Hatchery Stocks Research Articles

Genetic diversity of the Ruditapes decussatus and evidence of its hybridization with the alien R. philippinarum in the Western Mediterranean Sea

The introduction of alien species in marine ecosystems is often driven by the increasing demand of fishery resources. This is the case of the Manila clam (R. philippinarum), imported in Europe from Japan since the 1970s, to meet the growing demand for clams that the native species, the grooved carpet shell clam (Ruditapes decussatus), could not satisfy. Alien species introduction could threaten the genetic diversity and integrity of the native clam, also causing hybridization (i.e., gene flow from one species into the gene pool of another). Since R. philippinarum recently spread in a few important Mediterranean coastal areas, a combined approach based on morphological characteristics, length differences of two nuclear species-specific markers (ITS2, 5SrDNA) and the sequence of the mitochondrial gene cytochrome c oxidase subunit I (COI), was used to investigate the presence of hybrids in six Mediterranean wetlands (Sardinia, Italy). Eight individuals morphologically identified as R. decussatus were hybrids, having sequences specific to both R. decussatus and R. philippinarum in their nuclear DNA (ITS2 and 5SrDNA). Most of these individuals were found to be post-first generation (F1) hybrids indicating that F1-hybrids may be fertile. Secondly, to study the genetic diversity of R. decussatus in the Sardinian wetlands as well as in its whole distribution area, >380 new COI sequences from the eastern Atlantic Ocean and Mediterranean Sea were analysed along with those available from public databases. Mitochondrial COI data revealed variable haplotype and nucleotide diversities in different areas, which were not dependent on sample sizes. The aquaculture breeding activities and clam transplantation between different countries, along with the long pelagic larval dispersal and the commercial import of other bivalve species might have promoted gene exchange between different sites and thus higher diversity levels in a few wild populations. Our research, evaluating the genetic makeup of wild and hatchery stocks and clarifying the degree of hybridization, can contribute to develop further recommendations for conserving the genetic integrity of R. decussatus.

Contrasting patterns of sequence variation in steelhead populations reflect distinct evolutionary processes.

Multiple evolutionary processes influence genome-wide allele frequencies and quantifying effects of genetic drift, and multiple forms of selection remain challenging in natural populations. Here, we investigate variation at major effect loci in contrast to patterns of neutral drift across a wide collection of steelhead (Oncorhynchus mykiss) populations that have declined in abundance due to anthropogenic impacts. Whole-genome resequencing of 74 populations of steelhead revealed genome-wide patterns (~8 million SNPs) consistent with expected neutral population structure. However, allelic variation at major effect loci associated with adult migration timing (chromosome 28: GREB1L/ROCK1) and age at maturity (chromosome 25: SIX6) reflected how selection has acted on phenotypic variation in contrast with neutral structure. Variation at major effect loci was influenced by evolutionary processes with differing signals between the strongly divergent Coastal and Inland lineages, while allele frequencies within and among populations within the Inland lineage have been driven by local natural selection as well as recent anthropogenic influences. Recent anthropogenic effects appeared to have influenced the frequency of major effect alleles including artificial selection for specific traits in hatchery stocks with subsequent gene flow into natural populations. Selection from environmental factors at various scales has also likely influenced variation for major effect alleles. These results reveal evolutionary mechanisms that influence allele frequencies at major effect loci that are critical for conservation of phenotypic traits and life history variation of this protected species.

