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We review knowledge on applications of sustained aerobic swimming as a tool to promote productivity and welfare of farmed fish species. There has been extensive interest in whether providing active species with a current to swim against can promote growth. The results are not conclusive but the studies have varied in species, life stage, swimming speed applied, feeding regime, stocking density and other factors. Therefore, much remains to be understood about mechanisms underlying findings of ‘swimming‐enhanced growth’, in particular to demonstrate that swimming can improve feed conversion ratio and dietary protein retention under true aquaculture conditions. There has also been research into whether swimming can alleviate chronic stress, once again on a range of species and life stages. The evidence is mixed but swimming does improve recovery from acute stresses such as handling or confinement. Research into issues such as whether swimming can improve immune function and promote cognitive function is still at an early stage and should be encouraged. There is promising evidence that swimming can inhibit precocious sexual maturation in some species, so studies should be broadened to other species where precocious maturation is a problem. Swimming performance is a heritable trait and may prove a useful selection tool, especially if it is related to overall robustness. More research is required to better understand the advantages that swimming may provide to the fish farmer, in terms of production, mitigation and selection.

Temperature‐dependent sex determination (TSD) can be observed in multiple reptile and fish species. It is adaptive when varying environmental conditions advantage either males or females. A good knowledge of the thermosensitive period is key to understand how environmental changes may lead to changes in population sex ratio. Here, by manipulating temperature during development, we confirm that cold temperature (16°C) increases the proportion of fish that develop as females in European sea bass (Dicentrarchus labrax) until 56 days posthatching, but show that it has an opposite effect at later stages, with the proportion of males reaching ~90% after 230 days at 16°C. This is the first observation of opposite effects of temperature at different time periods on the sex ratio of a vertebrate. Our results highlight the potential complexity of environmental effects on sex determination.

In the context of parentage assignment using genomic markers, key issues are genotyping errors and an absence of parent genotypes because of sampling, traceability or genotyping problems. Most likelihood‐based parentage assignment software programs require a priori estimates of genotyping errors and the proportion of missing parents to set up meaningful assignment decision rules. We present here the R package APIS, which can assign offspring to their parents without any prior information other than the offspring and parental genotypes, and a user‐defined, acceptable error rate among assigned offspring. Assignment decision rules use the distributions of average Mendelian transmission probabilities, which enable estimates of the proportion of offspring with missing parental genotypes. APIS has been compared to other software (CERVUS, VITASSIGN) on a real European seabass (Dicentrarchus labrax) SNP data set. The type I error rate (false positives) was lower with APIS than with other software, especially when parental genotypes were missing, but the true positive rate was also lower, except when the theoretical exclusion power reached 0.99999. In general, APIS provided assignments that satisfied the user‐set acceptable error rate of 1% or 5%, even when tested on simulated data with high genotyping error rates (1% or 3%) and up to 50% missing sires. Because it uses the observed distribution of Mendelian transmission probabilities, APIS is best suited to assigning parentage when numerous offspring (>200) are genotyped. We have demonstrated that APIS is an easy‐to‐use and reliable software for parentage assignment, even when up to 50% of sires are missing.

The European sea bass (Dicentrarchus labrax L.) is a marine fish of key economic and cultural importance in Europe. It is now more an aquaculture than a fisheries species (>96% of the production in 2016), although modern rearing techniques date back only from the late 1980s. It also has high interest for evolutionary studies, as it is composed of two semispecies (Atlantic and Mediterranean lineages) that have come into secondary contact following the last glaciation. Based on quantitative genetics studies of most traits of interest over the past 10–15 years, selective breeding programs are now applied to this species, which is at the beginning of its domestication process. The availability of a good quality reference genome has accelerated the development of new genomic resources, including SNP arrays that will enable genomic selection to improve genetic gain. There is a need to improve feed efficiency, both for economic and environmental reasons, but this will require novel phenotyping approaches. Further developments will likely focus on the understanding of genotype‐by‐environment interactions, which will be important both for efficient breeding of farmed stocks and for improving knowledge of the evolution of natural populations. At the interface between both, the domestication process must be better understood to improve production and also to fully evaluate the possible impact of aquaculture escapees on wild populations. The latter is an important question for all large‐scale aquaculture productions.

Improving feed efficiency (FE) is key to reducing production costs in aquaculture and to achieving sustainability for the aquaculture industry. Feed costs account for 30–70% of total production costs in aquaculture; much work has been done on nutritional and husbandry approaches to improve FE but only a limited amount of research has been devoted to using genetics, despite its potential. This paper reviews past work to improve FE in fish using selective breeding and assess future directions. Direct selection on FE traits requires methods to measure individual feed consumption and estimate FE efficiently and accurately. This is particularly difficult to do in fish because of the environment in which they live. Many of the published studies on FE were found to be inaccurate because of methodological problems. The relatively low heritability estimates of FE traits in fish published to date are probably partly as a result of inaccurate measurements of feed intake. Improving ways to measure the individual feed intake with high accuracy will be critical to the successful application of genetics to improving FE. Indirect selection criteria that could be used to improve FE (including growth after starvation/refeeding, body composition, neuropeptides or hormone levels) are discussed. Promising approaches to measuring feed intake accurately that may enable these studies to be undertaken are identified. More work using these will be needed prior to assessing the practicality of the introduction of direct or indirect traits for FE in fish genetic improvement programmes.

Describing and explaining the geographic within-species variation in phenotypes (“phenogeography”) in the sea over a species distribution range is central to our understanding of a variety of eco-evolutionary topics. However, phenogeographic studies that have a large potential to investigate adaptive variation are overcome by phylogeographic studies, still mainly focusing on neutral markers. How genotypic and phenotypic data could covary over large geographic scales remains poorly understood in marine species. We crossed 75 noninbred sires (five origins) and 26 dams (two origins; each side of a hybrid zone) in a factorial diallel cross in order to investigate geographic variation for early survival and sex ratio in the metapopulation of the European sea bass (Dicentrarchus labrax), a highly prized marine fish species. Full-sib families (N = 1,950) were produced and reared in a common environment. Parentage assignment of 7,200 individuals was performed with seven microsatellite markers. Generalized linear models showed significant additive effects for both traits and pleiotropy between traits. A significant nonadditive genetic effect was detected. Different expression of traits and distinct relative performances were found for reciprocal crosses involving populations located on each side of the main hybrid zone located at the Almeria-Oran front, illustrating asymmetric reproductive isolation. The poor fitness performance observed for the Western Mediterranean population of sea bass is discussed as it represents the main source of seed hatchery production, but also because it potentially illustrates nonadaptive introgression and maladaptation.

Viral encephalopathy and retinopathy (VER), otherwise known as viral nervous necrosis (VNN), is a major devastating threat for aquatic animals. Betanodaviruses have been isolated in at least 70 aquatic animal species in marine and in freshwater environments throughout the world, with the notable exception of South America. In this review, the main features of betanodavirus, including its diversity, its distribution and its transmission modes in fish, are firstly presented. Then, the existing diagnosis and detection methods, as well as the different control procedures of this disease, are reviewed. Finally, the potential of selective breeding, including both conventional and genomic selection, as an opportunity to obtain resistant commercial populations, is examined.