Chum Salmon Populations Research Articles

Comparative morphology related to reproductive strategy in two chum salmon (Oncorhynchus keta) populations in the Yurappu River

Comparative morphology related to reproductive strategy in two chum salmon (Oncorhynchus keta) populations in the Yurappu River

Erratum to: An overview of salmon enhancement and the need to manage and monitor natural spawning in Hokkaido, Japan

The chum and pink salmon catches in Hokkaido, Japan have increased dramatically since the 1970s and the 1990s, respectively. In contrast, masu salmon catches have been steadily decreasing. Despite intensive hatchery development in Hokkaido, naturally spawning salmon populations persist based on results from a recent river survey. This paper focuses on the challenges of maintaining hatchery salmon populations while protecting natural chum, pink and masu salmon populations in Hokkaido. Two important initiatives related to meeting this ambitious goal are managing hatcheries in a way that minimizes negative interactions between natural and hatchery salmon populations, and initiating new efforts at restoring and rehabilitating degraded freshwater habitats. In addition, in order to maintain a balance of demand and supply in the domestic market through the exportation of extra salmon, Hokkaido has decided to enter full assessment to gain Marine Stewardship Council (MSC) certification of the Hokkaido chum salmon trap net fishery. This would involve a fundamental shift in fisheries management as practiced in Japan, specifically elevating the importance of managing the fishery in a way that conserves natural salmon populations. A key component of a new salmon management strategy is the establishment of a zone management framework based on the designation of stream units to spatially separate natural salmon from hatchery salmon to minimize negative effects of hatchery fish and to utilize effectively hatchery salmon for commercial fisheries. This effort is allied with similar initiatives in other Pacific Rim countries that are focusing on management reform to restore natural ecosystem function and maintain the coexistence of wild and hatchery salmon.

The genetic structure of chum salmon (Oncorhynchus keta Walbaum) populations inferred from the nucleotide variation of the mitochondrial DNA cytochrome b gene

The nucleotide sequences of a fragment of the mitochondrial DNA cytochrome b gene were determined in 12 chum salmon populations from the Russian Far East. The level of genetic diversity in the chum salmon populations from the Iturup Island, northern coast of the Sea of Okhotsk, and Anadyr' River was found to be higher than in the populations from Kamchatka and Sakhalin, which may be related to the history of their origin and dispersal. The proportions of intrapopulation genetic variability (F(ct)) and interpopulation genetic variability within the groups (F(sc)) account for 90.87 and 0.9%, respectively, and the intergroup component (F(st)) comprises 8.23%. The predominance of one haplotype, B1, which is common for all populations studied, and a low share of intergroup variability suggest the beginning of colonization by the species of the given region from a common source (group of founders) and a relatively recent time of divergence of the chum salmon populations from the region examined.

Perspectives on wild and hatchery salmon interactions at sea, potential climate effects on Japanese chum salmon, and the need for sustainable salmon fishery management reform in Japan

Pacific salmon (Oncorhynchus spp.) play an important role as a keystone species and provider of ecosystem services in the North Pacific ecosystem. We review our studies on recent production trends, marine carrying capacity, climate effects and biological interactions between wild and hatchery origin populations of Pacific salmon in the open sea, with a particular focus on Japanese chum salmon (O. keta). Salmon catch data indicates that the abundance of Pacific salmon increased since the 1976/77 ocean regime shift. Chum and pink salmon (O. gorbuscha) maintained high abundances with a sharp increase in hatchery-released populations since the late 1980s. Since the 1990s, the biomass contribution of hatchery returns to the total catch amounts to 50% for chum salmon, more than 10% for pink salmon, and less than 10% for sockeye salmon (O. nerka). We show evidence of density-dependence of growth and survival at sea and how it might vary across spatial scales, and we provide some new information on foraging plasticity that may offer new insight into competitive interactions. The marine carrying capacity of these three species is synchronized with long-term patterns in climate change. At the present time, global warming has positively affected growth and survival of Hokkaido populations of chum salmon. In the future, however, global warming may decrease the marine carrying capacity and the area of suitable habitat for chum salmon in the North Pacific Ocean. We outline future challenges for salmon sustainable conservation management in Japan, and recommend fishery management reform to sustain the hatchery-supported salmon fishery while conserving natural spawning populations.

