1
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Li YC, Gao ZL, Liu KJ, Tian JY, Yang BY, Rahman ZU, Yang LQ, Zhang SH, Li CT, Achilli A, Semino O, Torroni A, Kong QP. Mitogenome evidence shows two radiation events and dispersals of matrilineal ancestry from northern coastal China to the Americas and Japan. Cell Rep 2023:112413. [PMID: 37164007 DOI: 10.1016/j.celrep.2023.112413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 01/05/2023] [Accepted: 04/04/2023] [Indexed: 05/12/2023] Open
Abstract
Although it is widely recognized that the ancestors of Native Americans (NAs) primarily came from Siberia, the link between mitochondrial DNA (mtDNA) lineage D4h3a (typical of NAs) and D4h3b (found so far only in East China and Thailand) raises the possibility that the ancestral sources for early NAs were more variegated than hypothesized. Here, we analyze 216 contemporary (including 106 newly sequenced) D4h mitogenomes and 39 previously reported ancient D4h data. The results reveal two radiation events of D4h in northern coastal China, one during the Last Glacial Maximum and the other within the last deglaciation, which facilitated the dispersals of D4h sub-branches to different areas including the Americas and the Japanese archipelago. The coastal distributions of the NA (D4h3a) and Japanese lineages (D4h1a and D4h2), in combination with the Paleolithic archaeological similarities among Northern China, the Americas, and Japan, lend support to the coastal dispersal scenario of early NAs.
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Affiliation(s)
- Yu-Chun Li
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zong-Liang Gao
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Kai-Jun Liu
- Chengdu 23Mofang Biotechnology Co., Ltd., Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Jiao-Yang Tian
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Bin-Yu Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Zia Ur Rahman
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China; University of Chinese Academy of Sciences, Beijing 100049, China; Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, Yunnan 650204, China
| | - Li-Qin Yang
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China
| | - Su-Hua Zhang
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Cheng-Tao Li
- Shanghai Key Laboratory of Forensic Medicine, Shanghai Forensic Service Platform, Academy of Forensic Science, Ministry of Justice, Shanghai 200063, China
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, 27100 Pavia, Italy
| | - Qing-Peng Kong
- State Key Laboratory of Genetic Resources and Evolution/Key Laboratory of Healthy Aging Research of Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; CAS Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; KIZ/CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming, Yunnan, 650223, China; Kunming Key Laboratory of Healthy Aging Study, Kunming, Yunnan 650223, China.
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2
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Biogeographic origin and genetic characteristics of the peopling of Jeju Island based on lineage markers. Genes Genomics 2023; 45:307-318. [PMID: 36607592 DOI: 10.1007/s13258-022-01363-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2022] [Accepted: 12/26/2022] [Indexed: 01/07/2023]
Abstract
BACKGROUND Jeju Island is the largest island of South Korea, located southwest far from the mainland of Korea, and has a unique history and its own cultures that are distinguished from those of the other regions of the Korean mainland. However, the Jeju population has not been deeply investigated to date to understand their genetic structure, which may reflect their historical and geographical background. OBJECTIVE To identify the genetic characteristics and biogeographic origin of people of Jeju Island based on the statistical analysis of genetic data using lineage markers. METHODS 17 Y-STRs data for 615 unrelated males and mitochondrial DNA haplogroup data for 799 unrelated individuals residing on Jeju Island were generated, and analyzed to investigate genetic diversity and genetic characteristics using statistical methods including pairwise Fst or Rst, Analysis of molecular variance (AMOVA) and Multidimensional scaling (MDS). RESULTS For male individuals of Jeju Island, unique genetic characteristics were observed in the analysis of Y-STRs, including low haplotype diversity, strong association with surnames, genetic difference from other regions of Korea, and common genetic variation of the Y-STR loci known to be predominant in Northern populations, such as Mongolians. Statistical analysis of the mitochondrial DNA haplogroups also revealed similar results that showed low haplogroup diversity and high frequency of haplogroup Y prevalent mostly in ethnic populations around the Sea of Okhotsk in Northeastern Asia. All these results suggest that Jeju Island is genetically distinct from other regions of Korea, possibly being a subpopulation in Korea, and related closely to Northern Asian populations. CONCLUSION The findings in the genetic approach could support understanding of the historical background of Jeju Island that is consistent with evidence from other multidisciplinary studies.
