Cultured fish: integrative biology and management of domestication and interactions with wild fish

Hurricane-induced dramatic decline and natural recovery of a vulnerable sportfish population: Shoal bass (Micropterus cataractae) in the Chipola River, Florida

Freshwater fishes are among the most biodiverse vertebrate groups and among the most threatened by anthropogenic activities. Many occur in small and geographically restricted populations that are increasingly subject to catastrophic events (hurricanes, wildfires, extreme floods and droughts), but it has rarely been possible to assess the impacts of such events. Here we document the decline and recovery of a regularly monitored, small shoal bass (Micropterus cataractae) population in the Chipola River, Florida following a catastrophic hurricane disturbance. The Chipola River population has the lowest level of interspecific hybridization (over 90 % non-introgressed shoal bass) within the species' range, a census population size of 2165 (95 % CI [1,383, 3,801]) in 2009 and a genetically effective population size Ne of 135 (95 % CI [70, 472]). In 2018, Hurricane Michael devastated the Chipola River and watershed. A survey conducted in 2019 indicated a severe decline (91 %) in relative population abundance and a very low Ne at 21 (95 % CI [16, 29]). However, the detection of young-of-year fish indicated that the depleted population had experienced successful reproduction. In fall 2021, the census population had recovered to 1039 fish (95 % CI [660, 1,814]) and Ne at 40 (95 % CI [31, 50]). While the population has shown considerable resilience in the face of hurricane disturbance, it remains vulnerable to future catastrophic events and may also suffer a long-term reduction in its adaptive potential due to a relatively low effective population size. To address these threats, continued monitoring is necessitated and targeted measures such as translocation of non-introgressed individuals from neighboring populations or establishment of a captive population of sufficient effective population size may be required to conserve the species in the long term.

Comparative studies on the intestinal health of wild and cultured ricefield eel (Monopterus albus)

Fish intestinal health under intensive aquaculture mode plays an important role in growth, development, and immune function. The present study was aimed to systematically investigate the differences of intestinal health between wild and cultured Monopterus albus by biochemical parameters, histomorphology, and molecular biology. A total of 15 healthy M. albus per group, with an average body weight of 45 g, were sampled to analyze intestinal health parameters. Compared with wild fish, the cultured M. albus in the foregut had lower trypsin, lipase, SOD, CAT, T-AOC, and GSH-Px activities (P < 0.05) and higher amylase activity and MDA content (P < 0.05). The villus circumference and goblet cells in the cultured group were significantly lower than those in the wild group (P < 0.05). In addition, the cultured fish showed lower relative expression levels of occludin, zo-1, zo-2, claudin-12, claudin-15, mucin5, mucin15, lysozyme, complement 3, il-10, tgf-β1, tgf-β2, and tgf-β3 (P < 0.05) and higher il-1β, il-6, il-8, tnf-a, and ifnγ mRNA expressions than those of wild fish (P < 0.05). In terms of gut microbiota, the cultured group at the phylum level displayed higher percentages of Chlamydiae and Spirochaetes and lower percentages of Firmicutes, Bacteroidetes, Actinobacteria, Cyanobacteria, and Verrucomicrobia compared to the wild group (P < 0.05). At the genus level, higher abundances of Pseudomonadaceae_Pseudomonas and Spironema and lower abundances of Lactococcus and Cetobacterium were observed in the cultured group than in the wild group (P < 0.05). To our knowledge, this is the first investigation of the intestinal health status between wild and cultured M. albus in terms of biochemistry, histology, and molecular biology levels. Overall, the present study showed significant differences in intestinal health between wild and cultured M. albus and the main manifestations that wild M. albus had higher intestinal digestion, antioxidant capacity, and intestinal barrier functions than cultured M. albus. These results would provide theoretical basis for the subsequent upgrading of healthy aquaculture technology and nutrient regulation of intestinal health of cultured M. albus.

Biochemical, Histological, and Transcriptomic Analyses Reveal Underlying Differences in Flesh Quality between Wild and Farmed Ricefield Eel (Monopterus albus)

The present study aimed to systematically investigate the underlying differences in flesh quality between wild and farmed Monopterus albus. Fifteen healthy M. albus per group with an average body weight of 45 g were sampled to analyze muscle parameters by biochemical indicators, histomorphology, and molecular biology. Compared with the wild fish, the farmed M. albus in flesh had lower crude protein, collagen, lysine, histidine, total amino acids, SFA, n-3 PUFA contents, and n-3/n-6 ratio (p < 0.05), and higher moisture, crude lipid, crude ash, MUFA, n-6PUFA, and total PUFA contents (p < 0.05). The thawing loss, drip loss, steaming loss, and boiling loss in the farmed group were significantly higher, and hardness, springiness, cohesiveness, gumminess, chewiness, and resilience were significantly lower than those in the wild group (p < 0.05). In addition, higher muscle fiber density and lower muscle fiber diameter were observed in wild M. albus (p < 0.05). In muscle transcriptome profiling, differentially expressed genes and enriched pathways are primarily associated with muscle development, protein synthesis, catabolism, lipid metabolism, and immunity. To the best of our knowledge, this is the first investigation that compares the flesh quality between wild and farmed M. albus in terms of biochemistry, histology, and molecular biology levels. Overall, wild M. albus had a higher nutritional value and texture quality than farmed M. albus.

Genetic Diversity and Signatures of Selection in the Roughskin Sculpin (Trachidermus fasciatus) Revealed by Whole Genome Sequencing

The roughskin sculpin (Trachidermus fasciatus) is an endangered fish species in China. In recent years, artificial breeding technology has made significant progress, and the population of roughskin sculpin has recovered in the natural environment through enhancement programs and the release of juveniles. However, the effects of released roughskin sculpin on the genetic structure and diversity of wild populations remain unclear. Studies on genetic diversity analysis based on different types and numbers of molecular markers have yielded inconsistent results. In this study, we obtained 2,610,157 high-quality SNPs and 494,698 InDels through whole-genome resequencing of two farmed populations and one wild population. Both farmed populations showed consistent levels of genomic polymorphism and a slight increase in linkage compared with wild populations. The population structure of the two farmed populations was distinct from that of the wild population, but the degree of genetic differentiation was low (overall average Fst = 0.015). Selective sweep analysis showed that 523,529 genes were selected in the two farmed populations, and KEGG enrichment analysis showed that the selected genes were related to amino acid metabolism, which might be caused by artificial feeding. The findings of this study provide valuable additions to the existing genomic resources to help conserve roughskin sculpin populations.

