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, Wake Forest, NC
J. Gordon Burleigh, University of Florida
Ruchi Chaudhary, University of Florida
Lyndon M. Coghill, Field Museum of Natural History, Chicago, IL
Keith A. Crandall, George Washington University
Jiabin Deng, University of Florida
Bryan T. Drew, University of Nebraska-Kearney
Romina Gazis, Clark University
Karl Gude, Michigan State University
David S. Hibbett, Clark University
Laura A. Katz, Smith CollegeFollow
H. Dail Laughinghouse IV, Smith College
Emily Jane McTavish, University of Kansas
Peter E. Midford, Field Museum of Natural History, Chicago, IL
Christopher L. Owen, University of Florida
Richard H. Ree, Field Museum of Natural History, Chicago, IL
Jonathan A. Rees, Duke University
Douglas E. Soltis, University of Florida
Tiffani Williams, Texas A&M University
Karen A. Cranston, Duke University

Document Type

Article

Publication Date

10-13-2015

Publication Title

PNAS

Abstract

Reconstructing the phylogenetic relationships that unite all line- ages (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 tips— 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

phylogeny, taxonomy, tree of life, biodiversity, synthesis

Volume

112

Issue

41

First Page

12764

Last Page

12769

DOI

doi/10.1073/pnas.1423041112

Rights

© 2015 National Academy of Sciences

Comments

Archived as published.

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.; Laughinghouse IV, H. Dail; McTavish, Emily Jane; Midford, Peter E.; Owen, Christopher L.; Ree, Richard H.; Rees, Jonathan A.; Soltis, 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/2