Moore Notes 2 19 14

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Group Call

  • Participants: Katie, Jonathan, Tom, Josh, Stephen, Sarah, Ladan, Guillaume, Dongying
  • Data availability
    • Katie checked with Samantha
      • TARA is under wraps until publications (maybe April)
      • JCVI may release GOS Phase III data to CAMERA - she'll look into it for us
    • Guillaume will check in CAMERA for next call
    • Josh talked to people at GBMF postdoc meeting
      • Cody Sheik who works on deep sea vents
      • Josh talked to MBARI folks who work on submersible robots that collect sea water
  • Spring in-person meeting
    • Samantha Forde cannot attend weeks of Mar 25, Mar 31, Apr 28, May 19 plus Apr 17-18
    • Guillaume gone in June
    • Tom teaching early April until late June
    • Jonathan teaching early April until late June MWF
    • Jonathan going to GBMF on a Tuesday in May
  • Katie in Davis March 31
  • Protein family database meeting last Wednesday (see notes)
    • JGI (Nikos) will be doing 1000 more diverse genomes (GEBA phase 3)
  • Eisen lab seagrass grant funded
    • May include leaf metagenomes from globally sampled grasses
  • Sarah has a new project direction
    • Relevant publication: http://www.pnas.org/content/105/39/15076.full
    • Katie/Tom: gene family duplication and loss can significantly affect unifrac distance
    • Tom: extending this method to metagenomes involves producing taxonomic trees and genome cluster (unifrac) trees across samples
    • Katie: functional stability and convergence questions are very similar to what Patrick is doing with human gut samples
      • Patrick: Turnbaugh's resampling approach involved single genomes and a lot of the variance would wash out in community analysis
    • Jonathan: first look at universal marker genes to see what variance is
    • Sarah: can directly compare unifrac distance matrices without building trees
    • Tom/Katie: check out Sam's paper on tree errors and unifrac http://www.biomedcentral.com/1471-2164/14/419/abstract
    • Josh: good to think about underlying ecological process and neutral models for community assembly
      • Jonathan: what is the time scale? May need better models than the microorganisms ones
      • Ecological and evolutionary time scales are confounded with microbes
      • Josh: community composition as selection of OTUs from a pool vs. evolution of OTUs
      • Jonathan: what is the source pool when a community was assembled? If we don't know this, then it would be hard to disentangle habitat filtering from long term evolution with lateral gene transfer and convergent evolution '
      • Katie: what about thinking about a pool of genes rather than organisms?
      • Do we see a decoupling of taxonomic diversity and gene family diversity and - if so - is it niche selection?
      • Josh: See Elhanan Bornstein's work on sampling networks/pathways
    • Katie: need to think about how to directly, statically compare two or more unifrac distance matrices