Archive for March, 2016

FuturePhy clade workshops

OpenTree, FuturePhy and Arbor jointly held the first round of clade workshops in Gainesville at the end of February.  There were three taxon-focused groups taking part, studying barnacles, beetles, and catfish – each with a very diverse set of participants. Expertise in the room included taxonomy, systematics, ecology, phylogenetic methods, bioinformatics, genomes, ontologies, and scientific illustration (to name a few). While each group had different goals for progress in understanding the biology of their taxon of interest, each group required a unified tree merging taxonomic and phylogenetic information for their clade. Sounds like a job for OpenTree! In advance of the workshop, we created tree collections (ranked lists of published trees in OpenTree) for each clade, and completed the beta version of our new synthesis algorithm. While there was only limited curation of new studies in the lead up to the meeting, during the workshop participants imported more than 40 new published phylogenies into the OpenTree database and curated tree collections. Not only will this burst of skilled curation improve accuracy of the synthetic tree in the future, we were able to use our new rapid synthesis method to produce on-the-fly custom synthesis trees for each clade collection during the workshop. By reviewing these synthetic trees and updating the input trees and rankings, participant groups were able to simultaneously achieve a better understanding of the relationships in their clade of interest, and of the OpenTree synthesis procedure. These clade synthetic trees were an efficient and reproducible methods for providing a unified view of taxon relationships which could then be compared to publications and to expert-curated supertrees produced by grafting existing trees.

On the last day, we asked each group to list the top features they want from OpenTree. This list included:

  • Better conflict visualization – between published input trees, the synthetic tree of life, and the Open Tree Taxonomy
  • Ways to summarize / visualize the annotations file created along with the synthetic tree (this file includes information about sources that support & conflict with each edge).
  • Provide a method for proposing new taxa for tips in a phylogeny that cannot be mapped to OTT (and for collecting supporting information about these new taxa)
  • Include branch length and / or time information in the synthetic tree
  • More fine-grained control over synthesis (be able to mask part of an input tree, suppress poorly-supported branches)

Many thanks to all of the participants, and in particular to Nico Cellinese and Rob Guralnick for local logistics, and to the University of Florida Informatics Institute for hosting. It was an enjoyable and productive meeting for the OpenTree crew, and hopefully for all the attendees!