Hinchliff, C. E., S. A. Smith, J. F. Allman, J. G. Burleigh, R. Chaudhary, L. M. Coghill, K. A. Crandall, J. Deng, B. T. Drew, R. Gazis, K. Gude, D. S. Hibbett, L. A. Katz, H. D. Laughinghouse, E. J. McTavish, P. E. Midford, C. L. Owen, R. H. Ree, J. A. Rees, D. E. Soltis, T. Williams, and K. A. Cranston. 2015. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 201423041. [View article on publisher’s site]
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 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.