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.     

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.     

Phylogeographic Analysis of Chum Salmon Oncorhynchus keta Walbaum in Asian Populations Based on mtDNA Variation

We used restriction length polymorphism (RFLP) analysis of PCR-amplified fragments of mtDNA to study the genetic structure of chum salmon populations sampled in 1993–2000 during a spawning run in five rivers: Narva (Southern Primorye), Naiba (Sakhalin Island), Sernovodnaya (Kunashir Island, Southern Kuril Islands), Ola (northwestern coast of the Sea of Okhotsk), and Anadyr' (Chukotka Peninsula). In total, 49 haplotypes were identified in 193 fish. Heterogeneity tests showed highly significant (P = 0) differences among all sample pairs. The estimated time of independent divergence of the populations or population groups is in good agreement with the time of Pleistocene glaciations. This result suggests that it is cyclic global changes during this time period that were crucial in determining the within-species divergence in chum salmon. The types of mtDNA genetic variability and mismatch distribution between haplotypes in the populations indicate that the southern regions of the Sea of Okhotsk and Sea of Japan served as refugia for chum salmon during glaciation periods.     

Phylogenic and geographic analysis of chum salmon Oncorhynchus keta (Walbaum) in Asian populations based on mitochondrial DNA variation

We used restriction length polymorphism (RFLP) analysis of PCR-amplified fragments of mtDNA to study the genetic structure of chum salmon populations sampled in 1993-2000 during a spawning run in five rivers: Narva (Southern Primorye), Naiba (Sakhalin Island), Sernovodnaya (Kunashir Island, Southern Kuril Islands), Ola (northwestern coast of the Sea of Okhotsk), and Anadyr' (Chukotka Peninsula). In total, 49 haplotypes were identified in 193 fish. Heterogeneity tests showed highly significant (P = 0) differences among all sample pairs. The estimated time of independent divergence of the populations or population groups is in good agreement with the time of Pleistocene glaciations. This result suggests that it is cyclic global changes during this time period that were crucial in determining the within-species divergence in chum salmon. The types of mtDNA genetic variability and mismatch distribution between haplotypes in the populations indicate that the southern regions of the Sea of Okhotsk and Sea of Japan served as refugia for chum salmon during glaciation periods.     

Regional differentiation of North American Atlantic salmon at allozyme loci

Allozyme variation was characterised by starch gel electrophoresis at 23 enzyme coding loci and one regulatory locus in Atlantic salmon from 53 rivers in Eastern Canada, encompassing the majority of the species' North American range. Variation among rivers was highly heterogeneous and eight of the 15 polymorphisms showed regionally restricted distributions. Nearest neighbour joining (NJ) analysis and multi‐dimensional scaling suggest six distinct regional groups; Labrador/Ungava, Gulf of Saint Lawrence, Newfoundland (excluding Gulf rivers), the Atlantic shore/Southern Uplands of Nova Scotia, the inner Bay of Fundy, and the outer Bay of Fundy. Approximately 25% of observed genetic variation was distributed among these regions with a weak though significant overall correlation of genetic and geographic distance (Mantel Test, r  = 0·255, P  = 0·005). Collectively, the rivers showed consistent divergence from European populations with strong bootstrap support for the two clusters across loci in the NJ analysis. Mean heterozygosity was 0·061 for both continental groups, but the European population showed more than twice the variation among populations. F _ST values were 0·076 and 0·176 for North America and Europe, respectively, with an overall F _ST of 0·330.     

