Wild-origin Fish Research Articles

The estuarine growth and residency of juvenile Pacific salmon in North America: a compilation of empirical data

The value of estuaries as nursery habitat for juvenile anadromous salmon is likely variable across estuaries and species. Here, we compiled published empirical data on juvenile salmon estuarine growth and residency. We aimed to quantify the range and variability of these aspects for five species of Pacific salmon across estuaries, methodologies, and life histories. The majority of studies focused on Chinook and coho salmon, largely from their southern range. While there is some evidence of higher growth in wild-origin fish relative to hatchery-origin fish, the wide range of metrics employed made identification of trends among life histories challenging, and unification of reporting could strengthen future research. Different salmon life histories exhibited different residencies, with natural-origin subyearling coho exhibiting the longest mean residency (∼3 months) and 1+ sockeye salmon exhibiting the shortest (3.7 days). Across life histories, hatchery fish exhibited much shorter estuary residencies than wild fish. Collectively, our review highlights key patterns in salmon estuary ecology, identifies knowledge gaps, and lays the foundation for future studies to quantify the importance of estuaries for specific salmon.

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.

Offspring of first-generation hatchery steelhead trout (Oncorhynchus mykiss) grow faster in the hatchery than offspring of wild fish, but survive worse in the wild: Possible mechanisms for inadvertent domestication and fitness loss in hatchery salmon.

Salmonid fish raised in hatcheries often have lower fitness (number of returning adult offspring) than wild fish when both spawn in the wild. Body size at release from hatcheries is positively correlated with survival at sea. So one explanation for reduced fitness is that hatcheries inadvertently select for trait values that enhance growth rate under the unnatural environment of a hatchery, but that are maladaptive in the wild environment. A simple prediction of this hypothesis is that juveniles of hatchery origin should grow more quickly than fish of wild origin under hatchery conditions, but should have lower survival under wild conditions. We tested that hypothesis using multiple full sibling families of steelhead (Oncorhynchus mykiss) that were spawned using either two wild parents (WxW) or two first-generation hatchery (HxH) parents. Offspring from all the families were grown together under hatchery conditions and under semi-natural conditions in artificial streams. HxH families grew significantly faster in the hatchery, but had significantly lower survival in the streams. That we see this tradeoff after only a single generation of selection suggests that the traits involved are under very strong selection. We also considered one possible alteration to the hatchery environment that might reduce the intensity of selection among families in size at release. Here we tested whether reducing the fat content of hatchery feed would reduce the variance among families in body size. Although fish raised under a low-fat diet were slightly smaller, the variation among families in final size was unchanged. Thus, there is no evidence that reducing the fat content of hatchery feed would reduce the opportunity for selection among families on size at release.

Relative influences of microhabitat incubation conditions and genetic parentage effects on lake sturgeon (Acipenser fulvescens) offspring traits during early ontogeny

Knowledge on factors influencing traits during critical early growth periods is essential for predicting population persistence. Genetic effects and microhabitat stream conditions at female selected oviposition sites influence larval phenotypes. However, limited work has examined contributions of both factors across sequential ontogenetic stages for larvae of wild origin. Using a wild population of lake sturgeon (Acipenser fulvescens) from Black Lake, Michigan (USA), fertilized eggs were collected from stream substrate just prior to hatch at one-meter intervals along seven transect lines at an adult-selected spawning area. Microhabitat variables (depth, discharge, substrate size) were recorded at egg collection points. Body length, body area, and yolk-sac area were quantified for yolk-sac larvae (N = 359) at the time of hatch. Following the onset of exogenous feeding, larval growth was measured weekly for four weeks. Parentage was assigned using genetic-based analysis. Inter-individual variation in phenotypic traits quantified at hatch were attributed to stream microhabitat variables; mean depth had the largest influence. No additive genetic effects were detected at hatch. Post-emergence larval growth significantly varied within and among half-sibling groups with the greatest range in body size observed at 33 days post-hatch. Additive genetic variance and heritability increased with age. Results demonstrate that female-selected incubation habitats influenced traits at hatch for wild-origin fish, but effects do not persist to a sequential ontogenetic stage. Alternatively, growth after the onset of exogenous feeding was largely influenced by intrinsic (genetic) factors which must be considered when designing and implementing rehabilitation strategies for lake sturgeon and potentially other threatened riverine fishes.