Changes in the spatio-temporal genetic structure of Baltic sea trout (Salmo trutta L.) over two decades: direct and indirect effects of stocking

Several countries have implemented stocking programmes to enhance abundance and fish production by releases of hatchery-reared fish. However, due to fluctuations in population size, stocking history, and potential indirect effects of straying of hatchery-reared fish, it is often difficult to predict how these factors will affect genetic diversity and differentiation patterns among wild populations. This study characterized the population genetic structure and temporal variability of four Estonian sea trout populations by evaluating the degrees of direct and indirect genetic impacts of stocking over two decades using 14 microsatellite loci. Our results demonstrate considerable temporal change combined with weak genetic structuring among studied sea trout populations. We found a reduction of the overall level of genetic differentiation combined with the tendency for increased genetic diversity, and an effective number of breeders (Nb) over the study period. Furthermore, we found that immigration rates (m) from hatchery stocks were highest in the population subjected to direct stocking and in non-stocked populations that were located geographically closer to the stocked rivers. This work suggests that hatchery releases have influenced the genetic diversity and structuring of studied sea trout populations. However, the impact of hatchery releases on the adaptive variation and fitness-related traits in wild trout populations remains to be revealed by more informative genetic markers. This study illustrates the dynamic nature of the population genetic structure of sea trout and the value of long-term genetic monitoring for management and conservation.

PoolParty2: An integrated pipeline for analysing pooled or indexed low-coverage whole-genome sequencing data to discover the genetic basis of diversity.

Whole-genome sequencing data allow survey of variation from across the genome, reducing the constraint of balancing genome sub-sampling with estimating recombination rates and linkage between sampled markers and target loci. As sequencing costs decrease, low-coverage whole-genome sequencing of pooled or indexed-individual samples is commonly utilized to identify loci associated with phenotypes or environmental axes in non-model organisms. There are, however, relatively few publicly available bioinformatic pipelines designed explicitly to analyse these types of data, and fewer still that process the raw sequencing data, provide useful metrics of quality control and then execute analyses. Here, we present an updated version of a bioinformatics pipeline called PoolParty2 that can effectively handle either pooled or indexed DNA samples and includes new features to improve computational efficiency. Using simulated data, we demonstrate the ability of our pipeline to recover segregating variants, estimate their allele frequencies accurately, and identify genomic regions harbouring loci under selection. Based on the simulated data set, we benchmark the efficacy of our pipeline with another bioinformatic suite, angsd, and illustrate the compatibility and complementarity of these suites using angsd to generate genotype likelihoods as input for identifying linkage outlier regions using alignment files and variants provided by PoolParty2. Finally, we apply our updated pipeline to an empirical dataset of low-coverage whole genomic data from population samples of Columbia River steelhead trout (Oncorhynchus mykiss), results from which demonstrate the genomic impacts of decades of artificial selection in a prominent hatchery stock. Thus, we not only demonstrate the utility of PoolParty2 for genomic studies that combine sequencing data from multiple individuals, but also illustrate how it compliments other bioinformatics resources such as angsd.

Genomic diversity of wild and cultured Yesso scallop Mizuhopecten yessoensis from Japan and Canada.

The Yesso scallop Mizuhopecten yessoensis is an important aquaculture species that was introduced to Western Canada from Japan to establish an economically viable scallop farming industry. This highly fecund species has been propagated in Canadian aquaculture hatcheries for the past 40 years, raising questions about genetic diversity and genetic differences among hatchery stocks. In this study, we compare cultured Canadian and wild Japanese populations of Yesso scallop using double-digest restriction site-associated DNA (ddRAD) sequencing to genotype 21,048 variants in 71 wild-caught scallops from Japan, 65 scallops from the Vancouver Island University breeding population, and 37 scallops obtained from a commercial farm off Vancouver Island, British Columbia. The wild scallops are largely comprised of equally unrelated individuals, whereas cultured scallops are comprised of multiple families of related individuals. The polymorphism rate estimated in wild scallops was 1.7%, whereas in the cultured strains, it ranged between 1.35 and 1.07%. Interestingly, heterozygosity rates were highest in the cultured populations, which is likely due to shellfish hatchery practices of crossing divergent strains to gain benefits of heterosis and to avoid inbreeding. Evidence of founder effects and drift was observed in the cultured strains, including high genetic differentiation between cultured populations and between cultured populations and the wild population. Cultured populations had effective population sizes ranging from 9 to 26 individuals whereas the wild population was estimated at 25,048-56,291 individuals. Further, a depletion of low-frequency variants was observed in the cultured populations. These results indicate significant genetic diversity losses in cultured scallops in Canadian breeding programs.