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3
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Cooke NP, Mattiangeli V, Cassidy LM, Okazaki K, Stokes CA, Onbe S, Hatakeyama S, Machida K, Kasai K, Tomioka N, Matsumoto A, Ito M, Kojima Y, Bradley DG, Gakuhari T, Nakagome S. Ancient genomics reveals tripartite origins of Japanese populations. SCIENCE ADVANCES 2021; 7:eabh2419. [PMID: 34533991 PMCID: PMC8448447 DOI: 10.1126/sciadv.abh2419] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.
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Affiliation(s)
- Niall P. Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Japan
| | | | - Shin Onbe
- Kumakogen Board of Education, Kumakogen, Japan
| | | | - Kenichi Machida
- Toyama Prefectural Research Office for Archaeological Heritage, Toyama, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | | | | | - Masafumi Ito
- Foundation of Ishikawa Archaeological Artifacts Center, Kanazawa, Japan
| | - Yoshitaka Kojima
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Takashi Gakuhari
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
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4
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Sato T, Adachi N, Kimura R, Hosomichi K, Yoneda M, Oota H, Tajima A, Toyoda A, Kanzawa-Kiriyama H, Matsumae H, Koganebuchi K, Shimizu KK, Shinoda KI, Hanihara T, Weber A, Kato H, Ishida H. Whole-Genome Sequencing of a 900-Year-Old Human Skeleton Supports Two Past Migration Events from the Russian Far East to Northern Japan. Genome Biol Evol 2021; 13:6355032. [PMID: 34410389 PMCID: PMC8449830 DOI: 10.1093/gbe/evab192] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/15/2021] [Indexed: 12/18/2022] Open
Abstract
Recent studies on paleogenomics have reported some Paleolithic and Neolithic genomes that have provided new insights into the human population history in East and Northeast Asia. However, there remain some cases where more recent migration events need to be examined to elucidate the detailed formation process of local populations. Although the area around northern Japan is one of the regions archaeologically suggested to have been affected by migration waves after the Neolithic period, the genetic source of these migrations are still unclear. Thus, genomic data from such past migrant populations would be highly informative to clarify the detailed formation process of local populations in this region. Here, we report the genome sequence of a 900-year-old adult female (NAT002) belonging to the prehistoric Okhotsk people, who have been considered to be the past migrants to northern Japan after the Neolithic period. We found a close relationship between NAT002 and modern Lower Amur populations and past admixture events between the Amur, Jomon, and Kamchatka ancestries. The admixture dating suggested migration of Amur-related ancestry at approximately 1,600 BP, which is compatible with the archaeological evidence regarding the settlement of the Okhotsk people. Our results also imply migration of Kamchatka-related ancestry at approximately 2,000 BP. In addition, human leukocyte antigen (HLA) typing detected the HLA-B*40 allele, which is reported to increase the risk of arthritis, suggesting the genetic vulnerability of NAT002 to hyperostosis, which was observed around her chest clavicle.