Rhythm of relationships in a social fish over the course of a full year in the wild

BACKGROUND

Animals are expected to adjust their social behaviour to cope with challenges in their environment. Therefore, for fish populations in temperate regions with seasonal and daily environmental oscillations, characteristic rhythms of social relationships should be pronounced. To date, most research concerning fish social networks and biorhythms has occurred in artificial laboratory environments or over confined temporal scales of days to weeks. Little is known about the social networks of wild, freely roaming fish, including how seasonal and diurnal rhythms modulate social networks over the course of a full year. The advent of high-resolution acoustic telemetry enables us to quantify detailed social interactions in the wild over time-scales sufficient to examine seasonal rhythms at whole-ecosystems scales. Our objective was to explore the rhythms of social interactions in a social fish population at various time-scales over one full year in the wild by examining high-resolution snapshots of a dynamic social network.

METHODS

To that end, we tracked the behaviour of 36 adult common carp, Cyprinus carpio, in a 25 ha lake and constructed temporal social networks among individuals across various time-scales, where social interactions were defined by proximity. We compared the network structure to a temporally shuffled null model to examine the importance of social attraction, and checked for persistent characteristic groups over time.

RESULTS

The clustering within the carp social network tended to be more pronounced during daytime than nighttime throughout the year. Social attraction, particularly during daytime, was a key driver for interactions. Shoaling behavior substantially increased during daytime in the wintertime, whereas in summer carp interacted less frequently, but the interaction duration increased. Therefore, smaller, characteristic groups were more common in the summer months and during nighttime, where the social memory of carp lasted up to two weeks.

CONCLUSIONS

We conclude that social relationships of carp change diurnally and seasonally. These patterns were likely driven by predator avoidance, seasonal shifts in lake temperature, visibility, forage availability and the presence of anoxic zones. The techniques we employed can be applied generally to high-resolution biotelemetry data to reveal social structures across other fish species at ecologically realistic scales.

Disparate behavioral types in wild and reared juveniles of gilthead seabream

Fish differ consistently in behavior within the same species and population, reflecting distinct behavioral types (BTs). Comparing the behavior of wild and reared individuals provides an excellent opportunity to delve into the ecological and evolutionary consequences of BTs. In this work, we evaluated the behavioral variation of wild and reared juvenile gilthead seabreams, Sparus aurata, a highly relevant species for aquaculture and fisheries. We quantified behavioral variation along the five major axes of fish behavioral traits (exploration-avoidance, aggressiveness, sociability, shyness-boldness, and activity) using standardized behavioral tests and a deep learning tracking algorithm for behavioral annotation. Results revealed significant repeatability in all five behavior traits, suggesting high consistency of individual behavioral variation across the different axes in this species. We found reared fish to be more aggressive, social and active compared to their wild conspecifics. Reared individuals also presented less variance in their aggressiveness, lacking very aggressive and very tame individuals. Phenotypic correlation decomposition between behavioral types revealed two different behavioral syndromes: exploration-sociability and exploration-activity. Our work establishes the first baseline of repeatability scores in wild and reared gilthead seabreams, providing novel insight into the behavior of this important commercial species with implications for fisheries and aquaculture.

Ecosystem-based management outperforms species-focused stocking for enhancing fish populations

Ecosystem-based management is costly. Therefore, without rigorously showing that it can outperform traditional species-focused alternatives, its broad-scale adoption in conservation is unlikely. We present a large-scale replicated and controlled set of whole-lake experiments in fish conservation (20 lakes monitored over 6 years with more than 150,000 fish sampled) to examine the outcomes of ecosystem-based habitat enhancement (coarse woody habitat addition and shallow littoral zone creation) versus a widespread, species-focused alternative that has long dominated fisheries management practice (i.e., fish stocking). Adding coarse woody habitats alone did not, on average, enhance fish abundance, but creating shallow water habitat consistently did, especially for juvenile fish. Species-focused fish stocking completely failed. We provide strong evidence questioning the performance of species-focused conservation actions in aquatic ecosystems and instead recommend ecosystem-based management of key habitats.

Juvenile semi-wild fish have a higher metabolic rate than farmed fish

Fish from commercially farmed stocks are often released into the natural environment to supplement wild populations. This practice is often applied to salmonid fish as they are an essential fishery resource and also used for recreational angling. However, farmed fish tend to show lower survival rates after release than wild fish. For this reason, the release of semi-wild fish is increasingly used in Japan; these fish are generated using female fish from domesticated stocks and male fish of wild origin. The survival rate of released semi-wild fish is higher than that of farmed fish, but the reason for this is unknown. This study compared the metabolism and swimming performance of semi-wild and farmed masu salmon (Oncorynchus masou). The analyses showed that resting metabolic rate (RMR), maximum metabolic rate (MMR) and swimming speeds that minimize energy costs of travel (optimal swimming speed) were higher in semi-wild fish than in farmed fish. Critical swimming speed did not differ significantly between the two groups of fish. Semi-wild fish with high RMR may have a social status advantage over farmed fish because a previous study reported that SMR, which is the value closest to basal metabolism significantly affects feeding motivation. This means that individuals with higher social status may be more motivated to feed. As RMR is proportional to food requirements, then release programs should be planned taking food resources at the release site into consideration.

Size-age population structure of an endangered and anthropogenically introgressed northern Adriatic population of marble trout (Salmo marmoratus Cuv.): insights for its conservation and sustainable exploitation

Salmonid species are main actors in the Italian socio-ecological landscape of inland fisheries. We present novel data on the size-age structure of one of the remnant Italian populations of the critically endangered marble trout Salmo marmoratus, which co-occurs with other stocked non-native salmonids in a large glacial river of the Lake Maggiore basin (Northern Italy-Southern Switzerland). Like other Italian native trout populations, the Toce River marble trout population is affected by anthropogenic introgression with the non-native brown trout S. trutta. Our sample includes 579 individuals, mainly collected in the Toce River main channel. We estimated the length-weight relationship, described the population size-age structure, estimated the age-specific growth trajectories, and fit an exponential mortality model. A subset of the sample was also used to measure numerical and biomass density. The estimated asymptotic maximum length is ~105 cm total length (TL). Mean length at first maturity is ~55 cm TL, and mean length at maximum yield per recruit is ~68 cm TL. Approximately 45-70% of the population are estimated to die annually, along with a fishing annual mortality of ~37%, with an exploitation ratio of ~0.5. The frequency distribution of length classes in a sample collected by angling shows that ~80% of the individuals that could be retained according to the current recreational fishing regulations likely never reproduced, and large fish disproportionally contributing to recruitment are fished and retained. We identify possible overfishing risks posed by present regulations, and propose updated harvest-slot length limits to mitigate such risks. More detailed and long-term datasets on this system are needed to more specifically inform the fishery management and monitor the effects of any change in the management strategy on the size-age structure of the marble trout population of the Toce River.

