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BT 15.000 700.036 Td /F3 9.8 Tf  [(June 19, 2014)] TJ ET
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BT 26.250 635.283 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 615.329 Td /F1 9.8 Tf  [(As phylogenetic data becomes increasingly available, along with associated data on species� genomes, traits, and geographic )] TJ ET
BT 26.250 603.424 Td /F1 9.8 Tf  [(distributions, the need to ensure data availability and reuse become more and more acute. In this paper, we provide ten �simple )] TJ ET
BT 26.250 591.519 Td /F1 9.8 Tf  [(rules� that we view as best practices for data sharing in phylogenetic research. These rules will help lead towards a future )] TJ ET
BT 26.250 579.615 Td /F1 9.8 Tf  [(phylogenetics where data can easily be archived, shared, reused, and repurposed across a wide variety of projects.)] TJ ET
BT 26.250 543.012 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 523.058 Td /F1 9.8 Tf  [(Funding for this work comes from the NSF AVAToL \(https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503629\), grant )] TJ ET
BT 26.250 511.153 Td /F1 9.8 Tf  [(numbers #1208809 \(KC\), #1208270 \(MO\), and #1208912 \(LH & CL\). The funders had no role in study design, data collection )] TJ ET
BT 26.250 499.248 Td /F1 9.8 Tf  [(and analysis, decision to publish, or preparation of the manuscript. The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 470.146 Td /F4 12.0 Tf  [(Introduction)] TJ ET
BT 26.250 450.192 Td /F1 9.8 Tf  [(The amount of phylogenetic data has rapidly increased in its quality and availability over the past few decades. Additionally, )] TJ ET
BT 26.250 438.287 Td /F1 9.8 Tf  [(phylogenetic matrices and trees are often based on and need to be linked to data on traits, geographic distribution, and genetic / )] TJ ET
BT 26.250 426.382 Td /F1 9.8 Tf  [(genomic sequences. Despite the rapid growth in data generation, comparative data from published studies are too often )] TJ ET
BT 26.250 414.477 Td /F1 9.8 Tf  [(unavailable, incomplete, or incompatible thereby greatly limiting reproducibility and expansion of existing studies )] TJ ET
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BT 523.827 414.477 Td /F1 9.8 Tf  [(. A greater )] TJ ET
BT 26.250 402.573 Td /F1 9.8 Tf  [(focus on data integration and interoperability, even at the data collection phase of a project, allows for scalable, integrative )] TJ ET
BT 26.250 390.668 Td /F1 9.8 Tf  [(analyses that combine data from multiple sources )] TJ ET
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BT 243.002 392.175 Td /F4 8.7 Tf  [(3)] TJ ET
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BT 247.821 394.556 Td /F1 8.7 Tf  [(,)] TJ ET
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BT 250.230 392.175 Td /F4 8.7 Tf  [(4)] TJ ET
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BT 255.049 390.668 Td /F1 9.8 Tf  [(.)] TJ ET
BT 26.250 371.263 Td /F1 9.8 Tf  [(Modeled on other initiatives in science that have suggested practices to standardize and share data )] TJ ET
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BT 457.639 372.770 Td /F4 8.7 Tf  [(5)] TJ ET
0.271 0.267 0.267 rg
BT 462.457 371.263 Td /F1 9.8 Tf  [(, here we discuss )] TJ ET
BT 26.250 359.358 Td /F1 9.8 Tf  [(recommendations for data sharing that will allow the phylogenetics community to advance large scale research much more )] TJ ET
BT 26.250 347.454 Td /F1 9.8 Tf  [(efficiently. �We� in this case, are members of the three NSF-funded )] TJ ET
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BT 354.084 347.454 Td /F1 9.8 Tf  [( projects � )] TJ ET
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BT 401.771 347.454 Td /F1 9.8 Tf  [(Open Tree of Life)] TJ ET
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BT 477.646 347.454 Td /F1 9.8 Tf  [(, )] TJ ET
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BT 506.905 347.454 Td /F1 9.8 Tf  [( and )] TJ ET
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BT 528.590 347.454 Td /F1 9.8 Tf  [(Next-)] TJ ET
BT 26.250 335.549 Td /F1 9.8 Tf  [(generation Phenomics)] TJ ET
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BT 123.253 335.549 Td /F1 9.8 Tf  [(, although this manuscript was heavily influenced by a period of public commenting )] TJ ET
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BT 483.077 337.056 Td /F4 8.7 Tf  [(23)] TJ ET
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BT 492.714 335.549 Td /F1 9.8 Tf  [( \(see )] TJ ET
BT 26.250 323.644 Td /F1 9.8 Tf  [(Acknowledgements\).)] TJ ET
BT 26.250 304.239 Td /F1 9.8 Tf  [(We define phylogenetic data as the inputs, outputs and methodological details of a phylogenetic analysis. Current practices for )] TJ ET
BT 26.250 292.335 Td /F1 9.8 Tf  [(publication of these data too often limit reusability. For example, molecular alignments are rarely preserved and made available; )] TJ ET
BT 26.250 280.430 Td /F1 9.8 Tf  [(phenomic matrices do not always include full descriptions of characters and character states, character states do not follow )] TJ ET
BT 26.250 268.525 Td /F1 9.8 Tf  [(standardized anatomical language, and despite the availability of inexpensive digital photography, phenomic homology is rarely )] TJ ET
BT 26.250 256.620 Td /F1 9.8 Tf  [(documented with images; phylogenetic trees are too often published only as images instead of digital data files that we can read )] TJ ET
BT 26.250 244.716 Td /F1 9.8 Tf  [(into another software package; published trees often contain ambiguities in interpretation due to inconsistencies in methods, )] TJ ET
BT 26.250 232.811 Td /F1 9.8 Tf  [(software, and file formats; and tip labels \(terminal taxa\) in tree files and associated data matrices are not always meaningful or )] TJ ET
BT 26.250 220.906 Td /F1 9.8 Tf  [(comprehensible to anyone outside the original study. Because of these \(and other\) problems, phylogenetic comparative studies )] TJ ET
BT 26.250 209.001 Td /F1 9.8 Tf  [(can be difficult or impossible to replicate or expand upon. When these studies are replicated, inconsistencies can be impossible )] TJ ET
BT 26.250 197.097 Td /F1 9.8 Tf  [(to track down. As a result, advancement in the field is greatly slowed by very preventable issues.)] TJ ET
BT 26.250 177.692 Td /F1 9.8 Tf  [(If you are producing any kind of phylogenetic data as part of your research publications, your data are much more likely to have )] TJ ET
BT 26.250 165.787 Td /F1 9.8 Tf  [(an impact if they are easily understandable and reusable by others. In many cases, the raw data and output files from your )] TJ ET
BT 26.250 153.882 Td /F1 9.8 Tf  [(analysis require additional curation than what has historically been expected in order to ensure that they are easily reusable. )] TJ ET
BT 26.250 141.978 Td /F1 9.8 Tf  [(Here we propose a set of �best practices� for comparative biology. Our best practices include suggestions that will facilitate )] TJ ET
BT 26.250 130.073 Td /F1 9.8 Tf  [(reproduction and reuse of the input and output data from phylogenetic analyses. We encourage practices that enable )] TJ ET
BT 26.250 118.168 Td /F1 9.8 Tf  [(automated curation and access to phylogenetic comparative data. We also emphasize the importance of file validators, curation )] TJ ET
BT 26.250 106.263 Td /F1 9.8 Tf  [(tools, and software that outputs standardized and reusable data.)] TJ ET
BT 26.250 86.859 Td /F1 9.8 Tf  [(The best general solution is to make your data available in a public repository and in a format that has existing parsers )] TJ ET
BT 26.250 74.954 Td /F1 9.8 Tf  [(\(computer programs that can import the file\) and validation tools \(computer programs that determine if the file has valid )] TJ ET
BT 26.250 63.049 Td /F1 9.8 Tf  [(formatting and confirm that the data in the file can be easily extracted\). A variety of parsing tools exist for phylogenetic packages )] TJ ET
BT 26.250 51.144 Td /F1 9.8 Tf  [(such as Mesquite )] TJ ET
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BT 104.825 52.652 Td /F4 8.7 Tf  [(6)] TJ ET
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BT 109.644 51.144 Td /F1 9.8 Tf  [(, PAUP )] TJ ET
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BT 304.487 51.144 Td /F1 9.8 Tf  [( and CIPRES )] TJ ET
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BT 374.818 51.144 Td /F1 9.8 Tf  [( . Going a step further, the newly emerging )] TJ ET
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BT 149.567 39.240 Td /F1 9.8 Tf  [( formats are examples of file types that have a published digital schema \(format\) that allows for )] TJ ET
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BT 266.548 688.195 Td /F1 9.8 Tf  [(Curtis Lisle)] TJ ET
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BT 26.250 676.290 Td /F1 9.8 Tf  [(Cranston K, Harmon LJ, O'Leary MA, Lisle C. Best Practices for Data Sharing in Phylogenetic Research. PLOS Currents Tree )] TJ ET
BT 26.250 664.386 Td /F1 9.8 Tf  [(of Life. 2014 Jun 19 . Edition 1. doi: 10.1371/currents.tol.bf01eff4a6b60ca4825c69293dc59645.)] TJ ET
q
15.000 24.954 577.500 637.051 re W n
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BT 26.250 635.283 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 615.329 Td /F1 9.8 Tf  [(As phylogenetic data becomes increasingly available, along with associated data on species� genomes, traits, and geographic )] TJ ET
BT 26.250 603.424 Td /F1 9.8 Tf  [(distributions, the need to ensure data availability and reuse become more and more acute. In this paper, we provide ten �simple )] TJ ET
BT 26.250 591.519 Td /F1 9.8 Tf  [(rules� that we view as best practices for data sharing in phylogenetic research. These rules will help lead towards a future )] TJ ET
BT 26.250 579.615 Td /F1 9.8 Tf  [(phylogenetics where data can easily be archived, shared, reused, and repurposed across a wide variety of projects.)] TJ ET
BT 26.250 543.012 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 523.058 Td /F1 9.8 Tf  [(Funding for this work comes from the NSF AVAToL \(https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503629\), grant )] TJ ET
BT 26.250 511.153 Td /F1 9.8 Tf  [(numbers #1208809 \(KC\), #1208270 \(MO\), and #1208912 \(LH & CL\). The funders had no role in study design, data collection )] TJ ET
BT 26.250 499.248 Td /F1 9.8 Tf  [(and analysis, decision to publish, or preparation of the manuscript. The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 470.146 Td /F4 12.0 Tf  [(Introduction)] TJ ET
BT 26.250 450.192 Td /F1 9.8 Tf  [(The amount of phylogenetic data has rapidly increased in its quality and availability over the past few decades. Additionally, )] TJ ET
BT 26.250 438.287 Td /F1 9.8 Tf  [(phylogenetic matrices and trees are often based on and need to be linked to data on traits, geographic distribution, and genetic / )] TJ ET
BT 26.250 426.382 Td /F1 9.8 Tf  [(genomic sequences. Despite the rapid growth in data generation, comparative data from published studies are too often )] TJ ET
BT 26.250 414.477 Td /F1 9.8 Tf  [(unavailable, incomplete, or incompatible thereby greatly limiting reproducibility and expansion of existing studies )] TJ ET
0.267 0.267 0.267 rg
BT 511.781 415.985 Td /F4 8.7 Tf  [(1)] TJ ET
0.271 0.267 0.267 rg
BT 516.599 418.366 Td /F1 8.7 Tf  [(,)] TJ ET
0.267 0.267 0.267 rg
BT 519.009 415.985 Td /F4 8.7 Tf  [(2)] TJ ET
0.271 0.267 0.267 rg
BT 523.827 414.477 Td /F1 9.8 Tf  [(. A greater )] TJ ET
BT 26.250 402.573 Td /F1 9.8 Tf  [(focus on data integration and interoperability, even at the data collection phase of a project, allows for scalable, integrative )] TJ ET
BT 26.250 390.668 Td /F1 9.8 Tf  [(analyses that combine data from multiple sources )] TJ ET
0.267 0.267 0.267 rg
BT 243.002 392.175 Td /F4 8.7 Tf  [(3)] TJ ET
0.271 0.267 0.267 rg
BT 247.821 394.556 Td /F1 8.7 Tf  [(,)] TJ ET
0.267 0.267 0.267 rg
BT 250.230 392.175 Td /F4 8.7 Tf  [(4)] TJ ET
0.271 0.267 0.267 rg
BT 255.049 390.668 Td /F1 9.8 Tf  [(.)] TJ ET
BT 26.250 371.263 Td /F1 9.8 Tf  [(Modeled on other initiatives in science that have suggested practices to standardize and share data )] TJ ET
0.267 0.267 0.267 rg
BT 457.639 372.770 Td /F4 8.7 Tf  [(5)] TJ ET
0.271 0.267 0.267 rg
BT 462.457 371.263 Td /F1 9.8 Tf  [(, here we discuss )] TJ ET
BT 26.250 359.358 Td /F1 9.8 Tf  [(recommendations for data sharing that will allow the phylogenetics community to advance large scale research much more )] TJ ET
BT 26.250 347.454 Td /F1 9.8 Tf  [(efficiently. �We� in this case, are members of the three NSF-funded )] TJ ET
0.267 0.267 0.267 rg
BT 317.775 347.454 Td /F1 9.8 Tf  [(AVAToL)] TJ ET
0.271 0.267 0.267 rg
BT 354.084 347.454 Td /F1 9.8 Tf  [( projects � )] TJ ET
0.267 0.267 0.267 rg
BT 401.771 347.454 Td /F1 9.8 Tf  [(Open Tree of Life)] TJ ET
0.271 0.267 0.267 rg
