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).