Selective exploitation of early running fish may induce genetic and phenotypic changes in Atlantic salmon

Genetic evidence for the selective exploitation by anglers of early running fish was examined in four Iberian Atlantic salmon populations using protein and mtDNA markers. The populations studied had been exploited exclusively by anglers since 1949 during a fixed fishing season that ran approximately from March to July. Genetic variation at six protein loci was small and was accounted for by the MEP‐2 * and MDH‐3,4 * polymorphisms, which generally remained stable over time and were in Castle–Hardy–Weinberg equilibrium during the fishing season. Early running fish that had spent multiple winters at sea (MSW) generally had higher frequencies of the common MEP‐2 *(100) allele than did late running, one sea winter (1SW) grilse that were significantly smaller and tended to escape the fishery. Spawners differed from angler caught fish in their mtDNA frequencies and consistently had a lower sea‐age and a smaller body size. Spawners also smolted at an older age and displayed lower frequencies of the MEP‐2 *(100) allele in three of the four populations studied. These results suggest that in these rivers anglers selectively exploit a distinct component of the population and inadvertently cause a differential mortality of genetic types that is likely to be detrimental to population viability.     

Migration of Pacific Rim Chum Salmon on the High Seas: Insights from Genetic Data

Wild stocks of chum salmon, Oncorhynchus keta, have experienced recent declines in some areas of their range. Also, the release of hatchery chum salmon has escalated to nearly three billion fish annually. The decline of wild stocks and the unknown effects of hatchery fish combined with the uncertainty of future production caused by global climate change have renewed interest in the migratory patterns of chum salmon on the high seas. We studied the composition of high-seas mixtures of maturing and immature individuals using baseline data for 20 allozyme loci from 356 populations from throughout the Pacific Rim. Composition estimates were made from three time series. Two of these time series were from important coastal migratory corridors: the Shumagin Islands south of the Alaska Peninsula and the east coast of the Kamchatka Peninsula. The third was from chum salmon captured incidentally in the Bering Sea trawl fishery for walleye pollock. We also analyzed geographically dispersed collections of chum salmon captured in the month of July. The time series show dynamic changes in stock composition. The Shumagin Island corridor was used primarily by Northwest Alaskan and Asian populations in June; by the end of July stocks from the Alaska Peninsula and southern North America dominated the composition. The composition along the Kamchatka coast changed dramatically from primarily Russian stocks in May to primarily Japanese stocks in August; the previously undocumented presence of stocks from the Alaska Peninsula and Gulf of Alaska was also demonstrated. Immature chum salmon from throughout the Pacific Rim, including large proportions of southern North American stocks, contributed to the Bering Sea bycatch during the months of September and October. The migration routes of North American stocks is far more widespread than previously observed, and the Bering Sea is an important rearing area for maturing and immature chum salmon from throughout the species' range.     

Mitochondrial DNA variation in Pleistocene and modern Atlantic salmon from the Iberian glacial refugium

Current understanding of the postglacial colonization of Nearctic and Palearctic species relies heavily on inferences drawn from the phylogeographic analysis of contemporary generic variants. Modern postglacial populations are supposed to be representative of their Pleistocene ancestors, and their current distribution is assumed to reflect the different colonization success and dispersal patterns of refugial lineages. Yet, testing of phylogeographic models against ancestral genomes from glacial refugia has rarely been possible. Here we compare ND1 mitochondrial DNA variation in late Pleistocene (16,000-40,000 years before present), historical and contemporary Atlantic salmon (Salmo salar) populations from northern Spain and other regions of western Europe. Our study demonstrates the presence of Atlantic salmon in the Iberian glacial refugium during the last 40,000 years and points to the Iberian Peninsula as the likely source of the most common haplotype within the Atlantic lineage in Europe. However, our findings also suggest that there may have been significant changes in the genetic structure of the Iberian refugial stock since the last ice age, and question whether modern populations in refugial areas are representative of ice age populations. A common haplotype that persisted in the Iberian Peninsula during the Pleistocene last glacial maximum is now extremely rare or absent from European rivers, highlighting the need for caution when making phylogeographic inferences about the origin and distribution of modern genetic types.     

