Moore Notes 12 15 14

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Group Call

  • Participants: Katie, Tom, Josh, Patrick, Dongying, Guillaume, Sarah, Ladan
  • Call schedule next quarter
    • Mondays at 1:30pm
    • Every other week
    • Jan 12: Ladan
    • Jan 26: Sarah
    • Feb 9: Stephen
  • Shotmap
    • Tom and Stephen iterating
    • Waiting on text/updates from Patrick and Stacia
  • Stephen: project to cluster genomes into species groups
    • Based on sequence identity for a subset of the PhyEco markers
    • About 20K genomes map into 4K species clusters
    • Validated with IMG taxonomy and ANI genome-wide
    • Sharing this resource
      • Can share with group now
      • Plans to post online soon
      • Manuscript? Touch base with Dongying
    • Tom: compare to phylogenetic species concept, Dongying's TreeOTU, PhyloPhlan
  • Tom: Relating phylogenetic structure to ecology (slides)
    • Josh: abundance not equivalent to core/keystone but sampling issues make abundant taxa appear more ubiquitous
      • Also sampling means you can miss clades that are there - check out ecology literature on underestimating prevalence
    • OTU matrices are frequently sparse
    • Katie: Bayesian methods might help (prior probability of seeing a sequence in each sample would help get around sparsity)
    • Stephen: Interesting to look at different levels of prevalence, even endemics
    • Relationships between core, criticality, functional redundancy that isn't phylogenetically correlated