PT  - JOURNAL ARTICLE
AU  - Cody Hinchliff
AU  - Stephen A Smith
AU  - James F Allman
AU  - J Gordon Burleigh
AU  - Ruchi Chaudhary
AU  - Lyndon M Cognill
AU  - Keith A Crandall
AU  - Jiabin Deng
AU  - Bryan T Drew
AU  - Romina Gazis
AU  - Karl Gude
AU  - David S Hibbett
AU  - Laura A Katz
AU  - H Dail Laughinghouse IV
AU  - Emily Jane McTavish
AU  - Peter E. Midford
AU  - Christopher L Owen
AU  - Richard Ree
AU  - Jonathan A Rees
AU  - Doug E Soltis
AU  - Tiffani Williams
AU  - Karen Ann Cranston
TI  - Synthesis of phylogeny and taxonomy into a comprehensive tree of life
AID  - 10.1101/012260
DP  - 2015 Jan 01
TA  - bioRxiv
PG  - 012260
4099  - http://biorxiv.org/content/early/2015/07/29/012260.short
4100  - http://biorxiv.org/content/early/2015/07/29/012260.full
AB  - 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: 1) a novel comprehensive global reference taxonomy; and 2) 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. While 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.