population history

Henn BM, Gignoux CR, Jobin M, Granka JM, Macpherson JM, Kidd JM, Rodríguez-Botigué L, Ramachandran S, Hon L, Brisbin A, Lin AA, Underhill PA, Kidd KK, Norman PJ, Parham P, Bustamante CD, Mountain JL & Feldman MW 2011 Hunter-gatherer genomic diversity suggests a southern African origin for modern humans. PNAS 108:5154-5162.

  • we also calculated Fst between clusters using the cluster-specific allele frequencies generated from ADMIXTURE
  • the Fst is estimated here from the cluster-based allele frequencies rather than the population-based frequencies
  • much of the influence of recent migration on our estimates has been removed
  • ancient migration and mis-estimation of cluster-based frequencies are potential sources of bias in this approach
  • admixture between highly diverged populations, such as the Bushmen and Europeans, is likely to be detected and removed
  • LD estimates can be affected by recent admixture
  • we used a second statistic, Fst, to infer the location of origin within Africa
  • Fst was calculated from cluster-specific allele frequencies using the ADMIXTURE software
  • we still detect discrete population membership at k = 14
  • we used the inferred genetic clusters, rather than the population-based allele frequency estimates, to remove the effect of recent migration on Fst
  • this procedure will, for example, minimize the bias of European gene flow on allele frequency estimates from the South African and Namibian Bushmen samples
  • the cluster-based Fst estimate will better reflect the divergence of the Bushman population before arrival of recent migrants
  • this procedure does, however, decrease the number of independent points from 27 in the LD analysis to 13 within Africa
  • given that the Fst estimates are not collinear with the LD decay estimates (because the ADMIXTURE model does not take LD into account), this provides an additional line of evidence for a southern origin for modern humans