Impacts of hatchery release on genetic structure of rock carp <Emphasis Type="Italic">Procypris rabaudi</Emphasis> in the upper Yangtze River,China

Rock carp Procypris rabaudi is a vulnerable endemic fish in the upper Yangtze River. Hatchery release has been carried out as a major stock enhancement strategy for this species. Ten microsatellite loci were chosen to compare genetic variation between one wild population and two hatchery groups to evaluate the potential impacts of hatchery release on the genetic structure of the wild population. Two different models indicated strong evidence of recent bottlenecks in all groups. The hatchery groups were lower in the mean number of alleles per locus, allelic richness, and allelic diversity compared with the wild population. The 80% membership coefficient indicated that 14% of the wild fish could be assigned as hybrids of wild and hatchery fish. Our results suggested that hatchery release will further reduce the natural genetic diversity in the wild population, change the genetic structure of the rock carp population, and may not benefit restoration of this vulnerable fish species.     

Density‐dependent effects of eastern Kamchatka pink salmon (Oncorhynchus gorbuscha) and Japanese chum salmon (O. keta) on age‐specific growth of western Alaska chum salmon

Hatcheries release >4.5 billion juvenile Pacific salmon (Oncorhynchus spp.) into the North Pacific Ocean annually, raising concerns about competition with wild salmon populations. We used retrospective scale analysis to investigate how the growth of chum salmon (O. keta) from western Alaska is affected by the abundance of chum salmon from Japanese hatcheries and wild pink salmon (O. gorbuscha) from the Russian Far East. Over nearly five decades, the growth of Kuskokwim River chum salmon was negatively correlated with the abundance of Japanese hatchery chum salmon after accounting for the effects of sex and spring/summer sea‐surface temperature in the Bering Sea. An effect of wild eastern Kamchatka pink salmon abundance on the growth of Kuskokwim River salmon was detectable but modest compared to the intraspecific competitive effect. A decrease in Japanese hatchery chum salmon releases in 2011–2013 was not associated with increased growth of Bering Sea chum salmon. However, the abundance of wild chum salmon from the Russian Far East increased during that time, possibly obscuring reduced competition with hatchery chum salmon. Our results support previous evidence that chum salmon are affected by intraspecific competition, and to a lesser extent interspecific competition, in the North Pacific, underscoring that the effects of salmon hatchery production transcend national boundaries.     

Genetic heterozygosity and meristic character variance in a wild Atlantic salmon population and a hatchery strain derived from it

Heterozygosity at seven enzyme loci was compared with the degree of fluctuating asymmetry of three bilateral traits in a wild population of Atlantic salmon (Salmo salar L.) and a hatchery strain derived from it. In the wild population, average heterozygosity per fish was higher (p < 0.01) and average asymmetric value per fish was lower (p < 0.01), compared with the hatchery strain. Analyses at the intrapopulation level did not provide unequivocal support for the relationship between heterozygosity and developmental stability, with correlation between the number of heterozygous loci per fish and the asymmetric value per fish being non-significant. However, comparisons of asymmetric value per fish between homozygous and heterozygous individuals at separate loci indicated that heterozygotes had significantly lower asymmetry values per fish at IDDH-1* in the hatchery sample. These results are discussed in relation to the potential utility of fluctuating character asymmetry as an indicator of loss of heterozygosity in cultured Atlantic salmon stains.     

Genetic diversity within sea trout population from an intensively stocked southern Baltic river,based on microsatellite DNA analysis

Sea trout, Salmo trutta L., populations in the Slupia River basin have been affected by mass stocking with smolts and fry. This work is focused on a small‐scale differentiation in sea trout populations from one basin with a strong emphasis on the relationship between wild and hatchery origin fish. A total of 216 sea trout were genotyped at 10 microsatellite loci. Global F_ST obtained by amova was low at 0.0165. Pairwise F_ST were significant for all tests except wild and stocked adults. The highest pairwise difference was found between the hatchery sample and Kwacza (F_ST = 0.038). Analysis of the genetic structure revealed micro‐geographical differentiation with four subpopulations. The quality of the artificial spawning was found not to be adequate with a high risk of adverse effects to the whole population. All future stocking actions in the basin should consider the existing population structures.     