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Affiliation(s)
- Takehiro Sato
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan.,Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Graduate School of Medicine, University of Yamanashi, Chuo, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kazuyoshi Hosomichi
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Hiroki Oota
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Atsushi Toyoda
- Comparative Genomics Laboratory, National Institute of Genetics, Mishima, Japan
| | | | - Hiromi Matsumae
- Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan.,Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
| | - Kae Koganebuchi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.,Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Japan.,Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Kentaro K Shimizu
- Kihara Institute for Biological Research (KIBR), Yokohama City University, Yokohama, Japan.,Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Tsunehiko Hanihara
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Japan
| | - Andrzej Weber
- Department of Anthropology, University of Alberta, Edmonton, Alberta, Canada.,Research Centre "Baikal Region", Irkutsk State University, Irkutsk, Russia.,Laboratoire Méditerranéen de Préhistoire Europe Afrique (LAMPEA) - UMR 7269, Aix-Marseille Université, Aix-en-Provence, France
| | - Hirofumi Kato
- Centre for Ainu and Indigenous Studies, Hokkaido University, Sapporo, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
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5
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Mizuno F, Gojobori J, Kumagai M, Baba H, Taniguchi Y, Kondo O, Matsushita M, Matsushita T, Matsuda F, Higasa K, Hayashi M, Wang L, Kurosaki K, Ueda S. Population dynamics in the Japanese Archipelago since the Pleistocene revealed by the complete mitochondrial genome sequences. Sci Rep 2021; 11:12018. [PMID: 34121089 PMCID: PMC8200360 DOI: 10.1038/s41598-021-91357-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 05/25/2021] [Indexed: 12/14/2022] Open
Abstract
The Japanese Archipelago is widely covered with acidic soil made of volcanic ash, an environment which is detrimental to the preservation of ancient biomolecules. More than 10,000 Palaeolithic and Neolithic sites have been discovered nationwide, but few skeletal remains exist and preservation of DNA is poor. Despite these challenging circumstances, we succeeded in obtaining a complete mitogenome (mitochondrial genome) sequence from Palaeolithic human remains. We also obtained those of Neolithic (the hunting-gathering Jomon and the farming Yayoi cultures) remains, and over 2,000 present-day Japanese. The Palaeolithic mitogenome sequence was not found to be a direct ancestor of any of Jomon, Yayoi, and present-day Japanese people. However, it was an ancestral type of haplogroup M, a basal group of the haplogroup M. Therefore, our results indicate continuity in the maternal gene pool from the Palaeolithic to present-day Japanese. We also found that a vast increase of population size happened and has continued since the Yayoi period, characterized with paddy rice farming. It means that the cultural transition, i.e. rice agriculture, had significant impact on the demographic history of Japanese population.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.
| | - Jun Gojobori
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Hayama, Japan.
| | - Masahiko Kumagai
- Advanced Analysis Center, National Agriculture and Food Research Organization, Tsukuba, Japan
| | - Hisao Baba
- Department of Anthropology, National Museum of Nature and Science, Tokyo, Japan
| | - Yasuhiro Taniguchi
- Department of Archaeology, Faculty of Letters, Kokugakuin University, Tokyo, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | | | | | | | - Koichiro Higasa
- Department of Genome Analysis, Institute of Biomedical Science, Kansai Medical University, Hirakata, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Li Wang
- School of Medicine, Hangzhou Normal University, Hangzhou, China.
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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6
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Malyarchuk BA. [Genetic markers on the distribution of ancient marine hunters in Priokhotye]. Vavilovskii Zhurnal Genet Selektsii 2021; 24:539-544. [PMID: 33659839 PMCID: PMC7716533 DOI: 10.18699/vj20.646] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Представлен обзор сведений о генетическом полиморфизме современного и древнего населения
Севера Азии и Америки с целью реконструкции истории миграций древних морских охотников в Охотоморском
регионе. Проанализированы данные о полиморфизме митохондриальной ДНК и распространенности «арктиче-
ской» мутации – варианта rs80356779-A гена CPT1A. Известно, что «арктический» вариант гена CPT1A с высокой
частотой распространен в современных популяциях эскимосов, чукчей, коряков и других народов Охотоморско-
го региона, хозяйственный уклад которых связан с морским зверобойным промыслом. Согласно палеогеномным
данным, самые ранние находки «арктического» варианта гена CPT1A обнаружены у гренландских и канадских па-
леоэскимосов (4 тыс. лет назад), представителей токаревской культуры Северного Приохотья (3 тыс. лет назад) и
носителей культуры позднего дзёмона острова Хоккайдо (3.5–3.8 тыс. лет назад). Результаты анализа позволили
выявить несколько миграционных событий, связанных с распространением морских охотников в Охотоморском
регионе. Самая поздняя миграция, оставившая следы у носителей культуры эпи-дзёмон (2.0–2.5 тыс. лет назад),
привнесла с севера Приохотья на Хоккайдо и соседние территории Приамурья митохондриальную гаплогруппу
G1b и «арктический» вариант гена CPT1A. Следы более ранней миграции, также привнесшей «арктическую» мута-
цию, зарегистрированы у населения позднего дзёмона Хоккайдо (3.5–3.8 тыс. лет назад). Проведен филогенети-
ческий анализ митохондриальных геномов, относящихся к редкой гаплогруппе C1a, встречающейся у населения
Дальнего Востока и Японии, но в филогенетическом отношении родственной C1-гаплогруппам американских
индейцев. Результаты показали, что дивергенция митохондриальных линий в пределах гаплогруппы C1a проис-
ходила в диапазоне от 7.9 до 6.6 тыс. лет назад, а возраст японской ветви гаплогруппы C1a составляет ~5.2 тыс.