Evidence of Limited Recruitment of Pallid Sturgeon in the Lower Missouri River

AbstractPallid Sturgeon Scaphirhynchus albus are endemic to the Missouri and Mississippi river basins and are rare throughout their range. The species was listed as federally endangered with little to no evidence of natural recruitment. Since population augmentation was initiated as a recovery objective in the early 1990s, thousands of hatchery-origin Pallid Sturgeon have been stocked in the lower Missouri River (Gavins Point Dam [river kilometer 1,305.1] to the confluence of the Mississippi River [river kilometer 0.0]). Efforts to discriminate natural reproduction and recruitment of wild-origin Pallid Sturgeon from hatchery-origin fish has been hampered by tag loss in hatchery-origin sturgeon, inconsistent documentation of hatchery parental crosses, and the failure to collect tissue samples for genotyping all broodstock. However, the recent reconstruction of missing parental genotypes from known hatchery-origin progeny and from cryopreserved milt made it possible to examine Pallid Sturgeon recruitment. Therefore, our objectives were to 1) determine the likelihood that unmarked Pallid Sturgeon captured from the lower Missouri River were the result of natural recruitment and 2) examine the length distribution of wild- and hatchery-origin fish to determine if a difference exists by origin and examine the life-stage distribution. Genetic analysis showed that from 2003 to 2015, 358 “presumptive wild-origin” Pallid Sturgeon were captured in the lower Missouri River and the comparison between the length distributions of wild- and hatchery-origin fish did not provide any additional clarification into potential wild-origin fish. Low recruitment may be due to a small breeding population, high mortality of early life stages, hybridization with Shovelnose Sturgeon Scaphirhynchus platorynchus, or transport of drifting free embryos or larvae into inhospitable habitats. Determining what factors are limiting recruitment is the important next step for the recovery of Pallid Sturgeon in the lower Missouri River.

Assessing demographic effects of dams on diadromous fish: a case study for Atlantic salmon in the Penobscot River, Maine

Abstract Dams are a major contributor to the historic decline and current low abundance of diadromous fish. We developed a population viability analysis to assess demographic effects of dams on diadromous fish within a river system and demonstrated an application of the model with Atlantic salmon in the Penobscot River, Maine. We used abundance and distribution of wild- and hatchery-origin adult salmon throughout the watershed as performance metrics. Salmon abundance, distribution to upper reaches of the Penobscot watershed, and the number and proportion of wild-origin fish in the upper reaches of the Penobscot watershed increased when dams, particularly mainstem dams, were removed or passage efficiency was increased. Salmon abundance decreased as indirect latent mortality per dam was increased. Salmon abundance increased as marine or freshwater survival rates were increased, but the increase in abundance was larger when marine survival was increased than when freshwater survival was increased. Without hatchery supplementation, salmon abundance equalled zero with low marine and freshwater survival but increased when marine and freshwater survival rates were increased. Models, such as this one, that incorporate biological, environmental, and functional parameters can be used to predict ecological responses of fish populations and can help evaluate and prioritize management and restoration actions for diadromous fish.

Influence of immune-relevant genotype on the reproductive success of a salmonid alternative mating strategy.