Genetic diversity and population history of Tanichthys albonubes (Teleostei: Cyprinidae): Implications for conservation

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Genetic variation of wild and cultured populations of the Kuruma prawn Marsupenaeus japonicus (Bate 1888) using microsatellites

The microsatellite DNA technique was used to detect the genetic variations between wild and cultured populations of Kuruma prawn Marsupenaeus japonicus Bate 1888. All the six microsatellite loci screened in this study showed high polymorphism for their PIC (0.6701–0.8989), which was much more than the standard value of 0.5. A total of 73 alleles were observed over six loci from 93 shrimps. The mean number of allele locus ranged from 9.83 (cultured) to 11.83 (wild). The number of effective alleles varied from 6.86 (cultured) to 8.58 (wild). The average of observed heterozygosity (H_o) of populations varied from 0.6935 (cultured) to 0.7370 (wild), and that of expected heterozygosity (He) was 0.8169 (wild) and 0.8209 (cultured). Tests of Hardy–Weinberg showed that these loci deviated significantly or highly significantly in one or both populations. Compared with the wild population, the cultured population showed little reduction in genetic variation. The total number of alleles (71, 59) was not significantly (P=0.296) different between wild and cultured populations. The paired‐samples t test of observed heterozygosity and expected heterozygosity implied that there was no significant difference (P=0.572 and 0.891 respectively) between wild and cultured populations. However, some rare allele loss might have occurred in the cultured population. A total of 14 unique alleles were found in the wild population, but only two unique alleles were observed in the cultured population. Therefore, there is a need to monitor genetic variability of cultured population, and to improve the hatchery program for the conservation of wild Kuruma prawn resources.     

Genetic diversity and structure of domesticated strains of red sea bream,Pagrus major,inferred from microsatellite DNA markers

The genetic diversity and structure of nine domesticated strains of red sea bream used in a private hatchery were studied and compared to a wild population. A total of 313 individuals were genotyped at eight microsatellite loci. Average number of alleles per locus ranged from 5.5 to 9.4 in domesticated strains, but that of the wild population was 28.4. Heterozygosity of domesticated strains (ranged 0.697–0.804) was also lower compared to the wild population (0.952). Estimated Ne also decreased in all domesticated strains (ranged 10.3–126.0) compared to the wild population (1422.5). The UPGMA tree and 3‐D FCA showed that there were two main clusters containing domesticated strains, and the wild population was at the middle of both of the domesticated clusters. The STRUCTURE analysis also supported the phylogenetic analysis, and revealed three sub‐clusters in the domesticated strains. Pairwise F_ST revealed that all domesticated strains were statistically different from the wild population, and also the differentiation between domesticated strains was all statistically significant. Information on genetic diversity and structure of domesticated strains of red sea bream obtained in this study will be useful for future broodstock management and selective breeding programmes.     

Predation on wild and hatchery salmon by non‐native brown trout (Salmo trutta) in the Trinity River,California

Non‐native predators may interfere with conservation efforts for native species. For example, fisheries managers have recently become concerned that non‐native brown trout may impede efforts to restore native salmon and trout in California's Trinity River. However, the extent of brown trout predation on these species is unknown. We quantified brown trout predation on wild and hatchery‐produced salmon and trout in the Trinity River in 2015. We first estimated the total biomass of prey consumed annually by brown trout using a bioenergetics model and measurements of brown trout growth and abundance over a 64‐km study reach. Then, we used stable isotope analysis and gastric lavage to allocate total consumption to specific prey taxa. Although hatchery‐produced fish are primarily released in the spring, hatchery fish accounted for most of the annual consumption by large, piscivorous brown trout (>40 cm long). In all, the 1579 (95% CI 1,279–1,878) brown trout >20 cm long in the study reach ate 5,930 kg (95% CI 3,800–8,805 kg) of hatchery fish in 2015. Brown trout predation on hatchery fish was ca. 7% of the total biomass released from the hatchery. Brown trout only ate 924 kg (95% CI 60–3,526 kg) of wild fish in 2015, but this was potentially a large proportion of wild salmon production because wild fish were relatively small. As large brown trout rely heavily on hatchery‐produced fish, modifying hatchery practices to minimise predation may enhance survival of hatchery fish and potentially reduce the abundance of predatory brown trout.     