Reduced lifetime fitness (growth, body condition and survivability) of hatchery-reared tiger pufferfish Takifugu rubripes compared to wild counterparts

Tiger pufferfish Takifugu rubripes (order Tetraodontiformes, family Tetraodontidae) is a highly exploited species and stocks continue to decline, although hatchery-reared juveniles have been released since 1965 for stock enhancement. To determine why the stock has not recovered through hatchery-release practices, this study investigated and compared the population characteristics of wild and hatchery-origin fish. The length-mass relationship showed that hatchery-origin fish were skinnier, with males weighing less than 90% of the mass of wild males of the same length. The hepatosomatic index tended to be lower in hatchery-origin fish. Age was estimated using the otolith-based method, and the estimates were more accurate and precise than those obtained by the conventional vertebra-based method. At the age of 2.9 years, an age at which specimens were the most abundant in catches, hatchery-origin males weighed only 67% of wild males. The maximum observed age was 12 years for wild fish and 5 years for hatchery-origin fish. The instantaneous total mortality rates of hatchery-origin fish were more than twice as high as those of wild fish. In summary, the hatchery-origin fish had poor health status, poor growth and high mortality, and their fitness in natural environments was therefore hypothesized to be low throughout life.

Domestication of captive-bred masu salmon Oncorhynchus masou masou (Salmonidae) leads to a significant decrease in numbers of lateral line organs

Because captive-bred animals gradually adapt to artificial rearing environments due to evolving life history traits, such individuals sometimes show lessened performance in natural environments. The lateral line system, one of the principal sensory organs of fishes, varies according to habitat environments, sometimes differing even within the same species. A reduction in lateral line elements may also occur in successive generations of captive-bred fish. Such a reduction, involving neuromasts over the entire body, was examined for the first time in captive-bred masu salmon Oncorhynchus masou masou. The total number of neuromasts in captive-bred fish was ca. 10% lower than in wild-caught and F1 fishes, suggesting that the system in captive-bred fish had reduced in number due to domestication. Furthermore, differences in total neuromast numbers between captive-bred and wild fish were greater than between anadromous and fluvial populations of the species. The lower number of neuromasts could be one of the reasons behind the lower survival of captive-bred fish in natural environments.

Tissue-Specific and Differential Cold Responses in the Domesticated Cold Tolerant Fugu

Domestication can be defined as the artificial selection in animals to achieve morphological, physiological, and developmental conformity to human needs, with the aim of improving various limitations in species under a human feeding environment. The future sustainability of aquaculture may rely partly on the availability of numerous domesticated fish species. However, the underlying adaptive mechanisms that result in the domestication of fish are still unclear. Because they are poikilothermic, temperature is a key environmental element that affects the entire life of fish, so studying the association between physiological and behavioral changes in low-temperature domesticated fish can provide a model for understanding the response mechanisms of fish under cold stress. Through 5 generations and 10 years of artificial selection at low temperatures, we used cold-tolerant fugu as a biological model to compare transcriptome changes in brain and liver tissues to study the effects of cold stress on fish. It was found that the expression of genes such as apoptosis, p53, oxidative phosphorylation, and mitochondrial β-oxidation in the brain of cold-tolerant fugu was significantly lower than the wild type due to cold stress, while excessive energy metabolism would lead to the production of reactive oxygen species (ROS) and exacerbate the brain damage, thus causing rollover and coma. Meanwhile, under cold stress, the signaling pathways involved in glycogenolysis and lipid metabolism, such as insulin signaling, adipocytokines, and mTOR signaling pathways, were significantly up-regulated in the liver of cold-tolerant fugu. Although the mitochondrial β-oxidation pathway was increased in cold-tolerant fugu liver tissues, the transcriptome was not enriched in apoptotic. These phenomena predict that in response to low-temperature conditions, cold-tolerant fugu employs a dynamic inter-organ metabolic regulation strategy to cope with cold stress and reduce damage to brain tissues.

Effects of stocking at the parr stage on the reproductive fitness and genetic diversity of a wild population of Atlantic salmon (Salmo salar L.)

Captive-breeding programs are among the most adopted conservation practices to mitigate the loss of biodiversity, including genetic diversity. However, both genetic and nongenetic changes occurring in captivity can reduce the fitness of supplemented individuals, which complicate rehabilitation efforts. In the case of Atlantic salmon, the intensity of changes that occur in captivity and their impact on fitness will vary with the stocking practice adopted. In this study, we test whether salmon stocked at the parr stage have reduced reproductive success compared with their wild conspecifics and whether they contribute to increase genetic diversity in the targeted population. To do so, we use high-throughput microsatellite sequencing of 38 loci to accurately assign 2381 offspring to a comprehensive set of possible parents from a supplemented Atlantic salmon population in Québec, Canada. Captive-bred salmon stocked at the parr stage had fewer mates than their wild conspecifics, as well as a reduced relative reproductive success (RSS) compared with their wild counterparts. Nonetheless, in comparison with previous studies, stocking at the parr stage significantly improved RSS compared with salmon stocked as smolts and they displayed a reduction in reproductive success similar to salmon stocked as fry, which spend less time in captivity than parr. Moreover, supplementation of captive-bred salmon significantly contributed to increasing genetic diversity. These results should contribute to informing resource managers in determining the best stocking practice to enhance Atlantic salmon populations.

Inconsistent evolution and growth-survival tradeoffs in Gambusia affinis

Growth-survival tradeoffs may be a generalizable mechanism influencing trajectories of prey evolution. Here, we investigate evolutionary contributions to growth and survival in western mosquitofish (Gambusia affinis) from 10 populations from high- and low-predation ancestral environments. We assess (i) the degree to which evolutionary components of growth and survival are consistent or inconsistent across populations within ancestral predation environments, and (ii) whether growth and survival trade off at the population level. We measure growth and survival on groups of common-reared mosquitofish in pond mesocosms. We find that evolution of growth is consistent, with fish from low-predation ancestral environments showing higher growth, while the evolution of survival is inconsistent, with significant population-level divergence unrelated to ancestral predation environment. Such inconsistency prevents a growth-survival tradeoff across populations. Thus, the generalizability of contemporary evolution probably depends on local context of evolutionary tradeoffs, and a continued focus on singular selective agents (e.g. predators) without such local context will impede insights into generalizable evolutionary patterns.

