Smith ScholarWorks

Title

Synthesis of Phylogeny and Taxonomy into a Comprehensive Tree of Life

Authors

Cody E. Hinchliff, University of Michigan, Ann Arbor
Stephen A. Smith, University of Michigan, Ann Arbor
James F. Allman, Interrobang Corporation
J. Gordon Burleigh, University of Florida
Ruchi Chaudhary, University of Florida
Lyndon M. Coghill, Field Museum of Natural History
Keith A. Crandall, The George Washington University
Jiabin Deng, University of Florida
Bryan T. Drew, University of Nebraska at Kearney
Romina Gazis, Clark University
Karl Gude, Michigan State University
David S. Hibbett, Clark University
Laura A. Katz, Smith CollegeFollow
H. Dail Laughinghouse, Smith College
Emily Jane McTavish, University of Kansas, Lawrence
Peter E. Midford, Field Museum of Natural History
Christopher L. Owen, University of Florida
Richard H. Ree, Field Museum of Natural History
Jonathan A. Rees, Duke University
Douglas E. Soltisc, Florida Museum of Natural History
Tiffani Williams, Texas A&M University
Karen A. Cranston, Duke University

Document Type

Article

Publication Date

10-13-2015

Publication Title

Proceedings of the National Academy of Sciences of the United States of America

Abstract

Reconstructing the phylogenetic relationships that unite all lineages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny.We present a draft tree containing 2.3 million tipsâ€" the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. Our open source framework facilitates community comment and contribution, enabling the tree to be continuously updated when new phylogenetic and taxonomic data become digitally available. Although data coverage and phylogenetic conflict across the Open Tree of Life illuminate 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 for community contribution. This comprehensive tree 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, agriculture, and genomics.

Keywords

Biodiversity, Phylogeny, Synthesis, Taxonomy, Tree of life

Volume

112

Issue

41

First Page

12764

Last Page

12769

DOI

10.1073/pnas.1423041112

ISSN

00278424

Comments

Archived as published.

Freely available online through the PNAS open access option.

Recommended Citation

Hinchliff, Cody E.; Smith, Stephen A.; Allman, James F.; Burleigh, J. Gordon; Chaudhary, Ruchi; Coghill, Lyndon M.; Crandall, Keith A.; Deng, Jiabin; Drew, Bryan T.; Gazis, Romina; Gude, Karl; Hibbett, David S.; Katz, Laura A.; Dail Laughinghouse, H.; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltisc, Douglas E.; Williams, Tiffani; and Cranston, Karen A., "Synthesis of Phylogeny and Taxonomy into a Comprehensive Tree of Life" (2015). Biological Sciences: Faculty Publications, Smith College, Northampton, MA.
https://scholarworks.smith.edu/bio_facpubs/97