BT 477.646 347.454 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 483.067 347.454 Td /F1 9.8 Tf  [(Arbor)] TJ ET
0.271 0.267 0.267 rg
BT 506.905 347.454 Td /F1 9.8 Tf  [( and )] TJ ET
0.267 0.267 0.267 rg
BT 528.590 347.454 Td /F1 9.8 Tf  [(Next-)] TJ ET
BT 26.250 335.549 Td /F1 9.8 Tf  [(generation Phenomics)] TJ ET
0.271 0.267 0.267 rg
BT 123.253 335.549 Td /F1 9.8 Tf  [(, although this manuscript was heavily influenced by a period of public commenting )] TJ ET
0.267 0.267 0.267 rg
BT 483.077 337.056 Td /F4 8.7 Tf  [(23)] TJ ET
0.271 0.267 0.267 rg
BT 492.714 335.549 Td /F1 9.8 Tf  [( \(see )] TJ ET
BT 26.250 323.644 Td /F1 9.8 Tf  [(Acknowledgements\).)] TJ ET
BT 26.250 304.239 Td /F1 9.8 Tf  [(We define phylogenetic data as the inputs, outputs and methodological details of a phylogenetic analysis. Current practices for )] TJ ET
BT 26.250 292.335 Td /F1 9.8 Tf  [(publication of these data too often limit reusability. For example, molecular alignments are rarely preserved and made available; )] TJ ET
BT 26.250 280.430 Td /F1 9.8 Tf  [(phenomic matrices do not always include full descriptions of characters and character states, character states do not follow )] TJ ET
BT 26.250 268.525 Td /F1 9.8 Tf  [(standardized anatomical language, and despite the availability of inexpensive digital photography, phenomic homology is rarely )] TJ ET
BT 26.250 256.620 Td /F1 9.8 Tf  [(documented with images; phylogenetic trees are too often published only as images instead of digital data files that we can read )] TJ ET
BT 26.250 244.716 Td /F1 9.8 Tf  [(into another software package; published trees often contain ambiguities in interpretation due to inconsistencies in methods, )] TJ ET
BT 26.250 232.811 Td /F1 9.8 Tf  [(software, and file formats; and tip labels \(terminal taxa\) in tree files and associated data matrices are not always meaningful or )] TJ ET
BT 26.250 220.906 Td /F1 9.8 Tf  [(comprehensible to anyone outside the original study. Because of these \(and other\) problems, phylogenetic comparative studies )] TJ ET
BT 26.250 209.001 Td /F1 9.8 Tf  [(can be difficult or impossible to replicate or expand upon. When these studies are replicated, inconsistencies can be impossible )] TJ ET
BT 26.250 197.097 Td /F1 9.8 Tf  [(to track down. As a result, advancement in the field is greatly slowed by very preventable issues.)] TJ ET
BT 26.250 177.692 Td /F1 9.8 Tf  [(If you are producing any kind of phylogenetic data as part of your research publications, your data are much more likely to have )] TJ ET
BT 26.250 165.787 Td /F1 9.8 Tf  [(an impact if they are easily understandable and reusable by others. In many cases, the raw data and output files from your )] TJ ET
BT 26.250 153.882 Td /F1 9.8 Tf  [(analysis require additional curation than what has historically been expected in order to ensure that they are easily reusable. )] TJ ET
BT 26.250 141.978 Td /F1 9.8 Tf  [(Here we propose a set of �best practices� for comparative biology. Our best practices include suggestions that will facilitate )] TJ ET
BT 26.250 130.073 Td /F1 9.8 Tf  [(reproduction and reuse of the input and output data from phylogenetic analyses. We encourage practices that enable )] TJ ET
BT 26.250 118.168 Td /F1 9.8 Tf  [(automated curation and access to phylogenetic comparative data. We also emphasize the importance of file validators, curation )] TJ ET
BT 26.250 106.263 Td /F1 9.8 Tf  [(tools, and software that outputs standardized and reusable data.)] TJ ET
BT 26.250 86.859 Td /F1 9.8 Tf  [(The best general solution is to make your data available in a public repository and in a format that has existing parsers )] TJ ET
BT 26.250 74.954 Td /F1 9.8 Tf  [(\(computer programs that can import the file\) and validation tools \(computer programs that determine if the file has valid )] TJ ET
BT 26.250 63.049 Td /F1 9.8 Tf  [(formatting and confirm that the data in the file can be easily extracted\). A variety of parsing tools exist for phylogenetic packages )] TJ ET
BT 26.250 51.144 Td /F1 9.8 Tf  [(such as Mesquite )] TJ ET
0.267 0.267 0.267 rg
BT 104.825 52.652 Td /F4 8.7 Tf  [(6)] TJ ET
0.271 0.267 0.267 rg
BT 109.644 51.144 Td /F1 9.8 Tf  [(, PAUP )] TJ ET
0.267 0.267 0.267 rg
BT 144.325 52.652 Td /F4 8.7 Tf  [(7)] TJ ET
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BT 26.250 664.386 Td /F1 9.8 Tf  [(of Life. 2014 Jun 19 . Edition 1. doi: 10.1371/currents.tol.bf01eff4a6b60ca4825c69293dc59645.)] TJ ET
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BT 26.250 635.283 Td /F4 12.0 Tf  [(Abstract)] TJ ET
BT 26.250 615.329 Td /F1 9.8 Tf  [(As phylogenetic data becomes increasingly available, along with associated data on species� genomes, traits, and geographic )] TJ ET
BT 26.250 603.424 Td /F1 9.8 Tf  [(distributions, the need to ensure data availability and reuse become more and more acute. In this paper, we provide ten �simple )] TJ ET
BT 26.250 591.519 Td /F1 9.8 Tf  [(rules� that we view as best practices for data sharing in phylogenetic research. These rules will help lead towards a future )] TJ ET
BT 26.250 579.615 Td /F1 9.8 Tf  [(phylogenetics where data can easily be archived, shared, reused, and repurposed across a wide variety of projects.)] TJ ET
BT 26.250 543.012 Td /F4 12.0 Tf  [(Funding Statement)] TJ ET
BT 26.250 523.058 Td /F1 9.8 Tf  [(Funding for this work comes from the NSF AVAToL \(https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503629\), grant )] TJ ET
BT 26.250 511.153 Td /F1 9.8 Tf  [(numbers #1208809 \(KC\), #1208270 \(MO\), and #1208912 \(LH & CL\). The funders had no role in study design, data collection )] TJ ET
BT 26.250 499.248 Td /F1 9.8 Tf  [(and analysis, decision to publish, or preparation of the manuscript. The authors have declared that no competing interests exist.)] TJ ET
BT 26.250 470.146 Td /F4 12.0 Tf  [(Introduction)] TJ ET
BT 26.250 450.192 Td /F1 9.8 Tf  [(The amount of phylogenetic data has rapidly increased in its quality and availability over the past few decades. Additionally, )] TJ ET
BT 26.250 438.287 Td /F1 9.8 Tf  [(phylogenetic matrices and trees are often based on and need to be linked to data on traits, geographic distribution, and genetic / )] TJ ET
BT 26.250 426.382 Td /F1 9.8 Tf  [(genomic sequences. Despite the rapid growth in data generation, comparative data from published studies are too often )] TJ ET
BT 26.250 414.477 Td /F1 9.8 Tf  [(unavailable, incomplete, or incompatible thereby greatly limiting reproducibility and expansion of existing studies )] TJ ET
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BT 523.827 414.477 Td /F1 9.8 Tf  [(. A greater )] TJ ET
BT 26.250 402.573 Td /F1 9.8 Tf  [(focus on data integration and interoperability, even at the data collection phase of a project, allows for scalable, integrative )] TJ ET
BT 26.250 390.668 Td /F1 9.8 Tf  [(analyses that combine data from multiple sources )] TJ ET
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BT 255.049 390.668 Td /F1 9.8 Tf  [(.)] TJ ET
BT 26.250 371.263 Td /F1 9.8 Tf  [(Modeled on other initiatives in science that have suggested practices to standardize and share data )] TJ ET
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BT 457.639 372.770 Td /F4 8.7 Tf  [(5)] TJ ET
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BT 462.457 371.263 Td /F1 9.8 Tf  [(, here we discuss )] TJ ET
BT 26.250 359.358 Td /F1 9.8 Tf  [(recommendations for data sharing that will allow the phylogenetics community to advance large scale research much more )] TJ ET
BT 26.250 347.454 Td /F1 9.8 Tf  [(efficiently. �We� in this case, are members of the three NSF-funded )] TJ ET
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BT 26.250 335.549 Td /F1 9.8 Tf  [(generation Phenomics)] TJ ET
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BT 123.253 335.549 Td /F1 9.8 Tf  [(, although this manuscript was heavily influenced by a period of public commenting )] TJ ET
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BT 492.714 335.549 Td /F1 9.8 Tf  [( \(see )] TJ ET
BT 26.250 323.644 Td /F1 9.8 Tf  [(Acknowledgements\).)] TJ ET
BT 26.250 304.239 Td /F1 9.8 Tf  [(We define phylogenetic data as the inputs, outputs and methodological details of a phylogenetic analysis. Current practices for )] TJ ET
BT 26.250 292.335 Td /F1 9.8 Tf  [(publication of these data too often limit reusability. For example, molecular alignments are rarely preserved and made available; )] TJ ET
BT 26.250 280.430 Td /F1 9.8 Tf  [(phenomic matrices do not always include full descriptions of characters and character states, character states do not follow )] TJ ET
BT 26.250 268.525 Td /F1 9.8 Tf  [(standardized anatomical language, and despite the availability of inexpensive digital photography, phenomic homology is rarely )] TJ ET
BT 26.250 256.620 Td /F1 9.8 Tf  [(documented with images; phylogenetic trees are too often published only as images instead of digital data files that we can read )] TJ ET
BT 26.250 244.716 Td /F1 9.8 Tf  [(into another software package; published trees often contain ambiguities in interpretation due to inconsistencies in methods, )] TJ ET
BT 26.250 232.811 Td /F1 9.8 Tf  [(software, and file formats; and tip labels \(terminal taxa\) in tree files and associated data matrices are not always meaningful or )] TJ ET
BT 26.250 220.906 Td /F1 9.8 Tf  [(comprehensible to anyone outside the original study. Because of these \(and other\) problems, phylogenetic comparative studies )] TJ ET
BT 26.250 209.001 Td /F1 9.8 Tf  [(can be difficult or impossible to replicate or expand upon. When these studies are replicated, inconsistencies can be impossible )] TJ ET
BT 26.250 197.097 Td /F1 9.8 Tf  [(to track down. As a result, advancement in the field is greatly slowed by very preventable issues.)] TJ ET
BT 26.250 177.692 Td /F1 9.8 Tf  [(If you are producing any kind of phylogenetic data as part of your research publications, your data are much more likely to have )] TJ ET
BT 26.250 165.787 Td /F1 9.8 Tf  [(an impact if they are easily understandable and reusable by others. In many cases, the raw data and output files from your )] TJ ET
BT 26.250 153.882 Td /F1 9.8 Tf  [(analysis require additional curation than what has historically been expected in order to ensure that they are easily reusable. )] TJ ET
BT 26.250 141.978 Td /F1 9.8 Tf  [(Here we propose a set of �best practices� for comparative biology. Our best practices include suggestions that will facilitate )] TJ ET
BT 26.250 130.073 Td /F1 9.8 Tf  [(reproduction and reuse of the input and output data from phylogenetic analyses. We encourage practices that enable )] TJ ET
BT 26.250 118.168 Td /F1 9.8 Tf  [(automated curation and access to phylogenetic comparative data. We also emphasize the importance of file validators, curation )] TJ ET
BT 26.250 106.263 Td /F1 9.8 Tf  [(tools, and software that outputs standardized and reusable data.)] TJ ET
BT 26.250 86.859 Td /F1 9.8 Tf  [(The best general solution is to make your data available in a public repository and in a format that has existing parsers )] TJ ET
BT 26.250 74.954 Td /F1 9.8 Tf  [(\(computer programs that can import the file\) and validation tools \(computer programs that determine if the file has valid )] TJ ET
BT 26.250 63.049 Td /F1 9.8 Tf  [(formatting and confirm that the data in the file can be easily extracted\). A variety of parsing tools exist for phylogenetic packages )] TJ ET
BT 26.250 51.144 Td /F1 9.8 Tf  [(such as Mesquite )] TJ ET
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BT 26.250 767.476 Td /F1 9.8 Tf  [(validation by a computer. These new formats represent the future of standardization. Widespread implementation of such )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(formats will eliminate much of the curation work that now wastes the time of many scientists. Although many widely used )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(programs do not currently read and write these new XML formats, the field is moving in a direction to standardize )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(communication and archivation using XML. A compromise that works at present is to publish all of the data in plain text files with )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(documentation that describes the file contents, allowing for downstream use after some manual curation \(Nexus or TNT files, for )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(example, are both plain text format\). Neglecting to publish the data files at all, or requiring extensive reading of the manuscript in )] TJ ET
BT 26.250 696.048 Td /F1 9.8 Tf  [(order to make sense of the data, substantially reduced the interpretability, reusability and, ultimately, the value of your results. )] TJ ET
BT 26.250 684.143 Td /F1 9.8 Tf  [(The following rules give specific examples of how to make your phylogenetic data understandable and how to increase its )] TJ ET
