Figure 1 . Normalized WGS read depth coverage for four population-by-sex samples of individuals (Y-axis) along sex-linked region of Macquarie perch scaffold 633 (SEMN0100063, bases 93050-94150 (X-axis). Dartmouth females- DF (red), Yarra females- YF (orange), Dartmouth males- DM (light blue), Yarra males- YM (dark blue). Vertical lines indicate location of nine sex-linked loci located in this region (yellow- SNP, orange- indels; see Table 4). Mean female:male read depth ratio for these loci was 1.15, 1.13, 0.92, 0.83, 0.72, 0.68, 0.65, 1.49 and 1.07, respectively.
Figure 2 . Read depth coverage for reference and alternative alleles at nine consecutive sex-linked loci on Macquarie perch scaffold 633 region 93182-94017 for four population-by-sex samples: Dartmouth females- DF, Dartmouth males- DM, Yarra females- YF and Yarra males- YM. Dashed horizontal line indicates genome-wide average. Box colours: pink- female, blue- male, reference allele (Ref)- lighter shade, alternative allele (Alt)- darker shade. All loci are XY-homologs, except 93879 is a locus bearing recent-Y-specific polymorphism. PCR-RFLP sexing assay targets the alternative allele at 93229.