An evaluation of the effects of conservation and fishery enhancement hatcheries on wild populations of salmon

Brown trout in Oder estuary tributaries: genetic structure, stocking, and admixture

Several rivers that are tributaries of the Oder estuary are inhabited by Salmo trutta L, the most important of which are Ina, Gowienica, and Wołczenica. Both forms of the species, sea trout and resident brown trout, are present. All rivers are traditionally stocked with either sea trout from the neighboring Pomeranian river Rega basin or resident brown trout from various locations. To examine populations in these rivers in terms of genetic structure, genetic diversity, and origin, they were analyzed using 13 microsatellite loci. Relatedness was also assessed for fish stocked in the same year. The obtained genotypes were compared with breeding stocks used for stocking in Poland. The analyses revealed a significant genetic distance between adult individuals from Ina and Rega Rivers and fish caught during electrofishing. Strong kinship relationships were identified in the sampled areas, with high proportions of fish originating from stocking and their dominance in numbers over wild juveniles, primarily in smaller tributaries. Additionally, clear separation in the origin of stocked individuals was observed. Adult trout from Ina and Rega are genetically closer to northern brown trout lineages, providing crucial information for the management and biodiversity conservation of Polish Salmo trutta populations.

Competitive interactions affect introgression and population viability amidst maladaptive hybridization

The deliberate release of captive-bred individuals, the accidental escape of domesticated strains, or the invasion of closely related conspecifics into wild populations can all lead to introgressive hybridization, which poses a challenge for conservation and wildlife management. Rates of introgression and the magnitude of associated demographic impacts vary widely across ecological contexts. However, the reasons for this variation remain poorly understood. One rarely considered phenomenon in this context is soft selection, wherein relative trait values determine success in intraspecific competition for a limiting resource. Here we develop an eco-genetic model explicitly focussed on understanding the influence of such competitive interactions on the eco-evolutionary dynamics of wild populations experiencing an influx of foreign/domesticated individuals. The model is applicable to any taxon that experiences natural or human-mediated inputs of locally maladapted genotypes ('intrusion'), in addition to phenotype-dependent competition for a limiting resource (e.g. breeding sites, feeding territories). The effects of both acute and chronic intrusion depended strongly on the relative competitiveness of intruders versus locals. When intruders were competitively inferior, density-dependent regulation limited their reproductive success (ability to compete for limited spawning sites), which prevented strong introgression or population declines from occurring. In contrast, when intruders were competitively superior, this amplified introgression and led to increased maladaptation of the admixed population. This had negative consequences for population size and population viability. The results were sensitive to the intrusion level, the magnitude of reproductive excess, trait heritability and the extent to which intruders were maladapted relative to locals. Our findings draw attention to under-appreciated interactions between phenotype-dependent competitive interactions and maladaptive hybridization, which may be critical to determining the impact captive breeding programmes and domesticated escapees can have on otherwise self-sustaining wild populations.

Invasion status of hatchery-origin pink salmon in an unstocked river at the Shiretoko World Natural Heritage Site in northern Japan

Hatchery fish and their offspring (including hatchery-wild hybrids) have lower reproductive success than wild fish. Thus, the straying of hatchery fish may negatively impact wild populations, depending on the number of wild salmon returning and hatchery strays. We investigated the straying status of hatchery-origin pink salmon (Oncorhynchus gorbuscha), which have a higher straying rate than other salmonids, in an unstocked river at the Shiretoko World Natural Heritage Site, Japan. The hatchery strays accounted for 40.0% and 19.0% of the total samples in 2021 and 2022, respectively. These results indicate that hatchery pink salmon have invaded unstocked rivers and potentially genetically affect wild populations.

Selection among critically endangered landlocked salmon (Salmo salar m. sebago) families in survival and growth traits across early life stages and in different environments

Endangered wild fish populations are commonly supported by hatchery propagation. However, hatchery-reared fish experience very different selective pressures compared to their wild counterparts, potentially causing genotype-by-environment interactions (G × E) in essential fitness traits. We experimentally studied early selection in a critically endangered landlocked Atlantic salmon population, first from fertilization to the swim-up stage in a common hatchery setting, and thereafter until the age of 5 months in two contrasting rearing environments. Swim-up progeny were moved either to standard indoor hatchery tanks involving conventional husbandry or to seminatural outdoor channels providing only natural food. After the first summer, sampled survivors were assigned to their families by genotyping. Early survival until the swim-up stage was mostly determined by maternal effects, but also involved significant variation due to sires and full-sib families (potential genetic effects). High on-growing survival in hatchery tanks (88.7%) maintained a more even distribution among families (relative share 1.5%-4.2%) than the seminatural environment (0.0%-5.4%). This heterogeneity was mostly maternal, whereas no independent paternal effect occurred. Heritability estimates were high for body size traits in both environments (0.62-0.69). Genetic correlations between the environments were significantly positive for body size traits (0.67-0.69), and high body condition in hatchery was also genetically linked to rapid growth in the seminatural environment (0.54). Additive and phenotypic growth variation increased in the seminatural environment, but scaling effects probably played a less significant role for G × E, compared to re-ranking of genotypes. Our results suggest that not only maternal effects, but also genetic effects, direct selection according to the environmental conditions experienced. Consistently high genetic variation in growth implies that, despite its low overall genetic diversity and long history in captive rearing (>50 years), this landlocked Atlantic salmon population still possesses adaptive potential for response to change from hatchery rearing back to more natural conditions.

Estimating blue mussel (Mytilus edulis) connectivity and settlement capacity in mid-latitude fjord regions

The mussel industry faces challenges such as low and inconsistent levels of larvae settlement and poor-quality spat, leading to variable production. However, mussel farming remains a vital sustainable and environmentally responsible method for producing protein, fostering ecological responsibility in the aquaculture sector. We investigate the population connectivity and larval dispersion of blue mussels (Mytilus edulis) in Scottish waters, as a case study, using a multidisciplinary approach that combined genetic data and particle modelling. This research allows us to develop a thorough understanding of blue mussel population dynamics in mid-latitude fjord regions, to infer gene-flow patterns, and to estimate population divergence. Our findings reveal a primary south-to-north particle transport direction and the presence of five genetic clusters. We discover a significant and continuous genetic material exchange among populations within the study area, with our biophysical model's outcomes aligning with our genetic observations. Additionally, our model reveals a robust connection between the southwest coast and the rest of the west coast. This study will guide the preservation of mussel farming regions, ensuring sustainable populations that contribute to marine ecosystem health and resilience.

