Reproductive Strategies Explain Genetic Diversity in Atlantic Salmon, Salmo salar

Synopsis We investigated the relationship between conservation status and genetic variability in European and North American Atlantic salmon, Salmo salar, populations, many of which have suffered severe bottlenecks. A negative north--south cline exists for the status of population conservation in this species. A literature review of genetic variability and demographic parameters of wild Atlantic salmon populations resulted in no statistical associations between population conservation status and genetic variation at enzyme or VNTR loci. We found however, a negative relationship between male parr maturation rates and geographical latitude for both American and European populations. The increase in effective population size due to participation by mature male parr and the increased proportions of these males in smaller (southern) populations could explain the lack of expected relationship between genetic variation and conservation status.     

Allelic and haplotypic diversity at the major histocompatibility class II within domesticated Australian Atlantic salmon (Salmo salar L.)

Variation within the major histocompatibility (MH) class II alpha gene ( Sasa-DAA ) was compared between domesticated Australian Atlantic salmon and their ancestral Canadian population. The level of Sasa-DAA and MH class II beta gene ( Sasa-DAB ) sequence variation was also examined within the Australian population and compared with that published for European Atlantic salmon populations. In contrast to variation previously reported for non-coding microsatellite loci, a high level of MH class II allelic variation has been maintained within the domesticated Australian populations. Furthermore, a high level of Sasa-DAA and Sasa-DAB allele sequence diversity was also observed and exceeded that reported for other cultured Atlantic salmon populations. The number of Sasa-DAB allele sequences (14) surpassed the number of Sasa-DAA allele sequences (9) to produce 14 unique class II haplotypes. We conclude that the Australian Atlantic salmon populations show high MH class II allelic and haplotypic variation compared with both its ancestral Canadian population and other cultured Atlantic salmon populations.     

Genetic divergence at the NAD +-dependent malic enzyme locus in Atlantic salmon from Europe and North America

The distribution of genetic variation for NAD+ malic enzyme ( ME* ) polymorphism in the Atlantic salmon was assessed in both anadromous and resident populations. The analysis revealed a major allelic divergence between North America and Europe. The *80 variant occurred in 39 of 40 North American samples, ranging in frequency from 0 to 0.515. In contrast, it was detected in only three fish from two of the 35 European locations analysed. Eleven fish from two rivers in north-west France had the * 110 variant. While heterogeneity among North American populations was significant, no regional differentiation was apparent and anadromous and resident salmon were not found to differ.     

Microsatellite Variation in Populations of Atlantic Salmon from North Europe

Our aim was to investigate the level of genetic differentiation in northern European populations of Atlantic salmon, to establish the genetic relationship among major salmon populations in Russia and North Norway, and to compare these to populations from the western Atlantic lineage. Samples were collected along an east—west axis, from Pechora River in Russia to Restigouche River in Quebec, Canada. A total of 439 individual salmon were collected from seven rivers (sample sizes from 50 to 84 individuals). The samples were analysed for variation at four microsatellite loci; Ssa13.37, Ssa14, Ssa171 and Ssa171. Significant differences were found between most of the European populations, and the populations from the Tana and Pechora Rivers were most distinct. The samples from the Rivers Mezenskaya Pizhma and Emtsa in Arkhangelsk oblast in Russia were not significantly different from each other in an exact test of population differences. All other river pairs were significantly different. These results confirmed the deep genetic divergence between American and European salmon populations demonstrated in earlier studies, with alleles specific to continent found in three of the microsatellites.     

Mitochondrial DNA diversity in North American and European Atlantic salmon with emphasis on the Downeast rivers of Maine

The displacement loop and NADH-1 dehydrogenase regions of mitochondrial DNA (mtDNA) were amplified by the polymerase chain reaction in 954 Atlantic salmon and digested with 40 restriction endonucleases. Variation was detected with 10 enzymes, resulting in 21 composite haplotypes which were strongly patterned geographically with a major discontinuity observed between most North American (NA) and European salmon. Significant heterogeneity of haplotype frequencies was found within and among all classification levels (continent, country, and river). Haplotype frequencies were significantly different across continents, within European samples, within NA samples, within Canadian samples, within wild Maine samples, within captive Maine strains, and between captive and wild Maine strains. Nine haplotypes occurred only in NA, seven in Maine, three only in Maine, and 11 occurred only in Europe. Some Maine rivers had only a single haplotype, suggesting that effective population sizes may be low. The second most frequent European haplotype occurred in tributaries to one Newfoundland river. Gene trees based on parsimony and genetic distance suggest that the haplotypes are monophyletic within each continent, and that the haplotype found on both continents is intermediate between those of Europe and NA, suggesting common ancestry of all haplotypes.     

