EST-Microsatellite Types and Structural Scenarios in European Hake Fisheries

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).

Microsatellites as Molecular Markers with Applications in Exploitation and Conservation of Aquatic Animal Populations

“…The list includes freshwater, diadromous and marine species. For the study of the genetic structure of the European hake, Pita et al [ 177 ] distinguished several groups of microsatellite markers. The most commonly used sets of microsatellites are neutral.…”

“…Microsatellites detected in ESTs are characterized by high allelic diversity in regions of functional importance. This group of microsatellites includes neutral markers with non-functional (non-adaptive) polymorphisms, purified (fossil-adaptive) polymorphism, and stabilizing (adaptive) polymorphism located in the adaptive regions of the genome [ 177 ]. In the latter group of markers, outliers can occur.…”

“…Microsatellites have been most widely applied in research related to populations, fisheries and aquaculture beginning in the early 1990s [ 173 , 174 , 175 , 176 ]. The next generation sequencing (NGS) genome assay enables the identification of many thousands of microsatellites of which a dozen or so highly polymorphic loci are usually sufficient for population genetic and aquaculture applications, e.g., in [ 177 ]. This review is an attempt to summarize the applications of microsatellite DNA markers to studies of natural populations, aquaculture stocks, fisheries and conservation genetics of aquatic animals ( Figure 1 ).…”

Temporal uncoupling between demographic and genetic metrics in fisheries assessment: the European hake case study

“…For instance, the short-term unpredictability of N e following the postoverharvesting SSB plateau (Pita et al, 2017) might be reduced by increasing time-point estimates of N e before and after the postharvesting SSB plateau. The adequate dissection of marker sets such as bulks of microsatellites or SNPs into distinct functional categories, prevents the enforcement of marker types not reflecting the extent of population dynamics processes, i.e., Fossil Adaptive Polymorphic Systems (FAPS) sensu Pita et al (2022). Provided that the number of alleles per locus markedly outperformed other indicators across multiple in-silico situations, increasing the number of neutral microsatellites and sample number and size seems to dramatically increase power (Hoban et al, 2014).…”

“…This study aimed to provide a less biased estimation of N e from the Southern hake stock over four decades as compared to a previous 7-year sample frame. This timely collection was screened with microsatellite types expected to provide a differential erosion signal caused by overharvesting (Pita et al, 2022). Also, historical records of molecular variation in the mtDNA cytochrome b gene (cyt b) were used as a conservative control under purifying selection (Lundy et al, 1999;Pita et al, 2014).…”