Interpretation of variation across marker loci as evidence of selection

Population structure and history have similar effects on the genetic divers ity at all neutral loci. However, some marker loci may also have been stron gly influenced by natural selection. Selection shapes genetic diversity in a locus-specific manner. If we could identify those loci that have responde d to selection during the divergence of populations, then we may obtain bet ter estimates of the parameters of population history by excluding these lo ci. Previous attempts were made to identify outlier loci from the distribut ion of sample statistics under neutral models of population structure and h istory. Unfortunately these methods depend on assumptions about population structure and history that usually cannot be verified. In this article, we define new population-specific parameters of population divergence and cons truct sample statistics that are estimators of these parameters. We then us e the joint distribution of these estimators to identify outlier loci that may be subject to selection. We found that outlier loci are easier to recog nize when this joint distribution is conditioned on the total number of all elic states represented in the pooled sample at each locus. This is so beca use the conditional distribution is less sensitive to the values of nuisanc e parameters.