 0.267 0.267 rg BT 218.081 568.062 Td /F1 9.8 Tf [(\). Among other options, the user can choose that the target tree is the maximum )] TJ ET BT 26.250 556.158 Td /F1 9.8 Tf [(clade credibility \(MCC\) tree, which RootAnnotator will identify by running TreeAnnotator \(distributed with BEAST\))] TJ ET 0.267 0.267 0.267 rg BT 511.741 557.665 Td /F4 8.7 Tf [(6)] TJ ET 0.271 0.267 0.267 rg BT 516.560 556.158 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 519.555 Td /F4 12.0 Tf [(Phylogenetic analysis)] TJ ET BT 26.250 499.601 Td /F1 9.8 Tf [(To investigate the position of the root within the Zare clade, we used the alignment of concatenated coding sequences )] TJ ET BT 26.250 487.696 Td /F1 9.8 Tf [(published by Dudas and Rambaut \(2014\) \(available at )] TJ ET 0.267 0.267 0.267 rg BT 261.986 487.696 Td /F1 9.8 Tf [(https://github.com/evogytis/ebolaGuinea2014)] TJ ET 0.271 0.267 0.267 rg BT 457.093 487.696 Td /F1 9.8 Tf [(\) from which we removed all )] TJ ET BT 26.250 475.791 Td /F1 9.8 Tf [(sequences that did not belong to the Zare lineage)] TJ ET 0.267 0.267 0.267 rg BT 243.051 477.299 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 247.870 475.791 Td /F1 9.8 Tf [( . This dataset therefore comprised 23 ZEBOV sequences and the three )] TJ ET BT 26.250 463.887 Td /F1 9.8 Tf [(Guinea 2014 EBOV sequences. To assess the position of the root within the genus )] TJ ET BT 386.659 463.887 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 432.172 463.887 Td /F1 9.8 Tf [(, we also used an alignment of )] TJ ET BT 26.250 451.982 Td /F1 9.8 Tf [(concatenated coding sequences derived from Dudas and Rambaut \(2014\))] TJ ET 0.267 0.267 0.267 rg BT 345.991 453.489 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 350.810 451.982 Td /F1 9.8 Tf [( . This alignment included 5 sequences which were )] TJ ET BT 26.250 440.077 Td /F1 9.8 Tf [(selected to represent the five recognized species in the genus.)] TJ ET BT 26.250 420.672 Td /F1 9.8 Tf [(The first alignment was analyzed in BEAST using a GTR+? model of nucleotide substitution and assuming an uncorrelated )] TJ ET BT 26.250 408.768 Td /F1 9.8 Tf [(relaxed clock \(lognormal\) which was tip-calibrated. We performed these analyses under the same three distinct demographic )] TJ ET BT 26.250 396.863 Td /F1 9.8 Tf [(priors used by Dudas and Rambaut \(2014\) \(constant population size, exponential growth and Bayesian skyride\))] TJ ET 0.267 0.267 0.267 rg BT 506.925 398.370 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 511.744 396.863 Td /F1 9.8 Tf [( . The second )] TJ ET BT 26.250 384.958 Td /F1 9.8 Tf [(alignment was first analyzed in PhyML)] TJ ET 0.267 0.267 0.267 rg BT 192.059 386.465 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 201.696 384.958 Td /F1 9.8 Tf [( using a GTR+? model of nucleotide substitution. The resulting tree was analysed with )] TJ ET BT 26.250 373.053 Td /F1 9.8 Tf [(Path-O-Gen which did not evidence any strong clocklike signal \(a positive correlation of time and root-to-tip distances was only )] TJ ET BT 26.250 361.149 Td /F1 9.8 Tf [(marginally supported; R)] TJ ET BT 129.200 365.037 Td /F1 8.7 Tf [(2)] TJ ET BT 134.019 361.149 Td /F1 9.8 Tf [(: 0.43\). The second alignment was therefore analyzed in BEAST using a GTR+? model of nucleotide )] TJ ET BT 26.250 349.244 Td /F1 9.8 Tf [(substitution and assuming an uncorrelated relaxed clock \(lognormal\) which was not tip-calibrated. We performed these analyses )] TJ ET BT 26.250 337.339 Td /F1 9.8 Tf [(under two speciation priors \(Yule and Birth-Death process\).)] TJ ET BT 26.250 317.934 Td /F1 9.8 Tf [(Branch RPP were determined using RootAnnotator and plotted on the MCC tree)] TJ ET BT 371.995 317.934 Td /F4 9.8 Tf [(s)] TJ ET BT 377.416 317.934 Td /F1 9.8 Tf [(. 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ӤXE*<ׄnImMd&=[ZA$\KW;:n @{Pd1%}3'PCCCd(PYrOxZ21R;SStd4i6qQQ ,TN@^2@d+aiUI wu×f2ט3ߖToI! ݊ܪ[%,\$1,\MFNkbJ> endobj 224 0 obj << /Length 13130 >> stream q 15.000 54.123 577.500 722.877 re W n 0.965 0.965 0.965 rg 26.250 644.191 555.000 132.809 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 644.191 m 581.250 644.191 l 581.250 644.941 l 26.250 644.941 l f q 35.250 655.441 537.000 121.559 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 1: Maximum clade credibility tree of concatenated coding sequences belonging to the Zare clade.)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(MCC tree and branch root posterior probabilities \(RPP\) derived from the analysis run under a constant population size )] TJ ET BT 35.250 734.370 Td /F1 9.8 Tf [(model \(the two other models ended up with generating very similar results\) and an uncorrelated relaxed clock \(lognormal\). )] TJ ET BT 35.250 720.634 Td /F1 9.8 Tf [(In the top left corner the complete list of branches that appeared at least once in the posterior tree sample and the )] TJ ET BT 35.250 706.897 Td /F1 9.8 Tf [(according RPP. Note that two possible root locations \(6 and 7\) do not appear in the tree as the MCC tree did not comprise )] TJ ET BT 35.250 693.161 Td /F1 9.8 Tf [(the corresponding branches. All internal branches linking coloured clades/groups received very good support \(posterior )] TJ ET BT 35.250 679.425 Td /F1 9.8 Tf [(probability: 1.00\). The only exception was the branch defining the clade comprising Guinea 2014 EBOV and DRC )] TJ ET BT 35.250 665.689 Td /F1 9.8 Tf [(2007/2008 EBOV, which was only moderately supported \(posterior probability comprised between 0.56 and 0.68\).)] TJ ET Q BT 26.250 609.970 Td /F4 12.0 Tf [(Results and discussion)] TJ ET BT 26.250 590.016 Td /F1 9.8 Tf [(For the Zare lineage, the posterior tree samples that we analyzed \(one sample per demographic model\) did not comprise a )] TJ ET BT 26.250 578.111 Td /F1 9.8 Tf [(single tree whose root would be located on the branch leading to Guinea 2014 EBOV \(Figure 1\). Hence, under the assumption )] TJ ET BT 26.250 566.206 Td /F1 9.8 Tf [(of a relaxed molecular clock it seems extremely unlikely that this virus falls outside the genetic diversity of the Zare lineage. The )] TJ ET BT 26.250 554.301 Td /F1 9.8 Tf [(clock rooting approach implemented here therefore provides strong statistical support to the conclusion reached by Dudas and )] TJ ET BT 26.250 542.397 Td /F1 9.8 Tf [(Rambaut \(2014\))] TJ ET 0.267 0.267 0.267 rg BT 96.694 543.904 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 101.512 542.397 Td /F1 9.8 Tf [( . We also note that in our analyses the split of Guinea 2014 EBOV and the closest Central African EBOV was )] TJ ET BT 26.250 530.492 Td /F1 9.8 Tf [(inferred to have taken place in 1999 \(Bayesian skyride; 95% HPD interval 