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The Japanese scallop (Mizuhopecten yessoensis) is one of the main fishery products in Japan, but with the expansion of culture operations of the Japanese scallop, various problems have been encountered including high mortality, poor growth, poor seed production, and so on. Moreover, there is concern that many years of cultivation may have affected the genetic structure of the scallop population. To approach these problems and concerns, we developed microsatellite markers as a molecular tool for population genetic studies. By using 4 microsatellite markers as well as a mitochondrial marker, we investigated the genetic structure of samples from the islands of Hokkaido (14 populations) and Honshu (Tohoku, 3 populations) in Japan, and south Primorye (4 populations) in Russia. All the populations sampled had high genetic diversity (average expected heterozygosity, 0.7011 to 0.7622; haplotype diversity, 0.6090 to 0.8848), and almost all showed a tendency of homozygote excess, which was significant in 2 populations. Hierarchical analysis of molecular variance tests based on the microsatellite and mitochondrial markers indicated that the 3 geographic regions were genetically divergent from one another, with little evidence of divergence within regions. Homogeneity in allele frequency distributions between natural and cultured scallops and allele frequency stability over a period of 2 decades indicated that the culturing operations have probably not had a substantial effect on the genetic structure of the populations.

Seven segments of mitochondrial DNA (mtDNA), comprising 97% of the mitochondrial genome, were amplified by polymerase chain reaction (PCR) and examined for restriction site variation using 13 restriction endonucleases in three species of Pacific salmon: pink (Oncorhynchus gorbuscha), chum (O. keta) and sockeye (O. nerka) salmon. The distribution of variability across the seven mtDNA segments differed substantially among species. Little similarity in the distribution of variable restriction sites was found even between the mitochondrial genomes of the even- and odd-year broodlines of pink salmon. Significantly different levels of nucleotide diversity were detected among three groups of genes: six NADH-dehydrogenase genes had the highest; two rRNA genes had the lowest; and a group that included genes for ATPase and cytochrome oxidase subunits, the cytochrome b gene, and the control region had intermediate levels of nucleotide diversity. Genealogies of mtDNA haplotypes were reconstructed for each species, based on the variation in all mtDNA segments. The contributions of variation within different segments to resolution of the genealogical trees were compared within each species. With the exception of sockeye salmon, restriction site data from different genome segments tended to produce rather different trees (and hence rather different genealogies). In the majority of cases, genealogical information in different segments of mitochondrial genome was additive rather than congruent. This finding has a relevance to phylogeographic studies of other organisms and emphasizes the importance of not relying on a limited segment of the mtDNA genome to derive a phylogeographic structure.

Charrs of the genus Salvelinus (including Salvethymus) represent a monophyletic group of salmo nid fishes that diverged from the common ancestor without subdivision into subgenera. The phylogenesis of the genus is characterized by four cycles of mitochondrial genome divergence. The first one, belonging to the Late Miocene-the border between Miocene and Pliocene (6 to 4 million years ago)-was associated with the consecutive divergence of the S. fontinalis, S. namaycush, S. levanidovi, and S. leucomaenis basal branches. Two divergence events, including separation of the ancestral lineage of Western Pacific group of S. m. krascheninnikovi and the following segregation of the common ancestor into two mitochondrial phyla, happened within the period of 3 to 2 million years ago. The next cycle is attributed to the time interval of about 1 million years ago and includes the divergence of both phyla. In one phylum, a relatively quick isolation of Arctic and Eastern Pacific phylogroups, along with the divergence of the latter phylogroup into S. confluentus and S. m. lordi lineages, took place. At the same time, the second phylum diverged into the S. m. malma and S. alpinus phylogenetic groups. At the final stage (Middle to Late Pleistocene), differentiation of the taxa within the phylogenetic groups took place.

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-Phylogenetic analysis of charrs of the genus Salvelinus was performed using PCR-RFLP analysis of mitochondrial DNA (mtDNA). Three fragments of mtDNA (ND1/ND2, ND5/ND6 and Cyt b/D-loop) were amplified by PCR and examined for restriction site variation using 13 restriction endonucleases. Analysis of 313 sites of over 7672 bp of charr mtDNA was conducted. Six phylogenetic lineages of the mtDNA were revealed, corresponding to six separate charr taxa: Salvelinus leucomaenis Pallas; Salvelinus levanidovi Chereshnev, Skopetz & Gudkov; Salvelinus taranetzi Kaganovsky; Salvelinus malma krascheninnikovi Taranetz; Salvelinus malma malma Walbaum and Salvelinus alpinus alpinus. The Levanidov (S. levanidovi) and white-spotted (S. leucomaenis) charrs represented the most divergent lineages. These are probably closest to a common ancestor of the genus. Salvelinus taranetzi was the next divergent lineage. Salvelinus malma krascheninnikovi was placed between S. leucomaenis and S. taranetzi. Salvelinus malma malma and S. a. alpinus were sister taxa, and were on the last branch to diverge. The divergence between S. m. malma and S. a. alpinus inferred from mtDNA nucleotide sequences was 1.1%; between S. m. malma and S. taranetzi 2.8%; between S. m. malma and S. m. krascheninnikovi 4%; between S. taranetzi, S. m. krascheninnikovi and S. a. alpinus 2.8%. Salvelinus levanidovi and S. leucomaenis were almost equally remote from the other charrs by some 9% and 7%, respectively. The extent of genetic differences between the northern S. m. malma populations and the European S. a. alpinus populations indicates that they diverged recently. The existence of many putative charr species with different divergence times in northeastern Asia suggests that this region may be one of the centres of speciation of the genus Salvelinus.

A survey of mtDNA variation among populations of chum salmon Oncorhynchus keta around the Pacific Rim revealed four large population groups: Rim of the Sea of Japan, the Rim of the Okhotsk Sea and West Bering Sea, North‐west Alaska and Gulf of Alaska. The observed population structure appears to reflect isolation by distance with limited gene flow between regions and larger amounts of gene flow between populations within these four regions.