Julius B. Lucks/Meetings and Notes/SMBE2007/methods population genetics

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Monty Slatkin : The conditional allele frequency spectrum

Wed Jun 27 09:56:11 EDT 2007

  • w/ Svante Pavo

Words to Look Up

  • allele frequency spectrum
  • Gegenbauer polynomials
  • Fesenstein's law - 'Everything that is true is obvious.'


  • summarize large amount polymorphic sequence data from species
  • sample N chromosomes - f_i density of sites i at which i chromosomes carry derived allele
  • consider allele freq spectrum in light of dna sequence of closely-related species
    • neanderthal and human
  • whether neanderthal carriers derived allele or ancestral allele
    • use chimpanzee as an outgroup to decide which is derived and which ancestral
  • use Kimura's diffusion equation on 2 branches - look at joint spectrum
    • assumes randomly mating population
  • in case where have derived allele in neanderthal
    • freq spectrum in species 1 is uniform - indep of pop size and history of pop sizes
  • separated for longer-longer periods - more independant distributions
  • when sample single chrom of neanderthal - as if sampled single chrom from humans