Genetic differentiation among chum salmon, Oncorhynchus keta (Walbaum), from Primorye and Sakhalin

Mitochondrial DNA (mtDNA) was examined in six wild populations of chum salmon ( Oncorhynchus keta Walbaum) distributed over the Primorye Region which extends approximately 1000 km along the Sea of Japan coast, and six populations from Sakhalin, using restriction enzyme analysis. By means of two restriction enzymes ( Bam HI and Eco 81I) eight mtDNA clonal lines were revealed in the 346 chum salmon studied. Mitochondrial DNA variants grouped the fish into two major clusters representing the Primorye and Sakhalin regions. Analysis of different chum salmon generations showed stability in the temporal population genetic structure in the three Primorye populations studied, but instability in the Sakhalin population of the Naiba River. We succeeded in detecting four major mtDNA clonal variants in Primorye chum salmon. The geographic distribution of clonal frequencies in Primorye populations has a clinal U-shape associated with the north-south axis of the Primorye region. On the whole, Sakhalin populations are less heterogeneous than Primorye ones. Two hatchery-seeded stocks from south west Sakhalin showed no mtDNA clonal variation.     

Relationships of Palearctic and Nearctic 'glacial relict' Myoxocephalus sculpins from mitochondrial DNA data

The relationships among Myoxocephalus quadricornis complex fish from Arctic coastal waters and from 'glacial relict' populations in Nearctic and Palearctic postglacial lakes were assessed using mtDNA sequence data (1978 bp). A principal phylogeographical split separated the North American continental deepwater sculpin (M. q. thompsonii) from a lineage of the Arctic marine and North European landlocked populations of the fourhorn sculpin (M. q. quadricornis). The North American continental invasion took place several glaciation cycles ago in the Early-to-Middle Pleistocene (0.9% sequence divergence); the divergence of the European and Arctic populations was somewhat later (0.5% divergence). The Nearctic-Palearctic freshwater vicariance in Myoxocephalus, however, appears clearly younger than in similarly distributed 'glacial relict' crustacean taxa; the phylogeographical structure is more similar to that in other northern Holarctic freshwater fish complexes.     

The parasite-host relationships between the glochidia of the European pearl oyster Margaritifera margaritifera (Margaritiferidae: Bivalvia) and mass fish species in the European north of the USSR

Narrow specificity of larvae (glochidia) of Margaritifera margaritifera to salmon in the rivers of the Kola Peninsula was proved experimentally. It was found that in the gills of minnow, the other mass fish in the northern rivers of the USSR, larvae of M. margaritifera cannot develop and perish. Reasons causing the narrow specificity of M. margaritifera to Salmonidae are discussed.     

Occurrence and genetic typing of infectious hematopoietic necrosis virus in Kamchatka, Russia

Infectious hematopoietic necrosis virus (IHNV) is a well known rhabdoviral pathogen of salmonid fish in North America that has become established in Asia and Europe. On the Pacific coast of Russia, IHNV was first detected in hatchery sockeye from the Kamchatka Peninsula in 2001. Results of virological examinations of over 10,000 wild and cultured salmonid fish from Kamchatka during 1996 to 2005 revealed IHNV in several sockeye salmon Oncorhynchus nerka populations. The virus was isolated from spawning adults and from juveniles undergoing epidemics in both hatchery and wild sockeye populations from the Bolshaya watershed. No virus was detected in 2 other watersheds, or in species other than sockeye salmon. Genetic typing of 8 virus isolates by sequence analysis of partial glycoprotein and nucleocapsid genes revealed that they were genetically homogeneous and fell within the U genogroup of IHNV. In phylogenetic analyses, the Russian IHNV sequences were indistinguishable from the sequences of North American U genogroup isolates that occur throughout Alaska, British Columbia, Washington, and Oregon. The high similarity, and in some cases identity, between Russian and North American IHNV isolates suggests virus transmission or exposure to a common viral reservoir in the North Pacific Ocean.     

