Genetic studies on serum transferrins in Atlantic salmon

Published and unpublished data on genetic variation at the transferrin locus ( TF *) in Atlantic salmon from rivers in eastern North America sampled from 1968 to 1970 were reanalysed and compared with data for samples collected in 1998 from nine of the same rivers. Genetic differentiation among rivers was highly significant as was spatial differentiation among tributary samples within the Miramichi River system, the largest rivers studied. Comparison of allele frequencies in rivers also sampled in 1998 show no overall evidence of significant genetic change after 30 years, spanning 9 generations. The results strongly support the stability of the patterns of spatial genetic differentiation and support the occurrence in Atlantic salmon of reproductive isolation among rivers and among tributaries within large river systems.     

Genetic comparison of salmon from the White Sea and north-western Atlantic Ocean

Samples of salmon Salmo salar from the River Kachkovka and the River Nilma in northern Russia were analysed by starch gel electrophoresis and compared to three Norwegian stocks, the Neiden river in northern Norway and Øyreselv and Hopselv rivers on the west coast. The comparison included the following polymorphic loci: AAT-4 *, IDDH-2 *, IDHP-3 *, MDH- 3,4 *, MEP-2 *, ESTD * as well as the newly discovered polymorphic loci FBALD-3 * and TPI-3 *. Samples were run side by side on gels, and the alleles found in the Russian stocks were the same as those found in the Norwegian stocks, although the electrophoretic methods used lead to differences in designations of alleles. A polymorphism in ESTD * which involves a slow allele was commonly observed in the three northern populations of the Nilma, Kachkovka and Neiden rivers. This allele was absent in the other Norwegian stocks and in a major brood stock of farmed salmon in Norway. The IDHP-3 * 116 allele was found in unusually high frequencies in the northern populations. Thus, the variability observed at these two loci indicates a barrier to gene flow between the northern salmon stocks and the more southern stocks in the East Atlantic area.     

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.     

Population structure of Atlantic salmon from the Conne River, Newfoundland as determined from microsatellite DNA

Variation at four microsatellite loci was examined for three populations of Atlantic salmon Salmo salar from the Conne River, Newfoundland. Samples of wild parr were collected from the mainstem Conne River during 4 years, and from tributaries Twillick Brook and Bernard Brook during 2 years. No significant temporal variation was observed in allele frequencies at the Ssal4, Ssal97, Ssa202, and Ssa289 loci. No difference in allele frequencies was observed between parr from Bernard and Twillick brooks at any locus, but allele frequencies of mainstem Conne River parr were significantly different from those of the tributaries at Ssal4 and Ssa202, indicative of differentiation among local populations. Atlantic salmon from the Conne River system were well differentiated from those in Nova Scotia, Canada and from those in Europe.     

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.     

Intra- and interpopulation variability of southwestern Kamchatka sockeye salmon Oncorhynchus nerka inferred from the data on single nucleotide polymorphism

The variability of 45 single nucleotide polymorphism (SNP) loci was studied in nine samples of the sockeye salmon Oncorhynchus nerka from the rivers of southwestern Kamchatka. The Wahlund effect, gametic disequilibrium at some loci, and a decrease in interpopulation genetic diversity indices observed in samples from the Bolshaya River outlet can be attributed to the samples’ heterogeneity. Partitioning of the mixed samples using some biological characteristics of the individuals led to a noticeable decrease in the frequency of these phenomena. It was demonstrated that the allelic diversity between the populations within the river accounted for the larger part of genetic variation, as compared to the differentiation between the basins. The SNP loci responsible for intra- and interpopulation differentiation of sockeye salmon from the rivers of southwestern Kamchatka were identified. Some recommendations for field population genetic studies of Asian sockeye salmon were formulated.     