Genetic erosion in an endangered desert fish during a megadrought despite long-term supportive breeding.

Human water use combined with a recent megadrought have reduced river and stream flow through the southwest United States and led to periodic drying of formerly perennial river segments. Reductions in snowmelt runoff and increased extent of drying collectively threaten short-lived, obligate aquatic species, including the endangered Rio Grande silvery minnow (Hybognathus amarus). This species is subject to boom-and-bust population dynamics, under which large fluctuations in abundance are expected to lower estimates of effective population size and erode genetic diversity over time. Rates of diversity loss are also affected by additions of hatchery-origin fish used to supplement the wild population. We used demographic and genetic data from wild and hatchery individuals to examine the relationship of genetic diversity and effective population size to abundance over the last two decades. Genetic diversity was low during the early 2000s, but diversity and demographic metrics stabilized after the hatchery program was initiated and environmental conditions improved. Yet, from 2017 onward, allelic diversity declined (Cohen's d = 1.34) and remained low despite hatchery stocking and brief wild population recovery. Across the time series, single-sample estimates of effective population size based on linkage disequilibrium (LD Ne ) were positively associated (r = 0.53) with wild abundance and total abundance, but as the proportion of hatchery-origin spawners increased, LD Ne declined (r = -0.55). Megadrought limited wild spawner abundance and precluded refreshment of hatchery brood stocks with wild fish; hence, we predict a riverine population increasingly dominated by hatchery-origin individuals and accelerated loss of genetic diversity despite supplementation. We recommend an adaptive and accelerated management plan that integrates river flow management and hatchery operations to slow the pace of genetic diversity loss exacerbated by megadrought.

The Genetic Composition of Wild Steelhead Based on Spatial Proximity to a Hatchery

AbstractManagement of hatchery and wild stocks of steelhead Oncorhynchus mykiss within the same watershed requires careful consideration when management objectives include the use of the hatchery stock to meet fishery objectives while maintaining the genetic integrity of coexisting wild stocks. This scenario can be further complicated when management objectives for the hatchery stock include supplementation of natural production. The lower Clearwater River in Idaho provided an ideal location to evaluate hatchery steelhead genetic influence within a drainage with separate wild steelhead and supplementation management emphasis areas. We collected 813 genetic samples from wild juvenile steelhead from two sample years in 10 tributaries to the lower Clearwater River to explore genetic structure and assess hatchery influence. Overall, levels of genetic diversity of wild groups were comparable with those observed elsewhere in the Snake River basin. Estimates of effective population size of sample tributaries ranged from 22 to 198 spawners, with a median of 84. All but two tributaries had >50 spawners, and evidence of natural gene flow from other stocks was observed. Results of the study display three zones of hatchery influence in the lower Clearwater River: (1) no influence in lower tributaries with wild steelhead emphasis, (2) moderate influence in wild steelhead tributaries in close proximity to the hatchery facility, and (3) significant influence in hatchery‐supplementation tributaries. Interestingly, a number of wild steelhead reporting groups from elsewhere in the Snake River basin were observed in the assignments of study fish, suggesting movement of wild steelhead among larger drainage areas. Techniques outlined in this study can be used to monitor future hatchery influence in the Clearwater River drainage, track historic versus contemporary genetic influence in the drainage, and apply to other watersheds with hatchery and wild steelhead management objectives.

