local adaptation

Coop G, Witonsky D, Di Rienzo A & Pritchard JK 2010 Using environmental correlations to identify loci underlying local adaptation. Genetics 185:1411-1423.

• loci involved in local adaptation can potentially be identified by an unusual correlation between allele frequencies and important ecological variables or by extreme allele frequency differences between geographic regions
• such comparisons are complicated by differences in sample sizes and the neutral correlation of allele frequencies across populations due to shared history and gene flow
• we have developed a Bayesian method that estimates the empirical pattern of covariance in allele frequencies between populations from a set of markers and then uses this as a null model for a test at individual SNPs
• the sample frequencies of an allele across populations are drawn from a set of underlying population frequencies