Search

The Japanese wild population of the medaka fish (Oryzias latipes species complex) comprises two genetically distinct groups, the Northern and the Southern Populations, with boundary populations having a unique genotype. It is thought that the boundary populations have been formed through introgressive hybridization between the two groups, because they are fixed with the Northern alleles at two allozymic loci, with the Southern alleles at two other loci, and have a unique allele at one locus. In this study, we examined the genetic population structure of the boundary populations using genome-wide single nucleotide polymorphism (SNP) data. Most SNPs of the Toyooka population, a typical boundary population, were shared with the Northern Population, some were shared with the Southern Population, and the remaining SNPs were unique to this population, suggesting that the boundary populations originated and diverged from the Northern Population. Further analyses of different populations using SNPs at eight genomic loci indicated that the boundary populations at different locations share similar genomic constitutions, and can be genetically distinguished from typical Northern Populations by unique SNPs. In addition, the boundary populations in the Maruyama River Basin had Northern mitochondrial DNA (mtDNA), while others, from the Fukuda and Kishida River Basins and from the Kumihama Bay area, had Southern mtDNA. These findings suggested that the boundary populations originated from the Northern Population, and then their genomes diverged as a result of geographical isolation, followed by mtDNA introgression from the Southern Population that occurred independently in some populations.

Medaka (Oryzias latipes) is a small freshwater teleost fish that serves as a model vertebrate organism in various fields of biology including development, genetics, toxicology and evolution. The recent completion of the medaka genome sequencing project has promoted the use of medaka as a comparative and complementary material for research on other vertebrates such as zebrafish, sticklebacks, mice, and humans. The Japanese government has supported the development of Medaka Bioresources since 2002. The second term of the Medaka Bioresource Project started in 2007. The National Institute for Basic Biology and Niigata University were selected as the core organizations for this project. More than 400 strains including more than 300 spontaneous and induced mutants, 8 inbred lines, 21 transgenic lines, 20 medaka-related species and 66 wild stock lines of medaka are now being provided to the scientific community and educational non-profit organizations. In addition to these live fish, NBRP Medaka is also able to provide cDNA/EST clones such as full-length cDNA and BAC/fosmid clones covering 90% of the medaka genome. All these resources can be found on the NBRP Medaka website (http://shigen.lab.nig.ac.jp/medaka/), and users can order any resource using the shopping cart system. We believe these resources will facilitate the further use of medaka and help to promote new findings for this vertebrate species.

Teleosts comprise more than half of all vertebrate species and have adapted to a variety of marine and freshwater habitats. Their genome evolution and diversification are important subjects for the understanding of vertebrate evolution. Although draft genome sequences of two pufferfishes have been published, analysis of more fish genomes is desirable. Here we report a high-quality draft genome sequence of a small egg-laying freshwater teleost, medaka (Oryzias latipes). Medaka is native to East Asia and an excellent model system for a wide range of biology, including ecotoxicology, carcinogenesis, sex determination and developmental genetics. In the assembled medaka genome (700 megabases), which is less than half of the zebrafish genome, we predicted 20,141 genes, including approximately 2,900 new genes, using 5'-end serial analysis of gene expression tag information. We found single nucleotide polymorphisms (SNPs) at an average rate of 3.42% between the two inbred strains derived from two regional populations; this is the highest SNP rate seen in any vertebrate species. Analyses based on the dense SNP information show a strict genetic separation of 4 million years (Myr) between the two populations, and suggest that differential selective pressures acted on specific gene categories. Four-way comparisons with the human, pufferfish (Tetraodon), zebrafish and medaka genomes revealed that eight major interchromosomal rearrangements took place in a remarkably short period of approximately 50 Myr after the whole-genome duplication event in the teleost ancestor and afterwards, intriguingly, the medaka genome preserved its ancestral karyotype for more than 300 Myr.