Improved productivity of naturalized spring Chinook salmon following reintroduction from a hatchery stock in Lookingglass Creek, Oregon

Supplementation of depressed salmonid populations with hatchery production has been questioned due to domestication effects, which may reduce reproductive fitness. However, for extirpated populations, reintroduction typically requires use of hatchery stocks. We evaluated this strategy by monitoring the naturalization of spring Chinook salmon reintroduced to Lookingglass Creek, OR (Grande Ronde Basin), from a captive brood, hatchery stock. We compared the reproductive success (RS) of naturally spawning natural-origin relative (NOR) to hatchery-origin (HOR) adults across 9 brood years. Individual RS (the number of progeny produced) was estimated by pedigree reconstruction analyses, and then analyzed by generalized linear models to estimate the effect of parental origin, while controlling for potentially confounding covariates. When evaluating RS by juvenile progeny, NOR spawners were more likely to be reproductively successful, and when successful, produced more progeny on average than successful HOR counterparts. We found a similar advantage when evaluating RS by adult progeny, although the origin effect was not as important among successful spawners. Results suggest fish reintroduced from a hatchery stock possess the adaptive capacity to positively contribute to natural productivity and recovery goals.

Spatiotemporal distribution of Ceratonova shasta in the lower Columbia River Basin and effects of exposure on survival of juvenile chum salmon Oncorhynchus keta.

In the Columbia River Basin (CRB), USA, anthropogenic factors ranging from dam construction to land use changes have modified riverine flow and temperature regimes and degraded salmon habitat. These factors are directly implicated in native salmon and steelhead (Oncorhynchus species) population declines and also indirectly cause mortality by altering outcomes of ecological interactions. For example, attenuated flows and warmer water temperatures drive increased parasite densities and in turn, overwhelm salmonid resistance thresholds, resulting in high disease and mortality. Outcomes of interactions between the freshwater myxozoan parasite, Ceratonova shasta, and its salmonid hosts (e.g., coho O. kisutch and Chinook salmon O. tshawytscha) are well-described, but less is known about effects on chum salmon O. keta, which have a comparatively brief freshwater residency. The goal of this study was to describe the distribution of C. shasta relative to chum salmon habitat in the CRB and assess its potential to cause mortality in juvenile chum salmon (listed as threatened in the CRB under the U.S. Endangered Species Act). We measured C. shasta densities in water samples collected from chum salmon habitat throughout the lower CRB during the period of juvenile chum salmon outmigration, 2018–2020. In 2019, we exposed caged chum salmon fry from two hatchery stocks at three C. shasta-positive sites to assess infection prevalence and survival. Results demonstrated: (1) C. shasta was detected in spawning streams from which chum salmon have been extirpated but was not detected in contemporary spawning habitat while juvenile chum salmon were present, (2) spatiotemporal overlap occurs between C. shasta and juvenile chum salmon in the Columbia River mainstem, and (3) low densities of C. shasta caused lethal infection in chum salmon fry from both hatchery stocks. Collectively, our results suggest C. shasta may limit recovery of chum salmon now and in the future.

Growth and foraging behavior of hatchery propagated long-spined sea urchins, Diadema antillarum: Implications for aquaculture and restocking

Stocking hatchery propagated long-spined sea urchins Diadema antillarum is a priority option for recovery of this keystone herbivore on Caribbean reefs. However, information on captive culture of D. antillarum is very limited due to historical lack of successful juvenile production from gametes in the hatchery. In this study, hatchery propagated D. antillarum juveniles were cultured using two diets, commercially available herbivore pellets and dried nori, with the presence/absence of stony coral Acropora cervicornis skeleton to understand how diet and habitat complexity affect growth and behavior of juveniles. Juvenile urchin growth, and the diel pattern of feeding and foraging behavior were significantly affected by diet type. Juveniles fed dried nori gained significantly higher live weight and test diameter than those fed herbivore pellets. Juvenile urchins displayed nocturnal feeding and foraging behavior irrespective of diet types and presence/absence of coral structure. Presence/absence of coral structure did not affect growth and diel pattern of feeding and foraging behavior, but modulated habitat usage patterns. Survival of juveniles was neither affected by diet types nor the presence/absence of coral structure. This study concludes that dried nori is a superior diet to herbivore pellets for juvenile urchin culture. Since the presence of coral structure influenced habitat usage patterns, provision of rugose structure in captivity has the potential to convey the innate shelter seeking behavior of juvenile urchins.

