Variability of size-age indices and genetic variability of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> from the Western Coast of Kamchatka: Comparative analysis of methods of differentiation of local populations

Study of variability of size-age indices and polymorphism of 6 microsatellite loci, 5 loci of SNP, and accidentally amplified polymorphic DNA (RAPD) of sockeye salmon Oncorhynchus nerka of three largest populations from the western coast of Kamchatka Peninsula was performed. The efficiency of using different types of markers for the differentiation of populations and determination of the population belonging of sockeye salmon from lake-river systems of western Kamchatka was analyzed. Significant interpopulation differences were revealed from the frequencies of alleles of genetic markers and from a set of biological indices. It was established that genetic markers are characterized by a better differentiating capacity, as compared to biological characteristics. The most satisfactory results during determination of population belonging of sockeye salmon were obtained using an integrated data base of allele frequencies of microsatellite and SNP loci.     

Genetic differentiation of sockeye salmon Oncorhynchus nerka (Walbaum, 1792) populations of eastern Kamchatka

The interpopulation differentiation of the sockeye salmon Oncorhynchus nerka (Walbaum) from the Olyutorskiy and Karaginskiy districts and from the Kamchatka River basin was examined based on the allelic variation at eight microsatellite loci (Ots107, Oki1a, Oki1b, One104, One109, OtsG68, OtsG85, and Oki6). The genetic diversity of samples from the northern rivers was lower, compared to samples from the Kamchatka River basin. Significant heterogeneity was found in the allele-frequency distribution at microsatellite loci of sockeye salmon from the investigated localities. The degree of genetic similarity of populations corresponded to their geographic closeness. The differences between population groups greatly exceeded the level of interpopulation differentiation. The analyzed samples formed four relatively separate groups: Lake Azabachye, Kamchatka River basin, Karaginskiy area (including the Navyrinvayam River in the south of the Olyutorskiy district), and northern Olyutorskiy area. The identification likelihood estimates of eastern Kamchatkan sockeye salmon in mixed aggregations at the level of population groups were fairly high (67.2–81.8%), greatly exceeding the accuracy of identification of individual populations.     

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.     

The phylogeography of the asian sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>, inferred from the data on the variability of mitochondrial SNP loci: Analysis of scenarios for post-glacial expansion of the species over the asian coast of the pacific ocean

The variability of three single nucleotide polymorphism (SNP) loci in the mitochondrial DNA (mtSNP) is analyzed for sockeye salmon populations over a major part of the species range, from Chukotka to the Kuril Islands. Two basic mtSNP haplotypes, GCC and GTT, have been revealed in 20 sockeye samples from 15 lake–river systems on the Asian coast of the Pacific Ocean. In most of the samples, the ratio of the haplotypes is approximately equal. The GTT haplotype dominates the populations from the Kuril Islands (except Shumshu Island); only the GCC haplotype has been found in the sample from the Commander Islands. This geographic pattern of haplotype distribution was presumably caused by the historico-demographic events related to the formation of the Asian sockeye range in the Middle–Late Pleistocene, viz., fragmentation of the species range and subsequent secondary contact between previously diverged populations. These data provide a basis to consider different scenarios for the formation of the modern diversity of sockeye mtSNP haplotypes, all of which suggest multiple expansions of the species to Asian waters during the periods of oceanic transgression after the Pleistocene glaciations.     

The genetic population structure of lacustrine sockeye salmon, <Emphasis Type="Italic">Oncorhynchus nerka,</Emphasis> in Japan as the endangered species

Lacustrine sockeye salmon (Oncorhynchus nerka) are listed as an endangered species in Japan despite little genetic information on their population structure. In order to clarify the genetic diversity and structure of Japanese populations for evaluating on the bottleneck effect and an endangered species, we analyzed the ND5 region of mitochondrial DNA (mtDNA) and 45 single nucleotide polymorphisms (SNPs) in 640 lacustrine sockeye salmon in Japan and 80 anadromous sockeye salmon in Iliamna Lake of Alaska. The genetic diversity of the Japanese population in both mtDNA and SNPs was significantly less than that of the Iliamna Lake population. Moreover, all Japanese populations had SNP loci deviating from the HWE. In spite of low genetic diversity, the SNP analyses resulted that the Japanese population was significantly divided into three groups. These suggest that Japanese sockeye salmon populations should be protected as an endangered species and genetically disturbed by the hatchery program and transplantations.     