1996-2004\) or 2001 \(constant population size or )] TJ ET BT 26.250 518.587 Td /F1 9.8 Tf [(exponential growth; 95% HPD interval 1996-2003\), which comes very close to the GP-based estimates of Dudas and Rambaut )] TJ ET BT 26.250 506.682 Td /F1 9.8 Tf [(\(2002; 95% HPD interval 2000-2006\))] TJ ET 0.267 0.267 0.267 rg BT 186.111 508.190 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 190.930 506.682 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 487.278 Td /F1 9.8 Tf [(Depending on the demographic model, eight to nine root locations were identified within the Zare clade. Irrespective of the )] TJ ET BT 26.250 475.373 Td /F1 9.8 Tf [(demographic model, the same two branches were always identified as receiving the two highest RPP. The external branch )] TJ ET BT 26.250 463.468 Td /F1 9.8 Tf [(leading to the DRC 1976 ZEBOV strain \(Mayinga\) received RPP comprised between 0.62 and 0.69 whereas for the branch )] TJ ET BT 26.250 451.563 Td /F1 9.8 Tf [(defining the bipartition [DRC 1976/1977 ZEBOV strains|other ZEBOV strains] RPP were between 0.21 and 0.28. These results )] TJ ET BT 26.250 439.659 Td /F1 9.8 Tf [(mostly raise the question of the reciprocal monophyly of early DRC ZEBOV and all other ZEBOV strains \(only supported by the )] TJ ET BT 26.250 427.754 Td /F1 9.8 Tf [(second-to-best root location\).)] TJ ET 0.965 0.965 0.965 rg 26.250 54.123 555.000 363.750 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 417.873 m 581.250 417.873 l 581.250 417.123 l 26.250 417.123 l f q 450.000 0 0 348.000 35.250 60.123 cm /I12 Do Q q 35.250 54.123 537.000 0.000 re W n Q Q q 15.000 54.123 577.500 722.877 re W n 0.965 0.965 0.965 rg 26.250 644.191 555.000 132.809 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 644.191 m 581.250 644.191 l 581.250 644.941 l 26.250 644.941 l f q 35.250 655.441 537.000 121.559 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 1: Maximum clade credibility tree of concatenated coding sequences belonging to the Zare clade.)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(MCC tree and branch root posterior probabilities \(RPP\) derived from the analysis run under a constant population size )] TJ ET BT 35.250 734.370 Td /F1 9.8 Tf [(model \(the two other models ended up with generating very similar results\) and an uncorrelated relaxed clock \(lognormal\). )] TJ ET BT 35.250 720.634 Td /F1 9.8 Tf [(In the top left corner the complete list of branches that appeared at least once in the posterior tree sample and the )] TJ ET BT 35.250 706.897 Td /F1 9.8 Tf [(according RPP. Note that two possible root locations \(6 and 7\) do not appear in the tree as the MCC tree did not comprise )] TJ ET BT 35.250 693.161 Td /F1 9.8 Tf [(the corresponding branches. All internal branches linking coloured clades/groups received very good support \(posterior )] TJ ET BT 35.250 679.425 Td /F1 9.8 Tf [(probability: 1.00\). The only exception was the branch defining the clade comprising Guinea 2014 EBOV and DRC )] TJ ET BT 35.250 665.689 Td /F1 9.8 Tf [(2007/2008 EBOV, which was only moderately supported \(posterior probability comprised between 0.56 and 0.68\).)] TJ ET Q BT 26.250 609.970 Td /F4 12.0 Tf [(Results and discussion)] TJ ET BT 26.250 590.016 Td /F1 9.8 Tf [(For the Zare lineage, the posterior tree samples that we analyzed \(one sample per demographic model\) did not comprise a )] TJ ET BT 26.250 578.111 Td /F1 9.8 Tf [(single tree whose root would be located on the branch leading to Guinea 2014 EBOV \(Figure 1\). Hence, under the assumption )] TJ ET BT 26.250 566.206 Td /F1 9.8 Tf [(of a relaxed molecular clock it seems extremely unlikely that this virus falls outside the genetic diversity of the Zare lineage. The )] TJ ET BT 26.250 554.301 Td /F1 9.8 Tf [(clock rooting approach implemented here therefore provides strong statistical support to the conclusion reached by Dudas and )] TJ ET BT 26.250 542.397 Td /F1 9.8 Tf [(Rambaut \(2014\))] TJ ET 0.267 0.267 0.267 rg BT 96.694 543.904 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 101.512 542.397 Td /F1 9.8 Tf [( . We also note that in our analyses the split of Guinea 2014 EBOV and the closest Central African EBOV was )] TJ ET BT 26.250 530.492 Td /F1 9.8 Tf [(inferred to have taken place in 1999 \(Bayesian skyride; 95% HPD interval 1996-2004\) or 2001 \(constant population size or )] TJ ET BT 26.250 518.587 Td /F1 9.8 Tf [(exponential growth; 95% HPD interval 1996-2003\), which comes very close to the GP-based estimates of Dudas and Rambaut )] TJ ET BT 26.250 506.682 Td /F1 9.8 Tf [(\(2002; 95% HPD interval 2000-2006\))] TJ ET 0.267 0.267 0.267 rg BT 186.111 508.190 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 190.930 506.682 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 487.278 Td /F1 9.8 Tf [(Depending on the demographic model, eight to nine root locations were identified within the Zare clade. Irrespective of the )] TJ ET BT 26.250 475.373 Td /F1 9.8 Tf [(demographic model, the same two branches were always identified as receiving the two highest RPP. The external branch )] TJ ET BT 26.250 463.468 Td /F1 9.8 Tf [(leading to the DRC 1976 ZEBOV strain \(Mayinga\) received RPP comprised between 0.62 and 0.69 whereas for the branch )] TJ ET BT 26.250 451.563 Td /F1 9.8 Tf [(defining the bipartition [DRC 1976/1977 ZEBOV strains|other ZEBOV strains] RPP were between 0.21 and 0.28. These results )] TJ ET BT 26.250 439.659 Td /F1 9.8 Tf [(mostly raise the question of the reciprocal monophyly of early DRC ZEBOV and all other ZEBOV strains \(only supported by the )] TJ ET BT 26.250 427.754 Td /F1 9.8 Tf [(second-to-best root location\).)] TJ ET 0.965 0.965 0.965 rg 26.250 54.123 555.000 363.750 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 417.873 m 581.250 417.873 l 581.250 417.123 l 26.250 417.123 l f q 450.000 0 0 348.000 35.250 60.123 cm /I14 Do Q q 35.250 54.123 537.000 0.000 re W n Q Q q 15.000 54.123 577.500 722.877 re W n 0.965 0.965 0.965 rg 26.250 644.191 555.000 132.809 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 644.191 m 581.250 644.191 l 581.250 644.941 l 26.250 644.941 l f q 35.250 655.441 537.000 121.559 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 1: Maximum clade credibility tree of concatenated coding sequences belonging to the Zare clade.)] TJ ET BT 35.250 748.106 Td /F1 9.8 Tf [(MCC tree and branch root posterior probabilities \(RPP\) derived from the analysis run under a constant population size )] TJ ET BT 35.250 734.370 Td /F1 9.8 Tf [(model \(the two other models ended up with generating very similar results\) and an uncorrelated relaxed clock \(lognormal\). )] TJ ET BT 35.250 720.634 Td /F1 9.8 