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Anthropogenic pressures in estuaries may impair not only the fitness of organisms and the evolutionary processes necessary to the survival, but also the management of exploited marine resources. In order to assess these impacts, phenotypic and genotypic data pertaining to young-of-the-year (YOY) sole ( Solea solea ) were screened in differentially contaminated North East Atlantic estuaries ranging from Portugal (Mondego) to the English Channel (Seine). YOY sole inhabiting each estuary was found being phenotypically distinct from each other; each of them being impacted by pollution when comparing observed phenotypic data with published literature. According to the strong pollution in the Seine estuary, the corresponding YOY sole sample showed significantly lower body mass, size and condition factor compared to other samples. Using fifteen genetic markers, the Mondego estuary demonstrated low, but significant levels of genetic differentiation with most of the samples. Using neutrality tests, two loci were found to be putatively under directional selection ( Soso7 and Soso23 ), but only locus Soso7 demonstrated significant positive heterozygosity–fitness correlation (HFC) for body size and body mass, suggesting a possible ongoing adaptive process. The candidate locus MT associated to a detoxifying metallothionein gene did not show significant genetic differentiation, but ( i ) significant deficit in heterozygote in the Seine estuary as already reported in other coastal samples impacted by metallic contaminants, and ( ii ) significant positive HFC with body mass were found. Selective rather than demographic processes better explain an observed genetic structure in YOY sole and are predominantly associated with the heavily contaminated Seine estuary whose nursery function and capacity are degraded.

Populations of marine organisms are potentially affected by numerous selective pressures such as temperature and salinity, or anthropogenic pressures such as xenobiotics that may preclude adaptation to particular habitats. Such selective pressures may also affect their demography. Examples include modifications of the population dynamics through shifts in growth rate, and in life history traits affecting fitness such as size or age of first reproduction. However, the documentation of variation in phenotypically plastic traits specific to distinct environments cannot be taken as the ultimate proof that natural selection has occurred. Measurement of the impact of selection and subsequent local adaptation of fish populations based exclusively on morphological or physiological characters is one of the most difficult things to achieve because it depends on the use of phenotypic characters that closely match the genotype. Molecular markers can help to overcome this problem and, under some circumstances, can record the footprints of selection. A combination of polymorphisms that are under selection and those that are not can provide complementary information. In this paper, we review how and why selection can be detected at the molecular level, using genetic markers analysed in a population genetic framework. We then report and discuss case studies in fish.