Moore Notes 4 29 09

Group Chat

• Differences between diversity measures for different gene families and why
  • Knight paper
    • Why joining gene trees at the root? An "average" for UNIFRAC.
    • This is clustering not phylogenetics
    • How to interpret results? How do they know it is parallel loss and HGT (vs. duplication)?

• OTU and OPF finding (e.g. GOS)
  • Schloss paper
    • Josh just wants % similarity as a start
    • related to JG's trait-based biogeography paper
    • Could do protein-family based analyses, but need larger gene set beyond the markers (which shouldn't differ)
      • markers should be like OTUs, other genes might have a different pattern
      • makes sense along a gradient
      • but why should protein richness vary with increasing area?
    • paper idea: OPFs vs. area and OTUs vs. area (are their slopes related?)
      • phylogenetic, taxanomic, functional diversity (3 levels)
      • Is their protein function endism and spatial structure?

• Steve's analysis of DeLong data
  • Wants to compare diversity measures between samples
  • How to "average" diversity over 31 trees?
    • Could concatenate all the gene family alignments
  • Distance measure could be phylogenetically-based, algorithm shouldn't necessarily by tree-based
  • Compare to rRNA tree: bag of genes vs. bag of organisms.
  • Should get the same clustering of communities as Schloss paper, because the marker genes should not be environmentally biased.
    • This could be a test of how good the markers are
  • Not really enough data in DeLong to do this - Need GOS now.

• AMPHORA on GOS
  • CAMERA?
    • JE following up with CAMERA
  • Genbeo?
    • JG will email Srijak and Martin