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.     

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.     

Geographic heterogeneity in natural selection on an MHC locus in sockeye salmon

Balancing selection maintains high levels of polymorphism and heterozygosity in genes of the MHC (major histocompatibility complex) of vertebrate organisms, and promotes long evolutionary persistence of individual alleles and strongly differentiated allelic lineages. In this study, genetic variation at the MHC class II DAB-beta1 locus was examined in 31 populations of sockeye salmon (Oncorhynchus nerka) inhabiting the Fraser River drainage of British Columbia, Canada. Twenty-five percent of variation at the locus was partitioned among sockeye populations, as compared with 5% at neutral genetic markers. Geographic heterogeneity of balancing selection was detected among four regions in the Fraser River drainage and among lake systems within regions. High levels of beta1 allelic diversity and heterozygosity, as well as distributions of alleles and allelic lineages that were more even than expected for a neutral locus, indicated the presence of balancing selection in populations throughout much of the interior Fraser drainage. However, proximate populations in the upper Fraser region, and four of six populations from the lower Fraser drainage, exhibited much lower levels of genetic diversity and had beta1 allele frequency distributions in conformance with those expected for a neutral locus, or a locus under directional selection. Pair-wise FST values for beta1 averaged 0.19 and tended to exceed the corresponding values estimated for neutral loci at all levels of population structure, although they were lower among populations experiencing balancing selection than among other populations. The apparent heterogeneity in selection resulted in strong genetic differentiation between geographically proximate populations with and without detectable levels of balancing selection, in stark contrast to observations at neutral loci. The strong partitioning and complex structure of beta1 diversity within and among sockeye populations on a small geographic scale illustrates the value of incorporating adaptive variation into conservation planning for the species.     

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.     

Population cycles in voles and lemmings: state of the science and future directions

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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.     

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.     

Asynchrony in population dynamics of sockeye salmon in southwest Alaska

Ecologists have examined the synchronization of population dynamics across space as a means to understand how populations respond to climate variation. However, response diversity may reflect important variation among local population dynamics driven by population‐specific responses to regional environmental change. We used long‐term data on sockeye salmon Oncorhynchus nerka from pristine watersheds of southwestern Alaska to show that populations spawning in close proximity (<40 km) to one another have a limited degree of synchrony in their dynamics, even after accounting for density‐dependent processes. In fact, the dynamics of local populations of stream‐spawning sockeye salmon were no more coherent than those of stocks at a much coarser resolution across this region of Alaska. We examined four hypotheses to explain the observed patterns of asynchrony among stream‐spawning populations, and found that populations spawning in dissimilar habitats, and using different nursery lakes were less synchronized in their productivity. Similarity in the age structure of spawning adults was less correlated with synchrony in productivity. These results emphasize the importance of maintaining diverse spawning and rearing habitat for the conservation of Pacific salmon, and should guide conservation planning for Pacific salmon populations in regions where natural dynamics have been altered by habitat loss, hatchery practices, and over‐fishing.     

A three-species model explaining cyclic dominance of Pacific salmon

The four-year oscillations of the number of spawning sockeye salmon (Oncorhynchus nerka) that return to their native stream within the Fraser River basin in Canada are a striking example of population oscillations. The period of the oscillation corresponds to the dominant generation time of these fish. Various—not fully convincing—explanations for these oscillations have been proposed, including stochastic influences, depensatory fishing, or genetic effects. Here, we show that the oscillations can be explained as an attractor of the population dynamics, resulting from a strong resonance near a Neimark Sacker bifurcation. This explains not only the long-term persistence of these oscillations, but also reproduces correctly the empirical sequence of salmon abundance within one period of the oscillations. Furthermore, it explains the observation that these oscillations occur only in sockeye stocks originating from large oligotrophic lakes, and that they are usually not observed in salmon species that have a longer generation time.     

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.     