Hatchery supplementation provides a demographic boost but alters age composition of sockeye salmon in Auke Lake, Southeast Alaska

Evaluating salmon hatchery supplementation programs requires assessing not only program objectives but identifying potential risks to wild populations as well. Such evaluations can be hampered by difficulty in distinguishing between hatchery- and wild-born returning adults. Here, we conducted 3 years (2011-2013) of experimental hatchery supplementation of sockeye salmon in Auke Lake, Juneau, Alaska where a permanent weir allows sampling and genotyping of every returning adult (2008-2019). We identified both hatchery- and wild-born returning adults with parentage assignment, quantified the productivity (adult offspring/spawner) of hatchery spawners relative to that of wild spawners, and compared run timing, age, and size at age between hatchery- and wild-born adults. Hatchery-spawning females produced from approximately six to 50 times more returning adults than did naturally spawning females. Supplementation had no discernable effect on run timing and limited consequences for size at age, but we observed a distinct shift to younger age at maturity in the hatchery-born individuals in all three brood years. The shift appeared to be driven by hatchery-born fish being more likely to emigrate after one, rather than two, years in the lake but the cause is unknown. In cases when spawning or incubation habitat is limiting sockeye salmon production, hatchery supplementation can be effective for enhancing the number of returning adult fish but not without the risk of phenotypic change in the recipient population, which can be an undesired outcome of hatchery supplementation. This study adds to a growing body of evidence suggesting that phenotypic change within a single generation of captive spawning might be widespread in salmon hatchery programs.

Influence of Pediveliger Larvae Stocking Density on Settlement Efficiency and Seed Production in Captivity of Mytilus galloprovincialis in Amsa Bay, Tetouan

In mussel hatchery systems, the settlement process is a crucial element influencing seed yield. The current study assayed the influence of five densities of competent pediveliger larvae on settlement success and post-larvae production. We showed an inverse relationship between density and settlement efficiency, e.g., an attachment success of 99.4% at the lowest density (35 larvae/cm2) but only 9% at the highest density (210 larvae/cm2). However, post-larvae production was higher at intermediate larvae densities (70 larvae/cm2). The reimplementation of treatments upon post-larvae density after 6 weeks post settlement showed that the lowest-density groups bore both the highest post-larvae growth rate (22.24 ± 4.60 µm/day) and the largest head batch (48% of the size distribution), as compared to the higher-post-larvae-density groups. These results highlight the importance of optimizing both pediveliger larvae density and post-larvae density, to maximize high-quality seed yield in local hatcheries. Current rearing technologies would assure a timely commercial seed production to protect natural sea rocky beds in Alboran Sea coasts.

Tidal gradients, fine-scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha)

The homing behaviour of salmon is a remarkable natural phenomenon, critical for shaping the ecology and evolution of populations yet the spatial scale at which it occurs is poorly understood. This study investigated the spatial scale and mechanisms driving homing as depicted by spawning site-choice behaviour in pink salmon (Oncorhynchus gorbuscha) in Prince William Sound, Alaska. Molecular pedigree analyses of over 30,000 adult spawners in four streams revealed that pink salmon exhibit fine-scale site fidelity within a stream, returning to within <100 m of their parents. Homing behaviours were driven in part by a salinity gradient between intertidal and freshwater environments, with individuals incubated in freshwater environments more than twice as likely to spawn upstream of tidal influence than those incubated in the intertidal. Our findings challenge the traditional view that pink salmon populations are genetically and phenotypically homogenous due to their short freshwater residency as juveniles and high rates of dispersal as returning adults (i.e. straying). This study has important implications for rates of inbreeding, local adaptation and gene flow within populations, and is particularly relevant to the management of salmon hatcheries, given the high incidence of hatchery-origin pink salmon, reared in freshwater hatchery environments, that stray into wild populations of Prince William Sound.

ISOTHERMAL RECOMBINANT POLYMERASE AMPLIFICATION AND CRIPSR(CAS12A) ASSAY DETECTION OF RENIBACTERIUM SALMONINARUM AS AN EXAMPLE FOR WILDLIFE PATHOGEN DETECTION IN ENVIRONMENTAL DNA SAMPLES

Improving rapid detection methods for pathogens is important for research as we collectively aim to improve the health of ecosystems globally. In the northern hemisphere, the success of salmon (Oncorhynchus spp.) populations is vitally important to the larger marine, aquatic, and terrestrial ecosystems they inhabit. This has led to managers cultivating salmon in hatcheries and aquaculture to bolster their populations, but young salmon face many challenges, including diseases such as bacterial kidney disease (BKD). Early detection of the BKD causative agent, Renibacterium salmoninarum, is useful for managers to avoid outbreaks in hatcheries and aquaculture stocks to enable rapid treatment with targeted antibiotics. Isothermal amplification and CRIPSR-Cas12a systems may enable sensitive, relatively rapid, detection of target DNA molecules from environmental samples compared to quantitative PCR (qPCR) and culture methods. We used these technologies to develop a sensitive and specific rapid assay to detect R. salmoninarum from water samples using isothermal recombinase polymerase amplification (RPA) and an AsCas12a RNA-guided nuclease detection. The assay was specific to R. salmoninarum (0/10 co-occurring or closely related bacteria detected) and sensitive to 0.0128 pg/µL of DNA (approximately 20-40 copies/µL) within 10 min of Cas activity. This assay successfully detected R. salmoninarum environmental DNA in 14/20 water samples from hatcheries with known quantification for the pathogen via previous qPCR (70% of qPCR-positive samples). The RPA-CRISPR/AsCas12a assay had a limit of detection (LOD) of >10 copies/µL in the hatchery water samples and stochastic detection below 10 copies/µL, similar to but slightly higher than the qPCR assay. This LOD enables 37 C isothermal detection, potentially in the field, of biologically relevant levels of R. salmoninarum in water. Further research is needed to develop easy-to-use, cost-effective, sensitive RPA/CRISPR-AsCas12a assays for rapidly detecting low concentrations of wildlife pathogens in environmental samples.

Coproduction and modeling spatial contact networks prevent bias about infectious hematopoietic necrosis virus transmission for Snake River Basin salmonids