Growth, Yield and Profitability of Major Carps Culture in Coastal Homestead Ponds Stocked with Wild and Hatchery Fish Seed

Major carps, native freshwater fish in South Asian nations, are economically valuable fish species with high market demand. Coastal rural people can cultivate them in their own seasonal, largely underutilized, small homestead ponds with low input and understanding. However, the major problems with fish production in this region are the lack of quality carp seed and appropriate culture techniques. Therefore, this research was carried out on growth performance, survival rate, yield, feed conversion ratio (FCR), and profit of carp polyculture systems stocking with hatchery-produced and wild sourced fish seed in homestead ponds located in a coastal area along the Bay of Bengal. Three different treatments (T1–T3), each treatment with three replications, were designed for culturing carps, Gibelion catla, Labeo rohita, Labeo calbasu, and Cirrhinus mrigala using two local hatcheries seeds (T1 and T2), and wild seeds from the Halda River (T3). For all treatments, the stocked fish were maintained in the same size, weight, density, and ratio. Water quality parameters were measured at intervals of seven days, and the mean values were found to be within an acceptable range for fish farming and, in most cases, did not differ significantly from each other. The specific growth rate (SGR) was found higher in T3 for G. catla (1.16 ± 0.012%/day), L. rohita (1.19 ± 0.035%/day), and C. mrigala (1.06 ± 0.03%/day) and significantly differed (p < 0.05) among the treatments. Additionally, there were significant differences between the treatments in terms of ultimate weight, weight gain, survival rate, fish production, and return on investment (ROI) (p < 0.05). The lower FCR in T3 (2.65 ± 0.10) than in T1 (3.32 ± 0.31) and T2 (3.21 ± 0.33) indicated that stocking wild seed had higher profitability potentials. High genetic variety in the population of naturally occurring, free-living fish, resistance to disease, a high rate of survival, and the hardiness of wild seed are all factors that might contribute to the better performance of wild seed stock. However, the total yield and total return from the T3 treatment also emphasized that carp farming using wild seed is not viable because of the variable amount, high seed cost, low transportation facilities, and very small natural seed-stock supplies from the river. Inbreeding and reduced genetic variety in the hatchery stock could result in the production of poor-quality seed, which had an impact on the production performance in culture treatments stocked with hatchery seed.

Assessing Genetic Diversity of Wild Populations and Different Color Varieties for Genetic Improvement of Siamese Fighting Fish Betta splendens in Thailand.

To establish sustainable resources and founder populations for genetic improvement of the Siamese fighting fish Betta splendens, genetic diversity in wild and hatchery stocks was examined using mitochondrial (mt) DNA genes cytochrome b (cytb), 16S ribosomal DNA (16S rDNA), and cytochrome oxidase subunit I (COI), and eight microsatellite loci. Based on mtDNA sequences, restrictive levels of polymorphism (0, 3, and 1 substitutions) were observed in this study. For analysis of microsatellites, fluorescent multiplex PCR was developed, and subsequently identifying moderate levels of observed (Ho = 0.4488) and expected (He = 0.6627) heterozygosities and a high number of alleles per locus (15.125 alleles) for overall samples. Comparison of Siamese fighting fish from different sources revealed large genetic differences between pairs of farmed fish (eight groups) and between wild (three geographic locations) and farmed fish (P < 0.0031 following Bonferroni correction). This suggested limited exchanges of genetic resources between commercial farms. When different color varieties of B. splendens were compared, large genetic distances and significant FST estimates and genetic heterogeneity were found (P < 0.0031). Effective population sizes (Ne) were estimated and two farms (NP2-2BS and BK1-4BS) showed Ne greater than 10. Among color varieties, Multi-colors and Blue revealed reasonable Ne (large and 27.9), but lower Ne values (3.6-8.4) were found for the remaining color varieties. These results indicate an urgent need for the establishment of gene pool resources of B. splendens for effective genetic improvement of Siamese fighting fish in Thailand.