Tf [(In the top left corner the complete list of branches that appeared at least once in the posterior tree sample and the )] TJ ET BT 35.250 706.897 Td /F1 9.8 Tf [(according RPP. Note that two possible root locations \(6 and 7\) do not appear in the tree as the MCC tree did not comprise )] TJ ET BT 35.250 693.161 Td /F1 9.8 Tf [(the corresponding branches. All internal branches linking coloured clades/groups received very good support \(posterior )] TJ ET BT 35.250 679.425 Td /F1 9.8 Tf [(probability: 1.00\). The only exception was the branch defining the clade comprising Guinea 2014 EBOV and DRC )] TJ ET BT 35.250 665.689 Td /F1 9.8 Tf [(2007/2008 EBOV, which was only moderately supported \(posterior probability comprised between 0.56 and 0.68\).)] TJ ET Q BT 26.250 609.970 Td /F4 12.0 Tf [(Results and discussion)] TJ ET BT 26.250 590.016 Td /F1 9.8 Tf [(For the Zare lineage, the posterior tree samples that we analyzed \(one sample per demographic model\) did not comprise a )] TJ ET BT 26.250 578.111 Td /F1 9.8 Tf [(single tree whose root would be located on the branch leading to Guinea 2014 EBOV \(Figure 1\). Hence, under the assumption )] TJ ET BT 26.250 566.206 Td /F1 9.8 Tf [(of a relaxed molecular clock it seems extremely unlikely that this virus falls outside the genetic diversity of the Zare lineage. The )] TJ ET BT 26.250 554.301 Td /F1 9.8 Tf [(clock rooting approach implemented here therefore provides strong statistical support to the conclusion reached by Dudas and )] TJ ET BT 26.250 542.397 Td /F1 9.8 Tf [(Rambaut \(2014\))] TJ ET 0.267 0.267 0.267 rg BT 96.694 543.904 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 101.512 542.397 Td /F1 9.8 Tf [( . We also note that in our analyses the split of Guinea 2014 EBOV and the closest Central African EBOV was )] TJ ET BT 26.250 530.492 Td /F1 9.8 Tf [(inferred to have taken place in 1999 \(Bayesian skyride; 95% HPD interval 1996-2004\) or 2001 \(constant population size or )] TJ ET BT 26.250 518.587 Td /F1 9.8 Tf [(exponential growth; 95% HPD interval 1996-2003\), which comes very close to the GP-based estimates of Dudas and Rambaut )] TJ ET BT 26.250 506.682 Td /F1 9.8 Tf [(\(2002; 95% HPD interval 2000-2006\))] TJ ET 0.267 0.267 0.267 rg BT 186.111 508.190 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 190.930 506.682 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 487.278 Td /F1 9.8 Tf [(Depending on the demographic model, eight to nine root locations were identified within the Zare clade. Irrespective of the )] TJ ET BT 26.250 475.373 Td /F1 9.8 Tf [(demographic model, the same two branches were always identified as receiving the two highest RPP. The external branch )] TJ ET BT 26.250 463.468 Td /F1 9.8 Tf [(leading to the DRC 1976 ZEBOV strain \(Mayinga\) received RPP comprised between 0.62 and 0.69 whereas for the branch )] TJ ET BT 26.250 451.563 Td /F1 9.8 Tf [(defining the bipartition [DRC 1976/1977 ZEBOV strains|other ZEBOV strains] RPP were between 0.21 and 0.28. These results )] TJ ET BT 26.250 439.659 Td /F1 9.8 Tf [(mostly raise the question of the reciprocal monophyly of early DRC ZEBOV and all other ZEBOV strains \(only supported by the )] TJ ET BT 26.250 427.754 Td /F1 9.8 Tf [(second-to-best root location\).)] TJ ET 0.965 0.965 0.965 rg 26.250 54.123 555.000 363.750 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 417.873 m 581.250 417.873 l 581.250 417.123 l 26.250 417.123 l f q 450.000 0 0 348.000 35.250 60.123 cm /I16 Do Q q 35.250 54.123 537.000 0.000 re W n Q Q q 450.000 0 0 348.000 35.250 60.123 cm /I18 Do 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 Outbreaks)] TJ ET Q endstream endobj 225 0 obj << /Type /Annot /Subtype /Link /A 226 0 R /Border [0 0 0] /H /I /Rect [ 96.6937 543.1022 101.5124 551.9205 ] >> endobj 226 0 obj << /Type /Action >> endobj 227 0 obj << /Type /Annot /Subtype /Link /A 228 0 R /Border [0 0 0] /H /I /Rect [ 186.1110 507.3879 190.9297 516.2062 ] >> endobj 228 0 obj << /Type /Action >> endobj 229 0 obj << /Type /Annot /Subtype /Link /A 230 0 R /Border [0 0 0] /H /I /Rect [ 35.2500 60.1230 485.2500 408.1230 ] >> endobj 230 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/outbreaks/files/2014/05/Figure_2.png) >> endobj 231 0 obj << /Type /XObject /Subtype /Image /Width 600 /Height 464 /Filter /FlateDecode /DecodeParms << /Predictor 15 /Colors 1 /Columns 600 /BitsPerComponent 8>> /ColorSpace /DeviceGray /BitsPerComponent 8 /Length 12887>> stream xD_cffffff$3$I2I$$3I2I$I$Id$If23$$I+u]u]yyn{߻s=ϧss                      H ʺ2^ ?tm^俄>÷%^?CYHqgWEJ&5uUTuWsTBc]|/X(tVv@٭045ңf9̠ꂺ `5PbWKUV@lA-MF?sXˢIƒ*;f<Q%iQSO|\pUS%pl;0nǗu)`Ej=]G߃|:jՀt[+N;7l6y^_b)T>E3RlL̂0AeoWM:}Q Xm5ځ4U ASc=Szm%}:&֤|Р](),`W3:5вF&]^67[,bYXd^l;xLX;5Lo߰-H?Ǧ0Dvzh|?_xZs KcwKCIDCŲ_92hX!!Kqt]|Q&l@5y^!uݟI+&^7|Q'W38Ju&VbyyT`Jk")ϻ=.#i1OKXl٠HʚÆQper? }WZ,!KfT'\ @n8K>u>m_f݁?_U|>5 ]M3NQO@r @QYGDHf 3L,RsA]bM)s\Vs@#˲)9lZD!![պ<ʈ кyXK HckXk^ ~FWTrv́ږ+VbzEEOD&b]5X쟤8!k8Pu2N&jY&"cLG>Gv:4r0|0v5Wd CjZ]tͿ"0z+bi'zp$EpE?MdZjViE7LY TM8  _T4S/e-#'d*abe*FY@LgDX9p"sfl2Jne/Uf Qcs0maNKD om7_kP~A,(X w9_~1c/杩I/pC2^E_|6A, (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" ({=ޗ"HA.O OcS(" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" (" *oJDykX>IF'bg5^M,׷k;"+++Ӎ$Ktj_ dN,^JZbU|&g>oLL̦2rbbZB+ftf)> mk]Dff{ƕt[~Uq` ;8tT5@oL Ml`@ڟ-CPsE٩n |UKvH\L?hz(+'Y/1)_g}N^Psw6f腔$V\SHjV`h:5ՁaESS|ɶ6F}@s|х4ڄKVe?%;N:{&%XX3i55w=W㇠kyoj]!gTUuCL[e^CA Alku䒢vnCA@[+Z bXw:_ Lp~*boJOZG* 1 pVEZgg28+eYy>UÔKuJVXhtDu*pIl;o{ab]IJ&z>p9k\p^ɣ+%,/Ć iyձW\1%z GZ>,fݬR"{1e|ޫ[@n i GheZ_Z:4ZBͯ,ꈛtW/t@msl#OM!ZOOOx(Xfh\mAzFYkT͵k;bbMLSHti(F=n=ȩb$#s;{ u3j0DKAb};CLJYH"c'V@">w M)(dyN!m*ab@SIҨIكXĸHA,CS5-v O7 |͊ybu^$LkAmY,;Q+A _Gr&V٭Z4; %]oEL\o`˒ɶ`sT'( H77KCXDz-3"SHiQ%rzӿdl.B~)/| +ܯ^&/Tr%}Xi>Ω^LOb)-OV)b!b!Yp(wxq_i*#Q>\{RYP,D$}sc0)T>LK+YKI̕/_܀b!Xϵ`2stې.O.N ߻=lx1C aL^#ʌ7hZ`*[E]_@%fw:|})[gt>B(]bOX9`n #PfźNO+(\z>t\L _^B(|>ȅ8/4&U' OrD|X!}TBp.GbpΗrDJXOee_ >^B(w57MQ?*Ӷu[ alzaʸ3"hG\*ɱ|r{ aO@!ox< 7XHIO RSbb!ߑ//SX(X(X#ցagYqb!*v<|K8gu/^2("x??m.#eUb! 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K:(H7m+T!Ap .09B UHr0b;H Ɣ>P 0|HWQ\.GQg|Z[[G>Cr9(qfފC: B+NX~Aa(.\x+0AȰJ$({ȑ/|ҤIIIB: B% g[nmiiٵkעEnGd!PUF[<5&c555~ov!@ P`r9?{wa^qǎ S(*J#]qwi2,------=G>3gkFsm۶;w|'m| =4JBU`h#] /c~7tӺu0ꪫGQ8u,@>-Bmݖ# aE7X&k+JȋCk Lڂi]]]cǎ/ ('i;w{ p> q S2"m۶+W=z4 |`ԋ_}Gyd޼yqBF Ť|ӧO_z t( [7xc| PDcIogA ; @q 8Y&3Lu@am 44C(ܻÄ=Bi.\rDEƍ1cF .yW*r[~ǓΣ'$tY @q }Đ9g uD Phg۫5@ 5Z*-K&5L^XڀAN Y@q/W& *vv!ŕv;4]vΝQ͚5kӧOO/څQN0‹hժU֭կ~裏h!`t L f.Ӓ#<#sQo 5nƂ3UDQTLz}[lwL^c飉egn̐gk]vѢEZ4]X`t:G1c$m~AjK;\$6Ӌ #;uԘ1cqeeZB`"3(RTD$r,HHAP*ɓNzflS-BQl (*(֤2A $k4ζtmڴ\.8qbܹ-jllK9q4Mo` maz\_^z>+V>|g?Yz^EQX0O7|szdr]P^NY{{z-̚5kůcǂQښ;4xWϞ=;3=5 _b|׷m۶)S? ښL|bΠwf6TFmmm+Vxꩧof>R飹夻C  ,!HO6mٲeV^̧5e&۽{/>#T5.̝8.