Data from: Determinants of hierarchical genetic structure in Atlantic salmon populations: environmental factors vs. anthropogenic influences

Disentangling the effects of natural environmental features and
anthropogenic factors on the genetic structure of endangered populations
is an important challenge for conservation biology. Here we investigated
the combined influences of major environmental features and stocking with
non-native fish on the genetic structure and local adaptation of Atlantic
salmon (Salmo salar) populations. We used 17 microsatellite loci to
genotype 975 individuals originating from 34 French rivers. Bayesian
analyses revealed a hierarchical genetic structure into five
geographically distinct clusters. Coastal distance, geological substrate
and river length were strong predictors of population structure. Gene flow
was higher among rivers with similar geologies, suggesting local
adaptation to geological substrate. The effect of river length was mainly
due to one highly differentiated population that has the farthest spawning
grounds off the river mouth (up to 900 km) and the largest fish,
suggesting local adaptation to river length. We detected high levels of
admixture in stocked populations but also in neighboring ones, implying
large scale impacts of stocking through dispersal of
non-native-individuals. However, we found relatively few admixed
individuals suggesting a lower fitness of stocked fish and/or some
reproductive isolation between wild and stocked individuals. When
excluding stocked populations, genetic structure increased as did its
correlation with environmental factors. This study overall indicates that
geological substrate and river length are major environmental factors
influencing gene flow and potential local adaptation among Atlantic salmon
populations but that stocking with non-native individuals may ultimately
disrupt these natural patterns of gene flow among locally adapted
populations.