Phylogeny provides a mechanism through which to interpret the patterns and processes of evolution and to predict the responses of life to rapid environmental change. Phylogenies and phylogenetic methods are now being used to enhance agriculture, identify and combat diseases, conserve biodiversity, and predict responses to global climate change and to biological invasions.
Summarize existing knowledge into a tree that is:
1. Complete
2. Online
3. Updateable
Original funding (2012 - 2015): 11 PIs, 10 institutions
Supplement (2015 - present): Cranston, Holder, Smith
I. Publishing tree files not a community norm
A git-based data store for community-curated phylogenetic estimates. Bioinformatics (2015) 31 (17): 2794-2800
I. Publishing tree files not a community norm
II. Taxonomy resources are incomplete and out of date
bold = version 2.0
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rotl: R package wraps APIs |
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provides trees given species |
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imports trees for comparative analyses |
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Providing taxonomy feedback |
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Joint workshops, webinars |
U Michigan, September 2014
https://github.com/OpenTreeOfLife/hackathon
U Florida, February 2016
https://blog.opentreeoflife.org/2016/03/09/futurephy-clade-workshops/
Clade | Tips | Phylo tips | % phylo |
---|---|---|---|
Embryophyta | 296,611 | 14,425 | 4.9% |
Fungi | 309,631 | 628 | 0.2% |
Metazoa | 1,467,443 | 21,323 | 1.5% |
Insecta | 979,709 | 3098 | 0.3% |
Incorporate more trees from phylesystem
Import trees from TreeBASE, Dryad
Scrape trees from images
Incorporate more taxonomy feedback / resources
Encourage more community input of trees
Motivating producers of trees to contribute data
https://tree.opentreeoflife.org
Tree visualization
Branch lengths / divergence times
Links back to raw data (sequences, specimens)
Greatly expanding dark parts of the tree
Scientific American, March 2016
Need resources describing OTUs in microbial trees
(aka Tell Me More about “Prevotella dentalis ES 2772 DSM 3688”)
Have process for curating and synthesizing phylogenetic and taxonomic data into comprehensive tree of life
Have data and services available through APIs; in use by biodiversity informatics community
Need to motivate participation of systematics community by providing tools and services