Founding events influence genetic population structure of sockeye salmon (Oncorhynchus nerka) in Lake Clark, Alaska

Bottlenecks can have lasting effects on genetic population structure that obscure patterns of contemporary gene flow and drift. Sockeye salmon are vulnerable to bottleneck effects because they are a highly structured species with excellent colonizing abilities and often occupy geologically young habitats. We describe genetic divergence among and genetic variation within spawning populations of sockeye salmon throughout the Lake Clark area of Alaska. Fin tissue was collected from sockeye salmon representing 15 spawning populations of Lake Clark, Six-mile Lake, and Lake Iliamna. Allele frequencies differed significantly at 11 microsatellite loci in 96 of 105 pairwise population comparisons. Pairwise estimates of FST ranged from zero to 0.089. Six-mile Lake and Lake Clark populations have historically been grouped together for management purposes and are geographically proximate. However, Six-mile Lake populations are genetically similar to Lake Iliamna populations and are divergent from Lake Clark populations. The reduced allelic diversity and strong divergence of Lake Clark populations relative to Six-mile Lake and Lake Iliamna populations suggest a bottleneck associated with the colonization of Lake Clark by sockeye salmon. Geographic distance and spawning habitat differences apparently do not contribute to isolation and divergence among populations. However, temporal isolation based on spawning time and founder effects associated with ongoing glacial retreat and colonization of new spawning habitats contribute to the genetic population structure of Lake Clark sockeye salmon. Nonequilibrium conditions and the strong influence of genetic drift caution against using estimates of divergence to estimate gene flow among populations of Lake Clark sockeye salmon.     

Single-nucleotide polymorphism in populations of sockeye salmon Oncorhynchus nerka from Kamchatka Peninsula

The genetic variability of 45 single-nucleotide polymorphism loci was examined in the four largest wild populations of sockeye salmon Oncorhynchus nerka from drainages of the Asian coast of the Pacific Ocean (Eastern and Western Kamchatka). It was demonstrated that sockeye salmon from the Palana River were considerably different from all other populations examined. The most probable explanation of the observed differences is the suggestion on possible demographic events in the history of this population associated with the decrease in its effective number. To study the origin, colonization patterns, and evolution of Asian sockeye salmon, as well as to resolve some of the applied tasks, like population assignment and genetic identification, a differential approach to SNP-marker selection was suggested. Adaptively important loci that evolve under the pressure of balancing (stabilizing) selection were identified, owing to this fact the number of loci that provide the baseline classification error rates in the population assignment tests was reduced to 30. It was demonstrated that SNPs located in the MHC2 and GPH genes were affected by diversifying selection. Procedures for selecting single-nucleotide polymorphisms for phylogenetic studies of Asian sockeye salmon were suggested. Using principal-component analysis, 17 loci that adequately reproduce genetic differentiation within and among the regions of the origin of Kamchatka sockeye salmon were selected.     

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.     

Genetic Diversity in a Small Population of Sockeye Salmon Oncorhynchus nerkaWalbaum from the Ola River (the 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.     

Seasonal and interannual variations of sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>) microsatellite DNA in two Kamchatka lake-river systems

Seasonal and interannual variations in the sockeye salmon populations from two lake-river systems of the East and West Kamchatka were studied. Stability of allele and genotypic frequencies of six microsatellite DNA loci in the adjacent generations and spawning populations of the sockeye salmon of the Bol’shaya River was confirmed experimentally. The pairwise intersample differentiation (F _st) of the local sockeye salmon populations from the southwestern Kamchatka coast (Ozernaya and Bol’shaya Rivers) was almost 7 times higher than the corresponding values for the spawning populations of the Bol’shaya River sockeye salmon of the adjacent years; 15 times, for the adjacent Bol’shaya River sockeye salmon generations; and four times, for the seasonal races within the Kamchatka River.     