櫮W^ٸq]wyN{_L0`0駟~Gƍ4 E42ɘYCC3#k4v2G4wj(0>B mpoZM@/OCjaxر^z)YM$BH9)8䢯oڵ;vkjjҽrY rI.|7jR)_|W_~kg"dv`C:G޽{ׯ_dɒL4.Nr9n&MU:Prr힞5ku]͙Ia?s̤0 zSd!PrF3ͻ(֯_<2\rG?ڽ{wfժUӦMKJǸe^{^XrѣGO8wI&֦?"/BqhNggg{{+΃0 'O.a:նlrȑ|;ADQo~;w#-mٷo_]]>ff @UaJ^ {{{Gmmmk׮}jj_u۸qkc_Wf̘Q-@ȟ5>O?vL 8mڴ)sĉӧO;N|80 __ $?`K]"}Ǧ\r={̜93Sa\HA ]w?׿u׮]/0馛2U87{H *hÆ 6l8yٳ-Z4uG|sa<2r>)TAp >"E)T t_42va tw PA dOLw*6XƿkCNy@q |" X}ZC('㷽OO>[%>z W^`fPDv[`ArgܹMMMqfJ@tfΦ~'===^zr0s|]]ݮ]~wvv=scǎ7oYG}cƌ{gϞ!E4XСC}}}SNNTtNzeW) @ 6>dir_s:@'btUJR󥊢( ֑!G\/ ACj B΃r_ᗑ!PjF^0 K㷙@2,R)Lm߾}]]]QeTAp n:uj{IF!Pm!\.'!D]E֭kiiNUE2,ٶiӦE%e(*J~C]v%ScÇ7{Ǝ <0rU-[E{{{׮]{ϔL۽{(jGwK.$yiӦRo֭mmm]]]MMMAjw125Eȹޮ f0 .]:uȨ P`qaΙ3gΜ9={/׿А(P9w ./mMMMSSSzq@uÒe4̾v!Ò[zEfME B5;TsBQQ!YI @vJ endstream endobj 251 0 obj << /Type /Page /Parent 3 0 R /Annots [ 253 0 R 255 0 R 257 0 R 259 0 R 261 0 R 263 0 R 265 0 R 267 0 R 269 0 R 271 0 R 273 0 R 275 0 R ] /Contents 252 0 R >> endobj 252 0 obj << /Length 22780 >> stream q 15.000 47.873 577.500 729.127 re W n 0.965 0.965 0.965 rg 26.250 673.495 555.000 103.505 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 673.495 m 581.250 673.495 l 581.250 674.245 l 26.250 674.245 l f q 35.250 684.745 537.000 92.255 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 2: Maximum clade credibility tree of concatenated coding sequences representing the 5 species of the genus )] TJ ET BT 35.250 755.571 Td /F4 9.8 Tf [(Ebolavirus.)] TJ ET BT 35.250 736.201 Td /F1 9.8 Tf [(MCC tree and branch root posterior probabilities \(RPP\) derived from the analysis run under a Yule process \(a Birth-Death )] TJ ET BT 35.250 722.465 Td /F1 9.8 Tf [(process ended up with generating very similar results\) and an uncorrelated relaxed clock \(lognormal\). The clock was not )] TJ ET BT 35.250 708.729 Td /F1 9.8 Tf [(calibrated and the scale axis therefore is in substitution per site. RPP are reported in the list appearing at the left of the tree. )] TJ ET BT 35.250 694.993 Td /F1 9.8 Tf [(All internal branches received very good support \(posterior probability: 1.00\).)] TJ ET Q BT 26.250 656.472 Td /F1 9.8 Tf [(We also applied the clock rooting approach to the genus )] TJ ET BT 271.755 656.472 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 317.268 656.472 Td /F1 9.8 Tf [(. Two recent articles whose analyses included outgroup )] TJ ET BT 26.250 644.567 Td /F1 9.8 Tf [(sequences \(Marburg virus and Lloviu virus\) agreed on the monophyly of Bundibugyo, Ta Forest and Zare ebolaviruses but )] TJ ET BT 26.250 632.662 Td /F1 9.8 Tf [(supported different sisterships of this clade with Reston and Sudan ebolaviruses. In the phylogeny produced by Lauber and )] TJ ET BT 26.250 620.757 Td /F1 9.8 Tf [(Gorbalenya \(2012\) Reston ebolavirus was in sistership with the clade comprising Zare ebolavirus)] TJ ET 0.267 0.267 0.267 rg BT 447.274 622.265 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 456.912 620.757 Td /F1 9.8 Tf [( while in the phylogeny by )] TJ ET BT 26.250 608.853 Td /F1 9.8 Tf [(Carroll et al. \(2013\) Sudan and Reston ebolaviruses formed a sister clade to the clade comprising Zare ebolavirus)] TJ ET 0.267 0.267 0.267 rg BT 519.366 610.360 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 529.003 608.853 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 589.448 Td /F1 9.8 Tf [(Under both speciation priors we tested, five root locations were identified and among these three gathered >0.99 RPP \(Figure )] TJ ET BT 26.250 577.543 Td /F1 9.8 Tf [(2\). The branch defining the bipartition [Sudan, Reston|Bundibugyo, Ta Forest, Zare] received RPP 0.69 and 0.68 \(Yule and )] TJ ET BT 26.250 565.638 Td /F1 9.8 Tf [(Birth-Death process, respectively\), the external branch leading to Sudan ebolavirus RPP 0.19 and 0.18 and the external branch )] TJ ET BT 26.250 553.734 Td /F1 9.8 Tf [(leading to Reston ebolavirus RPP 0.12 and 0.13. Therefore, while the hypothesis put forward by Carroll et al. \(2013\) gets more )] TJ ET BT 26.250 541.829 Td /F1 9.8 Tf [(probabilistic support)] TJ ET 0.267 0.267 0.267 rg BT 112.947 543.336 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 122.584 541.829 Td /F1 9.8 Tf [( , our analyses underlines significant uncertainty and the existence of a third plausible root position. As )] TJ ET BT 26.250 529.924 Td /F1 9.8 Tf [(Reston ebolavirus is the only Asian ebolavirus \(all other ebolaviruses are African\), we note here that this new rooting scenario )] TJ ET BT 26.250 518.019 Td /F1 9.8 Tf [(would imply a geographical partitioning of the genetic diversity within the genus )] TJ ET BT 369.820 518.019 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 415.333 518.019 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 498.615 Td /F1 9.8 Tf [(In our view, these examples highlight the unique ability of clock rooting to capture uncertainty so as to root location. With )] TJ ET BT 26.250 486.710 Td /F1 9.8 Tf [(RootAnnotator it is now easily possible to establish short lists of plausible roots warranting further examination)] TJ ET 0.267 0.267 0.267 rg BT 499.856 488.217 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 509.494 486.710 Td /F1 9.8 Tf [( , even where )] TJ ET BT 26.250 474.805 Td /F1 9.8 Tf [(no obvious candidate roots exist \(e.g. in the absence of appropriate outgroups\). We hope that this tool will provide the many )] TJ ET BT 26.250 462.900 Td /F1 9.8 Tf [(biologists using Bayesian phylogenetics under clock models with a rationale to turn even more tree-like graphs into phylogenetic )] TJ ET BT 26.250 450.996 Td /F1 9.8 Tf [(trees.)] TJ ET BT 26.250 414.393 Td /F4 12.0 Tf [(Competing interests)] TJ ET BT 26.250 394.439 Td /F1 9.8 Tf [(The authors have declared that no competing interests exist.)] TJ ET BT 26.250 357.836 Td /F4 12.0 Tf [(Acknowledgements)] TJ ET BT 26.250 337.882 Td /F1 9.8 Tf [(The authors thank Paul Schpe for his help with the implementation of BEAST on a local server. SCS thanks the entire group )] TJ ET BT 568.721 337.882 Td /F1 9.8 Tf [(of )] TJ ET BT 26.250 325.977 Td /F1 9.8 Tf [(epidemiology of highly pathogenic microorganisms at the Robert Koch-Institute for stimulating discussions.)] TJ ET BT 26.250 296.875 Td /F4 12.0 Tf [(References)] TJ ET BT 26.250 269.421 Td /F1 9.8 Tf [(1.)] TJ ET BT 38.132 269.421 Td /F1 9.8 Tf [(Hall BG. Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol. 2013 May;30\(5\):1229-35. PubMed )] TJ ET BT 26.250 257.516 Td /F1 9.8 Tf [(PMID:23486614.)] TJ ET BT 26.250 238.111 Td /F1 9.8 Tf [(2.)] TJ ET BT 38.132 238.111 Td /F1 9.8 Tf [(Dudas G, Rambaut A. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak. PLOS Currents Outbreaks. 