Composition of the founding population of Iceland: biological distance and morphological variation in early historic Atlantic Europe

We examined the composition of the founding population of Iceland through the study of morphological traits in skeletons from Iceland, Ireland, Norway, and Greenland. This is the first study to address this issue from the Settlement Period of Iceland and contemporary samples from Ireland. We pose the following questions: 1) Was the founding population of Iceland of mixed or homogeneous origin? 2) Is there evidence for a significant Irish cohort in the founding population, as suggested in medieval Icelandic literature? Analysis of biodistance revealed that both Settlement Age and later samples from Iceland showed a greater degree of phenetic similarity to contemporary Viking Age Norwegians than to samples obtained from early medieval Ireland. Analysis of among‐individual morphological variation showed that the Settlement Age population of Iceland did not exhibit an increase in variation in comparison to other populations in the sample, suggesting a relatively homogenous origin. However, estimation of admixture between the Irish and Norwegian populations indicated that 66% of the Icelandic settlers were of Norwegian origin. Comparison of the Icelandic samples to hybrid samples produced by resampling the Viking Age Norwegian and early medieval Irish samples revealed that the Icelandic samples are much closer to the Norwegian samples than expected, based on a 66:34 mixture of Norwegian and Irish settlers. We conclude that the Settlement Age population of Iceland was predominantly (60–90%) of Norwegian origin. Although this population was relatively homogenous, our results do not preclude significant contributions from Ireland as well as other sources not represented in our analysis. Am J Phys Anthropol, 2003. © 2003 Wiley‐Liss, Inc.     

The effect of natural selection on estimates of genetic divergence among populations of the Atlantic salmon

The effect of natural selection on the _mMEP-2 * locus on measures of genetic divergence among Atlantic salmon populations was investigated by examining the pattern of change in the level of genetic differentiation (F_ST) averaged over loci when data on the _mMEP-2 * locus were either included or excluded. The level of F_ST among populations at various geographic scales was estimated from allele frequencies at up to four loci (_s AAT-4 *, IDDH-1 *, IDHP-3 *, and _mMEP-2 *). At smaller geographic scales (within river systems or limited geographic regions) levels of variance in _mMEP-2 * allele frequencies were reduced relative to mean levels. At larger geographic scales (across continents or the species range) variation in _mMEP-2 * allele frequencies was greater than mean levels. These results suggest an a priori hypothesis for the effect of selection on the _mMEP-2 * locus which may be applied in future studies on variation in protein coding or other (e.g. mini- and microsatellite) loci in the Atlantic salmon. It is recommended that estimates of gene flow among populations of the Atlantic salmon based on mean F _ST estimates which include data on the _mMEP-2 * locus should be viewed with caution.     

Microsatellite loci reveal highly significant genetic differentiation among Atlantic salmon (Salmo salar L.) stocks from the east coast of Canada

Allele frequency data from eight microsatellite loci provide evidence of highly significant genetic differentiation among stocks of Atlantic salmon Salmo salar L. from the Bay of Fundy, eastern and north-western Nova Scotia and Newfoundland. Estimates of genetic structure ( R _ST and θ) were significant both among all samples taken from the different geographical locations and among samples from geographical regions for which more than one stock was sampled. Samples from the Bay of Fundy taken from stocks which are phenotypically and behaviourally diverse showed particularly high levels of genetic structure. Rogers', allele sharing and (δμ)² distances also revealed significant differences among stock samples and were significantly correlated [Rogers' and (δμ)²] with sea distance between rivers. Results suggest that stocks of Atlantic salmon in eastern Canada are highly diverse genetically and that this should be an important consideration in any management programme for stocks in the area.     

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.     

