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).