Effective Size of the Early-Run Sockeye Salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> Population of Lake Azabach’e,Kamchatka Peninsula Evaluation of the Effect of Interaction between Subpopulations within a Subdivided Population

The effect of subdivision on the effective size (N _e) of the early-run sockeye salmon Oncorhynchus nerka population of Lake Azabach’e (Kamchatka Peninsula) has been studied. The mode of this effect is determined by the relative productivity of the subpopulations and its magnitude, by the rate of individual migration among subpopulations and genetic differentiation. If the contributions of subpopulations (offspring numbers) are different, genetic differentiation can reduce the N _e of the subdivided population. At equal subpopulation contributions, genetic differentiation always increases the N _e of the subdivided population in comparison with a panmictic population. We have found that all sockeye salmon subpopulations of Azabach’e Lake produce equal offspring numbers contributing to the next generation. The genetic differentiation between sockeye salmon subpopulations is low, and the subdivision increases the N _e of the early-run race with reference to the sum of the effective sizes of the subpopulations by as little as 2%.__________Translated from Genetika, Vol. 41, No. 5, 2005, pp. 680–685.Original Russian Text Copyright © 2005 by Efremov.     

Effective size of subpopulation of the early run sockeye salmon Oncorhynchus nerka from Azabach's Lake (Kamchatka): effect of density on variance of reproductive success

Using Parensky's approach for estimating the number of breeding pairs, we determined effective subpopulation size Ne in early-run sockeye salmon Oncorhynchus nerka from Azabach'e Lake (Kamchatka) in 1977 through 1981. On average (over years and populations), biased sex ratio decreased Ne by 7% as compared to the number of fish on the spawning sites (Ni). High density reduced the Ne/Ni ratio by 62-66% because some fish were excluded from spawning. Dominance polygyny as compared to monogamy and random union of gametes could reduce Ne by about 17%.     

Effective size of subpopulations in early-run sockeye salmon Oncorhynchus nerka from Azabach'e Lake (Kamchatka): the effect of relative reproductive success of different-year cohorts

The effect of variation in reproductive success of cohorts of different year of birth (within generation) on the effective subpopulation (breeding group) size in early-run sockeye salmon Oncorhynchus nerka from Azabach'e Lake (Kamchatka). The annual variation in census size and overlapping of year classes reduced the ratio of the effective subpopulation size to the census size by 7 to 88% in different subpopulations. The total effect of the variance of reproductive success in individual years and the variance of reproductive success of different cohorts reduced the effective size/census size ratio by 68-96%.     

Effective Size of Subpopulations in Early-Run Sockeye Salmon Oncorhynchus nerka from Azabach'e Lake (Kamchatka): The Effect of Relative Reproductive Success of Different-Year Cohorts

The effect of variation in reproductive success of cohorts of different year of birth (within generation) on the effective subpopulation (breeding group) size in early-run sockeye salmonOncorhynchus nerka from Azabach'e Lake (Kamchatka). The annual variation in census size and overlapping of year classes reduced the ratio of the effective subpopulation size to the census size by 7 to 88% in different subpopulations. The total effect of the variance of reproductive success in individual years and the variance of reproductive success of different cohorts reduced the effective size/census size ratio by 68–96%.     

Divergence of mitochondrial DNA in a population of sockeye salmon (Oncorhynchus nerka Walbaum) from Azabache'e lake (Kamchatka)

Variability of three PCR-amplified mtDNA regions was examined in five populations of sockeye salmon from Azabach'e Lake. Eighteen haplotypes were detected in 144 fish. Significant differences were found between seasonal races of sockeye salmon spawning in the lake. The short time of independent divergence between the seasonal races indicates that these races formed independently in each spawning region. No difference in mtDNA between lake samples of early sockeye salmon (subisolates) was revealed, which confirms the existence of gene flow between them. A high level of differences between the sockeye salmon spawning in the lake and spawning in the tributaries of the lake, the Bushuev and Lotnaya rivers, suggests that there were no migration between them during many generations and that the nature of spawning grounds (lake or river) is essential for within species differentiation in this species.     

