3.2.1 Genome-wide diversity and divergence
Genome-wide diversity, measured as nucleotide diversity (π ) and Watterson’s theta (Ɵ ), was considerably larger in Deme I than in Deme II (Table 2; Deme I π =0.0013 vs. Deme II π =0.00046). The average values for Ɵ were 0.0017 (Deme I) vs. 0.0008 (Deme II). Tajima’s D values were all below 0, with Deme II having a larger negative estimate (Table 2).
The genome-wide divergence between the two demes was high;F ST=0.13 using window size of 5 kb (Table 3); this value was largely consistent for other window sizes (Table S2) and agrees with estimates from the 96 SNP array (Table 3). The fraction to which windows were covered with data after quality and depth filtering did not affect F ST values (F ST=0.13 for all fraction depths; Table S3). To minimize stochastic errors linked with small window sizes, while not losing too much of data, we chose 5 kb windows with ≥80% fraction depth coverage. There was a strong correlation between Nei´s (1973)F ST from Pool-seq versusF ST from the 96 SNP array (r =0.78, p<0.001; Figure S4).