Effects of species, culture history, size and residency on relative competitive ability of salmonids

The relative competitive ability of juvenile farm and wild salmonids was investigated to provide insight into the potential effects of introduction of cultured salmon on wild Pacific salmonid ( Oncorhynchus ) species. Aquarium experiments involving equal contests ( i.e. size matched, simultaneously introduced individuals) indicated that two wild coho salmon Oncorhynchus kisutch populations were competitively equal to a farm coho salmon population. In equal contests between farm Atlantic salmon Salmo salar (Mowi strain) and these wild coho salmon populations or coastal cutthroat trout Oncorhynchus clarki clarki , Atlantic salmon were subordinate in all cases. When Atlantic salmon were given a residence advantage, however, they were competitively equal to both wild coho salmon populations, but remained subordinate to coastal cutthroat trout. When Atlantic salmon were given a 10–30% length advantage, they were competitively equal to one wild coho salmon population but remained subordinate to the other. In equal contests in semi-natural stream channels, both wild coho and farm Atlantic salmon grew significantly more in the presence of the other species than when alone. It appears that coho salmon obtain additional food ration by out competing Atlantic salmon, whereas Atlantic salmon were stimulated to feed more in the presence of coho salmon competitors. These results suggest that wild coho salmon and cutthroat trout should out compete farm Atlantic salmon of a similar size in nature. As the relative competitive ability of Atlantic salmon improves when they have a size and residence advantage, should feral populations become established, they may exist on a more equal competitive footing owing to the long freshwater residence of Atlantic salmon.     

Population structure of Atlantic salmon (Salmo salar L.): a range-wide perspective from microsatellite DNA variation

Atlantic salmon (n = 1682) from 27 anadromous river populations and two nonanadromous strains ranging from south-central Maine, USA to northern Spain were genotyped at 12 microsatellite DNA loci. This suite of moderate to highly polymorphic loci revealed 266 alleles (5-37/locus) range-wide. Statistically significant allelic and genotypic heterogeneity was observed across loci between all but one pairwise comparison. Significant isolation by distance was found within and between North American and European populations, indicating reduced gene flow at all geographical scales examined. North American Atlantic salmon populations had fewer alleles, fewer unique alleles (though at a higher frequency) and a shallower phylogenetic structure than European Atlantic salmon populations. We believe these characteristics result from the differing glacial histories of the two continents, as the North American range of Atlantic salmon was glaciated more recently and more uniformly than the European range. Genotypic assignment tests based on maximum-likelihood provided 100% correct classification to continent of origin and averaged nearly 83% correct classification to province of origin across continents. This multilocus method, which may be enhanced with additional polymorphic loci, provides fishery managers the highest degree of correct assignment to management unit of any technique currently available.     

Genetic Variation within and Between Domesticated Chinook Salmon, Oncorhynchus tshawytscha, Strains and their Progenitor Populations

Domesticated chinook salmon strains in British Columbia (BC), Canada are believed to have originated primarily from populations of the Big Qualicum (BQ) River and Robertson Creek (RC) on Vancouver Island in the early 1980s. The number of parental fish that gave rise to the domesticated strains and their subsequent breeding history during approximately five ensuing generations of domestication were not documented. Genetic variation at 13 microsatellite loci was examined in samples from two domesticated strains and the two progenitor populations to determine the genetic relationships among them. The domesticated strains had lower allelic diversity and tended to have lower levels of expected heterozygosity than did the BQ and RC progenitor populations. Only three alleles over all 13 loci were detected in the domesticated strains that were not present in the BQ and RC samples, whereas the progenitor strains possessed over 25 (BQ) and 43 (RC) private alleles. Genetic distance and F_ST values also indicated a closer relationship of the domesticated strains with the BQ than the RC population. One domesticated strain had a significant excess of heterozygosity compared with that expected under conditions of mutation-drift equilibrium, indicative of a recent genetic bottleneck. Genetic differentiation between the domesticated strains was as great as that distinguishing them from the progenitor populations, indicating that the genetic base of domesticated chinook salmon could be increased by hybridization. The existence of genetically distinct domesticated strains of chinook salmon in coastal BC generates the need for an evaluation of potential genetic interactions between domesticated escapees and natural spawning populations.     

