Shunpei Sato

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.

Genetic stock identification of chum salmon in the Bering Sea and North Pacific Ocean using mitochondrial DNA microarray.

A newly developed DNA microarray was applied to identify mitochondrial (mt) DNA haplotypes of more than 2200 chum salmon in the Bering Sea and North Pacific Ocean in September 2002 and also 2003, when the majority of maturing fish were migrating toward their natal river. The distribution of haplotypes occurring in Asian and North American fish in the surveyed area was similar in the 2xa0years. A conditional maximum likelihood method for estimation of stock compositions indicated that the Japanese stocks were distributed mainly in the north central Bering Sea, whereas the Russian stocks were mainly in the western Bering Sea. The North American stocks were abundant in the North Pacific Ocean around the Aleutian Islands. These results indicate that the Asian and North American stocks of chum salmon are nonrandomly distributed in the Bering Sea and the North Pacific Ocean, and further the oligonuleotide DNA microarray developed by us has a high potential for identification of stocks among mixed ocean aggregates of high-seas chum salmon.

Activity of the pituitary–gonadal axis is increased prior to the onset of spawning migration of chum salmon

SUMMARY The activity of the pituitary–gonadal axis (PG axis) in pre-migratory and homing chum salmon was examined because endocrine mechanisms underlying the onset of spawning migration remain unknown. Pre-migratory fish were caught in the central Bering Sea in June, July and September 2001, 2002 and 2003, and in the Gulf of Alaska in February 2006. They were classified into immature and maturing adults on the basis of gonadal development. The maturing adults commenced spawning migration to coastal areas by the end of summer, because almost all fish in the Bering Sea were immature in September. In the pituitaries of maturing adults, the copy numbers of FSHβ mRNA and the FSH content were 2.5- to 100-fold those of the immature fish. Similarly, the amounts of LHβ mRNA and LH content in the maturing adults were 100- to 1000-fold those of immature fish. The plasma levels of testosterone, 11-ketotestosterone and estradiol were higher than 10 nmol l–1 in maturing adults, but lower than 1.0 nmol l–1 in immature fish. The increase in the activity of the PG-axis components had already initiated in the maturing adults while they were still in the Gulf of Alaska in winter. In the homing adults, the pituitary contents and the plasma levels of gonadotropins and plasma sex steroid hormones peaked during upstream migration from the coast to the natal hatchery. The present results thus indicate that the seasonal increase in the activity of the PG axis is an important endocrine event that is inseparable from initiation of spawning migration of chum salmon.

Microsatellite Stock Identification of Chum Salmon on a Pacific Rim Basis

Abstract The variation at 14 microsatellite loci was analyzed for more than 53,000 chum salmon Oncorhynchus keta from 381 locations ranging from Korea to Washington State and used to estimate the stock composition of mixed-stock fishery samples. High resolution of the samples was possible, the number of reporting groups being distributed as follows: Korea = 1, Japan = 7, Russia = 8, Alaska = 15, Canadian Yukon River = 5, British Columbia = 16, and Washington State = 5. The number of alleles observed at a locus was related to the power of the locus in providing accurate estimates of the stock composition of single population mixtures. Approximately 800 alleles were observed across the 14 microsatellites, providing the basis for high-resolution stock identification. Analysis of known-origin samples indicated that accurate regional estimates of stock composition were obtained. The estimated stock compositions of mixed-fishery samples from coastal Japan, the Sea of Okhotsk, the western Pacific Ocean, the Gulf...

Population structure and stock identification of chum salmon Oncorhynchus keta from Japan determined by microsatellite DNA variation

Variation at 14 microsatellite loci was surveyed in 26 chum salmon Oncorhynchus keta populations from Japan, one population from West Kamchatka and three populations from North America to determine population structure. Microsatellites were then applied to estimate stock composition of chum salmon in mixed-stock fisheries. The genetic differentiation index (Fst) over all populations and loci was 0.031, with individual locus values ranging from 0.010 to 0.081. Seven regional populations were observed in Japanese chum salmon, with late-run populations from the Pacific Coast of Honshu the most distinct. Japanese populations displayed greater genetic diversity than did those in North America. Transplantation history in some Japanese river populations influenced their present genetic characteristics. Analysis of simulated mixtures from fishery sampling suggested that accurate and precise regional estimates of stock composition should be produced when the microsatellites were used to estimate stock compositions. Stock compositions for a 2005 sample of maturing, migrating chum salmon off the north-west coast of Hokkaido near the border of the Sea of Japan and the Sea of Okhotsk indicated that this region may be a migration corridor for Hokkaido populations from the Sea of Japan coast. Microsatellites have the ability to provide fine-scale resolution of stock composition in Japanese coastal fisheries.