Much remains unknown about variation in pathogen transmission across the geographic range of a free-ranging fish or animal species and about the influence of movement (associated with husbandry practices or animal behavior) on pathogen transmission. Salmonid hatcheries are an ideal system in which to study these processes. Salmonid hatcheries are managed for endangered species recovery, supplementation of threatened or at-risk fish stocks, support of fisheries, and ecosystem stability. Infectious hematopoietic necrosis virus (IHNV) is a rhabdovirus of significant concern to salmon aquaculture. Landscape IHNV transmission dynamics previously had been estimated only for salmonid hatcheries in the Lower Columbia River Basin (LCRB). The objectives of this study were to estimate IHNV transmission dynamics in a unique geographic region, the Snake River Basin (SRB), and to quantitatively estimate the effect of model coproduction on inference because previous assessments of coproduction have been qualitative. In contrast to the LCRB, the SRB has hatchery complexes consisting of a main hatchery and ≥1 satellite facility. Knowledge about hatchery complexes was held by a subset of project researchers but would not have been available to project modelers without coproduction. Project modelers generated and tested multiple versions of Bayesian susceptible-exposedinfected models to realistically represent the SRB and estimate the effect of coproduction. Models estimated the frequency of transmission routes, route-specific infection probabilities, and infection probabilities for combinations of salmonid hosts and IHNV lineages. Model results indicated that in the SRB, avoiding exposure to IHNV-positive adult salmonids is the most important action to prevent juvenile infections. Migrating adult salmonids exposed juvenile cohort-sites most frequently, and the infection probability was greatest following exposure to migrating adults. Without coproduction, the frequency of exposure by migrating adults would have been overestimated by 70 cohort-sites, and the infection probability following exposure to migrating adults would have been underestimated by∼0.09. The coproduced model had less uncertainty in the infection probability if no transmission route could be identified (Bayesian credible interval (BCI) width = 0.12) compared to the model without coproduction (BCI width = 0.34). Evidence for virus lineage MD specialization on steelhead and rainbow trout (both Oncorhynchus mykiss) was apparent without model coproduction. In the SRB, we found a greater probability of virus lineage UC infection in Chinook salmon (Oncorhynchus tshawytscha) compared to in O. mykiss, whereas in the LCRB, UC more clearly exhibited a generalist approach. Coproduction influenced estimates that depended on transmission routes, which operated differently at main hatcheries and satellite sites within hatchery complexes. Hatchery complexes are found outside of the SRB and are not specific to salmonid hatcheries alone. There is great potential for coproduction and modeling spatial contact networks to advance understanding about infectious disease transmission in complex production systems and surrounding free-ranging animal populations.

Parentage-based tagging and parentage analyses of stocked sea trout in Vistula River commercial catches

The longest Baltic River, the Vistula, historically hosted numerous sea trout populations. However, dam construction in the twentieth century drastically reduced the spawning migration rate. Reduced natural reproduction has resulted in a population collapse and, consequentially, a substantial reduction in catches. In response, like other Baltic countries, Poland has initiated an intensive stocking program, mainly involving smolt. Initially, stocking was conducted primarily with offspring of sea trout caught during spawning migration. Currently, due to difficulties in obtaining fish, most stocking involves fish from breeding stocks. Therefore, determining the proportion of fish derived from stocking has become an important issue. Experiments based on traditional tagging did not provide sufficient material for analysis; hence, we decided to use genetic methods based on analysis of relatedness. In this study, we performed parentage-based tagging and an analysis of the origins of parent animals used for artificial spawning in 2013, and offspring returning to the Vistula in subsequent years. We based the analysis on three different algorithms and compared the results, showing that the presented methods were effective for estimating mass stocking success. The study also indicated that a certain level of natural reproduction in the Vistula continues to occur. The proportion of sea trout from spawning in 2013 in Vistula sea trout catches from 2017 to 2018 was approximately 30%.

Fished or farmed: Life cycle impacts of salmon consumer decisions and opportunities for reducing impacts

Salmon is a nutritious and popular food among consumers predominantly in wealthy countries around the world. Since the mid-1990s farmed salmon production has exceeded wild salmon harvest, and is now 80 % of total global salmon supply. The environmental impacts of farmed salmon are frequently discussed and consumers are faced with a multitude of choices even after deciding to have salmon for dinner: species, production method, origin, product form. We present life cycle impacts of fresh and frozen salmon products, originating in purse seine fisheries for pink salmon and gill net fisheries for sockeye salmon in Alaska, when sold on markets in Europe and the United States. Norwegian salmon products are then modelled to the same markets in fresh and frozen form, based on literature data. Impact categories included were greenhouse gas emissions, marine eutrophication, marine ecotoxicity and land use. A fish in, fish out ratio is also calculated and differences in content of nutrients and contaminants described. Frozen products from wild sockeye and pink salmon had the lowest emissions in both markets. For consumers in the U.S. and Europe, wild salmon products have 46-86 % and 12-71 % lower greenhouse gas emissions than farmed Norwegian salmon, respectively, depending on species and product form. Farmed salmon also had higher land use, marine ecotoxic and eutrophying emissions and fish in, fish out ratio. Important differences exist in nutritional and contaminant content between the three types of salmon production. Improvement options as well as an optimized supply chain are modelled showing greenhouse gas reduction opportunities of 40-50 % also for the best performing chains. Results can be used as a baseline for improved data collection and emission reductions. Recommendations for consumers, industry and policymakers who can facilitate and even drive development towards more sustainable salmon products are provided.

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 relative fitness in hatchery‐origin Pink Salmon in two streams in Prince William Sound, Alaska

Previous studies generally report that hatchery‐origin Pacific Salmon (Oncorhynchus spp.) have lower relative reproductive success (RRS) than their natural‐origin counterparts. We estimated the RRS of Pink Salmon (O. gorbuscha) in Prince William Sound (PWS), Alaska using incomplete pedigrees. In contrast to other RRS studies, Pink Salmon have a short freshwater life history, freshwater habitats in PWS are largely unaltered by development, and sampling was conducted without the aid of dams or weirs resulting in incomplete sampling of spawning individuals. Pink Salmon released from large‐scale hatchery programs in PWS have interacted with wild populations for more than 15 generations. Hatchery populations were established from PWS populations but have subsequently been managed as separate broodstocks. Gene flow is primarily directional, from hatchery strays to wild populations. We used genetic‐based parentage analysis to estimate the RRS of a single generation of stray hatchery‐origin Pink Salmon in two streams, and across the odd‐ and even‐year lineages. Despite incomplete sampling, we assigned 1745 offspring to at least one parent. Reproductive success (RS), measured as sampled adult offspring that returned to their natal stream, was significantly lower for hatchery‐ vs. natural‐origin parents in both lineages, with RRS ranging from 0.03 to 0.47 for females and 0.05 to 0.86 for males. Generalized linear modeling for the even‐year lineage indicated that RRS was lower for hatchery‐origin fish, ranging from 0.42 to 0.60, after accounting for sample date (run timing), sample location within the stream, and fish length. Our results strongly suggest that hatchery‐origin strays have lower fitness in the wild. The consequences of reduced RRS on wild productivity depend on whether the mechanisms underlying reduced RRS are environmentally driven, and likely ephemeral, or genetically driven, and likely persistent across generations.

North American diadromous fishes: Drivers of decline and potential for recovery in the Anthropocene

Diadromous fishes migrate between freshwater and marine habitats to complete their life cycle, a complexity that makes them vulnerable to the adverse effects of current and past human activities on land and in the oceans. Many North American species are critically endangered, and entire populations have been lost. Major factors driving declines include overfishing, pollution, water withdrawals, aquaculture, non-native species, habitat degradation, over-zealous application of hatcheries designed to mitigate effects of other factors, and effects of climate change. Perhaps, the most broadly tractable and effective factors affecting diadromous fishes are removals of the dams that prevent or hinder their migrations, alter their environment, and often favor non-native biotic communities. Future survival of many diadromous fish populations may depend on this.

