Tests for sex-linked loci in Macquarie perch WGS-derived SNPs using population-by-sex pools
Median WGS depth coverage for 50 female and 50 male Macquarie perch was 16.3X per sample (range 11.3X- 93.0X; Supplementary Material S1). For the majority (75) of samples, coverage ranged from 11X to 20X; 25 libraries for Dartmouth individuals were re-sequenced due to insufficient yield during the first run, these had a range of coverage from 32X to 57X, with one outlier of 92X coverage.
Cochran-Mantel-Haenszel (CMH) tests applied to four pooled population-by-sex samples (each comprising 25 million paired-end reads in each of 25 individuals) detected 30 SNP loci strongly (p<1e-20) differentiated between males and females in all four population-by-sex comparisons (Table 3). Of these, 10 SNPs (nine on scaffold 633, SEMN01000633, and one on SEMN01000251) had two alleles in males but only one in females (with the exception of a single count of a second allele at one SNP), and the other 20 SNPs had two alleles in each sex but with different allele frequencies between sexes.
The eleven SNP loci with the lowest CMH test p-values (p<1e-24) were located on Macquarie perch scaffold 633, within a ~6.6-Kb region 90152-96798 (Table 3). For nine of these SNPs, all located within a ~3.8-Kb region 90152-94017, both female pools had a single allele present (the same allele in both populations), and both male pools had two alleles (the same two in both populations; Table 3). Five of these SNPs were located within a short 146-bp fragment 93182-93327 (hereafter, the ‘146-bp sexing region ’).
When the CMH test threshold was lowered to p<1e-5, there were 61,452 loci differentiated between male and female Macquarie perch pools (results in Supplementary Material S3). Of these, 1,711 loci in 644 scaffolds had one allele in female- and two in male pools, and 1,715 loci in 678 scaffolds had one allele in male- and two in female pools. Of the former set of scaffolds, scaffold 633 (length 274,905 bases), had the most loci (36) (Appendix C). Of these 36, together with three strongly (p<1e-20) differentiated loci that did not make this list because they had a single count for an alternative allele in females, 27 loci clustered within the ~6.3 Kb region 87668-94017 of scaffold 633 (Table C1). Two loci on scaffold 633 (p<1e-5) had one allele in male- and two in female pools (Table C1).