Genome-wide analysis of natural and restored eastern oyster populations reveals local adaptation and positive impacts of planting frequency and broodstock number

The release of captive-bred plants and animals has increased worldwide to augment declining species. However, insufficient attention has been given to understanding how neutral and adaptive genetic variation are partitioned within and among proximal natural populations, and the patterns and drivers of gene flow over small spatial scales, which can be important for restoration success. A seascape genomics approach was used to investigate population structure, local adaptation, and the extent to which environmental gradients influence genetic variation among natural and restored populations of Chesapeake Bay eastern oysters Crassostrea virginica. We also investigated the impact of hatchery practices on neutral genetic diversity of restored reefs and quantified the broader genetic impacts of large-scale hatchery-based bivalve restoration. Restored reefs showed similar levels of diversity as natural reefs, and striking relationships were found between planting frequency and broodstock numbers and genetic diversity metrics (effective population size and relatedness), suggesting that hatchery practices can have a major impact on diversity. Despite long-term restoration activities, haphazard historical translocations, and high dispersal potential of larvae that could homogenize allele frequencies among populations, moderate neutral population genetic structure was uncovered. Moreover, environmental factors, namely salinity, pH, and temperature, play a major role in the distribution of neutral and adaptive genetic variation. For marine invertebrates in heterogeneous seascapes, collecting broodstock from large populations experiencing similar environments to candidate sites may provide the most appropriate sources for restoration and ensure population resilience in the face of rapid environmental change. This is one of a few studies to demonstrate empirically that hatchery practices have a major impact on the retention of genetic diversity. Overall, these results contribute to the growing body of evidence for fine-scale genetic structure and local adaptation in broadcast-spawning marine species and provide novel information for the management of an important fisheries resource.

Growth-enhanced salmon modify stream ecosystem functioning

Use of fast-growing domesticated and/or genetically modified strains of fish is becoming increasingly common in aquaculture, increasing the likelihood of deliberate or accidental introductions into the wild. To date, their ecological impacts on ecosystems remain to be quantified. Here, using a controlled phenotype manipulation by implanting growth hormone in juvenile Atlantic salmon (Salmo salar), we found that growth-enhanced fish display changes in several phenotypic traits known to be important for ecosystem functioning, such as habitat use, morphology and excretion rate. Furthermore, these phenotypic changes were associated with significant impacts on the invertebrate community and key stream ecosystem functions such as primary production and leaf-litter decomposition. These findings provide novel evidence that introductions of growth-enhanced fish into the wild can affect the functioning of natural ecosystems and represent a form of intraspecific invasion. Consequently, environmental impact assessments of growth-enhanced organisms need to explicitly consider ecosystem-level effects.

Population Structure, Genetic Connectivity, and Signatures of Local Adaptation of the Giant Black Tiger Shrimp (Penaeus monodon) throughout the Indo-Pacific Region

The giant black tiger shrimp (Penaeus monodon) is native to the Indo-Pacific and is the second most farmed penaeid shrimp species globally. Understanding genetic structure, connectivity, and local adaptation among Indo-Pacific black tiger shrimp populations is important for informing sustainable fisheries management and aquaculture breeding programs. Population genetic and outlier detection analyses were undertaken using 10,593 genome-wide single nucleotide polymorphisms (SNPs) from 16 geographically disparate Indo-Pacific P. monodon populations. Levels of genetic diversity were highest for Southeast Asian populations and were lowest for Western Indian Ocean (WIO) populations. Both neutral (n = 9,930) and outlier (n = 663) loci datasets revealed a pattern of strong genetic structure of P. monodon corresponding with broad geographical regions and clear genetic breaks among samples within regions. Neutral loci revealed seven genetic clusters and the separation of Fiji and WIO clusters from all other clusters, whereas outlier loci revealed six genetic clusters and high genetic differentiation among populations. The neutral loci dataset estimated five migration events that indicated migration to Southeast Asia from the WIO, with partial connectivity to populations in both oceans. We also identified 26 putatively adaptive SNPs that exhibited significant Pearson correlation (P < 0.05) between minor allele frequency and maximum or minimum sea surface temperature. Matched transcriptome contig annotations suggest putatively adaptive SNPs involvement in cellular and metabolic processes, pigmentation, immune response, and currently unknown functions. This study provides novel genome-level insights that have direct implications for P. monodon aquaculture and fishery management practices.

Has stocking contributed to an increase in the rod catch of anadromous trout (Salmo trutta L.) in the Shetland Islands, UK?

The stocking of hatchery-origin fish into rivers and lakes has long been used in fisheries management to try to enhance catches, especially for trout and salmon species. Frequently, however, the long-term impacts of stocking programmes have not been evaluated. In this study, the authors investigate the contribution of a stocking programme undertaken to support the rod catch of sea trout in the Shetland Islands, UK. Once a highly productive recreational fishery, Shetland sea trout catches crashed in the mid-1990s. Around the time that stocking began, increases in rod catches were also reported, with advocates of the stocking highlighting the apparent success of the programme. Using a suite of genetic markers (microsatellites), this study explores the contribution of the stocking programme to the Shetland sea trout population. The authors found that the domesticated broodstock and wild spawned brown trout from seven streams were genetically distinct. Despite extensive stocking, wild spawned brown trout dominated, even in those streams with a long history of supplementation. The majority of sea trout caught and analysed were of wild origin - only a single individual was of pure stocked origin, with a small number of fish being of wild × stocked origins. This study suggests that stocking with a domesticated strain of brown trout has made only a very limited contribution to the Shetland Islands rod catch, and that the revival of sea trout numbers appears to be driven almost exclusively by recovery of trout spawned in the wild.

Wild Zebrafish Sentinels: Biological Monitoring of Site Differences Using Behavior and Morphology

Environmental change poses a devastating risk to human and environmental health. Rapid assessment of water conditions is necessary for monitoring, evaluating, and addressing this global health danger. Sentinels or biological monitors can be deployed in the field using minimal resources to detect water quality changes in real time, quickly and cheaply. Zebrafish (Danio rerio) are ideal sentinels for detecting environmental changes due to their biomedical tool kit, widespread geographic distribution, and well-characterized phenotypic responses to environmental disturbances. Here, we demonstrate the utility of zebrafish sentinels by characterizing phenotypic differences in wild zebrafish between two field sites in India. Site 1 was a rural environment with flowing water, low-hypoxic conditions, minimal human-made debris, and high iron and lead concentrations. Site 2 was an urban environment with still water, hypoxic conditions, plastic pollution, and high arsenic, iron, and chromium concentrations. We found that zebrafish from Site 2 were smaller, more cohesive, and less active than Site 1 fish. We also found sexually dimorphic body shapes within the Site 2, but not the Site 1, population. Advancing zebrafish sentinel research and development will enable rapid detection, evaluation, and response to emerging global health threats.