Identification of infectious agents in early marine Chinook and Coho salmon associated with cohort survival

Recent decades have seen an increased appreciation for the role infectious diseases can play in mass mortality events across a diversity of marine taxa. At the same time many Pacific salmon populations have declined in abundance as a result of reduced marine survival. However, few studies have explicitly considered the potential role pathogens could play in these declines. Using a multi-year dataset spanning 59 pathogen taxa in Chinook and Coho salmon sampled along the British Columbia coast, we carried out an exploratory analysis to quantify evidence for associations between pathogen prevalence and cohort survival and between pathogen load and body condition. While a variety of pathogens had moderate to strong negative correlations with body condition or survival for one host species in one season, we found that Tenacibaculum maritimum and Piscine orthoreovirus had consistently negative associations with body condition in both host species and seasons and were negatively associated with survival for Chinook salmon collected in the fall and winter. Our analyses, which offer the most comprehensive examination of associations between pathogen prevalence and Pacific salmon survival to date, suggest that pathogens in Pacific salmon warrant further attention, especially those whose distribution and abundance may be influenced by anthropogenic stressors.

Environment-driven reprogramming of gamete DNA methylation occurs during maturation and is transmitted intergenerationally in Atlantic Salmon

An epigenetic basis for transgenerational plasticity in animals is widely theorized, but convincing empirical support is limited by taxa-specific differences in the presence and role of epigenetic mechanisms. In teleost fishes, DNA methylation generally does not undergo extensive reprogramming and has been linked with environmentally induced intergenerational effects, but solely in the context of early life environmental differences. Using whole-genome bisulfite sequencing, we demonstrate that differential methylation of sperm occurs in response to captivity during the maturation of Atlantic Salmon (Salmo salar), a species of major economic and conservation significance. We show that adult captive exposure further induces differential methylation in an F1 generation that is associated with fitness-related phenotypic differences. Some genes targeted with differential methylation were consistent with genes differential methylated in other salmonid fishes experiencing early-life hatchery rearing, as well as genes under selection in domesticated species. Our results support a mechanism of transgenerational plasticity mediated by intergenerational inheritance of DNA methylation acquired late in life for salmon. To our knowledge, this is the first-time environmental variation experienced later in life has been directly demonstrated to influence gamete DNA methylation in fish.

The effects of environmental enrichment on hatchery-performance, smolt migration and capture rates in landlocked Atlantic salmon

Enrichment of rearing environment with natural elements has been suggested to improve the welfare and post-release survival of cultured fish. We studied the combined effects of shelter structures, periodical water flow and water level changes on pre- and post-release performance of critically endangered landlocked Atlantic salmon (Salmo salar m. sebago). Relative to standard (plain) rearing tanks, provision of enrichment improved fish condition factor and survival during the first year of rearing when most mortality was attributable to parasitic and bacterial infections. The consequent higher density in enriched tanks probably induced greater growth variation and more dorsal fin damages than found in fish of standard tanks. Possibly this was partly due to the applied changes in water level. Experimentally determined smolt migration tendency at age 3 did not differ, on average, between the rearing groups, but enriched-reared fish showed clearly less variation in total movement activity than standard-reared fish. Experimental angling in earthen ponds did not suggest divergent vulnerability between the differentially reared fish at age 3, but decreased condition during the preceding growth season increased vulnerability to fishing. Based on long-term post-stocking tag returns in large-lake fisheries, fish length at release but not rearing method affected the capture rates of fish released at age 2. When released at age 3 the fish grown in enriched environment had a higher risk to be captured with stationary gears and earlier by hook and line gears compared to standard-reared conspecifics. Earlier time of maximal smolt migration activity was associated with an increased risk of being captured. We suggest that environmental enrichment may modulate growth- and behavior-related qualities that indirectly increased the vulnerability to fishing in natural conditions but not in experimental setting. The favorable effects of enrichment on early survival encourages adopting enriched rearing practices in supportive breeding of landlocked salmon.

Population structure of chum salmon and selection on the markers collected for stock identification

Genetic stock identification (GSI) is a major management tool of Pacific salmon (Oncorhynchus Spp.) that has provided rich genetic baseline data of allozymes, microsatellites, and single-nucleotide polymorphisms (SNPs) across the Pacific Rim. Here, we analyzed published data sets for adult chum salmon (Oncorhynchus keta), namely 10 microsatellites, 53 SNPs, and a mitochondrial DNA locus (mtDNA3, control region, and NADH-3 combined) in samples from 495 locations in the same distribution range (n = 61,813). TreeMix analysis of the microsatellite loci identified the greatest convergence toward Japanese/Korean populations and suggested two admixture events from Japan/Korea to Russia and the Alaskan Peninsula. The SNPs had been purposively collected from rapidly evolving genes to increase the power of GSI. The largest expected heterozygosity was observed in Japanese/Korean populations for microsatellites, whereas it was largest in Western Alaskan populations for SNPs, reflecting the SNP discovery process. A regression of SNP population structures on those of microsatellites indicated the selection of the SNP loci according to deviations from the predicted structures. Specifically, we matched the sampling locations of the SNPs with those of the microsatellites and performed regression analyses of SNP allele frequencies on a 2-dimensional scaling (MDS) of matched locations obtained from microsatellite pairwise F ST values. The MDS first axis indicated a latitudinal cline in American and Russian populations, whereas the second axis showed differentiation of Japanese/Korean populations. The top five outlier SNPs included mtDNA3, U502241 (unknown), GnRH373, ras1362, and TCP178, which were identified by principal component analysis. We summarized the functions of 53 nuclear genes surrounding SNPs and the mtDNA3 locus by referring to a gene database system and propose how they may influence the fitness of chum salmon.

An evaluation of the potential factors affecting lifetime reproductive success in salmonids

Lifetime reproductive success (LRS), the number of offspring produced over an organism's lifetime, is a fundamental component of Darwinian fitness. For taxa such as salmonids with multiple species of conservation concern, understanding the factors affecting LRS is critical for the development and implementation of successful conservation management practices. Here, we reviewed the published literature to synthesize factors affecting LRS in salmonids including significant effects of hatchery rearing, life history, and phenotypic variation, and behavioral and spawning interactions. Additionally, we found that LRS is affected by competitive behavior on the spawning grounds, genetic compatibility, local adaptation, and hybridization. Our review of existing literature revealed limitations of LRS studies, and we emphasize the following areas that warrant further attention in future research: (1) expanding the range of studies assessing LRS across different life-history strategies, specifically accounting for distinct reproductive and migratory phenotypes; (2) broadening the variety of species represented in salmonid fitness studies; (3) constructing multigenerational pedigrees to track long-term fitness effects; (4) conducting LRS studies that investigate the effects of aquatic stressors, such as anthropogenic effects, pathogens, environmental factors in both freshwater and marine environments, and assessing overall body condition, and (5) utilizing appropriate statistical approaches to determine the factors that explain the greatest variation in fitness and providing information regarding biological significance, power limitations, and potential sources of error in salmonid parentage studies. Overall, this review emphasizes that studies of LRS have profoundly advanced scientific understanding of salmonid fitness, but substantial challenges need to be overcome to assist with long-term recovery of these keystone species in aquatic ecosystems.

