Open Tree of Life paper appears in PNAS

At last, the first major synthetic publication from the Open Tree of Life Project has appeared in PNAS. The article has 22 authors*, reflecting the complexity of the endeavor. The centerpiece of the project is a comprehensive tree of life that synthesizes diverse phylogenies, along with a newly-constructed global taxonomy, the “Open Tree Taxonomy” (OTT). The workflow for Open Tree of Life is represented in this figure from the supplement:

fig s1The synthetic tree is available on the Open Tree website, and is represented in this figure from the main text:

fig 1Part C of the figure indicates the number of source phylogenies that support each branch of the synthetic tree. Black lines indicate branches represented by phylogenetic analyses, whereas gray lines represent the parts of the tree supported only by taxonomy. This is a zoomed-out view, where each terminal represents at least 500 descendants; if every tip was a species, then much more of the tree would be gray, reflecting the still very incomplete sampling of known biodiversity in phylogenetic studies.

Mycologists will notice that the Fungi clade is mostly gray, while the flanking clades (animals and plants) are mostly black. This is not because fungal systematists have been inactive. In fact, the GitHub repository (see Fig. S1, above) contains over 1000 curated fungal phylogenies, but only 60 of these phylogenies are incorporated into the current synthesis. We are currently working with our partners in the project to get more fungal trees into the synthetic phylogeny.

Another issue with the fungal portion of Open Tree of Life concerns the taxonomic content of OTT. Most mycologists know that there are roughly 100,000 described species of fungi, but would be surprised to learn that OTT includes about 280,000 tips in the fungal branch of the tree. OTT draws on Index Fungorum, the NCBI taxonomy, and other sources, so the “extra” species (and other terminals) in the fungi reflect synonyms and other questionable entities populating those taxonomic databases. We are currently working to document the distribution of synonyms etc across clades and across databases, but cleaning up those resources is beyond the scope of this project (and will require coordinated effort by the fungal taxonomy community).

Mycologists and others should view the current tree not as a representation of the total knowledge of phylogenetic relationships, but rather as a framework for continued synthesis and augmentation of knowledge of the tree of life.

For the truly interested, I gave a talk on the Open Tree of Life at the The Second International Workshop on Ascomycete Systematics that can be viewed on YouTube.

*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 IV, Emily Jane McTavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams, and Karen A. Cranston. Synthesis of phylogeny and taxonomy into a comprehensive tree of life. PNAS 2015 ; published ahead of print September 18, 2015, doi:10.1073/pnas.1423041112