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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. However, 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. To overcome these difficulties, 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. Graham developed this method in collaboration with David Witonsky, Anna Di Rienzo and Jonathan Pritchard.

Required Modules


  • bayenv

System Variables

  • HPC_BAYENV_DIR - installation directory
  • HPC_BAYENV_BIN - executable directory
  • HPC_BAYENV_DOC - documentation directory
  • HPC_BAYENV_EXE - example directory


If you publish research that uses bayenv you have to cite it as follows:

Coop G., Witonsky D., Di Rienzo A., Pritchard J.K. Using Environmental Correlations to Identify Loci Underlying Local Adaptation. Genetics. 2010