Genetic relatedness and differentiation of hatchery populations of Asian seabass (Lates calcarifer) (Bloch, 1790) broodstock in Thailand inferred from microsatellite genetic markers

After more than 20 years of hatchery production of Asian seabass in Thailand, genetic information is still lacking for effective genetic management and a selective breeding programme. This study aimed to evaluate genetic status of existing hatchery populations and genetic consequences of a selective breeding attempt. We examined genetic relatedness in seven hatchery samples, including a selectively bred population (RACF‐F1), compared with three wild samples using 11 microsatellite loci. Genetic diversity and relatedness values within most hatchery samples, except for RACF‐F1, did not differ from those of wild populations (P > 0.05). RACF‐F1 had the lowest allelic diversity and effective population size (A_r = 6.99; N_e = 7.8) and highest relatedness values (mean r_xy = 0.075–0.204). Pairwise Φ_ST values, principal component analysis and model‐based cluster analyses revealed three genetically distinct hatchery groups: Eastern Thailand (CHN, RACF, NSCF and SKCF), Southern Thailand (NICA) and the Andaman Sea (STCF). Results suggest that exiting domestic populations capture reasonable amount of genetic variation and can be useful for a base population for genetic improvement programmes. In addition, given the rapid increase in relatedness that we observed in one selectively bred population, we recommend using selection methods and hatchery practices that reduce variability in family contribution in the subsequent generations.     

Maintenance of genetic variation in hatchery stocks of Atlantic salmon, Salmo salar L.: experiences from the River Bush, Northern Ireland

Abstract. An examination of biochemical-genetic variation at seven polymorphic loci was carried out among five year classes of wild Atlantic salmon, Salar L., in the R. Bush and in a hatchery strain derived from the wild population. Within some of the year classes, gene frequencies at several loci differed significantly between wild and artificially reared salmon. Highly significant temporal variation in gene frequencies was detected among successive year classes of the hatchery strain, while this was less significant among the wild salmon. Samples of wild salmon taken as 0+ and 1 + parr in the river showed no significant temporal variability in allelic frequencies. Heterozygosity levels among the wild and hatchery-reared salmon were comparable, averaging 0·185 and 0·176 respectively. The genetic variability of the artificially reared salmon is discussed in relation to numbers of broodstock and breeding regime used at the hatchery.     

Identification of differential broodstock contribution affecting genetic variability in hatchery stocks of Atlantic salmon (Salmo salar)

Supportive breeding of Atlantic salmon (Salmo salar) is commonly employed to maintain numbers of fish where the species has become locally endangered. Increasingly, one of the main aims of population management is the preservation of natural genetic diversity. If the stocks employed in supportive breeding exhibit reduced variation they can alter the natural pattern of genetic variation observed in wild populations. In northern Spain, wild adult salmon are caught every year from local rivers and artificially crossed in order to create supportive stocks. The offspring are hatchery reared until the juvenile stage, then released into the same river where their parents were caught. In the current study, our findings demonstrate that although adult broodstock exhibit a pattern of variation similar to the wild populations, variability at microsatellite loci was drastically reduced in the juveniles released into one of three rivers analyzed. The contribution of broodstock to this juvenile stock was examined by pedigree analysis. A restricted number of females contributing to the hatchery stock was identified as the main cause of loss in genetic variation, possibly due to overmaturity of some multi-sea-winter females. We suggest that better monitoring and control of parental contribution will help in solving the problem of loss of genetic diversity in hatchery populations.     

A set of highly polymorphic microsatellites useful for kinship and population analysis in turbot (Scophthalmus maximus L.)

