Microsatellite genetic variation between and within farmed and wild Atlantic salmon (Salmo salar) populations

Genetic diversity between three farmed and four wild populations of Atlantic salmon from Ireland and Norway were analysed using 15 microsatellite markers. High levels of polymorphism were observed over all populations with the average number of alleles and average heterozygosity at 17.8 and 0.70, respectively. Farmed salmon showed less genetic variability than wild salmon in terms of allelic diversity but not necessarily in terms of overall heterozygosity. Between farmed populations significant differences were observed in expected heterozygosity suggesting that more intensive breeding practices may have resulted in a further erosion of genetic variability. Phylogenetic analysis using either populations or individuals as nodes show a clustering of populations into two groups, farmed and wild. This suggests that founder effects and subsequent selection have had more effect on the genetic differentiation between these strains than geographical separation. This technology has great potential for use in aquaculture situation where levels of genetic variation could be monitored and inbreeding controlled in a commercial breeding progra.     

Susceptibility,behaviour, and retention of the parasitic salmon louse (Lepeophtheirus salmonis) differ with Atlantic salmon population origin

Atlantic salmon populations across the world have diverse ecological and evolutionary histories, from wild anadromous or landlocked, to domestication and genetic modification. The natural host behaviours confer protection from infestation by ectoparasitic salmon lice Lepeophtheirus salmonis, yet whether genetic origin results in different behaviours and thus susceptibility to infestation is unknown. In common garden experiments, we tested antiparasite behaviours, susceptibility and retention of salmon lice in wild anadromous, wild landlocked, domesticated and genetically modified domesticated strains. Within domesticated strains, we tested two infestation histories (previously infested and naïve) and a new phenotype (albino colouring). Farmed stocks initially acquired 24%–44% higher levels of parasite density than the wild and landlocked strains. Burst swimming and displacement behaviours were higher in the domesticated groups, and jumping was more prevalent in the domesticated strains. At 34 days post‐infestation, domesticated strains and the wild anadromous strain did not differ significantly from each other; however, landlocked salmon had increased infestation levels considerably. Domesticated strains lost ~20% (±9.9%–16.5%; 95% CI) of their initial parasite load, while parasite load increased by 5.5% (±30.1%) for wild salmon and 20.1% (±28.5%) in landlocked salmon. This study provides early evidence for diverged host–parasite interactions associated with domestication in this system.     

Residual genetic variability in domesticated populations of the Pacific blue shrimp (Litopenaeus stylirostris) of New Caledonia,French Polynesia and Hawaii and some management recommendations

The Latin American shrimp Litopenaeus stylirostris was introduced in three different Pacific islands (Tahiti, New Caledonia via Tahiti, and Hawaii) and hatchery-propagated for 7–25 generations to develop shrimp farming based on these domesticated stocks. Three microsatellite markers have been used in an attempt to assess the genetic bases of the populations available to start a selective breeding program. The comparison of eight hatchery stocks (five New Caledonian, two Hawaiian and one Tahitian stocks) and one wild Ecuadorian population showed a much lower variability in the domesticated stocks than in the wild population, especially in New Caledonia and Tahiti (2–3.7 vs. 14–27 alleles per locus; 20–60% vs. 90% expected heterozygosity). The Tahitian and the New Caledonian stocks share the same alleles, suggesting that the loss of alleles occurred during the common past of these populations. On the contrary, New Caledonian and Hawaiian populations share only one common allele at the three loci studied. Although the low genetic variability and the resulting inbreeding of the New Caledonian stocks do not seem to affect their present performance, the results of this study demonstrate the usefulness of the introduction of new stocks in order to increase the potential responses to new controlled or uncontrolled selective pressures. The introduction in New Caledonia of the Hawaiian domesticated stocks, which would provide the local shrimp industry with 40% of the allelic diversity of the species, is advised and preferred to the one of wild animals in order to take advantage (i) of the spontaneous selection which occurred during domestication and (ii) of their favourable sanitary “specific pathogen free” status (no presence of four viruses: WSV, YHV, IHHNV, TSV) which limits the risk of introduction of pathogens.     