Patterns of Hatchery‐Produced Returns of American Shad in the James River, Virginia

AbstractAmerican Shad Alosa sapidissima is an anadromous clupeid that once supported a robust fishery but has declined drastically throughout its native range due to overfishing, dam proliferation, and poor water quality. A hatchery program on the James River in Virginia was introduced in 1992 to support the recovery of stocks. Following a moratorium of the fishery enacted in 1994, a fisheries‐independent survey was initiated in 1998 to monitor the population recovery efforts and status of American Shad stocks in Virginia. This paper examined 22 years of monitoring data for the James River and determined the effect of hatchery inputs on the James River stock of American Shad. The spawning stock index increased from 2.57 in 1998 to a peak of 9.33 in 2003 but has generally been declining since and has been at very low levels in most recent years. The hatchery prevalence for female American Shad (i.e., the percentage of fish derived from the hatchery) ranged between 3.6% and 60.5%. Years with higher spawning stock index values were significantly correlated to higher percentages of hatchery fish returning to spawn. The stock–recruitment relationship was best explained by the Ricker model, which had the lowest residual standard error and Akaike information criterion value. A threshold level of hatchery‐released individuals (approximately 4 million larvae) was necessary to achieve the highest numbers of returning spawners, but stocking above 7 million larvae correlated with declining returns. Long‐term monitoring of the James River American Shad spawning population allowed for the critical examination of the contribution of hatchery individuals to the yearly spawning run and the relative success rate of each hatchery year‐class. From these data, we consider that the James River spawning stock of American Shad was dependent upon hatchery inputs, with ideal hatchery returns occurring during years of moderate levels of hatchery stocking.

Growth of Lahontan cutthroat trout from multiple sources re-introduced into Sagehen Creek, CA.

Lahontan cutthroat trout Oncorhynchus clarkii henshawi have experienced massive declines in their native range and are now a threatened species under the US Endangered Species Act. A key management goal for this species is re-establishing extirpated populations using translocations and conservation hatcheries. In California USA, two broodstocks (Pilot Peak and Independence Lake) are available for reintroduction, in addition to translocations from wild and naturalized sources. Pilot Peak and Independence Lake fish are hatchery stocks derived from native fish from the Truckee River basin and used for recovery activities in the western Geographic Management Unit Areas only, specifically within the Truckee River basin. Yet suitability of these sources for re-introduction in different ecosystem types remains an open and important topic. We conducted growth experiments using Lahontan cutthroat trout stocked into Sagehen Creek, CA, USA. Experiments evaluated both available broodstocks and a smaller sample of fish translocated representing a naturalized population of unknown origin from a nearby creek. Fish from the Independence Lake source had significantly higher growth in weight and length compared to the other sources. Further, Independence Lake fish were the only stock that gained weight on average over the duration of the experiment. Our experiments suggest fish from the Independence Lake brood stock should be considered in reintroduction efforts.

Genetic Diversity and Population Structure of Portunustrituberculatus in Released and Wild Populations Based on Microsatellite DNA Markers from the Yangtze Estuary