Major histocompatibility complex (MHC) and immune-relevant gene markers were used to evaluate differences in reproductive success (RS) among naturally spawning coho salmon Oncorhynchus kisutch mate pairs involving an alternative male reproductive phenotype, known as jacks. These mate pairs included both hatchery-reared and wild origin fish such that three classes were evaluated in two consecutive years (2005 and 2006) using a previously constructed multigenerational genetic pedigree: wild × wild (W × W), hatchery × hatchery (H × H) and wild × hatchery (W × H). Oncorhynchus kisutch jack mate pairs mated randomly based on immune-relevant genotype in both years; a result consistent with the opportunistic mating strategy of jacks. An association between greater number of alleles shared at three immune-relevant gene markers and increased RS was found for: W × H mate pairs in 2005 (BHMS429), W × H pairs in 2006 (SsalR016TKU) and W × W pairs in 2006 (OMM3085). No correlation between immune gene diversity and RS was found for H × H pairs in either year. The results suggest that the influence of immune-relevant genotype on mating success may be different for jacks when compared with previous studies of large adult male O. kisutch.

Loss of genetic variation in Greek hatchery populations of the European sea bass (Dicentrarchus labrax L.) as revealed by microsatellite DNA analysis

Genetic variation in four reared stocks of European sea bass Dicentrarchus labrax L., originating from Greek commercial farms, was assessed using five polymorphic microsatellite markers and was compared with that of three natural populations from Greece and France. The total number of alleles per marker ranged from 8 to 22 alleles, and hatchery samples showed the same levels of observed heterozygosity with samples from the wild but substantially smaller allelic richness and expected heterozygosity. The genetic differentiation of cultivated samples between them as well as from the wild origin fish was significant as indicated by Fst analysis. All population pairwise comparisons were statistically significant, except for the pair of the two natural Greek populations. Results of microsatellite DNA analysis herein showed a 37 % reduction of the mean allele number in the hatchery samples compared to the wild ones, suggesting random genetic drift and inbreeding events operating in the hatcheries. Knowledge of the genetic variation in D. labrax cultured populations compared with that in the wild ones is essential for setting up appropriate guidelines for proper monitoring and management of the stocks either under traditional practices or for the implementation of selective breeding programmes.

Contribution of wild-origin chinook salmon (Oncorhynchus tshawytcha) to the spawning run in the Salmon River, New York

We examined the contribution and distribution of wild-origin chinook salmon (Oncorhynchus tshawytcha) in the Salmon River, New York, during the 2005 spawning run. To determine the origin of each fish, we used scale metrics and a recently developed discriminant function model. We estimated that approximately 32% (∼20,000 individuals) of chinook salmon were of wild-origin and that there was a greater proportion of wild fish in younger age groups than in older groups (age-1 = 48.6%, age-2 = 47.2%, and age-3 = 21.1%). We also observed spatial differences in the distribution of wild- and hatchery-derived fish, with a higher proportion of wild-origin chinook salmon in the lower section of the river (47.5%) than in the upper sections (28.2%). The lowest proportion of wild fish was found in the Salmon River hatchery (12.4%), located in the upper section of the river. These findings suggest that wild-origin fish were more evenly distributed along the river, whereas hatchery fish were more likely to reach the upper parts of the river or enter the hatchery.

Impacts of supplementation: genetic diversity in supplemented and unsupplemented populations of summer chum salmon (Oncorhynchus keta) in Puget Sound (Washington, USA)

In supplementation programs, hatcheries employ wild-origin fish as brood stock and their offspring are allowed into wild spawning areas. Resource managers use supplementation to support imperiled salmonid populations, seeking to increase census size and possibly effective population size (Ne), while minimizing risks of genetic diversity loss and domestication from hatchery intervention. Here we document impacts of 5–10 years of supplementation on threatened summer-run chum salmon ( Oncorhynchus keta ) in Hood Canal (HC) and Strait of Juan de Fuca (SJF) in Washington State and compare them genetically with unsupplemented summer- and fall-run chum salmon from HC and South Puget Sound. Microsatellite allele frequencies identified four run-timing and geographic groups. HC and SJF summer chum salmon genetic relationships followed a metapopulation pattern of isolation by distance, similar to patterns prior to supplementation, suggesting that supplementation minimally impacted population structure. In most supplemented subpopulations, we detected no effects on diversity and Ne, but high variance in individual pairwise relatedness values indicated over-representation of family groups. In two subpopulations, hatchery impacts (decreased diversity and lower Ne) were confounded with extreme bottlenecks. Rebounds in census sizes in all subpopulations suggest that general survivorship has improved and that possible hatchery effects on genetic diversity will be overcome.

