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Harmon)] TJ ET 0.271 0.267 0.267 rg BT 95.066 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 100.487 688.195 Td /F1 9.8 Tf [(Jeffrey Baumes)] TJ ET 0.271 0.267 0.267 rg BT 168.220 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 173.641 688.195 Td /F1 9.8 Tf [(Charles Hughes)] TJ ET 0.271 0.267 0.267 rg BT 243.538 692.083 Td /F1 8.7 Tf [(1)] TJ ET BT 248.357 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 253.778 688.195 Td /F1 9.8 Tf [(Jorge Soberon)] TJ ET 0.271 0.267 0.267 rg BT 317.728 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 323.149 688.195 Td /F1 9.8 Tf [(Chelsea D Specht)] TJ ET 0.271 0.267 0.267 rg BT 401.725 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 407.146 688.195 Td /F1 9.8 Tf [(Wesley Turner)] TJ ET 0.271 0.267 0.267 rg BT 470.530 692.083 Td /F1 8.7 Tf [(2)] TJ ET BT 475.349 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 480.770 688.195 Td /F1 9.8 Tf [(Curtis Lisle)] TJ ET 0.271 0.267 0.267 rg BT 528.984 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 534.405 688.195 Td /F1 9.8 Tf [(Robert W. )] TJ ET BT 26.250 676.290 Td /F1 9.8 Tf [(Thacker)] TJ ET 0.271 0.267 0.267 rg BT 61.467 680.179 Td /F1 8.7 Tf [(3)] TJ ET BT 26.250 665.118 Td /F4 9.0 Tf [(1)] TJ ET BT 31.254 665.118 Td /F1 9.0 Tf [( University of Central Florida, )] TJ ET BT 149.784 665.118 Td /F4 9.0 Tf [(2)] TJ ET BT 154.788 665.118 Td /F1 9.0 Tf [( Kitware, Inc., )] TJ ET BT 211.812 665.118 Td /F4 9.0 Tf [(3)] TJ ET BT 216.816 665.118 Td /F1 9.0 Tf [( University of Alabama at Birmingham)] TJ ET BT 26.250 653.397 Td /F1 9.8 Tf [(Harmon LJ, Baumes J, Hughes C, Soberon J, Specht CD, Turner W, Lisle C, Thacker RW. Arbor: Comparative Analysis )] TJ ET BT 26.250 641.492 Td /F1 9.8 Tf [(Workflows for the Tree of Life. PLOS Currents Tree of Life. 2013 Jun 21 . Edition 1. doi: )] TJ ET BT 26.250 629.587 Td /F1 9.8 Tf [(10.1371/currents.tol.099161de5eabdee073fd3d21a44518dc.)] TJ ET q 15.000 24.432 577.500 602.774 re W n 0.271 0.267 0.267 rg BT 26.250 600.485 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 580.530 Td /F1 9.8 Tf [(We describe our efforts to develop a software package, Arbor, that will enable scientific research in all aspects of comparative )] TJ ET BT 26.250 568.626 Td /F1 9.8 Tf [(biology. This software will enable developmental biologists, geneticists, ecologists, geographers, paleobiologists, educators, and )] TJ ET BT 26.250 556.721 Td /F1 9.8 Tf [(students to analyze diverse types of comparative data at multiple phylogenetic and spatiotemporal scales using an intuitive )] TJ ET BT 26.250 544.816 Td /F1 9.8 Tf [(visual interface. Arbors user-defined workflows will be exported and shared so that entire analyses can be quickly replicated )] TJ ET BT 26.250 532.911 Td /F1 9.8 Tf [(with new or updated data. Arbor will also be designed to easily and seamlessly expand to include novel analytical tools as they )] TJ ET BT 26.250 521.007 Td /F1 9.8 Tf [(are developed. Here we describe the core components of Arbor, as well as provide details of one proposed test case to )] TJ ET BT 26.250 509.102 Td /F1 9.8 Tf [(illustrate the softwares key functionality.)] TJ ET BT 26.250 472.499 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 452.545 Td /F1 9.8 Tf [(This work was supported by the National Science Foundation \(DEB 1208912, 1208472, 1208340, and 1208666\).)] TJ ET BT 26.250 423.443 Td /F4 12.0 Tf [(Introduction)] TJ ET BT 26.250 403.488 Td /F1 9.8 Tf [(Scientists are making rapid progress building the Tree of Life, which promises to provide new insights into evolutionary )] TJ ET BT 26.250 391.584 Td /F1 9.8 Tf [(relationships across space and time. We now have available large-scale phylogenies \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 416.952 393.091 Td /F4 8.7 Tf [(1)] TJ ET BT 421.771 393.091 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 426.589 391.584 Td /F1 9.8 Tf [(\) and are accumulating massive )] TJ ET BT 26.250 379.679 Td /F1 9.8 Tf [(amounts of character and distributional data \(e.g. plant traits )] TJ ET 0.267 0.267 0.267 rg BT 288.545 381.186 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 293.363 379.679 Td /F1 9.8 Tf [(; mammalian traits )] TJ ET 0.267 0.267 0.267 rg BT 375.712 381.186 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 380.530 379.679 Td /F1 9.8 Tf [(; species occurrence data )] TJ ET 0.267 0.267 0.267 rg BT 494.332 381.186 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 499.151 379.679 Td /F1 9.8 Tf [(; gene )] TJ ET BT 26.250 367.774 Td /F1 9.8 Tf [(interactions )] TJ ET 0.267 0.267 0.267 rg BT 78.812 369.281 Td /F4 8.7 Tf [(6)] TJ ET 0.271 0.267 0.267 rg BT 83.631 367.774 Td /F1 9.8 Tf [(; microbiomes )] TJ ET 0.267 0.267 0.267 rg BT 147.016 369.281 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 151.834 367.774 Td /F1 9.8 Tf [(\). Together, these resources provide researchers with unique opportunities to investigate )] TJ ET BT 26.250 355.869 Td /F1 9.8 Tf [(processes that drive biological diversification at broad and deep phylogenetic scales \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 413.179 357.377 Td /F4 8.7 Tf [(8)] TJ ET BT 417.997 357.377 Td /F4 8.7 Tf [(9)] TJ ET BT 422.816 357.377 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 432.453 355.869 Td /F1 9.8 Tf [(\). Developing tools that enable )] TJ ET BT 26.250 343.965 Td /F1 9.8 Tf [(comparative analysis of various types of character data across large-scale phylogenies is essential to further our understanding )] TJ ET BT 26.250 332.060 Td /F1 9.8 Tf [(of fundamental evolutionary processes.)] TJ ET BT 26.250 312.655 Td /F1 9.8 Tf [(As a first draft of the Tree of Life emerges, it becomes increasingly clear that we lack the resources necessary to interpret the )] TJ ET BT 26.250 300.750 Td /F1 9.8 Tf [(evolution of character data across phylogenies at large scales. This is largely due to a lack of tools for the integration and )] TJ ET BT 26.250 288.846 Td /F1 9.8 Tf [(visualization of massive amounts of spatial, temporal, and character data and for placing this information into the comparative )] TJ ET BT 26.250 276.941 Td /F1 9.8 Tf [(framework provided by phylogenetic trees )] TJ ET 0.267 0.267 0.267 rg BT 209.404 278.448 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 219.041 276.941 Td /F1 9.8 Tf [(. Comparative analyses are hindered by the lack of scalable programs for studying )] TJ ET BT 26.250 265.036 Td /F1 9.8 Tf [(trait evolution, the heterogeneity of data formats, and the inability to integrate multiple analyses to enable novel discoveries )] TJ ET 0.267 0.267 0.267 rg BT 557.888 266.543 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 567.526 265.036 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 253.131 Td /F1 9.8 Tf [(Tools that successfully integrate very large phylogenetic trees with vast amounts of data associated with branch tips and nodes )] TJ ET BT 26.250 241.227 Td /F1 9.8 Tf [(will enable evolutionary biologists to visualize and investigate the processes that drive the evolution of organismal diversity.)] TJ ET BT 26.250 221.822 Td /F1 9.8 Tf [(Here we present an initial description of a new open-source software package, Arbor, which is currently in development. Funded )] TJ ET BT 26.250 209.917 Td /F1 9.8 Tf [(by the NSF AVAToL program, Arbor will allow us to harvest massive amounts of information from phylogenetic trees to facilitate )] TJ ET BT 26.250 198.012 Td /F1 9.8 Tf [(new discoveries about the evolution of life on Earth.)] TJ ET BT 26.250 161.410 Td /F4 12.0 Tf [(Arbor: a new vision for comparative analyses)] TJ ET BT 26.250 141.456 Td /F1 9.8 Tf [(To bring comparative biology up to speed with the emerging Tree of Life, we are developing Arbor)] TJ ET BT 447.860 141.456 Td /F4 9.8 Tf [(, )] TJ ET BT 453.281 141.456 Td /F1 9.8 Tf [(an extendable platform for )] TJ ET BT 26.250 129.551 Td /F1 9.8 Tf [(analyzing and visualizing evolutionary processes in a phylogenetic framework. Using Arbor workflows, researchers will be able )] TJ ET BT 26.250 117.646 Td /F1 9.8 Tf [(to investigate evolutionary questions across very large phylogenetic trees containing very large numbers of terminal units \(e.g. )] TJ ET BT 26.250 105.741 Td /F1 9.8 Tf [(species, populations, individuals\) using diverse types of character data \(e.g. traits, biogeography, ecological associations, )] TJ ET BT 26.250 93.837 Td /F1 9.8 Tf [(species interactions\). The goal of Arbor is to provide biologists with an immediate and intuitive interface for testing comparative )] TJ ET BT 26.250 81.932 Td /F1 9.8 Tf [(evolutionary questions across the Tree of Life and to enable them to quickly and efficiently communicate their findings to )] TJ ET BT 26.250 70.027 Td /F1 9.8 Tf [(scientific and general audiences.)] TJ ET BT 26.250 50.622 Td /F1 9.8 Tf [(We are currently developing and implementing flexible and extendable tools that interact through an intuitive visual workspace )] TJ ET BT 26.250 38.718 Td /F1 9.8 Tf [(in Arbor. As designed, Arbor workflows have three main benefits. First, Arbor will be flexible: the workspace allows end users to )] 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 [(Arbor: Comparative Analysis Workflows for the Tree of Life)] TJ ET Q 0.271 0.267 0.267 rg BT 15.000 700.036 Td /F3 9.8 Tf [(June 21, 2013)] TJ ET BT 74.846 700.036 Td /F3 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 79.721 700.036 Td /F3 9.8 Tf [(AVAToL)] TJ ET BT 26.250 688.195 Td /F1 9.8 Tf [(Luke J. Harmon)] TJ ET 0.271 0.267 0.267 rg BT 95.066 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 100.487 688.195 Td /F1 9.8 Tf [(Jeffrey Baumes)] TJ ET 0.271 0.267 0.267 rg BT 168.220 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 173.641 688.195 Td /F1 9.8 Tf [(Charles Hughes)] TJ ET 0.271 0.267 0.267 rg BT 243.538 692.083 Td /F1 8.7 Tf [(1)] TJ ET BT 248.357 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 253.778 688.195 Td /F1 9.8 Tf [(Jorge Soberon)] TJ ET 0.271 0.267 0.267 rg BT 317.728 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 323.149 688.195 Td /F1 9.8 Tf [(Chelsea D Specht)] TJ ET 0.271 0.267 0.267 rg BT 401.725 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 407.146 688.195 Td /F1 9.8 Tf [(Wesley Turner)] TJ ET 0.271 0.267 0.267 rg BT 470.530 692.083 Td /F1 8.7 Tf [(2)] TJ ET BT 475.349 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 480.770 688.195 Td /F1 9.8 Tf [(Curtis Lisle)] TJ ET 0.271 0.267 0.267 rg BT 528.984 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 534.405 688.195 Td /F1 9.8 Tf [(Robert W. )] TJ ET BT 26.250 676.290 Td /F1 9.8 Tf [(Thacker)] TJ ET 0.271 0.267 0.267 rg BT 61.467 680.179 Td /F1 8.7 Tf [(3)] TJ ET BT 26.250 665.118 Td /F4 9.0 Tf [(1)] TJ ET BT 31.254 665.118 Td /F1 9.0 Tf [( University of Central Florida, )] TJ ET BT 149.784 665.118 Td /F4 9.0 Tf [(2)] TJ ET BT 154.788 665.118 Td /F1 9.0 Tf [( Kitware, Inc., )] TJ ET BT 211.812 665.118 Td /F4 9.0 Tf [(3)] TJ ET BT 216.816 665.118 Td /F1 9.0 Tf [( University of Alabama at Birmingham)] TJ ET BT 26.250 653.397 Td /F1 9.8 Tf [(Harmon LJ, Baumes J, Hughes C, Soberon J, Specht CD, Turner W, Lisle C, Thacker RW. Arbor: Comparative Analysis )] TJ ET BT 26.250 641.492 Td /F1 9.8 Tf [(Workflows for the Tree of Life. PLOS Currents Tree of Life. 2013 Jun 21 . Edition 1. doi: )] TJ ET BT 26.250 629.587 Td /F1 9.8 Tf [(10.1371/currents.tol.099161de5eabdee073fd3d21a44518dc.)] TJ ET q 15.000 24.432 577.500 602.774 re W n 0.271 0.267 0.267 rg BT 26.250 600.485 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 580.530 Td /F1 9.8 Tf [(We describe our efforts to develop a software package, Arbor, that will enable scientific research in all aspects of comparative )] TJ ET BT 26.250 568.626 Td /F1 9.8 Tf [(biology. This software will enable developmental biologists, geneticists, ecologists, geographers, paleobiologists, educators, and )] TJ ET BT 26.250 556.721 Td /F1 9.8 Tf [(students to analyze diverse types of comparative data at multiple phylogenetic and spatiotemporal scales using an intuitive )] TJ ET BT 26.250 544.816 Td /F1 9.8 Tf [(visual interface. Arbors user-defined workflows will be exported and shared so that entire analyses can be quickly replicated )] TJ ET BT 26.250 532.911 Td /F1 9.8 Tf [(with new or updated data. Arbor will also be designed to easily and seamlessly expand to include novel analytical tools as they )] TJ ET BT 26.250 521.007 Td /F1 9.8 Tf [(are developed. Here we describe the core components of Arbor, as well as provide details of one proposed test case to )] TJ ET BT 26.250 509.102 Td /F1 9.8 Tf [(illustrate the softwares key functionality.)] TJ ET BT 26.250 472.499 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 452.545 Td /F1 9.8 Tf [(This work was supported by the National Science Foundation \(DEB 1208912, 1208472, 1208340, and 1208666\).)] TJ ET BT 26.250 423.443 Td /F4 12.0 Tf [(Introduction)] TJ ET BT 26.250 403.488 Td /F1 9.8 Tf [(Scientists are making rapid progress building the Tree of Life, which promises to provide new insights into evolutionary )] TJ ET BT 26.250 391.584 Td /F1 9.8 Tf [(relationships across space and time. We now have available large-scale phylogenies \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 416.952 393.091 Td /F4 8.7 Tf [(1)] TJ ET BT 421.771 393.091 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 426.589 391.584 Td /F1 9.8 Tf [(\) and are accumulating massive )] TJ ET BT 26.250 379.679 Td /F1 9.8 Tf [(amounts of character and distributional data \(e.g. plant traits )] TJ ET 0.267 0.267 0.267 rg BT 288.545 381.186 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 293.363 379.679 Td /F1 9.8 Tf [(; mammalian traits )] TJ ET 0.267 0.267 0.267 rg BT 375.712 381.186 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 380.530 379.679 Td /F1 9.8 Tf [(; species occurrence data )] TJ ET 0.267 0.267 0.267 rg BT 494.332 381.186 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 499.151 379.679 Td /F1 9.8 Tf [(; gene )] TJ ET BT 26.250 367.774 Td /F1 9.8 Tf [(interactions )] TJ ET 0.267 0.267 0.267 rg BT 78.812 369.281 Td /F4 8.7 Tf [(6)] TJ ET 0.271 0.267 0.267 rg BT 83.631 367.774 Td /F1 9.8 Tf [(; microbiomes )] TJ ET 0.267 0.267 0.267 rg BT 147.016 369.281 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 151.834 367.774 Td /F1 9.8 Tf [(\). Together, these resources provide researchers with unique opportunities to investigate )] TJ ET BT 26.250 355.869 Td /F1 9.8 Tf [(processes that drive biological diversification at broad and deep phylogenetic scales \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 413.179 357.377 Td /F4 8.7 Tf [(8)] TJ ET BT 417.997 357.377 Td /F4 8.7 Tf [(9)] TJ ET BT 422.816 357.377 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 432.453 355.869 Td /F1 9.8 Tf [(\). Developing tools that enable )] TJ ET BT 26.250 343.965 Td /F1 9.8 Tf [(comparative analysis of various types of character data across large-scale phylogenies is essential to further our understanding )] TJ ET BT 26.250 332.060 Td /F1 9.8 Tf [(of fundamental evolutionary processes.)] TJ ET BT 26.250 312.655 Td /F1 9.8 Tf [(As a first draft of the Tree of Life emerges, it becomes increasingly clear that we lack the resources necessary to interpret the )] TJ ET BT 26.250 300.750 Td /F1 9.8 Tf [(evolution of character data across phylogenies at large scales. This is largely due to a lack of tools for the integration and )] TJ ET BT 26.250 288.846 Td /F1 9.8 Tf [(visualization of massive amounts of spatial, temporal, and character data and for placing this information into the comparative )] TJ ET BT 26.250 276.941 Td /F1 9.8 Tf [(framework provided by phylogenetic trees )] TJ ET 0.267 0.267 0.267 rg BT 209.404 278.448 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 219.041 276.941 Td /F1 9.8 Tf [(. Comparative analyses are hindered by the lack of scalable programs for studying )] TJ ET BT 26.250 265.036 Td /F1 9.8 Tf [(trait evolution, the heterogeneity of data formats, and the inability to integrate multiple analyses to enable novel discoveries )] TJ ET 0.267 0.267 0.267 rg BT 557.888 266.543 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 567.526 265.036 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 253.131 Td /F1 9.8 Tf [(Tools that successfully integrate very large phylogenetic trees with vast amounts of data associated with branch tips and nodes )] TJ ET BT 26.250 241.227 Td /F1 9.8 Tf [(will enable evolutionary biologists to visualize and investigate the processes that drive the evolution of organismal diversity.)] TJ ET BT 26.250 221.822 Td /F1 9.8 Tf [(Here we present an initial description of a new open-source software package, Arbor, which is currently in development. Funded )] TJ ET BT 26.250 209.917 Td /F1 9.8 Tf [(by the NSF AVAToL program, Arbor will allow us to harvest massive amounts of information from phylogenetic trees to facilitate )] TJ ET BT 26.250 198.012 Td /F1 9.8 Tf [(new discoveries about the evolution of life on Earth.)] TJ ET BT 26.250 161.410 Td /F4 12.0 Tf [(Arbor: a new vision for comparative analyses)] TJ ET BT 26.250 141.456 Td /F1 9.8 Tf [(To bring comparative biology up to speed with the emerging Tree of Life, we are developing Arbor)] TJ ET BT 447.860 141.456 Td /F4 9.8 Tf [(, )] TJ ET BT 453.281 141.456 Td /F1 9.8 Tf [(an extendable platform for )] TJ ET BT 26.250 129.551 Td /F1 9.8 Tf [(analyzing and visualizing evolutionary processes in a phylogenetic framework. Using Arbor workflows, researchers will be able )] TJ ET BT 26.250 117.646 Td /F1 9.8 Tf [(to investigate evolutionary questions across very large phylogenetic trees containing very large numbers of terminal units \(e.g. )] TJ ET BT 26.250 105.741 Td /F1 9.8 Tf [(species, populations, individuals\) using diverse types of character data \(e.g. traits, biogeography, ecological associations, )] TJ ET BT 26.250 93.837 Td /F1 9.8 Tf [(species interactions\). The goal of Arbor is to provide biologists with an immediate and intuitive interface for testing comparative )] TJ ET BT 26.250 81.932 Td /F1 9.8 Tf [(evolutionary questions across the Tree of Life and to enable them to quickly and efficiently communicate their findings to )] TJ ET BT 26.250 70.027 Td /F1 9.8 Tf [(scientific and general audiences.)] TJ ET BT 26.250 50.622 Td /F1 9.8 Tf [(We are currently developing and implementing flexible and extendable tools that interact through an intuitive visual workspace )] TJ ET BT 26.250 38.718 Td /F1 9.8 Tf [(in Arbor. As designed, Arbor workflows have three main benefits. First, Arbor will be flexible: the workspace allows end users to )] 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 [(Arbor: Comparative Analysis Workflows for the Tree of Life)] TJ ET Q 0.271 0.267 0.267 rg BT 15.000 