Presentation at Symposium on sharing and delivery of reusable phylogenetic knowledge at TDWG conference 2013, http://wiki.tdwg.org/twiki/bin/view/Phylogenetics/PhyloSharingWorkshop2013
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Assembling a draft overall tree of life from phylogenetic trees and taxonomic databases
1. assembling a draft
overall tree of life from
phylogenetic trees and
taxonomic databases
Jonathan A Rees
US National Evolutionary Synthesis Center
Duke University
rees@nescent.org
TDWG, 31 October 2013
2. software team:
Jim Allman
Joseph Brown
Karen Cranston
Cody Hinchliff
Mark Holder
Jonathan Leto
Emily McTavish
Peter Midford
Rick Ree
Stephen Smith
funding:
US NSF
4. 1. collect phylogenetic trees for best
possible coverage of entire tree of life
Drew BT, Gazis R, Cabezas P, Swithers KS, Deng J, et al. (2013) Lost Branches on the Tree of
Life. PLoS Biol 11(9): e1001636. http://dx.doi.org/10.1371/journal.pbio.1001636
5. 2. normalize tips so that they match
between source trees
label
normalization
Hemsleya amabilis HS454
524163 Hemsleya amabilis
Theria
4267989 Theria in Arthropoda
Nicotiana suaveolans var
excelsior
232354 Nicotiana rotundifolia
Selysia prunifera
949305 Cayaponia prunifera
6. 3. synthesize a single ‘big tree’
algorithmically from the source trees
Smith SA, Brown JW, Hinchliff CE (2013) Analyzing and Synthesizing Phylogenies Using Tree
Alignment Graphs. PLoS Comput Biol 9(9): e1003223. http://dx.doi.org/10.1371/journal.pcbi.1003223
8. exposing provenance
• links to studies
• links to data deposits (e.g. treebase)
• links to taxonomic database records
• methods documentation
• versioning
9. reference taxonomy
• used for normalization, internal node
labeling, gap-filling
• need NCBI taxonomy
• supplement with GBIF
• patch system
• future: other sources
11. lessons
• NeXML and badgerfish are good
• machine-processable tip identity would
be awfully nice
• we were surprised by tree rooting
problem
• provenance is an uphill battle
• to be seen: github for data curation?