- 著者
- KAE KOGANEBUCHI HIROKI OOTA
- 出版者
- The Anthropological Society of Nippon
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- pp.2011302, (Released:2021-03-31)
- 被引用文献数
- 2
Ancient DNA analysis became paleogenomics once high-throughput sequencing technology was applied to ancient DNA sequencing. Paleogenomics based on whole-genome information from Neanderthals and Denisovans showed that small fragments of these genomes remain in the modern human genome, and corresponding studies of anatomical modern humans clarified the history of migration and expansion among Homo sapiens. Due to geographical and environmental conditions, paleogenomic studies have fallen behind in Eastern compared with Western Eurasia. Recently, however, various capture sequencing techniques, which can enrich ancient DNA, have been used in East Eurasia, and the field of paleogenomics has been further developed. This review briefly introduces the history of ancient DNA analysis leading to paleogenomics, outlines three sequencing stages (partial, draft, and complete genome sequencing) and capture methods, and discusses the necessity of high-quality sequencing for paleogenomes of Eastern Eurasia.
- 著者
- RYAN W. SCHMIDT KEN WAKABAYASHI DAISUKE WAKU TAKASHI GAKUHARI KAE KOGANEBUCHI MOTOYUKI OGAWA JORDAN K. KARSTEN MYKHAILO SOKHATSKY HIROKI OOTA
- 出版者
- The Anthropological Society of Nippon
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- pp.200205, (Released:2020-03-20)
- 被引用文献数
- 1
Verteba Cave (VC) in western Ukraine dates to the Eneolithic period (c. 5500 YBP), and contains the largest collection yet found of human skeletal remains associated with the Cucuteni–Tripolye culture. The subsistence economy of this people was based on agropastoralism, and included some of the largest and densest Middle Neolithic settlement sites in all of Europe. To understand further the evolutionary history of the Tripolye people, we examined population genetics patterns in mitochondrial DNA from ancient human remains excavated from VC chambers. From five commingled and secondary burial sites within the cave, we obtained 368 bp mtDNA HVR1 sequences from 22 individuals assignable to eight haplogroups: H (three haplotypes), HV (two haplotypes), W, K, and T. Overall nucleotide diversity is low (π = 0.00621). The two largest samples, from Chamber G3 and Site 7, were significantly differentiated with respect to haplotype composition: G3 (n = 8) is dominated by haplotype W (π = 0), whereas Site 7 (n = 15) is dominated by H haplotypes (π = 0.00439). Tajima’s D as an indication of population expansion was not significantly negative for the complete sample (D = –1.37) or for sites G3 (D = –0.973) and 7 (D = –1.35), which were analyzed separately. Individuals from the Tripolye culture buried at VC c. 5500 YBP had predominantly haplogroup H and related haplotypes. This contrasts with predominantly haplogroup U individuals in preEneolithic peoples from the same area, which suggests lack of genetic continuity in a site that has been dated to the Mesolithic. Peoples of the Tripolye culture are more closely related to other early European farmers than to Mesolithic hunter-gatherers and/or preEneolithic cultures.
- 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
- KAE KOGANEBUCHI HIROKI OOTA
- 出版者
- The Anthropological Society of Nippon
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- vol.129, no.1, pp.59-69, 2021 (Released:2021-04-27)
- 参考文献数
- 100
- 被引用文献数
- 2 2
Ancient DNA analysis became paleogenomics once high-throughput sequencing technology was applied to ancient DNA sequencing. Paleogenomics based on whole-genome information from Neanderthals and Denisovans showed that small fragments of these genomes remain in the modern human genome, and corresponding studies of anatomical modern humans clarified the history of migration and expansion among Homo sapiens. Due to geographical and environmental conditions, paleogenomic studies have fallen behind in Eastern compared with Western Eurasia. Recently, however, various capture sequencing techniques, which can enrich ancient DNA, have been used in East Eurasia, and the field of paleogenomics has been further developed. This review briefly introduces the history of ancient DNA analysis leading to paleogenomics, outlines three sequencing stages (partial, draft, and complete genome sequencing) and capture methods, and discusses the necessity of high-quality sequencing for paleogenomes of Eastern Eurasia.
- 著者
- DAISUKE WAKU TAKASHI GAKUHARI KAE KOGANEBUCHI MINORU YONEDA OSAMU KONDO TADAYUKI MASUYAMA YASUHIRO YAMADA HIROKI OOTA
- 出版者
- The Anthropological Society of Nippon
- 雑誌
- Anthropological Science (ISSN:09187960)
- 巻号頁・発行日
- pp.220129, (Released:2022-05-19)
- 被引用文献数
- 2
A draft whole genome sequence of a Jomon woman from the Ikawazu shell-mound site has been reported recently. The adult woman, IK002, was excavated with a child, IK001. Because of the burial situation with the child located above the adult, the two individuals were thought to be a mother–child relationship. In this study, we conducted a target capture sequencing, and obtained 258-fold coverage of the complete mitochondrial (mt) genome sequence of IK001. Comparing the mtDNA nucleotide sequences of IK001 and IK002, we found these were unambiguously different from each other. Thus, the mitogenome sequence analysis clarified that both have a non-mother–child relationship. This result sheds new light on the relationship between burial and kinship in Jomon archaeology.
- 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.