Whole-genome resequencing of large yellow croaker (Larimichthys crocea) reveals the population structure and signatures of environmental adaptation

Large yellow croaker is an economically important fish in China and East Asia. Despite its economic importance, genome-wide adaptions of domesticated large yellow croaker are largely unknown. Here, we performed whole-genome resequencing of 198 individuals of large yellow croaker obtained in the sea or from farmers in Zhoushan or Ningde. Population genomics analyses revealed the genetic population structure of our samples, reflecting the living environment. Each effective population size is estimated to be declining over generations. Moreover, we identified genetically differentiated genomic regions between the sea-captured population in the Zhoushan Sea area and that of the Ningde Sea area or between the sea-captured population and the farmed population in either area. Gene ontology analyses revealed the gene groups under selective sweep for the adaptation to the domesticated environment. All these results suggest that individuals of the large yellow croaker populations show genomic signatures of adaptation to different living environments.

Thermal tolerance and routine oxygen consumption of convict cichlid, Archocentrus nigrofasciatus, acclimated to constant temperatures (20 °C and 30 °C) and a daily temperature cycle (20 °C → 30 °C)

Organismal temperature tolerance and metabolic responses are correlated to recent thermal history, but responses to thermal variability are less frequently assessed. There is great interest in whether organisms that experience greater thermal variability can gain metabolic or tolerance advantages through phenotypic plasticity. We compared thermal tolerance and routine aerobic metabolism of Convict cichlid acclimated for 2 weeks to constant 20 °C, constant 30 °C, or a daily cycle of 20 → 30 °C (1.7 °C/h). Acute routine mass-specific oxygen consumption ([Formula: see text]O₂) and critical thermal maxima/minima (CTMax/CTMin) were compared between groups, with cycle-acclimated fish sampled from the daily minimum (20 °C, 0900 h) and maximum (30 °C, 1600 h). Cycle-acclimated fish demonstrated statistically similar CTMax at the daily minimum and maximum (39.0 °C, 38.6 °C) but distinct CTMin values, with CTMin 2.4 °C higher for fish sampled from the daily 30 °C maximum (14.8 °C) compared to the daily 20 °C minimum (12.4 °C). Measured acutely at 30 °C, [Formula: see text]O₂ decreased with increasing acclimation temperature; 20 °C acclimated fish had an 85% higher average [Formula: see text]O₂ than 30 °C acclimated fish. Similarly, acute [Formula: see text]O₂ at 20 °C was 139% higher in 20 °C acclimated fish compared to 30 °C acclimated fish. Chronic [Formula: see text]O₂ was measured in separate fish continually across the 20 → 30 °C daily cycle for all 3 acclimation groups. Chronic [Formula: see text]O₂ responses were very similar between groups between average individual hourly values, as temperatures increased or decreased (1.7 °C/h). Acute [Formula: see text]O₂ and thermal tolerance responses highlight "classic" trends, but dynamic, chronic trials suggest acclimation history has little effect on the relative change in oxygen consumption during a thermal cycle. Our results strongly suggest that the minimum and maximum temperatures experienced more strongly influence fish physiology, rather than the thermal cycle itself. This research highlights the importance of collecting data in both cycling and static (constant) thermal conditions, and further research should seek to understand whether ectotherm metabolism does respond uniquely to fluctuating temperatures.

Toward Genome-Based Selection in Asian Seabass: What Can We Learn From Other Food Fishes and Farm Animals?

Due to the steadily increasing need for seafood and the plateauing output of fisheries, more fish need to be produced by aquaculture production. In parallel with the improvement of farming methods, elite food fish lines with superior traits for production must be generated by selection programs that utilize cutting-edge tools of genomics. The purpose of this review is to provide a historical overview and status report of a selection program performed on a catadromous predator, the Asian seabass (Lates calcarifer, Bloch 1790) that can change its sex during its lifetime. We describe the practices of wet lab, farm and lab in detail by focusing onto the foundations and achievements of the program. In addition to the approaches used for selection, our review also provides an inventory of genetic/genomic platforms and technologies developed to (i) provide current and future support for the selection process; and (ii) improve our understanding of the biology of the species. Approaches used for the improvement of terrestrial farm animals are used as examples and references, as those processes are far ahead of the ones used in aquaculture and thus they might help those working on fish to select the best possible options and avoid potential pitfalls.

Restocking of Anabarilius grahami in Lake Fuxian, Southwest China: morphological and genetic effects

The restocking of the endangered Kanglang white minnow (Anabarilius grahami) in Lake Fuxian, China, has been conducted for 13 years. However, few studies have reported on the effectiveness of the captive breeding and release of this species. Here, we investigated variations in morphology, including body shape and skeletal deformities, and genetic features among hatchery-born and recaptured A. grahami from Lake Fuxian. Results showed that current hatchery-reared fish displayed a stubbier body shape than their wild conspecifics from the 1980s. Furthermore, high skeletal deformity ratios were found in two aquafarms (Luchong, 50%; Haikou, 45.2%), and the release of malformed fish elevated the skeletal deformity rate of wild stocks found near the Lake Fuxian release sites (west coast, 19.0%; east coast, 12.5%). Based on variations in the cytochrome b (cyt b) gene, existing A. grahami populations showed relatively high haplotype diversity and low nucleotide diversity. Hatchery populations exhibited reduced genetic variations based on microsatellite markers and reintroduction led to markedly lower genetic diversity around the west coast release sites of Lake Fuxian. Analysis of molecular variance (AMOVA) of cyt b and microsatellite analysis showed that the greatest genetic variations were found within populations, and genetic distance and Bayesian clustering analysis showed that the 14 populations clustered into one group. Based on morphological and genetic tests, we discuss corresponding recommendations, including release size, feed formulations, breeding strategies, and release tags, to minimize potential risks and improve hatchery practices for better restocking of this species.

When more is more: taking advantage of species diversity to move towards sustainable aquaculture

Human population growth has increased demand for food products, which is expected to double in coming decades. Until recently, this demand has been met by expanding agricultural area and intensifying agrochemical-based monoculture of a few species. However, this development pathway has been criticised due to its negative impacts on the environment and other human activities. Therefore, new production practices are needed to meet human food requirements sustainably in the future. Herein, we assert that polyculture practices can ensure the transition of aquaculture towards sustainable development. We review traditional and recent polyculture practices (ponds, recirculated aquaculture systems, integrated multi-trophic aquaculture, aquaponics, integrated agriculture-aquaculture) to highlight how they improve aquaculture through the coexistence and interactions of species. This overview highlights the importance of species compatibility (i.e. species that can live in the same farming environment without detrimental interactions) and complementarity (i.e. complementary use of available resources and/or commensalism/mutualism) to achieve efficient and ethical aquaculture. Overall, polyculture combines aspects of productivity, environmental protection, resource sharing, and animal welfare. However, several challenges must be addressed to facilitate polyculture development across the world. We developed a four-step conceptual framework for designing innovative polyculture systems. This framework highlights the importance of (i) using prospective approaches to consider which species to combine, (ii) performing integrated assessment of rearing environments to determine in which farming system a particular combination of species is the most relevant, (iii) developing new tools and strategies to facilitate polyculture system management, and (iv) implementing polyculture innovation for relevant stakeholders involved in aquaculture transitions.