BT 26.250 672.238 Td /F1 9.8 Tf  [(impact. )] TJ ET
0.267 0.267 0.267 rg
BT 60.385 672.238 Td /F1 9.8 Tf  [(Appendix 1)] TJ ET
0.271 0.267 0.267 rg
BT 109.164 672.238 Td /F1 9.8 Tf  [( lists the predominant file formats in phylogenetics and the benefits and downsides of each form.)] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(The following sections list ten simple rules for publishing and sharing phylogenetic data.)] TJ ET
BT 26.250 616.231 Td /F4 12.0 Tf  [(Rule 1: Manage your data as if sharing matters, right from the start)] TJ ET
BT 26.250 596.277 Td /F1 9.8 Tf  [(In the initial stages of your project, think about what you are going to share and in what form. Agree with your co-authors on )] TJ ET
BT 26.250 584.372 Td /F1 9.8 Tf  [(what your data legacy will be, how soon data will be shared, and how the data will be licensed. Do this by asking �What is )] TJ ET
BT 26.250 572.467 Td /F1 9.8 Tf  [(needed to reproduce our results?� Keep track of which versions of the data are actually used in the published analysis. )] TJ ET
BT 26.250 560.562 Td /F1 9.8 Tf  [(Assembling and analyzing your data while being cognizant of data sharing rules \(e.g., writing taxon names in full\) will, in the )] TJ ET
BT 26.250 548.658 Td /F1 9.8 Tf  [(long run, save curation time in the end. Ideally, manage your data package using tools such as github that store old versions )] TJ ET
BT 26.250 536.753 Td /F1 9.8 Tf  [(and allow you to keep notes \(e.g., descriptions of changes\) separate from the document. Resources such as MorphoBank )] TJ ET
BT 26.250 524.848 Td /F1 9.8 Tf  [(support collaboration during the data collection phase, and allow you to release your private data set to a public archive upon )] TJ ET
BT 26.250 512.943 Td /F1 9.8 Tf  [(publication.)] TJ ET
BT 26.250 476.341 Td /F4 12.0 Tf  [(Rule 2: Publish your data \(and not just pictures of your data!\))] TJ ET
BT 26.250 456.387 Td /F1 9.8 Tf  [(The word �publish� has taken on expanded meaning in the digital age. Previously, the most familiar connotation of the word )] TJ ET
BT 26.250 444.482 Td /F1 9.8 Tf  [(�publish� for scientists was to have a paper accepted and presented by a peer-reviewed academic journal. In the age of data )] TJ ET
BT 26.250 432.577 Td /F1 9.8 Tf  [(sharing and digital re-use policies, �publishing your data� means to deposit it in a digital archive that makes the data broadly )] TJ ET
BT 26.250 420.672 Td /F1 9.8 Tf  [(available to the community. A surprising number of phylogenetic studies publish matrices or trees only as a figure in a printed )] TJ ET
BT 26.250 408.768 Td /F1 9.8 Tf  [(journal article, a format that makes reuse at best challenging and often impossible. Publish character matrices, genetic )] TJ ET
BT 26.250 396.863 Td /F1 9.8 Tf  [(sequence alignments, and your phylogenetic trees as one or more digital files in a data repository such as )] TJ ET
0.267 0.267 0.267 rg
BT 484.714 396.863 Td /F1 9.8 Tf  [(TreeBASE)] TJ ET
0.271 0.267 0.267 rg
BT 530.774 396.863 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 536.195 396.863 Td /F1 9.8 Tf  [(Dryad)] TJ ET
0.271 0.267 0.267 rg
BT 562.198 396.863 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 384.958 Td /F1 9.8 Tf  [(MorphoBank)] TJ ET
0.271 0.267 0.267 rg
BT 81.523 384.958 Td /F1 9.8 Tf  [( or a )] TJ ET
0.267 0.267 0.267 rg
BT 103.743 384.958 Td /F1 9.8 Tf  [(DataOne)] TJ ET
0.271 0.267 0.267 rg
BT 142.762 384.958 Td /F1 9.8 Tf  [( member node. Include the kind of data that a colleague would need in order to verify your results, )] TJ ET
BT 26.250 373.053 Td /F1 9.8 Tf  [(build on your analysis, or include your data in a meta-analysis. If a standard format for your type of data is available \(e.g., )] TJ ET
BT 26.250 361.149 Td /F1 9.8 Tf  [(standard alignment formats for DNA\), use it \(see Appendix 1\). In all cases, use plain text formats \(for example, .txt or .csv files\) )] TJ ET
BT 26.250 349.244 Td /F1 9.8 Tf  [(rather than proprietary and non machine-readable formats such as Microsoft Office documents or PDFs.)] TJ ET
BT 26.250 312.641 Td /F4 12.0 Tf  [(Rule 3: CC0 maximizes ease of data reuse)] TJ ET
BT 26.250 292.687 Td /F1 9.8 Tf  [(Input data to a phylogenetic analysis are scientific facts, not subject to copyright, and performing a computational analysis on )] TJ ET
BT 26.250 280.782 Td /F1 9.8 Tf  [(scientific facts does not constitute the type of creative expression subject to copyright law )] TJ ET
0.267 0.267 0.267 rg
BT 413.179 282.290 Td /F4 8.7 Tf  [(24)] TJ ET
0.271 0.267 0.267 rg
BT 422.816 280.782 Td /F1 9.8 Tf  [( . Creative expression, such as )] TJ ET
BT 26.250 268.878 Td /F1 9.8 Tf  [(images, can be subject to copyright. Newer databases and initiatives, such as as )] TJ ET
0.267 0.267 0.267 rg
BT 376.870 268.878 Td /F1 9.8 Tf  [(Dryad)] TJ ET
0.271 0.267 0.267 rg
BT 402.873 268.878 Td /F1 9.8 Tf  [( and )] TJ ET
0.267 0.267 0.267 rg
BT 424.557 268.878 Td /F1 9.8 Tf  [(Open Tree of Life,)] TJ ET
0.271 0.267 0.267 rg
BT 503.142 268.878 Td /F1 9.8 Tf  [( require that )] TJ ET
BT 26.250 256.973 Td /F1 9.8 Tf  [(uploaded data be marked with an explicit )] TJ ET
0.267 0.267 0.267 rg
BT 205.631 256.973 Td /F1 9.8 Tf  [(CC0 waiver)] TJ ET
0.271 0.267 0.267 rg
BT 256.009 256.973 Td /F1 9.8 Tf  [(, which means that the author legally waives any claim to copyright. We )] TJ ET
BT 26.250 245.068 Td /F1 9.8 Tf  [(recommend using the CC0 waiver for phylogenetic data. The Dryad data repository points out )] TJ ET
0.267 0.267 0.267 rg
BT 432.133 245.068 Td /F1 9.8 Tf  [(three key benefits to CC0)] TJ ET
0.271 0.267 0.267 rg
BT 542.142 245.068 Td /F1 9.8 Tf  [(:)] TJ ET
BT 32.206 225.681 Td /F1 9.8 Tf  [(1.)] TJ ET
BT 45.750 225.663 Td /F1 9.8 Tf  [(Interoperability: CC0 is human and machine-readable, allowing people and services to easily determine terms of use.)] TJ ET
BT 32.206 202.526 Td /F1 9.8 Tf  [(1.)] TJ ET
BT 45.750 202.509 Td /F1 9.8 Tf  [(Universality: CC0 is widely recognized, covering all data and all countries.)] TJ ET
BT 32.206 186.872 Td /F1 9.8 Tf  [(2.)] TJ ET
BT 45.750 186.854 Td /F1 9.8 Tf  [(Simplicity: eliminates the need for humans to make, and respond to, individual data requests, allowing scientists to spend )] TJ ET
BT 45.750 174.949 Td /F1 9.8 Tf  [(their time doing science.)] TJ ET
BT 26.250 151.794 Td /F1 9.8 Tf  [(There are mature resources that contain phylogenetic data \(for example, Genbank, TreeBASE or Morphobank\) and have not )] TJ ET
BT 26.250 139.890 Td /F1 9.8 Tf  [(placed copyright licenses or waivers of any kind on gene sequences, trees, matrices and other associated data. It should be )] TJ ET
BT 26.250 127.985 Td /F1 9.8 Tf  [(understood by the phylogenetics community that those databases contain content to be shared and the very reason those )] TJ ET
BT 26.250 116.080 Td /F1 9.8 Tf  [(databases came into existence is to share their content to further scientific research. However, there may be legal issues )] TJ ET
BT 26.250 104.175 Td /F1 9.8 Tf  [(\(beyond the scope of this paper\) that come up when combining data that does not have explicit licensing, waivers or terms of )] TJ ET
BT 26.250 92.271 Td /F1 9.8 Tf  [(use.)] TJ ET
BT 26.250 63.168 Td /F4 12.0 Tf  [(Rule 4: Include a README file in your data package)] TJ ET
BT 26.250 43.214 Td /F1 9.8 Tf  [(A README file is a plain text file that describes the contents of your data package, generally listing each file in the package with )] TJ ET
Q
q
15.000 28.928 577.500 748.072 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(validation by a computer. These new formats represent the future of standardization. Widespread implementation of such )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(formats will eliminate much of the curation work that now wastes the time of many scientists. Although many widely used )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(programs do not currently read and write these new XML formats, the field is moving in a direction to standardize )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(communication and archivation using XML. A compromise that works at present is to publish all of the data in plain text files with )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(documentation that describes the file contents, allowing for downstream use after some manual curation \(Nexus or TNT files, for )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(example, are both plain text format\). Neglecting to publish the data files at all, or requiring extensive reading of the manuscript in )] TJ ET
BT 26.250 696.048 Td /F1 9.8 Tf  [(order to make sense of the data, substantially reduced the interpretability, reusability and, ultimately, the value of your results. )] TJ ET
BT 26.250 684.143 Td /F1 9.8 Tf  [(The following rules give specific examples of how to make your phylogenetic data understandable and how to increase its )] TJ ET
BT 26.250 672.238 Td /F1 9.8 Tf  [(impact. )] TJ ET
0.267 0.267 0.267 rg
BT 60.385 672.238 Td /F1 9.8 Tf  [(Appendix 1)] TJ ET
0.271 0.267 0.267 rg
BT 109.164 672.238 Td /F1 9.8 Tf  [( lists the predominant file formats in phylogenetics and the benefits and downsides of each form.)] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(The following sections list ten simple rules for publishing and sharing phylogenetic data.)] TJ ET
BT 26.250 616.231 Td /F4 12.0 Tf  [(Rule 1: Manage your data as if sharing matters, right from the start)] TJ ET
BT 26.250 596.277 Td /F1 9.8 Tf  [(In the initial stages of your project, think about what you are going to share and in what form. Agree with your co-authors on )] TJ ET
BT 26.250 584.372 Td /F1 9.8 Tf  [(what your data legacy will be, how soon data will be shared, and how the data will be licensed. Do this by asking �What is )] TJ ET
BT 26.250 572.467 Td /F1 9.8 Tf  [(needed to reproduce our results?� Keep track of which versions of the data are actually used in the published analysis. )] TJ ET
BT 26.250 560.562 Td /F1 9.8 Tf  [(Assembling and analyzing your data while being cognizant of data sharing rules \(e.g., writing taxon names in full\) will, in the )] TJ ET
BT 26.250 548.658 Td /F1 9.8 Tf  [(long run, save curation time in the end. Ideally, manage your data package using tools such as github that store old versions )] TJ ET
BT 26.250 536.753 Td /F1 9.8 Tf  [(and allow you to keep notes \(e.g., descriptions of changes\) separate from the document. Resources such as MorphoBank )] TJ ET
BT 26.250 524.848 Td /F1 9.8 Tf  [(support collaboration during the data collection phase, and allow you to release your private data set to a public archive upon )] TJ ET
BT 26.250 512.943 Td /F1 9.8 Tf  [(publication.)] TJ ET
BT 26.250 476.341 Td /F4 12.0 Tf  [(Rule 2: Publish your data \(and not just pictures of your data!\))] TJ ET
BT 26.250 456.387 Td /F1 9.8 Tf  [(The word �publish� has taken on expanded meaning in the digital age. Previously, the most familiar connotation of the word )] TJ ET
BT 26.250 444.482 Td /F1 9.8 Tf  [(�publish� for scientists was to have a paper accepted and presented by a peer-reviewed academic journal. In the age of data )] TJ ET
BT 26.250 432.577 Td /F1 9.8 Tf  [(sharing and digital re-use policies, �publishing your data� means to deposit it in a digital archive that makes the data broadly )] TJ ET
BT 26.250 420.672 Td /F1 9.8 Tf  [(available to the community. A surprising number of phylogenetic studies publish matrices or trees only as a figure in a printed )] TJ ET
BT 26.250 408.768 Td /F1 9.8 Tf  [(journal article, a format that makes reuse at best challenging and often impossible. Publish character matrices, genetic )] TJ ET
BT 26.250 396.863 Td /F1 9.8 Tf  [(sequence alignments, and your phylogenetic trees as one or more digital files in a data repository such as )] TJ ET
0.267 0.267 0.267 rg
BT 484.714 396.863 Td /F1 9.8 Tf  [(TreeBASE)] TJ ET
0.271 0.267 0.267 rg
BT 530.774 396.863 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 536.195 396.863 Td /F1 9.8 Tf  [(Dryad)] TJ ET
0.271 0.267 0.267 rg
BT 562.198 396.863 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 384.958 Td /F1 9.8 Tf  [(MorphoBank)] TJ ET
0.271 0.267 0.267 rg
BT 81.523 384.958 Td /F1 9.8 Tf  [( or a )] TJ ET
0.267 0.267 0.267 rg
BT 103.743 384.958 Td /F1 9.8 Tf  [(DataOne)] TJ ET
0.271 0.267 0.267 rg
BT 142.762 384.958 Td /F1 9.8 Tf  [( member node. Include the kind of data that a colleague would need in order to verify your results, )] TJ ET
BT 26.250 373.053 Td /F1 9.8 Tf  [(build on your analysis, or include your data in a meta-analysis. If a standard format for your type of data is available \(e.g., )] TJ ET
BT 26.250 361.149 Td /F1 9.8 Tf  [(standard alignment formats for DNA\), use it \(see Appendix 1\). In all cases, use plain text formats \(for example, .txt or .csv files\) )] TJ ET