700.036 Td /F3 9.8 Tf [(June 21, 2013)] TJ ET BT 74.846 700.036 Td /F3 9.8 Tf [()] TJ ET 0.267 0.267 0.267 rg BT 79.721 700.036 Td /F3 9.8 Tf [(AVAToL)] TJ ET BT 26.250 688.195 Td /F1 9.8 Tf [(Luke J. Harmon)] TJ ET 0.271 0.267 0.267 rg BT 95.066 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 100.487 688.195 Td /F1 9.8 Tf [(Jeffrey Baumes)] TJ ET 0.271 0.267 0.267 rg BT 168.220 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 173.641 688.195 Td /F1 9.8 Tf [(Charles Hughes)] TJ ET 0.271 0.267 0.267 rg BT 243.538 692.083 Td /F1 8.7 Tf [(1)] TJ ET BT 248.357 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 253.778 688.195 Td /F1 9.8 Tf [(Jorge Soberon)] TJ ET 0.271 0.267 0.267 rg BT 317.728 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 323.149 688.195 Td /F1 9.8 Tf [(Chelsea D Specht)] TJ ET 0.271 0.267 0.267 rg BT 401.725 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 407.146 688.195 Td /F1 9.8 Tf [(Wesley Turner)] TJ ET 0.271 0.267 0.267 rg BT 470.530 692.083 Td /F1 8.7 Tf [(2)] TJ ET BT 475.349 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 480.770 688.195 Td /F1 9.8 Tf [(Curtis Lisle)] TJ ET 0.271 0.267 0.267 rg BT 528.984 688.195 Td /F1 9.8 Tf [(, )] TJ ET 0.267 0.267 0.267 rg BT 534.405 688.195 Td /F1 9.8 Tf [(Robert W. )] TJ ET BT 26.250 676.290 Td /F1 9.8 Tf [(Thacker)] TJ ET 0.271 0.267 0.267 rg BT 61.467 680.179 Td /F1 8.7 Tf [(3)] TJ ET BT 26.250 665.118 Td /F4 9.0 Tf [(1)] TJ ET BT 31.254 665.118 Td /F1 9.0 Tf [( University of Central Florida, )] TJ ET BT 149.784 665.118 Td /F4 9.0 Tf [(2)] TJ ET BT 154.788 665.118 Td /F1 9.0 Tf [( Kitware, Inc., )] TJ ET BT 211.812 665.118 Td /F4 9.0 Tf [(3)] TJ ET BT 216.816 665.118 Td /F1 9.0 Tf [( University of Alabama at Birmingham)] TJ ET BT 26.250 653.397 Td /F1 9.8 Tf [(Harmon LJ, Baumes J, Hughes C, Soberon J, Specht CD, Turner W, Lisle C, Thacker RW. Arbor: Comparative Analysis )] TJ ET BT 26.250 641.492 Td /F1 9.8 Tf [(Workflows for the Tree of Life. PLOS Currents Tree of Life. 2013 Jun 21 . Edition 1. doi: )] TJ ET BT 26.250 629.587 Td /F1 9.8 Tf [(10.1371/currents.tol.099161de5eabdee073fd3d21a44518dc.)] TJ ET q 15.000 24.432 577.500 602.774 re W n 0.271 0.267 0.267 rg BT 26.250 600.485 Td /F4 12.0 Tf [(Abstract)] TJ ET BT 26.250 580.530 Td /F1 9.8 Tf [(We describe our efforts to develop a software package, Arbor, that will enable scientific research in all aspects of comparative )] TJ ET BT 26.250 568.626 Td /F1 9.8 Tf [(biology. This software will enable developmental biologists, geneticists, ecologists, geographers, paleobiologists, educators, and )] TJ ET BT 26.250 556.721 Td /F1 9.8 Tf [(students to analyze diverse types of comparative data at multiple phylogenetic and spatiotemporal scales using an intuitive )] TJ ET BT 26.250 544.816 Td /F1 9.8 Tf [(visual interface. Arbors user-defined workflows will be exported and shared so that entire analyses can be quickly replicated )] TJ ET BT 26.250 532.911 Td /F1 9.8 Tf [(with new or updated data. Arbor will also be designed to easily and seamlessly expand to include novel analytical tools as they )] TJ ET BT 26.250 521.007 Td /F1 9.8 Tf [(are developed. Here we describe the core components of Arbor, as well as provide details of one proposed test case to )] TJ ET BT 26.250 509.102 Td /F1 9.8 Tf [(illustrate the softwares key functionality.)] TJ ET BT 26.250 472.499 Td /F4 12.0 Tf [(Funding Statement)] TJ ET BT 26.250 452.545 Td /F1 9.8 Tf [(This work was supported by the National Science Foundation \(DEB 1208912, 1208472, 1208340, and 1208666\).)] TJ ET BT 26.250 423.443 Td /F4 12.0 Tf [(Introduction)] TJ ET BT 26.250 403.488 Td /F1 9.8 Tf [(Scientists are making rapid progress building the Tree of Life, which promises to provide new insights into evolutionary )] TJ ET BT 26.250 391.584 Td /F1 9.8 Tf [(relationships across space and time. We now have available large-scale phylogenies \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 416.952 393.091 Td /F4 8.7 Tf [(1)] TJ ET BT 421.771 393.091 Td /F4 8.7 Tf [(2)] TJ ET 0.271 0.267 0.267 rg BT 426.589 391.584 Td /F1 9.8 Tf [(\) and are accumulating massive )] TJ ET BT 26.250 379.679 Td /F1 9.8 Tf [(amounts of character and distributional data \(e.g. plant traits )] TJ ET 0.267 0.267 0.267 rg BT 288.545 381.186 Td /F4 8.7 Tf [(3)] TJ ET 0.271 0.267 0.267 rg BT 293.363 379.679 Td /F1 9.8 Tf [(; mammalian traits )] TJ ET 0.267 0.267 0.267 rg BT 375.712 381.186 Td /F4 8.7 Tf [(4)] TJ ET 0.271 0.267 0.267 rg BT 380.530 379.679 Td /F1 9.8 Tf [(; species occurrence data )] TJ ET 0.267 0.267 0.267 rg BT 494.332 381.186 Td /F4 8.7 Tf [(5)] TJ ET 0.271 0.267 0.267 rg BT 499.151 379.679 Td /F1 9.8 Tf [(; gene )] TJ ET BT 26.250 367.774 Td /F1 9.8 Tf [(interactions )] TJ ET 0.267 0.267 0.267 rg BT 78.812 369.281 Td /F4 8.7 Tf [(6)] TJ ET 0.271 0.267 0.267 rg BT 83.631 367.774 Td /F1 9.8 Tf [(; microbiomes )] TJ ET 0.267 0.267 0.267 rg BT 147.016 369.281 Td /F4 8.7 Tf [(7)] TJ ET 0.271 0.267 0.267 rg BT 151.834 367.774 Td /F1 9.8 Tf [(\). Together, these resources provide researchers with unique opportunities to investigate )] TJ ET BT 26.250 355.869 Td /F1 9.8 Tf [(processes that drive biological diversification at broad and deep phylogenetic scales \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 413.179 357.377 Td /F4 8.7 Tf [(8)] TJ ET BT 417.997 357.377 Td /F4 8.7 Tf [(9)] TJ ET BT 422.816 357.377 Td /F4 8.7 Tf [(10)] TJ ET 0.271 0.267 0.267 rg BT 432.453 355.869 Td /F1 9.8 Tf [(\). Developing tools that enable )] TJ ET BT 26.250 343.965 Td /F1 9.8 Tf [(comparative analysis of various types of character data across large-scale phylogenies is essential to further our understanding )] TJ ET BT 26.250 332.060 Td /F1 9.8 Tf [(of fundamental evolutionary processes.)] TJ ET BT 26.250 312.655 Td /F1 9.8 Tf [(As a first draft of the Tree of Life emerges, it becomes increasingly clear that we lack the resources necessary to interpret the )] TJ ET BT 26.250 300.750 Td /F1 9.8 Tf [(evolution of character data across phylogenies at large scales. This is largely due to a lack of tools for the integration and )] TJ ET BT 26.250 288.846 Td /F1 9.8 Tf [(visualization of massive amounts of spatial, temporal, and character data and for placing this information into the comparative )] TJ ET BT 26.250 276.941 Td /F1 9.8 Tf [(framework provided by phylogenetic trees )] TJ ET 0.267 0.267 0.267 rg BT 209.404 278.448 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 219.041 276.941 Td /F1 9.8 Tf [(. Comparative analyses are hindered by the lack of scalable programs for studying )] TJ ET BT 26.250 265.036 Td /F1 9.8 Tf [(trait evolution, the heterogeneity of data formats, and the inability to integrate multiple analyses to enable novel discoveries )] TJ ET 0.267 0.267 0.267 rg BT 557.888 266.543 Td /F4 8.7 Tf [(12)] TJ ET 0.271 0.267 0.267 rg BT 567.526 265.036 Td /F1 9.8 Tf [(. )] TJ ET BT 26.250 253.131 Td /F1 9.8 Tf [(Tools that successfully integrate very large phylogenetic trees with vast amounts of data associated with branch tips and nodes )] TJ ET BT 26.250 241.227 Td /F1 9.8 Tf [(will enable evolutionary biologists to visualize and investigate the processes that drive the evolution of organismal diversity.)] TJ ET BT 26.250 221.822 Td /F1 9.8 Tf [(Here we present an initial description of a new open-source software package, Arbor, which is currently in development. Funded )] TJ ET BT 26.250 209.917 Td /F1 9.8 Tf [(by the NSF AVAToL program, Arbor will allow us to harvest massive amounts of information from phylogenetic trees to facilitate )] TJ ET BT 26.250 198.012 Td /F1 9.8 Tf [(new discoveries about the evolution of life on Earth.)] TJ ET BT 26.250 161.410 Td /F4 12.0 Tf [(Arbor: a new vision for comparative analyses)] TJ ET BT 26.250 141.456 Td /F1 9.8 Tf [(To bring comparative biology up to speed with the emerging Tree of Life, we are developing Arbor)] TJ ET BT 447.860 141.456 Td /F4 9.8 Tf [(, )] TJ ET BT 453.281 141.456 Td /F1 9.8 Tf [(an extendable platform for )] TJ ET BT 26.250 129.551 Td /F1 9.8 Tf [(analyzing and visualizing evolutionary processes in a phylogenetic framework. Using Arbor workflows, researchers will be able )] TJ ET BT 26.250 117.646 Td /F1 9.8 Tf [(to investigate evolutionary questions across very large phylogenetic trees containing very large numbers of terminal units \(e.g. )] TJ ET BT 26.250 105.741 Td /F1 9.8 Tf [(species, populations, individuals\) using diverse types of character data \(e.g. traits, biogeography, ecological associations, )] TJ ET BT 26.250 93.837 Td /F1 9.8 Tf [(species interactions\). The goal of Arbor is to provide biologists with an immediate and intuitive interface for testing comparative )] TJ ET BT 26.250 81.932 Td /F1 9.8 Tf [(evolutionary questions across the Tree of Life and to enable them to quickly and efficiently communicate their findings to )] TJ ET BT 26.250 70.027 Td /F1 9.8 Tf [(scientific and general audiences.)] TJ ET BT 26.250 50.622 Td /F1 9.8 Tf [(We are currently developing and implementing flexible and extendable tools that interact through an intuitive visual workspace )] TJ ET BT 26.250 38.718 Td /F1 9.8 Tf [(in Arbor. As designed, Arbor workflows have three main benefits. 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Second, )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(Arbor will be extendable: software developers are able to quickly and easily add functionality without altering the details of )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(Arbors core implementation. Third, Arbor will be sharable: users will be able to save their Arbor workflows and share them with )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(others. As such, Arbor will be next generation software that enables tree-thinking and novel analyses at broad spatial and )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(temporal scales.)] TJ ET BT 26.250 700.452 Td /F1 9.8 Tf [(The Arbor development team \(see below\) brings together a variety of expertise in both biology and computer science. The )] TJ ET BT 26.250 688.548 Td /F1 9.8 Tf [(ongoing development of Arbor focuses on four components. First, we are developing the core of Arbor. 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Users will interact with )] TJ ET BT 26.250 512.943 Td /F1 9.8 Tf [(Arbor in an intuitive, visual way; building an Arbor workflow will have more in common with building a structure using Legos than )] TJ ET BT 26.250 501.039 Td /F1 9.8 Tf [(with programming a computer. 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This scalable )] TJ ET BT 26.250 390.801 Td /F1 9.8 Tf [(performance will come from the use of improved algorithms \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 306.923 392.308 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 316.561 390.801 Td /F1 9.8 Tf [(\) along with both fine-grained parallelism \(using )] TJ ET BT 26.250 378.896 Td /F1 9.8 Tf [(multithreaded execution of individual steps when possible in a workflow\) and coarse-grained parallelism \(executing multiple )] TJ ET BT 26.250 366.991 Td /F1 9.8 Tf [(steps of a workflow simultaneously on separate cores\). Arbor will run efficiently to develop and test workflow designs using )] TJ ET BT 26.250 355.086 Td /F1 9.8 Tf [(small and medium-size datasets on laptop and personal computers. Then, after a workflow idea has been expressed and )] TJ ET BT 26.250 343.182 Td /F1 9.8 Tf [(validated, the workflow can be run against tree-of-life scale data using a scalable computing resource. 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Users of workflow software create problem-specific workflows visually by connecting a series of data )] TJ ET BT 26.250 445.920 Td /F1 9.8 Tf [(manipulations and analyses in a series of steps. The underlying software system is able to automatically coordinate the )] TJ ET BT 26.250 434.015 Td /F1 9.8 Tf [(invocation of all of these steps during workflow execution \(see the test case described below for an example workflow design\).)] TJ ET BT 26.250 414.610 Td /F1 9.8 Tf [(We are designing Arbor as scalable software, with tree-of-life-scale analyses in mind from the beginning. Arbor will be able to )] TJ ET BT 26.250 402.705 Td /F1 9.8 Tf [(efficiently process both small and large datasets, ultimately extending to analyses across the entire Tree of Life. This scalable )] TJ ET BT 26.250 390.801 Td /F1 9.8 Tf [(performance will come from the use of improved algorithms \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 306.923 392.308 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 316.561 390.801 Td /F1 9.8 Tf [(\) along with both fine-grained parallelism \(using )] TJ ET BT 26.250 378.896 Td /F1 9.8 Tf [(multithreaded execution of individual steps when possible in a workflow\) and coarse-grained parallelism \(executing multiple )] TJ ET BT 26.250 366.991 Td /F1 9.8 Tf [(steps of a workflow simultaneously on separate cores\). Arbor will run efficiently to develop and test workflow designs using )] TJ ET BT 26.250 355.086 Td /F1 9.8 Tf [(small and medium-size datasets on laptop and personal computers. Then, after a workflow idea has been expressed and )] TJ ET BT 26.250 343.182 Td /F1 9.8 Tf [(validated, the workflow can be run against tree-of-life scale data using a scalable computing resource. To do this, the user will )] TJ ET BT 26.250 331.277 Td /F1 9.8 Tf [(transfer the workflow from the local computer to an Arbor instance running on a large, multiprocessing computer, a computation )] TJ ET BT 26.250 319.372 Td /F1 9.8 Tf [(cluster \(e.g., XSEDE; www.xsede.org\), or a similar cloud computational service to run a full-scale analysis.)] TJ ET BT 26.250 299.967 Td /F1 9.8 Tf [(Arbor will be modular software, extendable through a plug-in architecture that allows new analysis modules to be added to the )] TJ ET BT 26.250 288.063 Td /F1 9.8 Tf [(program \(similar to the modular design of Mesquite )] TJ ET 0.267 0.267 0.267 rg BT 248.950 289.570 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 258.587 288.063 Td /F1 9.8 Tf [(\). Arbor modules will be able to include algorithms written in a number of )] TJ ET BT 26.250 276.158 Td /F1 9.8 Tf [(languages \(e.g. R, Python, Perl, C, or C++\). Researchers who develop software for comparative analyses will have an )] TJ ET BT 26.250 264.253 Td /F1 9.8 Tf [(immediate user base if they integrate their program as an Arbor module, promoting and encouraging active use of Arbor by the )] TJ ET BT 26.250 252.348 Td /F1 9.8 Tf [(programming community. Arbors modular construction will allow new algorithms to become quickly available and usable with )] TJ ET BT 26.250 240.444 Td /F1 9.8 Tf [(data; scientists will be able to carry out comparative analyses that have not yet been imagined.)] TJ ET BT 26.250 221.039 Td /F1 9.8 Tf [(Instead of spending effort redeveloping yet another implementation of known algorithms, the Arbor team will focus initially on )] TJ ET BT 26.250 209.134 Td /F1 9.8 Tf [(integrating with existing external applications. Arbor will be able to work alongside proven systems like Mesquite, MrBayes, )] TJ ET BT 26.250 197.229 Td /F1 9.8 Tf [(BEAST, PHYLIP, ape, and others. At any point along the way, Arbors visualization tools can be used to examine intermediate )] TJ ET BT 26.250 185.325 Td /F1 9.8 Tf [(steps along an analysis workflow. All of the analyses in a workflow will be coordinated through the Arbor interface. This )] TJ ET BT 26.250 173.420 Td /F1 9.8 Tf [(integration represents an entirely new way to build novel comparative analyses.)] TJ ET BT 26.250 154.015 Td /F1 9.8 Tf [(Arbor will include a web services infrastructure, providing the ability to integrate with existing web-hosted services that offer )] TJ ET BT 26.250 142.110 Td /F1 9.8 Tf [(trees and data for analysis or perform algorithms useful for Arbor workflows \(e.g. Lifemapper, CIPRES, MAFFT, RAXML, )] TJ ET BT 26.250 130.206 Td /F1 9.8 Tf [(UniFrac, TreeBase, PorToL, OneZoom, and iPLANT\). We will also make specific connections to the other AVAToL projects )] TJ ET BT 26.250 118.301 Td /F1 9.8 Tf [(\(Open Tree of Life and Next-Generation Phenomics\). These connections will be facilitated by Arbors )] TJ ET BT 463.011 118.301 Td /F5 9.8 Tf [(dataIntegrator)] TJ ET BT 523.715 118.301 Td /F1 9.8 Tf [( module, )] TJ ET BT 26.250 106.396 Td /F1 9.8 Tf [(which will allow Arbor to access, integrate, and analyze phylogenetic, geospatial, ontogenetic, and morphological data together )] TJ ET BT 26.250 94.491 Td /F1 9.8 Tf [(in a single workflow.)] TJ ET BT 26.250 75.087 Td /F1 9.8 Tf [(Users will be able to export and share their workflows so that entire analyses can be quickly replicated with new or updated )] TJ ET BT 26.250 63.182 Td /F1 9.8 Tf [(data. Shared workflows will be stored at the DRYAD digital repository \(datadryad.org\) or a similar archive, so that users who )] TJ ET BT 26.250 51.277 Td /F1 9.8 Tf [(generate practical or compelling workflows receive direct credit via citations in scientific publications. We will encourage buy-in )] TJ ET BT 26.250 39.372 Td /F1 9.8 Tf [(from user communities by providing an interactive and intuitive visual exploratory workspace with a user-driven toolkit. This )] TJ ET Q q 15.000 25.087 577.500 751.913 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(link together custom-designed sets of statistical analyses geared toward the types of questions inherent to their data. Second, )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(Arbor will be extendable: software developers are able to quickly and easily add functionality without altering the details of )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(Arbors core implementation. Third, Arbor will be sharable: users will be able to save their Arbor workflows and share them with )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(others. As such, Arbor will be next generation software that enables tree-thinking and novel analyses at broad spatial and )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(temporal scales.)] TJ ET BT 26.250 700.452 Td /F1 9.8 Tf [(The Arbor development team \(see below\) brings together a variety of expertise in both biology and computer science. The )] TJ ET BT 26.250 688.548 Td /F1 9.8 Tf [(ongoing development of Arbor focuses on four components. First, we are developing the core of Arbor. This core will be a )] TJ ET BT 26.250 676.643 Td /F1 9.8 Tf [(phylogenetic comparative analysis platform with a flexible user interface that will leverage existing software, algorithms and web )] TJ ET BT 26.250 664.738 Td /F1 9.8 Tf [(services to allow scientists to address comparative evolutionary hypotheses at every scale across the Tree of Life. Second, we )] TJ ET BT 26.250 652.833 Td /F1 9.8 Tf [(are implementing shared data integration and