The occurrence and run timing of naturally spawning chum salmon in northern Japan

Since the late 20th century, the biomass of Pacific salmon Oncorhynchus spp. has increased. Hokkaido, northern Japan, is one of the main areas of chum salmon O. keta production in the North Pacific and intensive hatchery programs support the recent high abundance. However, proper management of naturally spawning populations is necessary to conserve healthy stocks of this species. In 2008, we started a program to assess the naturally spawning chum salmon populations in Hokkaido. Of the total of approximately 1,500 rivers in Hokkaido, 238 rivers with lengths of longer than 8 km (excluding those rivers used for hatchery broodstock collection) were surveyed in 2008 and 2009. The number of non-enhanced rivers found to contain naturally reproducing chum salmon was 59 (31.4% of surveyed rivers) and 50 (37.6% of surveyed rivers) rivers in 2008 and 2009, respectively. Including the rivers where hatchery broodstock were collected and rivers shorter than 8 km that contain naturally spawning chum salmon, chum salmon ascended at least 191 and 175 rivers in Hokkaido in 2008 and 2009, respectively. Repeated foot surveys indicated that the run timings of naturally spawning chum salmon may be affected by coastal commercial fisheries. This study showed that naturally spawning chum salmon remain in many rivers in Hokkaido where hatchery programs have been intensively conducted.

Evidence for competition at sea between Norton Sound chum salmon and Asian hatchery chum salmon

Increasing production of hatchery salmon over the past four decades has led to concerns about possible density-dependent effects on wild Pacific salmon populations in the North Pacific Ocean. The concern arises because salmon from distant regions overlap in the ocean, and wild salmon populations having low productivity may compete for food with abundant hatchery populations. We tested the hypothesis that adult length-at-age, age-at-maturation, productivity, and abundance of a Norton Sound, Alaska, chum salmon population were influenced by Asian hatchery chum salmon, which have become exceptionally abundant and surpassed the abundance of wild chum salmon in the North Pacific beginning in the early 1980s. We found that smaller adult length-at-age, delayed age-at-maturation, and reduced productivity and abundance of the Norton Sound salmon population were associated with greater production of Asian hatchery chum salmon since 1965. Modeling of the density-dependent relationship, while controlling for other influential variables, indicated that an increase in adult hatchery chum salmon abundance from 10 million to 80 million adult fish led to a 72% reduction in the abundance of the wild chum salmon population. These findings indicate that competition with hatchery chum salmon contributed to the low productivity and abundance of Norton Sound chum salmon, which includes several stocks that are classified as Stocks of Concern by the State of Alaska. This study provides new evidence indicating that large-scale hatchery production may influence body size, age-at-maturation, productivity and abundance of a distant wild salmon population.

Intraspecific polymorphism of mitochondrial cytochrome b gene fragment of the chum salmon (Oncorhynchus Keta Walbaum) from the rivers of eastern Kamchatka and the northern coast of the Sea of Okhotsk

The nucleotide sequence of a gene fragment of cytochrome b (cytb) was determined, and data on the variability of this mtDNA region in chum salmon from certain populations on the northern coast of the Sea of Okhotsk and eastern Kamchatka populations were obtained. It was shown that the Kamchatka chum salmon population is characterized by the lowest values of nucleotide (π) and haplotype (h) diversity. The higher level of genetic diversity of the Sea of Okhotsk population is most likely due to the history of formation and distribution. Statistically significant (p < 0.001) genetic differences (Fst) between the studied groups of populations were found. The Okhotsk and Kamchatka chum salmon populations differ from the Canada chum salmon population in the structure of the cytb gene and the amino acid sequence of the studied fragment of this enzyme.

Single nucleotide polymorphisms across a species’ range: implications for conservation studies of Pacific salmon

Studies of the oceanic and near-shore distributions of Pacific salmon, whose migrations typically span thousands of kilometres, have become increasingly valuable in the presence of climate change, increasing hatchery production and potentially high rates of bycatch in offshore fisheries. Genetics data offer considerable insights into both the migratory routes as well as the evolutionary histories of the species. However, these types of studies require extensive data sets from spawning populations originating from across the species' range. Single nucleotide polymorphisms (SNPs) have been particularly amenable for multinational applications because they are easily shared, require little interlaboratory standardization and can be assayed through increasingly efficient technologies. Here, we discuss the development of a data set for 114 populations of chum salmon through a collaboration among North American and Asian researchers, termed PacSNP. PacSNP is focused on developing the database and applying it to problems of international interest. A data set spanning the entire range of species provides a unique opportunity to examine patterns of variability, and we review issues associated with SNP development. We found evidence of ascertainment bias within the data set, variable linkage relationships between SNPs associated with ancestral groupings and outlier loci with alleles associated with latitude.

