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).