Assembling, Visualizing, and Analyzing the Tree of Life

Posts tagged “phylogenies

A push for fungal phylogenies in the Open Tree of Life

Screen Shot 2014-09-15 at 1.16.35 PMThe summer of 2014 was a busy one for the mycology group in the Open Tree of Life. Postdoctoral Fellow Romina Gazis gave presentations on the Open Tree of Life at the Annual Meeting of the Mycological Society of America (June 8-12, East Lansing, Michigan) and the International Mycological Congress (Aug. 3-8, Bangkok, Thailand). You can download the IMC presentation here.

Meanwhile, back in Worcester, we continued to compile published phylogenetic trees for incorporation into the Open Tree database. Our goal is to create a synthetic tree that represents, as closely as possible, our current understanding of the broad outlines of fungal phylogenetic relationships, based on molecular studies and taxonomy in Index Fungorum and other sources. We plan to use the tree as the centerpiece of a revision of “higher level” fungal taxonomy, updating a study that we published with seventy coauthors way back in 20071.

Dr. Romina Gazis is a postdoc at Clark University. Dr. Gazis specializes in systematics of endophytes, including symbionts of rubber trees (Hevea brasiliensis) and the newly-described class Xylonomycetes, and also works on phylogenies for the Open Tree of Life project.

Dr. Romina Gazis is a postdoc at Clark University. Dr. Gazis specializes in systematics of endophytes, including symbionts of rubber trees (Hevea brasiliensis) and the newly-described class Xylonomycetes, and also works on phylogenies for the Open Tree of Life project.

To this end, we reviewed the recent and not-so-recent fungal biology literature, emphasizing studies that made a major contribution to understanding of higher-level relationships. We thus identified 314 important studies that are a priority for inclusion in Open Tree of Life. The list of “critical” higher-level studies can be viewed here. Mycologists reading this blog post may wish to check our list of references, and let us know if we have missed anything! Please realize that at this point, we are prioritizing studies that resolve major clades, or that have particularly strong sampling of large groups.

Jiaqi Mei is an undergraduate research assistant at the Katz Lab at Smith College. Jiaqi has been working on gathering information on missing phylogenies for the Open Tree of Life project. Photo: Katz Lab

Having identified the critical higher-level analyses, our next job was to search for the phylogenies in TreeBase and upload them to Open Tree of Life via PhyloGrafter. We were assisted in this time-consuming work by Jiaqi Mei, an undergraduate from Laura Katz’s lab at Smith College who joined us for the summer. 119 of the 314 “higher level” studies (38%) had studies available in TreeBase or other sources. In contrast, Drew et al. (2013)2 found that only about 17% of published phylogenetic studies from all groups have available phylogenies . This evidently demonstrates that mycologists who look at “big picture” phylogenetic relationships are particularly conscientious about data deposition! Nonetheless, there were still many missing phylogenies, so Jiaqi and Romina initiated an e-mail campaign, reaching out to authors of the 195 critical higher-level studies for which we had no trees. We are very grateful to have received responses from almost 50 authors so far. If you are among those who replied to our plea for data, we want to take this opportunity to say Thank You! You should have received a note from us—if not, something may have been lost in transit—please write again!

Our immediate goal is to compile phylogenies that address higher-level relationships, but we are not neglecting fungal studies at low taxonomic levels. In fact, one of Jiaqi’s major tasks was to update our literature review of all fungal phylogenies, reviewing publications since the 2013 study of Drew et al.2, which included studies published up to 2012. Overall, we have identified 2314 fungal phylogenetic studies published since 2000 in 17 journals, of which 640 (28%) have associated treefiles.

It is hard to believe that the Open Tree of Life Project is already in its third year. Our major goal by the end of this academic year is to produce a synthetic phylogenetic tree that significantly updates the 2007 “AFTOL Classification”1 of Fungi, with direct connections to taxonomy and diverse phylogenetic studies. With the continued cooperation of the mycological community we are optimistic that we will reach this goal.

1Hibbett, D. S., M. Binder, J. F. Bischoff, M. Blackwell, P. F. Cannon, O. E. Eriksson, S. Huhndorf, T. James, P. M. Kirk, R. Lücking, T. Lumbsch, F. Lutzoni, P. B. Matheny, D. J. Mclaughlin, M. J. Powell, S. Redhead, C. L. Schoch, J. W. Spatafora, J. A. Stalpers, R. Vilgalys, M. C. Aime, A. Aptroot, R. Bauer, D. Begerow, G. L. Benny, L. A. Castlebury, P. W. Crous, Y.-C. Dai, W. Gams, D. M. Geiser, G. W. Griffith, C. Gueidan, D. L. Hawksworth, G. Hestmark, K. Hosaka, R. A. Humber, K. Hyde, J. E. Ironside, U. Kõljalg, C. P. Kurtzman, K.-H. Larsson, R. Lichtwardt, J. Longcore, J. Miądlikowska, A. Miller, J.-M. Moncalvo, S. Mozley-Standridge, F. Oberwinkler, E. Parmasto, V. Reeb, J. D. Rogers, C. Roux, L. Ryvarden, J. P. Sampaio, A. Schüßler, J. Sugiyama, R. G. Thorn, L. Tibell, W. A. Untereiner, C. Walker, Z. Wang, A. Weir, M. Weiß, M. M. White, K. Winka, Y.-J. Yao, N. Zhang. 2007. A higher-level phylogenetic classification of the Fungi. Mycological Research 111: 509-547. <http://www.clarku.edu/faculty/dhibbett/Reprints%20PDFs/Hibbett_et_al_AFTOL_class_2007.pdf>

2Drew, B.T., R. Gazis, P. Cabezas, K.S. Swithers, J. Deng, R. Rodriguez, L.A. Katz, K.A. Crandall, D.S. Hibbett, D.E. Soltis. 2013. Lost branches on the tree of life. PLOS Biology 11:e1001636. http://www.clarku.edu/faculty/dhibbett/Reprints%20PDFs/added_pdfs_Feb_2013/Drew_et_al_2013_LostBranchesOnTheTreeOfLife_PLOSbiology.pdf

David Hibbett is a professor of biology and PI of the Hibbett lab at Clark University.

Romina Gazis is a postdoc at Clark University. 

 


Building an API for the Open Tree of Life database

Do you want an app for this?

Screen Shot 2012-08-29 at 9.22.20 PMThe developers of the Open Tree of Life would like to know from the phylogenetic community what kind of information they want to extract from its database when the first draft is released later this year. With those preferences, it is possible to develop an API that gives scientists the opportunity to build their own websites or software packages that use the data.

An API (application programming interface) is a digital tool that allows one website or software program to “talk” to another website to dig up certain pieces of data. For instance, a lot of people use Tweetdeck to navigate the ongoing bombardment of messages in the Twittersphere. In that case, Tweetdeck is connecting to Twitter, through its API, to receive and order the messages according to the preferences of the user.

In case of the Open Tree of Life, an API gives researchers advanced access to the data of about two million species, the phylogenies that have been created to illustrate possible relationships between them, and the underlying data and methods of synthesis. “For example, it will be possible to select smaller trees for specific species or find out how many studies there are for a particular node within the database,” says Karen Cranston, the lead investigator of the project. (more…)


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