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.