Forest-obligate Sabethes mosquitoes suggest palaeoecological perturbations

The origin of tropical forest diversity has been hotly debated for decades. Although specific mechanisms vary, many such explanations propose some vicariance in the distribution of species during glacial cycles and several have been supported by genetic evidence in Neotropical taxa. However, no consensus exists with regard to the extent or time frame of the vicariance events. Here, we analyse the cytochrome oxidase II mitochondrial gene of 250 Sabethes albiprivus B mosquitoes sampled from western Sao Paulo in Brazil. There was very low population structuring among collection sites (Phi(ST)=0.03, P=0.04). Historic demographic analyses and the contemporary geographic distribution of genetic diversity suggest that the populations sampled are not at demographic equilibrium. Three distinct mitochondrial clades were observed in the samples, one of which differed significantly in its geographic distribution relative to the other two within a small sampling area (approximately 70 x 35 km). This fact, supported by the inability of maximum likelihood analyses to achieve adequate fits to simple models for the population demography of the species, suggests a more complex history, possibly involving disjunct forest refugia. This hypothesis is supported by a genetic signal of recent population growth, which is expected if population sizes of this forest-obligate insect increased during the forest expansions that followed glacial periods. Although a time frame cannot be reliably inferred for the vicariance event leading to the three genetic clades, molecular clock estimates place this at approximately 1 Myr before present.     

The synergistic effects of stochasticity and dispersal on population densities

Using laboratory experiments, simulation models, and analytical techniques, we examined the impact of dispersal on the mean densities of patchily distributed populations. Even when dispersal leads to no net additions or removals of individuals from a population, it may nonetheless increase mean population densities if the net immigration rate is positive when populations are growing and negative when they are declining. As a model system for exploring this phenomenon, we used the yeastlike fungus Aureobasidium pullulans. In a laboratory experiment, we showed that dispersal can both ensure persistence and increase mean population densities even when dispersal among populations causes no direct addition or loss of fungal cells. From the laboratory data, we constructed a plausible model of A. pullulans dynamics among apple leaves within an orchard. This simulation model demonstrated that the effect of dispersal on mean densities is enhanced by three factors: weak density dependence of the dynamics within populations, high environmental variability affecting population growth rates, and lack of synchrony among the fluctuations of populations. Using an analytical model, we showed that the underlying mechanisms for this phenomenon are general, suggesting that a large effect of dispersal on mean population densities is possible in many natural systems.     

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.     

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.     

Multi-annual density fluctuations and habitat size enhance genetic variability in two northern voles

In order to gain a better understanding of the consequences of population density cycles and landscape structure for the genetic composition in time and space of vole populations, we analyzed the multiannual genetic structure of the two numerically dominant, sympatric small rodent species of northernmost Fennoscandia. Red voles Myodes rutilus and grey-sided voles M. rufocanus were trapped in the subarctic birch forest along three fjords over five years. Along each fjord, there were four or five altitudinal transects each with five trapping stations. Spring and fall population densities were estimated from mark–recapture data. Grey-sided voles exhibited higher amplitude density fluctuations than red voles. Polymorphism at eight or nine microsatellite loci, determined in 1228 voles, was used to estimate local genetic diversity and differentiation among samples. Genetic diversity was higher in grey-sided voles than in red voles. Spring densities had no effect on local genetic diversity or on differentiation. The amplitude of density fluctuations and the extent of favorable habitat (sub-arctic birch forest) surrounding each site had a positive effect on genetic diversity, and the amplitude of density fluctuations had a negative effect on differentiation in red voles, for which fluctuating populations were compared with more stable populations. The harmonic mean of densities, reflecting average population sizes, had a negative effect on genetic diversity in red voles, but a positive effect in grey-sided voles, for which only fluctuating populations were compared. No other effects were significant for grey-sided voles. A temporal assignment test showed that the spatial structure was more stable in time for populations with more stable population dynamics. Altogether our results suggest that high amplitude density fluctuations lead to more gene flow and higher genetic diversity in vole populations.     

Ontogenetic Scaling of Foraging Rates and the Dynamics of a Size-Structured Consumer-Resource Model

The ontogenetic scaling of foraging capacity strongly influences the competitive ability of differently sized individuals within a species. We develop a physiologically structured model to investigate the effect of different ontogenetic size scalings of the attack rate on the population dynamics of a consumer-resource system. The resource is assumed to reproduce continuously whereas the consumer only reproduces at discrete time instants. Depending on the ontogenetic size scaling, the model exhibited recruit-driven cycles, stable fixed point dynamics, non-recruit juvenile-driven cycles, quasiperiodic orbits, or chaotic dynamics. The kind of dynamics observed was related to the maintenance resource levels required of differently sized individuals. Stable fixed point dynamics was, besides at the persistence boundary, only observed when the minimum resource levels were similar for newborns and mature individuals. The tendency for large population fluctuations over a wide range of the parameter space was due to the consumer's pulsed reproduction. Background mortality and length of season were major determinants of cycle length. Model dynamics strongly resembled empirically observed dynamics from fish and Daphnia populations with respect to both patterns and mechanisms. The non-recruit juvenile-driven dynamics is suggested to occur in populations with size-dependent interference or preemptive competition like cicada populations.     

