Moore GreenLabNotesJan-27-09

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