2.2 Screen for species and population specific variants
To screen for species- and population-specific markers, we estimated population differentiation (FST) for individual SNP loci using vcftools (Danecek et al., 2011) always comparing the respective focal population (ingroup) to all other samples (outgroup) (the workflow is also described in Fig. 2). For Crater Lakes Apoyo and XiloĆ”, we compared the focal species (ingroup) against all other sympatric species (outgroup). For the two great lake species, we used instead genome-wide-association (GWA) data for lip shape, which is a characteristic trait that differs between A. citrinellus andA. labiatus and correlates with FST in both lakes (Kautt et al., 2020). For each species and population, we extracted the 20 variants with the highest differentiation (FST) / genome-wide association (GWA).