The turbot (Scophthalmus maximus) is a flatfish species of great commercial value for aquaculture. In this study we describe the isolation and characterization of 30 novel highly polymorphic microsatellite markers in this species obtained from a genomic library enriched for seven short tandem repeated motifs. Much higher polymorphism (mean number of alleles: 13.37; mean expected heterozygosity: 0.869) and potential for parentage assignment than previously reported for microsatellites in turbot were found after the analysis of 24 wild individuals. Most loci conformed to Hardy–Weinberg expectations, excluding Sma‐USC20 and Sma‐USC28, which showed a high heterozygote deficit probably due to the presence of null alleles. No significant genotypic disequilibrium was observed between any pair of loci, suggesting no close linkage between them. These loci are potentially useful for kinship and population analysis in turbot.     

Wild origin and enriched environment promote foraging rate and learning to forage on natural prey of captive reared Atlantic salmon parr

Abstract – After release to the wild, captive reared salmon have shown lower foraging rates on natural prey and impaired ability to avoid natural predators and thus lower survival compared with wild‐born conspecifics. Here, we examine whether captive breeding influences learning of foraging on natural prey and how enriched rearing methods may improve foraging on natural prey by Atlantic salmon (Salmo salar) parr. We reared offspring of hatchery or wild salmon of the same population in either a standard or enriched environment at production‐scale densities. The enriched environment featured submerged overhead shelter, varying water current, depth and direction and consequently alterations in food dispersion. Parr reared in the enriched environment expressed higher feeding rates, and parr of wild origin started to forage earlier on natural prey. The enriched method promoted foraging of hatchery reared parr on natural prey and is easily applicable to commercial production of salmonids for reintroduction or stock enhancement purposes.     

Evolution of introduced Chinook salmon (Oncorhynchus tshawytscha) in Lake Huron: emergence of population genetic structure in less than 10 generations

Abstract – Population genetic structure was detected in Chinook salmon Oncorhynchus tshawytscha in their non‐native range of Lake Huron using microsatellite DNA. All Chinook salmon in this system descend from Green River, Washington cohorts, originally transplanted to Michigan hatcheries in the late 1960s. We tested for population genetic differentiation of age 0 fish collected from 13 rivers and two hatcheries in 2007. The amount of genetic differentiation among collection sites was low but statistically significant, with F_ST values ranging from 0.036 to 0.133 and R_ST values ranging from 0.008 to 0.157 for specific loci. Based on pairwise F_ST and R_ST values and Bayesian cluster analysis, the Maitland River population in the Main Basin of Lake Huron was genetically distinct from the remaining collection sites. Based on analysis of bycatch data from commercial gill net fisheries, Chinook salmon likely colonised the Main Basin by 1975 (10 generations ago) and the North Channel and southern Georgian Bay regions by 1980 (eight generations ago). Thus, population genetic structure has emerged in Lake Huron Chinook salmon in <10 generations.     

An evaluation of the contribution of hatchery stocking on population density and biomass: a lesson from masu salmon juveniles within a Japanese river system

Stocking is an important management tool for enhancing fisheries resources, but its actual contribution to fisheries resources is controversial, taking into consideration both the positive and negative effects. This study compared density and biomass of hatchery (otolith thermal marked) and wild masu salmon parr between stocked and unstocked rivers to evaluate the contribution of stocking with hatchery‐reared fish. Density and biomass of all fish did not differ between stocked and unstocked rivers. Moreover, density and biomass of wild fish in the stocked rivers were lower than those of the unstocked rivers. Density and biomass of hatchery fish in a non‐natural reproducing river were similar with those of all fish in natural reproducing rivers. These results indicate that hatchery stocking does not have positive effects on population density or biomass but replaces wild fish with hatchery fish and that non‐natural reproducing areas are more suitable as stocking sites.     

Microsatellite genetic variation in wild and hatchery populations of the sea cucumber (Apostichopus japonicus Selenka) from northern China

Farming of the sea cucumber Apostichopus japonicus (Selenka) started 20 years ago and is still in rapid expansion in China. In order to assess the genetic status of both wild and cultivated stocks of this species, we used eight microsatellite markers to estimate the level of genetic diversity within five hatchery stocks and two wild populations of A. japonicus, and compared the degree of genetic differentiation between them. High levels of polymorphism were observed over all loci. The mean alleles and expected heterozygosities over the seven stocks were 10.4–12.3 and 0.735–0.783 respectively. The results of the microsatellite survey provide no evidence to show that hatchery practice of the sea cucumber in China to date has significantly affected the genetic variability of the cultured stocks. Significant differentiation was found between most pairs of the hatchery stocks and wild populations (F_st range: 0.008–0.036), and no obvious difference was detected between the wild populations (F_st=0.008). The information on the genetic variation and differentiation obtained in this study can be applied for future genetic monitoring of A. japonicus aquaculture stocks and will be useful for future genetic improvement by selective breeding, and for designing suitable management guidelines for these genetic materials.     