Divergence of Mitochondrial DNA in Populations of Sockeye Salmon Oncorhynchus nerka Walbaum from Azabach'e Lake (Kamchatka)

Variability of three PCR-amplified mtDNA regions was examined in five populations of sockeye salmon from Azabach'e Lake. Eighteen haplotypes were detected in 144 fish. Significant differences were found between seasonal races of sockeye salmon spawning in the lake. The short time of independent divergence between the seasonal races indicates that these races formed independently in each spawning region. No difference in mtDNA between lake samples of early sockeye salmon (subisolates) was revealed, which confirms the existence of gene flow between them. A high level of differences between the sockeye salmon spawning in the lake and spawning in the tributaries of the lake, the Bushuev and Lotnaya rivers, suggests that there were no migration between them during many generations and that the nature of spawning grounds (lake or river) is essential for within-species differentiation in this species.     

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.     

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.     

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.     

Demographic and genetic consequences of population subdivision in Formosa land-locked salmon <Emphasis Type="Italic">Oncorhynchus masou formosanus</Emphasis>, the southernmost subspecies of the salmonids

A few studies have evaluated demographic and genetic consequences of population subdivision by damming on the population as a whole. Formosa landlocked salmon Oncorhynchus masou formosanus have persisted as a relatively large population that has recently been subdivided into seven subpopulations by erosion-control dams and a natural waterfall. The present study simulated the demographic and genetic dynamics of this subdivided salmon population using VORTEX, an individual-based stochastic model. Although the population as a whole did not experience extinction over 200 simulation years, the loss of genetic variation was often detrimental (>10% loss). Isolated headwater subpopulations frequently reached extinction. Even when the subpopulations did persist through the 200 years, they experienced dramatic loss of genetic variation, suggesting short-term genetic threats. Due to the unidirectional dispersal of the fish, the damming puts headwater subpopulations at higher risk of extinction and loss of genetic variation, which affects persistence of the population as a whole, particularly from a genetic perspective.     

Variation in smoltification age and its determinants in sockeye salmon of Lake Azabach’e

In this paper, we analyze scale samples of sexually mature sockeye salmon from Lake Azabach'e collected over many years and data on the abundance of zooplankton in this lake. For native juvenile sockeye salmon, the major limiting factor of growth and smoltification is food availability. During the observation period from 1977 to 1993, two-year-olds were the most numerous group among the downstream-migrating sockeye salmon. Short-term fluctuations in the proportion of one-year-old smolts during downstream migration are attributed to outbreaks of plankton due to the natural fertilization of the lake.     

Analysis of gene origin in the first adult returns to the Cultus sockeye salmon captive breeding program

Rigorous evaluation of the utility of captive breeding for the restoration of depleted wild salmonid fish populations has not been undertaken. In particular, little is known about the reproductive success of captively-bred individuals that are released back into an extant population and their capacity to assist in long-term population persistence. For the endangered Cultus Lake sockeye salmon population, we examined the potential genetic contribution of the first juvenile fish released from a captive breeding program upon their maturity in the natural Cultus Lake environment. Genetic analysis of 792 Cultus sockeye salmon that were spawned in captivity in 2004 and their adult progeny of 2007 and 2008 revealed a genetic bottleneck originating from 20 wild sockeye salmon hatchery-spawned at Cultus Lake in the previous generation. Pedigree analysis revealed that six of the 20 sockeye salmon spawned in 2001 (grandparents) gave rise to a majority of the hatchery spawners in 2004 (parents) and provided more than 30% of the genes in the progeny that survived to maturity in the wild. Allele frequencies and genetic diversity of the age three progeny that returned to Cultus Lake from their marine migration in 2007 reflected the bottleneck, but its genetic signature was faint among the more genetically diverse age four fish that returned in 2008. Two-generation analysis of gene origin among fish resulting from 2004 hatchery production indicated that they contained the genetic diversity expected from 36 effective ancestors.     