2014 )] TJ ET BT 26.250 226.206 Td /F1 9.8 Tf [(May 2. Edition 1. doi: 10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d.)] TJ ET BT 26.250 206.802 Td /F1 9.8 Tf [(3.)] TJ ET BT 38.132 206.802 Td /F1 9.8 Tf [(Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N, Soropogui B, Sow MS, Keta S, De Clerck H, )] TJ ET BT 26.250 194.897 Td /F1 9.8 Tf [(Tiffany A, Dominguez G, Loua M, Traor A, Koli M, Malano ER, Heleze E, Bocquin A, Mly S, Raoul H, Caro V, Cadar D, )] TJ ET BT 26.250 182.992 Td /F1 9.8 Tf [(Gabriel M, Pahlmann M, Tappe D, Schmidt-Chanasit J, Impouma B, Diallo AK, Formenty P, Van Herp M, Gnther S. )] TJ ET BT 26.250 171.087 Td /F1 9.8 Tf [(Emergence of Zaire Ebola Virus Disease in Guinea - Preliminary Report. N Engl J Med. 2014 Apr 16. PubMed PMID:24738640.)] TJ ET BT 26.250 151.683 Td /F1 9.8 Tf [(4.)] TJ ET BT 38.132 151.683 Td /F1 9.8 Tf [(Bergsten, J. \(2005\), A review of long-branch attraction. Cladistics, 21: 163193. doi: 10.1111/j.1096-0031.2005.00059.x)] TJ ET BT 26.250 132.278 Td /F1 9.8 Tf [(5.)] TJ ET BT 38.132 132.278 Td /F1 9.8 Tf [(Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006 )] TJ ET BT 26.250 120.373 Td /F1 9.8 Tf [(May;4\(5\):e88. PubMed PMID:16683862.)] TJ ET BT 26.250 100.968 Td /F1 9.8 Tf [(6.)] TJ ET BT 38.132 100.968 Td /F1 9.8 Tf [(Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. )] TJ ET BT 26.250 89.064 Td /F1 9.8 Tf [(2012 Aug;29\(8\):1969-73. PubMed PMID:22367748.)] TJ ET BT 26.250 69.659 Td /F1 9.8 Tf [(7.)] TJ ET BT 38.132 69.659 Td /F1 9.8 Tf [(Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007 Nov 8;7:214. )] TJ ET BT 26.250 57.754 Td /F1 9.8 Tf [(PubMed PMID:17996036.)] TJ ET Q q 15.000 47.873 577.500 729.127 re W n 0.965 0.965 0.965 rg 26.250 673.495 555.000 103.505 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 673.495 m 581.250 673.495 l 581.250 674.245 l 26.250 674.245 l f q 35.250 684.745 537.000 92.255 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 2: Maximum clade credibility tree of concatenated coding sequences representing the 5 species of the genus )] TJ ET BT 35.250 755.571 Td /F4 9.8 Tf [(Ebolavirus.)] TJ ET BT 35.250 736.201 Td /F1 9.8 Tf [(MCC tree and branch root posterior probabilities \(RPP\) derived from the analysis run under a Yule process \(a Birth-Death )] TJ ET BT 35.250 722.465 Td /F1 9.8 Tf [(process ended up with generating very similar results\) and an uncorrelated relaxed clock \(lognormal\). The clock was not )] TJ ET BT 35.250 708.729 Td /F1 9.8 Tf [(calibrated and the scale axis therefore is in substitution per site. RPP are reported in the list appearing at the left of the tree. )] TJ ET BT 35.250 694.993 Td /F1 9.8 Tf [(All internal branches received very good support \(posterior probability: 1.00\).)] TJ ET Q BT 26.250 656.472 Td /F1 9.8 Tf [(We also applied the clock rooting approach to the genus )] TJ ET BT 271.755 656.472 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 317.268 656.472 Td /F1 9.8 Tf [(. Two recent articles whose analyses included outgroup )] TJ ET BT 26.250 644.567 Td /F1 9.8 Tf [(sequences \(Marburg virus and Lloviu virus\) agreed on the monophyly of Bundibugyo, Ta Forest and Zare ebolaviruses but )] TJ ET BT 26.250 632.662 Td /F1 9.8 Tf [(supported different sisterships of this clade with Reston and Sudan ebolaviruses. In the phylogeny produced by Lauber and )] TJ ET BT 26.250 620.757 Td /F1 9.8 Tf [(Gorbalenya \(2012\) Reston ebolavirus was in sistership with the clade comprising Zare ebolavirus)] TJ ET 0.267 0.267 0.267 rg BT 447.274 622.265 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 456.912 620.757 Td /F1 9.8 Tf [( while in the phylogeny by )] TJ ET BT 26.250 608.853 Td /F1 9.8 Tf [(Carroll et al. \(2013\) Sudan and Reston ebolaviruses formed a sister clade to the clade comprising Zare ebolavirus)] TJ ET 0.267 0.267 0.267 rg BT 519.366 610.360 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 529.003 608.853 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 589.448 Td /F1 9.8 Tf [(Under both speciation priors we tested, five root locations were identified and among these three gathered >0.99 RPP \(Figure )] TJ ET BT 26.250 577.543 Td /F1 9.8 Tf [(2\). The branch defining the bipartition [Sudan, Reston|Bundibugyo, Ta Forest, Zare] received RPP 0.69 and 0.68 \(Yule and )] TJ ET BT 26.250 565.638 Td /F1 9.8 Tf [(Birth-Death process, respectively\), the external branch leading to Sudan ebolavirus RPP 0.19 and 0.18 and the external branch )] TJ ET BT 26.250 553.734 Td /F1 9.8 Tf [(leading to Reston ebolavirus RPP 0.12 and 0.13. Therefore, while the hypothesis put forward by Carroll et al. \(2013\) gets more )] TJ ET BT 26.250 541.829 Td /F1 9.8 Tf [(probabilistic support)] TJ ET 0.267 0.267 0.267 rg BT 112.947 543.336 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 122.584 541.829 Td /F1 9.8 Tf [( , our analyses underlines significant uncertainty and the existence of a third plausible root position. As )] TJ ET BT 26.250 529.924 Td /F1 9.8 Tf [(Reston ebolavirus is the only Asian ebolavirus \(all other ebolaviruses are African\), we note here that this new rooting scenario )] TJ ET BT 26.250 518.019 Td /F1 9.8 Tf [(would imply a geographical partitioning of the genetic diversity within the genus )] TJ ET BT 369.820 518.019 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 415.333 518.019 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 498.615 Td /F1 9.8 Tf [(In our view, these examples highlight the unique ability of clock rooting to capture uncertainty so as to root location. With )] TJ ET BT 26.250 486.710 Td /F1 9.8 Tf [(RootAnnotator it is now easily possible to establish short lists of plausible roots warranting further examination)] TJ ET 0.267 0.267 0.267 rg BT 499.856 488.217 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 509.494 486.710 Td /F1 9.8 Tf [( , even where )] TJ ET BT 26.250 474.805 Td /F1 9.8 Tf [(no obvious candidate roots exist \(e.g. in the absence of appropriate outgroups\). We hope that this tool will provide the many )] TJ ET BT 26.250 462.900 Td /F1 9.8 Tf [(biologists using Bayesian phylogenetics under clock models with a rationale to turn even more tree-like graphs into phylogenetic )] TJ ET BT 26.250 450.996 Td /F1 9.8 Tf [(trees.)] TJ ET BT 26.250 414.393 Td /F4 12.0 Tf [(Competing interests)] TJ ET BT 26.250 394.439 Td /F1 9.8 Tf [(The authors have declared that no competing interests exist.)] TJ ET BT 26.250 357.836 Td /F4 12.0 Tf [(Acknowledgements)] TJ ET BT 26.250 337.882 Td /F1 9.8 Tf [(The authors thank Paul Schpe for his help with the implementation of BEAST on a local server. SCS thanks the entire group )] TJ ET BT 568.721 337.882 Td /F1 9.8 Tf [(of )] TJ ET BT 26.250 325.977 Td /F1 9.8 Tf [(epidemiology of highly pathogenic microorganisms at the Robert Koch-Institute for stimulating discussions.)] TJ ET BT 26.250 296.875 Td /F4 12.0 Tf [(References)] TJ ET BT 26.250 269.421 Td /F1 9.8 Tf [(1.)] TJ ET BT 38.132 269.421 Td /F1 9.8 Tf [(Hall BG. Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol. 2013 May;30\(5\):1229-35. PubMed )] TJ ET BT 26.250 257.516 Td /F1 9.8 Tf [(PMID:23486614.)] TJ ET BT 26.250 238.111 Td /F1 9.8 Tf [(2.)] TJ ET BT 38.132 238.111 Td /F1 9.8 Tf [(Dudas G, Rambaut A. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak. PLOS Currents Outbreaks. 2014 )] TJ ET BT 26.250 226.206 Td /F1 9.8 Tf [(May 2. Edition 1. doi: 10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d.)] TJ ET BT 26.250 206.802 Td /F1 9.8 Tf [(3.)] TJ ET BT 38.132 206.802 Td /F1 9.8 Tf [(Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N, Soropogui B, Sow MS, Keta S, De Clerck H, )] TJ ET BT 26.250 194.897 Td /F1 9.8 Tf [(Tiffany A, Dominguez G, Loua M, Traor A, Koli M, Malano ER, Heleze E, Bocquin A, Mly S, Raoul H, Caro V, Cadar D, )] TJ ET BT 26.250 182.992 Td /F1 9.8 Tf [(Gabriel M, Pahlmann M, Tappe D, Schmidt-Chanasit J, Impouma B, Diallo AK, Formenty P, Van Herp M, Gnther S. )] TJ ET BT 26.250 171.087 Td /F1 9.8 Tf [(Emergence of Zaire Ebola Virus Disease in Guinea - Preliminary Report. N Engl J Med. 2014 Apr 16. PubMed PMID:24738640.)] TJ ET BT 26.250 151.683 Td /F1 9.8 Tf [(4.)] TJ ET BT 38.132 151.683 Td /F1 9.8 Tf [(Bergsten, J. \(2005\), A review of long-branch attraction. Cladistics, 21: 163193. doi: 10.1111/j.1096-0031.2005.00059.x)] TJ ET BT 26.250 132.278 Td /F1 9.8 Tf [(5.)] TJ ET BT 38.132 132.278 Td /F1 9.8 Tf [(Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006 )] TJ ET BT 26.250 120.373 Td /F1 9.8 Tf [(May;4\(5\):e88. PubMed PMID:16683862.)] TJ ET BT 26.250 100.968 Td /F1 9.8 Tf [(6.)] TJ ET BT 38.132 100.968 Td /F1 9.8 Tf [(Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. )] TJ ET BT 26.250 89.064 Td /F1 9.8 Tf [(2012 Aug;29\(8\):1969-73. PubMed PMID:22367748.)] TJ ET BT 26.250 69.659 Td /F1 9.8 Tf [(7.)] TJ ET BT 38.132 69.659 Td /F1 9.8 Tf [(Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007 Nov 8;7:214. )] TJ ET BT 26.250 57.754 Td /F1 9.8 Tf [(PubMed PMID:17996036.)] TJ ET Q q 15.000 47.873 577.500 729.127 re W n 0.965 0.965 0.965 rg 26.250 673.495 555.000 103.505 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 673.495 m 581.250 673.495 l 581.250 674.245 l 26.250 674.245 l f q 35.250 684.745 537.000 92.255 re W n 0.271 0.267 0.267 rg BT 35.250 767.476 Td /F4 9.8 Tf [(Fig. 2: Maximum clade credibility tree of concatenated coding sequences representing the 5 species of the genus )] TJ ET BT 35.250 755.571 Td /F4 9.8 Tf [(Ebolavirus.)] TJ ET BT 35.250 736.201 Td /F1 9.8 Tf [(MCC tree and branch root posterior probabilities \(RPP\) derived from the analysis run under a Yule process \(a Birth-Death )] TJ ET BT 35.250 722.465 Td /F1 9.8 Tf [(process ended up with generating very similar results\) and an uncorrelated relaxed clock \(lognormal\). The clock was not )] TJ ET BT 35.250 708.729 Td /F1 9.8 Tf [(calibrated and the scale axis therefore is in substitution per site. RPP are reported in the list appearing at the left of the tree. )] TJ ET BT 35.250 694.993 Td /F1 9.8 Tf [(All internal branches received very good support \(posterior probability: 1.00\).)] TJ ET Q BT 26.250 656.472 Td /F1 9.8 Tf [(We also applied the clock rooting approach to the genus )] TJ ET BT 271.755 656.472 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 317.268 656.472 Td /F1 9.8 Tf [(. Two recent articles whose analyses included outgroup )] TJ ET BT 26.250 644.567 Td /F1 9.8 Tf [(sequences \(Marburg virus and Lloviu virus\) agreed on the monophyly of Bundibugyo, Ta Forest and Zare ebolaviruses but )] TJ ET BT 26.250 632.662 Td /F1 9.8 Tf [(supported different sisterships of this clade with Reston and Sudan ebolaviruses. In the phylogeny produced by Lauber and )] TJ ET BT 26.250 620.757 Td /F1 9.8 Tf [(Gorbalenya \(2012\) Reston ebolavirus was in sistership with the clade comprising Zare ebolavirus)] TJ ET 0.267 0.267 0.267 rg BT 447.274 622.265 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 456.912 620.757 Td /F1 9.8 Tf [( while in the phylogeny by )] TJ ET BT 26.250 608.853 Td /F1 9.8 Tf [(Carroll et al. \(2013\) Sudan and Reston ebolaviruses formed a sister clade to the clade comprising Zare ebolavirus)] TJ ET 0.267 0.267 0.267 rg BT 519.366 610.360 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 529.003 608.853 Td /F1 9.8 Tf [( .)] TJ ET BT 26.250 589.448 Td /F1 9.8 Tf [(Under both speciation priors we tested, five root locations were identified and among these three gathered >0.99 RPP \(Figure )] TJ ET BT 26.250 577.543 Td /F1 9.8 Tf [(2\). The branch defining the bipartition [Sudan, Reston|Bundibugyo, Ta Forest, Zare] received RPP 0.69 and 0.68 \(Yule and )] TJ ET BT 26.250 565.638 Td /F1 9.8 Tf [(Birth-Death process, respectively\), the external branch leading to Sudan ebolavirus RPP 0.19 and 0.18 and the external branch )] TJ ET BT 26.250 553.734 Td /F1 9.8 Tf [(leading to Reston ebolavirus RPP 0.12 and 0.13. Therefore, while the hypothesis put forward by Carroll et al. \(2013\) gets more )] TJ ET BT 26.250 541.829 Td /F1 9.8 Tf [(probabilistic support)] TJ ET 0.267 0.267 0.267 rg BT 112.947 543.336 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 122.584 541.829 Td /F1 9.8 Tf [( , our analyses underlines significant uncertainty and the existence of a third plausible root position. As )] TJ ET BT 26.250 529.924 Td /F1 9.8 Tf [(Reston ebolavirus is the only Asian ebolavirus \(all other ebolaviruses are African\), we note here that this new rooting scenario )] TJ ET BT 26.250 518.019 Td /F1 9.8 Tf [(would imply a geographical partitioning of the genetic diversity within the genus )] TJ ET BT 369.820 518.019 Td /F5 9.8 Tf [(Ebolavirus)] TJ ET BT 415.333 518.019 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 498.615 Td /F1 9.8 Tf [(In our view, these examples highlight the unique ability of clock rooting to capture uncertainty so as to root location. With )] TJ ET BT 26.250 486.710 Td /F1 9.8 Tf [(RootAnnotator it is now easily possible to establish short lists of plausible roots warranting further examination)] TJ ET 0.267 0.267 0.267 rg BT 499.856 488.217 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 509.494 486.710 Td /F1 9.8 Tf [( , even where )] TJ ET BT 26.250 474.805 Td /F1 9.8 Tf [(no obvious candidate roots exist \(e.g. in the absence of appropriate outgroups\). We hope that this tool will provide the many )] TJ ET BT 26.250 462.900 Td /F1 9.8 Tf [(biologists using Bayesian phylogenetics