Endangered predators and endangered prey: Seasonal diet of Southern Resident killer whales

Understanding diet is critical for conservation of endangered predators. Southern Resident killer whales (SRKW) (Orcinus orca) are an endangered population occurring primarily along the outer coast and inland waters of Washington and British Columbia. Insufficient prey has been identified as a factor limiting their recovery, so a clear understanding of their seasonal diet is a high conservation priority. Previous studies have shown that their summer diet in inland waters consists primarily of Chinook salmon (Oncorhynchus tshawytscha), despite that species' rarity compared to some other salmonids. During other times of the year, when occurrence patterns include other portions of their range, their diet remains largely unknown. To address this data gap, we collected feces and prey remains from October to May 2004-2017 in both the Salish Sea and outer coast waters. Using visual and genetic species identification for prey remains and genetic approaches for fecal samples, we characterized the diet of the SRKWs in fall, winter, and spring. Chinook salmon were identified as an important prey item year-round, averaging ~50% of their diet in the fall, increasing to 70-80% in the mid-winter/early spring, and increasing to nearly 100% in the spring. Other salmon species and non-salmonid fishes, also made substantial dietary contributions. The relatively high species diversity in winter suggested a possible lack of Chinook salmon, probably due to seasonally lower densities, based on SRKW's proclivity to selectively consume this species in other seasons. A wide diversity of Chinook salmon stocks were consumed, many of which are also at risk. Although outer coast Chinook samples included 14 stocks, four rivers systems accounted for over 90% of samples, predominantly the Columbia River. Increasing the abundance of Chinook salmon stocks that inhabit the whales' winter range may be an effective conservation strategy for this population.

Differential migration in Pacific salmon and trout: Patterns and hypotheses

Migrations affect the population dynamics, life history, evolution, and connections of animals to natural ecosystems and humans. Many species and populations display partial migration (some individuals migrate and some do not), and differential migration (migration distance varies). Partial migration is widely distributed in fishes but the term differential migration is much less commonly applied, despite the occurrence of this phenomenon. This paper briefly reviews the extent of differential migration in Pacific salmon and trout (genus Oncorhynchus), a very extensively studied group. Three hypotheses are presented to explain the patterns among species: 1) phylogenetic relationships, 2) the prevalence of partial migration (i.e., variation in anadromy), and 3) life history patterns (iteroparous or semelparous, and duration spent feeding at sea prior to maturation). Each hypothesis has some support but none is consistent with all patterns. The prevalence of differential migration, ranging from essentially non-existent to common within a species, reflects phylogeny and life history, interacting with the geographic features of the region where juvenile salmon enter the ocean. Notwithstanding the uncertain evolution of this behavior, it has very clear implications for salmon conservation, as it strongly affects exposure to predators, patterns of fishery exploitation and also uptake of toxic contaminants.

Captive-bred populations of a partially migratory salmonid fish are unlikely to maintain migratory polymorphism in natural habitats

Variation in life history is fundamental to the long-term persistence of populations and species. Partial migration, in which both migratory and resident individuals are maintained in a population, is commonly found across animal taxa. However, human-induced habitat fragmentation continues to cause a rapid decline in the migratory phenotype in many natural populations. Using field and hatchery experiments, we demonstrated that despite both migrants and residents being maintained in captive environments, few individuals of the red-spotted masu salmon, Oncorhynchus masou ishikawae, became migrants in natural streams when released prior to the migration decision. Released fish rarely reached the threshold body size necessary to become migrants in natural streams, presumably owing to lower growth rates in natural than in captive environments. The decision to migrate is often considered a threshold trait in salmonids and other animal taxa. Our findings highlight the need for management programmes that acknowledge the effects of the environment on the determination of the migratory phenotypes of partially migratory species when releasing captive-bred individuals prior to their migratory decisions.

Differential DNA methylation in somatic and sperm cells of hatchery vs wild (natural-origin) steelhead trout populations

Environmental factors such as nutrition, stress, and toxicants can influence epigenetic programming and phenotypes of a wide variety of species from plants to humans. The current study was designed to investigate the impacts of hatchery spawning and rearing on steelhead trout (Oncorhynchus mykiss) vs the wild fish on a molecular level. Additionally, epigenetic differences between feeding practices that allow slow growth (2 years) and fast growth (1 year) hatchery trout were investigated. The sperm and red blood cells (RBC) from adult male slow growth/maturation hatchery steelhead, fast growth/maturation hatchery steelhead, and wild (natural-origin) steelhead were collected for DNA preparation to investigate potential alterations in differential DNA methylation regions (DMRs) and genetic mutations, involving copy number variations (CNVs). The sperm and RBC DNA both had a large number of DMRs when comparing the hatchery vs wild steelhead trout populations. The DMRs were cell type specific with negligible overlap. Slow growth/maturation compared to fast growth/maturation steelhead also had a larger number of DMRs in the RBC samples. A number of the DMRs had associated genes that were correlated to various biological processes and pathologies. Observations demonstrate a major epigenetic programming difference between the hatchery and wild natural-origin fish populations, but negligible genetic differences. Therefore, hatchery conditions and growth/maturation rate can alter the epigenetic developmental programming of the steelhead trout. Interestingly, epigenetic alterations in the sperm allow for potential epigenetic transgenerational inheritance of phenotypic variation to future generations. The impacts of hatchery exposures are not only important to consider on the fish exposed, but also on future generations and evolutionary trajectory of fish in the river populations.

Captive-bred Atlantic salmon released into the wild have fewer offspring than wild-bred fish and decrease population productivity

The release of captive-bred animals into the wild is commonly practised to restore or supplement wild populations but comes with a suite of ecological and genetic consequences. Vast numbers of hatchery-reared fish are released annually, ostensibly to restore/enhance wild populations or provide greater angling returns. While previous studies have shown that captive-bred fish perform poorly in the wild relative to wild-bred conspecifics, few have measured individual lifetime reproductive success (LRS) and how this affects population productivity. Here, we analyse data on Atlantic salmon from an intensely studied catchment into which varying numbers of captive-bred fish have escaped/been released and potentially bred over several decades. Using a molecular pedigree, we demonstrate that, on average, the LRS of captive-bred individuals was only 36% that of wild-bred individuals. A significant LRS difference remained after excluding individuals that left no surviving offspring, some of which might have simply failed to spawn, consistent with transgenerational effects on offspring survival. The annual productivity of the mixed population (wild-bred plus captive-bred) was lower in years where captive-bred fish comprised a greater fraction of potential spawners. These results bolster previous empirical and theoretical findings that intentional stocking, or non-intentional escapees, threaten, rather than enhance, recipient natural populations.

