Posts tagged “open data

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. 

 


Karen Cranston talks about open licensing and Dryad

Making scientific data available

 

In case you haven’t seen the video yet, Open Tree of Life investigator Karen Cranston talked about sharing research data in open access data repositories during the Creative Commons 10-year celebration in Raleigh, North Carolina, last December. She mainly focused on the use of CC0 for Dryad, which is a curated general-purpose repository that makes the data underlying scientific publications discoverable and freely reusable. Cranston also mentioned that data availability leads to more citations, which is highly valued in the academic community. You can access the presentation slides as well (link).


Interview with Open Tree of Life investigator

Crandall featured on PeerJ blog

Keith Crandall for bio low resOpen Tree of Life investigator Keith Crandall is featured on the blog of PeerJ, which is a peer-reviewed, open access journal on the Internet. Crandall is an Academic Editor for PeerJ and is the director of the Computational Biology Institute at George Washington University. He was the editor for the “living fossil” manuscript that got much news media attention last week. Here’s the link to the interview.


Connecting millions of data points in a graph database

Creating ‘Facebook’ for species

Neo4j screenshotThe Open Tree of Life database is not just a list with about two million species. Information is added about their special characteristics and possible relationships with others as well. “It may become tens or hundreds of million pieces of data when we are all done.”

Stephen Smith, an evolutionary biology professor at the University of Michigan, is working together with the other researchers of the Open Tree of Life project to develop the programs and tools that will be used to construct the full tree of life. Scientists from all over the world can then synthesize all the information in the database.

“We are currently building the back-end of the Open Tree of Life. We need to create software that allows us to put all our information in a graph network, so that we can easily retrieve the information that researchers are specifically looking for.” (more…)


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