2.1 Study system, samples and genomic data
The Midas cichlid species complex encompasses a total of — based on genetic clustering (Kautt et al., 2020) — at least 19 genetically distinguishable populations that include the 13 described species (Fig. 1). These include five crater lakes with only one species (Lakes Apoyeque, As. León, As, Managua, Masaya, and Tiscapa), one crater lake with six species (Lake Apoyo), one crater lake with four species (Lake Xiloá), and the great lakes Managua and Nicaragua that both harbor the same set of two species (A. citrinellus and A. labiatus ; Fig. 1). To find species and population-specific markers, we used genotype calls from a previous analysis of 453 re-sequenced Midas cichlid genomes, including all aforementioned species and lake populations (Kautt et al., 2020). Tissue samples were collected during field trips to Nicaragua (years 2003–2018).