3.5 Comparisons with other lakes
The genetic divergence between the two demes of Lakes Bunnersjöarna was similar to the lower estimates of divergence between fish from lakes with no migratory contact (Tables S10a, b-S11). Lake Ånnsjön is the closest lake, 8.5 km downstream of Lakes Bunnersjörna (Figure 1), and the most parsimonious source for the colonization of Lakes Bunnersjörna. Weir & Cockerham´s F ST for the 96 SNP array between Lake Ånnsjön and Deme I (F ST=0.12; Table S10a) was around half that of the divergence between the two demes (F ST=0.24) while F STbetween Lake Ånnsjön and Deme II was 0.36.
There are strong correlations for different types ofF ST values between population pairs from Pool-seq data and those from the SNP array data (Figure S10a, b). The TreeMix dendrogram from Pool-seq data (Figure 7; c.f. Appendix S1 for methods) and the neighbor-joining tree from SNP array data (Figure S11) illustrate how Deme II stands out as isolated and less connected to both Deme I and Lake Ånnsjön.
The nucleotide diversity estimated in brown trout from Bunnersjöarna Deme I (π =0.0013; Table 2) was of the same order of magnitude as estimates from other lakes where π ranged between 0.00104 to 0.00151 (Table S12), while π for Deme II was almost an order of magnitude lower (Table 2). The two individuals from Deme II showed higher average inbreeding levels measured as length of ROH (Figure 6a, Figure S12) and F ROH (Figure 6b, Figure S13) than brown trout in any of the other lakes. In contrast, Deme I individuals showed the lowest values. Long runs of homozygosity were also more frequent in Deme II than in any other lake (Table S7).