Data from: Spatio-temporal genetic structure and the effects of long-term fishing in two partially sympatric offshore demersal fishes

Environmental gradients have been shown to disrupt gene flow in marine
species, yet their influence in structuring populations at depth remains
poorly understood. The Cape hakes (Merluccius paradoxus and M. capensis)
are demersal species co-occurring in the Benguela Current system, where
decades of intense fishing resulted in severely depleted stocks in the
past. Previous studies identified conflicting mtDNA genetic substructuring
patterns and thus contrasting evolutionary trajectories for both species.
Using 10 microsatellite loci, the control region of mtDNA and employing a
seascape genetics approach, we investigated genetic connectivity and the
impact of prolonged exploitation in the two species, which are
characterized by different patterns of fishing pressure. Three consecutive
years were sampled covering the entire distribution (N = 2100 fishes).
Despite large estimated population sizes, both species exhibited low
levels of contemporary genetic diversity (0.581 < HE <
0.692), implying that fishing has had a significant impact on their
genetic composition and evolutionary trajectories. Further, for M.
paradoxus, significant temporal, but not spatial, divergence points to the
presence of genetic chaotic patchiness. In contrast, M. capensis exhibited
a clear latitudinal cline in genetic differentiation between Namibia and
South Africa (FST = 0.063, P < 0.05), with low (0.2% per
generation) estimates of contemporary gene flow. Seascape analyses reveal
an association with bathymetry and upwelling events, suggesting that
adaptation to local environmental conditions may drive genetic
differentiation in M. capensis. Importantly, our results highlight the
need for temporal sampling in disentangling the complex factors that
impact population divergence in marine fishes.