A striking example of the founder effect in the mollusc Littorina saxatilis

Two South African populations of Littorina saxatilis were examined by starch-gel electrophoresis at 16 enzyme loci and compared with 13 populations of North Atlantic saxatilis from both American and European coasts, and with six British populations of the closely related species Littorina arcana. The South African animals showed a severely reduced heterozygosity (– 0.052) compared with Atlantic populations of saxatilis ( = 0.181), and the mean genetic distance between the two areas was high ( = 0.203) compared with distances within the North Atlantic saxatilis populations (D = 0.034). In fact, the saxatilis from South Africa were genetically more distant from the North Atlantic samples of L. saxatilis than were the arcana from British shores. The reduced genetic heterozygosity and genetic divergence of the South African populations is attributed to founder effects following a postulated recent introduction by man.     

Chromosome polymorphisms track trans‐Atlantic divergence and secondary contact in Atlantic salmon

Pleistocene glaciations drove repeated range contractions and expansions shaping contemporary intraspecific diversity. Atlantic salmon (Salmo salar) in the western and eastern Atlantic diverged >600,000 years before present, with the two lineages isolated in different southern refugia during glacial maxima, driving trans‐Atlantic genomic and karyotypic divergence. Here, we investigate the genomic consequences of glacial isolation and trans‐Atlantic secondary contact using 108,870 single nucleotide polymorphisms genotyped in 80 North American and European populations. Throughout North America, we identified extensive interindividual variation and discrete linkage blocks within and between chromosomes with known trans‐Atlantic differences in rearrangements: Ssa01/Ssa23 translocation and Ssa08/Ssa29 fusion. Spatial genetic analyses suggest independence of rearrangements, with Ssa01/Ssa23 showing high European introgression (>50%) in northern populations indicative of post‐glacial trans‐Atlantic secondary contact, contrasting with low European ancestry genome‐wide (3%). Ssa08/Ssa29 showed greater intrapopulation diversity, suggesting a derived chromosome fusion polymorphism that evolved within North America. Evidence of potential selection on both genomic regions suggests that the adaptive role of rearrangements warrants further investigation in Atlantic salmon. Our study highlights how Pleistocene glaciations can influence large‐scale intraspecific variation in genomic architecture of northern species.     

Chromosomal differences between European and North American Atlantic salmon discovered by linkage mapping and supported by fluorescence in situ hybridization analysis

ABSTRACT: BACKGROUND: Geographical isolation has generated a distinct difference between Atlantic salmon of European and North American Atlantic origin. The European Atlantic salmon generally has 29 pairs of chromosomes and 74 chromosome arms whereas it has been reported that the North American Atlantic salmon has 27 chromosome pairs and an NF of 72. In order to predict the major chromosomal rearrangements causing these differences, we constructed a dense linkage map for Atlantic salmon of North American origin and compared it with the well-developed map for European Atlantic salmon. RESULTS: The presented male and female genetic maps for the North American subspecies of Atlantic salmon, contains 3,662 SNPs located on 27 linkage groups. The total lengths of the female and male linkage maps were 2,153 cM and 968 cM respectively, with males characteristically showing recombination only at the telomeres. We compared these maps with recently published SNP maps from European Atlantic salmon, and predicted three chromosomal reorganization events that we then tested using fluorescence in situ hybridization (FISH) analysis. The proposed rearrangements, which define the differences in the karyotypes of the North American Atlantic salmon relative to the European Atlantic salmon, include the translocation of the p arm of ssa01 to ssa23 and polymorphic fusions: ssa26 with ssa28, and ssa08 with ssa29. CONCLUSIONS: This study identified major chromosomal differences between European and North American Atlantic salmon. However, while gross structural differences were significant, the order of genetic markers at the fine-resolution scale was remarkably conserved. This is a good indication that information from the International Cooperation to Sequence the Atlantic salmon Genome, which is sequencing a European Atlantic salmon, can be transferred to Atlantic salmon from North America.     

Atlantic salmon colonization of the Russian Arctic coast: pioneers from North America

Previous studies of the ESTD * isozyme locus in the Atlantic salmon show the * 80 allele to be absent across the species' European range, with the exception of northern Russia, whereas the allele is nearly fixed in North American populations. The allele was found in samples from 15 out of 18 rivers on the Kola Peninsula and White sea coast and had frequencies that ranged from 0·017 to 0·363. Typing of fish in nine of these rivers for mtDNA variation in the ND1 gene region found variation characteristic of North American salmon in three Kola Peninsula populations and is the only part of Europe where such variants have been detected. The study area was completely glaciated during the late Pleistocene period and the restriction of the European distribution of these ESTD * and mtDNA variants to this area suggests that salmon that colonized the Russian Arctic coast rivers included fish of North American origin after the Pleistocene glacier had retreated.     