Genetic characterization of wild Dutch common carp (Cyprinus carpio L.)

Six male carp, caught in the water system surrounding the Anna Paulowna (AP) Polder in The Netherlands, were characterized using allozyme and microsatellite markers. At the sMDH‐A1,2* loci an allele was found, which has previously only been found in wild River Rhine and wild Vietnamese common carp. Microsatellite allele frequencies showed that these AP carp were significantly different from a group of carp originating from several different domesticated strains. Based on both allozyme and microsatellite data, the AP carp probably originated from a wild or feral self‐sustaining population.     

Juvenile river residence and performance of Snake River fall Chinook salmon

An animal's performance during its early life stage can greatly influence its survival to adulthood. Therefore, understanding aspects of early life history can be informative, particularly when designing management plans to rebuild a population. For a threatened population of fall Chinook salmon (Oncorhynchus tshawytscha) in the Snake River of Idaho, we reconstructed the early life history for 124 returning wild and hatchery adults using information recorded in their otoliths. Of our sampled wild adults (n = 61), 43% and 49% reared within the Snake River and Clearwater/Salmon rivers. We also found that only 21% of our sampled wild adults exhibited the historically common subyearling out‐migration strategy, in which juveniles exit freshwater shortly after hatching, while the remaining wild adults exhibited the yearling out‐migration strategy (i.e., individuals delay their freshwater exit). As expected, yearlings had, on average, a significantly larger body size than subyearlings at ocean entry. However, 35% of wild yearlings overlapped in size with wild subyearlings suggesting that spending more time in freshwater might not necessarily result in a larger body size. Lastly, we observed that variability in fork length at Snake River egress and ocean entry were best explained by migration strategy and where it reared, followed by hatch year and sex. Results from this study highlight the utility of adult otoliths in providing details about early life history, an understanding of which is critical to the conservation of Snake River fall Chinook salmon.     

长江鲢、草鱼原种——人繁群体生长差异与生化遗传变化↑（*）

用完全随机区组设计的方法在三个池塘中进行了源于长江的鲢，草鱼原种与封闭人繁群体子三代１龄鱼种阶段的生长比较试验。结果表明；原种鲢，草鱼的体长绝对增长高出封闭人繁子三代群体１７－２１％，相对增长快１３－１８％；体重绝对增重高出２５－２６％，相对增重快１５－２０％。但这些差异均未达数理统计上差异显著的标准。     

Impact of stocked Atlantic salmon (Salmo salar L.) on habitat use by the wild population

Laffaille P. Impact of stocked Atlantic salmon (Salmo salar L.) on habitat use by the wild population.
Ecology of Freshwater Fish 2011: 20: 67–73. © 2010 John Wiley & Sons A/S Abstract – We investigated the summer habitat occupied by populations of young‐of‐the‐year wild and stocked (farmed populations released into the native range) Atlantic salmon under allopatric and sympatric conditions. Under allopatric conditions, farmed and wild salmon occupied habitats with the same characteristics. The salmon preferentially occupied the riffle areas. However, under sympatric conditions, the fish occupied meso‐ and micro‐habitats with different characteristics. Wild salmon avoided habitats used by farmed salmon and preferred glide areas with considerable vegetation cover. This study suggests that differences in the pattern of habitats used by young Atlantic salmon were both size‐ and origin‐dependent and may result from intra‐species competition between farmed and wild populations. Given that stocking with farmed Atlantic salmon is carried out intensively to enhance recreational angling or to conserve salmon populations, this study warns that this can have a negative impact on the extant wild Atlantic salmon population.