EST-Microsatellite Types and Structural Scenarios in European Hake Fisheries

SIMPLE SUMMARY: The conservation of the maximum genetic background from all genomic regions matters for sustainability in the changing global scenario. This study focused the importance of integrating such genetic variation in order to infer meaningful units for management and sustainability. We show that knowledge that can be obtained from different marker types should be goal-oriented, i.e., remnant patterns of selection pressures and extreme drift episodes (directional markers, i.e., the evolutionary genetic background), current evolutionary novelty and adaptive potential for fisheries’ sustainability (balanced markers, i.e., the potential genetic drive of the species), and demographic dynamics of genetic relevance for fisheries’ management (neutral markers, i.e., the present-day fishery structure and connectivity). In particular, special attention should be paid to the variation in supergenes or balancing markers, which are a rich source of evolutionary novelty and can be crucial for species welfare and survival. ABSTRACT: A fishery’s structure and connectivity are priors to its effective management. A successful description of such processes depends on both the sampling design and the choice of adequate genetic markers. EST markers are perfusing the studies of marine metapopulations and are believed to provide access to functional polymorphisms. However, the assumed adaptive role of outlier EST loci might not be generalizable. EST-microsatellites represent the upper polymorphic boundary in these regions because of their high mutation rate. We have subclassified the polymorphisms of EST-microsatellites to assess their structural contribution in the European hake, a paradigmatic and highly mobile marine species (HMMS). Because of the counterbalanced forces between directional markers (15%) and balanced markers (23%), the whole marker set offers the same structural situation as the one observed with neutral markers (62%), i.e., k = 2 gene pools. In contrast to outlier EST- microsatellites, neutral EST subsets allow one to measure crucial population phenomena for fisheries’ management. The high inter-population divergence of outlier EST-microsatellites is compatible with drifted post-selection genomic regions rather than with ongoing local selective pressures. The structural scenario in hake is explainable by a limited gene flow across the Almería-Oran Front (AOF) and by the within-basin IBD pattern of connectivity plus drift-related demographic events. This study highlights how polymorphic properties of EST-microsatellite types can be useful to address mutually excluding research tasks in fisheries, i.e., to address its evolutionary history (directional markers or FAPS: Fossil Adaptive Polymorphic Systems); to delineate management units (neutral markers or NAPS: Non Adaptive Polymorphic Systems); or to ensure sustainability (balanced markers or APS: Adaptive Polymorphic Systems).