Long‐term declines in body size and shifts in run timing of Atlantic salmon in Ireland

Records extending back from three to seven decades from Atlantic salmon Salmo salar fisheries on the Blackwater, Newport and Owenduff River systems in Ireland, were used to test the hypothesis that there have been progressive declines in size and associated shifts in run timing. They showed identical patterns in four respects: 1) peaks of catch, in spring (March to April) and summer (June to July), 2) the largest fish were caught in the spring, with declines in size over the summer and a slight increase in autumn, 3) marked declines over time in average size and in the proportion of the Atlantic salmon taken in spring and 4) reductions in size in most months at all three sites. Correlations were also detected in average fish mass among the rivers over time (especially the Owenduff and Newport systems), showing a slight rise from the late 1960s until the late 1970s, followed by a steep decline. Data from an electronic counter on the Blackwater showed a reduction in the abundance of early migrants. The early fish were apparently much more vulnerable to fishing than later migrants, so the catch records overstated the abundance of early fish. These long‐term declines in size, which have been noted elsewhere, may be due to other factors in addition to changes in marine productivity. Specifically, reduction in the abundance of large, spring‐running Atlantic salmon may be due to selection resulting from heavy angler exploitation.     

Movements of salmon Salmo salar (L.) to and from Irish waters

Fish tagged as kelts at a number of Irish stations have been recaptured outside Irish waters along the coasts of Great Britain, Norway and West Greenland. Salmon tagged as smolts in three Irish rivers have been recaptured off the coast of West Greenland and one off the Faroes. Sixteen fish tagged as smolts in Denmark, Great Britain and Sweden were recaptured in Irish rivers or on the coastline of Ireland. Clean salmon tagged in the open sea have travelled to the coasts of Great Britain and a single fish travelled to southern Sweden. Feeding salmon tagged off West Greenland, in the Labrador sea and off the Faroes have been recaptured in Irish waters.     

Genetic drift and the population history of the Irish travellers

The Irish Travellers are an itinerant group in Ireland that has been socially isolated. Two hypotheses have been proposed concerning the genetic origin of the Travellers: (1) they are genetically related to Roma populations in Europe that share a nomadic lifestyle or (2) they are of Irish origin, and genetic differences from the rest of Ireland reflect genetic drift. These hypotheses were tested using data on 33 alleles from 12 red blood cell polymorphism loci. Comparison with other European, Roma, and Indian populations shows that the Travellers are genetically distinct from the Roma and Indian populations and most genetically similar to Ireland, in agreement with earlier genetic analyses of the Travellers. However, the Travellers are still genetically distinct from other Irish populations, which could reflect some external gene flow and/or the action of genetic drift in a small group that was descended from a small number of founders. In order to test the drift hypothesis, we analyzed genetic distances comparing the Travellers to four geographic regions in Ireland. These distances were then compared with adjusted distances that account for differential genetic drift using a method developed by Relethford (Hum Biol 68 ( 1996 ) 29–44). The unadjusted distances show the genetic distinctiveness of the Travellers. After adjustment for the expected effects of genetic drift, the Travellers are equidistant from the other Irish samples, showing their Irish origins and population history. The observed genetic differences are thus a reflection of genetic drift, and there is no evidence of any external gene flow. Am J Phys Anthropol, 2013. © 2012 Wiley Periodicals, Inc.     

Genetic Structure of Chum Salmon (Oncorhynchus keta) Populations in the Lower Columbia River: Are Chum Salmon in Cascade Tributaries Remnant Populations?

The lower Columbia River drainage once supported a run of over a million chum salmon. By the late 1950s, the run had decreased to often a few hundred fish. With the exception of Grays River near the coast and an aggregation of chum salmon spawning in creeks and the main stem near Bonneville Dam in the Columbia Gorge, most populations were thought to be extinct. However, chum salmon consistently return in low numbers to tributaries originating in the Cascade Range: the Cowlitz, Lewis, and Washougal rivers. To assess whether Cascade spawners were strays or remnants of former populations, chum salmon from the Coastal, Cascade and Gorge ecoregional zones were characterized at 17 microsatellite loci. Significant heterogeneity in genotype distributions was detected between zones and collections formed regional groups in a neighbor-joining tree. Cascade collections had higher allelic richness and private alleles, and the Cowlitz River supported genetically divergent fall and summer runs, the only summer chum salmon run extant in the Columbia River drainage. We propose that chum salmon in the Cascade zone are remnants of original populations. We attribute the divergence between zonal groups to diverse ecological conditions in each zone, which promoted regional genetic adaptation, and to genetic drift experienced in small populations.     

