How to detect polymorphisms undergoing selection in marine fishes? A review of methods and case studies, including flatfishes

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.