Tests for sex-linked loci in Macquarie perch WGS-derived SNPs using population-by-sex pools
Cochran-Mantel-Haenszel (CMH) tests applied to four in-silicoMacquarie perch population-by-sex pools tested 1,492,004 SNP loci, of which 4.1% were differentiated p<1e-5 between male and female pools (Supplementary Material S3) and 0.25% had sex-specific alleles in both populations, with a similar number of male- and female-specific alleles (Table 2). The 274,905-bp long scaffold 633 had the most loci with male-specific alleles (40 of 1831), two thirds of which clustered within a ~6.2 Kb region (87120-93327; Appendix B; Table B2). Of 30 SNP loci most strongly differentiated between male and female pools (CMH p<1e-20), nine were loci with male-specific alleles located within a ~3.8-Kb region 90152-94017 of scaffold 633 (Table B1). Of these nine loci, five clustered within a short 146-bp fragment (93182-93327; hereafter, ‘the 146-bp sexing region ’). Fifteen additional scaffolds had smaller clusters of 3-6 loci with male-specific alleles (CMH p<1e-5), and eight scaffolds had clusters of 3-4 loci with female-specific alleles (Appendix B, Table B3).