лет. Пока неизвестно, связана ли эта миграция с распространением «арктического» варианта гена CPT1A или же
присутствие C1a-гаплотипов у населения островов Японии маркирует собой еще один, более ранний, эпизод
миграционной истории, связывающей население северо-западной Пацифики и Северной Америки.
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Affiliation(s)
- B A Malyarchuk
- Institute of Biological Problems of the North of the Far-East Branch of the Russian Academy of Sciences, Magadan, Russia
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7
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ADACHI NOBORU, KANZAWA-KIRIYAMA HIDEAKI, NARA TAKASHI, KAKUDA TSUNEO, NISHIDA IWAO, SHINODA KENICHI. Ancient genomes from the initial Jomon period: new insights into the genetic history of the Japanese archipelago. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.2012132] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NOBORU ADACHI
- Department of Legal Medicine, Graduate School of Medicine, University of Yamanashi, Chuo
| | | | - TAKASHI NARA
- Department of Rehabilitation, Department of Medical Technology, Niigata University of Health and Welfare, Niigata
| | - TSUNEO KAKUDA
- Department of Legal Medicine, Graduate School of Medicine, University of Yamanashi, Chuo
| | | | - KEN-ICHI SHINODA
- Department of Anthropology, National Museum of Nature and Science, Tsukuba
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8
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Eisenhofer R, Kanzawa-Kiriyama H, Shinoda KI, Weyrich LS. Investigating the demographic history of Japan using ancient oral microbiota. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190578. [PMID: 33012223 PMCID: PMC7702792 DOI: 10.1098/rstb.2019.0578] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
While microbial communities in the human body (microbiota) are now commonly associated with health and disease in industrialised populations, we know very little about how these communities co-evolved and changed with humans throughout history and deep prehistory. We can now examine these communities by sequencing ancient DNA preserved within calcified dental plaque (calculus), providing insights into the origins of disease and their links to human history. Here, we examine ancient DNA preserved within dental calculus samples and their associations with two major cultural periods in Japan: the Jomon period hunter–gatherers approximately 3000 years before present (BP) and the Edo period agriculturalists 400–150 BP. We investigate how human oral microbiomes have changed in Japan through time and explore the presence of microorganisms associated with oral diseases (e.g. periodontal disease, dental caries) in ancient Japanese populations. Finally, we explore oral microbial strain diversity and its potential links to ancient demography in ancient Japan by performing phylogenomic analysis of a widely conserved oral species—Anaerolineaceae oral taxon 439. This research represents, to our knowledge, the first study of ancient oral microbiomes from Japan and demonstrates that the analysis of ancient dental calculus can provide key information about the origin of non-infectious disease and its deep roots with human demography. This article is part of the theme issue ‘Insights into health and disease from ancient biomolecules’.
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Affiliation(s)
- Raphael Eisenhofer
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia
| | | | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Laura S Weyrich
- Australian Centre for Ancient DNA, University of Adelaide, Adelaide, Australia.,Department of Anthropology and the Huck Institutes of Life Sciences, The Pennsylvania State University, University Park, PA, USA
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9
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Mizuno F, Taniguchi Y, Kondo O, Hayashi M, Kurosaki K, Ueda S. A study of 8,300-year-old Jomon human remains in Japan using complete mitogenome sequences obtained by next-generation sequencing. Ann Hum Biol 2020; 47:555-559. [PMID: 32674620 DOI: 10.1080/03014460.2020.1797164] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Ancient human remains have been assigned to their mitochondrial DNA (mtDNA) haplogroups. To obtain efficiently deep and reliable nucleotide sequences of ancient DNA of interest, we achieved target enrichment followed by next-generation sequencing (NGS). Complete mitochondrial genome (mitogenome) sequences were obtained for three human remains from the Iyai rock-shelter site of the Initial Jomon Period in Japan. All the Jomon mitogenomes belong to haplogroup N9b, but no sequences among them were identical. High genetic diversity was clarified even among the Jomon human remains belonging to haplogroup N9b, which has been described as a haplogroup representing the Jomon people.
