Moore GreenLabNotesJan-27-09

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January 27 2009 meeting

Jess Green, Jess Bryant, James O'Dwyer, Steven Kembel

Short term goals

Steve's short term goals

  • develop/modify existing methods/code to measure phylogenetic diversity in metagenomic data sets
  • analyze phylogenetic diversity in metagenomic data sets (deLong), relate phylogenetic diversity to taxonomic diversity, environmental gradients
    • compare different gene families/tree inference methods as part of paper - initial focus on DeLong data
  • evaluate methods for building phylogenetic trees from metagenomic reads
    • we have metagenomic reads and 16S PCR for DeLong from Dongying and Srijak
    • try different tree building methods with these
      • so far the metagenomic reads are very short/fragmented and not placed well on a tree even with use of reference alignment
    • Steve/Jess B. to develop pipeline to do this

James' short term goals

  • develop spatially explicit neutral predictions of phylogenetic diversity (add phylogenetic component to spatial neutral models)
  • develop neutral predictions for more general set of patterns (extend F(r) statitics to higher orders, related similarity metrics (incorporate phylogeny, species area, etc.))

To do

  • circulate phylogenetic diversity measures reviews (Jess chapter, Vamosi et al, Steve EL draft)
  • develop tree building pipeline and share with iSEEM group
    • email Sam/Jenna re: simulations
    • email Srijak/Dongying re: tree building pipelines
  • add pages for individual projects to Green/iSEEM wikis