Geographical and temporal mitochondrial DNA variability in populations of pink salmon

Pink salmon Oncorhynchus gorbuscha from odd and even year generations in rivers of Sakhalin Island, Kuril Island, Kamchatka Peninsula, and Alaska were investigated with five informative restriction endonucleases for mtDNA variation. The odd and even generations from the same rivers of South Sakhalin differed greatly. The time of divergence between the two broodlines was estimated at 0.9-1.1 Myr. The variability of mtDNA in odd year generations was higher than in even year generations and may have been due to' founder' and/or' bottleneck' effects. The differences among river populations within the Sakhalin region in 1991-1993 were not significant and this confirms the highly migratory nature of pink compared with other Pacific salmon. The mtDNA samples revealed statistically significant differences between regions. The northern populations (Kamchatka, Alaska) were less diverse in number and frequency of haplotypes than the southern populations (Sakhalin). This suggests that pink salmon originated in the Sakhalin-Kuril region and that a founder effect during the spread of this species may have restricted the mtDNA variability in other regions.     

Geographical patterns in the population genetics of Atlantic salmon, Salmo salar L., on U.S.S.R. territory, as evidence for colonization routes

From data on interpopulation genetic structure of the Atlantic salmon from the rivers of the Barents, White and Baltic Sea basins on U.S.S.R. territory, it is suggested that salmon colonized the Onega and Pechora River basins from the Baltic drainage as the last ice-sheet receded, and that the Kola Peninsula rivers were colonized separately from the Barents Sea area.     

Selective effect of the duration of the critical temperature period on some allozyme loci of Atlantic salmon Salmo salar L. (Salmonidae)

Genetic structure of juvenile fish from the populations of the Atlantic salmon Salmo salar inhabiting the rivers of Murmansk oblast, Arkhangelsk oblast, and Karelia, as well as of juveniles from hatcheries was examined at five allozymic loci: aspartate aminotransferase (AAT-4*), isocitrate dehydrogenase (IDHP-3*), iditol dehydrogenase (IDDH-2*), esterase D (ESTD*), and malic enzyme (MEP-2*). High genetic differentiation of both natural and “hatchery” juvenile fish was revealed. It was demonstrated that the gene pool of juveniles at three of the five loci tested was to a considerable degree formed by natural selection. In this case, the role of limiting factor was played by the duration of critical temperature regime in the rivers. The differentiation factors for juveniles from nature were not established, however, their clusterization pattern pointed to a possible role of natural selection in this process.     

Isolation by distance and selection effects on genetic structure of sardines Sardina pilchardus Walbaum

Allozyme data were used to analyse the genetic structure of Sardina pilchardus populations. Fifty samples from 15 locations between the North Sea and Mauritania, including samples from the Azores, Madeira and the Mediterranean Sea, were surveyed. A weak but significant structure was found between all samples ( F _ST= 0.057, P < 0·001). This structure results from a change in the most common allele of SOD* between the North African and the Azores populations separated by the greatest distance. This locus seemed to be under selective pressure according to the test of neutrality, and the variations in allele frequencies may be explained due to isolation by distance (IBD) of coastal populations (from Mauritania to the North Sea) ( r = 0·86, P < 0·001). When SOD* was removed from the analyses, IBD was not observed in coastal populations ( r = 0·236, P > 0·05) but was observed over the whole range ( r = 0·321, P = 0·05). The genetic structure of S. pilchardus is driven by both IBD and selective processes.     

Sexual genotype markers absent from small numbers of male New Zealand Oncorhynchus tshawytscha

In New Zealand chinook salmon Oncorhynchus tshawytscha , sexual genotype did not correspond to phenotype in 1·6% of male fish, contrasting starkly with North American chinook populations, where inconsistencies between female genotype and phenotype have been observed at frequencies up to 84%.     

Population structure of lake‐type and river‐type sockeye salmon in transboundary rivers of northern British Columbia

The population structure of 'lake‐type' and 'river‐type' sockeye salmon Oncorhynchus nerka , primarily in transboundary rivers in northern British Columbia, was examined with a survey of microsatellite variation. Variation at 14 microsatellite loci was surveyed from c . 3000 lake‐type and 3200 river‐type sockeye salmon from 47 populations in six river drainages in British Columbia. The mean F _ST for the 14 microsatellite loci and 47 populations was 0·068, and 0·034 over all river‐type populations. River‐type sockeye salmon were more genetically diverse than lake‐type sockeye salmon, with expected heterozygosity of river‐type sockeye salmon 0·72 and with an average 12·7 alleles observed per locus, whereas expected heterozygosity of lake‐type sockeye salmon was 0·65 with and average 10·5 alleles observed per locus. River drainage of origin was a significant unit of population structure. There was clear evidence of genetic differentiation among river‐type populations of sockeye salmon from different drainages over a broad geographic range in British Columbia.     