Discovery and surveillance of viruses from salmon in British Columbia using viral immune-response biomarkers, metatranscriptomics, and high-throughput RT-PCR

The emergence of infectious agents poses a continual economic and environmental challenge to aquaculture production, yet the diversity, abundance, and epidemiology of aquatic viruses are poorly characterised. In this study, we applied salmon host transcriptional biomarkers to identify and select fish in a viral disease state, but only those that were negative for known viruses based on RT-PCR screening. These fish were selected for metatranscriptomic sequencing to discover potential viral pathogens of dead and dying farmed Atlantic (Salmo salar) and Chinook (Oncorhynchus tshawytscha) salmon in British Columbia (BC). We found that the application of the biomarker panel increased the probability of discovering viruses in aquaculture populations. We discovered two viruses that have not previously been characterised in Atlantic salmon farms in BC (Atlantic salmon calicivirus and Cutthroat trout virus-2), as well as partially sequenced three putative novel viruses. To determine the epidemiology of the newly discovered or emerging viruses, we conducted high-throughput reverse transcription polymerase chain reaction (RT-PCR) and screened over 9,000 farmed and wild salmon sampled over one decade. Atlantic salmon calicivirus and Cutthroat trout virus-2 were in more than half of the farmed Atlantic salmon we tested. Importantly we detected some of the viruses we first discovered in farmed Atlantic salmon in Chinook salmon, suggesting a broad host range. Finally, we applied in situ hybridisation to determine infection and found differing cell tropism for each virus tested. Our study demonstrates that continual discovery and surveillance of emerging viruses in these ecologically important salmon will be vital for management of both aquaculture and wild resources in the future.

Infectious hematopoietic necrosis virus specialization in a multihost salmonid system

Many pathogens interact and evolve in communities where more than one host species is present, yet our understanding of host-pathogen specialization is mostly informed by laboratory studies with single species. Managing diseases in the wild, however, requires understanding how host-pathogen specialization affects hosts in diverse communities. Juvenile salmonid mortality in hatcheries caused by infectious hematopoietic necrosis virus (IHNV) has important implications for salmonid conservation programs. Here, we evaluate evidence for IHNV specialization on three salmonid hosts and assess how this influences intra- and interspecific transmission in hatchery-reared salmonids. We expect that while more generalist viral lineages should pose an equal risk of infection across host types, viral specialization will increase intraspecific transmission. We used Bayesian models and data from 24 hatcheries in the Columbia River Basin to reconstruct the exposure history of hatcheries with two IHNV lineages, MD and UC, allowing us to estimate the probability of juvenile infection with these lineages in three salmonid host types. Our results show that lineage MD is specialized on steelhead trout and perhaps rainbow trout (both Oncorhynchus mykiss), whereas lineage UC displayed a generalist phenotype across steelhead trout, rainbow trout, and Chinook salmon. Furthermore, our results suggest the presence of specialist-generalist trade-offs because, while lineage UC had moderate probabilities of infection across host types, lineage MD had a small probability of infection in its nonadapted host type, Chinook salmon. Thus, in addition to quantifying probabilities of infection of socially and economically important salmonid hosts with different IHNV lineages, our results provide insights into the trade-offs that viral lineages incur in multihost communities. Our results suggest that knowledge of the specialist/generalist strategies of circulating viral lineages could be useful in salmonid conservation programs to control disease.

Restored river habitat provides a natural spawning area for a critically endangered landlocked Atlantic salmon population

Supplementing endangered fish populations with captive bred individuals is a common practice in conservation management. The aim of supplementary releases from hatchery broodstocks is to maintain the viability of populations by maintaining their genetic diversity. Landlocked Lake Saimaa salmon (Salmo salar m. sebago) has been critically endangered for the past half-century. As a result of anthropogenic disturbance, especially construction of hydroelectric power plants, the Lake Saimaa salmon has become completely dependent on hatchery broodstock. Recently, habitat restoration has been done in one of the former spawning rivers with the aim of creating a new natural spawning ground for the critically endangered population. Hatchery fish releases have also been revised so that in addition to juveniles, adult fish from the hatchery and from the wild have been released into the restored river. We assessed here if a restored river stretch can be used as a natural spawning ground and juvenile production area with the aim of improving genetic diversity of the critically endangered Lake Saimaa salmon. By constructing a pedigree of the released adults, and juveniles sampled from the restored river, we found that the majority of the released adults had produced offspring in the river. We also found that wild-caught spawners that were released into the restored river had much higher reproductive success than hatchery-reared parents that were released into the restored river at the same time. We found no significant differences in genetic diversity between the parent and offspring generations. Meanwhile, relatedness among different groups of adults and juveniles varied a lot. For example, while the hatchery-reared females were on average half-siblings, wild-caught females showed no significant relatedness. This highlights the importance of using pedigree information in planning the conservation and management of endangered populations, especially when artificial propagation is involved.

Multiple decades of stocking has resulted in limited hatchery introgression in wild brook trout (Salvelinus fontinalis) populations of Nova Scotia

Many populations of freshwater fishes are threatened with losses, and increasingly, the release of hatchery individuals is one strategy being implemented to support wild populations. However, stocking of hatchery individuals may pose long-term threats to wild populations, particularly if genetic interactions occur between wild and hatchery individuals. One highly prized sport fish that has been heavily stocked throughout its range is the brook trout (Salvelinus fontinalis). In Nova Scotia, Canada, hatchery brook trout have been stocked since the early 1900s, and despite continued stocking efforts, populations have suffered declines in recent decades. Before this study, the genetic structure of brook trout populations in the province was unknown; however, given the potential negative consequences associated with hatchery stocking, it is possible that hatchery programs have adversely affected the genetic integrity of wild populations. To assess the influence of hatchery supplementation on wild populations, we genotyped wild brook trout from 12 river systems and hatchery brook trout from two major hatcheries using 100 microsatellite loci. Genetic analyses of wild trout revealed extensive population genetic structure among and within river systems and significant isolation-by-distance. Hatchery stocks were genetically distinct from wild populations, and most populations showed limited to no evidence of hatchery introgression (<5% hatchery ancestry). Only a single location had a substantial number of hatchery-derived trout and was located in the only river where a local strain is used for supplementation. The amount of hatchery stocking within a watershed did not influence the level of hatchery introgression. Neutral genetic structure of wild populations was influenced by geography with some influence of climate and stocking indices. Overall, our study suggests that long-term stocking has not significantly affected the genetic integrity of wild trout populations, highlighting the variable outcomes of stocking and the need to evaluate the consequences on a case-by-case basis.

