Moore Notes 7 8 09

Group Call

• Steve: genome-wide trees from gene family trees
  • ML works OK in HOT/ALOHA, does not work in larger data sets
  • how to incorporate differences in rate between gene families/sites
  • Sam saw a paper about improving NJ (will send article)
  • Jenna: can you mark the reference alignments with a correction factor?
  • What would the correction factor be? e.g. Dongying's phylogenetic signal estimates
  • Morgan: what is the goal? Take reads from different families (AMPHORA) and place on genome reference tree.
  • Sam: similar to problem with a read within a gene family

• James & Josh
  • Will talk on Friday about connecting their projects
  • James finishing up theory paper on shape of taxa-area releationship
  • relates to species turn-over with distance
  • goal: to find ways to directly collaborate

• Jenna is in Woods Hole
  • project: taxa area relationships at micron scale
  • generate islands on a slide, drop in bay/pond, laser dissect, sequence 16S in each "plot"
  • Josh: we need data, especially if you separate little plots by different distances
    • Would it be possible to census a slide completely? or on a grid? (like Serpentine data set)

• Sam: simulations
  • fixed bug with Martin
  • AMPHORA only maps some metaSim reads to profile
  • Is it OK to have a random number of reads/taxa per run of simulation? Steve: Yes.
  • How many reads do we want? 5-30,000 reads per gene family
  • How many taxa? Check GOS 16S rRNA species abundance distribution estimates
  • How many reference genomes included? Start with 100-200, uniform? top 100 based on maxPD?
    • don't want to use it for the reads, just the reference genomes (use uniform for reads)

• Josh: GOS OTUs update
  • emailed Quince:
    • they made 16S shotgun read based OTUs
    • but not on a sample-by-sample basis
  • try Rusch?
  • try mapping OTUs back to samples via reads?

• Jenna wants to look at population level variation and simulating that
  • less diverse environment
  • Tom is also thinking about this since there isn't much real data (except e.g. acid mine)
  • could modify Sam's simulator (different input set)
  • possibly with a genome evolution simulator like ROSE

• Annual Meeting
  • possible date: Dec 15-18
  • let JE know if you can't make it then