Synthesis of phylogeny and taxonomy into a comprehensive tree of life
Cody E. Hinchliff,Stephen A. Smith,James F. Allman,J. Gordon Burleigh,Ruchi Chaudhary,Lyndon M. Coghill,Keith A. Crandall,Jiabin Deng,Bryan T. Drew,Romina Gazis,Karl Gude,David S. Hibbett,Laura A. Katz,H. Dail Laughinghouse,Emily Jane McTavish,Peter E. Midford,Christopher L. Owen,Richard H. Ree,Jonathan Rees,Douglas E. Soltis,Tiffani L. Williams,Karen Cranston +21 more
TLDR
This study is the first, to the knowledge, to apply an efficient and automated process for assembling published trees into a complete tree of life, and presents a draft tree containing 2.3 million tips—the Open Tree of Life.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.read more
Citations
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Book ChapterDOI
I. the origin of species by means of natural selection
AsaHG Gray,A. Hunter Dupree +1 more
Journal ArticleDOI
BEAST 2.5: An advanced software platform for Bayesian evolutionary analysis.
Remco R. Bouckaert,Remco R. Bouckaert,Timothy G. Vaughan,Timothy G. Vaughan,Joëlle Barido-Sottani,Joëlle Barido-Sottani,Sebastián Duchêne,Mathieu Fourment,Alexandra Gavryushkina,Joseph Heled,Graham Jones,Denise Kühnert,Nicola De Maio,Michael Matschiner,Fábio K. Mendes,Nicola F. Müller,Nicola F. Müller,Huw A. Ogilvie,Louis du Plessis,Alex Popinga,Andrew Rambaut,David A. Rasmussen,Igor Siveroni,Marc A. Suchard,Chieh-Hsi Wu,Dong Xie,Chi Zhang,Tanja Stadler,Tanja Stadler,Alexei J. Drummond +29 more
TL;DR: A series of major new developments in the BEAST 2 core platform and model hierarchy that have occurred since the first release of the software, culminating in the recent 2.5 release are described.
Journal ArticleDOI
A new view of the tree of life
Laura A. Hug,Laura A. Hug,Brett J. Baker,Karthik Anantharaman,Christopher T. Brown,Alexander J. Probst,Cindy J. Castelle,Cristina N. Butterfield,Alex W Hernsdorf,Yuki Amano,Kotaro Ise,Yohey Suzuki,Natasha Dudek,David A. Relman,David A. Relman,Kari M. Finstad,Ronald Amundson,Brian C. Thomas,Jillian F. Banfield,Jillian F. Banfield +19 more
TL;DR: New genomic data from over 1,000 uncultivated and little known organisms, together with published sequences, are used to infer a dramatically expanded version of the tree of life, with Bacteria, Archaea and Eukarya included.
Journal ArticleDOI
How many species of mammals are there
TL;DR: The Mammal Diversity Database (MDD) is presented, a digital, publically accessible, and updateable list of all mammalian species, now available online: https://mammaldiversity.org.
Journal ArticleDOI
Multispecies coalescent delimits structure, not species
Jeet Sukumaran,L. Lacey Knowles +1 more
TL;DR: It is shown that the multispecies coalescent diagnoses genetic structure, not species, and that it does not statistically distinguish structure associated with population isolation vs. species boundaries.
References
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I. the origin of species by means of natural selection
AsaHG Gray,A. Hunter Dupree +1 more
Journal ArticleDOI
The global diversity of birds in space and time
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