Genetic diversity in a Tasmanian hatchery population of Atlantic salmon (Salmo salar L.) compared with its Canadian progenitor population

The level of genetic diversity in a cultured Atlantic salmon (Salmo salar) population from Tasmania, Australia was examined at 11 microsatellite loci and compared with that in its progenitor population from the River Philip in Nova Scotia, Canada. The reference progenitor population consisted of archived scales collected from wild River Philip salmon in 1971 and 1972, not long after salmon from this river were imported into Australia in the mid‐1960s. The Tasmanian hatchery stock had a significant reduction in the mean number of alleles (31–43%) and mean allelic richness (28–39%) across all microsatellite loci compared with the wild Canadian population. Mean heterozygosity levels remained unchanged. Estimates of per‐generation effective population sizes for the Tasmanian population, based on allele frequency temporal variance with the wild progenitor population, ranged from 102–207 individuals and reflected hatchery records.     

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.     

Prespawning migratory behaviour of wild and farmed Atlantic salmon, Salmo salar L, in a north Norwegian river

The migration patterns of wild and released farmed Atlantic salmon, Salmo salar L., were studied by radio-telemetry during migration from entering a river to after spawning. The wild salmon were caught during return migration in bagnets and the farmed salmon were produced in a near by fish farm. Both groups were tagged and released at sea near the river mouth of the River Alta, North Norway. A pronounced individual variation in migration pattern was observed. No significant differences was found between wild and farmed salmon in the distance from entering the river mouth to the place of the first stop (recorded in the same pool for 5 days or longer) and the days from entering the river mouth to arrival at the first stop. For both wild and farmed salmon, mean migration speed was 2.6 km day¹, varying from 0.4 to 11.0 km day^-1. A larger proportion of farmed salmon distributed to the upper part of the river at spawning; mean distances from the river mouth were 30.1 and 19.1 km. respectively. Farmed salmon spent a significantly longer time from entering the river to reaching the area occupied during spawning.     

Genetic comparison of experimental farmed strains and wild Icelandic populations of Atlantic cod (Gadus morhua L.)

Microsatellite DNA loci and the Pantophysin locus (Pan I) were used to investigate levels of genetic diversity within farmed strains of Atlantic cod Gadus morhua and to compare them with the wild source population. A total of 282 farmed samples originating from a spawning ground off the south-west coast of Iceland were sampled in the years 2002 and 2003, and 258 wild cod were collected at the same spawning ground in the same years. The farmed strains exhibited a lower mean number of alleles and allelic diversity than the wild samples at the microsatellite loci. Significant differences were observed between wild and farmed samples both in allele and genotype frequencies at the Pan I locus. We argue that the genetic divergence of wild and farmed samples of Atlantic cod may be due to a small number of effective founding breeders contributing to the genetic variation of the farmed strains, inducing a reduction in allelic diversity. We discuss the potential effect of breeding practices on the genetic diversity of Atlantic cod.     

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.     

Genetic Introgression Between Arctic Charr (Salvelinus Alpinus) and Brook Trout (Salvelinus Fontinalis) in Bavarian Hatchery Stocks Inferred from Nuclear and Mitochondrial DNA Markers

Nuclear insulin-like growth factor 2 gene (IGF-2), growth hormone 1 gene (GH-1) and internal transcribed spacer 1 (ITS-1) of the ribosomal DNA as well as the mitochondrial NADH-3 and NADH-4 dehydrogenase genes (ND-3/4) exhibited species-specific restriction fragment patterns and three microsatellite loci (Sfo18, Ssa85 and Ssa197) had non-overlapping allele size ranges in Arctic charr and brook trout and were used as diagnostic markers for testing genetic purity of hatchery stocks and wild populations of Arctic charr and brook trout in Bavaria, Germany. Screening of four wild populations (three in Arctic charr and one in brook trout) revealed only a single hybrid (back-cross to brook trout) individual in L. Starnberg. In contrast, in three (out of five) hatchery stocks of Arctic charr and in both hatchery stocks of brook trout hybrids were detected with the frequency from 3 to 100%. Three hatchery stocks (SS2, SA and BS1) represent a hybrid swarm because they contained a very high proportion of hybrids (from 83 to 100%) and most or all hybrid individuals had alien alleles at only one or a few of six unlinked diagnostic loci, indicating that post-F₁ hybrids represent the majority of individuals in these stocks and introgression has taken place. Release or escape of introgressed individuals from hatcheries into natural water bodies should be avoided in order to protect the biological diversity and genetic integrity of native fish populations.     