basic analysis tools for Arbor. These modular tools will provide basic visualization )] TJ ET BT 26.250 640.929 Td /F1 9.8 Tf [(and fast, scalable algorithms for comparative analyses across a given phylogeny \(i.e. lineage-specific trait diversification\) or )] TJ ET BT 26.250 629.024 Td /F1 9.8 Tf [(between two topologies \(i.e. co-diversification, species interactions\). Third, we are using a set of three test cases to develop )] TJ ET BT 26.250 617.119 Td /F1 9.8 Tf [(Arbor into software that can solve fundamental problems in evolutionary biology. These test cases will stimulate rapid )] TJ ET BT 26.250 605.214 Td /F1 9.8 Tf [(development of numerous Arbor modules that are directly inspired by biological applications across the Tree of Life. Fourth, we )] TJ ET BT 26.250 593.310 Td /F1 9.8 Tf [(are developing four outreach initiatives to ensure that Arbor has a broader impact in advancing science, education and public )] TJ ET BT 26.250 581.405 Td /F1 9.8 Tf [(education in comparative evolutionary biology.)] TJ ET BT 26.250 544.802 Td /F4 12.0 Tf [(The Arbor core: workflows and web services promote flexible and dynamic analyses)] TJ ET BT 26.250 524.848 Td /F1 9.8 Tf [(The Arbor interface will be a radical departure from currently existing software for comparative analyses. Users will interact with )] TJ ET BT 26.250 512.943 Td /F1 9.8 Tf [(Arbor in an intuitive, visual way; building an Arbor workflow will have more in common with building a structure using Legos than )] TJ ET BT 26.250 501.039 Td /F1 9.8 Tf [(with programming a computer. By using a modular open-source interface and web services, we will encourage the development )] TJ ET BT 26.250 489.134 Td /F1 9.8 Tf [(of new tools and simultaneously enhance interoperability among existing tools.)] TJ ET BT 26.250 469.729 Td /F1 9.8 Tf [(Arbor takes inspiration from existing workflow software, especially ParaView )] TJ ET 0.267 0.267 0.267 rg BT 356.765 471.236 Td /F4 8.7 Tf [(13)] TJ ET 0.271 0.267 0.267 rg BT 366.403 469.729 Td /F1 9.8 Tf [( \(also see Galaxy )] TJ ET 0.267 0.267 0.267 rg BT 444.432 471.236 Td /F4 8.7 Tf [(14)] TJ ET 0.271 0.267 0.267 rg BT 454.069 469.729 Td /F1 9.8 Tf [( and the iPlant Discovery )] TJ ET BT 26.250 457.824 Td /F1 9.8 Tf [(Environment)] TJ ET 0.267 0.267 0.267 rg BT 80.977 459.332 Td /F4 8.7 Tf [(33)] TJ ET 0.271 0.267 0.267 rg BT 90.614 457.824 Td /F1 9.8 Tf [(\). Users of workflow software create problem-specific workflows visually by connecting a series of data )] TJ ET BT 26.250 445.920 Td /F1 9.8 Tf [(manipulations and analyses in a series of steps. The underlying software system is able to automatically coordinate the )] TJ ET BT 26.250 434.015 Td /F1 9.8 Tf [(invocation of all of these steps during workflow execution \(see the test case described below for an example workflow design\).)] TJ ET BT 26.250 414.610 Td /F1 9.8 Tf [(We are designing Arbor as scalable software, with tree-of-life-scale analyses in mind from the beginning. Arbor will be able to )] TJ ET BT 26.250 402.705 Td /F1 9.8 Tf [(efficiently process both small and large datasets, ultimately extending to analyses across the entire Tree of Life. This scalable )] TJ ET BT 26.250 390.801 Td /F1 9.8 Tf [(performance will come from the use of improved algorithms \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 306.923 392.308 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 316.561 390.801 Td /F1 9.8 Tf [(\) along with both fine-grained parallelism \(using )] TJ ET BT 26.250 378.896 Td /F1 9.8 Tf [(multithreaded execution of individual steps when possible in a workflow\) and coarse-grained parallelism \(executing multiple )] TJ ET BT 26.250 366.991 Td /F1 9.8 Tf [(steps of a workflow simultaneously on separate cores\). Arbor will run efficiently to develop and test workflow designs using )] TJ ET BT 26.250 355.086 Td /F1 9.8 Tf [(small and medium-size datasets on laptop and personal computers. Then, after a workflow idea has been expressed and )] TJ ET BT 26.250 343.182 Td /F1 9.8 Tf [(validated, the workflow can be run against tree-of-life scale data using a scalable computing resource. To do this, the user will )] TJ ET BT 26.250 331.277 Td /F1 9.8 Tf [(transfer the workflow from the local computer to an Arbor instance running on a large, multiprocessing computer, a computation )] TJ ET BT 26.250 319.372 Td /F1 9.8 Tf [(cluster \(e.g., XSEDE; www.xsede.org\), or a similar cloud computational service to run a full-scale analysis.)] TJ ET BT 26.250 299.967 Td /F1 9.8 Tf [(Arbor will be modular software, extendable through a plug-in architecture that allows new analysis modules to be added to the )] TJ ET BT 26.250 288.063 Td /F1 9.8 Tf [(program \(similar to the modular design of Mesquite )] TJ ET 0.267 0.267 0.267 rg BT 248.950 289.570 Td /F4 8.7 Tf [(16)] TJ ET 0.271 0.267 0.267 rg BT 258.587 288.063 Td /F1 9.8 Tf [(\). Arbor modules will be able to include algorithms written in a number of )] TJ ET BT 26.250 276.158 Td /F1 9.8 Tf [(languages \(e.g. R, Python, Perl, C, or C++\). Researchers who develop software for comparative analyses will have an )] TJ ET BT 26.250 264.253 Td /F1 9.8 Tf [(immediate user base if they integrate their program as an Arbor module, promoting and encouraging active use of Arbor by the )] TJ ET BT 26.250 252.348 Td /F1 9.8 Tf [(programming community. Arbors modular construction will allow new algorithms to become quickly available and usable with )] TJ ET BT 26.250 240.444 Td /F1 9.8 Tf [(data; scientists will be able to carry out comparative analyses that have not yet been imagined.)] TJ ET BT 26.250 221.039 Td /F1 9.8 Tf [(Instead of spending effort redeveloping yet another implementation of known algorithms, the Arbor team will focus initially on )] TJ ET BT 26.250 209.134 Td /F1 9.8 Tf [(integrating with existing external applications. Arbor will be able to work alongside proven systems like Mesquite, MrBayes, )] TJ ET BT 26.250 197.229 Td /F1 9.8 Tf [(BEAST, PHYLIP, ape, and others. At any point along the way, Arbors visualization tools can be used to examine intermediate )] TJ ET BT 26.250 185.325 Td /F1 9.8 Tf [(steps along an analysis workflow. All of the analyses in a workflow will be coordinated through the Arbor interface. This )] TJ ET BT 26.250 173.420 Td /F1 9.8 Tf [(integration represents an entirely new way to build novel comparative analyses.)] TJ ET BT 26.250 154.015 Td /F1 9.8 Tf [(Arbor will include a web services infrastructure, providing the ability to integrate with existing web-hosted services that offer )] TJ ET BT 26.250 142.110 Td /F1 9.8 Tf [(trees and data for analysis or perform algorithms useful for Arbor workflows \(e.g. Lifemapper, CIPRES, MAFFT, RAXML, )] TJ ET BT 26.250 130.206 Td /F1 9.8 Tf [(UniFrac, TreeBase, PorToL, OneZoom, and iPLANT\). We will also make specific connections to the other AVAToL projects )] TJ ET BT 26.250 118.301 Td /F1 9.8 Tf [(\(Open Tree of Life and Next-Generation Phenomics\). These connections will be facilitated by Arbors )] TJ ET BT 463.011 118.301 Td /F5 9.8 Tf [(dataIntegrator)] TJ ET BT 523.715 118.301 Td /F1 9.8 Tf [( module, )] TJ ET BT 26.250 106.396 Td /F1 9.8 Tf [(which will allow Arbor to access, integrate, and analyze phylogenetic, geospatial, ontogenetic, and morphological data together )] TJ ET BT 26.250 94.491 Td /F1 9.8 Tf [(in a single workflow.)] TJ ET BT 26.250 75.087 Td /F1 9.8 Tf [(Users will be able to export and share their workflows so that entire analyses can be quickly replicated with new or updated )] TJ ET BT 26.250 63.182 Td /F1 9.8 Tf [(data. Shared workflows will be stored at the DRYAD digital repository \(datadryad.org\) or a similar archive, so that users who )] TJ ET BT 26.250 51.277 Td /F1 9.8 Tf [(generate practical or compelling workflows receive direct credit via citations in scientific publications. We will encourage buy-in )] TJ ET BT 26.250 39.372 Td /F1 9.8 Tf [(from user communities by providing an interactive and intuitive visual exploratory workspace with a user-driven toolkit. 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Tool use could be tracked to demonstrate user action and )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(efficiency, providing feedback on which programs are being used and combined. Workflows will capture the provenance of )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(ideas by automatically generating a list of references to be cited by end-users.)] TJ ET BT 26.250 695.159 Td /F4 12.0 Tf [(What will I be able to do with Arbor?)] TJ ET BT 26.250 675.205 Td /F1 9.8 Tf [(Arbor will begin by implementing the most commonly used existing comparative algorithms. We have started from the most )] TJ ET BT 26.250 663.300 Td /F1 9.8 Tf [(flexible current platform for comparative methods, the statistical computer programming language R, home to several widely )] TJ ET BT 26.250 651.396 Td /F1 9.8 Tf [(used phylogenetic analyses packages including ape )] TJ ET 0.267 0.267 0.267 rg BT 253.327 652.903 Td /F4 8.7 Tf [(17)] TJ ET 0.271 0.267 0.267 rg BT 262.965 651.396 Td /F1 9.8 Tf [(, GEIGER )] TJ ET 0.267 0.267 0.267 rg BT 309.024 652.903 Td /F4 8.7 Tf [(18)] TJ ET 0.271 0.267 0.267 rg BT 318.661 651.396 Td /F1 9.8 Tf [(, picante )] TJ ET 0.267 0.267 0.267 rg BT 358.227 652.903 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 367.864 651.396 Td /F1 9.8 Tf [(, and diversitree )] TJ ET 0.267 0.267 0.267 rg BT 439.936 652.903 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 449.573 651.396 Td /F1 9.8 Tf [(. The comparative algorithms )] TJ ET BT 26.250 639.491 Td /F1 9.8 Tf [(from these packages especially ape will form the initial basis for Arbors core analysis infrastructure. We will also focus on )] TJ ET BT 26.250 627.586 Td /F1 9.8 Tf [(developing and implementing new algorithms that can be applied efficiently to very large datasets \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 470.626 629.093 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 480.263 627.586 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 608.181 Td /F1 9.8 Tf [(Arbor will allow users to link analyses as a series of steps in a workflow. To facilitate this process, we will spend effort to extend )] TJ ET BT 26.250 596.277 Td /F1 9.8 Tf [(the flexible and scalable data structures already implemented in ParaView and/or VTK \(the Visualization Toolkit )] TJ ET 0.267 0.267 0.267 rg BT 508.534 597.784 Td /F4 8.7 Tf [(22)] TJ ET 0.271 0.267 0.267 rg BT 518.171 596.277 Td /F1 9.8 Tf [(\) to be useful )] TJ ET BT 26.250 584.372 Td /F1 9.8 Tf [(for a wide array of evolutionary analyses. Phylogenetic tree data structures are initially based on designs implemented in the )] TJ ET BT 26.250 572.467 Td /F1 9.8 Tf [(ape and phylobase R packages. Our project will study and refine the design of tree and data structures for scalability and )] TJ ET BT 26.250 560.562 Td /F1 9.8 Tf [(efficiency.)] TJ ET BT 26.250 541.158 Td /F1 9.8 Tf [(We will include powerful tree-based selection and query operations in Arbors analytical capabilities through the )] TJ ET BT 507.988 541.158 Td /F5 9.8 Tf [(treeManipulator)] TJ ET BT 26.250 529.253 Td /F1 9.8 Tf [(module. For example, Arbor will be able to locate sets of species that co-occur at a particular place and time, and to plot those )] TJ ET BT 26.250 517.348 Td /F1 9.8 Tf [(species on a phylogenetic tree. This type of analysis, combining phylogenetic, geospatial, temporal, and other evolutionary )] TJ ET BT 26.250 505.443 Td /F1 9.8 Tf [(traits, will take advantage of the rich filtering and selection operations implemented in Arbors analysis framework. These steps )] TJ ET BT 26.250 493.539 Td /F1 9.8 Tf [(can then be chained together to form problem-specific workflows.)] TJ ET BT 26.250 474.134 Td /F1 9.8 Tf [(A strength of Arbor will be the )] TJ ET BT 156.851 474.134 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 193.696 474.134 Td /F1 9.8 Tf [( module, which will use a mature set of interactive graphical tools already extensively )] TJ ET BT 26.250 462.229 Td /F1 9.8 Tf [(tested by the scientific visualization and data-mining communities. VTK-based visualizations have previously been implemented )] TJ ET BT 26.250 450.324 Td /F1 9.8 Tf [(in interactive user interfaces running on all major computing platforms \(Windows, Mac, Linux, and various custom )] TJ ET BT 26.250 438.420 Td /F1 9.8 Tf [(supercomputer architectures\). The VTK library itself is open-source and has been steadily evolving and expanding since its )] TJ ET BT 26.250 426.515 Td /F1 9.8 Tf [(initial releases. In the past few years, the Visualization Toolkit has been extended to include informatics and information )] TJ ET BT 26.250 414.610 Td /F1 9.8 Tf [(visualization tools to VTK, making VTK a premier information visualization platform that includes pre-built interactive )] TJ ET BT 26.250 402.705 Td /F1 9.8 Tf [(visualization views )] TJ ET 0.267 0.267 0.267 rg BT 109.144 404.213 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 118.782 402.705 Td /F1 9.8 Tf [(. The )] TJ ET BT 143.713 402.705 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 180.558 402.705 Td /F1 9.8 Tf [( module will take advantage of these views to include visualizations specific to comparative )] TJ ET BT 26.250 390.801 Td /F1 9.8 Tf [(analyses. We will also allow users to interface with OneZoom, a new tool for visualizing very large phylogenetic trees )] TJ ET 0.267 0.267 0.267 rg BT 531.807 392.308 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 541.444 390.801 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 371.396 Td /F1 9.8 Tf [(We will employ a set of three test cases to develop Arbor into software that can address fundamental questions in evolutionary )] TJ ET BT 26.250 359.491 Td /F1 9.8 Tf [(biology. Test cases have been selected for their overarching biological relevance, but also to deliberately challenge and drive )] TJ ET BT 26.250 347.586 Td /F1 9.8 Tf [(software development. These test cases include: \(I\) )] TJ ET BT 251.680 347.586 Td /F5 9.8 Tf [(The Evolutionary Process of Spatial Diversification)] TJ ET BT 469.505 347.586 Td /F1 9.8 Tf [(, using species )] TJ ET BT 26.250 335.682 Td /F1 9.8 Tf [(distribution data, phylogenetic relationships, and temporal data to understand processes underlying biogeographic patterns and )] TJ ET BT 26.250 323.777 Td /F1 9.8 Tf [(ecological niche differentiation; \(II\) )] TJ ET BT 176.897 323.777 Td /F5 9.8 Tf [(The Evolution of Symbiotic Communities)] TJ ET BT 351.910 323.777 Td /F1 9.8 Tf [(, using natural evolutionary replicates to understand )] TJ ET BT 26.250 311.872 Td /F1 9.8 Tf [(the tempo and mode of evolution in species interactions and the evolution of phylogenetic community structure; \(III\) )] TJ ET BT 525.362 311.872 Td /F5 9.8 Tf [(The )] TJ ET BT 26.250 299.967 Td /F5 9.8 Tf [(Evolution of Complex Interactions)] TJ ET BT 171.476 299.967 Td /F1 9.8 Tf [(, using novel evolutionary models and analytical algorithms to understand functional )] TJ ET BT 26.250 288.063 Td /F1 9.8 Tf [(diversification during macroevolution and the evolution of interaction networks. Below we describe one test case in more detail )] TJ ET BT 26.250 276.158 Td /F1 9.8 Tf [(to give an idea of the potential of the Arbor framework for enabling novel analyses.)] TJ ET BT 26.250 239.555 Td /F4 12.0 Tf [(Arbor Test Case: The Evolutionary Process of Spatial Diversification)] TJ ET BT 26.250 219.601 Td /F1 9.8 Tf [(The geographic range of a species is a crucial feature of its evolution. Species ranges are determined by both contemporary )] TJ ET BT 26.250 207.696 Td /F1 9.8 Tf [(and historical factors )] TJ ET 0.267 0.267 0.267 rg BT 118.368 209.204 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 128.005 207.696 Td /F1 9.8 Tf [(. Currently, species distribution models \(SDMs\) focus on the impact of contemporary abiotic factors in )] TJ ET BT 26.250 195.792 Td /F1 9.8 Tf [(structuring species ranges )] TJ ET 0.267 0.267 0.267 rg BT 144.917 197.299 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 154.555 195.792 Td /F1 9.8 Tf [(. By contrast, biogeographic models \(such as Lagrange )] TJ ET 0.267 0.267 0.267 rg BT 395.711 197.299 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 405.348 195.792 Td /F1 9.8 Tf [(\) consider how species ranges change )] TJ ET BT 26.250 183.887 Td /F1 9.8 Tf [(through time due to dispersal, speciation, and extinction )] TJ ET 0.267 0.267 0.267 rg BT 269.581 185.394 Td /F4 8.7 Tf [(27)] TJ ET BT 279.218 185.394 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 288.855 183.887 Td /F1 9.8 Tf [(. Arbor will allow users to integrate both approaches to allow )] TJ ET BT 26.250 171.982 Td /F1 9.8 Tf [(comprehensive analyses of the evolution of species ranges over time.)] TJ ET BT 26.250 152.577 Td /F1 9.8 Tf [(For this test case, we will combine locality data with dated phylogenetic trees and paleoclimate data to model species )] TJ ET BT 26.250 140.673 Td /F1 9.8 Tf [(distributions over time. Our test case analyses will focus on two main goals: \(I\) including historical data in SDMs; and \(II\) )] TJ ET BT 26.250 128.768 Td /F1 9.8 Tf [(including information about species niches in biogeographic models.)] TJ ET BT 26.250 109.363 Td /F1 9.8 Tf [(To include historical data in Species Distribution Models \(SDMs\), the Arbor data integration module \()] TJ ET BT 459.199 109.363 Td /F5 9.8 Tf [(dataIntegrator)] TJ ET BT 519.902 109.363 Td /F1 9.8 Tf [(\) will query )] TJ ET BT 26.250 97.458 Td /F1 9.8 Tf [(occurrence data \(e.g, VertNet [)] TJ ET 0.267 0.267 0.267 rg BT 159.562 97.458 Td /F1 9.8 Tf [(vertnet.org)] TJ ET 0.271 0.267 0.267 rg BT 206.167 97.458 Td /F1 9.8 Tf [(], GBIF [)] TJ ET 0.267 0.267 0.267 rg BT 242.476 97.458 Td /F1 9.8 Tf [(www.gbif.org)] TJ ET 0.271 0.267 0.267 rg BT 298.821 97.458 Td /F1 9.8 Tf [(], iDigBio [)] TJ ET 0.267 0.267 0.267 rg BT 343.252 97.458 Td /F1 9.8 Tf [(www.idigbio.org)] TJ ET 0.271 0.267 0.267 rg BT 412.057 97.458 Td /F1 9.8 Tf [(], or others\) to obtain locality )] TJ ET BT 26.250 85.554 Td /F1 9.8 Tf [(information for individuals from many species within a clade, and climate data servers to obtain climate data for each locality. An )] TJ ET BT 26.250 73.649 Td /F1 9.8 Tf [(intuitive visual output will enable the user to effectively curate occurrence data, selecting data points that are relevant for the )] TJ ET BT 26.250 61.744 Td /F1 9.8 Tf [(analysis. A distribution model for each of these species using the curated occurrence data will be constructed using an )] TJ ET BT 26.250 49.839 Td /F5 9.8 Tf [(openModeller)] TJ ET BT 85.316 49.839 Td /F1 9.8 Tf [( module \(based on openmodeller.sourceforge.net\) and LifeMapper \(lifemapper.org\), an existing set of web )] TJ ET BT 26.250 37.935 Td /F1 9.8 Tf [(services and tools. )] TJ ET