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).