Progress Toward the Rehabilitation of Lake Trout ( Salvelinus namaycush) in South Bay, Lake Huron

Our objective was to evaluate the status of lake trout Salvelinus namaycush rehabilitation in South Bay, Lake Huron. Standardized surveys were conducted to quantify natural recruitment, annual mortality, and the contribution of wild-versus hatchery-origin lake trout. Some indicators suggest a high level of natural recruitment. The spawning population was comprised of multiple ages, and the mean age of spawners (8.4 years for females, 7.9 years for males) was at least 1 year older than the age at 50% maturity (5.8 years). Estimated annual total mortality rates (0.20–0.25) and sea-lamprey induced mortality rates (0.02) were less than maximum allowable values. The proportion of wild-origin fish captured was high among spawners but varied among sampling programs (42% in fall trap nets, 70% in fall gill nets, and 88% in summer gill nets). A strong year class (1997) could be tracked from 2001 to 2005. Few fish were captured from early (< 1996) or later (1999–2002) year classes. Possible explanations for low natural recruitment during these later years include declining spawning habitat quality caused by low water levels and/or invasion of non-native mussels ( Dreissena spp.) and/or direct or indirect effects of alewife ( Alosa pseudoharengus).

The effects of hatchery domestication on competitive dominance of juvenile spring Chinook salmon (Oncorhynchus tshawytscha)

We tested the null hypotheses that competitive dominance among juvenile Chinook salmon (Oncorhynchus tshawytscha) in contest and scramble experiments would not be affected by domestication selection after one generation of state-of-the-art hatchery culture. Dyadic challenges of size-matched juvenile fish were conducted after a 6-day acclimation in 113.4 L aquaria. Differences in dominance and frequency of different types of agonistic interactions used were not significantly different in contest (n = 505) or scramble (n = 363) competition experiments (P &gt; 0.05). However, wild origin fish were more aggressive than hatchery origin fish in both types of experiments (P ≤ 0.05). Furthermore, wild origin fish gained more weight than hatchery origin fish during contest experiments, and hatchery origin fish lost less weight than wild origin fish in scramble experiments (P ≤ 0.05). Dominant fish, regardless of origin, grew more than subordinate fish in both contest and scramble experiments (P ≤ 0.05). Our results indicate that aggression, and growth mediated by competition, can be affected by domestication after only one generation of state-of-the-art hatchery culture; however, impacts to competitive dominance appear to be small.

Genetic structure and genetic relatedness of a hatchery stock of Senegal sole ( Solea senegalensis) inferred by microsatellites

Solea senegalensis is a fish species in an early stage of domestication. A commercial hatchery in southern Spain experienced a dramatic failure in spawning and embryo survival, after incorporation into the broodstock of fish reared in their hatchery. To assess the impact of management on the stock quality, a population genetics study was made of adult broodstock present at this hatchery in 2000. The broodstock was composed of a group of fish of wild origin and two more groups from F 1 progeny. A set of eight microsatellite loci was used to compare genetic variability among the three groups and to establish the relationships between pairs of individuals within each group. Individuals from F 1 origin showed a substantial reduction in genetic variability when compared to those from the wild. There was a greater than 50% decrease in the number of alleles per locus corrected by sample size and 16% and 26% reductions in H e values in the two F 1 groups, respectively. The degree of genetic relationship between individuals, evaluated by the relatedness estimator, rxy, and by graphical approaches, revealed a high proportion, almost 75%, of full-sibs and half-sibs in both F 1 groups, which might account for the reduction in overall variability. The high proportion of siblings also suggests a reproductive pattern in this stock in which few individuals breed successfully. This mating behaviour, along with factors inherent to selection and management systems, might be responsible for the negative effects on the reproductive capacity of the stock.