Comparison of linkage groups to SNP cohorts identified in previous work
Using the PC loading plateaus described above and in Trevoy et al. (2019), we identified and extracted scaffolds from the draft female assembly (Keeling et al., 2013c) that had the highest loadings for each of the first four axes (Supp. Tab. 7). The 48 draft scaffolds identified from PC 1, which Trevoy et al. (2019) found to be related to geography, contained 101 SNPs and had top BLAST hits to 16 scaffolds in the final female assembly. Chromosome 4 contained 66 of these SNPs. PC 2 contained 214 SNPs on 60 draft scaffolds. With only one exception, all of these draft scaffolds had their top BLAST hits on the neo-X chromosome in the female assembly. This is consistent with the sex-based clustering along PC 2 found in Trevoy et al. (2019). PC 3 contained 50 SNPs on 11 draft scaffolds. These draft scaffolds aligned to chromosome 4, and 9 of them were also found in PC 1. Of the 68 unique SNPs from PCs 1 and 3 that corresponded to female chromosome 4, 13 were located within the region of elevated FST and Tajima’s D on that chromosome, as described above (Supp. Tab. 8). Finally, two draft scaffolds containing 25 SNPs from PC 4 matched to chromosome 9 in the final female assembly.