Population structure of chum salmon Oncorhynchus keta in the Russian Far East, as revealed by microsatellite markers

Chum salmon populations in the Russian Far East have a complex multi-level genetic structure. A total of 53 samples (2446 fish) were grouped into five major regional clusters: the southern Kurils, eastern Sakhalin, southwestern Sakhalin, the Amur River, and a northern cluster. The northern cluster consists of chum salmon populations from a vast geographical region, including Chukotka, Kamchatka, and the continental coast of the Sea of Okhotsk. However, the degree of its genetic differentiation is low, 1.9%. In contrast, the southern population cluster exhibits much higher variation; for example, differentiation between chum salmon groups within Sakhalin Island reaches 4.6%, and the differentiation between Iturup Island and Sakhalin Island chum salmon is 7.7%. This suggests that southern populations of Asian chum salmon have a more ancient evolutionary history than northern populations. In contrast to the available data, our study indicates a great deviation of southwestern Sakhalin populations from other Sakhalin chum salmon. The Russian Far East chum salmon are genetically diverse and show statistically significant differentiation even within small geographic localities. This can be used to assign samples of unknown origins to definite local populations.

Impacts of supplementation: genetic diversity in supplemented and unsupplemented populations of summer chum salmon (Oncorhynchus keta) in Puget Sound (Washington, USA)

In supplementation programs, hatcheries employ wild-origin fish as brood stock and their offspring are allowed into wild spawning areas. Resource managers use supplementation to support imperiled salmonid populations, seeking to increase census size and possibly effective population size (Ne), while minimizing risks of genetic diversity loss and domestication from hatchery intervention. Here we document impacts of 5–10 years of supplementation on threatened summer-run chum salmon ( Oncorhynchus keta ) in Hood Canal (HC) and Strait of Juan de Fuca (SJF) in Washington State and compare them genetically with unsupplemented summer- and fall-run chum salmon from HC and South Puget Sound. Microsatellite allele frequencies identified four run-timing and geographic groups. HC and SJF summer chum salmon genetic relationships followed a metapopulation pattern of isolation by distance, similar to patterns prior to supplementation, suggesting that supplementation minimally impacted population structure. In most supplemented subpopulations, we detected no effects on diversity and Ne, but high variance in individual pairwise relatedness values indicated over-representation of family groups. In two subpopulations, hatchery impacts (decreased diversity and lower Ne) were confounded with extreme bottlenecks. Rebounds in census sizes in all subpopulations suggest that general survivorship has improved and that possible hatchery effects on genetic diversity will be overcome.

Spatiotemporal change in growth of two populations of Asian chum salmon in relation to intraspecific interaction

Spatiotemporal changes in growth patterns of chum salmon Oncorhynchus keta that returned to the Ishikari (Japan) and Namdae (Korea) rivers in 1984–1998 were investigated using scale analysis. Juvenile chum salmon from both populations left coastal marine areas after spring at a size of over 8 cm fork length (FL). In summer, juvenile salmon from the Namdae River entered the Okhotsk Sea at a larger FL than did Ishikari River juveniles. There were no significant differences in annual growth between populations of 1-, 2-, and 4-year-old fish. For 3-year-old fish, however, Namdae River salmon had significantly higher synchronous and sympatric growth than did Ishikari River salmon. Mean FL of adults was also larger in Namdae River salmon than in Ishikari River salmon. Analysis of covariance (ANCOVA) results showed (1) negative linear relations between FL and catch, (2) homogeneous slopes of those relations at regional and species levels, and (3) nonhomogeneous slopes at the population level, indicating that density-dependent effects on growth were most significant at this level. We concluded that growth of chum salmon was concurrently influenced by stronger effects of intrapopulation competition and weaker effects of inter- and intraspecific interactions in the Bering Sea.

Patterns of genetic diversity in population complexes of pacific chum salmon Oncorhynchus keta Walbaum, from Asia and America, inferred from allozyme polymorphism data

Based on the data of Russian and foreign researchers, a database, consisting of 100 allozyme-coding loci examined in 288 chum salmon populations from Asia and Northern America, was constructed. Using G-test, genetic heterogeneity of Asian population samples of chum salmon was evaluated. Correlations between the frequencies of major alleles and geographic latitude of the mouths of native rivers were estimated. Using the methods of Nei and Cavalli-Sforza and Edwards, for different local chum salmon stock groups the genetic distances at the number of polymorphic enzyme loci were determined. Analysis of these distances made it possible to evaluate the patterns of genetic diversity in regional population groups from the Russian Far East, Japan, and North America. The proportions of genetic variation at each hierarchical level, identified in accordance with the geographical positions of the populations, were estimated through partitioning of variation in Asian populations into within and between-population components. It was demonstrated that intraspecific genetic structure of chum salmon corresponded geographic subdivision into regional population groups.