Genetic Differentiation in Hatchery and Stocked Populations of Sea Trout in the Southern Baltic: Selection Evidence at SNP Loci

The impacts and interactions between hatchery-bred fish and wild fish populations has been a topic of active investigation in recent decades. In some instances, the benefits of stocking can be overshadowed by negative effects such as genetic introgression with natural populations, loss of genetic diversity, and dilution of local adaptations. Methods that facilitate the identification of stocked fish enable us to estimate not only the effectiveness of stocking but also the level of natural reproduction and the degree of hybridization. The longest Baltic river, the Vistula, also has the second highest discharge. Historically, it hosted numerous populations of the anadromous form of brown trout (sea trout); however, dam construction has since interfered with and reduced spawning migration to a rate that is much lower than before. Reduced spawning has resulted in a population collapse and a negative flow-on effect on commercial catches. In response, Poland (along with many other Baltic countries) initiated an intensive stocking program which continues today and which sees the average annual release of 700,000 smolts. As a consequence, today’s main-river and inshore catches come from stock-enhanced populations. High-throughput single-nucleotide polymorphism (SNP) genotyping was performed on samples of sea trout from southern Baltic populations; results suggest that a significant portion of the sea trout catches in the Vistula mouth region have direct hatchery origin and indicate the presence of Pomeranian specimens. SNP loci identified as outliers indicate a potential selection pressure that may be related with effects of hatchery breeding and mixing with natural populations. The brown trout SNP array applied in this study showed high effectiveness not only for population differentiation, but more importantly, it emerged as a sensitive tool to provide evidence of detection selection.

Resurgence of an apex marine predator and the decline in prey body size

Recent recoveries of marine mammal populations worldwide have heightened concerns for their potential impacts on global fisheries. While predator-induced reductions in prey abundance have been documented, trait-mediated changes in life-history characteristics are rarely considered. Here we provide a striking example of the impact of a resurging apex marine predator on a commercially important fish species through changes in prey life-history traits. We find that widespread declines in the body size of Chinook salmon over the past 50 y can be explained by intensified predation by growing populations of resident killer whales that selectively feed on large Chinook salmon, thus revealing a potential conflict between salmon fisheries and marine mammal conservation objectives.

In light of recent recoveries of marine mammal populations worldwide and heightened concern about their impacts on marine food webs and global fisheries, it has become increasingly important to understand the potential impacts of large marine mammal predators on prey populations and their life-history traits. In coastal waters of the northeast Pacific Ocean, marine mammals have increased in abundance over the past 40 to 50 y, including fish-eating killer whales that feed primarily on Chinook salmon. Chinook salmon, a species of high cultural and economic value, have exhibited marked declines in average size and age throughout most of their North American range. This raises the question of whether size-selective predation by marine mammals is generating these trends in life-history characteristics. Here we show that increased predation since the 1970s, but not fishery selection alone, can explain the changes in age and size structure observed for Chinook salmon populations along the west coast of North America. Simulations suggest that the decline in mean size results from the selective removal of large fish and an evolutionary shift toward faster growth and earlier maturation caused by selection. Our conclusion that intensifying predation by fish-eating killer whales contributes to the continuing decline in Chinook salmon body size points to conflicting management and conservation objectives for these two iconic species.

Conservation and Management of Salmon in the Age of Genomics

Salmon were among the first nonmodel species for which systematic population genetic studies of natural populations were conducted, often to support management and conservation. The genomics revolution has improved our understanding of the evolutionary ecology of salmon in two major ways: (a) Large increases in the numbers of genetic markers (from dozens to 10⁴-10⁶) provide greater power for traditional analyses, such as the delineation of population structure, hybridization, and population assignment, and (b) qualitatively new insights that were not possible with traditional genetic methods can be achieved by leveraging detailed information about the structure and function of the genome. Studies of the first type have been more common to date, largely because it has taken time for the necessary tools to be developed to fully understand the complex salmon genome. We expect that the next decade will witness many new studies that take full advantage of salmonid genomic resources.

The role of recombination on genome-wide patterns of local ancestry exemplified by supplemented brook charr populations

Assessing the immediate and long-term evolutionary consequences of human-mediated hybridization is of major concern for conservation biology. Several studies have documented how selection in interaction with recombination modulates introgression at a genome-wide scale, but few have considered the dynamics of this process within and among chromosomes. Here, we used an exploited freshwater fish, the brook charr (Salvelinus fontinalis), for which decades of stocking practices have resulted in admixture between wild populations and an introduced domestic strain, to assess both the temporal dynamics and local chromosomal variation in domestic ancestry. We provide a detailed picture of the domestic ancestry patterns across the genome using about 33,000 mapped single nucleotide polymorphisms genotyped in 611 individuals from 24 supplemented populations. For each lake, we distinguished early- and late-generation hybrids using information regarding admixture tracts. To assess the selective outcomes following admixture we then evaluated the relationship between recombination and admixture proportions at three different scales: the whole genome, chromosomes and within 2-Mb windows. This allowed us to detect a wide range of evolutionary mechanisms varying along the genome, as reflected by the finding of favoured or disfavoured introgression of domestic haplotypes. Among these, the main factor modulating local ancestry was probably the presence of deleterious recessive mutations in the wild populations, which can be efficiently hidden to selection in the presence of long admixture tracts. Overall, our results emphasize the relevance of taking into consideration local ancestry information to assess both the temporal and the chromosomal variation in local admixture ancestry toward better understanding post-hybridization evolutionary outcomes.

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.

Comparison of infectious agents detected from hatchery and wild juvenile Coho salmon in British Columbia, 2008-2018

Infectious diseases are potential contributors to decline in Coho salmon (Oncorhynchus kisutch) populations. Although pathogens are theoretically considered to pose higher risk in high-density rearing environments like hatcheries, there is no direct evidence that hatchery-origin Coho salmon increase the transmission of infectious agents to sympatric wild populations. This study was undertaken to compare prevalence, burden, and diversity of infectious agents between hatchery-reared and wild juvenile Coho salmon in British Columbia (BC), Canada. In total, 2,655 juvenile Coho salmon were collected between 2008 and 2018 from four regions of freshwater and saltwater in BC. High-throughput microfluidics qPCR was employed for simultaneous detection of 36 infectious agents from mixed-tissue samples (gill, brain, heart, liver, and kidney). Thirty-one agents were detected at least once, including ten with prevalence >5%. Candidatus Brachiomonas cysticola, Paraneuclospora theridion, and Parvicapsula pseudobranchiocola were the most prevalent agents. Diversity and burden of infectious agents were substantially higher in marine environment than in freshwater. In Mainland BC, infectious burden and diversity were significantly lower in hatchery smolts than in wild counterparts, whereas in other regions, there were no significant differences. Observed differences in freshwater were predominantly driven by three parasites, Loma salmonae, Myxobolus arcticus, and Parvicapsula kabatai. In saltwater, there were no consistent differences in agent prevalence between hatchery and wild fish shared among the west and east coasts of Vancouver Island. Although some agents showed differential infectious patterns between regions, annual variations likely contributed to this signal. Our findings do not support the hypothesis that hatchery smolts carry higher burdens of infectious agents than conspecific wild fish, reducing the potential risk of transfer to wild smolts at this life stage. Moreover, we provide a baseline of infectious agents in juvenile Coho salmon that will be used in future research and modeling potential correlations between infectious profiles and marine survival.