Microsatellite Identification of Canadian Sockeye Salmon Rearing in the Bering Sea

Abstract The stock composition of sockeye salmon Oncorhynchus nerka caught in the central Bering Sea in the summer of 2009 was estimated to evaluate migration patterns of salmon of Canadian origin, which have not been demonstrated previously to rear in the Bering Sea. The variation at 14 microsatellites was analyzed for 450 immature sockeye salmon, and a baseline of 387 populations from Japan, Russia, Alaska, Canada, and Washington State was used to determine the stock composition of the fish sampled. Sockeye salmon originating from Alaska were the most abundant in the catch, comprising 86.0% of all sockeye salmon caught, the catch being dominated by sockeye salmon of Bristol Bay origin. Russian-origin sockeye salmon accounted for 10.2% of the catch, while Canadian-origin sockeye salmon accounted for 3.8% of the catch. Salmon from Canada were estimated to originate from the Fraser River, Rivers Inlet (Owikeno Lake), the Skeena River (Babine Lake), the Stikine River, and the Alsek River, British Columbia. ...

Genetic Structure and Diversity of Japanese Chum Salmon Populations Inferred from Single-Nucleotide Polymorphism Markers

AbstractWe estimated the genetic structure and diversity of Japanese Chum Salmon Oncorhynchus keta populations using single-nucleotide polymorphism (SNP) markers to support the management and assessment of the Japanese salmon hatchery program. A total of 5,571 individuals from 57 Japanese Chum Salmon populations were genotyped with 52 markers. A neighbor-joining tree, principal coordinate analysis, analysis of molecular variance, and average pairwise FST values indicated the existence of eight regional groups, six in Hokkaido and two in Honshu. Weak but significant isolation by distance was found within the populations of Hokkaido and the Pacific Ocean coast of Honshu. These results suggest that the genetic differentiation among the eight regional groups is small but distinct and occurred through low or restricted gene flow. Furthermore, our results also suggest the persistence of the historical genetic structure (or remnants of it) in extant populations in Japan despite the operation of a hatchery progra...

Nonrandom distribution of chum salmon stocks in the Bering Sea and the North Pacific Ocean estimated using mitochondrial DNA microarray

More than 1,000 age-identified chum salmon Oncorhynchus keta collected at 23 stations in the Bering Sea and the North Pacific Ocean in June to July 2003 were used to estimate their origin of stocks using a DNA microarray developed for analyzing the mitochondrial (mt)DNA haplotypes. The observed haplotype distribution was nearly the same as that reported previously for fish collected in September 2002 and 2003 in the present surveyed areas. A conditional maximum-likelihood method for estimation of stock compositions indicated that the Japanese stocks mainly distributed in north central Bering Sea, whereas the Russian stocks were mainly in western Bering Sea. The North American stocks were abundant in eastern Bering Sea and around the Aleutian Islands. Such an area-specific stock composition was not significantly different between mature and immature fish. Thus, the combined results of 2xa0years suggest that the distribution of chum salmon is nonrandom in the surveyed areas in summer and autumn, and that fish of the same origin migrate together to the same area irrespective of age.

Genetic variation of Japanese pink salmon populations inferred from nucleotide sequence analysis of the mitochondrial DNA control region

To estimate genetic variation and structure of pink salmon (Oncorhynchus gorbuscha) populations in Hokkaido, Japan, we analyzed the nucleotide sequence of about 500xa0bp in a variable portion of the 5′ end of the mitochondrial DNA control region for even- and odd-year broodlines. Sixty-seven haplotypes were detected in the examined individuals. Among these, 25 haplotypes were unique to the even-year broodline, while another 30 haplotypes were unique to the odd-year broodline. Five and three length-heteroplasmic haplotypes were detected in the even-year broodline and odd-year broodline, respectively. The distribution pattern of the 67 haplotypes was different among populations between both broodlines, while not different among populations within the same broodline. The haplotype and nucleotide diversity were higher for even-year broodline populations than for odd-year broodline populations, suggesting greater genetic variation within populations of the even-year broodline. Analysis of molecular variance and pairwise fixation index estimates also demonstrated strong genetic differentiation between even- and odd-year broodlines, although there was no genetic differentiation among populations within the same year broodline. The neutrality tests and mismatch distribution analysis indicate that the demographic history of pink salmon in Japan differs between even- and odd-year populations. Together, these results suggest strong reproductive isolation between the even- and odd-year broodlines of pink salmon, and high gene flow with broodlines due to straying.

Artificial and natural cross breeding between Atlantic salmon and salmonids currently present in Japan

We evaluated the potential for hybridization between Atlantic salmon and salmonids currently present in Japan. We performed artificial and natural crosses and tested for hybridization using short interspersed elements. We documented the occurrence of hybrids and gynogenesis following artificial crossing. However, the survival rate of these offspring was low (<2xa0% to the fry stage). We were unable to obtain viable offspring from natural crosses of Atlantic salmon and chum salmon or masu salmon. Our results suggest that there is little risk of hybridization between Atlantic salmon and salmonids that are currently present in the wild in Japan. Furthermore, our results suggest that gynogenesis may occur naturally.