The nuclear genome: Neutral and adaptive markers in fisheries science

Advances in DNA sequencing methods now allow for the whole information content of a eukaryotic genome to be rapidly unveiled and screened at relatively affordable costs. The availability of millions of genetic polymorphisms for screening genetic variation in natural populations provides fisheries geneticists with a new generation of more powerful methods, which is causing a rapid turnover of the molecular markers used in stock identification. Microsatellite analysis is expected to be gradually replaced by the screening of known single nucleotide polymorphisms (SNPs), and restriction-assisted fragment-based techniques, such as amplified fragment length polymorphisms (AFLPs), are being superseded by newly developed reduced genomic representation approaches. Overall, our ability to understand the patterns and processes in wild exploited populations is taking a huge forward leap through the application of population genomic approaches. However, the astounding biological diversity of harvested species and the practicalities associated with fisheries management require a judicious assessment and validation of new methodologies and the refinement of analytical approaches. The plethora of available tools and concepts warrant clarity of purpose and continued efforts to improve communication between geneticists, fishery managers, and policy makers.