Here we critically review the scale and extent of adaptive genetic variation in Atlantic salmon (Salmo salar L.), an important model system in evolutionary and conservation biology that provides fundamental insights into population persistence, adaptive response and the effects of anthropogenic change. We consider the process of adaptation as the end product of natural selection, one that can best be viewed as the degree of matching between phenotype and environment. We recognise three potential sources of adaptive variation: heritable variation in phenotypic traits related to fitness, variation at the molecular level in genes influenced by selection, and variation in the way genes interact with the environment to produce phenotypes of varying plasticity. Of all phenotypic traits examined, variation in body size (or in correlated characters such as growth rates, age of seaward migration or age at sexual maturity) generally shows the highest heritability, as well as a strong effect on fitness. Thus, body size in Atlantic salmon tends to be positively correlated with freshwater and marine survival, as well as with fecundity, egg size, reproductive success, and offspring survival. By contrast, the fitness implications of variation in behavioural traits such as aggression, sheltering behaviour, or timing of migration are largely unknown. The adaptive significance of molecular variation in salmonids is also scant and largely circumstantial, despite extensive molecular screening on these species. Adaptive variation can result in local adaptations (LA) when, among other necessary conditions, populations live in patchy environments, exchange few or no migrants, and are subjected to differential selective pressures. Evidence for LA in Atlantic salmon is indirect and comes mostly from ecological correlates in fitness-related traits, the failure of many translocations, the poor performance of domesticated stocks, results of a few common-garden experiments (where different populations were raised in a common environment in an attempt to dissociate heritable from environmentally induced phenotypic variation), and the pattern of inherited resistance to some parasites and diseases. Genotype x environment interactions occurr for many fitness traits, suggesting that LA might be important. However, the scale and extent of adaptive variation remains poorly understood and probably varies, depending on habitat heterogeneity, environmental stability and the relative roles of selection and drift. As maladaptation often results from phenotype-environment mismatch, we argue that acting as if populations are not locally adapted carries a much greater risk of mismanagement than acting under the assumption for local adaptations when there are none. As such, an evolutionary approach to salmon conservation is required, aimed at maintaining the conditions necessary for natural selection to operate most efficiently and unhindered. This may require minimising alterations to native genotypes and habitats to which populations have likely become ad...

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Efficient sea-lice control remains one of the most important challenges for the salmon farming industry. The use of wrasse (Labridae) as cleaner fish offers an alternative to medicines for sea-lice control, but wrasse tend to become inactive in winter. Lumpfish (Cyclopterus lumpus) continue to feed on sea-lice at low temperatures, and commercial production has escalated from thousands of fish in 2010 to well over 30 million juveniles deployed in 2016. However, production still relies on the capture of wild broodstock, which may not be sustainable. To meet global industry needs, lumpfish production needs to increase to reach c. 50 million fish annually and this can only come from aquaculture. We review current production methods and the use of lumpfish in sea cages and identify some of the main challenges and bottlenecks facing lumpfish intensification. Our gap analysis indicates that the areas in most need of research include better control of maturation for year-round production; formulation of appropriate diets; artificial selection of elite lines with desirable traits; and development of vaccines for certified, disease-free juvenile production. The welfare of farmed lumpfish also needs to be better quantified, and more information is needed on optimal densities and tank design. Finally, the risk of farmed lumpfish escaping from net pens needs to be critically assessed, and we argue that it might be beneficial to recover cleaner fish from salmon cages after the production cycle, perhaps using them as broodstock, for export to the Asian food markets or for the production of animal feeds.

Variation in the microbiome has a fundamental influence on host health, ecology, and evolution, but the scope and basis of this variation are not fully understood. We identified considerable variation in skin and gut microbial communities between seven wild and captive populations of Atlantic salmon, reflecting divergent environmental conditions and fish genetic diversity. In particular, we found very pronounced differences in the intestinal microbiomes of wild and hatchery-reared fish, likely reflecting differences in diet. Our results offer an insight into how the microbiome potentially contributes to the generation of local adaptations in this species and how domestication alters intestinal microbial communities, highlighting future research directions in these areas.

Aquaculture is a major source of invasive aquatic species, despite the fact that cultured organisms often have low genetic diversity and tend to be maladapted to survive in the wild. Yet, to what extent aquaculture escapees become established by means of high propagule pressure and multiple origins is not clear. We analysed the genetic diversity of 15 established populations and four farmed stocks of non-native rainbow trout in Chile, a species first introduced for recreational fishing around 1900, but which has in recent decades escaped in large numbers from fish farms and become widespread. Aquaculture propagule pressure was a good predictor of the incidence of farm escapees, which represented 16% of all free-ranging rainbow trout and were present in 80% of the study rivers. Hybrids between farm escapes and established trout were present in all rivers at frequencies ranging between 7 and 69%, and population admixture was positively correlated with genetic diversity. We suggest that non-native salmonids introduced into the Southern Hemisphere could benefit from admixture because local adaptations may not have yet developed, and there may be initially little fitness loss resulting from outbreeding depression.