Moore Notes 10 20 10

Group Call

• Steve: PLoS paper has been in review for 2 months - should hear soon.

• Morgan: Gerstein lab paper uses ARCGIS data - might be useful for niche mapping

• PhylOTU revision
  • Rebecca's streamlining by putting code into C sped it up a lot!
    • Will share code with every one
    • Dongying can use it for pruning large trees
  • Also found tree pruning bug (removeAncestralNode function in BioPerl)
    • This is called by smoothing function
    • Accuracy improves after fixing the bug
    • Scaled threshold is closer to PID threshold, e.g., 0.03 is now 0.06, not 0.15 at 80% accuracy
    • Threshold of 0.15 is 90% accuracy
  • Will redo simulations this week
    • Initial results show little correlation between average PD of sources and accuracy
    • Using SILVA and/or other simulations with many reads compared to number of reference sequences to make sure we cover a good range of PD (an order of magnitude more PD)
  • Will work with Steve to redo the GOS analysis

• Niche mapping
  • Talked to Catherine Graham at Stony Brook about bias in environmental layers
    • Pick layers that you expect to drive diversity
    • Layers shouldn't have pairwise coefficient of determination >0.75
    • Appropriate granularity
  • Using these, picked 15 variables from Reddy et al
    • Only the multiple salinity and multiple temperature variables are highly correlated
    • Pick 8 to use
    • Might want to drop coral and estuary (many zero values globally)
  • May want to add: ocean PH, depth (e.g., area in cell <100m), tidal range
  • Could do more than once with different layers
  • What are the criteria for picking relevant variables?
  • Could add a neutral or random layer is a control
  • Estimation versus model selection etc. (after thresholding)
  • Sampling bias layer can be fed into MaxEnt to correct for this bias
    • Might want to account for size of sample: number of bp or number of reads or measure of species coverage
    • Goal is to remove regions of low diversity due to not sampling
  • Try to wrap this up soon: goal to submit before winter break
  • Journal?
    • General biology journal: Nature, Science, PLoS Biology, PNAS