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Synthesis of phylogeny and taxonomy into a comprehensive tree of life

Stephen A. Smith, View ORCID ProfileKaren A. Cranston, View ORCID ProfileJames F. Allman, View ORCID ProfileJoseph W. Brown, View ORCID ProfileGordon Burleigh, View ORCID ProfileRuchi Chaudhary, View ORCID ProfileLyndon M. Coghill, View ORCID ProfileKeith A. Crandall, View ORCID ProfileJiabin Deng, View ORCID ProfileBryan T. Drew, View ORCID ProfileRomina Gazis, View ORCID ProfileKarl Gude, View ORCID ProfileDavid S. Hibbett, View ORCID ProfileCody Hinchliff, View ORCID ProfileLaura A. Katz, View ORCID ProfileH. Dail Laughinghouse IV, View ORCID ProfileEmily Jane McTavish, View ORCID ProfileChristopher L. Owen, View ORCID ProfileRichard Ree, View ORCID ProfileJonathan A. Rees, View ORCID ProfileDouglas E. Soltis, View ORCID ProfileTiffani Williams
doi: https://doi.org/10.1101/012260
Stephen A. Smith
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Karen A. Cranston
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James F. Allman
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Joseph W. Brown
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Gordon Burleigh
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Ruchi Chaudhary
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Lyndon M. Coghill
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Keith A. Crandall
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Jiabin Deng
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Bryan T. Drew
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Romina Gazis
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Karl Gude
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David S. Hibbett
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Cody Hinchliff
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Laura A. Katz
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H. Dail Laughinghouse IV
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Emily Jane McTavish
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Christopher L. Owen
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Richard Ree
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Jonathan A. Rees
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Douglas E. Soltis
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Tiffani Williams
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Abstract

Reconstructing the phylogenetic relationships that unite all biological lineages (the tree of life) is a grand challenge of biology. However, the paucity of readily available homologous character data across disparately related lineages renders direct phylogenetic inference currently untenable. Our best recourse towards realizing the tree of life is therefore the synthesis of existing collective phylogenetic knowledge available from the wealth of published primary phylogenetic hypotheses, together with taxonomic hierarchy information for unsampled taxa. We combined phylogenetic and taxonomic data to produce a draft tree of life – the Open Tree of Life – containing 2.3 million tips. Realization of this draft tree required the assembly of two resources that should prove valuable to the community: 1) a novel comprehensive global reference taxonomy, and 2) a database of published phylogenetic trees mapped to this common taxonomy. Our open source framework facilitates community comment and contribution, enabling a continuously updatable tree when new phylogenetic and taxonomic data become digitally available. While data coverage and phylogenetic conflict across the Open Tree of Life illuminates significant gaps in both the underlying data available for phylogenetic reconstruction and the publication of trees as digital objects, the tree provides a compelling starting point from which we can continue to improve through community contributions. Having a comprehensive tree of life will fuel fundamental research on the nature of biological diversity, ultimately providing up-to-date phylogenies for downstream applications in comparative biology, ecology, conservation biology, climate change studies, agriculture, and genomics.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted December 15, 2014.
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Synthesis of phylogeny and taxonomy into a comprehensive tree of life
Stephen A. Smith, Karen A. Cranston, James F. Allman, Joseph W. Brown, Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Cody Hinchliff, Laura A. Katz, H. Dail Laughinghouse IV, Emily Jane McTavish, Christopher L. Owen, Richard Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams
bioRxiv 012260; doi: https://doi.org/10.1101/012260
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Synthesis of phylogeny and taxonomy into a comprehensive tree of life
Stephen A. Smith, Karen A. Cranston, James F. Allman, Joseph W. Brown, Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Cody Hinchliff, Laura A. Katz, H. Dail Laughinghouse IV, Emily Jane McTavish, Christopher L. Owen, Richard Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams
bioRxiv 012260; doi: https://doi.org/10.1101/012260

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