A very interesting paper that addresses the question of whether a selective sweep proceeds from standing variation (i.e., an allele already exists in the population, perhaps for a long time, and becomes "advantageous" only when it is paired with the right environmental stimulus), or from a new mutation (i.e., the selection pressure begins first, and a new allele appears by mutation and gets positively selected).
This question is of interest to me, because it might help interpret the occurrence of alleles that may be selected in one core region -where, perhaps, the selection pressure is highest, or they've had the most time to increase in frequency- but also occur at low or even trace frequencies in many more regions.
If selection occurs from standing neutral variation, then the occurrence of the allele in a wide geographical region is not particulary noteworthy; presumably the allele occurred at such frequencies in many places, but became selected in a few.
On the other hand, if an allele occurs from de novo mutation, then it's low frequency occurrence outside its core region is evidence of gene flow, and perhaps recent one. This gene flow may be facilitated by the selection pressure itself (i.e., when people move with the technology, e.g., milk, that creates this pressure in the first place).
PLoS Genet 8(10): e1003011. doi:10.1371/journal.pgen.1003011
Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation
Benjamin M. Peter et al.
An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminating between models of selection and providing estimates of the age of selected alleles and the selection coefficients acting on them. We use simulations to assess the power and accuracy of our method and apply it to seven of the strongest sweeps currently known in humans. We identify two genes, ASPM and PSCA, that are most likely affected by selection on standing variation; and we find three genes, ADH1B, LCT, and EDAR, in which the adaptive alleles seem to have swept from a new mutation. We also confirm evidence of selection for one further gene, TRPV6. In one gene, G6PD, neither neutral models nor models of selective sweeps fit the data, presumably because this locus has been subject to balancing selection.