Genetic variation at isozyme loci in blue whiting from the north-east Atlantic

Genetic variation in blue whiting Micromesistius poutassou was investigated by starch gel electrophoresis of enzymes in tissue extracts. A total of 130 specimens from the spawning areas west of the British Isles were collected from trawl catches in 1990 ( n = 30) and 1992 ( n = 100). In 25 tissue enzyme loci screened for genetic variants in the 1990 sample, polymorphisms (0.95 criterion) were found at IDDH-2 *, IDHP-2 * and PGM-1 *, giving a frequency of polymorphic loci of P _0.95= 0.12. In pooled samples the average heterozygosity per locus was estimated at H _e =0.043 and the effective number of alleles per locus at 2.20, 1.45 and 1.53, respectively, for IDDH-2 *, IDHP-2 * and PGM-1 *.     

Geographical variation of allele frequencies at the LDH-A* locus in the arctic grayling Thymallus arcticus Pall. and in the European grayling Thymallus arcticus L

The allele frequencies of LDH-A* locus were studied in the population of Siberian grayling from the Kozhym River (Pechora basin) and in the population of European grayling from Pechora, Mezen', and Vym' rivers (Northern Dvina basin). In samples of both species (n = 134), three LDH-A phenotypes have been identified in total, which proved to be under the control of two alleles: LDH-A*100 and LDH-A*50. The alternative alleles of LDH-A* locus were identified in the populations of Siberian grayling from Kozhym River and in the population of European grayling from the same river and other Pechora tributaries, namely, LDH-A*100 and LDH-A*50 in the Siberian and the European grayling, respectively. However, in the European grayling populations from the Mezen' and Vym' rivers, both alleles occur at the frequencies of the rare LDH-A*100 allele of 0.143 and 0.222, respectively. According to the published data, the frequency of LDH-A*100 allele increases in the European grayling populations of northwestern (Finland) and southern (France) rivers, reaching 0.872 and 1.000 in Rhone and Loire, respectively, i.e., the values characteristic of the Siberian grayling populations.     

Comparative survey of within-river genetic structure in Atlantic salmon; relevance for management and conservation

In wild populations, defining the spatial scale at which management and conservation practices should focus remains challenging. In Atlantic salmon, compelling evidence suggests that genetic structure within rivers occurs, casting doubt on the underlying premise of the river-based management approach for this species. However, no comparisons of within-river genetic structure across different systems have been performed yet to assess the generality of this pattern. We compared the within-river genetic structure of four important salmon rivers in North America and evaluated the extent of genetic differentiation among their main tributaries. We found a hierarchical genetic structure at the river and tributary levels in most water systems, except in the Miramichi where panmixia could not be rejected. In the other cases, genetic differentiation between most tributaries was significant and could be as high as that found between rivers of the same geographical region. More importantly, the extent of genetic differentiation between tributaries varied greatly among water systems, from well differentiated (θ_ST = 0.035) to undifferentiated (θ_ST = −0.0003), underlying the difficulty in generalizing the ubiquity of within-river genetic structure in Atlantic salmon. Thus, this study underlines the importance of evaluating the genetic structure of Atlantic salmon in large water systems on a case by case basis in order to define the most appropriate spatial scale and focal unit for efficient management and conservation actions. The potential consequences of management at an inappropriate spatial scale are discussed.     

