Moore Notes 12 15 14

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