BT 109.700 37.935 Td /F5 9.8 Tf [(openModeller)] TJ ET BT 168.766 37.935 Td /F1 9.8 Tf [( will use the integration capabilities of Arbor to incorporate both current distribution data and )] TJ ET Q q 15.000 23.649 577.500 753.351 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(toolkit can be expanded to include novel analytical tools as later modules are developed to serve the scientific community. )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(Furthermore, we plan to quantify the impact of Arbor in real time. Tool use could be tracked to demonstrate user action and )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(efficiency, providing feedback on which programs are being used and combined. Workflows will capture the provenance of )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(ideas by automatically generating a list of references to be cited by end-users.)] TJ ET BT 26.250 695.159 Td /F4 12.0 Tf [(What will I be able to do with Arbor?)] TJ ET BT 26.250 675.205 Td /F1 9.8 Tf [(Arbor will begin by implementing the most commonly used existing comparative algorithms. We have started from the most )] TJ ET BT 26.250 663.300 Td /F1 9.8 Tf [(flexible current platform for comparative methods, the statistical computer programming language R, home to several widely )] TJ ET BT 26.250 651.396 Td /F1 9.8 Tf [(used phylogenetic analyses packages including ape )] TJ ET 0.267 0.267 0.267 rg BT 253.327 652.903 Td /F4 8.7 Tf [(17)] TJ ET 0.271 0.267 0.267 rg BT 262.965 651.396 Td /F1 9.8 Tf [(, GEIGER )] TJ ET 0.267 0.267 0.267 rg BT 309.024 652.903 Td /F4 8.7 Tf [(18)] TJ ET 0.271 0.267 0.267 rg BT 318.661 651.396 Td /F1 9.8 Tf [(, picante )] TJ ET 0.267 0.267 0.267 rg BT 358.227 652.903 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 367.864 651.396 Td /F1 9.8 Tf [(, and diversitree )] TJ ET 0.267 0.267 0.267 rg BT 439.936 652.903 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 449.573 651.396 Td /F1 9.8 Tf [(. The comparative algorithms )] TJ ET BT 26.250 639.491 Td /F1 9.8 Tf [(from these packages especially ape will form the initial basis for Arbors core analysis infrastructure. We will also focus on )] TJ ET BT 26.250 627.586 Td /F1 9.8 Tf [(developing and implementing new algorithms that can be applied efficiently to very large datasets \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 470.626 629.093 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 480.263 627.586 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 608.181 Td /F1 9.8 Tf [(Arbor will allow users to link analyses as a series of steps in a workflow. To facilitate this process, we will spend effort to extend )] TJ ET BT 26.250 596.277 Td /F1 9.8 Tf [(the flexible and scalable data structures already implemented in ParaView and/or VTK \(the Visualization Toolkit )] TJ ET 0.267 0.267 0.267 rg BT 508.534 597.784 Td /F4 8.7 Tf [(22)] TJ ET 0.271 0.267 0.267 rg BT 518.171 596.277 Td /F1 9.8 Tf [(\) to be useful )] TJ ET BT 26.250 584.372 Td /F1 9.8 Tf [(for a wide array of evolutionary analyses. Phylogenetic tree data structures are initially based on designs implemented in the )] TJ ET BT 26.250 572.467 Td /F1 9.8 Tf [(ape and phylobase R packages. Our project will study and refine the design of tree and data structures for scalability and )] TJ ET BT 26.250 560.562 Td /F1 9.8 Tf [(efficiency.)] TJ ET BT 26.250 541.158 Td /F1 9.8 Tf [(We will include powerful tree-based selection and query operations in Arbors analytical capabilities through the )] TJ ET BT 507.988 541.158 Td /F5 9.8 Tf [(treeManipulator)] TJ ET BT 26.250 529.253 Td /F1 9.8 Tf [(module. For example, Arbor will be able to locate sets of species that co-occur at a particular place and time, and to plot those )] TJ ET BT 26.250 517.348 Td /F1 9.8 Tf [(species on a phylogenetic tree. This type of analysis, combining phylogenetic, geospatial, temporal, and other evolutionary )] TJ ET BT 26.250 505.443 Td /F1 9.8 Tf [(traits, will take advantage of the rich filtering and selection operations implemented in Arbors analysis framework. These steps )] TJ ET BT 26.250 493.539 Td /F1 9.8 Tf [(can then be chained together to form problem-specific workflows.)] TJ ET BT 26.250 474.134 Td /F1 9.8 Tf [(A strength of Arbor will be the )] TJ ET BT 156.851 474.134 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 193.696 474.134 Td /F1 9.8 Tf [( module, which will use a mature set of interactive graphical tools already extensively )] TJ ET BT 26.250 462.229 Td /F1 9.8 Tf [(tested by the scientific visualization and data-mining communities. VTK-based visualizations have previously been implemented )] TJ ET BT 26.250 450.324 Td /F1 9.8 Tf [(in interactive user interfaces running on all major computing platforms \(Windows, Mac, Linux, and various custom )] TJ ET BT 26.250 438.420 Td /F1 9.8 Tf [(supercomputer architectures\). The VTK library itself is open-source and has been steadily evolving and expanding since its )] TJ ET BT 26.250 426.515 Td /F1 9.8 Tf [(initial releases. In the past few years, the Visualization Toolkit has been extended to include informatics and information )] TJ ET BT 26.250 414.610 Td /F1 9.8 Tf [(visualization tools to VTK, making VTK a premier information visualization platform that includes pre-built interactive )] TJ ET BT 26.250 402.705 Td /F1 9.8 Tf [(visualization views )] TJ ET 0.267 0.267 0.267 rg BT 109.144 404.213 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 118.782 402.705 Td /F1 9.8 Tf [(. The )] TJ ET BT 143.713 402.705 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 180.558 402.705 Td /F1 9.8 Tf [( module will take advantage of these views to include visualizations specific to comparative )] TJ ET BT 26.250 390.801 Td /F1 9.8 Tf [(analyses. We will also allow users to interface with OneZoom, a new tool for visualizing very large phylogenetic trees )] TJ ET 0.267 0.267 0.267 rg BT 531.807 392.308 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 541.444 390.801 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 371.396 Td /F1 9.8 Tf [(We will employ a set of three test cases to develop Arbor into software that can address fundamental questions in evolutionary )] TJ ET BT 26.250 359.491 Td /F1 9.8 Tf [(biology. Test cases have been selected for their overarching biological relevance, but also to deliberately challenge and drive )] TJ ET BT 26.250 347.586 Td /F1 9.8 Tf [(software development. These test cases include: \(I\) )] TJ ET BT 251.680 347.586 Td /F5 9.8 Tf [(The Evolutionary Process of Spatial Diversification)] TJ ET BT 469.505 347.586 Td /F1 9.8 Tf [(, using species )] TJ ET BT 26.250 335.682 Td /F1 9.8 Tf [(distribution data, phylogenetic relationships, and temporal data to understand processes underlying biogeographic patterns and )] TJ ET BT 26.250 323.777 Td /F1 9.8 Tf [(ecological niche differentiation; \(II\) )] TJ ET BT 176.897 323.777 Td /F5 9.8 Tf [(The Evolution of Symbiotic Communities)] TJ ET BT 351.910 323.777 Td /F1 9.8 Tf [(, using natural evolutionary replicates to understand )] TJ ET BT 26.250 311.872 Td /F1 9.8 Tf [(the tempo and mode of evolution in species interactions and the evolution of phylogenetic community structure; \(III\) )] TJ ET BT 525.362 311.872 Td /F5 9.8 Tf [(The )] TJ ET BT 26.250 299.967 Td /F5 9.8 Tf [(Evolution of Complex Interactions)] TJ ET BT 171.476 299.967 Td /F1 9.8 Tf [(, using novel evolutionary models and analytical algorithms to understand functional )] TJ ET BT 26.250 288.063 Td /F1 9.8 Tf [(diversification during macroevolution and the evolution of interaction networks. Below we describe one test case in more detail )] TJ ET BT 26.250 276.158 Td /F1 9.8 Tf [(to give an idea of the potential of the Arbor framework for enabling novel analyses.)] TJ ET BT 26.250 239.555 Td /F4 12.0 Tf [(Arbor Test Case: The Evolutionary Process of Spatial Diversification)] TJ ET BT 26.250 219.601 Td /F1 9.8 Tf [(The geographic range of a species is a crucial feature of its evolution. Species ranges are determined by both contemporary )] TJ ET BT 26.250 207.696 Td /F1 9.8 Tf [(and historical factors )] TJ ET 0.267 0.267 0.267 rg BT 118.368 209.204 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 128.005 207.696 Td /F1 9.8 Tf [(. Currently, species distribution models \(SDMs\) focus on the impact of contemporary abiotic factors in )] TJ ET BT 26.250 195.792 Td /F1 9.8 Tf [(structuring species ranges )] TJ ET 0.267 0.267 0.267 rg BT 144.917 197.299 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 154.555 195.792 Td /F1 9.8 Tf [(. By contrast, biogeographic models \(such as Lagrange )] TJ ET 0.267 0.267 0.267 rg BT 395.711 197.299 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 405.348 195.792 Td /F1 9.8 Tf [(\) consider how species ranges change )] TJ ET BT 26.250 183.887 Td /F1 9.8 Tf [(through time due to dispersal, speciation, and extinction )] TJ ET 0.267 0.267 0.267 rg BT 269.581 185.394 Td /F4 8.7 Tf [(27)] TJ ET BT 279.218 185.394 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 288.855 183.887 Td /F1 9.8 Tf [(. Arbor will allow users to integrate both approaches to allow )] TJ ET BT 26.250 171.982 Td /F1 9.8 Tf [(comprehensive analyses of the evolution of species ranges over time.)] TJ ET BT 26.250 152.577 Td /F1 9.8 Tf [(For this test case, we will combine locality data with dated phylogenetic trees and paleoclimate data to model species )] TJ ET BT 26.250 140.673 Td /F1 9.8 Tf [(distributions over time. Our test case analyses will focus on two main goals: \(I\) including historical data in SDMs; and \(II\) )] TJ ET BT 26.250 128.768 Td /F1 9.8 Tf [(including information about species niches in biogeographic models.)] TJ ET BT 26.250 109.363 Td /F1 9.8 Tf [(To include historical data in Species Distribution Models \(SDMs\), the Arbor data integration module \()] TJ ET BT 459.199 109.363 Td /F5 9.8 Tf [(dataIntegrator)] TJ ET BT 519.902 109.363 Td /F1 9.8 Tf [(\) will query )] TJ ET BT 26.250 97.458 Td /F1 9.8 Tf [(occurrence data \(e.g, VertNet [)] TJ ET 0.267 0.267 0.267 rg BT 159.562 97.458 Td /F1 9.8 Tf [(vertnet.org)] TJ ET 0.271 0.267 0.267 rg BT 206.167 97.458 Td /F1 9.8 Tf [(], GBIF [)] TJ ET 0.267 0.267 0.267 rg BT 242.476 97.458 Td /F1 9.8 Tf [(www.gbif.org)] TJ ET 0.271 0.267 0.267 rg BT 298.821 97.458 Td /F1 9.8 Tf [(], iDigBio [)] TJ ET 0.267 0.267 0.267 rg BT 343.252 97.458 Td /F1 9.8 Tf [(www.idigbio.org)] TJ ET 0.271 0.267 0.267 rg BT 412.057 97.458 Td /F1 9.8 Tf [(], or others\) to obtain locality )] TJ ET BT 26.250 85.554 Td /F1 9.8 Tf [(information for individuals from many species within a clade, and climate data servers to obtain climate data for each locality. An )] TJ ET BT 26.250 73.649 Td /F1 9.8 Tf [(intuitive visual output will enable the user to effectively curate occurrence data, selecting data points that are relevant for the )] TJ ET BT 26.250 61.744 Td /F1 9.8 Tf [(analysis. A distribution model for each of these species using the curated occurrence data will be constructed using an )] TJ ET BT 26.250 49.839 Td /F5 9.8 Tf [(openModeller)] TJ ET BT 85.316 49.839 Td /F1 9.8 Tf [( module \(based on openmodeller.sourceforge.net\) and LifeMapper \(lifemapper.org\), an existing set of web )] TJ ET BT 26.250 37.935 Td /F1 9.8 Tf [(services and tools. )] TJ ET BT 109.700 37.935 Td /F5 9.8 Tf [(openModeller)] TJ ET BT 168.766 37.935 Td /F1 9.8 Tf [( will use the integration capabilities of Arbor to incorporate both current distribution data and )] TJ ET Q q 15.000 23.649 577.500 753.351 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(toolkit can be expanded to include novel analytical tools as later modules are developed to serve the scientific community. )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(Furthermore, we plan to quantify the impact of Arbor in real time. Tool use could be tracked to demonstrate user action and )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(efficiency, providing feedback on which programs are being used and combined. Workflows will capture the provenance of )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(ideas by automatically generating a list of references to be cited by end-users.)] TJ ET BT 26.250 695.159 Td /F4 12.0 Tf [(What will I be able to do with Arbor?)] TJ ET BT 26.250 675.205 Td /F1 9.8 Tf [(Arbor will begin by implementing the most commonly used existing comparative algorithms. We have started from the most )] TJ ET BT 26.250 663.300 Td /F1 9.8 Tf [(flexible current platform for comparative methods, the statistical computer programming language R, home to several widely )] TJ ET BT 26.250 651.396 Td /F1 9.8 Tf [(used phylogenetic analyses packages including ape )] TJ ET 0.267 0.267 0.267 rg BT 253.327 652.903 Td /F4 8.7 Tf [(17)] TJ ET 0.271 0.267 0.267 rg BT 262.965 651.396 Td /F1 9.8 Tf [(, GEIGER )] TJ ET 0.267 0.267 0.267 rg BT 309.024 652.903 Td /F4 8.7 Tf [(18)] TJ ET 0.271 0.267 0.267 rg BT 318.661 651.396 Td /F1 9.8 Tf [(, picante )] TJ ET 0.267 0.267 0.267 rg BT 358.227 652.903 Td /F4 8.7 Tf [(19)] TJ ET 0.271 0.267 0.267 rg BT 367.864 651.396 Td /F1 9.8 Tf [(, and diversitree )] TJ ET 0.267 0.267 0.267 rg BT 439.936 652.903 Td /F4 8.7 Tf [(20)] TJ ET 0.271 0.267 0.267 rg BT 449.573 651.396 Td /F1 9.8 Tf [(. The comparative algorithms )] TJ ET BT 26.250 639.491 Td /F1 9.8 Tf [(from these packages especially ape will form the initial basis for Arbors core analysis infrastructure. We will also focus on )] TJ ET BT 26.250 627.586 Td /F1 9.8 Tf [(developing and implementing new algorithms that can be applied efficiently to very large datasets \(e.g. )] TJ ET 0.267 0.267 0.267 rg BT 470.626 629.093 Td /F4 8.7 Tf [(15)] TJ ET 0.271 0.267 0.267 rg BT 480.263 627.586 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 608.181 Td /F1 9.8 Tf [(Arbor will allow users to link analyses as a series of steps in a workflow. To facilitate this process, we will spend effort to extend )] TJ ET BT 26.250 596.277 Td /F1 9.8 Tf [(the flexible and scalable data structures already implemented in ParaView and/or VTK \(the Visualization Toolkit )] TJ ET 0.267 0.267 0.267 rg BT 508.534 597.784 Td /F4 8.7 Tf [(22)] TJ ET 0.271 0.267 0.267 rg BT 518.171 596.277 Td /F1 9.8 Tf [(\) to be useful )] TJ ET BT 26.250 584.372 Td /F1 9.8 Tf [(for a wide array of evolutionary analyses. Phylogenetic tree data structures are initially based on designs implemented in the )] TJ ET BT 26.250 572.467 Td /F1 9.8 Tf [(ape and phylobase R packages. Our project will study and refine the design of tree and data structures for scalability and )] TJ ET BT 26.250 560.562 Td /F1 9.8 Tf [(efficiency.)] TJ ET BT 26.250 541.158 Td /F1 9.8 Tf [(We will include powerful tree-based selection and query operations in Arbors analytical capabilities through the )] TJ ET BT 507.988 541.158 Td /F5 9.8 Tf [(treeManipulator)] TJ ET BT 26.250 529.253 Td /F1 9.8 Tf [(module. For example, Arbor will be able to locate sets of species that co-occur at a particular place and time, and to plot those )] TJ ET BT 26.250 517.348 Td /F1 9.8 Tf [(species on a phylogenetic tree. This type of analysis, combining phylogenetic, geospatial, temporal, and other evolutionary )] TJ ET BT 26.250 505.443 Td /F1 9.8 Tf [(traits, will take advantage of the rich filtering and selection operations implemented in Arbors analysis framework. These steps )] TJ ET BT 26.250 493.539 Td /F1 9.8 Tf [(can then be chained together to form problem-specific workflows.)] TJ ET BT 26.250 474.134 Td /F1 9.8 Tf [(A strength of Arbor will be the )] TJ ET BT 156.851 474.134 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 193.696 474.134 Td /F1 9.8 Tf [( module, which will use a mature set of interactive graphical tools already extensively )] TJ ET BT 26.250 462.229 Td /F1 9.8 Tf [(tested by the scientific visualization and data-mining communities. VTK-based visualizations have previously been implemented )] TJ ET BT 26.250 450.324 Td /F1 9.8 Tf [(in interactive user interfaces running on all major computing platforms \(Windows, Mac, Linux, and various custom )] TJ ET BT 26.250 438.420 Td /F1 9.8 Tf [(supercomputer architectures\). The VTK library itself is open-source and has been steadily evolving and expanding since its )] TJ ET BT 26.250 426.515 Td /F1 9.8 Tf [(initial releases. In the past few years, the Visualization Toolkit has been extended to include informatics and information )] TJ ET BT 26.250 414.610 Td /F1 9.8 Tf [(visualization tools to VTK, making VTK a premier information visualization platform that includes pre-built interactive )] TJ ET BT 26.250 402.705 Td /F1 9.8 Tf [(visualization views )] TJ ET 0.267 0.267 0.267 rg BT 109.144 404.213 Td /F4 8.7 Tf [(23)] TJ ET 0.271 0.267 0.267 rg BT 118.782 402.705 Td /F1 9.8 Tf [(. The )] TJ ET BT 143.713 402.705 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 180.558 402.705 Td /F1 9.8 Tf [( module will take advantage of these views to include visualizations specific to comparative )] TJ ET BT 26.250 390.801 Td /F1 9.8 Tf [(analyses. We will also allow users to interface with OneZoom, a new tool for visualizing very large phylogenetic trees )] TJ ET 0.267 0.267 0.267 rg BT 531.807 392.308 Td /F4 8.7 Tf [(11)] TJ ET 0.271 0.267 0.267 rg BT 541.444 390.801 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 371.396 Td /F1 9.8 Tf [(We will employ a set of three test cases to develop Arbor into software that can address fundamental questions in evolutionary )] TJ ET BT 26.250 359.491 Td /F1 9.8 Tf [(biology. Test cases have been selected for their overarching biological relevance, but also to deliberately challenge and drive )] TJ ET BT 26.250 347.586 Td /F1 9.8 Tf [(software development. These test cases include: \(I\) )] TJ ET BT 251.680 347.586 Td /F5 9.8 Tf [(The Evolutionary Process of Spatial Diversification)] TJ ET BT 469.505 347.586 Td /F1 9.8 Tf [(, using species )] TJ ET BT 26.250 335.682 Td /F1 9.8 Tf [(distribution data, phylogenetic relationships, and temporal data to understand processes underlying biogeographic patterns and )] TJ ET BT 26.250 323.777 Td /F1 9.8 Tf [(ecological niche differentiation; \(II\) )] TJ ET BT 176.897 323.777 Td /F5 9.8 Tf [(The Evolution of Symbiotic Communities)] TJ ET BT 351.910 323.777 Td /F1 9.8 Tf [(, using natural evolutionary replicates to understand )] TJ ET BT 26.250 311.872 Td /F1 9.8 Tf [(the tempo and mode of evolution in species interactions and the evolution of phylogenetic community structure; \(III\) )] TJ ET BT 525.362 311.872 Td /F5 9.8 Tf [(The )] TJ ET BT 26.250 299.967 Td /F5 9.8 Tf [(Evolution of Complex Interactions)] TJ ET BT 171.476 299.967 Td /F1 9.8 Tf [(, using novel evolutionary models and analytical algorithms to understand functional )] TJ ET BT 26.250 288.063 Td /F1 9.8 Tf [(diversification during macroevolution and the evolution of interaction networks. Below