Biological Impacts of the Elwha River Dams and Potential Salmonid Responses to Dam Removal

The Elwha River dams have disconnected the upper and lower Elwha watershed for over 94 years. This has disrupted salmon migration and reduced salmon habitat by 90%. Several historical salmonid populations have been extirpated, and remaining populations are dramatically smaller than estimated historical population size. Dam removal will reconnect upstream habitats which will increase salmonid carrying capacity, and allow the downstream movement of sediment and wood leading to long-term aquatic habitat improvements. We hypothesize that salmonids will respond to the dam removal by establishing persistent, self-sustaining populations above the dams within one to two generations. We collected data on the impacts of the Elwha River dams on salmonid populations and developed predictions of species-specific response dam removal. Coho (Oncorhynchus kisutch), Chinook (O. tshawytscha), and steelhead (O. mykiss) will exhibit the greatest spatial extent due to their initial population size, timing, ability to maneuver past natural barriers, and propensity to utilize the reopened alluvial valleys. Populations of pink (O. gorbuscha), chum (O. keta), and sockeye (O. nerka) salmon will follow in extent and timing because of smaller extant populations below the dams. The initially high sediment loads will increase stray rates from the Elwha and cause deleterious effects in the egg to outmigrant fry stage for all species. Dam removal impacts will likely cause a lag in recolonization and population rebuilding. These negative sediment effects will be locally buffered by the extent of functioning floodplain, and management attempts to minimize sediment impacts. Resident life forms of char (Salvelinus confluentus), rainbow trout (O. mykiss), and cutthroat (O. clarki) will positively interact with their anadromous counterparts resulting in a positive population level response.

Sex ratio control in pink salmon (Oncorhynchus gorbuscha and chum salmon (O. keta) populations: The possible causes and mechanisms of changes in the sex ratio

Long-term changes in the sex ratio have been studied in pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) populations of Kamchatka and Sakhalin. It has been demonstrated that these changes are an adaptation to population dynamics: an increase in the population size is accompanied by a shift towards a higher proportion of males; a decrease in population size, by a shift towards a higher proportion of females. The correspondence between morphological and molecular characters in populations of the two species has been analyzed in order to determine the mechanism of sex ratio control. In some pink salmon and chum salmon populations, there is a discrepancy between sex identifications based on morphological characters and molecular markers. This discrepancy is assumed to be accounted for by sex inversion mechanisms, which may be population- or region-specific. In two cases, it has been found that the sex ratio discrepancy in populations is related to the numbers of fish in subsequent generations. These findings suggest that sex inversion may be related to population size control.

Interregional differentiation of chum salmon from Sakhalin and South Kurils inferred from microsatellite markers

Variability at ten microsatellite loci was examined in wild and hatchery populations of chum salmon from the Sakhalin Island and Southern Kuril Islands, Iturup and Kunashir. Substantial genetic differences between Sakhalin and South Kurils chum salmon (the differentiation theta reached 6.0%) were revealed. Statistically significant differences between chum salmon from Iturup and that from Kunashir were demonstrated, as well as between the chum salmon populations from different rivers within the islands. It was shown that in different types of population comparisons, required different marker sets most informative were.

Differentiation of chum salmon Oncorhynchus keta Wallbaum populations as revealed with microsatellite and allozyme markers: A comparative study

The character and extent of population differentiation in chum salmon Oncorhynchus keta from Sakhalin and Iturup were comparatively studied with 10 microsatellite and 12 allozyme markers. It was demonstrated with the example of allozyme polymorphism at the EstD locus that the effect of an individual locus with one major allele is capable of distorting the total picture of population differentiation. Multiallelic microsatellites were more efficient in revealing the genetic structure of chum salmon populations at the levels of differences between regional populations and between the stocks of individual rivers of the same region.