Size-selective and sex-selective predation by brown bears on sockeye salmon

Breeding activity increases the vulnerability of many animals to predation, and such predation can affect the subset of animals successfully reproducing. To study the ways in which predation might affect the evolution of Pacific salmon, we measured the intensity and selectivity of predation by bears (primarily brown bears, Ursus arctos) on mature sockeye salmon (Oncorhynchus nerka) breeding in a series of small, spring-fed ponds and creeks near Pedro Bay, Alaska, from 1994 to 1998. Bears killed male salmon more often than females; males constituted 60% of the kills but only 35% of the salmon that died of senescence. The bears also killed fish that were larger, on average, than those dying of senescence (males: 462 vs 452 mm; females: 453 vs 443 mm). The level of predation varied greatly, from 4% (females) and 10% (males) in 1994 to 100% of both sexes in 1996 and 1997. The rate of predation also varied among habitats, being lower in larger ponds than in smaller, shallower ponds and the very small interconnecting creeks. Despite the intense and size-selective predation, the salmon in safer habitats (large ponds) were not larger than those in riskier habitats, and salmon densities were only slightly higher in the safer areas. Compared to a nearby population that experiences no bear predation (Woody Island), the male sockeye salmon from the Pedro Pond system had shallower bodies (i.e., less exposure in shallow water) for a given length, consistent with the hypothesis that selective predation can affect the extent of sexual dimorphism among populations. However, the average length at age for both males and females was greater in the Pedro Pond fish, indicating that selective factors besides predation affect length. Overall, the results indicate that bears can be an agent of natural selection within (and perhaps between) sockeye salmon populations, and predation can greatly affect reproductive success among individuals and years for the population as a whole. Received: 6 April 1999 / Accepted: 1 June 1999     

Improved viability of populations with diverse life-history portfolios

A principle shared by both economists and ecologists is that a diversified portfolio spreads risk, but this idea has little empirical support in the field of population biology. We found that population growth rates (recruits per spawner) and life-history diversity as measured by variation in freshwater and ocean residency were negatively correlated across short time periods (one to two generations), but positively correlated at longer time periods, in nine Bristol Bay sockeye salmon populations. Further, the relationship between variation in growth rate and life-history diversity was consistently negative. These findings strongly suggest that life-history diversity can both increase production and buffer population fluctuations, particularly over long time periods. Our findings provide new insights into the importance of biocomplexity beyond spatio-temporal aspects of populations, and suggest that maintaining diverse life-history portfolios of populations may be crucial for their resilience to unfavourable conditions like habitat loss and climate change.     

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.     

The best in all possible worlds? A quantitative genetic study of geographic variation in the meadow vole,Microtus pennsylvanicus

The meadow vole, Microtus pennsylvanicus , is the most widely distributed Microtus species in North America. Across its range, it shows marked demographic differences, experiences a large range of climatic conditions, and varies considerably in body size and life-history characteristics. To study the genetic basis of the geographic variation in size and life history of this species, we subjected three populations, one from central Canada and two from eastern Canada, to quantitative genetic analysis in the lab. We studied the variance and covariance of several size and growth variables as well as age and size at maturity by means of population crosses, full-sib analysis, and parent-offspring regressions. We found that the phenotypic differences among these populations are almost entirely due to environmental effects. However, within populations, additive genetic and maternal effects explain most of the variation. We discuss possible explanations for the lack of genetic differences among the populations and speculate that a similar reaction norm is maintained in all populations through heterogeneity in the temporal or spatial environment that the populations experience. The heterogeneity may be mediated through population density fluctuations, climatic variation, or variation in site productivity. Thus, we hypothesize that M. pennsylvanicus has evolved to be the best in all possible worlds rather than in one actual world. This study highlights the crucial importance of maternal and environmental effects on the size, growth, and life history of small rodents.