Microsatellite DNA Data Indicate Distinct Native Populations of Kokanee, Oncorhynchus nerka, Persist in the Lake Sammamish Basin, Washington

Large-scale introductions of resident and anadromous salmonids from exogenous sources and urbanization have led to major changes in, and concern for the fate of, indigenous fish populations of the Lake Sammamish/Lake Washington Basin. Specifically, introductions of kokanee (the resident form of Oncorhynchus nerka) from the Lake Whatcom Hatchery and sockeye (the anadromous form of O. nerka) from Baker Lake have caused uncertainty about the ancestry of the kokanee that currently spawn in the basin. We used nine microsatellite loci to investigate the inter-relationships of kokanee populations that spawn in streams in the Sammamish sub-basin, sockeye salmon populations that share spawning areas with the kokanee, Lake Whatcom Hatchery kokanee and Baker Lake sockeye, and an outgroup, Meadow Creek kokanee, from Lake Kootenay which drains into the upper Columbia River. We observed high levels of genetic variation (5–49 alleles per locus). Explicit tests of population sub-division revealed that collections from most spawning aggregations differed from each other. Observed allele frequency distributions strongly suggest that natural spawning kokanee in the basin are not descended from recent Lake Whatcom stock introductions. We found no compelling evidence to suggest that the kokanee sampled from spawning areas within the Lake Sammamish sub-basin have resulted from, or been altered substantially by, past introductions of non-native kokanee or sockeye.     

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.     

Genetic variability and population structure of sockeye salmon from the Asian Coast of Pacific Ocean

Variability of six microsatellite loci and 45 single nucleotide polymorphism (SNP) loci was analyzed in 17 samples of sockeye salmon from 10 major spawning watersheds on the Asian coast of the Pacific Ocean. On the basis of the analysis of SNP loci variability of sockeye salmon in the examined part of the range, five population groups were identified, including local stocks from the Palana, Okhota, and Kamchatka rivers, as well as the population groups of Southwestern Kamchatka, and Northeastern Kamchatka and Chukotka. Rather different pattern of samples differentiation was obtained by estimating variability of six microsatellite DNA loci. Regional complexes of the eastern and western coasts of Kamchatka were identified. Moreover, sockeye salmon from the Palana River fell into the cluster of Western Kamchatka populations, while the population from the Okhota River and Meynypilgin lake–river system (Chukotka), confined to the subperiphery of the range, where the most differentiated from the others. The possible reasons for the discrepancies and high divergence of the Palana River and the Okhota River sockeye salmon populations, inferred from the SNP markers analysis, are discussed.     

Seasonal and interannual variations of sockeye salmon (Oncorhynchus nerka) microsatellite DNA in two Kamchatka lake-river systems

Seasonal and interannual variations in the sockeye salmon populations from two lake-river systems of the East and West Kamchatka were studied. Stability of allele and genotypic frequencies of six microsatellite DNA loci in the adjacent generations and spawning populations of the sockeye salmon of the Bol'shaya River was confirmed experimentally. The pairwise intersample differentiation (F(st)) of the local sockeye salmon populations from the southwestern Kamchatka coast (Ozernaya and Bol'shaya Rivers)was almost 7 times higher than the corresponding values for the spawning populations of the Bol'shaya River sockeye salmon of the adjacent years; 15 times, for the adjacent Bol'shaya River sockeye salmon generations; and four times, for the seasonal races within the Kamchatka River.     

Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (<Emphasis Type="Italic">Oncorhynchus nerka</Emphasis>) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

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.     

Tendencies of Density Dynamics in Reophilic and Lacustrine Sockeye Salmon Oncorhynchus nerkain the Basin of Azabach'e Lake

Temporal series of density in the spawners of two sockeye salmon populations from Azabach'e Lake (Kamchatka River basin) were analyzed using periodic functions. It has been found that the quality of describing the density dynamics for sockeye salmon by such models is very high (R ²= 0.943 and R ²= 0.905 for early and late populations, respectively). The density (for early sockeye salmon) and total number (for late sockeye salmon) distributions of the reproductive fraction of the populations have been developed and analyzed.     