Factors affecting river entry of adult Atlantic salmon in a small river

In this study, effects of stock origin, fish size, water flow and temperature on time of river ascent of adult Atlantic salmon Salmo salar were tested. Brood stocks were collected in eight Norwegian rivers situated between 59 and 69° N. The fish were reared to smolts, individually tagged and released in the River Imsa, south-west Norway (59° N). Adults from all stocks approached the Norwegian coast concurrently, but Atlantic salmon ≥70 cm in natural tip length entered coastal water slightly earlier during summer than smaller fish. Atlantic salmon <70 cm, however, ascended the river significantly earlier and at lower water flow and higher water temperature than larger fish. Although largest in size, the fish from the northern populations (62–69° N) ascended the River Imsa almost 1 month earlier than those from the south (59–60° N). They seemed less restricted by the environmental factors than the fish originating from the more southern rivers. There was no apparent trend among years in time of river ascent. Maximum ascent per day occurred at water discharges between 12·5 and 15 m³ s⁻¹ and at water temperatures between 10 and 12·5° C. There was a significant positive correlation between water flow and river ascent during the first part of the upstream run from July to September with best correlation for September, when multiple regression analysis indicated that water temperature had an additional positive effect. Stock origin, fish size and water discharge were important variables influencing the upstream migration of Atlantic salmon in small rivers.     

MOLECULAR GENETIC EVIDENCE FOR PARALLEL LIFE-HISTORY EVOLUTION WITHIN A PACIFIC SALMON (SOCKEYE SALMON AND KOKANEE,ONCORHYNCHUS NERKA)

The Pacific salmon Oncorhynchus nerka typically occurs as a sea-run form (sockeye salmon) or may reside permanently in lakes (kokanee) thoughout its native North Pacific. We tested whether such geographically extensive ecotypic variation resulted from parallel evolutionary divergence thoughout the North Pacific or whether the two forms are monophyletic groups by examining allelic variation between sockeye salmon and kokanee at two minisatellite DNA repeat loci and in mitochondrial DNA (mtDNA) Bgl II restriction sites. Our examination of over 750 fish from 24 populations, ranging from Kamchatka to the Columbia River, identified two major genetic groups of North Pacific O. nerka: a “northwestern” group consisting of fish from Kamchatka, western Alaska, and northwestern British Columbia, and a “southern” group consisting of sockeye salmon and kokanee populations from the Fraser and Columbia River systems. Maximum-likelihood analysis accompanied by bootstrapping provided strong support for these two genetic groups of O. nerka; the populations did not cluster by migratory form, but genetic affinities were organized more strongly by geographic proximity. The two major genetic groups resolved in our study probably stem from historical isolation and dispersal of O. nerka from two major Wisconsinan glacial refugia in the North Pacific. There were significant minisatellite DNA allele frequency differences between sockeye salmon and kokanee populations from different parts of the same watershed, between populations spawning in different tributaries of the same lake, and also between sympatric populations spawning in the same stream at the same time. MtDNA Bgl II restriction site variation was significant between sockeye salmon and kokanee spawning in different parts of the same major watershed but not between forms spawning in closer degrees of reproductive sympatry. Patterns of genetic affinity and allele sharing suggested that kokanee have arisen from sea-run sockeye salmon several times independently in the North Pacific. We conclude that sockeye salmon and kokanee are para- and polyphyletic, respectively, and that the present geographic distribution of the ecotypes results from parallel evolutionary origins of kokanee from sockeye (divergences between them) thoughout the North Pacific.