- 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.
- 著者
- Takehiro Sato Tetsuya Amano Hiroko Ono Hajime Ishida Haruto Kodera Hirofumi Matsumura Minoru Yoneda Ryuichi Masuda
- 出版者
- The Anthropological Society of Nippon
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- vol.117, no.3, pp.171-180, 2009 (Released:2009-12-17)
- 参考文献数
- 39
- 被引用文献数
- 38 45
In order to further understand the genetic status of the Okhotsk people, who were distributed in southern coastal regions of the Okhotsk Sea during the 5th–13th centuries, nucleotide variations in the hypervariable region (HVR) and the coding regions of mitochondrial DNA (mtDNA) were analyzed. Targeting the coding regions provides reliable genetic information even from ancient DNAs that may have suffered post-mortem damage. MtDNA haplogroups of 38 individuals were classified according to mtDNA lineages known in northeastern Asian people. Comparisons of mtDNA haplogroup frequencies between the Okhotsk people and other Asian populations revealed that the genetic structures of the Okhotsk people are very similar to those of populations currently living around lower regions of the Amur River and the Ainu of Hokkaido. The results support our previous study on molecular phylogeny of mtDNA HVR 1 sequences, and strongly suggest that the Okhotsk people originated around the lower regions of the Amur River and became an intermediate of gene flow from the continental Sakhalin people to the Ainu.
- 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.
- 著者
- ANGELA R. LIEVERSE DAISUKE KUBO REBECCA L. BOURGEOIS HIROFUMI MATSUMURA MINORU YONEDA HAJIME ISHIDA
- 出版者
- The Anthropological Society of Nippon
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- pp.2108281, (Released:2021-11-16)
- 被引用文献数
- 2
This paper discusses a probable case of pediatric mandibular osteomyelitis (OM) from the east Hokkaido Okhotsk (5th–13th century AD) site of Moyoro, Japan. The remains of a young child present an unusual mandibular lesion exhibiting two main features: (1) cortical thickening reflecting periosteal new bone formation, and (2) lytic alveolar destruction with associated antemortem tooth loss. The lesion was examined macroscopically, microscopically, and via computed tomography imaging. A differential diagnosis—considering lesion appearance, location, and the age of the child—is most consistent with OM, while alveolar and dental involvement suggest an odontogenic source such as an infected tooth germ. The infection appears to have been active at the time of death and chronic (i.e. of 4+ weeks) in duration, an interpretation supported by enamel hypoplastic evidence of physiological stress in the preceding 12–18 months. The lesion’s unique appearance highlights the diverse manifestation of OM, especially in the jaws and in the absence of modern therapeutic treatment. Despite being considered a relatively common condition among non-adult individuals in the past, surprisingly few cases of pediatric OM have been reported from archaeological contexts. This case, only the second documented on a mandible, contributes to the general paucity of paleopathological literature on OM.
- 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
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.
- 著者
- MASATOMI KUDAKA HITOSHI FUKASE RYOSUKE KIMURA TSUNEHIKO HANIHARA HIROFUMI MATSUMURA AIKO SASO TADAHIKO FUKUMINE HAJIME ISHIDA
- 出版者
- 日本人類学会
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- pp.121125, (Released:2013-02-19)
- 被引用文献数
- 6 13
Twelve metric variables of the humerus, radius, femur, and tibia were investigated in 11 male samples from northeastern and eastern Asian populations. Variations among regions and correlations between latitude and respective measurements and indices were calculated and a principal component analysis was conducted to elucidate human limb bone characteristics. Significant correlation and marginally significant correlation were found for the maximum subtrochanteric diameter (r = 0.662, P = 0.027) and the platymeric index (r = -0.583, P = 0.060) with latitude, respectively, suggesting that the femur of northern Asians had a wide and flat subtrochanteric shape. The second principal component of the principal component analysis shows that the northeastern samples with comparatively long shaft length and thin and flat shaft diameters were discriminated from the southern samples; the second principal component was significantly correlated with latitude (r = -0.743, P = 0.009). The estimated Fst value of 0.432–0.336 shows that the variation in limb bone measurements across regions is rather large, at approximately two or three times the low levels of interregional variation (0.078–0.180) in analyses of cranial and dental data. Limb bone morphology has been repeatedly proposed to be more strongly influenced by environmental and nutritional factors than cranial and dental traits, but this study is the first to confirm it on the basis of statistical analysis.
- 著者
- NARUYA SAITOU RYOSUKE KIMURA HITOSHI FUKASE AKIRA YOGI SADAYUKI MURAYAMA HAJIME ISHIDA
- 出版者
- 日本人類学会
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- vol.119, no.3, pp.231-237, 2011 (Released:2011-12-21)
- 参考文献数
- 62
- 被引用文献数
- 2 5 3
Two mainland Japanese males were examined with a computer tomography (CT) X-ray scanner to reconstruct three-dimensional CT simulation images of their cranial anatomy and to check for the presence/absence of 23 nonmetric cranial traits. Surface anatomy for scoring 19 nonmetric cranial variations was clearly observed among the 23 variations. Evaluation of the four other traits might have been disturbed due to dental treatment history, small variations in the images, or X-ray radiation condition. However, these disturbances could be overcome by a combination of simple thin-sliced CT images and magnetic resonance imaging. We have thus developed a new anatomical field for elucidating human morphology.