we describe one test case in more detail )] TJ ET BT 26.250 276.158 Td /F1 9.8 Tf [(to give an idea of the potential of the Arbor framework for enabling novel analyses.)] TJ ET BT 26.250 239.555 Td /F4 12.0 Tf [(Arbor Test Case: The Evolutionary Process of Spatial Diversification)] TJ ET BT 26.250 219.601 Td /F1 9.8 Tf [(The geographic range of a species is a crucial feature of its evolution. Species ranges are determined by both contemporary )] TJ ET BT 26.250 207.696 Td /F1 9.8 Tf [(and historical factors )] TJ ET 0.267 0.267 0.267 rg BT 118.368 209.204 Td /F4 8.7 Tf [(24)] TJ ET 0.271 0.267 0.267 rg BT 128.005 207.696 Td /F1 9.8 Tf [(. Currently, species distribution models \(SDMs\) focus on the impact of contemporary abiotic factors in )] TJ ET BT 26.250 195.792 Td /F1 9.8 Tf [(structuring species ranges )] TJ ET 0.267 0.267 0.267 rg BT 144.917 197.299 Td /F4 8.7 Tf [(25)] TJ ET 0.271 0.267 0.267 rg BT 154.555 195.792 Td /F1 9.8 Tf [(. By contrast, biogeographic models \(such as Lagrange )] TJ ET 0.267 0.267 0.267 rg BT 395.711 197.299 Td /F4 8.7 Tf [(26)] TJ ET 0.271 0.267 0.267 rg BT 405.348 195.792 Td /F1 9.8 Tf [(\) consider how species ranges change )] TJ ET BT 26.250 183.887 Td /F1 9.8 Tf [(through time due to dispersal, speciation, and extinction )] TJ ET 0.267 0.267 0.267 rg BT 269.581 185.394 Td /F4 8.7 Tf [(27)] TJ ET BT 279.218 185.394 Td /F4 8.7 Tf [(28)] TJ ET 0.271 0.267 0.267 rg BT 288.855 183.887 Td /F1 9.8 Tf [(. Arbor will allow users to integrate both approaches to allow )] TJ ET BT 26.250 171.982 Td /F1 9.8 Tf [(comprehensive analyses of the evolution of species ranges over time.)] TJ ET BT 26.250 152.577 Td /F1 9.8 Tf [(For this test case, we will combine locality data with dated phylogenetic trees and paleoclimate data to model species )] TJ ET BT 26.250 140.673 Td /F1 9.8 Tf [(distributions over time. Our test case analyses will focus on two main goals: \(I\) including historical data in SDMs; and \(II\) )] TJ ET BT 26.250 128.768 Td /F1 9.8 Tf [(including information about species niches in biogeographic models.)] TJ ET BT 26.250 109.363 Td /F1 9.8 Tf [(To include historical data in Species Distribution Models \(SDMs\), the Arbor data integration module \()] TJ ET BT 459.199 109.363 Td /F5 9.8 Tf [(dataIntegrator)] TJ ET BT 519.902 109.363 Td /F1 9.8 Tf [(\) will query )] TJ ET BT 26.250 97.458 Td /F1 9.8 Tf [(occurrence data \(e.g, VertNet [)] TJ ET 0.267 0.267 0.267 rg BT 159.562 97.458 Td /F1 9.8 Tf [(vertnet.org)] TJ ET 0.271 0.267 0.267 rg BT 206.167 97.458 Td /F1 9.8 Tf [(], GBIF [)] TJ ET 0.267 0.267 0.267 rg BT 242.476 97.458 Td /F1 9.8 Tf [(www.gbif.org)] TJ ET 0.271 0.267 0.267 rg BT 298.821 97.458 Td /F1 9.8 Tf [(], iDigBio [)] TJ ET 0.267 0.267 0.267 rg BT 343.252 97.458 Td /F1 9.8 Tf [(www.idigbio.org)] TJ ET 0.271 0.267 0.267 rg BT 412.057 97.458 Td /F1 9.8 Tf [(], or others\) to obtain locality )] TJ ET BT 26.250 85.554 Td /F1 9.8 Tf [(information for individuals from many species within a clade, and climate data servers to obtain climate data for each locality. An )] TJ ET BT 26.250 73.649 Td /F1 9.8 Tf [(intuitive visual output will enable the user to effectively curate occurrence data, selecting data points that are relevant for the )] TJ ET BT 26.250 61.744 Td /F1 9.8 Tf [(analysis. A distribution model for each of these species using the curated occurrence data will be constructed using an )] TJ ET BT 26.250 49.839 Td /F5 9.8 Tf [(openModeller)] TJ ET BT 85.316 49.839 Td /F1 9.8 Tf [( module \(based on openmodeller.sourceforge.net\) and LifeMapper \(lifemapper.org\), an existing set of web )] TJ ET BT 26.250 37.935 Td /F1 9.8 Tf [(services and tools. )] TJ ET BT 109.700 37.935 Td /F5 9.8 Tf [(openModeller)] TJ ET BT 168.766 37.935 Td /F1 9.8 Tf [( will use the integration capabilities of Arbor to incorporate both current distribution data and )] 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 187 0 obj << /Type /Annot /Subtype /Link /A 188 0 R /Border [0 0 0] /H /I /Rect [ 253.3275 652.1012 262.9648 660.9195 ] >> endobj 188 0 obj << /Type /Action >> endobj 189 0 obj << /Type /Annot /Subtype /Link /A 190 0 R /Border [0 0 0] /H /I /Rect [ 309.0238 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The results can then be visualized using the )] TJ ET BT 26.250 731.762 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 63.095 731.762 Td /F1 9.8 Tf [( module.)] TJ ET 0.965 0.965 0.965 rg 26.250 415.876 555.000 306.005 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 721.881 m 581.250 721.881 l 581.250 721.131 l 26.250 721.131 l f 26.250 415.876 m 581.250 415.876 l 581.250 416.626 l 26.250 416.626 l f q 452.250 0 0 186.750 35.250 525.381 cm /I4 Do Q q 35.250 427.126 537.000 92.255 re W n 0.271 0.267 0.267 rg BT 35.250 509.857 Td /F4 9.8 Tf [(Fig. 1: Proposed phyloFlow workflow for the test case developed in the text. Information processing flows from )] TJ ET BT 35.250 497.952 Td /F4 9.8 Tf [(remote sources to five phyloFlow modules.)] TJ ET BT 35.250 478.582 Td /F1 9.8 Tf [(First, the dataIntegrator \(A\) combines phylogenetic, distributional, and climactic data sources. openModeller \(B\) then )] TJ ET BT 35.250 464.846 Td /F1 9.8 Tf [(creates species distribution models, and Lagrange \(C\) tests historical biogeographic hypotheses incorporating those )] TJ ET BT 35.250 451.110 Td /F1 9.8 Tf [(models. Next, phyloView allows geographic \(D\) and phylogenetic \(E\) visualization of results. Outputs are directed to the )] TJ ET BT 35.250 437.374 Td /F1 9.8 Tf [(dataOutput module \(F\), which can save results both locally and remotely.)] TJ ET Q BT 26.250 398.853 Td /F1 9.8 Tf [(We show a hypothetical workflow for this test case in Figure 1. The entire workflow has already been demonstrated \(outside of )] TJ ET BT 26.250 386.948 Td /F1 9.8 Tf [(Arbor\) in a pilot study )] TJ ET 0.267 0.267 0.267 rg BT 121.079 388.455 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 130.716 386.948 Td /F1 9.8 Tf [( using a virtual species on a spatially realistic matrix of 144 cells, and climate modeled in 130 time steps )] TJ ET BT 26.250 375.043 Td /F1 9.8 Tf [(\(back to 140,000 years before present\). We )] TJ ET BT 217.009 375.043 Td /F1 9.8 Tf [(will also be able to use the comparative capabilities of Arbor to constrain niche )] TJ ET BT 26.250 363.138 Td /F1 9.8 Tf [(models to follow patterns expected if species response to abiotic factors follows evolutionary history \(i.e., closely related )] TJ ET BT 26.250 351.234 Td /F1 9.8 Tf [(species have niches that are more similar to one another than distantly related species\). This will allow the user to directly test )] TJ ET BT 26.250 339.329 Td /F1 9.8 Tf [(for phylogenetic structure in historic and extant species distribution patterns. We will use the New World genus )] TJ ET BT 504.731 339.329 Td /F5 9.8 Tf [(Aphelocoma)] TJ ET BT 26.250 327.424 Td /F1 9.8 Tf [(\(scrub jays\), which has 9 phylogenetic species, as a biological application of this test case. The phylogeny of the clade is well )] TJ ET BT 26.250 315.519 Td /F1 9.8 Tf [(established )] TJ ET 0.267 0.267 0.267 rg BT 78.276 317.027 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 87.913 315.519 Td /F1 9.8 Tf [( and predictions of Pleistocene ranges have been made )] TJ ET 0.267 0.267 0.267 rg BT 331.254 317.027 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 340.891 315.519 Td /F1 9.8 Tf [(, but without consideration to the historical trajectories )] TJ ET BT 26.250 303.615 Td /F1 9.8 Tf [(of climatic factors and the phylogenetic history of the clade. We will use the new methods and algorithms implemented in Arbor )] TJ ET BT 26.250 291.710 Td /F1 9.8 Tf [(to model scrub jay species distributions while incorporating paleoclimatic and phylogenetic data.)] TJ ET BT 26.250 272.305 Td /F1 9.8 Tf [(To include information about species niches in biogeographic models, we will use the )] TJ ET BT 397.988 272.305 Td /F5 9.8 Tf [(Lagrange)] TJ ET BT 439.182 272.305 Td /F1 9.8 Tf [( module to test hypotheses )] TJ ET BT 26.250 260.400 Td /F1 9.8 Tf [(about the processes that govern range changes over time. Currently, the Lagrange program can fit process-based models of )] TJ ET BT 26.250 248.496 Td /F1 9.8 Tf [(changes in species ranges through time by modeling speciation, extinction, and dispersal among a set of geographic regions. )] TJ ET BT 26.250 236.591 Td /F1 9.8 Tf [(One can either assume that dispersal rates among these regions are constant or make modifications based on hypothesized )] TJ ET BT 26.250 224.686 Td /F1 9.8 Tf [(patterns of geographic connections through time. The )] TJ ET BT 259.831 224.686 Td /F5 9.8 Tf [(Lagrange)] TJ ET BT 301.024 224.686 Td /F1 9.8 Tf [( module in Arbor will allow us to modify transition rates as a )] TJ ET BT 26.250 212.781 Td /F1 9.8 Tf [(function of historical climate, directly testing whether geographic range shifts affect biogeographic processes. As a supplemental )] TJ ET BT 26.250 200.877 Td /F1 9.8 Tf [(biological application, we will use this approach to investigate the diversification of )] TJ ET BT 381.735 200.877 Td /F5 9.8 Tf [(Heliconia)] TJ ET BT 421.827 200.877 Td /F1 9.8 Tf [( plants and their hummingbird )] TJ ET BT 26.250 188.972 Td /F1 9.8 Tf [(pollinators. As these are Andean taxa that diversify during uplift activity, this test case will address the common biogeographical )] TJ ET BT 26.250 177.067 Td /F1 9.8 Tf [(hypothesis that the Andean uplift and subsequent diversification of ecological niche space led to the )] TJ ET BT 458.740 177.067 Td /F5 9.8 Tf [(in situ)] TJ ET BT 484.207 177.067 Td /F1 9.8 Tf [( diversification of )] TJ ET BT 26.250 165.162 Td /F1 9.8 Tf [(local lineages, and that current species distribution is largely driven by historical distributions and shifts in climatic factors )] TJ ET 0.267 0.267 0.267 rg BT 548.606 166.670 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 558.244 165.162 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 128.560 Td /F4 12.0 Tf [(Arbor outreach)] TJ ET BT 26.250 108.606 Td /F1 9.8 Tf [(Our outreach and education efforts integrate four main goals to ensure that Arbor plays a meaningful role in advancing science )] TJ ET BT 26.250 96.701 Td /F1 9.8 Tf [(and education in comparative evolutionary biology. As part of the development of Arbor, we will )] TJ ET BT 438.646 96.701 Td /F4 9.8 Tf [(\(1\))] TJ ET BT 450.560 96.701 Td /F1 9.8 Tf [( create novel educational )] TJ ET BT 26.250 84.796 Td /F1 9.8 Tf [(programs targeted to K-12 and the general public in collaboration with several public science centers; )] TJ ET BT 465.195 84.796 Td /F4 9.8 Tf [(\(2\))] TJ ET BT 477.109 84.796 Td /F1 9.8 Tf [( explicitly involve )] TJ ET BT 26.250 72.891 Td /F1 9.8 Tf [(diverse researchers and students, providing training both in software development and in using Arbor through hackathons and )] TJ ET BT 26.250 60.987 Td /F1 9.8 Tf [(workshops; )] TJ ET BT 78.266 60.987 Td /F4 9.8 Tf [(\(3\))] TJ ET BT 90.181 60.987 Td /F1 9.8 Tf [( engage undergraduates as well as graduate students and postdoctoral fellows in the development of Arbor; and )] TJ ET BT 26.250 49.082 Td /F4 9.8 Tf [(\(4\))] TJ ET BT 38.165 49.082 Td /F1 9.8 Tf [( leverage and augment research conducted by other NSF-supported Tree of Life and Dimensions of Biodiversity projects.)] TJ ET Q q 15.000 39.201 577.500 737.799 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(the phylogenetic relationships of species into SDMs. Using these data, the )] TJ ET BT 349.238 767.476 Td /F5 9.8 Tf [(openModeller)] TJ ET BT 408.304 767.476 Td /F1 9.8 Tf [( module will be able to project species )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(ranges onto past climatic layers using species distribution models combined with paleoclimatic data, given the phylogenetic )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(relationships of the species and the temporal scale of their ancestral distributions. The results can then be visualized using the )] TJ ET BT 26.250 731.762 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 63.095 731.762 Td /F1 9.8 Tf [( module.)] TJ ET 0.965 0.965 0.965 rg 26.250 415.876 555.000 306.005 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 721.881 m 581.250 721.881 l 581.250 721.131 l 26.250 721.131 l f 26.250 415.876 m 581.250 415.876 l 581.250 416.626 l 26.250 416.626 l f q 452.250 0 0 186.750 35.250 525.381 cm /I6 Do Q q 35.250 427.126 537.000 92.255 re W n 0.271 0.267 0.267 rg BT 35.250 509.857 Td /F4 9.8 Tf [(Fig. 1: Proposed phyloFlow workflow for the test case developed in the text. Information processing flows from )] TJ ET BT 35.250 497.952 Td /F4 9.8 Tf [(remote sources to five phyloFlow modules.)] TJ ET BT 35.250 478.582 Td /F1 9.8 Tf [(First, the dataIntegrator \(A\) combines phylogenetic, distributional, and climactic data sources. openModeller \(B\) then )] TJ ET BT 35.250 464.846 Td /F1 9.8 Tf [(creates species distribution models, and Lagrange \(C\) tests historical biogeographic hypotheses incorporating those )] TJ ET BT 35.250 451.110 Td /F1 9.8 Tf [(models. Next, phyloView allows geographic \(D\) and phylogenetic \(E\) visualization of results. Outputs are directed to the )] TJ ET BT 35.250 437.374 Td /F1 9.8 Tf [(dataOutput module \(F\), which can save results both locally and remotely.)] TJ ET Q BT 26.250 398.853 Td /F1 9.8 Tf [(We show a hypothetical workflow for this test case in Figure 1. The entire workflow has already been demonstrated \(outside of )] TJ ET BT 26.250 386.948 Td /F1 9.8 Tf [(Arbor\) in a pilot study )] TJ ET 0.267 0.267 0.267 rg BT 121.079 388.455 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 130.716 386.948 Td /F1 9.8 Tf [( using a virtual species on a spatially realistic matrix of 144 cells, and climate modeled in 130 time steps )] TJ ET BT 26.250 375.043 Td /F1 9.8 Tf [(\(back to 140,000 years before present\). We )] TJ ET BT 217.009 375.043 Td /F1 9.8 Tf [(will also be able to use the comparative capabilities of Arbor to constrain niche )] TJ ET BT 26.250 363.138 Td /F1 9.8 Tf [(models to follow patterns expected if species response to abiotic factors follows evolutionary history \(i.e., closely related )] TJ ET BT 26.250 351.234 Td /F1 9.8 Tf [(species have niches that are more similar to one another than distantly related species\). This will allow the user to directly test )] TJ ET BT 26.250 339.329 Td /F1 9.8 Tf [(for phylogenetic structure in historic and extant species distribution patterns. We will use the New World genus )] TJ ET BT 504.731 339.329 Td /F5 9.8 Tf [(Aphelocoma)] TJ ET BT 26.250 327.424 Td /F1 9.8 Tf [(\(scrub jays\), which has 9 phylogenetic species, as a biological application of this test case. The phylogeny of the clade is well )] TJ ET BT 26.250 315.519 Td /F1 9.8 Tf [(established )] TJ ET 0.267 0.267 0.267 rg BT 78.276 317.027 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 87.913 315.519 Td /F1 9.8 Tf [( and predictions of Pleistocene ranges have been made )] TJ ET 0.267 0.267 0.267 rg BT 331.254 317.027 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 340.891 315.519 Td /F1 9.8 Tf [(, but without consideration to the historical trajectories )] TJ ET BT 26.250 303.615 Td /F1 9.8 Tf [(of climatic factors and the phylogenetic history of the clade. We will use the new methods and algorithms implemented in Arbor )] TJ ET BT 26.250 291.710 Td /F1 9.8 Tf [(to model scrub jay species distributions while incorporating paleoclimatic and phylogenetic data.)] TJ ET BT 26.250 272.305 Td /F1 9.8 Tf [(To include information about species niches in biogeographic models, we will use the )] TJ ET BT 397.988 272.305 Td /F5 9.8 Tf [(Lagrange)] TJ ET BT 439.182 272.305 Td /F1 9.8 Tf [( module to test hypotheses )] TJ ET BT 26.250 260.400 Td /F1 9.8 Tf [(about the processes that govern range changes over time. Currently, the Lagrange program can fit process-based models of )] TJ ET BT 26.250 248.496 Td /F1 9.8 Tf [(changes in species ranges through time by modeling speciation, extinction, and dispersal among a set of geographic regions. )] TJ ET BT 26.250 236.591 Td /F1 9.8 Tf [(One can either assume that dispersal rates among these regions are constant or make modifications based on hypothesized )] TJ ET BT 26.250 224.686 Td /F1 9.8 Tf [(patterns of geographic connections through time. The )] TJ ET BT 259.831 224.686 Td /F5 9.8 Tf [(Lagrange)] TJ ET BT 301.024 224.686 Td /F1 9.8 Tf [( module in Arbor will allow us to modify transition rates as a )] TJ ET BT 26.250 212.781 Td /F1 9.8 Tf [(function of historical climate, directly testing whether geographic range shifts affect biogeographic processes. As a supplemental )] TJ ET BT 26.250 200.877 Td /F1 9.8 Tf [(biological application, we will use this approach to investigate the diversification of )] TJ ET BT 381.735 200.877 Td /F5 9.8 Tf [(Heliconia)] TJ ET BT 421.827 200.877 Td /F1 9.8 Tf [( plants and their hummingbird )] TJ ET BT 26.250 188.972 Td /F1 9.8 Tf [(pollinators. As these are Andean taxa that diversify during uplift activity, this test case will address the common biogeographical )] TJ ET BT 26.250 177.067 Td /F1 9.8 Tf [(hypothesis that the Andean uplift and subsequent diversification of ecological niche space led to the )] TJ ET BT 458.740 177.067 Td /F5 9.8 Tf [(in situ)] TJ ET BT 484.207 177.067 Td /F1 9.8 Tf [( diversification of )] TJ ET BT 26.250 165.162 Td /F1 9.8 Tf [(local lineages, and that current species distribution is largely driven by historical distributions and shifts in climatic factors )] TJ ET 0.267 0.267 0.267 rg BT 548.606 166.670 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 558.244 165.162 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 128.560 Td /F4 12.0 Tf [(Arbor outreach)] TJ ET BT 26.250 108.606 Td /F1 9.8 Tf [(Our outreach and education efforts integrate four main goals to ensure that Arbor plays a meaningful role in advancing science )] TJ ET BT 26.250 96.701 Td /F1 9.8 Tf [(and education in comparative evolutionary biology. As part of the development of Arbor, we will )] TJ ET BT 438.646 96.701 Td /F4 9.8 Tf [(\(1\))] TJ ET BT 450.560 96.701 Td /F1 9.8 Tf [( create novel educational )] TJ ET BT 26.250 84.796 Td /F1 9.8 Tf [(programs targeted to K-12 and the general public in collaboration with several public science centers; )] TJ ET BT 465.195 84.796 Td /F4 9.8 Tf [(\(2\))] TJ ET BT 477.109 84.796 Td /F1 9.8 Tf [( explicitly involve )] TJ ET BT 26.250 72.891 Td /F1 9.8 Tf [(diverse researchers and students, providing training both in software development and in using Arbor through hackathons and )] TJ ET BT 26.250 60.987 Td /F1 9.8 Tf [(workshops; )] TJ ET BT 78.266 60.987 Td /F4 9.8 Tf [(\(3\))] TJ ET BT 90.181 60.987 Td /F1 9.8 Tf [( engage undergraduates as well as graduate students and postdoctoral fellows in the