Moore Notes 4 29 09

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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.
    • CAMERA?
      • JE following up with CAMERA
    • Genbeo?
      • JG will email Srijak and Martin