The genetic impacts of fishing have been difficult to demonstrate in wild populations, due to the phenotypic plasticity of many life history traits that respond to both biological and physical parameters as well as selection pressures. Selection is likely to be fishery specific and dependent upon the interaction between fishing gear and the average size and age at onset of sexual maturity of the target species. Measured genetic impacts in enhanced fisheries range from no detectable change to complete replacement of local stocks. Protocols have been developed that enable hatchery managers to minimize genetic change by careful choice of the origin and number of parents used for seed production.
Species extinction, and threatened and endangered aquatic species, are most common in freshwater and estuarine environments and produced by habitat loss and degradation rather than direct impacts of fishing. However, marine fishes with low reproductive rates, large size at onset of sexual maturity, and restricted distributions, such as the coelacanth, and some sharks and rays, are vulnerable to exploitation. In addition industrial fisheries are disrupting ecosystems. Many collapsed stocks have maintained relatively large population sizes and would not be expected to lose genetic diversity.
Fishing also impacts on a range of non-target species and those with low population sizes and low reproductive rates that include sharks, turtles, albatrosses and marine mammals are vulnerable to accidental harvesting. In many managed fisheries, measures are being put in place to reduce mortalities on non-target species through gear restrictions and local closures. The move towards large-scale marine protected areas and seasonal closures will contribute to the conservation of non-target species. Illegal harvesting of protected species and overfishing of quota species in high seas fisheries urgently requires new initiatives in conservation and sustainable management. Most genetic problems relate to overfishing and, while biological solutions to problems of overfishing seem obvious, such as reducing fleet size in industrial fisheries and creating closed areas in artisanal fisheries, the socio-political measures to resolve the conflict between long-term conservation goals and short-term economic gains will be difficult to implement.