Lessons learned and remaining uncertainties
The lack of XY-gametologous loci in DArT SNPs in either perch species and other fish with homomorphic sex chromosomes (Nguyen et al., 2021) suggests that approaches other than reduced-representation sequencing may be required to identify sex-linked loci in systems with young sex chromosomes. Methylation-sensitive approaches, such as DArTseq, will also have low power in detecting cis-regulatory regions that play a role of sex-determining loci, because these regions might be methylated in adults. Successful detection of a short XY-gametologous locus in Macquarie perch using WGS data also implies that lack of sex-linked markers in reduced-representation data cannot be used as evidence for lack of sex chromosomes in a species. Acquiring WGS data for known-sex samples from other populations will be crucial for improving our understanding of sex determination in this and other percichthyid species. The set of 22 Macquarie perch loci with male-specific alleles (including eight XY-gametologous loci; Fig. 1) may not have the power to predict the genotypic or phenotypic sex in some populations of Macquarie perch, due to fast sex chromosome turnover and/or presence of environmental sex-reversal. At least some of these loci appear to be autosomally-inherited in golden perch, and in more distant relatives from the family Percichthyidae (Murray cod and trout cod), suggesting independent evolution of the Macquarie perch sex-determining locus. However, these properties make these markers a great resource for studying sex chromosome turnover across populations and species.
Whilst SOX1b appears to be a promising novel candidate sex-determining gene, it is possible that we missed other important sex-linked regions due to the highly repetitive nature of the fish genomes precluding efficient short-read mapping, or due to our draft genome missing relevant loci. Alternatively, polygenic sex-determination in Macquarie perch is possible, given the many sex-linked loci detected and some clustering of sex-specific alleles in scaffolds other than 633. In sea bass Dicentrarchus labrax at least four loci are associated with sex determination (Palaiokostas et al., 2015). Also, both XY and ZW sex-determining systems are present on different chromosomes in some Metriaclima cichlids, with epistasis between genotypes at two loci controlling sex (Ser, Roberts, & Kocher, 2010). Three alleles (X, Y, and W) segregate at the sex-determination locus and interact in platyfish Xiphophorus maculatus (Schultheis et al., 2009). Structural genomic variation can also play a major role in adaptation, speciation and sex determination (Mérot, Oomen, Tigano, & Wellenreuther, 2020; Natri et al., 2019), and the role of sex-linked deletions and other structural variants in sex determination of Macquarie perch and other percichthyids remains to be clarified (Appendix H).