Transcriptome analysis of the growth performance of hybrid mandarin fish after food conversion

During recent years, China has become a hotspot for the domestication of mandarin fish, and this is of great commercial value. Although the food preference of domesticated mandarin fish has been studied, little is known about genes regulating their growth. We raised hybrid mandarin fish on artificial feed for 3 months, the results showed that the survival rate of hybrid mandarin fish was 60.00%. Their total length and body weight were 18.34 ±0.43 cm and 100.44 ±4.87 g. The absolute length and weight gain rates were 0.14 cm/d and 1.08 g/d, respectively. Finally, RNA sequencing (RNA-Seq) was performed to identify potential genes and pathways activated in response to growth performance. The transcriptome analysis generated 68, 197 transcripts and 45,871 unigenes. Among them, 1025 genes were up-regulated and 593 genes were down-regulated between the fast- and slow-growth fish. Finally, we obtained 32 differentially expressed genes, which were mainly related to fatty acid biosynthesis (e.g. FASN and ACACB), collecting duct acid secretion (e.g. ATP6E and KCC4), cell cycle (e.g. CDC20 and CCNB), and the insulin-like growth factor (IGF) system (IGFBP1). These pathways might be related to the growth of hybrid mandarin fish. In addition, more potential single nucleotide polymorphisms (SNPs) were detected in the fast-growth fish than in the slow-growth fish. The results suggest that the interaction of metabolism and abundant alleles might determine the growth of hybrid mandarin fish after food conversion.

Whole genome re-sequencing reveals recent signatures of selection in three strains of farmed Nile tilapia (Oreochromis niloticus)

Nile tilapia belongs to the second most cultivated group of fish in the world, mainly because of its favorable characteristics for production. Genetic improvement programs and domestication process of Nile tilapia may have modified the genome through selective pressure, leaving signals that can be detected at the molecular level. In this work, signatures of selection were identified using genome-wide SNP data, by two haplotype-based (iHS and Rsb) and one F_ST based method. Whole-genome re-sequencing of 326 individuals from three strains (A, B and C) of farmed tilapia maintained in Brazil and Costa Rica was carried out using Illumina HiSeq 2500 technology. After applying conventional SNP-calling and quality-control filters, ~ 1.3 M high-quality SNPs were inferred and used as input for the iHS, Rsb and F_ST based methods. We detected several candidate genes putatively subjected to selection in each strain. A considerable number of these genes are associated with growth (e.g. NCAPG, KLF3, TBC1D1, TTN), early development (e.g. FGFR3, PFKFB3), and immunity traits (e.g. NLRC3, PIGR, MAP1S). These candidate genes represent putative genomic landmarks that could be associated to traits of biological and commercial interest in farmed Nile tilapia.

Are bivalves susceptible to domestication selection? Using starvation tolerance to test for potential trait changes in eastern oyster larvae

Conservation efforts are increasingly being challenged by a rapidly changing environment, and for some aquatic species the use of captive rearing or selective breeding is an attractive option. However, captivity itself can impose unintended artificial selection known as domestication selection (adaptation to culture conditions) and is relatively understudied for most marine species. To test for domestication selection in marine bivalves, we focused on a fitness-related trait (larval starvation resistance) that could be altered under artificial selection. Using larvae produced from a wild population of Crassostrea virginica and a selectively bred, disease-resistant line we measured growth and survival during starvation versus standard algal diet conditions. Larvae from both lineages showed a remarkable resilience to food limitation, possibly mediated by an ability to utilize dissolved organic matter for somatic maintenance. Water chemistry analysis showed dissolved organic carbon in filtered tank water to be at concentrations similar to natural river water. We observed that survival in larvae produced from the aquaculture line was significantly lower compared to larvae produced from wild broodstock (8 ± 3% and 21 ± 2%, respectively) near the end of a 10-day period with no food (phytoplankton). All larval cohorts had arrested growth and depressed respiration during the starvation period and took at least two days to recover once food was reintroduced before resuming growth. Respiration rate recovered rapidly and final shell length was similar between the two treatments Phenotypic differences between the wild and aquaculture lines suggest potential differences in the capacity to sustain extended food limitation, but this work requires replication with multiple selection lines and wild populations to make more general inferences about domestication selection. With this contribution we explore the potential for domestication selection in bivalves, discuss the physiological and fitness implications of reduced starvation tolerance, and aim to inspire further research on the topic.

Differential effects of the urban heat island on thermal responses of freshwater fishes from unmanaged and managed systems

A lack of understanding exists regarding how freshwater species will respond to increases in temperature associated with ongoing changes in climate. Non-urban to urban thermal gradients generated by urban heat islands can serve as models to characterize the effects of relatively consistent increases in temperature on freshwater ecosystems over several decades. This study investigates the apparent responses of two freshwater fish species, Campostoma anomalum (Central Stoneroller) and Lepomis macrochirus (Bluegill), to directional changes in temperature over the past century across the non-urban to urban gradient in the Saint Louis, Missouri region in the central United States. Differences in air temperature across this gradient have increased by approximately 3 °C since 1920. Critical thermal maximum (CTMax) assays were conducted on individuals from fish populations across this gradient from either streams (C. anomalum) or ponds (L. macrochirus) to assess whether thermal tolerance is associated with water temperature among sites. According to expectations based on the effect of an urban heat island, maximum water temperature at stream sites was positively correlated with percent urban landcover around the sites. Moreover, CTMax among populations of C. anomalum was positively correlated with maximum water temperature at each site, suggesting that this species has likely responded to increases in temperature over the past several decades. There was no relationship between percent urban landcover and maximum water temperature in the pond systems. There was also no relationship between CTMax and maximum water temperature among L. macrochirus populations. The pond systems and populations of L. macrochirus are highly managed, which may limit local physical and biological responses to increases in air temperature. Results suggest that freshwater habitats in urban environments and the species inhabiting these areas are responding differently to recent increases in air temperature, highlighting the complexity of the physical and biological components of these systems.