BT 26.250 349.244 Td /F1 9.8 Tf  [(rather than proprietary and non machine-readable formats such as Microsoft Office documents or PDFs.)] TJ ET
BT 26.250 312.641 Td /F4 12.0 Tf  [(Rule 3: CC0 maximizes ease of data reuse)] TJ ET
BT 26.250 292.687 Td /F1 9.8 Tf  [(Input data to a phylogenetic analysis are scientific facts, not subject to copyright, and performing a computational analysis on )] TJ ET
BT 26.250 280.782 Td /F1 9.8 Tf  [(scientific facts does not constitute the type of creative expression subject to copyright law )] TJ ET
0.267 0.267 0.267 rg
BT 413.179 282.290 Td /F4 8.7 Tf  [(24)] TJ ET
0.271 0.267 0.267 rg
BT 422.816 280.782 Td /F1 9.8 Tf  [( . Creative expression, such as )] TJ ET
BT 26.250 268.878 Td /F1 9.8 Tf  [(images, can be subject to copyright. Newer databases and initiatives, such as as )] TJ ET
0.267 0.267 0.267 rg
BT 376.870 268.878 Td /F1 9.8 Tf  [(Dryad)] TJ ET
0.271 0.267 0.267 rg
BT 402.873 268.878 Td /F1 9.8 Tf  [( and )] TJ ET
0.267 0.267 0.267 rg
BT 424.557 268.878 Td /F1 9.8 Tf  [(Open Tree of Life,)] TJ ET
0.271 0.267 0.267 rg
BT 503.142 268.878 Td /F1 9.8 Tf  [( require that )] TJ ET
BT 26.250 256.973 Td /F1 9.8 Tf  [(uploaded data be marked with an explicit )] TJ ET
0.267 0.267 0.267 rg
BT 205.631 256.973 Td /F1 9.8 Tf  [(CC0 waiver)] TJ ET
0.271 0.267 0.267 rg
BT 256.009 256.973 Td /F1 9.8 Tf  [(, which means that the author legally waives any claim to copyright. We )] TJ ET
BT 26.250 245.068 Td /F1 9.8 Tf  [(recommend using the CC0 waiver for phylogenetic data. The Dryad data repository points out )] TJ ET
0.267 0.267 0.267 rg
BT 432.133 245.068 Td /F1 9.8 Tf  [(three key benefits to CC0)] TJ ET
0.271 0.267 0.267 rg
BT 542.142 245.068 Td /F1 9.8 Tf  [(:)] TJ ET
BT 32.206 225.681 Td /F1 9.8 Tf  [(1.)] TJ ET
BT 45.750 225.663 Td /F1 9.8 Tf  [(Interoperability: CC0 is human and machine-readable, allowing people and services to easily determine terms of use.)] TJ ET
BT 32.206 202.526 Td /F1 9.8 Tf  [(1.)] TJ ET
BT 45.750 202.509 Td /F1 9.8 Tf  [(Universality: CC0 is widely recognized, covering all data and all countries.)] TJ ET
BT 32.206 186.872 Td /F1 9.8 Tf  [(2.)] TJ ET
BT 45.750 186.854 Td /F1 9.8 Tf  [(Simplicity: eliminates the need for humans to make, and respond to, individual data requests, allowing scientists to spend )] TJ ET
BT 45.750 174.949 Td /F1 9.8 Tf  [(their time doing science.)] TJ ET
BT 26.250 151.794 Td /F1 9.8 Tf  [(There are mature resources that contain phylogenetic data \(for example, Genbank, TreeBASE or Morphobank\) and have not )] TJ ET
BT 26.250 139.890 Td /F1 9.8 Tf  [(placed copyright licenses or waivers of any kind on gene sequences, trees, matrices and other associated data. It should be )] TJ ET
BT 26.250 127.985 Td /F1 9.8 Tf  [(understood by the phylogenetics community that those databases contain content to be shared and the very reason those )] TJ ET
BT 26.250 116.080 Td /F1 9.8 Tf  [(databases came into existence is to share their content to further scientific research. However, there may be legal issues )] TJ ET
BT 26.250 104.175 Td /F1 9.8 Tf  [(\(beyond the scope of this paper\) that come up when combining data that does not have explicit licensing, waivers or terms of )] TJ ET
BT 26.250 92.271 Td /F1 9.8 Tf  [(use.)] TJ ET
BT 26.250 63.168 Td /F4 12.0 Tf  [(Rule 4: Include a README file in your data package)] TJ ET
BT 26.250 43.214 Td /F1 9.8 Tf  [(A README file is a plain text file that describes the contents of your data package, generally listing each file in the package with )] TJ ET
Q
q
15.000 28.928 577.500 748.072 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(validation by a computer. These new formats represent the future of standardization. Widespread implementation of such )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(formats will eliminate much of the curation work that now wastes the time of many scientists. Although many widely used )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(programs do not currently read and write these new XML formats, the field is moving in a direction to standardize )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(communication and archivation using XML. A compromise that works at present is to publish all of the data in plain text files with )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(documentation that describes the file contents, allowing for downstream use after some manual curation \(Nexus or TNT files, for )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(example, are both plain text format\). Neglecting to publish the data files at all, or requiring extensive reading of the manuscript in )] TJ ET
BT 26.250 696.048 Td /F1 9.8 Tf  [(order to make sense of the data, substantially reduced the interpretability, reusability and, ultimately, the value of your results. )] TJ ET
BT 26.250 684.143 Td /F1 9.8 Tf  [(The following rules give specific examples of how to make your phylogenetic data understandable and how to increase its )] TJ ET
BT 26.250 672.238 Td /F1 9.8 Tf  [(impact. )] TJ ET
0.267 0.267 0.267 rg
BT 60.385 672.238 Td /F1 9.8 Tf  [(Appendix 1)] TJ ET
0.271 0.267 0.267 rg
BT 109.164 672.238 Td /F1 9.8 Tf  [( lists the predominant file formats in phylogenetics and the benefits and downsides of each form.)] TJ ET
BT 26.250 652.833 Td /F1 9.8 Tf  [(The following sections list ten simple rules for publishing and sharing phylogenetic data.)] TJ ET
BT 26.250 616.231 Td /F4 12.0 Tf  [(Rule 1: Manage your data as if sharing matters, right from the start)] TJ ET
BT 26.250 596.277 Td /F1 9.8 Tf  [(In the initial stages of your project, think about what you are going to share and in what form. Agree with your co-authors on )] TJ ET
BT 26.250 584.372 Td /F1 9.8 Tf  [(what your data legacy will be, how soon data will be shared, and how the data will be licensed. Do this by asking �What is )] TJ ET
BT 26.250 572.467 Td /F1 9.8 Tf  [(needed to reproduce our results?� Keep track of which versions of the data are actually used in the published analysis. )] TJ ET
BT 26.250 560.562 Td /F1 9.8 Tf  [(Assembling and analyzing your data while being cognizant of data sharing rules \(e.g., writing taxon names in full\) will, in the )] TJ ET
BT 26.250 548.658 Td /F1 9.8 Tf  [(long run, save curation time in the end. Ideally, manage your data package using tools such as github that store old versions )] TJ ET
BT 26.250 536.753 Td /F1 9.8 Tf  [(and allow you to keep notes \(e.g., descriptions of changes\) separate from the document. Resources such as MorphoBank )] TJ ET
BT 26.250 524.848 Td /F1 9.8 Tf  [(support collaboration during the data collection phase, and allow you to release your private data set to a public archive upon )] TJ ET
BT 26.250 512.943 Td /F1 9.8 Tf  [(publication.)] TJ ET
BT 26.250 476.341 Td /F4 12.0 Tf  [(Rule 2: Publish your data \(and not just pictures of your data!\))] TJ ET
BT 26.250 456.387 Td /F1 9.8 Tf  [(The word �publish� has taken on expanded meaning in the digital age. Previously, the most familiar connotation of the word )] TJ ET
BT 26.250 444.482 Td /F1 9.8 Tf  [(�publish� for scientists was to have a paper accepted and presented by a peer-reviewed academic journal. In the age of data )] TJ ET
BT 26.250 432.577 Td /F1 9.8 Tf  [(sharing and digital re-use policies, �publishing your data� means to deposit it in a digital archive that makes the data broadly )] TJ ET
BT 26.250 420.672 Td /F1 9.8 Tf  [(available to the community. A surprising number of phylogenetic studies publish matrices or trees only as a figure in a printed )] TJ ET
BT 26.250 408.768 Td /F1 9.8 Tf  [(journal article, a format that makes reuse at best challenging and often impossible. Publish character matrices, genetic )] TJ ET
BT 26.250 396.863 Td /F1 9.8 Tf  [(sequence alignments, and your phylogenetic trees as one or more digital files in a data repository such as )] TJ ET
0.267 0.267 0.267 rg
BT 484.714 396.863 Td /F1 9.8 Tf  [(TreeBASE)] TJ ET
0.271 0.267 0.267 rg
BT 530.774 396.863 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 536.195 396.863 Td /F1 9.8 Tf  [(Dryad)] TJ ET
0.271 0.267 0.267 rg
BT 562.198 396.863 Td /F1 9.8 Tf  [(, )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 384.958 Td /F1 9.8 Tf  [(MorphoBank)] TJ ET
0.271 0.267 0.267 rg
BT 81.523 384.958 Td /F1 9.8 Tf  [( or a )] TJ ET
0.267 0.267 0.267 rg
BT 103.743 384.958 Td /F1 9.8 Tf  [(DataOne)] TJ ET
0.271 0.267 0.267 rg
BT 142.762 384.958 Td /F1 9.8 Tf  [( member node. Include the kind of data that a colleague would need in order to verify your results, )] TJ ET
BT 26.250 373.053 Td /F1 9.8 Tf  [(build on your analysis, or include your data in a meta-analysis. If a standard format for your type of data is available \(e.g., )] TJ ET
BT 26.250 361.149 Td /F1 9.8 Tf  [(standard alignment formats for DNA\), use it \(see Appendix 1\). In all cases, use plain text formats \(for example, .txt or .csv files\) )] TJ ET
BT 26.250 349.244 Td /F1 9.8 Tf  [(rather than proprietary and non machine-readable formats such as Microsoft Office documents or PDFs.)] TJ ET
BT 26.250 312.641 Td /F4 12.0 Tf  [(Rule 3: CC0 maximizes ease of data reuse)] TJ ET
BT 26.250 292.687 Td /F1 9.8 Tf  [(Input data to a phylogenetic analysis are scientific facts, not subject to copyright, and performing a computational analysis on )] TJ ET
BT 26.250 280.782 Td /F1 9.8 Tf  [(scientific facts does not constitute the type of creative expression subject to copyright law )] TJ ET
0.267 0.267 0.267 rg
BT 413.179 282.290 Td /F4 8.7 Tf  [(24)] TJ ET
0.271 0.267 0.267 rg
BT 422.816 280.782 Td /F1 9.8 Tf  [( . Creative expression, such as )] TJ ET
BT 26.250 268.878 Td /F1 9.8 Tf  [(images, can be subject to copyright. Newer databases and initiatives, such as as )] TJ ET
0.267 0.267 0.267 rg
BT 376.870 268.878 Td /F1 9.8 Tf  [(Dryad)] TJ ET
0.271 0.267 0.267 rg
BT 402.873 268.878 Td /F1 9.8 Tf  [( and )] TJ ET
0.267 0.267 0.267 rg
BT 424.557 268.878 Td /F1 9.8 Tf  [(Open Tree of Life,)] TJ ET
0.271 0.267 0.267 rg
BT 503.142 268.878 Td /F1 9.8 Tf  [( require that )] TJ ET
BT 26.250 256.973 Td /F1 9.8 Tf  [(uploaded data be marked with an explicit )] TJ ET
0.267 0.267 0.267 rg
BT 205.631 256.973 Td /F1 9.8 Tf  [(CC0 waiver)] TJ ET
0.271 0.267 0.267 rg
BT 256.009 256.973 Td /F1 9.8 Tf  [(, which means that the author legally waives any claim to copyright. We )] TJ ET
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BT 26.250 743.667 Td /F1 9.8 Tf  [(README file for your data package, note that meaningful file names can simplify description of the package and subsequent )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(understanding by reviewers or users.)] TJ ET
BT 26.250 695.159 Td /F4 12.0 Tf  [(Rule 5: Provide meaningful labels for taxa)] TJ ET
BT 26.250 675.205 Td /F1 9.8 Tf  [(The labels that you use for terminal taxa \(�tips�\) in your tree should be meaningful to someone not familiar with your study. )] TJ ET
BT 26.250 663.300 Td /F1 9.8 Tf  [(Avoid using lab codes, abbreviations or common names. Use full taxon names \(not abbreviations like �)] TJ ET
BT 467.886 663.300 Td /F5 9.8 Tf  [(C. elegans)] TJ ET
BT 514.491 663.300 Td /F1 9.8 Tf  [(�\) or use )] TJ ET
BT 26.250 651.396 Td /F1 9.8 Tf  [(identifiers from an online database \(e.g., NCBI, Paleobiology Database\). For studies where Linnaean taxon names are not )] TJ ET
BT 26.250 639.491 Td /F1 9.8 Tf  [(appropriate or not sufficient \(for example, studies that contain multiple individuals per species, studies containing unnamed taxa )] TJ ET
BT 26.250 627.586 Td /F1 9.8 Tf  [(or microbial studies where strain is important\), use a consistent format for names that includes additional information such as )] TJ ET
BT 26.250 615.681 Td /F1 9.8 Tf  [(specimen numbers, strains or accession number. Increasingly, online databases used in phylogenetic work contain information )] TJ ET
BT 26.250 603.777 Td /F1 9.8 Tf  [(about taxa, strains, specimens, etc \(GenBank, PaleoDB, GBIF, SILVA\) and we encourage linking taxon labels to online )] TJ ET
BT 26.250 591.872 Td /F1 9.8 Tf  [(resources to help disambiguate and cross-reference other data. XML file formats allow you to do this within the same file. )] TJ ET
BT 26.250 579.967 Td /F1 9.8 Tf  [(Alternately, provide a mapping file that lists the taxon names in a phylogeny and the corresponding entity in an online resource. )] TJ ET
BT 26.250 568.062 Td /F1 9.8 Tf  [(For phenomic data, MorphoBank provides a single data management and publishing platform that allows dynamic linking of )] TJ ET
BT 26.250 556.158 Td /F1 9.8 Tf  [(taxon labels to online resources.)] TJ ET
BT 26.250 519.555 Td /F4 12.0 Tf  [(Rule 6: Use the same taxon labels across different data elements or files)] TJ ET
BT 26.250 499.601 Td /F1 9.8 Tf  [(The taxon names in your phylogenetic tree should match those in the alignment, character matrix, and other data elements, )] TJ ET