Conservation through the lens of (mal)adaptation: Concepts and meta-analysis

Evolutionary approaches are gaining popularity in conservation science, with diverse strategies applied in efforts to support adaptive population outcomes. Yet conservation strategies differ in the type of adaptive outcomes they promote as conservation goals. For instance, strategies based on genetic or demographic rescue implicitly target adaptive population states whereas strategies utilizing transgenerational plasticity or evolutionary rescue implicitly target adaptive processes. These two goals are somewhat polar: adaptive state strategies optimize current population fitness, which should reduce phenotypic and/or genetic variance, reducing adaptability in changing or uncertain environments; adaptive process strategies increase genetic variance, causing maladaptation in the short term, but increase adaptability over the long term. Maladaptation refers to suboptimal population fitness, adaptation refers to optimal population fitness, and (mal)adaptation refers to the continuum of fitness variation from maladaptation to adaptation. Here, we present a conceptual classification for conservation that implicitly considers (mal)adaptation in the short-term and long-term outcomes of conservation strategies. We describe cases of how (mal)adaptation is implicated in traditional conservation strategies, as well as strategies that have potential as a conservation tool but are relatively underutilized. We use a meta-analysis of a small number of available studies to evaluate whether the different conservation strategies employed are better suited toward increasing population fitness across multiple generations. We found weakly increasing adaptation over time for transgenerational plasticity, genetic rescue, and evolutionary rescue. Demographic rescue was generally maladaptive, both immediately after conservation intervention and after several generations. Interspecific hybridization was adaptive only in the F1 generation, but then rapidly leads to maladaptation. Management decisions that are made to support the process of adaptation must adequately account for (mal)adaptation as a potential outcome and even as a tool to bolster adaptive capacity to changing conditions.

Artificial selection on reproductive timing in hatchery salmon drives a phenological shift and potential maladaptation to climate change

The timing of breeding migration and reproduction links generations and substantially influences individual fitness. In salmonid fishes, such phenological events (seasonal return to freshwater and spawning) vary among populations but are consistent among years, indicating local adaptation in these traits to prevailing environmental conditions. Changing reproductive phenology has been observed in many populations of Atlantic and Pacific salmon and is sometimes attributed to adaptive responses to climate change. The sockeye salmon spawning in the Cedar River near Seattle, Washington, USA, have displayed dramatic changes in spawning timing over the past 50 years, trending later through the early 1990s, and becoming earlier since then. We explored the patterns and drivers of these changes using generalized linear models and mathematical simulations to identify possible environmental correlates of the changes, and test the alternative hypothesis that hatchery propagation caused inadvertent selection on timing. The trend toward later spawning prior to 1993 was partially explained by environmental changes, but the rapid advance in spawning since was not. Instead, since its initiation in 1991, the hatchery has, on average, selected for earlier spawning, and, depending on trait heritability, could have advanced spawning by 1-3 weeks over this period. We estimated heritability of spawning date to be high (h 2 ~0.8; 95% CI: 0.5-1.1), so the upper end of this range is not improbable, though at lower heritabilities a smaller effect would be expected. The lower reproductive success of early spawners and relatively low survival of early emerging juveniles observed in recent years suggest that artificial and natural selection are acting in opposite directions. The fitness costs of early spawning may be exacerbated by future warming; thus, the artificially advanced phenology could reduce the population's productivity. Such artificial selection is known in many salmon hatcheries, so there are broad consequences for the productivity of wild populations comingled with hatchery-produced fish.

Population correlates of rapid captive-induced maladaptation in a wild fish

Understanding the extent to which captivity generates maladaptation in wild species can inform species recovery programs and elucidate wild population responses to novel environmental change. Although rarely quantified, effective population size (N e ) and genetic diversity should influence the magnitude of plastic and genetic changes manifested in captivity that reduce wild fitness. Sexually dimorphic traits might also mediate consequences of captivity. To evaluate these relationships, we generated >600 full- and half-sibling families from nine wild brook trout populations, reared them for one generation under common, captive environmental conditions and contrasted several fitness-related traits in wild versus captive lines. We found substantial variation in lifetime success (lifetime survival and reproductive success) and life history traits among wild populations after just one captive generation (fourteen- and threefold ranges across populations, respectively). Populations with lower heterozygosity showed lower captive lifetime success, suggesting that captivity generates maladaptation within one generation. Greater male-biased mortality in captivity occurred in populations having disproportionately higher growth rates in males than females. Wild population N e and allelic diversity had little or no influence on captive trait expression and lifetime success. Our results have four conservation implications: (i) Trait values and lifetime success were highly variable across populations following one generation of captivity. (ii) Maladaptation induced by captive breeding might be particularly intense for the very populations practitioners are most interested in conserving, such as those with low heterozygosity. (iii) Maladaptive sex differences in captivity might be associated with population-dependent growth costs of reproduction. (iv) Heterozygosity can be a good indicator of short-term, intraspecific responses to novel environmental change.

Climate vulnerability assessment for Pacific salmon and steelhead in the California Current Large Marine Ecosystem

Major ecological realignments are already occurring in response to climate change. To be successful, conservation strategies now need to account for geographical patterns in traits sensitive to climate change, as well as climate threats to species-level diversity. As part of an effort to provide such information, we conducted a climate vulnerability assessment that included all anadromous Pacific salmon and steelhead (Oncorhynchus spp.) population units listed under the U.S. Endangered Species Act. Using an expert-based scoring system, we ranked 20 attributes for the 28 listed units and 5 additional units. Attributes captured biological sensitivity, or the strength of linkages between each listing unit and the present climate; climate exposure, or the magnitude of projected change in local environmental conditions; and adaptive capacity, or the ability to modify phenotypes to cope with new climatic conditions. Each listing unit was then assigned one of four vulnerability categories. Units ranked most vulnerable overall were Chinook (O. tshawytscha) in the California Central Valley, coho (O. kisutch) in California and southern Oregon, sockeye (O. nerka) in the Snake River Basin, and spring-run Chinook in the interior Columbia and Willamette River Basins. We identified units with similar vulnerability profiles using a hierarchical cluster analysis. Life history characteristics, especially freshwater and estuary residence times, interplayed with gradations in exposure from south to north and from coastal to interior regions to generate landscape-level patterns within each species. Nearly all listing units faced high exposures to projected increases in stream temperature, sea surface temperature, and ocean acidification, but other aspects of exposure peaked in particular regions. Anthropogenic factors, especially migration barriers, habitat degradation, and hatchery influence, have reduced the adaptive capacity of most steelhead and salmon populations. Enhancing adaptive capacity is essential to mitigate for the increasing threat of climate change. Collectively, these results provide a framework to support recovery planning that considers climate impacts on the majority of West Coast anadromous salmonids.