development of Arbor; and )] TJ ET BT 26.250 49.082 Td /F4 9.8 Tf [(\(4\))] TJ ET BT 38.165 49.082 Td /F1 9.8 Tf [( leverage and augment research conducted by other NSF-supported Tree of Life and Dimensions of Biodiversity projects.)] TJ ET Q q 15.000 39.201 577.500 737.799 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(the phylogenetic relationships of species into SDMs. Using these data, the )] TJ ET BT 349.238 767.476 Td /F5 9.8 Tf [(openModeller)] TJ ET BT 408.304 767.476 Td /F1 9.8 Tf [( module will be able to project species )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(ranges onto past climatic layers using species distribution models combined with paleoclimatic data, given the phylogenetic )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(relationships of the species and the temporal scale of their ancestral distributions. The results can then be visualized using the )] TJ ET BT 26.250 731.762 Td /F5 9.8 Tf [(phyloVis)] TJ ET BT 63.095 731.762 Td /F1 9.8 Tf [( module.)] TJ ET 0.965 0.965 0.965 rg 26.250 415.876 555.000 306.005 re f 0.267 0.267 0.267 rg 0.267 0.267 0.267 RG 26.250 721.881 m 581.250 721.881 l 581.250 721.131 l 26.250 721.131 l f 26.250 415.876 m 581.250 415.876 l 581.250 416.626 l 26.250 416.626 l f q 452.250 0 0 186.750 35.250 525.381 cm /I8 Do Q q 35.250 427.126 537.000 92.255 re W n 0.271 0.267 0.267 rg BT 35.250 509.857 Td /F4 9.8 Tf [(Fig. 1: Proposed phyloFlow workflow for the test case developed in the text. Information processing flows from )] TJ ET BT 35.250 497.952 Td /F4 9.8 Tf [(remote sources to five phyloFlow modules.)] TJ ET BT 35.250 478.582 Td /F1 9.8 Tf [(First, the dataIntegrator \(A\) combines phylogenetic, distributional, and climactic data sources. openModeller \(B\) then )] TJ ET BT 35.250 464.846 Td /F1 9.8 Tf [(creates species distribution models, and Lagrange \(C\) tests historical biogeographic hypotheses incorporating those )] TJ ET BT 35.250 451.110 Td /F1 9.8 Tf [(models. Next, phyloView allows geographic \(D\) and phylogenetic \(E\) visualization of results. Outputs are directed to the )] TJ ET BT 35.250 437.374 Td /F1 9.8 Tf [(dataOutput module \(F\), which can save results both locally and remotely.)] TJ ET Q BT 26.250 398.853 Td /F1 9.8 Tf [(We show a hypothetical workflow for this test case in Figure 1. The entire workflow has already been demonstrated \(outside of )] TJ ET BT 26.250 386.948 Td /F1 9.8 Tf [(Arbor\) in a pilot study )] TJ ET 0.267 0.267 0.267 rg BT 121.079 388.455 Td /F4 8.7 Tf [(29)] TJ ET 0.271 0.267 0.267 rg BT 130.716 386.948 Td /F1 9.8 Tf [( using a virtual species on a spatially realistic matrix of 144 cells, and climate modeled in 130 time steps )] TJ ET BT 26.250 375.043 Td /F1 9.8 Tf [(\(back to 140,000 years before present\). We )] TJ ET BT 217.009 375.043 Td /F1 9.8 Tf [(will also be able to use the comparative capabilities of Arbor to constrain niche )] TJ ET BT 26.250 363.138 Td /F1 9.8 Tf [(models to follow patterns expected if species response to abiotic factors follows evolutionary history \(i.e., closely related )] TJ ET BT 26.250 351.234 Td /F1 9.8 Tf [(species have niches that are more similar to one another than distantly related species\). This will allow the user to directly test )] TJ ET BT 26.250 339.329 Td /F1 9.8 Tf [(for phylogenetic structure in historic and extant species distribution patterns. We will use the New World genus )] TJ ET BT 504.731 339.329 Td /F5 9.8 Tf [(Aphelocoma)] TJ ET BT 26.250 327.424 Td /F1 9.8 Tf [(\(scrub jays\), which has 9 phylogenetic species, as a biological application of this test case. The phylogeny of the clade is well )] TJ ET BT 26.250 315.519 Td /F1 9.8 Tf [(established )] TJ ET 0.267 0.267 0.267 rg BT 78.276 317.027 Td /F4 8.7 Tf [(30)] TJ ET 0.271 0.267 0.267 rg BT 87.913 315.519 Td /F1 9.8 Tf [( and predictions of Pleistocene ranges have been made )] TJ ET 0.267 0.267 0.267 rg BT 331.254 317.027 Td /F4 8.7 Tf [(31)] TJ ET 0.271 0.267 0.267 rg BT 340.891 315.519 Td /F1 9.8 Tf [(, but without consideration to the historical trajectories )] TJ ET BT 26.250 303.615 Td /F1 9.8 Tf [(of climatic factors and the phylogenetic history of the clade. We will use the new methods and algorithms implemented in Arbor )] TJ ET BT 26.250 291.710 Td /F1 9.8 Tf [(to model scrub jay species distributions while incorporating paleoclimatic and phylogenetic data.)] TJ ET BT 26.250 272.305 Td /F1 9.8 Tf [(To include information about species niches in biogeographic models, we will use the )] TJ ET BT 397.988 272.305 Td /F5 9.8 Tf [(Lagrange)] TJ ET BT 439.182 272.305 Td /F1 9.8 Tf [( module to test hypotheses )] TJ ET BT 26.250 260.400 Td /F1 9.8 Tf [(about the processes that govern range changes over time. Currently, the Lagrange program can fit process-based models of )] TJ ET BT 26.250 248.496 Td /F1 9.8 Tf [(changes in species ranges through time by modeling speciation, extinction, and dispersal among a set of geographic regions. )] TJ ET BT 26.250 236.591 Td /F1 9.8 Tf [(One can either assume that dispersal rates among these regions are constant or make modifications based on hypothesized )] TJ ET BT 26.250 224.686 Td /F1 9.8 Tf [(patterns of geographic connections through time. The )] TJ ET BT 259.831 224.686 Td /F5 9.8 Tf [(Lagrange)] TJ ET BT 301.024 224.686 Td /F1 9.8 Tf [( module in Arbor will allow us to modify transition rates as a )] TJ ET BT 26.250 212.781 Td /F1 9.8 Tf [(function of historical climate, directly testing whether geographic range shifts affect biogeographic processes. As a supplemental )] TJ ET BT 26.250 200.877 Td /F1 9.8 Tf [(biological application, we will use this approach to investigate the diversification of )] TJ ET BT 381.735 200.877 Td /F5 9.8 Tf [(Heliconia)] TJ ET BT 421.827 200.877 Td /F1 9.8 Tf [( plants and their hummingbird )] TJ ET BT 26.250 188.972 Td /F1 9.8 Tf [(pollinators. As these are Andean taxa that diversify during uplift activity, this test case will address the common biogeographical )] TJ ET BT 26.250 177.067 Td /F1 9.8 Tf [(hypothesis that the Andean uplift and subsequent diversification of ecological niche space led to the )] TJ ET BT 458.740 177.067 Td /F5 9.8 Tf [(in situ)] TJ ET BT 484.207 177.067 Td /F1 9.8 Tf [( diversification of )] TJ ET BT 26.250 165.162 Td /F1 9.8 Tf [(local lineages, and that current species distribution is largely driven by historical distributions and shifts in climatic factors )] TJ ET 0.267 0.267 0.267 rg BT 548.606 166.670 Td /F4 8.7 Tf [(32)] TJ ET 0.271 0.267 0.267 rg BT 558.244 165.162 Td /F1 9.8 Tf [(.)] TJ ET BT 26.250 128.560 Td /F4 12.0 Tf [(Arbor outreach)] TJ ET BT 26.250 108.606 Td /F1 9.8 Tf [(Our outreach and education efforts integrate four main goals to ensure that Arbor plays a meaningful role in advancing science )] TJ ET BT 26.250 96.701 Td /F1 9.8 Tf [(and education in comparative evolutionary biology. As part of the development of Arbor, we will )] TJ ET BT 438.646 96.701 Td /F4 9.8 Tf [(\(1\))] TJ ET BT 450.560 96.701 Td /F1 9.8 Tf [( create novel educational )] TJ ET BT 26.250 84.796 Td /F1 9.8 Tf [(programs targeted to K-12 and the general public in collaboration with several public science centers; )] TJ ET BT 465.195 84.796 Td /F4 9.8 Tf [(\(2\))] TJ ET BT 477.109 84.796 Td /F1 9.8 Tf [( explicitly involve )] TJ ET BT 26.250 72.891 Td /F1 9.8 Tf [(diverse researchers and students, providing training both in software development and in using Arbor through hackathons and )] TJ ET BT 26.250 60.987 Td /F1 9.8 Tf [(workshops; )] TJ ET BT 78.266 60.987 Td /F4 9.8 Tf [(\(3\))] TJ ET BT 90.181 60.987 Td /F1 9.8 Tf [( engage undergraduates as well as graduate students and postdoctoral fellows in the development of Arbor; and )] TJ ET BT 26.250 49.082 Td /F4 9.8 Tf [(\(4\))] TJ ET BT 38.165 49.082 Td /F1 9.8 Tf [( leverage and augment research conducted by other NSF-supported Tree of Life and Dimensions of Biodiversity projects.)] TJ ET Q q 452.250 0 0 186.750 35.250 525.381 cm /I10 Do 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 285 0 obj << /Type /Annot /Subtype /Link /A 286 0 R /Border [0 0 0] /H /I /Rect [ 35.2500 525.3810 487.5000 712.1310 ] >> endobj 286 0 obj << /Type /Action /S /URI /URI (http://currents.plos.org/treeoflife/files/2012/12/figure4_final1.png) >> endobj 287 0 obj << /Type /XObject /Subtype /Image /Width 603 /Height 249 /Filter /FlateDecode /DecodeParms << /Predictor 15 /Colors 1 /Columns 603 /BitsPerComponent 8>> /ColorSpace /DeviceGray /BitsPerComponent 8 /Length 651>> stream xA 0 =" ʝ<2;E[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TE[TEe3> endstream endobj 288 0 obj << /Type /XObject /Subtype /Image /Width 603 /Height 249 /SMask 287 0 R /Filter /FlateDecode /DecodeParms << /Predictor 15 /Colors 3 /Columns 603 /BitsPerComponent 8>> /ColorSpace /DeviceRGB /BitsPerComponent 8 /Length 93586>> stream x}w^E۾ͶlMF@04XC)b>E  "Eji$gSvl6_w̽߷ arg9SOs !hڷ6лG $)GasEHY,G}$^Rk? \a@k %V( [(6PHba :h"NTlwKDH;tI Vi҆"$n@9YTJ q z{DFr8I3FJiE4]*:LX FDӯT`iG̖p٤OJbb/8|aI|]{YT–:LBo(-WXa9I0!s]Dh8P";i*AaeHj $8aqN,X R 3Hv, JƕKaY EҾ$%˕=B)kACcMbheˋ4qD5JHcY9ܭ± )9q DRErd4 L[(ց@; ť-J"J +֧'@}!]cPYWjNJ6uXA $z>-f"=ǰ%v>vlڔC #4{$;=-?zlx.\6* |"iK>\G+pۈhF,?Et U|5*bA^V;̎čN=pK?!%fY1" .-\iy amVr5zE!p„aVgƶcJ$a͛ i))[hIL.A*z(`^Vz9IaF I!}p@%FHG-FOR“$ g-),>1!ٲRjt@(f Bh 3Ф(q,lVۻ  Gz#T(*TŒb].TYTN8u=(̤kzq5,!3~84j;FIg^G62;\Ҽot2ڱ <INuDiDQf>n//DB ђÝSKB*b^_!2) E"a qceƛQ<j-3d(%VOp\0R[acbMqpkR`f#8ҌܣwX.f,\wJ)xZHqBj!jfZ;ӏo7eZpM RN&3JyaD q$ez}/ʖ}9!>HW04elEɘ:3%lL8 G p)yAa)š1ePaKJ@ /(Iao /p= C҈ibE#Mvp ,>bE ϼqu۬ƔA'R5{O}}~C?Bґq'Min|Hlzs2:xxd3IㅫYLtVܼmJwXfd5 /f$Ý̠QBB iaF!MӈfLGP@X e;AaK@. 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This interface will be a )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(streamlined version of Arbor with a graphically appealing interface and more limited data analysis options to facilitate student )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(use. Rich but appropriate data sets will be selected from the parent project so that students can explore a variety of evolutionary )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(scenarios \(e.g., co-diversification, ecological niches through time\) and investigate multiple questions. Lesson plans will provide )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(background information and explicit suggestions for instructors regarding how these materials can best be incorporated into )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(classrooms to teach evolution, systematics, comparative biology, and the process of science.)] TJ ET BT 26.250 659.445 Td /F4 12.0 Tf [(The Arbor team)] TJ ET BT 26.250 639.491 Td /F1 9.8 Tf [(The arbor team includes both biologists and computer scientists. Biologists include Bob Thacker \(University of Alabama at )] TJ ET BT 26.250 627.586 Td /F1 9.8 Tf [(Birmingham\), Chelsea Specht \(University of California, Berkeley\), Jorge Soberon \(University of Kansas\), and Luke Harmon )] TJ ET BT 26.250 615.681 Td /F1 9.8 Tf [(\(University of Idaho\). We span a range of biological expertise and interests, including symbiosis, genetics, developmental )] TJ ET BT 26.250 603.777 Td /F1 9.8 Tf [(biology, species distributions, and comparative methods. Computer scientists include Charlie Hughes \(University of Central )] TJ ET BT 26.250 591.872 Td /F1 9.8 Tf [(Florida\) and Curt Lisle \(KnowledgeVis\). We are also working closely with a team of programmers from KitWare, led by Wes )] TJ ET BT 26.250 579.967 Td /F1 9.8 Tf [(Turner and Jeff Baumes. The computer scientists have extensive expertise with workflow software, visualization, user )] TJ ET BT 26.250 568.062 Td /F1 9.8 Tf [(interaction and statistical analyses of large datasets.)] TJ ET BT 26.250 531.460 Td /F4 12.0 Tf [(Community involvement: how you can get involved now with Arbor)] TJ ET BT 26.250 511.506 Td /F1 9.8 Tf [(Although the Arbor team is small now, we will grow more inclusive through a series of planned training courses and hackathons. )] TJ ET BT 26.250 499.601 Td /F1 9.8 Tf [(Training courses will be geared towards teaching end-users how to obtain and analyze data using Arbor workflows, while )] TJ ET BT 26.250 487.696 Td /F1 9.8 Tf [(hackathons will help programmers get up to speed and create new modules for Arbor. The first of these meetings will take place )] TJ ET BT 26.250 475.791 Td /F1 9.8 Tf [(in late 2013. We will also be offering sabbaticals to postdoctoral scholars who are actively generating phylogenetic and )] TJ ET BT 26.250 463.887 Td /F1 9.8 Tf [(comparative data that could be analyzed within Arbor. These 3-6 month appointments allow postdocs to work closely with the )] TJ ET BT 26.250 451.982 Td /F1 9.8 Tf [(Arbor team to integrate their data into Arbor and design novel Arbor workflows that are suited to their particular questions, )] TJ ET BT 26.250 440.077 Td /F1 9.8 Tf [(thereby immediately developing the capacity of Arbor to serve the scientific community. We encourage community feedback )] TJ ET BT 26.250 428.172 Td /F1 9.8 Tf [(and involvement at every step of the process; the goal of the Arbor team is to produce efficient and open-source software that )] TJ ET BT 26.250 416.268 Td /F1 9.8 Tf [(will enable scientists, students, and educators to understand the Tree of Life in new ways. Everyone is free to provide )] TJ ET BT 26.250 404.363 Td /F1 9.8 Tf [(comments or suggestions either here on the PLOS Currents page or via our website \()] TJ ET 0.267 0.267 0.267 rg BT 394.741 404.363 Td /F1 9.8 Tf [(http://www.arborworkflows.com/)] TJ ET 0.271 0.267 0.267 rg BT 532.353 404.363 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 367.760 Td /F4 12.0 Tf [(Conclusion)] TJ ET BT 26.250 347.806 Td /F1 9.8 Tf [(We are rapidly approaching a rough draft for the Tree of Life. As phylogenetic trees become more reliable, larger, and more )] TJ ET BT 26.250 335.901 Td /F1 9.8 Tf [(complete, the need for integrative approaches to analyze and understand those trees and their evolutionary significance )] TJ ET BT 26.250 323.997 Td /F1 9.8 Tf [(becomes critical. Arbor will allow users to test key evolutionary hypotheses with methods that are new and flexible using )] TJ ET BT 26.250 312.092 Td /F1 9.8 Tf [(massive amounts of data. Arbors most unique feature is allowing users to create sharable and citable workflows that combine )] TJ ET BT 26.250 300.187 Td /F1 9.8 Tf [(methods in new and unanticipated ways. We are building the Tree of Life, but we do not yet know what it can tell us about the )] TJ ET BT 26.250 288.282 Td /F1 9.8 Tf [(process of evolution. Arbor will allow us to harvest massive amounts of new information from the Tree of Life and facilitate new )] TJ ET BT 26.250 276.378 Td /F1 9.8 Tf [(discoveries about organismal evolution.)] TJ ET BT 26.250 239.775 Td /F4 12.0 Tf [(References)] TJ ET BT 26.250 212.321 Td /F1 9.8 Tf [(1.)] TJ ET BT 38.132 212.321 Td /F1 9.8 Tf [(Bininda-Emonds OR, Cardillo M, Jones KE, MacPhee RD, Beck RM, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A. )] TJ ET BT 26.250 200.416 Td /F1 9.8 Tf [(The delayed rise of present-day mammals. Nature. 2007 Mar 29;446\(7135\):507-12. PubMed PMID:17392779.)] TJ ET BT 26.250 181.011 Td /F1 9.8 Tf [(2.)] TJ ET BT 38.132 181.011 Td /F1 9.8 Tf [(Smith SA, Beaulieu JM, Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and )] TJ ET BT 26.250 169.107 Td /F1 9.8 Tf [(supermatrix approaches. BMC Evol Biol. 2009 Feb 11;9:37. PubMed PMID:19210768.)] TJ ET BT 26.250 149.702 Td /F1 9.8 Tf [(3.)] TJ ET BT 38.132 149.702 Td /F1 9.8 Tf [(Kattge J, Daz S, Lavorel S, Prentice IC, Leadley P, Bnisch G, Garnier E, and 128 others. 2011. TRY - a global database of )] TJ ET BT 26.250 137.797 Td /F1 9.8 Tf [(plant traits. Global Change Biology 17: 2905-2935.)] TJ ET BT 26.250 118.392 Td /F1 9.8 Tf [(4.)] TJ ET BT 38.132 118.392 Td /F1 9.8 Tf [(Jones KE, Bielby J, Cardillo M, Fritz SA, O'Dell J, Orme CDL, Safi K, Sechrest W, Boakes EH, Carbone C, Connolly C, Cutts )] TJ ET BT 26.250 106.488 Td /F1 9.8 Tf [(MJ, Foster JK, Grenyer R, Habib M, Plaster CA, Price SA, Rigby EA, Rist J, Teacher A, Bininda-Emonds ORP, Gittleman JL, )] TJ ET BT 26.250 94.583 Td /F1 9.8 Tf [(Mace GM, Purvis A. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently )] TJ ET BT 26.250 82.678 Td /F1 9.8 Tf [(extinct mammals. Ecology 90: 2648.)] TJ ET BT 26.250 63.273 Td /F1 9.8 Tf [(5.)] TJ ET BT 38.132 63.273 Td /F1 9.8 Tf [(Guralnick R, Hill A. Biodiversity informatics: automated approaches for documenting global biodiversity patterns and )] TJ ET BT 26.250 51.369 Td /F1 9.8 Tf [(processes. Bioinformatics. 