BT 26.250 487.696 Td /F1 9.8 Tf  [(whether they are in the same file or different files. In cases where you must use different taxon labels across your study, include )] TJ ET
BT 26.250 475.791 Td /F1 9.8 Tf  [(explicit information about how one set of labels maps to another. The best solution is to use a file format that allows for this )] TJ ET
BT 26.250 463.887 Td /F1 9.8 Tf  [(mapping within the file \(e.g. NeXML, PhyloML, STK-XML )] TJ ET
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BT 26.250 451.982 Td /F1 9.8 Tf  [(Appendix 1\). An alternate is to include the mapping information in a separate text file.)] TJ ET
BT 26.250 415.379 Td /F4 12.0 Tf  [(Rule 7: Provide all of the data and scripts needed to replicate your analyses)] TJ ET
BT 26.250 395.425 Td /F1 9.8 Tf  [(Rather than simply describing your analysis in the Methods section of a publication, also deposit in a public data repository any )] TJ ET
BT 26.250 383.520 Td /F1 9.8 Tf  [(input files and/or scripts that you used to produce the phylogeny. For example, publishing a MrBayes block, BEAST XML or R )] TJ ET
BT 26.250 371.616 Td /F1 9.8 Tf  [(script ensures that all of the inference parameters and default values are clearly stated. If you ran the analysis using command-)] TJ ET
BT 26.250 359.711 Td /F1 9.8 Tf  [(line options rather than putting the commands in a file, for example with RaXML )] TJ ET
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BT 26.250 347.806 Td /F1 9.8 Tf  [(you used in a README file. Include in the data package all alignment files needed to rerun your analyses. If trees are )] TJ ET
BT 26.250 335.901 Td /F1 9.8 Tf  [(reconstructed from multiple alignments, each alignment should be made available. Which alignment corresponds to which )] TJ ET
BT 26.250 323.997 Td /F1 9.8 Tf  [(published tree should be explicit. In the case of concatenated alignments, provide metadata about the beginning and end of )] TJ ET
BT 26.250 312.092 Td /F1 9.8 Tf  [(each gene \(e.g., in NEXUS, a SETS block with CHARSET or CHARPARTITION commands\).)] TJ ET
BT 26.250 275.489 Td /F4 12.0 Tf  [(Rule 8: Provide information about the tree as well as the tree itself)] TJ ET
BT 26.250 255.535 Td /F1 9.8 Tf  [(A tree topology is difficult to interpret and of minimal use without associated information. The )] TJ ET
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BT 26.250 243.630 Td /F1 9.8 Tf  [(Phylogenetic Analysis)] TJ ET
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BT 26.250 231.726 Td /F1 9.8 Tf  [(as branch lengths, branch length units, support values, and rooting. When publishing your data, ensure that the data package )] TJ ET
BT 26.250 219.821 Td /F1 9.8 Tf  [(contains sufficient information for comprehension and reusability, either in the phylogeny files themselves or in an associated )] TJ ET
BT 26.250 207.916 Td /F1 9.8 Tf  [(README file. Rooting is a particularly problematic annotation, as changes in rooting can greatly impact phylogenetic )] TJ ET
BT 26.250 196.011 Td /F1 9.8 Tf  [(statements, and the tree file output from software is often not rooted in the same way as the figures in the paper. If a tree is )] TJ ET
BT 26.250 184.107 Td /F1 9.8 Tf  [(rooted in the paper, publish your data file with the tree rooted in the same way. It is best to indicate rooting through the )] TJ ET
BT 26.250 172.202 Td /F1 9.8 Tf  [(orientation of the tree itself \(for example, in a Newick string, the outermost parentheses indicate the root\), rather than annotating )] TJ ET
BT 26.250 160.297 Td /F1 9.8 Tf  [(the root separately from the tree structure using software-specific commands \(for example, using the unrooted [&U] annotation )] TJ ET
BT 26.250 148.392 Td /F1 9.8 Tf  [(or stating an outgroup that differs from the rooting implied by the tree structure\).)] TJ ET
BT 26.250 111.790 Td /F4 12.0 Tf  [(Rule 9: Provide complete and easily reusable information about characters, character states, )] TJ ET
BT 26.250 97.138 Td /F4 12.0 Tf  [(and the specimens from which they are derived)] TJ ET
BT 26.250 77.184 Td /F1 9.8 Tf  [(For phenomic matrices \(and combined matrices by extension\), if you need to add a new taxon to an existing matrix or a new set )] TJ ET
BT 26.250 65.279 Td /F1 9.8 Tf  [(of characters to an existing matrix, having easily accessible information about characters and states make the original data )] TJ ET
BT 26.250 53.374 Td /F1 9.8 Tf  [(much easier to expand upon.)] TJ ET
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BT 26.250 731.762 Td /F1 9.8 Tf  [(understanding by reviewers or users.)] TJ ET
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BT 26.250 675.205 Td /F1 9.8 Tf  [(The labels that you use for terminal taxa \(�tips�\) in your tree should be meaningful to someone not familiar with your study. )] TJ ET
BT 26.250 663.300 Td /F1 9.8 Tf  [(Avoid using lab codes, abbreviations or common names. Use full taxon names \(not abbreviations like �)] TJ ET
BT 467.886 663.300 Td /F5 9.8 Tf  [(C. elegans)] TJ ET
BT 514.491 663.300 Td /F1 9.8 Tf  [(�\) or use )] TJ ET
BT 26.250 651.396 Td /F1 9.8 Tf  [(identifiers from an online database \(e.g., NCBI, Paleobiology Database\). For studies where Linnaean taxon names are not )] TJ ET
BT 26.250 639.491 Td /F1 9.8 Tf  [(appropriate or not sufficient \(for example, studies that contain multiple individuals per species, studies containing unnamed taxa )] TJ ET
BT 26.250 627.586 Td /F1 9.8 Tf  [(or microbial studies where strain is important\), use a consistent format for names that includes additional information such as )] TJ ET
BT 26.250 615.681 Td /F1 9.8 Tf  [(specimen numbers, strains or accession number. Increasingly, online databases used in phylogenetic work contain information )] TJ ET
BT 26.250 603.777 Td /F1 9.8 Tf  [(about taxa, strains, specimens, etc \(GenBank, PaleoDB, GBIF, SILVA\) and we encourage linking taxon labels to online )] TJ ET
BT 26.250 591.872 Td /F1 9.8 Tf  [(resources to help disambiguate and cross-reference other data. XML file formats allow you to do this within the same file. )] TJ ET
BT 26.250 579.967 Td /F1 9.8 Tf  [(Alternately, provide a mapping file that lists the taxon names in a phylogeny and the corresponding entity in an online resource. )] TJ ET
BT 26.250 568.062 Td /F1 9.8 Tf  [(For phenomic data, MorphoBank provides a single data management and publishing platform that allows dynamic linking of )] TJ ET
BT 26.250 556.158 Td /F1 9.8 Tf  [(taxon labels to online resources.)] TJ ET
BT 26.250 519.555 Td /F4 12.0 Tf  [(Rule 6: Use the same taxon labels across different data elements or files)] TJ ET
BT 26.250 499.601 Td /F1 9.8 Tf  [(The taxon names in your phylogenetic tree should match those in the alignment, character matrix, and other data elements, )] TJ ET
BT 26.250 487.696 Td /F1 9.8 Tf  [(whether they are in the same file or different files. In cases where you must use different taxon labels across your study, include )] TJ ET
BT 26.250 475.791 Td /F1 9.8 Tf  [(explicit information about how one set of labels maps to another. The best solution is to use a file format that allows for this )] TJ ET
BT 26.250 463.887 Td /F1 9.8 Tf  [(mapping within the file \(e.g. NeXML, PhyloML, STK-XML )] TJ ET
0.267 0.267 0.267 rg
BT 273.880 465.394 Td /F4 8.7 Tf  [(17)] TJ ET
0.271 0.267 0.267 rg
BT 283.518 463.887 Td /F1 9.8 Tf  [( , or a TaxaAssociation block in a Mesquite-style NEXUS file; see )] TJ ET
BT 26.250 451.982 Td /F1 9.8 Tf  [(Appendix 1\). An alternate is to include the mapping information in a separate text file.)] TJ ET
BT 26.250 415.379 Td /F4 12.0 Tf  [(Rule 7: Provide all of the data and scripts needed to replicate your analyses)] TJ ET
BT 26.250 395.425 Td /F1 9.8 Tf  [(Rather than simply describing your analysis in the Methods section of a publication, also deposit in a public data repository any )] TJ ET
BT 26.250 383.520 Td /F1 9.8 Tf  [(input files and/or scripts that you used to produce the phylogeny. For example, publishing a MrBayes block, BEAST XML or R )] TJ ET
BT 26.250 371.616 Td /F1 9.8 Tf  [(script ensures that all of the inference parameters and default values are clearly stated. If you ran the analysis using command-)] TJ ET
BT 26.250 359.711 Td /F1 9.8 Tf  [(line options rather than putting the commands in a file, for example with RaXML )] TJ ET
0.267 0.267 0.267 rg
BT 371.985 361.218 Td /F4 8.7 Tf  [(18)] TJ ET
0.271 0.267 0.267 rg
BT 381.622 359.711 Td /F1 9.8 Tf  [( or Muscle )] TJ ET
0.267 0.267 0.267 rg
BT 429.300 361.218 Td /F4 8.7 Tf  [(19)] TJ ET
0.271 0.267 0.267 rg
BT 438.937 359.711 Td /F1 9.8 Tf  [(, include the full command that )] TJ ET
BT 26.250 347.806 Td /F1 9.8 Tf  [(you used in a README file. Include in the data package all alignment files needed to rerun your analyses. If trees are )] TJ ET
BT 26.250 335.901 Td /F1 9.8 Tf  [(reconstructed from multiple alignments, each alignment should be made available. Which alignment corresponds to which )] TJ ET
BT 26.250 323.997 Td /F1 9.8 Tf  [(published tree should be explicit. In the case of concatenated alignments, provide metadata about the beginning and end of )] TJ ET
BT 26.250 312.092 Td /F1 9.8 Tf  [(each gene \(e.g., in NEXUS, a SETS block with CHARSET or CHARPARTITION commands\).)] TJ ET
BT 26.250 275.489 Td /F4 12.0 Tf  [(Rule 8: Provide information about the tree as well as the tree itself)] TJ ET
BT 26.250 255.535 Td /F1 9.8 Tf  [(A tree topology is difficult to interpret and of minimal use without associated information. The )] TJ ET
0.267 0.267 0.267 rg
BT 427.258 255.535 Td /F1 9.8 Tf  [(Minimum Information About a )] TJ ET
BT 26.250 243.630 Td /F1 9.8 Tf  [(Phylogenetic Analysis)] TJ ET
0.271 0.267 0.267 rg
BT 121.079 243.630 Td /F1 9.8 Tf  [( \(MIAPA\) checklist )] TJ ET
0.267 0.267 0.267 rg
BT 203.427 245.138 Td /F4 8.7 Tf  [(20)] TJ ET
0.271 0.267 0.267 rg
BT 213.064 243.630 Td /F1 9.8 Tf  [( provides a reference list of useful tree annotations. This includes information such )] TJ ET
BT 26.250 231.726 Td /F1 9.8 Tf  [(as branch lengths, branch length units, support values, and rooting. When publishing your data, ensure that the data package )] TJ ET
BT 26.250 219.821 Td /F1 9.8 Tf  [(contains sufficient information for comprehension and reusability, either in the phylogeny files themselves or in an associated )] TJ ET
BT 26.250 207.916 Td /F1 9.8 Tf  [(README file. Rooting is a particularly problematic annotation, as changes in rooting can greatly impact phylogenetic )] TJ ET
BT 26.250 196.011 Td /F1 9.8 Tf  [(statements, and the tree file output from software is often not rooted in the same way as the figures in the paper. If a tree is )] TJ ET
BT 26.250 184.107 Td /F1 9.8 Tf  [(rooted in the paper, publish your data file with the tree rooted in the same way. It is best to indicate rooting through the )] TJ ET
BT 26.250 172.202 Td /F1 9.8 Tf  [(orientation of the tree itself \(for example, in a Newick string, the outermost parentheses indicate the root\), rather than annotating )] TJ ET
BT 26.250 160.297 Td /F1 9.8 Tf  [(the root separately from the tree structure using software-specific commands \(for example, using the unrooted [&U] annotation )] TJ ET
BT 26.250 148.392 Td /F1 9.8 Tf  [(or stating an outgroup that differs from the rooting implied by the tree structure\).)] TJ ET
BT 26.250 111.790 Td /F4 12.0 Tf  [(Rule 9: Provide complete and easily reusable information about characters, character states, )] TJ ET
BT 26.250 97.138 Td /F4 12.0 Tf  [(and the specimens from which they are derived)] TJ ET
BT 26.250 77.184 Td /F1 9.8 Tf  [(For phenomic matrices \(and combined matrices by extension\), if you need to add a new taxon to an existing matrix or a new set )] TJ ET
BT 26.250 65.279 Td /F1 9.8 Tf  [(of characters to an existing matrix, having easily accessible information about characters and states make the original data )] TJ ET
BT 26.250 53.374 Td /F1 9.8 Tf  [(much easier to expand upon.)] TJ ET
Q
q
15.000 43.493 577.500 733.507 re W n
0.271 0.267 0.267 rg
BT 26.250 767.476 Td /F1 9.8 Tf  [(a description of its contents. Dryad has examples of data packages well-documented using README files )] TJ ET
0.267 0.267 0.267 rg
BT 485.231 768.983 Td /F4 8.7 Tf  [(13)] TJ ET
0.271 0.267 0.267 rg
BT 494.869 771.364 Td /F1 8.7 Tf  [(,)] TJ ET
0.267 0.267 0.267 rg
BT 497.278 768.983 Td /F4 8.7 Tf  [(14)] TJ ET
0.271 0.267 0.267 rg
BT 506.915 771.364 Td /F1 8.7 Tf  [(,)] TJ ET
0.267 0.267 0.267 rg
BT 509.325 768.983 Td /F4 8.7 Tf  [(15)] TJ ET
0.271 0.267 0.267 rg
BT 518.962 767.476 Td /F1 9.8 Tf  [( . Such files )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(can also be stored in the Documents folder on MorphoBank )] TJ ET
0.267 0.267 0.267 rg
BT 285.834 757.079 Td /F4 8.7 Tf  [(16)] TJ ET
0.271 0.267 0.267 rg
