Population diversity
There were marked differences between the European and Japanese
populations in their levels of linkage disequilibria. The European
population possessed strong linkage disequilibrium, with slow LD decay,
while the Japanese population demonstrated a more rapid LD decay (Figure
6). The European population possessed a lower genetic diversity (π =
0.00028, number of SNPs = 18,982) compared to the Japanese population (π
= 0.00235, number of SNPs = 231,952; Table 2). The higher level of
genetic diversity in the Japanese population was observed throughout the
entire genome (Figure 7). Nevertheless, the Japanese population
possessed some genomic regions of lower genetic diversity, specifically
in scaffolds 1 and 3 (which are the same genomic regions as where the
isolate ICMP18202 from New Zealand shared ancestry to the Japanese
population; Figure 5). In contrast, the European population had more
narrow genomic regions of high genetic diversity (Figure 7). Both
populations showed high inbreeding coefficients, with an average
FIS of 0.978 for the European and 0.520 for the Japanese
population (Table 1).
The average Tajima’s D values calculated using 10 kb genomic windows
along the genome were higher in the Japanese population than in the
European population (0.724 versus -0.079, Table 2).