Genetic diversity of Asian chum salmon Oncorhynchus keta (Salmonidae, Salmoniformes) and the dynamics of gene pools in Sakhalin populations under artificial reproduction

The estimates of genetic diversity in populations of chum salmon Oncorhynchus keta from different regions of Sakhalin Island, Iturup Island, and the Anadyr’ River were obtained on the basis of analysis of allozyme variability. These estimates together with our published earlier data on chum salmon from the Amur River basin and the rivers of the northern coast of the Sea of Okhotsk demonstrate pronounced regional genetic differentiation in the Asian part of the fish range. The intraregional level of interpopulation genetic diversity was maximum on Sakhalin Island (GST = 6.6%) and was small on Iturup Island (GST = 0.9%) and the northern coast of the Sea of Okhotsk (GST = 0.6%). Interpopulation genetic diversity of Sakhalin chum salmon was almost commensurable to the diversity of the whole pool of studied Asian populations (GST = 7.6%) and would be presented more completely in baselines assigned for genetic identification of mixed stocks. It was demonstrated that the character and degree of genetic differentiation between populations of chum salmon from the main hatcheries situated in different regions of the Sakhalin oblast and connected to one another by numerous transplantations of fertilized eggs did not change significantly during an approximately 20-year period of our observation, and this fact suggests low efficiency of such transplantations.

Number of Alleles as a Predictor of the Relative Assignment Accuracy of Short Tandem Repeat (STR) and Single‐Nucleotide‐Polymorphism (SNP) Baselines for Chum Salmon

AbstractShort tandem repeat (STR) markers, which exhibit many alleles per locus, are commonly used to assign fish to their populations of origin. Single‐nucleotide polymorphisms (SNPs), which have many technical advantages over STRs, typically exhibit only two alleles per locus. Simulation studies have indicated that the number of independent alleles is a good predictor of the accuracy of genetic markers for fishery applications. Extant STR baselines for salmon Oncorhynchus spp. contain hundreds of alleles, and it has been estimated that hundreds of SNP markers will need to be developed before the SNP baselines will be comparable to the STR baselines. We compared 15 STRs exhibiting 349 independent alleles with 61 SNPs exhibiting 66 independent alleles for accuracy in assigning individuals to closely related populations of chum salmon O. keta. The SNP baseline yielded slightly higher mean accuracies for proportional assignment and comparable accuracies for individual assignment. Based on the number of independent alleles in each baseline, the SNP baseline performed considerably better than the STR baseline. We suggest that this discrepancy is due to the fact that the simulation studies do not capture the impacts of the different strategies commonly employed for discovering and selecting STR and SNP markers.

Genetic Analysis of Asian Chum Salmon Populations Based on Microsatellite DNA Variation

We examined the genetic variability of Asian chum salmon (Oncorhynchus keta) populations using nuclear microsatellite (ms) DNA analysis with four polymorphic loci (OKM4, OKM5, OKM7, and OKM8) in 397 individuals from nine populations, including one in Korea, seven in Japan, and one in Russia. The msDNA gene diversity was highest in the Japanese populations, suggesting greater genetic variation in the populations in Japan than in populations in Korea and Russia. The pairwise <TEX>$F_{ST}$</TEX> estimates based on our msDNA data showed that the Korean population was genetically different from the Japanese and Russian populations, and there were higher <TEX>$F_{ST}$</TEX> estimates between Hokkaido and Honshu populations than between other population pairs. A neighbor-joining tree showed that the Korean population was distinct from two other clusters, representing the populations in Honshu and the populations in Hokkaido and Russia. These results suggest that the observed population genetic patterns of Asian chum salmon might be influenced by low or restricted gene flow.

Genetic diversity of north Okhotsk Sea chum salmon populations with natural and artificial reproduction

The variability of 32 enzyme loci was studied in chum salmon populations with different types of reproduction—natural, mixed, and artificial—in some Magadan Region rivers. Among the populations studied, the values of mean heterozygosity and allele number per locus did not differ significantly. We found evidence of definite temporal stability of the populations, and also found that their genetic variability was expressed only slightly but still remained in spite of periodic egg transplantations between rivers. Statistically significant spatial genetic differentiation of the populations accounted for 0.55 to 0.76% of the total variation and the mean inter-year differentiation accounted for 0.30% of the total. Significant temporal (seasonal) genetic subdivision was revealed in chum salmon of the Tauy River. The populations of the Okhotsk Sea coast are very similar genetically to the east Sakhalin populations. The industrial chum salmon population founded and reproduced artificially in the Kulkuty River preserves the genetic similarity of the donor Yama River chum salmon. In the industrial population, we observed a tendency toward reduction of genetic variation over time. The contribution of the Yama population to the gene pool of the Ola chum salmon, (both by natural reproduction and by farming) is small in spite of many large-scale transplantations. However, the consequences of those transplantations are revealed by means of linkage disequilibrium analysis.