BT 295.471 755.571 Td /F1 9.8 Tf  [( where they can be shared during peer review. When writing your )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(README file for your data package, note that meaningful file names can simplify description of the package and subsequent )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(understanding by reviewers or users.)] TJ ET
BT 26.250 695.159 Td /F4 12.0 Tf  [(Rule 5: Provide meaningful labels for taxa)] TJ ET
BT 26.250 675.205 Td /F1 9.8 Tf  [(The labels that you use for terminal taxa \(�tips�\) in your tree should be meaningful to someone not familiar with your study. )] TJ ET
BT 26.250 663.300 Td /F1 9.8 Tf  [(Avoid using lab codes, abbreviations or common names. Use full taxon names \(not abbreviations like �)] TJ ET
BT 467.886 663.300 Td /F5 9.8 Tf  [(C. elegans)] TJ ET
BT 514.491 663.300 Td /F1 9.8 Tf  [(�\) or use )] TJ ET
BT 26.250 651.396 Td /F1 9.8 Tf  [(identifiers from an online database \(e.g., NCBI, Paleobiology Database\). For studies where Linnaean taxon names are not )] TJ ET
BT 26.250 639.491 Td /F1 9.8 Tf  [(appropriate or not sufficient \(for example, studies that contain multiple individuals per species, studies containing unnamed taxa )] TJ ET
BT 26.250 627.586 Td /F1 9.8 Tf  [(or microbial studies where strain is important\), use a consistent format for names that includes additional information such as )] TJ ET
BT 26.250 615.681 Td /F1 9.8 Tf  [(specimen numbers, strains or accession number. Increasingly, online databases used in phylogenetic work contain information )] TJ ET
BT 26.250 603.777 Td /F1 9.8 Tf  [(about taxa, strains, specimens, etc \(GenBank, PaleoDB, GBIF, SILVA\) and we encourage linking taxon labels to online )] TJ ET
BT 26.250 591.872 Td /F1 9.8 Tf  [(resources to help disambiguate and cross-reference other data. XML file formats allow you to do this within the same file. )] TJ ET
BT 26.250 579.967 Td /F1 9.8 Tf  [(Alternately, provide a mapping file that lists the taxon names in a phylogeny and the corresponding entity in an online resource. )] TJ ET
BT 26.250 568.062 Td /F1 9.8 Tf  [(For phenomic data, MorphoBank provides a single data management and publishing platform that allows dynamic linking of )] TJ ET
BT 26.250 556.158 Td /F1 9.8 Tf  [(taxon labels to online resources.)] TJ ET
BT 26.250 519.555 Td /F4 12.0 Tf  [(Rule 6: Use the same taxon labels across different data elements or files)] TJ ET
BT 26.250 499.601 Td /F1 9.8 Tf  [(The taxon names in your phylogenetic tree should match those in the alignment, character matrix, and other data elements, )] TJ ET
BT 26.250 487.696 Td /F1 9.8 Tf  [(whether they are in the same file or different files. In cases where you must use different taxon labels across your study, include )] TJ ET
BT 26.250 475.791 Td /F1 9.8 Tf  [(explicit information about how one set of labels maps to another. The best solution is to use a file format that allows for this )] TJ ET
BT 26.250 463.887 Td /F1 9.8 Tf  [(mapping within the file \(e.g. NeXML, PhyloML, STK-XML )] TJ ET
0.267 0.267 0.267 rg
BT 273.880 465.394 Td /F4 8.7 Tf  [(17)] TJ ET
0.271 0.267 0.267 rg
BT 283.518 463.887 Td /F1 9.8 Tf  [( , or a TaxaAssociation block in a Mesquite-style NEXUS file; see )] TJ ET
BT 26.250 451.982 Td /F1 9.8 Tf  [(Appendix 1\). An alternate is to include the mapping information in a separate text file.)] TJ ET
BT 26.250 415.379 Td /F4 12.0 Tf  [(Rule 7: Provide all of the data and scripts needed to replicate your analyses)] TJ ET
BT 26.250 395.425 Td /F1 9.8 Tf  [(Rather than simply describing your analysis in the Methods section of a publication, also deposit in a public data repository any )] TJ ET
BT 26.250 383.520 Td /F1 9.8 Tf  [(input files and/or scripts that you used to produce the phylogeny. For example, publishing a MrBayes block, BEAST XML or R )] TJ ET
BT 26.250 371.616 Td /F1 9.8 Tf  [(script ensures that all of the inference parameters and default values are clearly stated. If you ran the analysis using command-)] TJ ET
BT 26.250 359.711 Td /F1 9.8 Tf  [(line options rather than putting the commands in a file, for example with RaXML )] TJ ET
0.267 0.267 0.267 rg
BT 371.985 361.218 Td /F4 8.7 Tf  [(18)] TJ ET
0.271 0.267 0.267 rg
BT 381.622 359.711 Td /F1 9.8 Tf  [( or Muscle )] TJ ET
0.267 0.267 0.267 rg
BT 429.300 361.218 Td /F4 8.7 Tf  [(19)] TJ ET
0.271 0.267 0.267 rg
BT 438.937 359.711 Td /F1 9.8 Tf  [(, include the full command that )] TJ ET
BT 26.250 347.806 Td /F1 9.8 Tf  [(you used in a README file. Include in the data package all alignment files needed to rerun your analyses. If trees are )] TJ ET
BT 26.250 335.901 Td /F1 9.8 Tf  [(reconstructed from multiple alignments, each alignment should be made available. Which alignment corresponds to which )] TJ ET
BT 26.250 323.997 Td /F1 9.8 Tf  [(published tree should be explicit. In the case of concatenated alignments, provide metadata about the beginning and end of )] TJ ET
BT 26.250 312.092 Td /F1 9.8 Tf  [(each gene \(e.g., in NEXUS, a SETS block with CHARSET or CHARPARTITION commands\).)] TJ ET
BT 26.250 275.489 Td /F4 12.0 Tf  [(Rule 8: Provide information about the tree as well as the tree itself)] TJ ET
BT 26.250 255.535 Td /F1 9.8 Tf  [(A tree topology is difficult to interpret and of minimal use without associated information. The )] TJ ET
0.267 0.267 0.267 rg
BT 427.258 255.535 Td /F1 9.8 Tf  [(Minimum Information About a )] TJ ET
BT 26.250 243.630 Td /F1 9.8 Tf  [(Phylogenetic Analysis)] TJ ET
0.271 0.267 0.267 rg
BT 121.079 243.630 Td /F1 9.8 Tf  [( \(MIAPA\) checklist )] TJ ET
0.267 0.267 0.267 rg
BT 203.427 245.138 Td /F4 8.7 Tf  [(20)] TJ ET
0.271 0.267 0.267 rg
BT 213.064 243.630 Td /F1 9.8 Tf  [( provides a reference list of useful tree annotations. This includes information such )] TJ ET
BT 26.250 231.726 Td /F1 9.8 Tf  [(as branch lengths, branch length units, support values, and rooting. When publishing your data, ensure that the data package )] TJ ET
BT 26.250 219.821 Td /F1 9.8 Tf  [(contains sufficient information for comprehension and reusability, either in the phylogeny files themselves or in an associated )] TJ ET
BT 26.250 207.916 Td /F1 9.8 Tf  [(README file. Rooting is a particularly problematic annotation, as changes in rooting can greatly impact phylogenetic )] TJ ET
BT 26.250 196.011 Td /F1 9.8 Tf  [(statements, and the tree file output from software is often not rooted in the same way as the figures in the paper. If a tree is )] TJ ET
BT 26.250 184.107 Td /F1 9.8 Tf  [(rooted in the paper, publish your data file with the tree rooted in the same way. It is best to indicate rooting through the )] TJ ET
BT 26.250 172.202 Td /F1 9.8 Tf  [(orientation of the tree itself \(for example, in a Newick string, the outermost parentheses indicate the root\), rather than annotating )] TJ ET
BT 26.250 160.297 Td /F1 9.8 Tf  [(the root separately from the tree structure using software-specific commands \(for example, using the unrooted [&U] annotation )] TJ ET
BT 26.250 148.392 Td /F1 9.8 Tf  [(or stating an outgroup that differs from the rooting implied by the tree structure\).)] TJ ET
BT 26.250 111.790 Td /F4 12.0 Tf  [(Rule 9: Provide complete and easily reusable information about characters, character states, )] TJ ET
BT 26.250 97.138 Td /F4 12.0 Tf  [(and the specimens from which they are derived)] TJ ET
BT 26.250 77.184 Td /F1 9.8 Tf  [(For phenomic matrices \(and combined matrices by extension\), if you need to add a new taxon to an existing matrix or a new set )] TJ ET
BT 26.250 65.279 Td /F1 9.8 Tf  [(of characters to an existing matrix, having easily accessible information about characters and states make the original data )] TJ ET
BT 26.250 53.374 Td /F1 9.8 Tf  [(much easier to expand upon.)] 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

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BT 26.250 696.048 Td /F1 9.8 Tf  [(easier to organize this information if a plan to do so is developed at the start of the project, not at the end.)] TJ ET
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BT 45.750 533.658 Td /F1 9.8 Tf  [(Sharing and re-use of phylogenetic trees \(and associated data\) to facilitate synthesis )] TJ ET
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BT 26.250 411.281 Td /F4 12.0 Tf  [(The future of data sharing in phylogenetics)] TJ ET
BT 26.250 391.327 Td /F1 9.8 Tf  [(Our vision in this paper is a future where phylogenetic data are seamlessly archived, shared, reused, and repurposed across a )] TJ ET
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BT 26.250 307.994 Td /F1 9.8 Tf  [(who develop and enforce data sharing requirements; and by end-users, who can embrace the culture of data sharing and reuse )] TJ ET
BT 26.250 296.089 Td /F1 9.8 Tf  [(that promises to transform comparative biology.)] TJ ET
BT 26.250 259.487 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 239.532 Td /F1 9.8 Tf  [(During assembly of these guidelines, we asked the community to contribute rules that would benefit their efforts in phylogenetic )] TJ ET
BT 26.250 227.628 Td /F1 9.8 Tf  [(data publishing, reviewing or integration. The public comment document is available on Figshare \(see references; Cranston )] TJ ET
BT 26.250 215.723 Td /F1 9.8 Tf  [(2014\). We are grateful to the following individuals who contributed via public comment: David Blackburn, Joseph Brown, Alex )] TJ ET
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BT 26.250 180.009 Td /F1 9.8 Tf  [(Vision, Aki Watanabe, Jo Wolfe and April Wright.)] TJ ET
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BT 26.250 627.586 Td /F1 9.8 Tf  [(1\) will change every year. Your data may pose a special challenge for sharing that only you can address. Improve your )] TJ ET
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BT 396.370 572.467 Td /F1 9.8 Tf  [(http://datadryad.org/pages/jdap)] TJ ET
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37.109 560.671 36.925 560.227 36.925 559.780 c
36.925 559.333 37.109 558.889 37.425 558.573 c
37.741 558.258 38.185 558.074 38.631 558.074 c
39.078 558.074 39.522 558.258 39.838 558.573 c
40.154 558.889 40.337 559.333 40.337 559.780 c f
BT 45.750 556.812 Td /F1 9.8 Tf  [(Data archiving in ecology and evolution: best practices )] TJ ET
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BT 283.650 558.320 Td /F4 8.7 Tf  [(21)] TJ ET
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37.109 537.516 36.925 537.072 36.925 536.625 c
36.925 536.179 37.109 535.735 37.425 535.419 c
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39.078 534.919 39.522 535.103 39.838 535.419 c
40.154 535.735 40.337 536.179 40.337 536.625 c f
BT 45.750 533.658 Td /F1 9.8 Tf  [(Sharing and re-use of phylogenetic trees \(and associated data\) to facilitate synthesis )] TJ ET
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37.109 521.861 36.925 521.417 36.925 520.970 c
36.925 520.524 37.109 520.080 37.425 519.764 c
37.741 519.448 38.185 519.264 38.631 519.264 c
39.078 519.264 39.522 519.448 39.838 519.764 c
40.154 520.080 40.337 520.524 40.337 520.970 c f
BT 45.750 518.003 Td /F1 9.8 Tf  [(Open Data and the Social Contract for Scientific Publishing )] TJ ET
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BT 303.160 519.510 Td /F4 8.7 Tf  [(22)] TJ ET
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39.522 506.838 39.078 507.022 38.631 507.022 c
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37.109 506.206 36.925 505.762 36.925 505.316 c
36.925 504.869 37.109 504.425 37.425 504.109 c
37.741 503.793 38.185 503.609 38.631 503.609 c
39.078 503.609 39.522 503.793 39.838 504.109 c
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BT 45.750 502.348 Td /F1 9.8 Tf  [(The Panton Principles: )] TJ ET
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BT 146.546 502.348 Td /F1 9.8 Tf  [(http://pantonprinciples.org/)] TJ ET
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39.522 483.683 39.078 483.867 38.631 483.867 c
38.185 483.867 37.741 483.683 37.425 483.368 c
37.109 483.052 36.925 482.608 36.925 482.161 c
36.925 481.714 37.109 481.270 37.425 480.954 c
37.741 480.639 38.185 480.455 38.631 480.455 c
39.078 480.455 39.522 480.639 39.838 480.954 c
40.154 481.270 40.337 481.714 40.337 482.161 c f
BT 45.750 479.193 Td /F1 9.8 Tf  [(Sharing Publication-Related Data and Materials: Responsibilities of Authorship in the Life Sciences \(National Research )] TJ ET
BT 45.750 467.289 Td /F1 9.8 Tf  [(Council \(US\), 2003\): )] TJ ET
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39.522 456.124 39.078 456.308 38.631 456.308 c
38.185 456.308 37.741 456.124 37.425 455.808 c
37.109 455.492 36.925 455.048 36.925 454.601 c
36.925 454.155 37.109 453.711 37.425 453.395 c
37.741 453.079 38.185 452.895 38.631 452.895 c
39.078 452.895 39.522 453.079 39.838 453.395 c
40.154 453.711 40.337 454.155 40.337 454.601 c f
