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
- Katie checked with Samantha
- 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