2009 Feb 15;25\(4\):421-8. PubMed PMID:19129210.)] TJ ET Q q 15.000 41.488 577.500 735.512 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(We plan to develop a software interface, selected data sets, and lesson plans that will allow middle school, high school, and )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(undergraduate students to engage with authentic scientific data as they develop tree-thinking skills. This interface will be a )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(streamlined version of Arbor with a graphically appealing interface and more limited data analysis options to facilitate student )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(use. Rich but appropriate data sets will be selected from the parent project so that students can explore a variety of evolutionary )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(scenarios \(e.g., co-diversification, ecological niches through time\) and investigate multiple questions. Lesson plans will provide )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(background information and explicit suggestions for instructors regarding how these materials can best be incorporated into )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(classrooms to teach evolution, systematics, comparative biology, and the process of science.)] TJ ET BT 26.250 659.445 Td /F4 12.0 Tf [(The Arbor team)] TJ ET BT 26.250 639.491 Td /F1 9.8 Tf [(The arbor team includes both biologists and computer scientists. Biologists include Bob Thacker \(University of Alabama at )] TJ ET BT 26.250 627.586 Td /F1 9.8 Tf [(Birmingham\), Chelsea Specht \(University of California, Berkeley\), Jorge Soberon \(University of Kansas\), and Luke Harmon )] TJ ET BT 26.250 615.681 Td /F1 9.8 Tf [(\(University of Idaho\). We span a range of biological expertise and interests, including symbiosis, genetics, developmental )] TJ ET BT 26.250 603.777 Td /F1 9.8 Tf [(biology, species distributions, and comparative methods. Computer scientists include Charlie Hughes \(University of Central )] TJ ET BT 26.250 591.872 Td /F1 9.8 Tf [(Florida\) and Curt Lisle \(KnowledgeVis\). We are also working closely with a team of programmers from KitWare, led by Wes )] TJ ET BT 26.250 579.967 Td /F1 9.8 Tf [(Turner and Jeff Baumes. The computer scientists have extensive expertise with workflow software, visualization, user )] TJ ET BT 26.250 568.062 Td /F1 9.8 Tf [(interaction and statistical analyses of large datasets.)] TJ ET BT 26.250 531.460 Td /F4 12.0 Tf [(Community involvement: how you can get involved now with Arbor)] TJ ET BT 26.250 511.506 Td /F1 9.8 Tf [(Although the Arbor team is small now, we will grow more inclusive through a series of planned training courses and hackathons. )] TJ ET BT 26.250 499.601 Td /F1 9.8 Tf [(Training courses will be geared towards teaching end-users how to obtain and analyze data using Arbor workflows, while )] TJ ET BT 26.250 487.696 Td /F1 9.8 Tf [(hackathons will help programmers get up to speed and create new modules for Arbor. The first of these meetings will take place )] TJ ET BT 26.250 475.791 Td /F1 9.8 Tf [(in late 2013. We will also be offering sabbaticals to postdoctoral scholars who are actively generating phylogenetic and )] TJ ET BT 26.250 463.887 Td /F1 9.8 Tf [(comparative data that could be analyzed within Arbor. These 3-6 month appointments allow postdocs to work closely with the )] TJ ET BT 26.250 451.982 Td /F1 9.8 Tf [(Arbor team to integrate their data into Arbor and design novel Arbor workflows that are suited to their particular questions, )] TJ ET BT 26.250 440.077 Td /F1 9.8 Tf [(thereby immediately developing the capacity of Arbor to serve the scientific community. We encourage community feedback )] TJ ET BT 26.250 428.172 Td /F1 9.8 Tf [(and involvement at every step of the process; the goal of the Arbor team is to produce efficient and open-source software that )] TJ ET BT 26.250 416.268 Td /F1 9.8 Tf [(will enable scientists, students, and educators to understand the Tree of Life in new ways. Everyone is free to provide )] TJ ET BT 26.250 404.363 Td /F1 9.8 Tf [(comments or suggestions either here on the PLOS Currents page or via our website \()] TJ ET 0.267 0.267 0.267 rg BT 394.741 404.363 Td /F1 9.8 Tf [(http://www.arborworkflows.com/)] TJ ET 0.271 0.267 0.267 rg BT 532.353 404.363 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 367.760 Td /F4 12.0 Tf [(Conclusion)] TJ ET BT 26.250 347.806 Td /F1 9.8 Tf [(We are rapidly approaching a rough draft for the Tree of Life. As phylogenetic trees become more reliable, larger, and more )] TJ ET BT 26.250 335.901 Td /F1 9.8 Tf [(complete, the need for integrative approaches to analyze and understand those trees and their evolutionary significance )] TJ ET BT 26.250 323.997 Td /F1 9.8 Tf [(becomes critical. Arbor will allow users to test key evolutionary hypotheses with methods that are new and flexible using )] TJ ET BT 26.250 312.092 Td /F1 9.8 Tf [(massive amounts of data. Arbors most unique feature is allowing users to create sharable and citable workflows that combine )] TJ ET BT 26.250 300.187 Td /F1 9.8 Tf [(methods in new and unanticipated ways. We are building the Tree of Life, but we do not yet know what it can tell us about the )] TJ ET BT 26.250 288.282 Td /F1 9.8 Tf [(process of evolution. Arbor will allow us to harvest massive amounts of new information from the Tree of Life and facilitate new )] TJ ET BT 26.250 276.378 Td /F1 9.8 Tf [(discoveries about organismal evolution.)] TJ ET BT 26.250 239.775 Td /F4 12.0 Tf [(References)] TJ ET BT 26.250 212.321 Td /F1 9.8 Tf [(1.)] TJ ET BT 38.132 212.321 Td /F1 9.8 Tf [(Bininda-Emonds OR, Cardillo M, Jones KE, MacPhee RD, Beck RM, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A. )] TJ ET BT 26.250 200.416 Td /F1 9.8 Tf [(The delayed rise of present-day mammals. Nature. 2007 Mar 29;446\(7135\):507-12. PubMed PMID:17392779.)] TJ ET BT 26.250 181.011 Td /F1 9.8 Tf [(2.)] TJ ET BT 38.132 181.011 Td /F1 9.8 Tf [(Smith SA, Beaulieu JM, Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and )] TJ ET BT 26.250 169.107 Td /F1 9.8 Tf [(supermatrix approaches. BMC Evol Biol. 2009 Feb 11;9:37. PubMed PMID:19210768.)] TJ ET BT 26.250 149.702 Td /F1 9.8 Tf [(3.)] TJ ET BT 38.132 149.702 Td /F1 9.8 Tf [(Kattge J, Daz S, Lavorel S, Prentice IC, Leadley P, Bnisch G, Garnier E, and 128 others. 2011. TRY - a global database of )] TJ ET BT 26.250 137.797 Td /F1 9.8 Tf [(plant traits. Global Change Biology 17: 2905-2935.)] TJ ET BT 26.250 118.392 Td /F1 9.8 Tf [(4.)] TJ ET BT 38.132 118.392 Td /F1 9.8 Tf [(Jones KE, Bielby J, Cardillo M, Fritz SA, O'Dell J, Orme CDL, Safi K, Sechrest W, Boakes EH, Carbone C, Connolly C, Cutts )] TJ ET BT 26.250 106.488 Td /F1 9.8 Tf [(MJ, Foster JK, Grenyer R, Habib M, Plaster CA, Price SA, Rigby EA, Rist J, Teacher A, Bininda-Emonds ORP, Gittleman JL, )] TJ ET BT 26.250 94.583 Td /F1 9.8 Tf [(Mace GM, Purvis A. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently )] TJ ET BT 26.250 82.678 Td /F1 9.8 Tf [(extinct mammals. Ecology 90: 2648.)] TJ ET BT 26.250 63.273 Td /F1 9.8 Tf [(5.)] TJ ET BT 38.132 63.273 Td /F1 9.8 Tf [(Guralnick R, Hill A. Biodiversity informatics: automated approaches for documenting global biodiversity patterns and )] TJ ET BT 26.250 51.369 Td /F1 9.8 Tf [(processes. Bioinformatics. 2009 Feb 15;25\(4\):421-8. PubMed PMID:19129210.)] TJ ET Q q 15.000 41.488 577.500 735.512 re W n 0.271 0.267 0.267 rg BT 26.250 767.476 Td /F1 9.8 Tf [(We plan to develop a software interface, selected data sets, and lesson plans that will allow middle school, high school, and )] TJ ET BT 26.250 755.571 Td /F1 9.8 Tf [(undergraduate students to engage with authentic scientific data as they develop tree-thinking skills. This interface will be a )] TJ ET BT 26.250 743.667 Td /F1 9.8 Tf [(streamlined version of Arbor with a graphically appealing interface and more limited data analysis options to facilitate student )] TJ ET BT 26.250 731.762 Td /F1 9.8 Tf [(use. Rich but appropriate data sets will be selected from the parent project so that students can explore a variety of evolutionary )] TJ ET BT 26.250 719.857 Td /F1 9.8 Tf [(scenarios \(e.g., co-diversification, ecological niches through time\) and investigate multiple questions. Lesson plans will provide )] TJ ET BT 26.250 707.952 Td /F1 9.8 Tf [(background information and explicit suggestions for instructors regarding how these materials can best be incorporated into )] TJ ET BT 26.250 696.048 Td /F1 9.8 Tf [(classrooms to teach evolution, systematics, comparative biology, and the process of science.)] TJ ET BT 26.250 659.445 Td /F4 12.0 Tf [(The Arbor team)] TJ ET BT 26.250 639.491 Td /F1 9.8 Tf [(The arbor team includes both biologists and computer scientists. Biologists include Bob Thacker \(University of Alabama at )] TJ ET BT 26.250 627.586 Td /F1 9.8 Tf [(Birmingham\), Chelsea Specht \(University of California, Berkeley\), Jorge Soberon \(University of Kansas\), and Luke Harmon )] TJ ET BT 26.250 615.681 Td /F1 9.8 Tf [(\(University of Idaho\). We span a range of biological expertise and interests, including symbiosis, genetics, developmental )] TJ ET BT 26.250 603.777 Td /F1 9.8 Tf [(biology, species distributions, and comparative methods. Computer scientists include Charlie Hughes \(University of Central )] TJ ET BT 26.250 591.872 Td /F1 9.8 Tf [(Florida\) and Curt Lisle \(KnowledgeVis\). We are also working closely with a team of programmers from KitWare, led by Wes )] TJ ET BT 26.250 579.967 Td /F1 9.8 Tf [(Turner and Jeff Baumes. The computer scientists have extensive expertise with workflow software, visualization, user )] TJ ET BT 26.250 568.062 Td /F1 9.8 Tf [(interaction and statistical analyses of large datasets.)] TJ ET BT 26.250 531.460 Td /F4 12.0 Tf [(Community involvement: how you can get involved now with Arbor)] TJ ET BT 26.250 511.506 Td /F1 9.8 Tf [(Although the Arbor team is small now, we will grow more inclusive through a series of planned training courses and hackathons. )] TJ ET BT 26.250 499.601 Td /F1 9.8 Tf [(Training courses will be geared towards teaching end-users how to obtain and analyze data using Arbor workflows, while )] TJ ET BT 26.250 487.696 Td /F1 9.8 Tf [(hackathons will help programmers get up to speed and create new modules for Arbor. The first of these meetings will take place )] TJ ET BT 26.250 475.791 Td /F1 9.8 Tf [(in late 2013. We will also be offering sabbaticals to postdoctoral scholars who are actively generating phylogenetic and )] TJ ET BT 26.250 463.887 Td /F1 9.8 Tf [(comparative data that could be analyzed within Arbor. These 3-6 month appointments allow postdocs to work closely with the )] TJ ET BT 26.250 451.982 Td /F1 9.8 Tf [(Arbor team to integrate their data into Arbor and design novel Arbor workflows that are suited to their particular questions, )] TJ ET BT 26.250 440.077 Td /F1 9.8 Tf [(thereby immediately developing the capacity of Arbor to serve the scientific community. We encourage community feedback )] TJ ET BT 26.250 428.172 Td /F1 9.8 Tf [(and involvement at every step of the process; the goal of the Arbor team is to produce efficient and open-source software that )] TJ ET BT 26.250 416.268 Td /F1 9.8 Tf [(will enable scientists, students, and educators to understand the Tree of Life in new ways. Everyone is free to provide )] TJ ET BT 26.250 404.363 Td /F1 9.8 Tf [(comments or suggestions either here on the PLOS Currents page or via our website \()] TJ ET 0.267 0.267 0.267 rg BT 394.741 404.363 Td /F1 9.8 Tf [(http://www.arborworkflows.com/)] TJ ET 0.271 0.267 0.267 rg BT 532.353 404.363 Td /F1 9.8 Tf [(\).)] TJ ET BT 26.250 367.760 Td /F4 12.0 Tf [(Conclusion)] TJ ET BT 26.250 347.806 Td /F1 9.8 Tf [(We are rapidly approaching a rough draft for the Tree of Life. As phylogenetic trees become more reliable, larger, and more )] TJ ET BT 26.250 335.901 Td /F1 9.8 Tf [(complete, the need for integrative approaches to analyze and understand those trees and their evolutionary significance )] TJ ET BT 26.250 323.997 Td /F1 9.8 Tf [(becomes critical. Arbor will allow users to test key evolutionary hypotheses with methods that are new and flexible using )] TJ ET BT 26.250 312.092 Td /F1 9.8 Tf [(massive amounts of data. Arbors most unique feature is allowing users to create sharable and citable workflows that combine )] TJ ET BT 26.250 300.187 Td /F1 9.8 Tf [(methods in new and unanticipated ways. We are building the Tree of Life, but we do not yet know what it can tell us about the )] TJ ET BT 26.250 288.282 Td /F1 9.8 Tf [(process of evolution. Arbor will allow us to harvest massive amounts of new information from the Tree of Life and facilitate new )] TJ ET BT 26.250 276.378 Td /F1 9.8 Tf [(discoveries about organismal evolution.)] TJ ET BT 26.250 239.775 Td /F4 12.0 Tf [(References)] TJ ET BT 26.250 212.321 Td /F1 9.8 Tf [(1.)] TJ ET BT 38.132 212.321 Td /F1 9.8 Tf [(Bininda-Emonds OR, Cardillo M, Jones KE, MacPhee RD, Beck RM, Grenyer R, Price SA, Vos RA, Gittleman JL, Purvis A. )] TJ ET BT 26.250 200.416 Td /F1 9.8 Tf [(The delayed rise of present-day mammals. Nature. 2007 Mar 29;446\(7135\):507-12. PubMed PMID:17392779.)] TJ ET BT 26.250 181.011 Td /F1 9.8 Tf [(2.)] TJ ET BT 38.132 181.011 Td /F1 9.8 Tf [(Smith SA, Beaulieu JM, Donoghue MJ. Mega-phylogeny approach for comparative biology: an alternative to supertree and )] TJ ET BT 26.250 169.107 Td /F1 9.8 Tf [(supermatrix approaches. BMC Evol Biol. 2009 Feb 11;9:37. PubMed PMID:19210768.)] TJ ET BT 26.250 149.702 Td /F1 9.8 Tf [(3.)] TJ ET BT 38.132 149.702 Td /F1 9.8 Tf [(Kattge J, Daz S, Lavorel S, Prentice IC, Leadley P, Bnisch G, Garnier E, and 128 others. 2011. TRY - a global database of )] TJ ET BT 26.250 137.797 Td /F1 9.8 Tf [(plant traits. Global Change Biology 17: 2905-2935.)] TJ ET BT 26.250 118.392 Td /F1 9.8 Tf [(4.)] TJ ET BT 38.132 118.392 Td /F1 9.8 Tf [(Jones KE, Bielby J, Cardillo M, Fritz SA, O'Dell J, Orme CDL, Safi K, Sechrest W, Boakes EH, Carbone C, Connolly C, Cutts )] TJ ET BT 26.250 106.488 Td /F1 9.8 Tf [(MJ, Foster JK, Grenyer R, Habib M, Plaster CA, Price SA, Rigby EA, Rist J, Teacher A, Bininda-Emonds ORP, Gittleman JL, )] TJ ET BT 26.250 94.583 Td /F1 9.8 Tf [(Mace GM, Purvis A. 2009. PanTHERIA: a species-level database of life history, ecology, and geography of extant and recently )] TJ ET BT 26.250 82.678 Td /F1 9.8 Tf [(extinct mammals. Ecology 90: 2648.)] TJ ET BT 26.250 63.273 Td /F1 9.8 Tf [(5.)] TJ ET BT 38.132 63.273 Td /F1 9.8 Tf [(Guralnick R, Hill A. Biodiversity informatics: automated approaches for documenting global biodiversity patterns and )] TJ ET BT 26.250 51.369 Td /F1 9.8 Tf [(processes. Bioinformatics. 2009 Feb 15;25\(4\):421-8. PubMed PMID:19129210.)] TJ ET 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 325 0 obj << /Type /Annot /Subtype /Link /A 326 0 R /Border [0 0 0] /H /I /Rect [ 394.7415 403.4611 532.3530 413.3817 ] >> endobj 326 0 obj << /Type /Action /S /URI /URI (http://www.arborworkflows.com/) >> endobj 327 0 obj << /Type /Annot /Subtype /Link /A 328 0 R /Border [0 0 0] /H /I /Rect [ 394.7415 403.4611 532.3530 413.3817 ] >> endobj 328 0 obj << /Type /Action /S /URI /URI (http://www.arborworkflows.com/) >> endobj 329 0 obj << /Type /Annot /Subtype /Link /A 330 0 R /Border [0 0 0] /H /I /Rect [ 394.7415 403.4611 532.3530 413.3817 ] >> endobj 330 0 obj << /Type /Action /S /URI /URI (http://www.arborworkflows.com/) >> endobj 331 0 obj << /Type /Page /Parent 3 0 R /Contents 332 0 R >> endobj 332 0 obj << /Length 22042 >> stream 0.271 0.267 0.267 rg q 15.000 52.477 577.500 724.523 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(6.)] TJ ET BT 38.132 759.976 Td /F1 9.8 Tf [(Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011 )] TJ ET BT 26.250 736.167 Td /F1 9.8 Tf [(Jan;39\(Database issue\):D698-704. PubMed PMID:21071413.)] TJ ET BT 26.250 716.762 Td /F1 9.8 Tf [(7.)] TJ ET BT 38.132 716.762 Td /F1 9.8 Tf [(Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, )] TJ ET BT 26.250 704.857 Td /F1 9.8 Tf [(Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, )] TJ ET BT 26.250 692.952 Td /F1 9.8 Tf [(Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature. 2012 May 9;486\(7402\):222-7. PubMed )] TJ ET BT 26.250 681.048 Td /F1 9.8 Tf [(PMID:22699611.)] TJ ET BT 26.250 661.643 Td /F1 9.8 Tf [(8.)] TJ ET BT 38.132 661.643 Td /F1 9.8 Tf [(Moles AT, Ackerly DD, Webb CO, Tweddle JC, Dickie JB, Westoby M. A brief history of seed size. Science. 2005 Jan )] TJ ET BT 26.250 649.738 Td /F1 9.8 Tf [(28;307\(5709\):576-80. PubMed PMID:15681384.)] TJ ET BT 26.250 630.333 Td /F1 9.8 Tf [(9.)] TJ ET BT 38.132 630.333 Td /F1 9.8 Tf [(Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Harmon LJ. Nine exceptional radiations )] TJ ET BT 26.250 618.429 Td /F1 9.8 Tf [(plus high turnover explain species diversity in jawed vertebrates. Proc Natl Acad Sci U S A. 2009 Aug 11;106\(32\):13410-4. )] TJ ET BT 26.250 606.524 Td /F1 9.8 Tf [(PubMed PMID:19633192.)] TJ ET BT 26.250 587.119 Td /F1 9.8 Tf [(10.)] TJ ET BT 43.553 587.119 Td /F1 9.8 Tf [(Meredith RW, Jane?ka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simo TL, Stadler T, )] TJ ET BT 26.250 575.214 Td /F1 9.8 Tf [(Rabosky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, Williams TL, Robinson TJ, Burk-Herrick A, Westerman M, Ayoub )] TJ ET BT 26.250 563.310 Td /F1 9.8 Tf [(NA, Springer MS, Murphy WJ. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. )] TJ ET BT 26.250 551.405 Td /F1 9.8 Tf [(Science. 2011 Oct 28;334\(6055\):521-4. PubMed PMID:21940861.)] TJ ET BT 26.250 532.000 Td /F1 9.8 Tf [(11.)] TJ ET BT 43.553 532.000 Td /F1 9.8 Tf [(Rosindell J, Harmon LJ. OneZoom: A Fractal Explorer for the Tree of Life. PLoS Biol. 2012 Oct;10\(10\):e1001406. PubMed )] TJ ET BT 26.250 520.095 Td /F1 9.8 Tf [(PMID:23091419.)] TJ ET BT 26.250 500.691 Td /F1 9.8 Tf [(12.)] TJ ET BT 43.553 500.691 Td /F1 9.8 Tf [(Reichman OJ, Jones MB, Schildhauer MP. Challenges and opportunities of open data in ecology. Science. 2011 Feb )] TJ ET BT 26.250 488.786 Td /F1 9.8 Tf [(11;331\(6018\):703-5. PubMed PMID:21311007.)] TJ ET BT 26.250 469.381 Td /F1 9.8 Tf [(13.)] TJ ET BT 43.553 469.381 Td /F1 9.8 Tf [(Ahrens J, Geveci B, Law C. 2005. ParaView: An End User Tool for Large Data Visualization. in The Visualization )] TJ ET BT 26.250 457.476 Td /F1 9.8 Tf [(Handbook, C. D. Hansen and C. R. Johnson, Eds.. Elsevier: Burlington, MA.)] TJ ET BT 26.250 438.072 Td /F1 9.8 Tf [(14.)] TJ ET BT 43.553 438.072 Td /F1 9.8 Tf [(Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and )] TJ ET BT 26.250 426.167 Td /F1 9.8 Tf [(transparent computational research in the life sciences. Genome Biol. 2010;11\(8\):R86. PubMed PMID:20738864.)] TJ ET BT 26.250 406.762 Td /F1 9.8 Tf [(15.)] TJ ET BT 43.553 406.762 Td /F1 9.8 Tf [(Freckleton RP. Fast likelihood calculations for comparative analyses. Methods in Ecology and Evolution2012; 3: 940-947.)] TJ ET BT 26.250 387.357 Td /F1 9.8 Tf [(16.)] TJ ET BT 43.553 387.357 Td /F1 9.8 Tf [(Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. 2011; Version 2.75 )] TJ ET BT 26.250 375.453 Td /F1 9.8 Tf [(http://mesquiteproject.org.)] TJ ET BT 26.250 356.048 Td /F1 9.8 Tf [(17.)] TJ ET BT 43.553 356.048 Td /F1 9.8 Tf [(Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 2004 Jan )] TJ ET BT 26.250 344.143 Td /F1 9.8 Tf [(22;20\(2\):289-90. PubMed PMID:14734327.)] TJ ET BT 26.250 324.738 Td /F1 9.8 Tf [(18.)] TJ ET BT 43.553 324.738 Td /F1 9.8 Tf [(Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. GEIGER: investigating evolutionary radiations. Bioinformatics. )] TJ ET BT 26.250 312.834 Td /F1 9.8 Tf [(2008 Jan 1;24\(1\):129-31. PubMed PMID:18006550.)] TJ ET BT 26.250 293.429 Td /F1 9.8 Tf [(19.)] TJ ET BT 43.553 293.429 Td /F1 9.8 Tf [(Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. Picante: R tools for )] TJ ET BT 26.250 281.524 Td /F1 9.8 Tf [(integrating phylogenies and ecology. Bioinformatics. 2010 Jun 1;26\(11\):1463-4. PubMed PMID:20395285.)] TJ ET BT 26.250 262.119 Td /F1 9.8 Tf [(20.)] TJ ET BT 43.553 262.119 Td /F1 9.8 Tf [(Fitzjohn RJ. Diversitree: comparative phylogenetic analyses of diversification in R. In press, Methods in Ecology and )] TJ ET BT 26.250 250.215 Td /F1 9.8 Tf [(Evolution.)] TJ ET BT 26.250 230.810 Td /F1 9.8 Tf [(21.)] TJ ET BT 43.553 230.810 Td /F1 9.8 Tf [(Schroeder, W., K. Martin, and B. Lorensen. 2006. Visualization Toolkit: An Object-Oriented Approach to 3D Graphics, 4th )] TJ ET BT 26.250 218.905 Td /F1 9.8 Tf [(Edition. Kitware, Inc.: Clifton, NY.)] TJ ET BT 26.250 199.500 Td /F1 9.8 Tf [(22.)] TJ ET BT 43.553 199.500 Td /F1 9.8 Tf [(Schroeder W, Martin K, Lorensen B. Visualization Toolkit: An Object-Oriented Approach to 3D Graphics, 2006, 4th Edition. )] TJ ET BT 26.250 187.596 Td /F1 9.8 Tf [(Kitware, Inc.: Clifton, NY.)] TJ ET BT 26.250 168.191 Td /F1 9.8 Tf [(23.)] TJ ET BT 43.553 168.191 Td /F1 9.8 Tf [(Wylie B, Shead T, Baumes J. Information visualization in VTK: the titan project. Tutorial presented at IEEE Visualization )] TJ ET BT 26.250 156.286 Td /F1 9.8 Tf [(Conference, 2008; Available online at http://titan.sandia.gov/media/Information_Visualization_in_VTK.pdf)] TJ ET BT 26.250 136.881 Td /F1 9.8 Tf [(24.)] TJ ET BT 43.553 136.881 Td /F1 9.8 Tf [(Peterson AT, Sobern J, Pearson RG, Anderson RP, Martnez-Meyer E, Nakamura M, Arajo MB. Ecological Niches and )] TJ ET BT 26.250 124.977 Td /F1 9.8 Tf [(Geographic Distributions. 