BT 45.750 451.634 Td /F1 9.8 Tf  [(Data One best practices guide: )] TJ ET
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BT 182.318 451.634 Td /F1 9.8 Tf  [(http://www.dataone.org/all-best-practices)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 411.281 Td /F4 12.0 Tf  [(The future of data sharing in phylogenetics)] TJ ET
BT 26.250 391.327 Td /F1 9.8 Tf  [(Our vision in this paper is a future where phylogenetic data are seamlessly archived, shared, reused, and repurposed across a )] TJ ET
BT 26.250 379.422 Td /F1 9.8 Tf  [(wide variety of projects. This can be facilitated by a few changes in �standard practices� in phylogenetics, many of which are )] TJ ET
BT 26.250 367.518 Td /F1 9.8 Tf  [(already partially underway. For example, analyses will likely move from desktops onto the web; data file formats are already )] TJ ET
BT 26.250 355.613 Td /F1 9.8 Tf  [(moving from structured text, unique to each application, to standardized and validatable files; controlled vocabularies and )] TJ ET
BT 26.250 343.708 Td /F1 9.8 Tf  [(ontologies are providing consistent, machine-readable language across projects; and character data is increasingly tied to )] TJ ET
BT 26.250 331.803 Td /F1 9.8 Tf  [(databases of ontological information and image files that fully describe and document those characters. This transition can be )] TJ ET
BT 26.250 319.899 Td /F1 9.8 Tf  [(aided by software developers, who can write software that uses interoperable data formats; by journal editors and reviewers )] TJ ET
BT 26.250 307.994 Td /F1 9.8 Tf  [(who develop and enforce data sharing requirements; and by end-users, who can embrace the culture of data sharing and reuse )] TJ ET
BT 26.250 296.089 Td /F1 9.8 Tf  [(that promises to transform comparative biology.)] TJ ET
BT 26.250 259.487 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 239.532 Td /F1 9.8 Tf  [(During assembly of these guidelines, we asked the community to contribute rules that would benefit their efforts in phylogenetic )] TJ ET
BT 26.250 227.628 Td /F1 9.8 Tf  [(data publishing, reviewing or integration. The public comment document is available on Figshare \(see references; Cranston )] TJ ET
BT 26.250 215.723 Td /F1 9.8 Tf  [(2014\). We are grateful to the following individuals who contributed via public comment: David Blackburn, Joseph Brown, Alex )] TJ ET
BT 26.250 203.818 Td /F1 9.8 Tf  [(Dececchi, Nick Gardner, Bastian Greshake, Mark Holder, Patricia Holroyd, Randall Irmis, Rutger Jansma, Graeme Lloyd, Paula )] TJ ET
BT 26.250 191.913 Td /F1 9.8 Tf  [(Mabee, Mark Miller, Ross Mounce, Chris Mungall, Jason Pardo, Cynthia Parr, William H. Piel, Arlin Stoltzfus, Wes Turner, Todd )] TJ ET
BT 26.250 180.009 Td /F1 9.8 Tf  [(Vision, Aki Watanabe, Jo Wolfe and April Wright.)] TJ ET
BT 26.250 150.906 Td /F4 12.0 Tf  [(APPENDIX 1)] TJ ET
BT 26.250 113.754 Td /F4 12.0 Tf  [(File formats for phylogenetic data)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 93.800 Td /F1 9.8 Tf  [(Download PDF)] TJ ET
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BT 26.250 57.197 Td /F4 12.0 Tf  [(References)] TJ ET
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BT 26.250 767.476 Td /F1 9.8 Tf  [(Phenomic data are far more reusable if the character names and states are embedded in the same file as the matrix itself, if the )] TJ ET
BT 26.250 755.571 Td /F1 9.8 Tf  [(format being used permits this practice \(e.g., Nexus, TNT\). An impediment to reuse is the storage of a matrix without such )] TJ ET
BT 26.250 743.667 Td /F1 9.8 Tf  [(information and separate pdf or Microsoft Word file with the character names and states. Archive any ordering \(weighting\) rules )] TJ ET
BT 26.250 731.762 Td /F1 9.8 Tf  [(used in the analyses of the character data, either in that file, so that they are readily readable by tree search programs or at the )] TJ ET
BT 26.250 719.857 Td /F1 9.8 Tf  [(very least in a separate file. Whenever practical, include journal citation/source of character state information to each character. )] TJ ET
BT 26.250 707.952 Td /F1 9.8 Tf  [(That way, errors or conflicts can be easily tracked down to the original source and corrected. As noted in the Rule 1, it is much )] TJ ET
BT 26.250 696.048 Td /F1 9.8 Tf  [(easier to organize this information if a plan to do so is developed at the start of the project, not at the end.)] TJ ET
BT 26.250 659.445 Td /F4 12.0 Tf  [(Rule 10: Educate yourself on data management practices in your field)] TJ ET
BT 26.250 639.491 Td /F1 9.8 Tf  [(Technology is changing and standards for data archiving will evolve over time. Formats and databases in use today \(Appendix )] TJ ET
BT 26.250 627.586 Td /F1 9.8 Tf  [(1\) will change every year. Your data may pose a special challenge for sharing that only you can address. Improve your )] TJ ET
BT 26.250 615.681 Td /F1 9.8 Tf  [(expertise by reading what has been written on data archiving in your field and in related fields and by consulting with colleagues )] TJ ET
BT 26.250 603.777 Td /F1 9.8 Tf  [(or the help documentation of different software packages. This list provides a good starting point but is not meant to be )] TJ ET
BT 26.250 591.872 Td /F1 9.8 Tf  [(comprehensive:)] TJ ET
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BT 26.250 411.281 Td /F4 12.0 Tf  [(The future of data sharing in phylogenetics)] TJ ET
BT 26.250 391.327 Td /F1 9.8 Tf  [(Our vision in this paper is a future where phylogenetic data are seamlessly archived, shared, reused, and repurposed across a )] TJ ET
BT 26.250 379.422 Td /F1 9.8 Tf  [(wide variety of projects. This can be facilitated by a few changes in �standard practices� in phylogenetics, many of which are )] TJ ET
BT 26.250 367.518 Td /F1 9.8 Tf  [(already partially underway. For example, analyses will likely move from desktops onto the web; data file formats are already )] TJ ET
BT 26.250 355.613 Td /F1 9.8 Tf  [(moving from structured text, unique to each application, to standardized and validatable files; controlled vocabularies and )] TJ ET
BT 26.250 343.708 Td /F1 9.8 Tf  [(ontologies are providing consistent, machine-readable language across projects; and character data is increasingly tied to )] TJ ET
BT 26.250 331.803 Td /F1 9.8 Tf  [(databases of ontological information and image files that fully describe and document those characters. This transition can be )] TJ ET
BT 26.250 319.899 Td /F1 9.8 Tf  [(aided by software developers, who can write software that uses interoperable data formats; by journal editors and reviewers )] TJ ET
BT 26.250 307.994 Td /F1 9.8 Tf  [(who develop and enforce data sharing requirements; and by end-users, who can embrace the culture of data sharing and reuse )] TJ ET
BT 26.250 296.089 Td /F1 9.8 Tf  [(that promises to transform comparative biology.)] TJ ET
BT 26.250 259.487 Td /F4 12.0 Tf  [(Acknowledgements)] TJ ET
BT 26.250 239.532 Td /F1 9.8 Tf  [(During assembly of these guidelines, we asked the community to contribute rules that would benefit their efforts in phylogenetic )] TJ ET
BT 26.250 227.628 Td /F1 9.8 Tf  [(data publishing, reviewing or integration. The public comment document is available on Figshare \(see references; Cranston )] TJ ET
BT 26.250 215.723 Td /F1 9.8 Tf  [(2014\). We are grateful to the following individuals who contributed via public comment: David Blackburn, Joseph Brown, Alex )] TJ ET
BT 26.250 203.818 Td /F1 9.8 Tf  [(Dececchi, Nick Gardner, Bastian Greshake, Mark Holder, Patricia Holroyd, Randall Irmis, Rutger Jansma, Graeme Lloyd, Paula )] TJ ET
BT 26.250 191.913 Td /F1 9.8 Tf  [(Mabee, Mark Miller, Ross Mounce, Chris Mungall, Jason Pardo, Cynthia Parr, William H. Piel, Arlin Stoltzfus, Wes Turner, Todd )] TJ ET
BT 26.250 180.009 Td /F1 9.8 Tf  [(Vision, Aki Watanabe, Jo Wolfe and April Wright.)] TJ ET
BT 26.250 150.906 Td /F4 12.0 Tf  [(APPENDIX 1)] TJ ET
BT 26.250 113.754 Td /F4 12.0 Tf  [(File formats for phylogenetic data)] TJ ET
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BT 26.250 421.545 Td /F1 9.8 Tf  [(11.)] TJ ET
BT 43.553 421.545 Td /F1 9.8 Tf  [(Vos, R. A., Balhoff, J. P., Caravas, J. A., Holder, M. T., Lapp, H., Maddison, W. P., ... & Stoltzfus, A. \(2012\). NeXML: rich, )] TJ ET
BT 26.250 409.641 Td /F1 9.8 Tf  [(extensible, and verifiable representation of comparative data and metadata. Systematic biology, 61\(4\), 675-689.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 401.155 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 382.605 Td /F1 9.8 Tf  [(12.)] TJ ET
BT 43.553 382.605 Td /F1 9.8 Tf  [(Han, M. V., & Zmasek, C. M. \(2009\). phyloXML: XML for evolutionary biology and comparative genomics. BMC )] TJ ET
BT 26.250 370.700 Td /F1 9.8 Tf  [(bioinformatics, 10\(1\), 356.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 362.214 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 343.664 Td /F1 9.8 Tf  [(13.)] TJ ET
BT 43.553 343.664 Td /F1 9.8 Tf  [(Clark LV, Jasieniuk M \(2012\) Data from: Spontaneous hybrids between native and exotic Rubus in the Western United )] TJ ET
BT 26.250 331.759 Td /F1 9.8 Tf  [(States produce offspring both by apomixis and by sexual recombination. Dryad Digital Repository. doi:10.5061/dryad.m466f)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 323.273 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 304.723 Td /F1 9.8 Tf  [(14.)] TJ ET
BT 43.553 304.723 Td /F1 9.8 Tf  [(Blackwood CB, Smemo KA, Kershner MW, Feinstein LM, Valverde-Barrantes OJ \(2013\) Data from: Decay of ecosystem )] TJ ET
BT 26.250 292.818 Td /F1 9.8 Tf  [(differences and decoupling of tree community-soil environment relationships at ecotones. Dryad Digital Repository. )] TJ ET
BT 26.250 280.914 Td /F1 9.8 Tf  [(doi:10.5061/dryad.85cb4)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 272.428 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 253.878 Td /F1 9.8 Tf  [(15.)] TJ ET
BT 43.553 253.878 Td /F1 9.8 Tf  [(Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR \(2011\) Data from: SAT�-II: very fast and )] TJ ET
BT 26.250 241.973 Td /F1 9.8 Tf  [(accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Dryad Digital Repository. )] TJ ET
BT 26.250 230.068 Td /F1 9.8 Tf  [(doi:10.5061/dryad.n9r3h)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 221.582 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 203.032 Td /F1 9.8 Tf  [(16.)] TJ ET
BT 43.553 203.032 Td /F1 9.8 Tf  [(O'Leary, M. A., Bloch, J. I., Flynn, J. J., Gaudin, T. J., Giallombardo, A., Giannini, N. P., ... & Cirranello, A. L. \(2013\). Data )] TJ ET
BT 26.250 191.127 Td /F1 9.8 Tf  [(from: The placental mammal ancestor and the post�K-Pg radiation of placentals. MorphBank Project 773.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 182.641 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 164.091 Td /F1 9.8 Tf  [(17.)] TJ ET
BT 43.553 164.091 Td /F1 9.8 Tf  [(Davis, K. E., & Hill, J. \(2010\). The supertree tool kit. BMC research notes, 3\(1\), 95.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 155.606 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 137.055 Td /F1 9.8 Tf  [(18.)] TJ ET
BT 43.553 137.055 Td /F1 9.8 Tf  [(Stamatakis, A. \(2014\). RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. )] TJ ET
BT 26.250 125.151 Td /F1 9.8 Tf  [(Bioinformatics, btu033.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 116.665 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 98.115 Td /F1 9.8 Tf  [(19.)] TJ ET
BT 43.553 98.115 Td /F1 9.8 Tf  [(Edgar, R. C. \(2004\). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids )] TJ ET
BT 26.250 86.210 Td /F1 9.8 Tf  [(research, 32\(5\), 1792-1797.)] TJ ET
BT 26.250 66.805 Td /F1 9.8 Tf  [(20.)] TJ ET
BT 43.553 66.805 Td /F1 9.8 Tf  [(Leebens-Mack, J., Vision, T., Brenner, E., Bowers, J. E., Cannon, S., Clement, M. J., ... & Zmasek, C. \(2006\). Taking the )] TJ ET
BT 26.250 54.900 Td /F1 9.8 Tf  [(first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis \(MIAPA\). )] TJ ET
Q
q
15.000 40.615 577.500 736.385 re W n
0.271 0.267 0.267 rg
BT 26.250 759.976 Td /F1 9.8 Tf  [(1.)] TJ ET
BT 38.132 759.976 Td /F1 9.8 Tf  [(Drew, B. T., Gazis, R., Cabezas, P., Swithers, K. S., Deng, J., Rodriguez, R., ... & Soltis, D. E. \(2013\). Lost branches on the )] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(tree of life. PLoS biology, 11\(9\), e1001636.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 739.586 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 721.035 Td /F1 9.8 Tf  [(2.)] TJ ET
BT 38.132 721.035 Td /F1 9.8 Tf  [(Stoltzfus, A., O'meara, B., Whitacre, J., Mounce, R., Gillespie, E. L., Kumar, S., ... & Vos, R. A. \(2012\). Sharing and re-use of )] TJ ET
BT 26.250 709.131 Td /F1 9.8 Tf  [(phylogenetic trees \(and associated data\) to facilitate synthesis. BMC research notes, 5\(1\), 574.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 700.645 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 682.095 Td /F1 9.8 Tf  [(3.)] TJ ET
