文献一覧: Shoji KAWAMURA (著者)

1 0 0 0 OA Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders

著者: KAE KOGANEBUCHI TAKAFUMI KATSUMURA SHIGEKI NAKAGOME HAJIME ISHIDA SHOJI KAWAMURA HIROKI OOTA THE ASIAN ARCHIVAL DNA REPOSITORY CONSORTIUM
出版者: The Anthropological Society of Nippon
雑誌: Anthropological Science (ISSN:09187960)
巻号頁・発行日: vol.120, no.3, pp.199-208, 2012 (Released:2012-12-21)
参考文献数: 40
被引用文献数: 15 18

Understanding the phylogenetic relationship between Hokkaido Ainu and Ryukyu islanders has been of great interest in human genetics, archaeology, and anthropology. We examined short tandem repeat (STR) polymorphisms on autosomes and Y-chromosomes for Ainu, and compared this with data from Ryukyu islanders. A statistical test for nine autosomal (A-STR) loci gave no indication that the Ainu had experienced any bottleneck effect(s). The genetic distances (Rst) based on the A-STR data consistently showed substantial differentiation between the Ainu and all other populations. The haplotype analysis based on Y-chromosomal (Y-STR) data revealed 10 distinct haplotypes found in 19 Ainu males; 7 out of 10 were Ainu-specific haplotypes, whereas two haplotypes were shared with two males from main-island Okinawa and Miyako island, respectively, indicating a strong, close relationship between the Ainu and the Ryukyu islanders. The time to the most recent common ancestor of the Y-lineages obtained in the Ainu and the Ryukyu islanders was estimated to be 37745 years ago. Overall, the A-STR showed uniqueness of the Ainu, and the Y-STR haplotypes revealed strong evidence for a link between the two indigenous populations of the Hokkaido and the Ryukyu islands.

2023-06-12 19:03:54
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1 0 0 0 OA Genetic variation of olfactory receptor gene family in a Japanese population

著者: MUHAMMAD SHOAIB AKHTAR RYUICHI ASHINO HIROKI OOTA HAJIME ISHIDA YOSHIHITO NIIMURA KAZUSHIGE TOUHARA AMANDA D. MELIN SHOJI KAWAMURA
出版者: The Anthropological Society of Nippon
雑誌: Anthropological Science (ISSN:09187960)
巻号頁・発行日: pp.211024, (Released:2022-01-20)
被引用文献数: 3

The olfactory receptor (OR) gene family is comprised of hundreds of intact and disrupted genes in humans. The compositions and copy number variation (CNV) of disrupted and intact OR genes among individuals is expected to cause variation in olfactory perception. However, little is known about OR genetic variation in many human populations. In this study, we used targeted capture enrichment and massive parallel short-read sequencing methods to examine genetic variation of OR genes, as well as of neutral genome regions as references, for 69 anonymized unrelated Japanese individuals. The capture probes were designed for 398 intact OR genes in the human reference genome hg38, and 85 neutral references. Probes were also designed for four unannotated and 99 ‘nearly-intact’ (hg38-pseudo) OR genes in hg38 and 53 chimpanzee OR genes in the Pantro3.0 genome database with no orthologs in hg38. All the hg38 OR genes and one Pantro 3.0 OR gene were retrieved. The mean sequencing depth was significantly higher than that of the 1000 Genomes Project. A total of 30 OR genes from hg38-intact and hg38-pseudo categories were newly found to be segregating pseudogenes. One hg38-pseudo OR gene was intact in all individuals. CNV was detected in 63 OR genes. Tajima’s D analysis for OR genes and neutral references was consistent with balancing selection to maintain allelic differences in intact OR genes. These results demonstrate that the targeted capture by probes with diversity-oriented design is far more effective than a whole-genome approach to retrieve OR genes and achieve high-depth sequencing and thus to reveal polymorphisms for the OR multigene family. The composition of OR genes in the human reference genome hg38 does not necessarily represent those in many humans, implying higher perceptual variation than previously thought. The current study inspires further investigation with a similar approach at a global scale.

2022-01-23 12:35:33
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1 0 0 0 OA Target capture of bitter taste receptor gene repertoire from dietarily divergent cercopithecid genomes

著者: Min HOU Masahiro HAYASHI Ryuichi ASHINO Amanda D. MELIN Shoji KAWAMURA
出版者: Primate Society of Japan
雑誌: 霊長類研究 Supplement
巻号頁・発行日: pp.32-33, 2020 (Released:2021-04-23)

Taste perception is fundamental in dietary selection for many animals. Bitter taste perception is important not only in dietary selection but also in preventing animals from ingesting potentially toxic compounds. Previous studies have revealed evolutionary divergence of the bitter taste receptor gene (TAS2R) repertoire in mammals, including primates, using publicly available whole genome sequence (WGS) data. Plant tissues contain more toxic compounds than animal tissues do. Herbivores could have less TAS2R genes because they are predicted to be more tolerant and less sensitive to bitter compounds to ingest poisons. On the other hand, herbivores could have more TAS2R genes because they are predicted to be in need of selecting and ingesting bitter plants which other animals avoid. Cercopithecid (African and Asian) monkeys are an excellent subject for studying adaptive evolution of bitter sensation because they have diverged into folivores (colobines) and omnivores (cercopithecines). However, only a few genera have been studied in this context. Dependence on WGS data is also potentially problematic due to its inherent incompleteness especially for multigene families such as TAS2Rs. In this study, we employed the target capture (TC) method specifically probing TAS2Rs followed by massive-parallel sequencing for nine cercopithecid species (seven cercopithecines: two Papio, two Macaca, one each of Cercopithecus, Chlorocebus and Erythrocebus species; two colobines: one each of Semnopithecus and Colobus species). We show that TC is far more effective than WGS in retrieving gene sequence and distinguishing intact and disrupted genes. We also find bitter taste gene composition differs among the species. Further studies are required to investigate whether difference of gene composition result in difference of receptor sensitivity and behavioral reactivity to bitter compounds.

2022-01-05 17:31:30
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1 0 0 0 OA Autosomal and Y-chromosomal STR markers reveal a close relationship between Hokkaido Ainu and Ryukyu islanders

著者: KAE KOGANEBUCHI TAKAFUMI KATSUMURA SHIGEKI NAKAGOME HAJIME ISHIDA SHOJI KAWAMURA HIROKI OOTA THE ASIAN ARCHIVAL DNA REPOSITORY CONSORTIUM
出版者: The Anthropological Society of Nippon
雑誌: Anthropological Science (ISSN:09187960)
巻号頁・発行日: pp.120322, (Released:2012-06-26)
被引用文献数: 9 18

2017-10-28 20:13:09
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