Portunus trituberculatus is an important economic species of crab that is artificially bred and released in the Yangtze River Estuary and its adjacent sea areas. Based on six microsatellite markers, we investigate the genetic diversity and structure of 101 P. trituberculatus specimens collected from two hatcheries in Nantong and Zhoushan that participated in stock enhancement in the year 2019. We compared these with 124 wild specimens caught from 13 localities in the estuary. Analysis of several genetic diversity parameters (NA, RS, I, HO, HE, FIS, and FST) for the 15 populations demonstrates that both released and wild populations possess relatively rich genetic diversity. Furthermore, the released groups demonstrate no less genetic variation between themselves than do the wild crabs. Most FIS values are greater than zero, which shows inbreeding is common among specimens with geographically open sites. However, insufficient sampling may have led to a wide distribution of null alleles, a Hardy–Weinberg test disequilibrium in microsatellite markers PN22 and P04, and a lack of crab genetic diversity in site 14. All populations (except locality 14) have not suffered the bottleneck effect. Four subgroups can be seen to roughly spread longitudinally along the sample area by performing pairwise comparisons of genetic distance and FST values among the populations. No obvious topological heterogeneity is discovered among the four subgroups in a phylogenetic tree. The existence of genetic exchange and differentiation among the subgroups is also verified using structure analysis. Therefore, based on this evidence, we propose that the hatchery stock enhancements performed in Nantong and Zhoushan result in no reduction in genetic diversity for wild populations in the Yangtze Estuary in 2019.

If You Build It, Will They Come? An Environmental DNA Assessment of Fish Assemblages on Artificial Reefs in the Northern Gulf of Mexico

AbstractGlobally, estuarine and marine fisheries have declined over the past century, and a variety of approaches have been employed in an attempt to improve fisheries, including the development of protected areas, implementation of catch regulations, hatchery stocking, and habitat augmentation. The focus of this study was to assess the impact of the introduction of artificial reefs on the fish assemblages in the northern Gulf of Mexico (nGOM). Unfortunately, assessing the success of artificial reefs has been problematic due to the high turbidity of the region and the difficulty of using traditional sampling gears to assess species diversity at reefs. To accomplish this, we gathered environmental DNA metabarcode data (12S) to assess the impact of reef age (1–19 years), construction material (limestone, concrete, shell, and oil and gas), and season on the fish assemblages at nine artificial reefs in the nGOM. The results indicate higher species richness at reefs versus paired control sites as well as differences between seasons, reef materials, and reef positions. Our results suggest that this technique is a viable method of monitoring ray‐finned fish species on artificial reefs and can provide baseline information on the fish assemblages associated with artificial reefs in the nGOM.

Genomic Hatchery Introgression in Brown Trout (Salmo trutta L.): Development of a Diagnostic SNP Panel for Monitoring the Impacted Mediterranean Rivers

Brown trout (Salmo trutta L.) populations have been restocked during recent decades to satisfy angling demand and counterbalance the decline of wild populations. Millions of fertile brown trout individuals were released into Mediterranean and Atlantic rivers from hatcheries with homogeneous central European stocks. Consequently, many native gene pools have become endangered by introgressive hybridization with those hatchery stocks. Different genetic tools have been used to identify and evaluate the degree of introgression starting from pure native and restocking reference populations (e.g., LDH-C* locus, microsatellites). However, due to the high genetic structuring of brown trout, the definition of the "native pool" is hard to achieve. Additionally, although the LDH-C* locus is useful for determining the introgression degree at the population level, its consistency at individual level is far from being accurate, especially after several generations were since releases. Accordingly, the development of a more powerful and cost-effective tool is essential for an appropriate monitoring to recover brown-trout-native gene pools. Here, we used the 2b restriction site-associated DNA sequencing (2b-RADseq) and Stacks 2 with a reference genome to identify single-nucleotide polymorphisms (SNPs) diagnostic for hatchery-native fish discrimination in the Atlantic and Mediterranean drainages of the Iberian Peninsula. A final set of 20 SNPs was validated in a MassARRAY® System genotyping by contrasting data with the whole SNP dataset using samples with different degree of introgression from those previously recorded. Heterogeneous introgression impact was confirmed among and within river basins, and was the highest in the Mediterranean Slope. The SNP tool reported here should be assessed in a broader sample scenario in Southern Europe considering its potential for monitoring recovery plans.