Migration patterns and navigation cues of Atlantic salmon post-smolts migrating from 12 rivers through the coastal zones around the Irish Sea

The freshwater phase of the first seaward migration of juvenile Atlantic salmon (Salmo salar) is relatively well understood when compared with our understanding of the marine phase of their migration. In 2021, 1008 wild and 60 ranched Atlantic salmon smolts were tagged with acoustic transmitters in 12 rivers in England, Scotland, Northern Ireland and Ireland. Large marine receiver arrays were deployed in the Irish Sea at two locations: at the transition of the Irish Sea into the North Atlantic between Ireland and Scotland, and between southern Scotland and Northern Ireland, to examine the early phase of the marine migration of Atlantic salmon smolts. After leaving their natal rivers' post-smolt migration through the Irish Sea was rapid with minimum speeds ranging from 14.03 to 38.56 km.day⁻¹ for Atlantic salmon smolts that entered the Irish Sea directly from their natal river, to 9.69–39.94 km.day⁻¹ for Atlantic salmon smolts that entered the Irish Sea directly from their natal estuary. Population minimum migration success through the study area was strongly correlated with the distance of travel, populations further away from the point of entry to the open North Atlantic exhibited lower migration success. Post-smolts from different populations experienced different water temperatures on entering the North Atlantic. This was largely driven by the timing of their migration and may have significant consequences for feeding and ultimately survivorship. The influence of water currents on post-smolt movement was investigated using data from previously constructed numerical hydrodynamic models. Modeled water current data in the northern Irish Sea showed that post-smolts had a strong preference for migrating when the current direction was at around 283° (west-north-west) but did not migrate when exposed to strong currents in other directions. This is the most favorable direction for onward passage from the Irish Sea to the continental shelf edge current, a known accumulation point for migrating post-smolts. These results strongly indicate that post-smolts migrating through the coastal marine environment are: (1) not simply migrating by current following (2) engage in active directional swimming (3) have an intrinsic sense of their migration direction and (4) can use cues other than water current direction to orientate during this part of their migration.     

After 100 years: hydroelectric dam-induced life-history divergence and population genetic changes in sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>)

Understanding the impact of barriers and habitat fragmentation on the ecology and genetics of species is of broad interest to many biologists. In aquatic systems, hydroelectric dams often present an impenetrable barrier to migratory fish and can have negative effects on their persistence. Hydroelectric dams constructed in the Coquitlam and Alouette Rivers in the Fraser River drainage (British Columbia, Canada) in the early 1900s were thought to have led to complete loss of anadromous sockeye salmon from both rivers. For both reservoirs, recent water release programs resulted in the unexpected downstream migration of juvenile sockeye salmon and the subsequent upstream migration of adults towards the reservoir 2 years later. Here we investigate the evolutionary impact of dams on the sockeye salmon migration behavior by investigating the genetic distinction between migratory and non-migratory individuals within the Alouette and Coquitlam reservoirs. We also compare historical and contemporary genetic connectivity among 11 Lower Fraser River sockeye sites to infer recent population connectivity changes that might have been influenced by anthropogenic activities. Our molecular genetic analyses show a genetic distinction between the sea-run and resident individuals from the Coquitlam reservoir and population splitting time estimates suggest a very recent divergence between them. These results indicate a genetic component to migration behavior. For our broader survey from 11 sites, our comparisons suggest a general decline in gene flow, with a few interesting exceptions. In summary, our results suggest (i) early stage divergence between life history forms of sockeye salmon within one reservoir, and (ii) recent changes in genetic connectivity among Lower Fraser River populations; both of these results have potential recovery implications for historically migratory populations that were affected by anthropogenic barriers such as hydroelectric dams.     

Genetic diversity in a small population of sockeye salmon, Oncorhynchus nerka (Walbaum) from the Ola river (northern coast of the Okhotsk sea)]

The genetic structure of a small sockeye salmon population from the Ola River (Tauyskaya Inlet, the Okhotsk Sea) was shown to exhibit high heterogeneity. Significant differences of LDH-B2* and ALAT-2* gene frequencies were detected not only among samples within the spawner and juvenile groups but also between spawners and juveniles as a whole. The average heterozygosity of sockeye salmon from the Ola River was considerably lower than the corresponding values for other Asian populations. The Ola sockeye salmon is genetically similar to the population from the Pakhach River of the northwestern Kamchatka Peninsula but different from other Kamchatka populations and the Okhota River population. A hypothesis explaining the genetic differentiation of Asian sockeye populations is advanced.