The effect of the infectious hematopoietic necrosis virus on the population of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> (Salmoniformes,Salmonidae) from Lake Nachikinskoe

The results of virological examination of adult sockeye salmon Oncorhynchus nerka in Lake Nachikinskoe from 2003 to 2008 demonstrated high values of prevalence of the infectious hematopoietic necrosis virus (IHNV) in the fish population (up to 100%). In the studied water reservoir there are optimal conditions for the development and revealing of the epizootic of infectious hematopoietic necrosis (IHN). In Lake Nachikinskoe, two natural epizootics of IHN in juvenile sockeye salmon were recorded in 2003 and 2006. The tendencies for change of prevalence of IHNV by years were analyzed, and their relation to the numbers of adult sockeye salmon at the spawning grounds of Lake Nachikinskoe was determined. The correlation of IHNV prevalence with the numbers of adult sockeye salmon in the studied water reservoir is direct but insignificant (r _s = 0.695, p < 0.05). It was shown that the epizootic of 2003 could affect the fact that fish return in 2007 and 2008 was minimum for the considered time interval while the numbers of their parents were, on the other hand, very high.     

Effective Size of Subpopulations in Early-Run Sockeye Salmon Oncorhynchus nerkafrom Azabach'e Lake (Kamchatka): The Effect of Density on Variance of Reproductive Success

Using Parensky's approach for estimating the number of breeding pairs, we determined effective subpopulation size N _e in early-run sockeye salmon Oncorhynchus nerka from Azabach'e Lake (Kamchatka) in 1977 through 1981. On average (over years and populations), biased sex ratio decreased N _e by 7% as compared to the number of fish on the spawning sites (N _i). High density reduced the N _e/N _i ratio by 62–66% because some fish were excluded from spawning. Dominance polygyny as compared to monogamy and random union of gametes could reduce N _e by about 17%.     

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 of sockeye salmon <Emphasis Type="Italic">Oncorhynchus nerka</Emphasis> Walbaum of Kamchatka and the Commander Islands based on analysis of the variability of microsatellite DNA

The genetic diversity of the resident and migratory forms of sockeye salmon is investigated in 14 populations from various water bodies of Kamchatka and the Commander Islands by ten loci of microsatellite DNA. There are considerable differences in the frequencies of alleles among the populations of kokanee from Lake Kronotskoe, the residual form of sockeye salmon from Lake Kopylie, and other populations analyzed. Clustering of samples corresponds to their geographic position. No differences in the frequencies of alleles of the investigated loci are found between two forms of resident sockeye salmon from Kronotskoe Lake. In the sockeye salmon from the Commander Islands, a relatively low genetic diversity is found, as well as the greatest remoteness from the other Kamchatka group.     

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.     

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.     

Juvenile habitat partitioning and relative productivity in allochronically isolated sockeye salmon (Oncorhynchus nerka)

Allochronic divergence, like spatial isolation, may contribute to population diversity and adaptation, however the challenges for tracking habitat utilization in shared environments are far greater. Adult Klukshu River (Yukon, Canada) sockeye salmon, Oncorhynchus nerka, return as genetically distinct "early" and "late" runs. Early and late adult spawning populations (1999 and 2000) and their subsequent fry (sampled at 7 sites in 2000 and at 8 sites in 2001 throughout Klukshu Lake and River) were genotyped at eight microsatellite loci. Bayesian assignment was used to determine the spatial distribution of early versus late fry; although intermixed, the distribution of fry significantly differed in Klukshu Lake and in the Klukshu River in 2001, based on crosstab analyses. Late-run fry predominated in Klukshu Lake at all sites, while early-run fry were most common in the north and south of Klukshu Lake and in Klukshu River. Early-run spawners had significantly higher relative productivity (early life survival) than late-run fish (2.9 times more fry produced per early-run adult in 2000, and 9.2 times more in 2001). This study demonstrates spatial habitat partitioning and differences in the contribution of allochronically isolated populations to fry abundance, and highlights annual variability that likely contributes to recruitment variation.     

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.