distinguishing between selective sweeps from standing variation and from a de novo mutation区分选择性清洁工从站从新创变异和突变.pdfVIP

Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation 1 1,2 1,2 Benjamin M. Peter *, Emilia Huerta-Sanchez , Rasmus Nielsen 1 Department of Integrative Biology, University of California Berkeley, Berkeley, California, United States of America, 2 Department of Statistics, University of California Berkeley, Berkeley, California, United States of America Abstract 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. Citation: Peter BM, Huerta-Sanchez E, Nielsen R (2012) Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation. PLoS Genet 8(10): e1003011. doi:10.1371/journal.pgen.1003011 Editor: Mikkel H. Schierup, Aarhus University