Fisheries genomics is an emerging field that advocates the application of genomic tools to address questions in fisheries management. Genomic approaches bring a new paradigm for fisheries management by making it possible to integrate adaptive diversity to understand fundamental aspects of fisheries resources. Hence, this review is focused on the relevance of genomic approaches to solve fisheries-specific questions. Particularly the detection of adaptive diversity (outlier loci) provides unprecedented opportunity to understand bio-complexity, increased power to trace processed sample origin to allow enforcement and the potential to understand the genetic basis of micro-evolutionary effects of fisheries-induced evolution and climate change. The understanding of adaptive diversity patterns will be the cornerstone of the future links between fisheries and genomics. These studies will help stakeholders anticipate the potential effects of fishing or climate change on the resilience of fisheries stocks; consequently, in the near future, fisheries sciences might integrate evolutionary principles with fisheries management.

Effective fishery management strategies should be based on stock delimitation and knowledge of the spatial scale at which species are distributed. However, a mismatch often occurs between biological and management units of fishery resources. The green abalone (Haliotis fulgens) supports an important artisanal fishery in the west coast of the Baja California Peninsula (BCP), Mexico, which has shown a declining tendency despite the several management measures. Thus, the aim of this study was to characterize the spatial patterns of neutral genomic variation of green abalone along the BCP to test whether the genomic structure patterns support the current green abalone management areas. To test this hypothesis, a set of 2,170 putative neutral single nucleotide polymorphisms discovered by a double digest restriction-site associated DNA approach was used on 10 locations along the BCP. The results revealed a population structure with three putative groups: Guadalupe Island and northern and southern BCP locations. The contemporary gene flow might be explained by local oceanographic features, where it is bidirectional within the southern region but with a predominant southward flow from the northern region. These findings indicated that the administrative areas did not match the biological units ofH. fulgensfishery; hence, the stock assessment and management areas should be revised.

Conservation of the evolutionary legacy of endangered species is a key component for long-term persistence. Totoaba is a long-lived fish endemic to the Gulf of California and is considered critically endangered. There is currently a debate concerning its conservation status and whether it can be used as a fishery resource. Unfortunately, basic information on biological and genetic population structure of the species is lacking. We sampled 313 individuals and employed 16 microsatellite loci and 3 mitochondrial DNA markers (16S, 547 pb; COI, 619 pb; control region, 650 pb) to assess population structure and demography of totoaba in the Gulf of California, with samples from locations that encompass nearly all of its recognized geographic distribution. We could not reject a hypothesis of panmixia for totoaba, using nuclear or mitochondrial markers. Demographic analysis of mtDNA suggests a sudden population expansion model. The results have important implications for totoaba conservation because poaching is a significant conservation challenge and could have additive negative effects over the single population of totoaba in the Gulf of California.

Several worldwide marine fish stocks need to recover from collapse or overexploitation. However, the effects of a fishery collapse at the genetic level are still largely unknown, as is the extent of reduction in genetic diversity caused by fisheries and the consequences for extinction risk. Here we present a case study of totoaba, the first marine fish considered as critically endangered. We assessed 16 microsatellite loci to determine whether the demographic collapse of the species resulted in a loss of genetic diversity. Our data indicate that genetic diversity of totoaba is in the range of values observed for fish with similar biological traits without a documented fishery collapse. Contemporary demographic analysis indicated no loss of genetic diversity. Long-term genealogical analysis showed a substantial reduction in effective population size. However, the time and causal effects for population decline cannot be inferred because of the large uncertainty in estimates. Our results indicate that the totoaba in the Gulf of California has not suffered a measurable contemporary reduction in genetic diversity, and that genetic diversity is driven by long-term climatic events. Estimates of current effective size indicate that it is large enough that genetic factors may not be a major problem for conservation. We conclude that the recent fishery collapse of totoaba did not have sufficient consequences at the genetic level to increase the risk of extinction from genetic drift. However, selective effects of fishing on the adaptive potential in totoaba remain unclear.