RT Journal Article
SR Electronic
T1 Synthesis of phylogeny and taxonomy into a comprehensive tree of life
JF bioRxiv
FD Cold Spring Harbor Laboratory
SP 012260
DO 10.1101/012260
A1 Stephen A. Smith
A1 Karen A. Cranston
A1 James F. Allman
A1 Joseph W. Brown
A1 Gordon Burleigh
A1 Ruchi Chaudhary
A1 Lyndon M. Coghill
A1 Keith A. Crandall
A1 Jiabin Deng
A1 Bryan T. Drew
A1 Romina Gazis
A1 Karl Gude
A1 David S. Hibbett
A1 Cody Hinchliff
A1 Laura A. Katz
A1 H. Dail Laughinghouse IV
A1 Emily Jane McTavish
A1 Christopher L. Owen
A1 Richard Ree
A1 Jonathan A. Rees
A1 Douglas E. Soltis
A1 Tiffani Williams
YR 2014
UL http://biorxiv.org/content/early/2014/12/05/012260.1.abstract
AB 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.