A two-phase approach to elicit and measure beliefs on management strategies: Fishers supportive and aware of trade-offs associated with stock enhancement

Understanding fisher beliefs and attitudes towards specific management strategies can help inform and improve fisheries management, and thus stock sustainability. Previous studies highlight a lack of fisher awareness regarding environmental issues influencing the systems they utilise and the negative impacts of specific strategies, such as stock enhancement. Our study used a two-phase approach to first elicit and then measure the strength of common fishers' beliefs and associated attitudes regarding stock enhancement. Specifically, this research focused on recreational fishers of an estuarine crab fishery (Portunus armatus) in south-western Australia. The results demonstrate that recreational fishers believe stock enhancement could have strong positive outcomes, but also recognise that this management strategy could lead to some negative outcomes, though the latter are perceived as less likely to happen. This contrasts with previous research on fisheries stocking and demonstrates the value of using the two-phase approach to clarify fishers' perceptions of particular management approaches. To reduce fisher dissatisfaction with management actions, careful communication on the benefits and costs of stock enhancement is recommended. Our study highlights the significance of integrating social sciences into fisheries research, and the need to better understand fishing community beliefs to ensure effective management of the fishery.

A pilot study of the performance of captive-reared delta smelt Hypomesus transpacificus in a semi-natural environment

A captive breeding programme was developed in 2008 for delta smelt Hypomesus transpacificus in reaction to dramatic population decline over several decades. We took 526 sub-adult captive-reared delta smelt and cultured them for 200 days without providing artificial food or water quality management to assess their performance once released in the wild. The results indicated captive-reared sub-adult delta smelt could survive in a semi-natural environment with uncontrolled water quality and naturally produced wild prey through spawning and into their post spawning phase.

Multiple Selection Signatures in Farmed Atlantic Salmon Adapted to Different Environments Across Hemispheres

Domestication of Atlantic salmon started approximately 40 years ago, using artificial selection through genetic improvement programs. Selection is likely to have imposed distinctive signatures on the salmon genome, which are often characterized by high genetic differentiation across population and/or reduction in genetic diversity in regions associated to traits under selection. The identification of such selection signatures may give insights into the candidate genomic regions of biological and commercial interest. Here, we used three complementary statistics to detect selection signatures, two haplotype-based (iHS and XP-EHH), and one F_ST-based method (BayeScan) among four populations of Atlantic salmon with a common genetic origin. Several regions were identified for these techniques that harbored genes, such as kind1 and chp2, which have been associated with growth-related traits or the kcnb2 gene related to immune system in Atlantic salmon, making them particularly relevant in the context of aquaculture. Our results provide candidate genes to inform the evolutionary and biological mechanisms controlling complex selected traits in Atlantic salmon.

The relationship between semen seminal plasma ions and sperm cell velocities of wild-caught longspine scraper, Capoeta trutta

In this study, semen seminal plasma contents and the motility of sperm cells were determined in Capoeta trutta via a computer-assisted sperm analysis system. In addition, we evaluated the relationship between semen seminal plasma ions and the velocities of sperm cells. Although the predominant ions were K ( 206.84 ± 20.61  mg L- 1 ) and Na ( 128.06 ± 23.82  mg L- 1 ) in the semen seminal plasma, Ca ( 14.05 ± 4.13  mg L- 1 ) and Mg ( 3.35 ± 0.44  mg L- 1 ) were not predominate according to our results. However, partially strong relationships between the curvilinear velocity value (VCL) and K (R 2 = 0.67 ; p < 0.05 ) were found, while it was moderate with Mg (R 2 = 0.48 ; p < 0.05 ). There was a weak relationship with Na (R 2 = 0.17 ; p < 0.05 ) and Ca (R 2 = 0.34 ; p < 0.05 ). In our results, while the trace metals were determined as Zn > Al > B > Li > Cu in semen seminal plasma, they are not correlated with sperm cell velocities. Finally, we hope that the present information on the motility parameters of Capoeta trutta in this paper will eventually help artificial insemination in reproduction practices.

A Conservation Hatchery Population of Delta Smelt Shows Evidence of Genetic Adaptation to Captivity After 9 Generations

Genetic adaptation to captivity is a concern for threatened and endangered species held in conservation hatcheries. Here, we present evidence of genetic adaptation to captivity in a conservation hatchery for the endangered delta smelt (Fish Conservation and Culture Laboratory, University of California Davis; FCCL). The FCCL population is genetically managed with parentage analysis and the addition of wild fish each year. Molecular monitoring indicates little loss of genetic variation and low differentiation between the wild and conservation populations. Yet, we found an increase in offspring survival to reproductive maturity during the subsequent spawning season (recovery rate) in crosses that included one or both cultured parents. Crosses with higher levels of hatchery ancestry tend to produce a greater number of offspring that are recovered the following year. The recovery rate of a cross decreases when offspring are raised in a tank with fish of high levels of hatchery ancestry. We suggest changes in fish rearing practices at the FCCL to reduce genetic adaptation to captivity, as delta smelt numbers in the wild continue to decline and the use of FCCL fish for reintroduction becomes more likely.

Tracking genetic diversity in a large-scale oyster restoration program: effects of hatchery propagation and initial characterization of diversity on restored vs. wild reefs

The release of hatchery-propagated fish and shellfish is occurring on a global scale, but the genetic impacts of these practices are often not fully understood and rarely monitored. Slow recovery of depleted eastern oyster populations in the Chesapeake Bay, USA has prompted a hatchery-based restoration program focused in the Choptank River, Maryland consisting of the mass release of hatchery-produced juveniles from local, wild broodstock. To evaluate potential genetic effects of this program, we (1) examined changes in genetic diversity (allelic richness, heterozygosity) and the effective number of breeders (Nb) over the hatchery production cycle with microsatellite-based parentage of natural, mass- and controlled-spawned cohorts, and (2) compared genetic diversity and effective population size (Ne) of a restored reef to wild source populations. Mass-spawned cohorts showed high variance in reproductive contribution, particularly among males, leading to a 45% average reduction in Nb from spawning adult numbers and higher relatedness-lower magnitude reductions in heterozygosity and significant reductions in allelic richness were also observed. While controlled-spawns (single-male fertilizations of pooled eggs) reduced male variance, overall reproductive variance (Vk) remained high. Finally, oysters sampled from a restored reef displayed comparable Ne, genetic diversity, and relatedness to samples from wild populations, with no significant genetic differentiation among them. Overall, the hatchery-based results and initial field-based population genetic analyses suggest that despite reductions in diversity from parents to offspring owing to high Vk, enhancement with rotated, wild broodstock appears to have maintained genetic diversity in a restored reef population compared to proximal wild populations.