under clock models with a rationale to turn even more tree-like graphs into phylogenetic )] TJ ET BT 26.250 450.996 Td /F1 9.8 Tf [(trees.)] TJ ET BT 26.250 414.393 Td /F4 12.0 Tf [(Competing interests)] TJ ET BT 26.250 394.439 Td /F1 9.8 Tf [(The authors have declared that no competing interests exist.)] TJ ET BT 26.250 357.836 Td /F4 12.0 Tf [(Acknowledgements)] TJ ET BT 26.250 337.882 Td /F1 9.8 Tf [(The authors thank Paul Schpe for his help with the implementation of BEAST on a local server. SCS thanks the entire group )] TJ ET BT 568.721 337.882 Td /F1 9.8 Tf [(of )] TJ ET BT 26.250 325.977 Td /F1 9.8 Tf [(epidemiology of highly pathogenic microorganisms at the Robert Koch-Institute for stimulating discussions.)] TJ ET BT 26.250 296.875 Td /F4 12.0 Tf [(References)] TJ ET BT 26.250 269.421 Td /F1 9.8 Tf [(1.)] TJ ET BT 38.132 269.421 Td /F1 9.8 Tf [(Hall BG. Building phylogenetic trees from molecular data with MEGA. Mol Biol Evol. 2013 May;30\(5\):1229-35. PubMed )] TJ ET BT 26.250 257.516 Td /F1 9.8 Tf [(PMID:23486614.)] TJ ET BT 26.250 238.111 Td /F1 9.8 Tf [(2.)] TJ ET BT 38.132 238.111 Td /F1 9.8 Tf [(Dudas G, Rambaut A. Phylogenetic Analysis of Guinea 2014 EBOV Ebolavirus Outbreak. PLOS Currents Outbreaks. 2014 )] TJ ET BT 26.250 226.206 Td /F1 9.8 Tf [(May 2. Edition 1. doi: 10.1371/currents.outbreaks.84eefe5ce43ec9dc0bf0670f7b8b417d.)] TJ ET BT 26.250 206.802 Td /F1 9.8 Tf [(3.)] TJ ET BT 38.132 206.802 Td /F1 9.8 Tf [(Baize S, Pannetier D, Oestereich L, Rieger T, Koivogui L, Magassouba N, Soropogui B, Sow MS, Keta S, De Clerck H, )] TJ ET BT 26.250 194.897 Td /F1 9.8 Tf [(Tiffany A, Dominguez G, Loua M, Traor A, Koli M, Malano ER, Heleze E, Bocquin A, Mly S, Raoul H, Caro V, Cadar D, )] TJ ET BT 26.250 182.992 Td /F1 9.8 Tf [(Gabriel M, Pahlmann M, Tappe D, Schmidt-Chanasit J, Impouma B, Diallo AK, Formenty P, Van Herp M, Gnther S. )] TJ ET BT 26.250 171.087 Td /F1 9.8 Tf [(Emergence of Zaire Ebola Virus Disease in Guinea - Preliminary Report. N Engl J Med. 2014 Apr 16. PubMed PMID:24738640.)] TJ ET BT 26.250 151.683 Td /F1 9.8 Tf [(4.)] TJ ET BT 38.132 151.683 Td /F1 9.8 Tf [(Bergsten, J. \(2005\), A review of long-branch attraction. Cladistics, 21: 163193. doi: 10.1111/j.1096-0031.2005.00059.x)] TJ ET BT 26.250 132.278 Td /F1 9.8 Tf [(5.)] TJ ET BT 38.132 132.278 Td /F1 9.8 Tf [(Drummond AJ, Ho SY, Phillips MJ, Rambaut A. Relaxed phylogenetics and dating with confidence. PLoS Biol. 2006 )] TJ ET BT 26.250 120.373 Td /F1 9.8 Tf [(May;4\(5\):e88. PubMed PMID:16683862.)] TJ ET BT 26.250 100.968 Td /F1 9.8 Tf [(6.)] TJ ET BT 38.132 100.968 Td /F1 9.8 Tf [(Drummond AJ, Suchard MA, Xie D, Rambaut A. Bayesian phylogenetics with BEAUti and the BEAST 1.7. Mol Biol Evol. )] TJ ET BT 26.250 89.064 Td /F1 9.8 Tf [(2012 Aug;29\(8\):1969-73. PubMed PMID:22367748.)] TJ ET BT 26.250 69.659 Td /F1 9.8 Tf [(7.)] TJ ET BT 38.132 69.659 Td /F1 9.8 Tf [(Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol Biol. 2007 Nov 8;7:214. )] TJ ET BT 26.250 57.754 Td /F1 9.8 Tf [(PubMed PMID:17996036.)] 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 Outbreaks)] TJ ET Q endstream endobj 253 0 obj << /Type /Annot /Subtype /Link /A 254 0 R /Border [0 0 0] /H /I /Rect [ 447.2745 621.4629 456.9118 630.2812 ] >> endobj 254 0 obj << /Type /Action >> endobj 255 0 obj << /Type /Annot /Subtype /Link /A 256 0 R /Border [0 0 0] /H /I /Rect [ 519.3660 609.5582 529.0033 618.3765 ] >> endobj 256 0 obj << /Type /Action >> endobj 257 0 obj << /Type /Annot /Subtype /Link /A 258 0 R /Border [0 0 0] /H /I /Rect [ 112.9470 542.5344 122.5843 551.3527 ] >> endobj 258 0 obj << /Type /Action >> endobj 259 0 obj << /Type /Annot /Subtype /Link /A 260 0 R /Border [0 0 0] /H /I /Rect [ 499.8562 487.4154 509.4936 496.2337 ] >> endobj 260 0 obj << /Type /Action >> endobj 261 0 obj << /Type /Annot /Subtype /Link /A 262 0 R /Border [0 0 0] /H /I /Rect [ 447.2745 621.4629 456.9118 630.2812 ] >> endobj 262 0 obj << /Type /Action >> endobj 263 0 obj << /Type /Annot /Subtype /Link /A 264 0 R /Border [0 0 0] /H /I /Rect [ 519.3660 609.5582 529.0033 618.3765 ] >> endobj 264 0 obj << /Type /Action >> endobj 265 0 obj << /Type /Annot /Subtype /Link /A 266 0 R /Border [0 0 0] /H /I /Rect [ 112.9470 542.5344 122.5843 551.3527 ] >> endobj 266 0 obj << /Type /Action >> endobj 267 0 obj << /Type /Annot /Subtype /Link /A 268 0 R /Border [0 0 0] /H /I /Rect [ 499.8562 487.4154 509.4936 496.2337 ] >> endobj 268 0 obj << /Type /Action >> endobj 269 0 obj << /Type /Annot /Subtype /Link /A 270 0 R /Border [0 0 0] /H /I /Rect [ 447.2745 621.4629 456.9118 630.2812 ] >> endobj 270 0 obj << /Type /Action >> endobj 271 0 obj << /Type /Annot /Subtype /Link /A 272 0 R /Border [0 0 0] /H /I /Rect [ 519.3660 609.5582 529.0033 618.3765 ] >> endobj 272 0 obj << /Type /Action >> endobj 273 0 obj << /Type /Annot /Subtype /Link /A 274 0 R /Border [0 0 0] /H /I /Rect [ 112.9470 542.5344 122.5843 551.3527 ] >> endobj 274 0 obj << /Type /Action >> endobj 275 0 obj << /Type /Annot /Subtype /Link /A 276 0 R /Border [0 0 0] /H /I /Rect [ 499.8562 487.4154 509.4936 496.2337 ] >> endobj 276 0 obj << /Type /Action >> endobj 277 0 obj << /Type /Page /Parent 3 0 R /Contents 278 0 R >> endobj 278 0 obj << /Length 9076 >> stream 0.271 0.267 0.267 rg q 15.000 475.810 577.500 301.190 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(8.)] TJ ET BT 38.132 759.976 Td /F1 9.8 Tf [(Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001 Aug;17\(8\):754-5. )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(PubMed PMID:11524383.)] TJ ET BT 26.250 728.667 Td /F1 9.8 Tf [(9.)] TJ ET BT 38.132 728.667 Td /F1 9.8 Tf [(Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003 Aug )] TJ ET BT 26.250 716.762 Td /F1 9.8 Tf [(12;19\(12\):1572-4. PubMed PMID:12912839.)] TJ ET BT 26.250 697.357 Td /F1 9.8 Tf [(10.)] TJ ET BT 43.553 697.357 Td /F1 9.8 Tf [(Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. )] TJ ET BT 26.250 685.452 Td /F1 9.8 Tf [(MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012 )] TJ ET BT 26.250 673.548 Td /F1 9.8 Tf [(May;61\(3\):539-42. PubMed PMID:22357727.)] TJ ET BT 26.250 654.143 Td /F1 9.8 Tf [(11.)] TJ ET BT 43.553 654.143 Td /F1 9.8 Tf [(Boykin LM, Kubatko LS, Lowrey TK. Comparison of methods for rooting phylogenetic trees: a case study using Orcuttieae )] TJ ET BT 26.250 642.238 Td /F1 9.8 Tf [(\(Poaceae: Chloridoideae\). Mol Phylogenet Evol. 2010 Mar;54\(3\):687-700. PubMed PMID:19931622.)] TJ ET BT 26.250 622.833 Td /F1 9.8 Tf [(12.)] TJ ET BT 43.553 622.833 Td /F1 9.8 Tf [(Renner SS, Grimm GW, Schneeweiss GM, Stuessy TF, Ricklefs RE. Rooting and dating maples \(Acer\) with an )] TJ ET BT 26.250 610.929 Td /F1 9.8 Tf [(uncorrelated-rates molecular clock: implications for north American/Asian disjunctions. Syst Biol. 2008 Oct;57\(5\):795-808. )] TJ ET BT 26.250 599.024 Td /F1 9.8 Tf [(PubMed PMID:18853365.)] TJ ET BT 26.250 579.619 Td /F1 9.8 Tf [(13.)] TJ ET BT 43.553 579.619 Td /F1 9.8 Tf [(Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-)] TJ ET BT 26.250 567.714 Td /F1 9.8 Tf [(likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010 May;59\(3\):307-21. PubMed PMID:20525638.)] TJ ET BT 26.250 548.310 Td /F1 9.8 Tf [(14.)] TJ ET BT 43.553 548.310 Td /F1 9.8 Tf [(Carroll SA, Towner JS, Sealy TK, McMullan LK, Khristova ML, Burt FJ, Swanepoel R, Rollin PE, Nichol ST. Molecular )] TJ ET BT 26.250 536.405 Td /F1 9.8 Tf [(evolution of viruses of the family Filoviridae based on 97 whole-genome sequences. J Virol. 