Spatial and temporal patterns in microsatellite DNA variation of wild Atlantic salmon, Salmo salar, in Irish rivers

Abstract  Two sequential year classes of Atlantic salmon parr, Salmo salar L., from 13 rivers throughout Ireland, genotyped at four widely used microsatellite loci, displayed comparable levels of intra-sample genetic variability to elsewhere in the species range. Temporal allele frequency differences were observed in only one riverine sample, whereas significant spatial differences were evident in all cases, with an overall F _ST value of 0.03. These spatial differences imply a high degree of natal homing. Two tributaries of a single major river system displayed variability comparable with that within the entire study, suggesting that large rivers may contain several separate tributary populations. Isolation-by-distance analysis suggests the presence of regional structure, which may have been obscured by inclusion of samples from some smaller rivers in Donegal Bay in the north west that are probably affected by incursions of cultured salmon from a nearby ranching operation. Although limited by the small number of loci screened, individual assignment analysis gave levels of self-assignment which would suggest that mixed stock analysis would be feasible as a management tool in Irish salmon fisheries, given the inclusion of larger numbers of microsatellite loci and more extensive coverage of salmon producing rivers.     

Migratory behaviour of adult wild and escaped farmed Atlantic salmon, Salmo salar L., before, during and after spawning in a Norwegian river

The migratory behaviour of adult wild and escaped farmed Atlantic salmon, Salmo salar L., before, during after spawning in the River Namsen, Norway, was analysed using radio telemetry. The fish were caught, radio tagged and released into the fjord between 7 and 25 km from the river mouth. A significantly higher proportion of wild (74%) than farmed (43%) salmon was subsequently recorded in the river. Wild salmon (33%) were more frequently captured in the sea and in rivers than farmed salmon (14%). The migration speed from release to passing a data logger 11 km upstream from the river mouth was not significantly different between wild (20.6 km day^?1) and farmed (19.8 km day^?1) salmon. Wild salmon tagged when water flow in the river was increasing had a significantly higher migration speed than wild salmon tagged when water flow was decreasing. This was not true for farmed salmon. Farmed salmon were distributed significantly higher up the river than wild salmon during spawning, although both types of fish were found together in spawning areas. Thus, there was no geographical isolation to prevent spawning between wild and escaped farmed salmon. Farmed salmon had significantly more and longer up- and downstream movements than wild salmon during the spawning period. Unlike farmed salmon, the number of riverine movements by wild salmon increased significantly when variation in water flow increased. A smaller proportion of wild (9%) than farmed (77%) salmon survived through the winter after spawning.     

Population genetic structure of lumpfish along the Norwegian coast: aquaculture implications

The potential for genetic contamination of stocks arising from translocation and subsequent release or escape of translocated and/or genetically mixed stocks may be a significant risk to wild populations. In this context, we undertook a population genetic survey of stocks of lumpfish (Cyclopterus lumpus) along the Norwegian coast to establish the existing genetic population structure, which will aid the development of policy of the species’ use as cleaner fish in salmonid aquaculture. This was done by using 14 microsatellite loci and 287 specimens collected at five fishing grounds, covering most of the Norwegian coastline from south to north, with additional 18 samples of first-generation reared fish from a fish farm outside Tromsø (North Norway). Overall, there was no indication of significant spatial genetic structuring or of positive correlation between geographic and genetic distance among the wild lumpfish samples. These results suggest that, should translocated individuals escape from aquaculture in Norway, this will probably have little to no impact on the genetic composition of the local fish population.     

Genetic differentiation of wild and hatchery Oujiang color common carp: potential application to the identification of escapees

The escape or release of cultured and domesticated organisms into the wild poses a threat to the genetic integrity of natural populations. Based on data from 17 microsatellite loci, the genetic differentiation between wild and hatchery Oujiang color common carp Cyprinus carpio var. color was investigated, and its potential application for identifying the escapees of hatchery strains was assessed using Bayesian genetic assignment. No significant differences were observed between pooled hatchery and pooled wild populations in terms of allelic richness (A _R), observed heterozygosity (H _O), and inbreeding coefficient (F _IS). Analysis of molecular variance and pairwise F _ST comparisons suggested significant genetic differentiation between hatchery strains and between hatchery and wild populations, which was further confirmed by principal components analysis and Bayesian clustering analysis. Bayesian genetic alignment showed high self-assignment accuracy (ranging from 86.0 to 96.0%) in the original populations, demonstrating the ability of this technique to identify hatchery Oujiang color common carp escapees in the wild population.     