BT 38.132 682.095 Td /F1 9.8 Tf  [(O�Leary, M. A., & Kaufman, S. \(2011\). MorphoBank: phylophenomics in the �cloud�. Cladistics, 27\(5\), 529-537.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 673.609 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 655.059 Td /F1 9.8 Tf  [(4.)] TJ ET
BT 38.132 655.059 Td /F1 9.8 Tf  [(Parr, C. S., Guralnick, R., Cellinese, N., & Page, R. D. \(2012\). Evolutionary informatics: unifying knowledge about the )] TJ ET
BT 26.250 643.154 Td /F1 9.8 Tf  [(diversity of life. Trends in ecology & evolution, 27\(2\), 94-103.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 634.668 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 616.118 Td /F1 9.8 Tf  [(5.)] TJ ET
BT 38.132 616.118 Td /F1 9.8 Tf  [(Sandve, G. K., Nekrutenko, A., Taylor, J., & Hovig, E. \(2013\). Ten simple rules for reproducible computational research. )] TJ ET
BT 26.250 604.213 Td /F1 9.8 Tf  [(PLoS computational biology, 9\(10\), e1003285.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 595.727 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 577.177 Td /F1 9.8 Tf  [(6.)] TJ ET
BT 38.132 577.177 Td /F1 9.8 Tf  [(Maddison, W. P. and D.R. Maddison. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.75 )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 568.691 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 550.141 Td /F1 9.8 Tf  [(7.)] TJ ET
BT 38.132 550.141 Td /F1 9.8 Tf  [(Swofford, D. L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony \(*and Other Methods\). Version 4. Sinauer Associates, )] TJ ET
BT 26.250 538.236 Td /F1 9.8 Tf  [(Sunderland, Massachusetts)] TJ ET
BT 26.250 518.832 Td /F1 9.8 Tf  [(8.)] TJ ET
BT 38.132 518.832 Td /F1 9.8 Tf  [(Goloboff, P. A., Farris, J. S., & Nixon, K. C. \(2008\). TNT, a free program for phylogenetic analysis. Cladistics, 24\(5\), 774-786.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 510.346 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 491.796 Td /F1 9.8 Tf  [(9.)] TJ ET
BT 38.132 491.796 Td /F1 9.8 Tf  [(Piel, W. H., Donoghue, M. J., Sanderson, M. J., & Netherlands, L. U. T. \(2000\). TreeBASE: a database of phylogenetic )] TJ ET
BT 26.250 479.891 Td /F1 9.8 Tf  [(information. In Proceedings of the 2nd International Workshop of Species 2000.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 471.405 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 452.855 Td /F1 9.8 Tf  [(10.)] TJ ET
BT 43.553 452.855 Td /F1 9.8 Tf  [(Miller, M. A., Pfeiffer, W., & Schwartz, T. \(2011, July\). The CIPRES science gateway: a community resource for )] TJ ET
BT 26.250 440.950 Td /F1 9.8 Tf  [(phylogenetic analyses. In Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery \(p. 41\). ACM.)] TJ ET
BT 26.250 421.545 Td /F1 9.8 Tf  [(11.)] TJ ET
BT 43.553 421.545 Td /F1 9.8 Tf  [(Vos, R. A., Balhoff, J. P., Caravas, J. A., Holder, M. T., Lapp, H., Maddison, W. P., ... & Stoltzfus, A. \(2012\). NeXML: rich, )] TJ ET
BT 26.250 409.641 Td /F1 9.8 Tf  [(extensible, and verifiable representation of comparative data and metadata. Systematic biology, 61\(4\), 675-689.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 401.155 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 382.605 Td /F1 9.8 Tf  [(12.)] TJ ET
BT 43.553 382.605 Td /F1 9.8 Tf  [(Han, M. V., & Zmasek, C. M. \(2009\). phyloXML: XML for evolutionary biology and comparative genomics. BMC )] TJ ET
BT 26.250 370.700 Td /F1 9.8 Tf  [(bioinformatics, 10\(1\), 356.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 362.214 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 343.664 Td /F1 9.8 Tf  [(13.)] TJ ET
BT 43.553 343.664 Td /F1 9.8 Tf  [(Clark LV, Jasieniuk M \(2012\) Data from: Spontaneous hybrids between native and exotic Rubus in the Western United )] TJ ET
BT 26.250 331.759 Td /F1 9.8 Tf  [(States produce offspring both by apomixis and by sexual recombination. Dryad Digital Repository. doi:10.5061/dryad.m466f)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 323.273 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 304.723 Td /F1 9.8 Tf  [(14.)] TJ ET
BT 43.553 304.723 Td /F1 9.8 Tf  [(Blackwood CB, Smemo KA, Kershner MW, Feinstein LM, Valverde-Barrantes OJ \(2013\) Data from: Decay of ecosystem )] TJ ET
BT 26.250 292.818 Td /F1 9.8 Tf  [(differences and decoupling of tree community-soil environment relationships at ecotones. Dryad Digital Repository. )] TJ ET
BT 26.250 280.914 Td /F1 9.8 Tf  [(doi:10.5061/dryad.85cb4)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 272.428 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 253.878 Td /F1 9.8 Tf  [(15.)] TJ ET
BT 43.553 253.878 Td /F1 9.8 Tf  [(Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR \(2011\) Data from: SAT�-II: very fast and )] TJ ET
BT 26.250 241.973 Td /F1 9.8 Tf  [(accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Dryad Digital Repository. )] TJ ET
BT 26.250 230.068 Td /F1 9.8 Tf  [(doi:10.5061/dryad.n9r3h)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 221.582 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 203.032 Td /F1 9.8 Tf  [(16.)] TJ ET
BT 43.553 203.032 Td /F1 9.8 Tf  [(O'Leary, M. A., Bloch, J. I., Flynn, J. J., Gaudin, T. J., Giallombardo, A., Giannini, N. P., ... & Cirranello, A. L. \(2013\). Data )] TJ ET
BT 26.250 191.127 Td /F1 9.8 Tf  [(from: The placental mammal ancestor and the post�K-Pg radiation of placentals. MorphBank Project 773.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 182.641 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 164.091 Td /F1 9.8 Tf  [(17.)] TJ ET
BT 43.553 164.091 Td /F1 9.8 Tf  [(Davis, K. E., & Hill, J. \(2010\). The supertree tool kit. BMC research notes, 3\(1\), 95.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 155.606 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 137.055 Td /F1 9.8 Tf  [(18.)] TJ ET
BT 43.553 137.055 Td /F1 9.8 Tf  [(Stamatakis, A. \(2014\). RAxML Version 8: A tool for Phylogenetic Analysis and Post-Analysis of Large Phylogenies. )] TJ ET
BT 26.250 125.151 Td /F1 9.8 Tf  [(Bioinformatics, btu033.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 116.665 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 98.115 Td /F1 9.8 Tf  [(19.)] TJ ET
BT 43.553 98.115 Td /F1 9.8 Tf  [(Edgar, R. C. \(2004\). MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic acids )] TJ ET
BT 26.250 86.210 Td /F1 9.8 Tf  [(research, 32\(5\), 1792-1797.)] TJ ET
BT 26.250 66.805 Td /F1 9.8 Tf  [(20.)] TJ ET
BT 43.553 66.805 Td /F1 9.8 Tf  [(Leebens-Mack, J., Vision, T., Brenner, E., Bowers, J. E., Cannon, S., Clement, M. J., ... & Zmasek, C. \(2006\). Taking the )] TJ ET
BT 26.250 54.900 Td /F1 9.8 Tf  [(first steps towards a standard for reporting on phylogenies: Minimum Information About a Phylogenetic Analysis \(MIAPA\). )] TJ ET
Q
q
15.000 40.615 577.500 736.385 re W n
0.271 0.267 0.267 rg
BT 26.250 759.976 Td /F1 9.8 Tf  [(1.)] TJ ET
BT 38.132 759.976 Td /F1 9.8 Tf  [(Drew, B. T., Gazis, R., Cabezas, P., Swithers, K. S., Deng, J., Rodriguez, R., ... & Soltis, D. E. \(2013\). Lost branches on the )] TJ ET
BT 26.250 748.071 Td /F1 9.8 Tf  [(tree of life. PLoS biology, 11\(9\), e1001636.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 739.586 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 721.035 Td /F1 9.8 Tf  [(2.)] TJ ET
BT 38.132 721.035 Td /F1 9.8 Tf  [(Stoltzfus, A., O'meara, B., Whitacre, J., Mounce, R., Gillespie, E. L., Kumar, S., ... & Vos, R. A. \(2012\). Sharing and re-use of )] TJ ET
BT 26.250 709.131 Td /F1 9.8 Tf  [(phylogenetic trees \(and associated data\) to facilitate synthesis. BMC research notes, 5\(1\), 574.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 700.645 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 682.095 Td /F1 9.8 Tf  [(3.)] TJ ET
BT 38.132 682.095 Td /F1 9.8 Tf  [(O�Leary, M. A., & Kaufman, S. \(2011\). MorphoBank: phylophenomics in the �cloud�. Cladistics, 27\(5\), 529-537.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 673.609 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 655.059 Td /F1 9.8 Tf  [(4.)] TJ ET
BT 38.132 655.059 Td /F1 9.8 Tf  [(Parr, C. S., Guralnick, R., Cellinese, N., & Page, R. D. \(2012\). Evolutionary informatics: unifying knowledge about the )] TJ ET
BT 26.250 643.154 Td /F1 9.8 Tf  [(diversity of life. Trends in ecology & evolution, 27\(2\), 94-103.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 634.668 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 616.118 Td /F1 9.8 Tf  [(5.)] TJ ET
BT 38.132 616.118 Td /F1 9.8 Tf  [(Sandve, G. K., Nekrutenko, A., Taylor, J., & Hovig, E. \(2013\). Ten simple rules for reproducible computational research. )] TJ ET
BT 26.250 604.213 Td /F1 9.8 Tf  [(PLoS computational biology, 9\(10\), e1003285.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 595.727 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 577.177 Td /F1 9.8 Tf  [(6.)] TJ ET
BT 38.132 577.177 Td /F1 9.8 Tf  [(Maddison, W. P. and D.R. Maddison. 2011. Mesquite: a modular system for evolutionary analysis. Version 2.75 )] TJ ET
0.267 0.267 0.267 rg
BT 26.250 568.691 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 550.141 Td /F1 9.8 Tf  [(7.)] TJ ET
BT 38.132 550.141 Td /F1 9.8 Tf  [(Swofford, D. L. 2002. PAUP*. Phylogenetic Analysis Using Parsimony \(*and Other Methods\). Version 4. Sinauer Associates, )] TJ ET
BT 26.250 538.236 Td /F1 9.8 Tf  [(Sunderland, Massachusetts)] TJ ET
BT 26.250 518.832 Td /F1 9.8 Tf  [(8.)] TJ ET
BT 38.132 518.832 Td /F1 9.8 Tf  [(Goloboff, P. A., Farris, J. S., & Nixon, K. C. \(2008\). TNT, a free program for phylogenetic analysis. Cladistics, 24\(5\), 774-786.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 510.346 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 491.796 Td /F1 9.8 Tf  [(9.)] TJ ET
BT 38.132 491.796 Td /F1 9.8 Tf  [(Piel, W. H., Donoghue, M. J., Sanderson, M. J., & Netherlands, L. U. T. \(2000\). TreeBASE: a database of phylogenetic )] TJ ET
BT 26.250 479.891 Td /F1 9.8 Tf  [(information. In Proceedings of the 2nd International Workshop of Species 2000.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 471.405 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 452.855 Td /F1 9.8 Tf  [(10.)] TJ ET
BT 43.553 452.855 Td /F1 9.8 Tf  [(Miller, M. A., Pfeiffer, W., & Schwartz, T. \(2011, July\). The CIPRES science gateway: a community resource for )] TJ ET
BT 26.250 440.950 Td /F1 9.8 Tf  [(phylogenetic analyses. In Proceedings of the 2011 TeraGrid Conference: Extreme Digital Discovery \(p. 41\). ACM.)] TJ ET
BT 26.250 421.545 Td /F1 9.8 Tf  [(11.)] TJ ET
BT 43.553 421.545 Td /F1 9.8 Tf  [(Vos, R. A., Balhoff, J. P., Caravas, J. A., Holder, M. T., Lapp, H., Maddison, W. P., ... & Stoltzfus, A. \(2012\). NeXML: rich, )] TJ ET
BT 26.250 409.641 Td /F1 9.8 Tf  [(extensible, and verifiable representation of comparative data and metadata. Systematic biology, 61\(4\), 675-689.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 401.155 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 382.605 Td /F1 9.8 Tf  [(12.)] TJ ET
BT 43.553 382.605 Td /F1 9.8 Tf  [(Han, M. V., & Zmasek, C. M. \(2009\). phyloXML: XML for evolutionary biology and comparative genomics. BMC )] TJ ET
BT 26.250 370.700 Td /F1 9.8 Tf  [(bioinformatics, 10\(1\), 356.)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 362.214 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 343.664 Td /F1 9.8 Tf  [(13.)] TJ ET
BT 43.553 343.664 Td /F1 9.8 Tf  [(Clark LV, Jasieniuk M \(2012\) Data from: Spontaneous hybrids between native and exotic Rubus in the Western United )] TJ ET
BT 26.250 331.759 Td /F1 9.8 Tf  [(States produce offspring both by apomixis and by sexual recombination. Dryad Digital Repository. doi:10.5061/dryad.m466f)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 323.273 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 304.723 Td /F1 9.8 Tf  [(14.)] TJ ET
BT 43.553 304.723 Td /F1 9.8 Tf  [(Blackwood CB, Smemo KA, Kershner MW, Feinstein LM, Valverde-Barrantes OJ \(2013\) Data from: Decay of ecosystem )] TJ ET
BT 26.250 292.818 Td /F1 9.8 Tf  [(differences and decoupling of tree community-soil environment relationships at ecotones. Dryad Digital Repository. )] TJ ET
BT 26.250 280.914 Td /F1 9.8 Tf  [(doi:10.5061/dryad.85cb4)] TJ ET
0.267 0.267 0.267 rg
BT 26.250 272.428 Td /F1 7.5 Tf  [(REFERENCE LINK)] TJ ET
0.271 0.267 0.267 rg
BT 26.250 253.878 Td /F1 9.8 Tf  [(15.)] TJ ET
BT 43.553 253.878 Td /F1 9.8 Tf  [(Liu K, Warnow TJ, Holder MT, Nelesen SM, Yu J, Stamatakis AP, Linder CR \(2011\) Data from: SAT�-II: very fast and )] TJ ET
BT 26.250 241.973 Td /F1 9.8 Tf  [(accurate simultaneous estimation of multiple sequence alignments and phylogenetic trees. Dryad Digital Repository. )] TJ ET
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