Distribution of genetic variation in the growth hormone 1 gene in Atlantic salmon (Salmo salar) populations from Europe and North America

The level and hierarchical distribution of genetic variation in complete sequences of the Atlantic salmon (Salmo salar) growth hormone (GH1) gene were investigated in populations from Europe and North America with a view to inferring the major evolutionary forces affecting genetic variation at this locus. Seventeen polymorphic sites were identified in complete sequences from nine populations, with levels of noncoding (intron and untranslated region sequences) nucleotide diversity being similar to those observed in other species. No variation, however, was observed in exonic sequences, indicating that nucleotide diversity in the Atlantic salmon GH1 gene is three and 25 times less than that estimated for human and Drosophila coding sequences, respectively. This suggests that purifying selection is the predominant contemporary force controlling the molecular evolution of GH1 coding sequences. Comparison of haplotype relationships within and between populations indicated that differentiation between populations from Europe and North America was greater than within-continent comparisons. However, several haplotypes observed in the northernmost European populations were more similar to those observed in North American than to any other haplotypes observed in Europe. This is most likely to be a result of historical, rather than contemporary, gene flow. Neutrality test statistics, such as Tajima's D, were significantly positive in the European populations in which North American-like haplotypes were observed. Although a positive Tajima's D is commonly interpreted as the signal of balancing selection, a more likely explanation in this case is that either historical migration or ascertainment bias, rather than within population local adaptation, has given rise to an excess of intermediate frequency alleles.     

Conservation genomics of Atlantic salmon: SNPs associated with QTLs for adaptive traits in parr from four trans-Atlantic backcrosses

European Atlantic salmon (Salmo salar) differ in skin pigmentation and shape from the North American lineage of Atlantic salmon but the genetic basis of these differences are poorly understood. We created four large (N=300) backcross families by crossing F1 hybrid male siblings to two females from the European and two from the North American aquacultural strains. We recorded 15 morphological landmarks and two skin pigmentation, three growth and three condition traits on parr. The backcross families were genotyped for at least 129 SNPs (single nucleotide polymorphisms) within expressed sequence tags (ESTs) spaced throughout the Atlantic salmon linkage map. The high polymorphism and low rates of crossover in our hybrid sires provided enough statistical power to detect 79 significant associations between SNP markers and quantitative traits after experiment-wide permutation analysis for all families within traits. Linkage group AS22 contained a quantitative trait loci (QTL) for parr mark number; its homolog AS24 contained a large QTL, which explained 26% of the phenotypic variance in parr mark contrast. We found 25 highly significant QTLs for body shape and fin position on seven different linkage groups, and 16 for growth and condition on six different linkage groups. QTL(s) for pectoral fin position, caudal peduncle position, late parr growth and condition index were associated with an SNP on linkage group AS1, which was linked to the sex-determining locus. Our work adds to the evidence that much of the variation in growth rate, shape and skin pigmentation observed among Atlantic salmon parr from different natal streams is genetic.     

Implications for introgression: has selection for fast growth altered the size threshold for precocious male maturation in domesticated Atlantic salmon?

Background

Mature male parr (MMP) represent an important alternative life-history strategy in Atlantic salmon populations. Previous studies indicate that the maturation size threshold for male parr varies among wild populations and is influenced by individual growth, environmental conditions, and genetics. More than ten generations of breeding have resulted in domesticated salmon displaying many genetic differences to wild salmon, including greatly increased growth rates. This may have resulted in domesticated fish with the potential to outgrow the size threshold for early maturation, or evolution of the size threshold of the trait itself. To investigate this, we performed a common-garden experiment under farming conditions using 4680 salmon from 39 families representing four wild, two wild-domesticated hybrid, and two domesticated strains.

Results

Domesticated salmon outgrew wild salmon 2–5-fold, and hybrids displayed intermediate growth. Overall, the numbers of MMP varied greatly among families and strains: averaging 4–12% in domesticated, 18–25% in hybrid, and 43–74% in the wild populations. However, when the influence of growth was accounted for, by dividing fish into lower and upper size modes, no difference in the incidence of MMP was detected among domesticated and wild strains in either size mode. In the lower size mode, hybrids displayed significantly lower incidences of mature males than their wild parental strains. No consistent differences in the body size of MMP, connected to domestication, was detected.