Comparative analysis of STR and SNP polymorphism in the populations of sockeye salmon (Oncorhynchus nerka) from Eastern and Western Kamchatka

Sockeye salmon samples from five largest lacustrine-riverine systems of Kamchatka Peninsula were tested for polymorphism at six microsatellite (STR) and five single nucleotide polymorphism (SNP) loci. Statistically significant genetic differentiation among local populations from this part of the species range examined was demonstrated. The data presented point to pronounced genetic divergence of the populations from two geographical regions, Eastern and Western Kamchatka. For sockeye salmon, the individual identification test accuracy was higher for microsatellites compared to similar number of SNP markers. Pooling of the STR and SNP allele frequency data sets provided the highest accuracy of the individual fish population assignment.     

Recent local adaptation of sockeye salmon to glacial spawning habitats

Salmonids spawn in highly diverse habitats, exhibit strong genetic population structuring, and can quickly colonize newly created habitats with few founders. Spawning traits often differ among populations, but it is largely unknown if these differences are adaptive or due to genetic drift. To test if sockeye salmon (Oncorhynchus nerka) populations are adapted to glacial, beach, and tributary spawning habitats, we examined variation in heritable phenotypic traits associated with spawning in 13 populations of wild sockeye salmon in Lake Clark, Alaska. These populations were commonly founded between 100 and 400 hundred sockeye salmon generations ago and exhibit low genetic divergence at 11 microsatellite loci (F _ST < 0.024) that is uncorrelated with spawning habitat type. We found that mean P _ST (phenotypic divergence among populations) exceeded neutral F _ST for most phenotypic traits measured, indicating that phenotypic differences among populations could not be explained by genetic drift alone. Phenotypic divergence among populations was associated with spawning habitat differences, but not with neutral genetic divergence. For example, female body color was lighter and egg color was darker in glacial than non-glacial habitats. This may be due to reduced sexual selection for red spawning color in glacial habitats and an apparent trade-off in carotenoid allocation to body and egg color in females. Phenotypic plasticity is an unlikely source of phenotypic differences because Lake Clark sockeye salmon spend nearly all their lives in a common environment. Our data suggest that Lake Clark sockeye salmon populations are adapted to spawning in glacial, beach and tributary habitats and provide the first evidence of a glacial spawning ecotype in salmonids. Glacial spawning habitats are often young (i.e., <200 years old) and ephemeral. Thus, local adaptation of sockeye salmon to glacial habitats appears to have occurred recently.     

Parallel and nonparallel genome‐wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon

Little is known about the genetic basis differentiating resident and anadromous forms found in many salmonid species. Using a medium‐density SNP array, we documented genomic diversity and divergence at 2336 genetically mapped loci among three pairs of North American anadromous and freshwater Atlantic salmon populations. Our results show that across the genome, freshwater populations have lower diversity and a smaller proportion of private polymorphism relative to anadromous populations. Moreover, differentiation was more pronounced among freshwater than among anadromous populations at multiple spatial scales, suggesting a large effect of genetic drift in these isolated freshwater populations. Using nonhierarchical and hierarchical genome scans, we identified hundreds of markers spread across the genome that are potentially under divergent selection between anadromous and freshwater populations, but few outlier loci were repeatedly found in all three freshwater–anadromous comparisons. Similarly, a sliding window analysis revealed numerous regions of high divergence that were nonparallel among the three comparisons. These last results show little evidence for the parallel evolution of alleles selected for in freshwater populations, but suggest nonparallel adaptive divergence at many loci of small effects distributed through the genome. Overall, this study emphasizes the important role of genetic drift in driving genome‐wide reduction in diversity and divergence in freshwater Atlantic salmon populations and suggests a complex multigenic basis of adaptation to resident and anadromous strategies with little parallelism.