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The software package Stacks (version 1.20,  as described in the following.
We ran “populations” separately for the lab strain and wild fish, each with defining minimum number of individuals required for a locus in each population as 1 (-p 1) and minimum stack depth required for individuals at a locus as 3 (-m 3) excluding over-merged loci (-B blacklisted markers, generated with a custom python script [ To identify potential sex-associated RAD loci by differences in coverage in male and female genomes, we used the sequencing reads of the two fathers to construct reference loci with ustacks (-m 3, -M 4).
Such degenerated, heteromorphic sex chromosomes are exemplified by the mammalian Y chromosome or the avian W; in contrast to this, sex chromosomes in fish, if present at all, are often homomorphic and differentiation is not detectable by karyotyping , which stands in sharp contrast to other vertebrate clades, especially to birds or mammals, where an entire class shares the same sex chromosomal system with sex being determined at fertilization.
So far, sex determination has been studied only in a small fraction of the over 30,000 described teleost species.
Fish were then fin-clipped and kept for an additional three months to confirm sexing by visual gonad inspection after dissection.
The analysis included the two parents of each cross as well as 28 sons and 27 daughters for the lab strain and 20 sons and 20 daughters for the Chipwa cross.
Here, we investigated the genetic basis of sex determination in a cichlid from Lake Tanganyika, examined here.