Conclusions

Our data demonstrate: 1- no evidence for the evolution of the size threshold for MMP in domesticated salmon, 2- the vastly lower incidence of MMP in domesticated strains under aquaculture conditions is primarily due to their genetically increased growth rate causing them to outgrow the size threshold for early maturation, 3- the incidence of MMP is likely to overlap among domesticated and wild salmon in the natural habitat where they typically display overlapping growth, although hybrid offspring may display lower incidences of mature male parr. These results have implications for wild salmon populations that are exposed to introgression from domesticated escapees.

     

A review of genetic variation in Atlantic salmon, Salmo salar L., and its importance for stock identification, enhancement programmes and aquaculture

The increasing exploitation of Atlantic salmon as a food source and sport fish demands a better understanding of salmon genetics and the dynamics of Atlantic salmon populations. Surveys of salmon populations for protein electrophoretic variation reveal that the average heterozygosity in Salmo salar is low and that four gene loci account for more than 95% of the total electrophoretically detectable variation. Populations that have been studied by this means fall into one of three groups: Western Atlantic, Eastern Atlantic or Baltic. However, biochemical genetics involving starch gel electrophoresis cannot be used routinely to identify the continent of origin of an Atlantic salmon, let alone its native river. The mitochondrial genome can be used to identify North American or European salmon with the aid of restriction endonucleases that have six base pair recognition sites. Restriction endonucleases that recognize four base pairs appear to be able to identify salmon from a particular river system. There has been a move from protein variation to mitochondrial DNA variation and this will inevitably lead to more extensive studies on the nuclear genome. Chromosomal studies suggest differences between salmon from Europe and North America but these have been hampered by lack of good banding procedures. Preliminary studies using cloned segments of salmonid genomes suggest that repeated sequences such as the genes for ribosomal RNA will be most useful for identifying specific stocks of Atlantic salmon. The need for continued genetic studies on the Atlantic salmon and the relevance and importance of the results of this research for stock identification, enhancement programmes, aquaculture and basic science are discussed.     

Identification of quantitative genetic components of fitness variation in farmed,hybrid and native salmon in the wild

Feral animals represent an important problem in many ecosystems due to interbreeding with wild conspecifics. Hybrid offspring from wild and domestic parents are often less adapted to local environment and ultimately, can reduce the fitness of the native population. This problem is an important concern in Norway, where each year, hundreds of thousands of farm Atlantic salmon escape from fish farms. Feral fish outnumber wild populations, leading to a possible loss of local adaptive genetic variation and erosion of genetic structure in wild populations. Studying the genetic factors underlying relative performance between wild and domesticated conspecific can help to better understand how domestication modifies the genetic background of populations, and how it may alter their ability to adapt to the natural environment. Here, based upon a large-scale release of wild, farm and wild x farm salmon crosses into a natural river system, a genome-wide quantitative trait locus (QTL) scan was performed on the offspring of 50 full-sib families, for traits related to fitness (length, weight, condition factor and survival). Six QTLs were detected as significant contributors to the phenotypic variation of the first three traits, explaining collectively between 9.8 and 14.8% of the phenotypic variation. The seventh QTL had a significant contribution to the variation in survival, and is regarded as a key factor to understand the fitness variability observed among salmon in the river. Interestingly, strong allelic correlation within one of the QTL regions in farmed salmon might reflect a recent selective sweep due to artificial selection.     

A standardized method for quantifying unidirectional genetic introgression

Genetic introgression of domesticated to wild conspecifics is of great concern to the genetic integrity and viability of the wild populations. Therefore, we need tools that can be used for monitoring unidirectional gene flow from domesticated to wild populations. A challenge to quantitation of unidirectional gene flow is that both the donor and the recipient population may be genetically substructured and that the subpopulations are subjected to genetic drift and may exchange migrants between one another. We develop a standardized method for quantifying and monitoring domesticated to wild gene flow and demonstrate its usefulness to farm and wild Atlantic salmon as a model species. The challenge of having several wild and farm populations was circumvented by in silico generating one analytical center point for farm and wild salmon, respectively. Distributions for the probability that an individual is wild were generated from individual‐based analyses of observed wild and farm genotypes using STRUCTURE. We show that estimates of proportions of the genome being of domesticated origin in a particular wild population can be obtained without having a historical reference sample for the same population. The main advantages of the method presented are the standardized way in which genetic processes within and between populations are taken into account, and the individual‐based analyses giving estimates for each individual independent of other individuals. The method makes use of established software, and as long as genetic markers showing generic genetic differences between domesticated and wild populations are available, it can be applied to all species with unidirectional gene flow. Results from our method are easy to interpret and understand, and will serve as a powerful tool for management, especially because there is no need for a specific historical wild reference sample.