2013 Mar;87\(5\):2608-16. PubMed )] TJ ET BT 26.250 524.500 Td /F1 9.8 Tf [(PMID:23255795.)] TJ ET BT 26.250 505.095 Td /F1 9.8 Tf [(15.)] TJ ET BT 43.553 505.095 Td /F1 9.8 Tf [(Lauber C, Gorbalenya AE. Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences. )] TJ ET BT 26.250 493.191 Td /F1 9.8 Tf [(Viruses. 2012 Sep;4\(9\):1425-37. PubMed PMID:23170166.)] TJ ET Q q 15.000 475.810 577.500 301.190 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(8.)] TJ ET BT 38.132 759.976 Td /F1 9.8 Tf [(Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001 Aug;17\(8\):754-5. )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(PubMed PMID:11524383.)] TJ ET BT 26.250 728.667 Td /F1 9.8 Tf [(9.)] TJ ET BT 38.132 728.667 Td /F1 9.8 Tf [(Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003 Aug )] TJ ET BT 26.250 716.762 Td /F1 9.8 Tf [(12;19\(12\):1572-4. PubMed PMID:12912839.)] TJ ET BT 26.250 697.357 Td /F1 9.8 Tf [(10.)] TJ ET BT 43.553 697.357 Td /F1 9.8 Tf [(Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. )] TJ ET BT 26.250 685.452 Td /F1 9.8 Tf [(MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012 )] TJ ET BT 26.250 673.548 Td /F1 9.8 Tf [(May;61\(3\):539-42. PubMed PMID:22357727.)] TJ ET BT 26.250 654.143 Td /F1 9.8 Tf [(11.)] TJ ET BT 43.553 654.143 Td /F1 9.8 Tf [(Boykin LM, Kubatko LS, Lowrey TK. Comparison of methods for rooting phylogenetic trees: a case study using Orcuttieae )] TJ ET BT 26.250 642.238 Td /F1 9.8 Tf [(\(Poaceae: Chloridoideae\). Mol Phylogenet Evol. 2010 Mar;54\(3\):687-700. PubMed PMID:19931622.)] TJ ET BT 26.250 622.833 Td /F1 9.8 Tf [(12.)] TJ ET BT 43.553 622.833 Td /F1 9.8 Tf [(Renner SS, Grimm GW, Schneeweiss GM, Stuessy TF, Ricklefs RE. Rooting and dating maples \(Acer\) with an )] TJ ET BT 26.250 610.929 Td /F1 9.8 Tf [(uncorrelated-rates molecular clock: implications for north American/Asian disjunctions. Syst Biol. 2008 Oct;57\(5\):795-808. )] TJ ET BT 26.250 599.024 Td /F1 9.8 Tf [(PubMed PMID:18853365.)] TJ ET BT 26.250 579.619 Td /F1 9.8 Tf [(13.)] TJ ET BT 43.553 579.619 Td /F1 9.8 Tf [(Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-)] TJ ET BT 26.250 567.714 Td /F1 9.8 Tf [(likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010 May;59\(3\):307-21. PubMed PMID:20525638.)] TJ ET BT 26.250 548.310 Td /F1 9.8 Tf [(14.)] TJ ET BT 43.553 548.310 Td /F1 9.8 Tf [(Carroll SA, Towner JS, Sealy TK, McMullan LK, Khristova ML, Burt FJ, Swanepoel R, Rollin PE, Nichol ST. Molecular )] TJ ET BT 26.250 536.405 Td /F1 9.8 Tf [(evolution of viruses of the family Filoviridae based on 97 whole-genome sequences. J Virol. 2013 Mar;87\(5\):2608-16. PubMed )] TJ ET BT 26.250 524.500 Td /F1 9.8 Tf [(PMID:23255795.)] TJ ET BT 26.250 505.095 Td /F1 9.8 Tf [(15.)] TJ ET BT 43.553 505.095 Td /F1 9.8 Tf [(Lauber C, Gorbalenya AE. Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences. )] TJ ET BT 26.250 493.191 Td /F1 9.8 Tf [(Viruses. 2012 Sep;4\(9\):1425-37. PubMed PMID:23170166.)] TJ ET Q q 15.000 475.810 577.500 301.190 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(8.)] TJ ET BT 38.132 759.976 Td /F1 9.8 Tf [(Huelsenbeck JP, Ronquist F. MRBAYES: Bayesian inference of phylogenetic trees. Bioinformatics. 2001 Aug;17\(8\):754-5. )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(PubMed PMID:11524383.)] TJ ET BT 26.250 728.667 Td /F1 9.8 Tf [(9.)] TJ ET BT 38.132 728.667 Td /F1 9.8 Tf [(Ronquist F, Huelsenbeck JP. MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics. 2003 Aug )] TJ ET BT 26.250 716.762 Td /F1 9.8 Tf [(12;19\(12\):1572-4. PubMed PMID:12912839.)] TJ ET BT 26.250 697.357 Td /F1 9.8 Tf [(10.)] TJ ET BT 43.553 697.357 Td /F1 9.8 Tf [(Ronquist F, Teslenko M, van der Mark P, Ayres DL, Darling A, Hhna S, Larget B, Liu L, Suchard MA, Huelsenbeck JP. )] TJ ET BT 26.250 685.452 Td /F1 9.8 Tf [(MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space. Syst Biol. 2012 )] TJ ET BT 26.250 673.548 Td /F1 9.8 Tf [(May;61\(3\):539-42. PubMed PMID:22357727.)] TJ ET BT 26.250 654.143 Td /F1 9.8 Tf [(11.)] TJ ET BT 43.553 654.143 Td /F1 9.8 Tf [(Boykin LM, Kubatko LS, Lowrey TK. Comparison of methods for rooting phylogenetic trees: a case study using Orcuttieae )] TJ ET BT 26.250 642.238 Td /F1 9.8 Tf [(\(Poaceae: Chloridoideae\). Mol Phylogenet Evol. 2010 Mar;54\(3\):687-700. PubMed PMID:19931622.)] TJ ET BT 26.250 622.833 Td /F1 9.8 Tf [(12.)] TJ ET BT 43.553 622.833 Td /F1 9.8 Tf [(Renner SS, Grimm GW, Schneeweiss GM, Stuessy TF, Ricklefs RE. Rooting and dating maples \(Acer\) with an )] TJ ET BT 26.250 610.929 Td /F1 9.8 Tf [(uncorrelated-rates molecular clock: implications for north American/Asian disjunctions. Syst Biol. 2008 Oct;57\(5\):795-808. )] TJ ET BT 26.250 599.024 Td /F1 9.8 Tf [(PubMed PMID:18853365.)] TJ ET BT 26.250 579.619 Td /F1 9.8 Tf [(13.)] TJ ET BT 43.553 579.619 Td /F1 9.8 Tf [(Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-)] TJ ET BT 26.250 567.714 Td /F1 9.8 Tf [(likelihood phylogenies: assessing the performance of PhyML 3.0. Syst Biol. 2010 May;59\(3\):307-21. PubMed PMID:20525638.)] TJ ET BT 26.250 548.310 Td /F1 9.8 Tf [(14.)] TJ ET BT 43.553 548.310 Td /F1 9.8 Tf [(Carroll SA, Towner JS, Sealy TK, McMullan LK, Khristova ML, Burt FJ, Swanepoel R, Rollin PE, Nichol ST. Molecular )] TJ ET BT 26.250 536.405 Td /F1 9.8 Tf [(evolution of viruses of the family Filoviridae based on 97 whole-genome sequences. J Virol. 2013 Mar;87\(5\):2608-16. PubMed )] TJ ET BT 26.250 524.500 Td /F1 9.8 Tf [(PMID:23255795.)] TJ ET BT 26.250 505.095 Td /F1 9.8 Tf [(15.)] TJ ET BT 43.553 505.095 Td /F1 9.8 Tf [(Lauber C, Gorbalenya AE. Genetics-based classification of filoviruses calls for expanded sampling of genomic sequences. )] TJ ET BT 26.250 493.191 Td /F1 9.8 Tf [(Viruses. 2012 Sep;4\(9\):1425-37. 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