2011; Princeton University Press, Princeton, NJ.)] TJ ET BT 26.250 105.572 Td /F1 9.8 Tf [(25.)] TJ ET BT 43.553 105.572 Td /F1 9.8 Tf [(Elith J, Leathwick JR. Species distribution models: ecological explanation and prediction across space and time. Annual )] TJ ET BT 26.250 93.667 Td /F1 9.8 Tf [(Review of Ecology, Evolution, and Systematics 2009; 40:677-697.)] TJ ET BT 26.250 74.262 Td /F1 9.8 Tf [(26.)] TJ ET BT 43.553 74.262 Td /F1 9.8 Tf [(Ree RH, Moore BR, Webb CO, Donoghue MJ. A likelihood framework for inferring the evolution of geographic range on )] TJ ET BT 26.250 62.358 Td /F1 9.8 Tf [(phylogenetic trees. Evolution. 2005 Nov;59\(11\):2299-311. PubMed PMID:16396171.)] TJ ET Q q 15.000 52.477 577.500 724.523 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(6.)] TJ ET BT 38.132 759.976 Td /F1 9.8 Tf [(Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011 )] TJ ET BT 26.250 736.167 Td /F1 9.8 Tf [(Jan;39\(Database issue\):D698-704. PubMed PMID:21071413.)] TJ ET BT 26.250 716.762 Td /F1 9.8 Tf [(7.)] TJ ET BT 38.132 716.762 Td /F1 9.8 Tf [(Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, )] TJ ET BT 26.250 704.857 Td /F1 9.8 Tf [(Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, )] TJ ET BT 26.250 692.952 Td /F1 9.8 Tf [(Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature. 2012 May 9;486\(7402\):222-7. PubMed )] TJ ET BT 26.250 681.048 Td /F1 9.8 Tf [(PMID:22699611.)] TJ ET BT 26.250 661.643 Td /F1 9.8 Tf [(8.)] TJ ET BT 38.132 661.643 Td /F1 9.8 Tf [(Moles AT, Ackerly DD, Webb CO, Tweddle JC, Dickie JB, Westoby M. A brief history of seed size. Science. 2005 Jan )] TJ ET BT 26.250 649.738 Td /F1 9.8 Tf [(28;307\(5709\):576-80. PubMed PMID:15681384.)] TJ ET BT 26.250 630.333 Td /F1 9.8 Tf [(9.)] TJ ET BT 38.132 630.333 Td /F1 9.8 Tf [(Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Harmon LJ. Nine exceptional radiations )] TJ ET BT 26.250 618.429 Td /F1 9.8 Tf [(plus high turnover explain species diversity in jawed vertebrates. Proc Natl Acad Sci U S A. 2009 Aug 11;106\(32\):13410-4. )] TJ ET BT 26.250 606.524 Td /F1 9.8 Tf [(PubMed PMID:19633192.)] TJ ET BT 26.250 587.119 Td /F1 9.8 Tf [(10.)] TJ ET BT 43.553 587.119 Td /F1 9.8 Tf [(Meredith RW, Jane?ka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simo TL, Stadler T, )] TJ ET BT 26.250 575.214 Td /F1 9.8 Tf [(Rabosky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, Williams TL, Robinson TJ, Burk-Herrick A, Westerman M, Ayoub )] TJ ET BT 26.250 563.310 Td /F1 9.8 Tf [(NA, Springer MS, Murphy WJ. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. )] TJ ET BT 26.250 551.405 Td /F1 9.8 Tf [(Science. 2011 Oct 28;334\(6055\):521-4. PubMed PMID:21940861.)] TJ ET BT 26.250 532.000 Td /F1 9.8 Tf [(11.)] TJ ET BT 43.553 532.000 Td /F1 9.8 Tf [(Rosindell J, Harmon LJ. OneZoom: A Fractal Explorer for the Tree of Life. PLoS Biol. 2012 Oct;10\(10\):e1001406. PubMed )] TJ ET BT 26.250 520.095 Td /F1 9.8 Tf [(PMID:23091419.)] TJ ET BT 26.250 500.691 Td /F1 9.8 Tf [(12.)] TJ ET BT 43.553 500.691 Td /F1 9.8 Tf [(Reichman OJ, Jones MB, Schildhauer MP. Challenges and opportunities of open data in ecology. Science. 2011 Feb )] TJ ET BT 26.250 488.786 Td /F1 9.8 Tf [(11;331\(6018\):703-5. PubMed PMID:21311007.)] TJ ET BT 26.250 469.381 Td /F1 9.8 Tf [(13.)] TJ ET BT 43.553 469.381 Td /F1 9.8 Tf [(Ahrens J, Geveci B, Law C. 2005. ParaView: An End User Tool for Large Data Visualization. in The Visualization )] TJ ET BT 26.250 457.476 Td /F1 9.8 Tf [(Handbook, C. D. Hansen and C. R. Johnson, Eds.. Elsevier: Burlington, MA.)] TJ ET BT 26.250 438.072 Td /F1 9.8 Tf [(14.)] TJ ET BT 43.553 438.072 Td /F1 9.8 Tf [(Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and )] TJ ET BT 26.250 426.167 Td /F1 9.8 Tf [(transparent computational research in the life sciences. Genome Biol. 2010;11\(8\):R86. PubMed PMID:20738864.)] TJ ET BT 26.250 406.762 Td /F1 9.8 Tf [(15.)] TJ ET BT 43.553 406.762 Td /F1 9.8 Tf [(Freckleton RP. Fast likelihood calculations for comparative analyses. Methods in Ecology and Evolution2012; 3: 940-947.)] TJ ET BT 26.250 387.357 Td /F1 9.8 Tf [(16.)] TJ ET BT 43.553 387.357 Td /F1 9.8 Tf [(Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. 2011; Version 2.75 )] TJ ET BT 26.250 375.453 Td /F1 9.8 Tf [(http://mesquiteproject.org.)] TJ ET BT 26.250 356.048 Td /F1 9.8 Tf [(17.)] TJ ET BT 43.553 356.048 Td /F1 9.8 Tf [(Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 2004 Jan )] TJ ET BT 26.250 344.143 Td /F1 9.8 Tf [(22;20\(2\):289-90. PubMed PMID:14734327.)] TJ ET BT 26.250 324.738 Td /F1 9.8 Tf [(18.)] TJ ET BT 43.553 324.738 Td /F1 9.8 Tf [(Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. GEIGER: investigating evolutionary radiations. Bioinformatics. )] TJ ET BT 26.250 312.834 Td /F1 9.8 Tf [(2008 Jan 1;24\(1\):129-31. PubMed PMID:18006550.)] TJ ET BT 26.250 293.429 Td /F1 9.8 Tf [(19.)] TJ ET BT 43.553 293.429 Td /F1 9.8 Tf [(Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. Picante: R tools for )] TJ ET BT 26.250 281.524 Td /F1 9.8 Tf [(integrating phylogenies and ecology. Bioinformatics. 2010 Jun 1;26\(11\):1463-4. PubMed PMID:20395285.)] TJ ET BT 26.250 262.119 Td /F1 9.8 Tf [(20.)] TJ ET BT 43.553 262.119 Td /F1 9.8 Tf [(Fitzjohn RJ. Diversitree: comparative phylogenetic analyses of diversification in R. In press, Methods in Ecology and )] TJ ET BT 26.250 250.215 Td /F1 9.8 Tf [(Evolution.)] TJ ET BT 26.250 230.810 Td /F1 9.8 Tf [(21.)] TJ ET BT 43.553 230.810 Td /F1 9.8 Tf [(Schroeder, W., K. Martin, and B. Lorensen. 2006. Visualization Toolkit: An Object-Oriented Approach to 3D Graphics, 4th )] TJ ET BT 26.250 218.905 Td /F1 9.8 Tf [(Edition. Kitware, Inc.: Clifton, NY.)] TJ ET BT 26.250 199.500 Td /F1 9.8 Tf [(22.)] TJ ET BT 43.553 199.500 Td /F1 9.8 Tf [(Schroeder W, Martin K, Lorensen B. Visualization Toolkit: An Object-Oriented Approach to 3D Graphics, 2006, 4th Edition. )] TJ ET BT 26.250 187.596 Td /F1 9.8 Tf [(Kitware, Inc.: Clifton, NY.)] TJ ET BT 26.250 168.191 Td /F1 9.8 Tf [(23.)] TJ ET BT 43.553 168.191 Td /F1 9.8 Tf [(Wylie B, Shead T, Baumes J. Information visualization in VTK: the titan project. Tutorial presented at IEEE Visualization )] TJ ET BT 26.250 156.286 Td /F1 9.8 Tf [(Conference, 2008; Available online at http://titan.sandia.gov/media/Information_Visualization_in_VTK.pdf)] TJ ET BT 26.250 136.881 Td /F1 9.8 Tf [(24.)] TJ ET BT 43.553 136.881 Td /F1 9.8 Tf [(Peterson AT, Sobern J, Pearson RG, Anderson RP, Martnez-Meyer E, Nakamura M, Arajo MB. Ecological Niches and )] TJ ET BT 26.250 124.977 Td /F1 9.8 Tf [(Geographic Distributions. 2011; Princeton University Press, Princeton, NJ.)] TJ ET BT 26.250 105.572 Td /F1 9.8 Tf [(25.)] TJ ET BT 43.553 105.572 Td /F1 9.8 Tf [(Elith J, Leathwick JR. Species distribution models: ecological explanation and prediction across space and time. Annual )] TJ ET BT 26.250 93.667 Td /F1 9.8 Tf [(Review of Ecology, Evolution, and Systematics 2009; 40:677-697.)] TJ ET BT 26.250 74.262 Td /F1 9.8 Tf [(26.)] TJ ET BT 43.553 74.262 Td /F1 9.8 Tf [(Ree RH, Moore BR, Webb CO, Donoghue MJ. A likelihood framework for inferring the evolution of geographic range on )] TJ ET BT 26.250 62.358 Td /F1 9.8 Tf [(phylogenetic trees. Evolution. 2005 Nov;59\(11\):2299-311. PubMed PMID:16396171.)] TJ ET Q q 15.000 52.477 577.500 724.523 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(6.)] TJ ET BT 38.132 759.976 Td /F1 9.8 Tf [(Stark C, Breitkreutz BJ, Chatr-Aryamontri A, Boucher L, Oughtred R, Livstone MS, Nixon J, Van Auken K, Wang X, Shi X, )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(Reguly T, Rust JM, Winter A, Dolinski K, Tyers M. The BioGRID Interaction Database: 2011 update. Nucleic Acids Res. 2011 )] TJ ET BT 26.250 736.167 Td /F1 9.8 Tf [(Jan;39\(Database issue\):D698-704. PubMed PMID:21071413.)] TJ ET BT 26.250 716.762 Td /F1 9.8 Tf [(7.)] TJ ET BT 38.132 716.762 Td /F1 9.8 Tf [(Yatsunenko T, Rey FE, Manary MJ, Trehan I, Dominguez-Bello MG, Contreras M, Magris M, Hidalgo G, Baldassano RN, )] TJ ET BT 26.250 704.857 Td /F1 9.8 Tf [(Anokhin AP, Heath AC, Warner B, Reeder J, Kuczynski J, Caporaso JG, Lozupone CA, Lauber C, Clemente JC, Knights D, )] TJ ET BT 26.250 692.952 Td /F1 9.8 Tf [(Knight R, Gordon JI. Human gut microbiome viewed across age and geography. Nature. 2012 May 9;486\(7402\):222-7. PubMed )] TJ ET BT 26.250 681.048 Td /F1 9.8 Tf [(PMID:22699611.)] TJ ET BT 26.250 661.643 Td /F1 9.8 Tf [(8.)] TJ ET BT 38.132 661.643 Td /F1 9.8 Tf [(Moles AT, Ackerly DD, Webb CO, Tweddle JC, Dickie JB, Westoby M. A brief history of seed size. Science. 2005 Jan )] TJ ET BT 26.250 649.738 Td /F1 9.8 Tf [(28;307\(5709\):576-80. PubMed PMID:15681384.)] TJ ET BT 26.250 630.333 Td /F1 9.8 Tf [(9.)] TJ ET BT 38.132 630.333 Td /F1 9.8 Tf [(Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Harmon LJ. Nine exceptional radiations )] TJ ET BT 26.250 618.429 Td /F1 9.8 Tf [(plus high turnover explain species diversity in jawed vertebrates. Proc Natl Acad Sci U S A. 2009 Aug 11;106\(32\):13410-4. )] TJ ET BT 26.250 606.524 Td /F1 9.8 Tf [(PubMed PMID:19633192.)] TJ ET BT 26.250 587.119 Td /F1 9.8 Tf [(10.)] TJ ET BT 43.553 587.119 Td /F1 9.8 Tf [(Meredith RW, Jane?ka JE, Gatesy J, Ryder OA, Fisher CA, Teeling EC, Goodbla A, Eizirik E, Simo TL, Stadler T, )] TJ ET BT 26.250 575.214 Td /F1 9.8 Tf [(Rabosky DL, Honeycutt RL, Flynn JJ, Ingram CM, Steiner C, Williams TL, Robinson TJ, Burk-Herrick A, Westerman M, Ayoub )] TJ ET BT 26.250 563.310 Td /F1 9.8 Tf [(NA, Springer MS, Murphy WJ. Impacts of the Cretaceous Terrestrial Revolution and KPg extinction on mammal diversification. )] TJ ET BT 26.250 551.405 Td /F1 9.8 Tf [(Science. 2011 Oct 28;334\(6055\):521-4. PubMed PMID:21940861.)] TJ ET BT 26.250 532.000 Td /F1 9.8 Tf [(11.)] TJ ET BT 43.553 532.000 Td /F1 9.8 Tf [(Rosindell J, Harmon LJ. OneZoom: A Fractal Explorer for the Tree of Life. PLoS Biol. 2012 Oct;10\(10\):e1001406. PubMed )] TJ ET BT 26.250 520.095 Td /F1 9.8 Tf [(PMID:23091419.)] TJ ET BT 26.250 500.691 Td /F1 9.8 Tf [(12.)] TJ ET BT 43.553 500.691 Td /F1 9.8 Tf [(Reichman OJ, Jones MB, Schildhauer MP. Challenges and opportunities of open data in ecology. Science. 2011 Feb )] TJ ET BT 26.250 488.786 Td /F1 9.8 Tf [(11;331\(6018\):703-5. PubMed PMID:21311007.)] TJ ET BT 26.250 469.381 Td /F1 9.8 Tf [(13.)] TJ ET BT 43.553 469.381 Td /F1 9.8 Tf [(Ahrens J, Geveci B, Law C. 2005. ParaView: An End User Tool for Large Data Visualization. in The Visualization )] TJ ET BT 26.250 457.476 Td /F1 9.8 Tf [(Handbook, C. D. Hansen and C. R. Johnson, Eds.. Elsevier: Burlington, MA.)] TJ ET BT 26.250 438.072 Td /F1 9.8 Tf [(14.)] TJ ET BT 43.553 438.072 Td /F1 9.8 Tf [(Goecks J, Nekrutenko A, Taylor J. Galaxy: a comprehensive approach for supporting accessible, reproducible, and )] TJ ET BT 26.250 426.167 Td /F1 9.8 Tf [(transparent computational research in the life sciences. Genome Biol. 2010;11\(8\):R86. PubMed PMID:20738864.)] TJ ET BT 26.250 406.762 Td /F1 9.8 Tf [(15.)] TJ ET BT 43.553 406.762 Td /F1 9.8 Tf [(Freckleton RP. Fast likelihood calculations for comparative analyses. Methods in Ecology and Evolution2012; 3: 940-947.)] TJ ET BT 26.250 387.357 Td /F1 9.8 Tf [(16.)] TJ ET BT 43.553 387.357 Td /F1 9.8 Tf [(Maddison WP, Maddison DR. Mesquite: a modular system for evolutionary analysis. 2011; Version 2.75 )] TJ ET BT 26.250 375.453 Td /F1 9.8 Tf [(http://mesquiteproject.org.)] TJ ET BT 26.250 356.048 Td /F1 9.8 Tf [(17.)] TJ ET BT 43.553 356.048 Td /F1 9.8 Tf [(Paradis E, Claude J, Strimmer K. APE: Analyses of Phylogenetics and Evolution in R language. Bioinformatics. 2004 Jan )] TJ ET BT 26.250 344.143 Td /F1 9.8 Tf [(22;20\(2\):289-90. PubMed PMID:14734327.)] TJ ET BT 26.250 324.738 Td /F1 9.8 Tf [(18.)] TJ ET BT 43.553 324.738 Td /F1 9.8 Tf [(Harmon LJ, Weir JT, Brock CD, Glor RE, Challenger W. GEIGER: investigating evolutionary radiations. Bioinformatics. )] TJ ET BT 26.250 312.834 Td /F1 9.8 Tf [(2008 Jan 1;24\(1\):129-31. PubMed PMID:18006550.)] TJ ET BT 26.250 293.429 Td /F1 9.8 Tf [(19.)] TJ ET BT 43.553 293.429 Td /F1 9.8 Tf [(Kembel SW, Cowan PD, Helmus MR, Cornwell WK, Morlon H, Ackerly DD, Blomberg SP, Webb CO. Picante: R tools for )] TJ ET BT 26.250 281.524 Td /F1 9.8 Tf [(integrating phylogenies and ecology. Bioinformatics. 2010 Jun 1;26\(11\):1463-4. PubMed PMID:20395285.)] TJ ET BT 26.250 262.119 Td /F1 9.8 Tf [(20.)] TJ ET BT 43.553 262.119 Td /F1 9.8 Tf [(Fitzjohn RJ. Diversitree: comparative phylogenetic analyses of diversification in R. In press, Methods in Ecology and )] TJ ET BT 26.250 250.215 Td /F1 9.8 Tf [(Evolution.)] TJ ET BT 26.250 230.810 Td /F1 9.8 Tf [(21.)] TJ ET BT 43.553 230.810 Td /F1 9.8 Tf [(Schroeder, W., K. Martin, and B. Lorensen. 2006. Visualization Toolkit: An Object-Oriented Approach to 3D Graphics, 4th )] TJ ET BT 26.250 218.905 Td /F1 9.8 Tf [(Edition. Kitware, Inc.: Clifton, NY.)] TJ ET BT 26.250 199.500 Td /F1 9.8 Tf [(22.)] TJ ET BT 43.553 199.500 Td /F1 9.8 Tf [(Schroeder W, Martin K, Lorensen B. Visualization Toolkit: An Object-Oriented Approach to 3D Graphics, 2006, 4th Edition. )] TJ ET BT 26.250 187.596 Td /F1 9.8 Tf [(Kitware, Inc.: Clifton, NY.)] TJ ET BT 26.250 168.191 Td /F1 9.8 Tf [(23.)] TJ ET BT 43.553 168.191 Td /F1 9.8 Tf [(Wylie B, Shead T, Baumes J. Information visualization in VTK: the titan project. Tutorial presented at IEEE Visualization )] TJ ET BT 26.250 156.286 Td /F1 9.8 Tf [(Conference, 2008; Available online at http://titan.sandia.gov/media/Information_Visualization_in_VTK.pdf)] TJ ET BT 26.250 136.881 Td /F1 9.8 Tf [(24.)] TJ ET BT 43.553 136.881 Td /F1 9.8 Tf [(Peterson AT, Sobern J, Pearson RG, Anderson RP, Martnez-Meyer E, Nakamura M, Arajo MB. Ecological Niches and )] TJ ET BT 26.250 124.977 Td /F1 9.8 Tf [(Geographic Distributions. 2011; Princeton University Press, Princeton, NJ.)] TJ ET BT 26.250 105.572 Td /F1 9.8 Tf [(25.)] TJ ET BT 43.553 105.572 Td /F1 9.8 Tf [(Elith J, Leathwick JR. Species distribution models: ecological explanation and prediction across space and time. Annual )] TJ ET BT 26.250 93.667 Td /F1 9.8 Tf [(Review of Ecology, Evolution, and Systematics 2009; 40:677-697.)] TJ ET BT 26.250 74.262 Td /F1 9.8 Tf [(26.)] TJ ET BT 43.553 74.262 Td /F1 9.8 Tf [(Ree RH, Moore BR, Webb CO, Donoghue MJ. A likelihood framework for inferring the evolution of geographic range on )] TJ ET BT 26.250 62.358 Td /F1 9.8 Tf [(phylogenetic trees. Evolution. 2005 Nov;59\(11\):2299-311. PubMed PMID:16396171.)] TJ ET 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 333 0 obj << /Type /Page /Parent 3 0 R /Contents 334 0 R >> endobj 334 0 obj << /Length 7294 >> stream 0.271 0.267 0.267 rg q 15.000 530.929 577.500 246.071 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(27.)] TJ ET BT 43.553 759.976 Td /F1 9.8 Tf [(Ree RH, Smith SA. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(cladogenesis. Syst Biol. 2008 Feb;57\(1\):4-14. PubMed PMID:18253896.)] TJ ET BT 26.250 728.667 Td /F1 9.8 Tf [(28.)] TJ ET BT 43.553 728.667 Td /F1 9.8 Tf [(Ree RH, Sanmartin I. Prospects and challenges for parametric models in historical biogeographical inference. Journal of )] TJ ET BT 26.250 716.762 Td /F1 9.8 Tf [(Biogeography 2009; 36:1211-1220.)] TJ ET BT 26.250 697.357 Td /F1 9.8 Tf [(29.)] TJ ET BT 43.553 697.357 Td /F1 9.8 Tf [(Barve NV, Barve V, Jimnez-Valverde A, Lira-Noriega A Maher SP, Peterson AT, Sobern J, Villalobos F. The crucial role )] TJ ET BT 26.250 685.452 Td /F1 9.8 Tf [(of the accessible area in ecological niche modeling and species distribution modeling. 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Am Nat. 2007 Oct;170\(4\):602-16. PubMed PMID:17891738.)] TJ ET BT 26.250 560.214 Td /F1 9.8 Tf [(33.)] TJ ET BT 43.553 560.214 Td /F1 9.8 Tf [(Lenards A, Merchant N, Stanzione D. Building an environment to facilitate discoveries for plant sciences. Proceedings of the )] TJ ET BT 26.250 548.310 Td /F1 9.8 Tf [(2011 ACM workshop on Gateway computing environments 2011; 51-58.)] TJ ET Q q 15.000 530.929 577.500 246.071 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(27.)] TJ ET BT 43.553 759.976 Td /F1 9.8 Tf [(Ree RH, Smith SA. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(cladogenesis. Syst Biol. 2008 Feb;57\(1\):4-14. PubMed PMID:18253896.)] TJ ET BT 26.250 728.667 Td /F1 9.8 Tf [(28.)] TJ ET BT 43.553 728.667 Td /F1 9.8 Tf [(Ree RH, Sanmartin I. Prospects and challenges for parametric models in historical biogeographical inference. 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Reconstructing the Pleistocene geography of the Aphelocoma jays )] TJ ET BT 26.250 610.929 Td /F1 9.8 Tf [(\(Corvidae\). Diversity and Distributions 2004; 10: 237-246.)] TJ ET BT 26.250 591.524 Td /F1 9.8 Tf [(32.)] TJ ET BT 43.553 591.524 Td /F1 9.8 Tf [(Rangel TF, Diniz-Filho JA, Colwell RK. Species richness and evolutionary niche dynamics: a spatial pattern-oriented )] TJ ET BT 26.250 579.619 Td /F1 9.8 Tf [(simulation experiment. Am Nat. 2007 Oct;170\(4\):602-16. PubMed PMID:17891738.)] TJ ET BT 26.250 560.214 Td /F1 9.8 Tf [(33.)] TJ ET BT 43.553 560.214 Td /F1 9.8 Tf [(Lenards A, Merchant N, Stanzione D. Building an environment to facilitate discoveries for plant sciences. Proceedings of the )] TJ ET BT 26.250 548.310 Td /F1 9.8 Tf [(2011 ACM workshop on Gateway computing environments 2011; 51-58.)] TJ ET Q q 15.000 530.929 577.500 246.071 re W n 0.271 0.267 0.267 rg BT 26.250 759.976 Td /F1 9.8 Tf [(27.)] TJ ET BT 43.553 759.976 Td /F1 9.8 Tf [(Ree RH, Smith SA. Maximum likelihood inference of geographic range evolution by dispersal, local extinction, and )] TJ ET BT 26.250 748.071 Td /F1 9.8 Tf [(cladogenesis. Syst Biol. 2008 Feb;57\(1\):4-14. PubMed PMID:18253896.)] TJ ET BT 26.250 728.667 Td /F1 9.8 Tf [(28.)] TJ ET BT 43.553 728.667 Td /F1 9.8 Tf [(Ree RH, Sanmartin I. Prospects and challenges for parametric models in historical biogeographical inference. Journal of )] TJ ET BT 26.250 716.762 Td /F1 9.8 Tf [(Biogeography 2009; 36:1211-1220.)] TJ ET BT 26.250 697.357 Td /F1 9.8 Tf [(29.)] TJ ET BT 43.553 697.357 Td /F1 9.8 Tf [(Barve NV, Barve V, Jimnez-Valverde A, Lira-Noriega A Maher SP, Peterson AT, Sobern J, Villalobos F. The crucial role )] TJ ET BT 26.250 685.452 Td /F1 9.8 Tf [(of the accessible area in ecological niche modeling and species distribution modeling. 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