The quest for successful Atlantic salmon restoration: perspectives, priorities, and maxims

AbstractAtlantic salmon is often a focal species of restoration efforts throughout the north Atlantic and it is therefore an excellent case study for how best to design programmes to address and mitigate threats and correct population declines. This perspective is written to promote the work that has been accomplished towards restoration of Atlantic salmon populations and synthesize how we believe the lessons can be used effectively to support efforts by management agencies to restore populations. We reviewed where restoration is needed for Atlantic salmon, agreed on definitions for three levels of successful restoration, and then applied these criteria to 49 published papers focused on Atlantic salmon restoration. We identified 16 successful examples of restoration among 49 papers reviewed and discussed what interventions led to success versus failure. We then addressed key questions about when hatchery stocking should be used as part of a restoration measure and whether local restoration efforts are enough when these wide-ranging species encounter broad-scale changes in the north Atlantic, specifically related to issues of climate change and to marine survival. We advise to avoid restoration as much as possible by protecting and managing existing populations and when restoration is necessary, problems should be identified and addressed in partnership with river users. With appropriate resources and research to resolve ongoing mysteries, restoration of lost Atlantic salmon populations is absolutely feasible.

The Abundance and Distribution of Hatchery and Naturally Produced Chinook Salmon in Columbia River Estuary Nearshore Habitat

AbstractColumbia River hatcheries release millions of juvenile Chinook Salmon Oncorhynchus tshawytscha to support fisheries and mitigate for historical productivity declines from dam construction and upriver habitat losses. Recent federal biological opinions for Federal Columbia River Power System operations also have mandated restoration of estuarine rearing habitats to mitigate for mortality of naturally produced (NP) salmon at main‐stem dams. We compared genetic stock compositions, distributions, abundances, and length frequencies of hatchery‐marked and unmarked Chinook Salmon to evaluate the extent of hatchery influence on nearshore estuarine habitat use and the potential for interactions between hatchery‐origin (HO) and NP salmon. Cumulative Chinook Salmon releases from all hatcheries in 2010 and 2011 dictated estuarine stock composition, abundance, and life histories during the spring–summer migration peak. Naturally produced salmon from the lower Columbia River populations, including many fry migrants, were most abundant, but larger HO juveniles also frequented nearshore sites, where their total biomass often equaled or exceeded that of NP fish. Large releases of a single stock of origin (Spring Creek Group fall run) in April and May created sharp pulses in the estuary entry timing of fingerling‐sized salmon and dominated abundance and stock composition at some sites. Successive releases from scores of hatcheries during spring and early summer ensured a consistent presence of HO salmon near shore, regardless of the habitat‐specific residence times of individual fish. Overall, the historical replacement of diverse wild populations with fewer hatchery stocks of a narrow size range and migration timing has intensified nearshore habitat use during the spring–summer migration peak and reduced life history variation of Columbia River Chinook Salmon. Such changes could undermine the fish conservation goals of both hatchery mitigation and estuary restoration programs.

English

Population genetic structure of cultured fish species is vital for improving the fisheries management and stock enhancement programs. The genetic variability and population genetic structure at fourteen microsatellite loci of a total 210 individuals of Cyprinus carpio from six selected hatcheries were analyzed. The data obtained through microsatellite markers showed a low- to-moderate level of genetic diversity in terms of allele numbers (Na), allelic richness (Ar), effective allele numbers (Nae) and observed heterozygosity (Ho) in all the populations. At the examined loci, 32 out of 84 possible tests were observed to be significantly (P&lt;0.05) deviated from the Hardy-Weinberg equilibrium. Maximal gene flow (Nm) and lower population differentiation (FST) was experienced among populations. However, significant (P&lt;0.05) differentiation was observed among some populations. An analysis of the distribution of genetic variation indicated within individual was very high (69.07%), while, among individuals within populations and among populations was low (29.56% and 1.37%, respectively). Recent bottleneck was detected with the shifted mode. Phylogenetic neighbor joining tree analysis showed the two distinct clusters. The inferences of this study would be helpful for setting up effective management strategies for the better conservation of genetic integrity in the hatchery stocks of C. carpio.