†Locus used for PCR-RFLP sexing assay
‡Two females had low read count for these SNPs, but reference allele was present
§One male had low read count for these SNPs but alternative allele was present
Figure 1. Visual summary of individual genotypes for sex-linked loci for 50 individual male Macquarie perch (numbered columns) for scaffold 633 region 90152-94017 (data in Supplementary Material S4). Loci with male-specific alleles: homozygote for the reference allele light blue, heterozygote- intermediate blue, homozygotes for alternative allele- dark blue. XY-gametologs: homozygotes for the reference allele- light yellow, heterozygotes- light orange, homozygotes for alternative allele- dark orange. Loci numbered in red text are XY-gametologous indels, black text-SNPs. All females were homozygous for the reference alleles at these loci (as per colour-coded genotype in the last column). Y-linked alleles for loci 1-13 appear in four distinct linkage patterns: (i) two loci: 1 and 9 (26 males); (ii) ten loci: 2, 3, 5-8, 10-13 (8 males); (iii) 10 loci: 1, 4-8, 10-13 (7 males); and (iv) 4 loci: 1, 7-9 (1 male).