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