2011 working group Tu iPToL-BIEN Phylogenetics¶

• together with BIEN, doing phylogenetic hypothesis testing
• slow to get a tree to do this
• first tree from iPToL last month
• blending tree with BIEN data
• perpetual tree
• OTU mapping
• use TNRS to take BIEN taxa, iPToL taxa and normalize them so they can be mapped together
• iPToL has ~116,000 names; BIEN has ~22,000 names
• periods, hyphens turned into underscores
• names don't precisely map to taxonomy b/c have gone through encoding for RAXML
• Phylocom (phylomatic software) crashes on invalid names
• using Phylocom for initial pruning of tree
• Biophylo libraries: powerful, but took 5 hours to parse 70,000 name tree
• BIEN names are genus and species for which hyphens are retained
• deleted names from iPToL not found in BIEN list genera (iPToL down to ~44,000 names) and vice versa (BIEN down to ~21,000 names)
• sp taxa handled individually
• TNRS doesn't have sp fungi
• iPToL using NCBI names
• clip tree using MRCA for first pass
• remove suffixes after f, var, subsp, subpp, var nov, x, sp -> canonicalize (sp preserved if no duplicate)
• which iPToL con-generic species can be deleted b/c not in BIEN (BIEN down to ~19,000 names)
• removes names from tree if missing
• don't keep species not in BIEN
• replace species with zero-length polytomy and use for clade (BIEN up to ~20,000 names)
• can't join by higher taxa
• 7000 BIEN names can't be added accurately b/c >1 congeneric name in iPToL
• where to attach nodes
• software says node attaches in a certain place, doesn't give conservative placement
• cultivated hybrids, varieties under one another
• put in clade that gives misleading evolution signal: put at base or tip?
• points to root of subtree, not physically attached
• queries that find reciprocal monophyly
• Dendroscope for viewing phylogenetic trees
• name prefixed w/ O: original tree
• preserve structure inside clades
• interact with database instead of taking tree as input
• Perl script query_vtol.pl: finds MRCA of two species
• Find map names that might descend from MRCA or direct ancestor
• %s in output tell whether could be in clade
• Felsenstein's independent contrast
• discrete or continuous character value for node
• clip out subtree w/ branch names -> Bayesian filter -> randomly put missing species in tree according to branch length
• use that w/ independent contrast or calculations
• clade by clade analysis to get scored value for node
• Phylocom creates giant polytomies, soft polytomies
• instead calculate optimized value w/ optimized trees
• never have tree that perfectly has all BIEN species
• technique to randomly resolve polytomies
• add missing species using skeletal backbone
• TB of data
• missing species: ~19,000 names
• TROPICOS classification
• deeper mapping than genera
• use TNRS API to script it all
• but want whole NCBI tree to clip out non-? plants
• script into pipeline
• forks output into fine, coarse mapping trees
• make pipeline completely automated
• for some eco-phylo questions, more conservative tree
• biases like rare species more likely to be floaters b/c not sequenced
• single vs multi-sequenced trees
• shunk iPToL tree and then expanded it with BIEN
• get original data from matrices of subset to generate support values
• inflate w/ missing BIEN species
• degree of conservatism in geographic trait, range values
• need both trees
• trait evolution: more highly resolved taxa
• communities: catch by genus/family rather than throwing out species
• better tree than what ecologists have available/typically work with
• Phylocom software: genus phylogeny -> create polytomies at tips for species
  • assumes species put into genera correctly
• species-level tree from iPToL -> add missing species
• iPToL: someone works on perpetual tree engine? will e-mail out
• scripts could be moved over to service tacked on to perpetual tree to get BIEN tree
• phylo people don't like own trees b/c worried they are wrong
• supermatrix approach, not supertree
• pull out tree-based data -> parallel supertree
• want to have script that takes big tree and adds timepoints, rate smoothing, age
• data much better than what currently have access to
• NCBI classification -> tree (molecular biology side)
• get use case for what would need to do this on the fly from BIEN
• API to framework?

Afternoon¶

• two groups: science-related and BIEN 3.0
• details of things for BIEN domain: data discussion (across the hall)
  • walk through data structure
  • warehouse database
  • outline of primary constraints
• science group
  • focal areas to continue working
  • outline primary goals