295 François Pompanon and Aurélie Bonin (eds.), Data Production and Analysis in Population Genomics: Methods and Protocols, Methods in Molecular Biology, vol. 888, DOI 10.1007/978-1-61779-870-2_17, © Springer Science+Business Media New York 2012 Chapter 17 Use of Qualitative Environmental and Phenotypic Variables in the Context of Allele Distribution Models: Detecting Signatures of Selection in the Genome of Lake Victoria Cichlids Stéphane Joost, Michael Kalbermatten, Etienne Bezault, and Ole Seehausen Abstract When searching for loci possibly under selection in the genome, an alternative to population genetics theo- retical models is to establish allele distribution models (ADM) for each locus to directly correlate allelic frequencies and environmental variables such as precipitation, temperature, or sun radiation. Such an approach implementing multiple logistic regression models in parallel was implemented within a comput- ing program named MATSAM. Recently, this application was improved in order to support qualitative envi- ronmental predictors as well as to permit the identification of associations between genomic variation and individual phenotypes, allowing the detection of loci involved in the genetic architecture of polymorphic characters. Here, we present the corresponding methodological developments and compare the results produced by software implementing population genetics theoretical models ( DFDIST and BAYESCAN) and ADM ( MATSAM) in an empirical context to detect signatures of genomic divergence associated with specia- tion in Lake Victoria cichlid fishes. Key words: Genome scans, Signature of selection, Genotype × phenotype association, Environmental variables, Logistic regression, Cichlid fishes, Seascape genetics On the basis of data produced by genome scans, the main approach to identify loci under directional selection – or likely to be linked to genomic regions under directional selection – is to use population genetics theoretical models to detect outlier molecular markers showing a larger genetic differentiation than expected under the neutral hypothesis (1–3). 1. Introduction