We examined the gene sequences of mitochondrial cytochrome b (cyt b) in two Japanese wood mouse species, Apodemus speciosus (n = 89) and A. argenteus (n = 46), which are distributed on the four main islands of Japan (Hokkaido, Honshu, Shikoku, and Kyushu) and on the small islands surrounding them. Apodemus speciosus, the larger of the two species, showed substantial genetic variation, with a maximum of 3% sequence divergence, and remarkable phylogenetic subdivision with two major clades. One clade represents haplotypes from a central region, including Honshu, Shikoku, Kyushu, and their adjacent islands; the other clade includes haplotypes from Hokkaido and the peripheral islands, forming four subclades: a) Hokkaido, b) Sado Island, c) Satsunan Islands, and d) the Izu Islands. Sequence divergence among the four subclades was 1.0 to 1.5%, implying that A. speciosus colonized these geographic regions 0.2 to 0.3 million years ago, assuming a substitution rate of 2.4% per million years. The population on the Izu Islands has preserved haplotypes that are distinct from those in any other region, providing good evidence for the natural colonization of the volcanic islands of the Izu Islands. The cyt b sequence variation had no relation to the karyotypic dimorphism for the eastern (2n = 48) and western (2n = 46) geographic groups, between which a strict border exists at central Honshu. On the other hand, Apodemus argenteus, the smaller of the two species, showed a similar level of sequence divergence (maximum of 3%) but no substantial geographic differentiation: populations in Hokkaido, Sado, and Yakushima shared similar haplotypes with each of the central populations, suggesting that genetic exchanges occurred among the localities in the last 0.15 million years. The apparent genetic structure of the mitochondrial DNA found in the A. speciosus population might be caused solely by long-term existence in insular regions, presumably due to ecological superiority relative to A. argenteus.

We conducted a polymerase chain reaction--restriction fragment length polymorphism (PCR-RFLP) analysis of the mitochondrial cytochrome b gene to elucidate the detailed genetic population structure of Japanese wild populations of medaka, Oryzias latipes. The analysis of 1,225 specimens collected from 303 sites identified 67 mitotypes. Subsequently we determined the nucleotide sequences of the complete cytochrome b gene (1141-bp) to clarify the phylogenetic relationships among mitotypes. The phylogenetic tree based on nucleotide sequences indicated three major clades (A, B and C) that differed by 11.3-11.8%, corresponding to three clusters previously identified by RFLP analysis of entire mitochondrial DNAs. The geographic distribution of mitotypes in clades A and B was fully concordant with the Northern and Southern Populations defined by allozymes. Clade A could be subdivided into three subclades and clade B into eleven, with sequence divergences among subclades of 1.3-5.8%. Each distribution of mitotypes in subclades roughly corresponded to that of mtDNA haplotypes in subclusters previously identified. Mitotypes in clade C were found only in the Kanto district. The phylogenetic relationships and the estimated divergence times suggest that three Japanese clades originated from a common ancestor and were separated during the Pliocene, and that the regional differentiation of subclades was closely connected with the geological history of the Quaternary. This study has also demonstrated the possibility of artificial disturbance of natural distribution especially in the Kanto district and the superior efficacy of PCR-RFLP analysis as a simple method for detecting genetic variation and artificial gene flow of medaka.

Taxonomic analysis has previously revealed that the species of moles that inhabit Japan are characterized by exceptional species richness and a high level of endemism. Here, we focused on the evolutionary history of the four Japanese mole species of the genera Euroscapter and Mogera, examining mitochondrial cytochrome b (cyt b) gene sequences and comparing them with those of continental Mogera wogura (Korean and Russian populations), M. insularis from Taiwan, and Talpa europaea and T. altaica from the western and central Eurasian continent, respectively. Our data support the idea that in a radiation center somewhere on the Eurasian continent, a parental stock evolved to modern mole-like morph and radiated several times intermittently during the course of the evolution, spreading its branches to other peripheral geographic domains at each stage of the radiation. Under this hypothesis, the four lineages of Japanese mole species, E. mizura, M. tokudae, M. imaizumii, and M. wogura, could be explained to have immigrated to Japan in this order. Mogera wogura and M. imaizumii showed substantial amounts of geographic variation and somewhat complicated distributions of the cyt b gene types. These intraspecific variations are likely to be associated with the expansion processes of moles in the Japanese Islands during the Pleistocene glacial ages.

An analysis by restriction endonuclease digestion of ribosomal DNA (rDNA) was carried out in natural populations of Apodemus speciosus, a field mouse that is endemic to Japan. Two restriction sites, the EcoRI (E3) and DraI (D4) sites, in the nontranscribed spacer region downstream from the gene for 28S RNA showed polymorphism within and between individuals in the populations from the Japanese main islands. By contrast, populations from the small adjoining islands which are thought to have separated from the main islands 1-2 x 10(4) years ago showed relatively low levels of polymorphism within and between individuals, i.e., one of the polymorphic bands in the case of each enzyme was predominant in these populations, irrespective of the variants. These results indicate that the rate of fixation of site variations depends on population size and that the direction of fixation is random. Furthermore, each polymorphic restriction site seems to be fixed independently.