Allozyme genetic analysis in hatchery strains and wild blue shrimp, Penaeus (Litopenaeus) stylirostris (Stimpson), from the Gulf of California

We conducted a population genetic analysis of Penaeus stylirostris to describe the genetic variability in two wild samples (Guaymas and Peñasco) and in two cultivated strains (A and B), and to determine the relationship among samples. Seventeen enzymatic systems and general proteins were used to visualize 31 loci. Of the 31 loci, 11 polymorphic loci (35%) were detected in all the organisms, with an average heterozygosity of 0.10 and an average of 1.8 per locus. There were no significant differences among the four samples of observed heterozygosity or percentage of polymorphic loci. According to Hardy–Weinberg, both cultivated strains showed disequilibrium in more loci than the wild samples. Guaymas showed linkage disequilibrium in five pairs of polymorphic loci, Peñasco samples in two pairs, A in seven pairs, and B in nine pairs. Peñasco and both cultivated lineages showed evidence of recent reductions in their effective populations size. Based on the comparisons of F_st values, and the distribution of the allelic frequencies, the cultivated strains were significantly different from the two wild populations. There is evidence that strain B originated from A and the discrepancies between the strains are probably the result of genetic drift and a founder effect.     

Spatial correlation patterns in coastal environmental variables and survival rates of salmon in the north-east Pacific Ocean

We examined spatial correlations for three coastal variables [upwelling index, sea surface temperature (SST), and sea surface salinity (SSS)] that might affect juvenile salmon ( Oncorhynchus spp.) during their early marine life. Observed correlation patterns in environmental variables were compared with those in survival rates of pink ( O. gorbuscha ), chum ( O. keta ), and sockeye ( O. nerka ) salmon stocks to help identify appropriate variables to include in models of salmon productivity. Both the upwelling index and coastal SST were characterized by strong positive correlations at short distances, which declined slowly with distance in the winter months, but much more rapidly in the summer. The SSS had much weaker and more variable correlations at all distances throughout the year. The distance at which stations were no longer correlated (spatial decorrelation scale) was largest for the upwelling index (> 1000 km), intermediate for SST (400–800 km in summer), and shortest for SSS (< 400 km). Survival rate indices of salmon showed moderate positive correlations among adjacent stocks that decreased to zero at larger distances. Spatial decorrelation scales ranged from approximately 500 km for sockeye salmon to approximately 1000 km for chum salmon. We conclude that variability in the coastal marine environment during summer, as well as variability in salmon survival rates, are dominated by regional scale variability of several hundred to 1000 km. The correlation scale for SST in the summer most closely matched the observed correlation scales for survival rates of salmon, suggesting that regional-scale variations in coastal SST can help explain the observed regional-scale covariation in survival rates among salmon stocks.     

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.     

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 variability in four hatchery strains of coho salmon, Oncorhynchus kisutch (Walbaum), in Chile

Coho salmon, Oncorhynchus kisutch (Walbaum), is intensively cultured in Chile. An increasing proportion of the eggs necessary to sustain the culture are locally produced by some hatcheries. However, there is no information about the origin or the genetic variability in these strains. The present study analysed allozymic variability and its distribution within and between some commercial strains of coho salmon in southern Chile. The genetic variability was estimated using horizontal starch gel electrophoresis. Samples of coho salmon were obtained randomly from four Chilean hatcheries. Twenty‐five enzymatic systems were examined, representing 51 enzymatic loci. Eight loci showed variability in at least one strain, which represented a total polymorphism (P) of 15.7%. Only the PGM‐1* locus was variable in all strains. The remaining loci were fixed in at least one strain. Total heterozygosity (H_T) and within population heterozygosity (H_S) were 0.35% and 0.36% respectively. The index of genetic diversity (G_ST) was 1.5%. The results confirm previous reports of low genetic variability in cultured strains of coho salmon in Chile, below that observed in their native range, which suggests loss of the genetic variability caused by genetic drift or other causes in these strains.     

Genetic differentiation among Atlantic salmon reared in sea‐cages reveals a non‐random distribution of genetic material from a breeding programme to commercial production

Seven samples, each consisting of approximately 50 Atlantic salmon, were collected from five marine farms in Norway. These farms reported to rear fish originating from the same commercial breed; however, all samples followed a unique route of production from breeder to marine farm via egg, fry and smolt producers. A group of farmed escapees (n=50) were also captured. Following genotyping with 18 microsatellite loci, the global F_ST was 0.083, and pair‐wise values were as high as 0.158. Four clusters, with varying degrees of genetic differentiation, were identified among samples from the farms, and the source of the escapees was identified successfully. It is suggested that the genetic differences observed among samples from the farms were created through the process of genetic drift, facilitated by parallel sub‐strains, extensive within‐strain selection and low to moderate numbers of adults contributing to batches of eggs. In conclusion, this study has demonstrated that genetic identification of escaped Atlantic salmon, back to the farm of origin, may be possible even when farms rear fish reported to originate from a single breeder.