Are model organisms representative for climate change research? Testing thermal tolerance in wild and laboratory zebrafish populations

Model organisms can be useful for studying climate change impacts, but it is unclear whether domestication to laboratory conditions has altered their thermal tolerance and therefore how representative of wild populations they are. Zebrafish in the wild live in fluctuating thermal environments that potentially reach harmful temperatures. In the laboratory, zebrafish have gone through four decades of domestication and adaptation to stable optimal temperatures with few thermal extremes. If maintaining thermal tolerance is costly or if genetic traits promoting laboratory fitness at optimal temperature differ from genetic traits for high thermal tolerance, the thermal tolerance of laboratory zebrafish could be hypothesized to be lower than that of wild zebrafish. Furthermore, very little is known about the thermal environment of wild zebrafish and how close to their thermal limits they live. Here, we compared the acute upper thermal tolerance (critical thermal maxima; CT_max) of wild zebrafish measured on-site in West Bengal, India, to zebrafish at three laboratory acclimation/domestication levels: wild-caught, F₁ generation wild-caught and domesticated laboratory AB-WT line. We found that in the wild, CT_max increased with increasing site temperature. Yet at the warmest site, zebrafish lived very close to their thermal limit, suggesting that they may currently encounter lethal temperatures. In the laboratory, acclimation temperature appeared to have a stronger effect on CT_max than it did in the wild. The fish in the wild also had a 0.85-1.01°C lower CT_max compared to all laboratory populations. This difference between laboratory-held and wild populations shows that environmental conditions can affect zebrafish's thermal tolerance. However, there was no difference in CT_max between the laboratory-held populations regardless of the domestication duration. This suggests that thermal tolerance is maintained during domestication and highlights that experiments using domesticated laboratory-reared model species can be appropriate for addressing certain questions on thermal tolerance and global warming impacts.

Hatchery-reared enhancement program for silver carp (Hypophthalmichthys molitrix) in the middle Yangtze River: monitoring the effectiveness based on parentage analysis

Introduction

A hatchery-reared silver carp (Hypophthalmichthys molitrix) program has been intensively carried out since 2010 to enhance the rapidly declining fisheries production in the middle Yangtze River. However, only a little information regarding the effectiveness of the enhancement program has been reported. In this context, this study investigates on an enhancement program through monitoring the efficacy based on parentage analysis.

Methods

A total of 1,529 hatchery-reared fish and 869 larvae were sampled from the middle Yangtze River in 2016 and 2017 and were genotyped by thirteen microsatellite loci. Based on the results of parentage analysis the larvae were divided into three populations: (1) larvae population with both parents being hatchery-reared fish (=R), (2) larvae population with only a male or a female parent being hatchery-reared fish (=H), and (3) larvae population with no hatchery-reared fish parent (=W). The following analyses were also carried out: (1) assessing the contribution of hatchery-reared offspring to larval resources, and (2) evaluating the genetic effect of stock enhancement on the wild population.

Results

In total, 10.37% and 11.56% of larvae were identified as the offspring produced by hatchery-reared fish released in 2016 and 2017, respectively. In 2017, some of the larvae were assigned unambiguously to hatchery-reared fish released in 2016. In terms of the number of offspring produced, the hatchery-reared fish have shown significant variations. No significant differences were found among all the larvae populations concerning genetic parameters for diversity. High levels of genetic diversity of all larvae populations were obtained. Low F _STvalues obtained from pairwise F _ST analysis, as well as the analysis of molecular variance (AMOVA), revealed high genetic structural similarity among all the larvae populations. The genetic composition of the W larvae population in 2017 was different from that of all other larvae populations (all larvae populations in 2016, and R and H larvae populations in 2017), as demonstrated from the results of STRUCTURE and PCA analyses.

Conclusion

It was demonstrated that hatchery-reared fish are successful in producing the offspring in the natural environment during multiple years, which might assist in increasing the abundance of larvae. The hatchery-reared fish had variations in terms of the success rates on reproduction. Also, the hatchery-reared enhancement program had no significant effect on the genetic diversity or the genetic structure of wild populations. However, the genetic component of the W larvae population in 2017 was changed as compared to 2016, which was not due to the hatchery-reared enhancement program for silver carp. This could be due to flooding, but the specific causes need further studies. Our results clearly show the necessity to continuously inspect the genetic impact of the enhancement program so that historical information can be utilized for further research.

A Global Assessment of Welfare in Farmed Fishes: The FishEthoBase

Fish welfare is an essential issue that needs to be tackled by the aquaculture industry. In order to address it, studies have been limited to a small number of species and the information is generally scattered. In order to have a consistent overview of the welfare of farmed fishes, we present the FishEthoBase, an open-access database that ultimately aims to provide information on the welfare of all fish species currently farmed worldwide. Presently with 41 species, this database is directed to all stakeholders in the field and targets not only to bridge the gaps between them but also to provide scientific information to improve the welfare of fish. The current text explains the database and presents an analysis of the welfare scores of 41 species, suggesting that (i) the general welfare state of farmed fishes is poor, (ii) there is some potential for improvement and (iii) this potential is related to research on species’ needs, but (iv) there are many remaining knowledge gaps and (v) current fish farming technologies do not seem to fully address welfare issues. The existence of a framework, such as the FishEthoBase, is proposed as fundamental to the design of strategies that improve the welfare of farmed fish.

Life history and temporal variability of escape events interactively determine the fitness consequences of aquaculture escapees on wild populations

Domesticated individuals are likely to be maladaptive in the wild due to adaptation to captivity. Escaped aquaculture fish can cause unintended fitness and demographic consequences for their wild conspecifics through interbreeding and competition. Escape events from different sources exhibit great heterogeneity in their frequencies and magnitudes, ranging from rare but large spillover during a storm, to continuous low-level leakage caused by operational errors. The timescale of escape events determines the distribution of gene flow from aquaculture to the wild. The evolutionary consequences of this variation in timescale will depend on the degree of generation overlap and the focal species' life history attributes, especially those under selection in aquaculture (e.g., growth rate, which can influence additional demographically important traits such as age at maturity). To evaluate the effects of variable escape both within and across generations, we construct an age-structured model of coupled genetic and demographic dynamics and parameterize it for species with contrasting life history characteristics (Salmo salar and Gadus morhua). Our results are consistent with earlier discrete-generation models that constant, low-level spillover can have a greater impact than rare, large pulses of leakage, even after accounting for the averaging effects of overlapping generations. The age-structured model also allows detailed evaluation of the role of different life history traits, which reveals that species with longer generation times might experience greater fitness consequences of aquaculture spillover but are less sensitive to variability in spillover. Additionally, environment-induced earlier maturity of escapees can increase the fitness effects on wild fish, especially those with shorter generation times. Our results suggest that effective management to minimize the unintended fitness consequences of aquaculture releases might require extensive monitoring efforts on constant, low-level spillover and assessment of the focal species' life history characteristics.