1. Whole-Genome Sequencing of Six Mauritian Cynomolgus Macaques (Macaca fascicularis) Reveals a Genome-Wide Pattern of Polymorphisms under Extreme Population Bottleneck.

    Genome Biology and Evolution 7(3):821 (2015) PMID 25805843

    Cynomolgus macaques (Macaca fascicularis) were introduced to the island of Mauritius by humans around the 16th century. The unique demographic history of the Mauritian cynomolgus macaques provides the opportunity to not only examine the genetic background of well-established nonhuman primates fo...
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  2. Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.

    Genome Biology and Evolution 6(9):2527 (2014) PMID 25364802 PMCID PMC4202324

    Many studies on conserved noncoding sequences (CNSs) have found that CNSs are enriched significantly in regulatory sequence elements. We conducted whole-genome analysis on plant CNSs to identify lineage-specific CNSs in eudicots, monocots, angiosperms,and vascular plants based on the premise tha...
  3. Lineage-specific conserved noncoding sequences of plant genomes: their possible role in nucleosome positioning.

    Genome Biology and Evolution 6(9):2527 (2014) PMID 25364802 PMCID PMC4202324

    Many studies on conserved noncoding sequences (CNSs) have found that CNSs are enriched significantly in regulatory sequence elements. We conducted whole-genome analysis on plant CNSs to identify lineage-specific CNSs in eudicots, monocots, angiosperms,and vascular plants based on the premise tha...
  4. An integrative evolution theory of histo-blood group ABO and related genes.

    Scientific reports 4:6601 (2014) PMID 25307962

    The ABO system is one of the most important blood group systems in transfusion/transplantation medicine. However, the evolutionary significance of the ABO gene and its polymorphism remained unknown. We took an integrative approach to gain insights into the significance of the evolutionary proces...
  5. An integrative evolution theory of histo-blood group ABO and related genes.

    Scientific reports 4:6601 (2014) PMID 25307962

    The ABO system is one of the most important blood group systems in transfusion/transplantation medicine. However, the evolutionary significance of the ABO gene and its polymorphism remained unknown. We took an integrative approach to gain insights into the significance of the evolutionary proces...
  6. A hypervariable STR polymorphism in the CFI gene: southern origin of East Asian-specific group H alleles.

    Legal Medicine 15(5):239 (2013) PMID 23688582

    Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a deeper ant...
  7. A hypervariable STR polymorphism in the CFI gene: Southern origin of East Asian-specific group H alleles

    Legal Medicine 15(5):239 (2013)

    Previous studies of four populations revealed that a hypervariable short tandem repeat (iSTR) in intron 7 of the human complement factor I (CFI) gene on chromosome 4q was unique, with 17 possible East Asian-specific group H alleles observed at relatively high frequencies. To develop a ...
  8. Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes.

    Journal of Human Genetics 58(7):446 (2013) PMID 23739127

    Changes in gene expression have been proposed to have an important role in the evolutionary changes in phenotypes. Interspecific changes in gene expression can result not only from genetic changes in regulatory regions but also from epigenetic changes in such regions. Here we report the identifi...
  9. Regional DNA methylation differences between humans and chimpanzees are associated with genetic changes, transcriptional divergence and disease genes.

    Journal of Human Genetics 58(7):446 (2013) PMID 23739127

    Changes in gene expression have been proposed to have an important role in the evolutionary changes in phenotypes. Interspecific changes in gene expression can result not only from genetic changes in regulatory regions but also from epigenetic changes in such regions. Here we report the identifi...
  10. The PNarec method for detection of ancient recombinations through phylogenetic network analysis

    Molecular Phylogenetics and Evolution 66(2):507 (2013)

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  11. The PNarec method for detection of ancient recombinations through phylogenetic network analysis.

    Molecular Phylogenetics and Evolution 66(2):507 (2013) PMID 23022140

    Recombinations are known to disrupt bifurcating tree structure of gene genealogies. Although recently occurred recombinations are easily detectable by using conventional methods, recombinations may have occurred at any time. We devised a new method for detecting ancient recombinations through ph...
  12. The PNarec method for detection of ancient recombinations through phylogenetic network analysis.

    Molecular Phylogenetics and Evolution 66(2):507 (2013) PMID 23022140

    Recombinations are known to disrupt bifurcating tree structure of gene genealogies. Although recently occurred recombinations are easily detectable by using conventional methods, recombinations may have occurred at any time. We devised a new method for detecting ancient recombinations through ph...
  13. Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain.

    Genome Biology and Evolution 5(1):140 (2013) PMID 23267051 PMCID PMC3595034

    Vertebrate genomes include gene regulatory elements in protein-noncoding regions. A part of gene regulatory elements are expected to be conserved according to their functional importance, so that evolutionarily conserved noncoding sequences (CNSs) might be good candidates for those elements. In ...
  14. Vertebrate paralogous conserved noncoding sequences may be related to gene expressions in brain.

    Genome Biology and Evolution 5(1):140 (2013) PMID 23267051 PMCID PMC3595034

    Vertebrate genomes include gene regulatory elements in protein-noncoding regions. A part of gene regulatory elements are expected to be conserved according to their functional importance, so that evolutionarily conserved noncoding sequences (CNSs) might be good candidates for those elements. In ...
  15. Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders.

    Genome Biology and Evolution 5(12):2330 (2013) PMID 24259317 PMCID PMC3879966

    Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein-coding gene regulatory functions. We examined the abundance and genomic distribution of CNSs in four mammalian orders: primates, rodents, carnivores, and cetartiodactyls. We defined the two thres...
  16. Admixture patterns and genetic differentiation in negrito groups from West Malaysia estimated from genome-wide SNP data.

    Human Biology 85(1-3):173 (2013) PMID 24297225

    Southeast Asia houses various culturally and linguistically diverse ethnic groups. In Malaysia, where the Malay, Chinese, and Indian ethnic groups form the majority, there exist minority groups such as the "negritos" who are believed to be descendants of the earliest settlers of Southeast Asia. ...
  17. Heterogeneous tempo and mode of conserved noncoding sequence evolution among four mammalian orders.

    Genome Biology and Evolution 5(12):2330 (2013) PMID 24259317 PMCID PMC3879966

    Conserved noncoding sequences (CNSs) of vertebrates are considered to be closely linked with protein-coding gene regulatory functions. We examined the abundance and genomic distribution of CNSs in four mammalian orders: primates, rodents, carnivores, and cetartiodactyls. We defined the two thres...
  18. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations.

    Journal of Human Genetics 57(12):787 (2012) PMID 23135232

    The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes an...
  19. The history of human populations in the Japanese Archipelago inferred from genome-wide SNP data with a special reference to the Ainu and the Ryukyuan populations.

    Journal of Human Genetics 57(12):787 (2012) PMID 23135232

    The Japanese Archipelago stretches over 4000 km from north to south, and is the homeland of the three human populations; the Ainu, the Mainland Japanese and the Ryukyuan. The archeological evidence of human residence on this Archipelago goes back to >30 000 years, and various migration routes an...
  20. Evolutionary history of continental southeast Asians: "early train" hypothesis based on genetic analysis of mitochondrial and autosomal DNA data.

    Molecular Biology and Evolution 29(11):3513 (2012) PMID 22729749

    The population history of the indigenous populations in island Southeast Asia is generally accepted to have been shaped by two major migrations: the ancient "Out of Africa" migration ∼50,000 years before present (YBP) and the relatively recent "Out of Taiwan" expansion of Austronesian agricultur...