4.3 Comparison to other lakes
The comparison with eight other lakes showed that Deme II in Bunnersjöarna stands out as less genetically variable, more inbred, and more isolated than any other population. For the other populations, nucleotide diversity was around 0.001 (Table 2; Table S12). This is in line with what we have observed previously from brown trout of the same geographic area using the Salmo salar reference genome for mapping (Kurland et al., 2019). Our estimate is considerably lower than that observed using dd-RADseq for brown trout populations of the Atlantic lineage (same lineage as our study system) held in a hatchery in south-western France withπ =0.004 and for wild Mediterranean lineage populations withπ =0.005 (Leitwein, Gagnaire, Desmarais, Berrebi, & Guinand, 2018). Again, Deme II stands out as an extreme in comparison with other brown trout populations with genome wide nucleotide diversity of below 0.0005 (Table 2).