User:Tara K. Luckau/Notebook/Team ConGen/2011/11/07

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Contents


Structure

  • continued from yesterday ...


Things I learned from chatting with Rulon

  • standard is to run a few iterations of each value of K
  • do NOT unclick "Compute probability of data (for estimating K)" ... this generates the Ln P(D) statistic that is reported in publications
  • can average the Ln P(D) values for each value of K ... the most positive value of Ln P(D) is the K that Structure likes best


  • did it... came up with:
  • averaging the 3 iterations of each value of K ... K=1 gives most positive Ln P(D) ... :(


GENEPOP

Option 1 - Hardy-Weinberg exact test
sub-option 3 - exact tests
Option 2 - Linkage disequilibrium
sub-option 1 - each pair of loci, log likelihood ratio
Option 3 - Population Differentiation
sub-option 3 - genotypic differentiation for all populations
Option 5 - Basic Information
sub-option 1 - basic info (genotypic matrices, number observed/expected homozygoes/heterozygotes, allele frequencies)
  • saved all output to GenePop folder


  • using Riley et al 2006 as framework for which analyses to run
  • they report (in supplement, Table S2) observed and expected heterozygosities for each locus as well as overall
  • where do they get that from GenePop?
    • looks like they gotta calculate it themselves:
Ho = (number observed heterozygotes) / (number observed heterozygotes + number observed homozygotes)
Ho overall = average of each locus Ho
but don't know how they get an 'overall' for each locus - it's not the average


Things I learned from chatting with Rulon

  • try FSTAT ... see if that'll give you Ho straight up



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