Individual genotypes of 1 416 brook trout genotyped at 14 779 high-quality SNPs for studying local adaptation and maladaptation in small populations

Investigating the relative importance of
neutral versus selective processes governing the
accumulation of genetic variants is a key goal in both evolutionary and
conservation biology. This is particularly true in the context of small
populations, where genetic drift can counteract the effect of selection.
Using Brook Charr (Salvelinus fontinalis) from Québec, Canada as a case
study, we investigated the importance of
demographic versus selective processes governing the
accumulation of both adaptive and maladaptive mutations in
closed versus open and connected populations to assess
gene flow effect. This was achieved by using 14 779 high-quality filtered
SNPs genotyped among 1 416 fish representing 50 populations from three
life history types: lacustrine (closed populations), riverine and
anadromous (connected populations). Using the Provean algorithm, we
observed a considerable accumulation of putative deleterious mutations
across populations. The absence of correlation between the
occurrence of putatively beneficial or deleterious mutations and local
recombination rate supports the hypothesis that genetic drift
might be the main driver of the accumulation of such variants.
However, despite a lower genetic diversity observed in lacustrine
than in riverine or anadromous populations, lacustrine populations do not
exhibit more deleterious mutations than the two other history types,
suggesting that the negative effect of genetic drift in lacustrine
populations may be mitigated by that of relaxed purifying
selection. Moreover, we also identified genomic regions
associated with anadromy, as well as an overrepresentation of transposable
elements associated with variation in environmental variables, thus
supporting the importance of transposable elements in
adaptation.