Moore Notes 10 27 09

Group Call

• JE is making an offer to Guillaume

• Simulation discussion: schedule a skype call for this topic early next week, especially who is going to do what

• Annual Meeting
  • Sessions can take different format
  • Feedback and planning, not just progress updates
  • Each postdoc should plan to lead a ~2 hour session

• Progress report updates
  • Dongying:
    • GEBA Nature paper
      • tree-based selection of genomes for sequencing (100 initial genomes)
      • linear curve for new proteins - many more out there
      • greengenes db is "only the tip of the iceberg"
      • used protein-family identification pipeline (developed for iSEEM)
    • 63 Actinobacterial genomes (18 new from GEBA) as a test of ability to identify universal marker genes for a specific clade
      • 136 candidate markers for this clade
      • MCL clustering: all vs. all blast scores as distances
      • candidate markers: score each cluster (i.e. family) for evenness, universality (using HMM profile to search), phylogenetic informativeness (does taxa tree match gene tree?)
      • greedy (single-linkage) clustering algorithm to add a few more families
      • checked if actually one single copy per genome: most, but not all are
    • Discussion
      • JG: impact of phylogenetic breadth on studies of diversity, e.g. in plant studies
      • JE: could use it for a particular data set to extend the taxonomy (e.g. 16S tree)
      • next steps: apply to metagenomic data
      • TS: Don't yet know if these markers occur outside Actinobacteria, JE: idea is to score marker sets for informativeness in different clades (and not use them for clades where we don't expect them to work)
      • JG: How much Actinobacteria in GOS? JE: not a large fraction in most samples (different from Shewanella contamination issue)
      • JE: may help us look at the rare taxa, SK: yes, this will be helpful if we can normalize for different numbers of sequences
  • Steve: [has given updates on many previous calls, quick update/summary]
    • AMPHORA and RAxML to build phylogenetic tree for HOT/ALOHA depth series data
    • Measure diversity using phylogenetic diversity measure
      • taxanomic diversity does not vary with depth
      • PD does vary with depth (most diversity at intermediate depths)
      • also looked at beta-diversity with UNIFRAC (similar results)
      • results are quite robust (e.g. if use different bootstrap trees)
    • Future work ideas
      • See if Actinobacteria marker genes show a similar pattern
      • See if extended AMPHORA marker gene sets show a similar pattern
      • TS: are there more photosynthetic organisms in the shallow samples?, SK: yes, especially Prochlorococcus, TS: could check if photosynthetic proteins (rather than taxa) show a similar pattern