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Affiliation(s)
- Fuzuki Mizuno
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Yasuhiro Taniguchi
- Department of Archaeology, Faculty of Letters, Kokugakuin University, Tokyo, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Michiko Hayashi
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Kunihiko Kurosaki
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Legal Medicine, Toho University School of Medicine, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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10
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Dryomov SV, Starikovskaya EB, Nazhmidenova AM, Morozov IV, Sukernik RI. Genetic legacy of cultures indigenous to the Northeast Asian coast in mitochondrial genomes of nearly extinct maritime tribes. BMC Evol Biol 2020; 20:83. [PMID: 32660486 PMCID: PMC7359603 DOI: 10.1186/s12862-020-01652-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Accepted: 07/06/2020] [Indexed: 11/27/2022] Open
Abstract
Background We have described the diversity of complete mtDNA sequences from ‘relic’ groups of the Russian Far East, primarily the Nivkhi (who speak a language isolate with no clear relatedness to any others) and Oroki of Sakhalin, as well as the sedentary Koryak from Kamchatka and the Udegey of Primorye. Previous studies have shown that most of their traditional territory was dramatically reshaped by the expansion of Tungusic-speaking groups. Results Overall, 285 complete mitochondrial sequences were selected for phylogenetic analyses of published, revised and new mitogenomes. To highlight the likely role of Neolithic expansions in shaping the phylogeographical landscape of the Russian Far East, we focus on the major East Eurasian maternal lineages (Y1a, G1b, D4m2, D4e5, M7a2, and N9b) that are restricted to the coastal area. To obtain more insight into autochthonous populations, we removed from the phylogeographic analysis the G2a, G3a2, M8a1, M9a1, and C4b1 lineages, also found within our samples, likely resulting from admixture between the expanding proto-Tungus and the indigenous Paleoasiatic groups with whom they assimilated. Phylogenetic analysis reveals that unlike the relatively diverse lineage spectrum observed in the Amur estuary and northwestern Sakhalin, the present-day subpopulation on the northeastern coast of the island is relatively homogenous: a sole Y1a sublineage, conspicuous for its nodal mutation at m.16189 T > C!, includes different haplotypes. Sharing of the Y1a-m.16189 T > C! sublineages and haplotypes among the Nivkhi, Ulchi and sedentary Koryak is also evident. Aside from Y1a, the entire tree approach expands our understanding of the evolutionary history of haplogroups G1, D4m, N9b, and M7a2. Specifically, we identified the novel haplogroup N9b1 in Primorye, which implies a link between a component of the Udegey ancestry and the Hokkaido Jomon. Conclusions Through a comprehensive dataset of mitochondrial genomes retained in autochthonous populations along the coast between Primorye and the Bering Strait, we considerably extended the sequence diversity of these populations to provide new features based on the number and timing of founding lineages. We emphasize the value of integrating genealogical information with genetic data for reconstructing the population history of indigenous groups dramatically impacted by twentieth century resettlement and social upheavals.
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Affiliation(s)
- Stanislav V Dryomov
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation
| | - Elena B Starikovskaya
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation
| | - Azhar M Nazhmidenova
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation
| | - Igor V Morozov
- Institute of Biological Chemistry and Fundamental Medicine, SBRAS, Novosibirsk, Russian Federation.,Novosibirsk State University, Novosibirsk, Russian Federation
| | - Rem I Sukernik
- Laboratory of Human Molecular Genetics, Institute of Molecular and Cellular Biology, SBRAS, Novosibirsk, Russian Federation.
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Chaubey G, van Driem G. Munda languages are father tongues, but Japanese and Korean are not. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e19. [PMID: 37588351 PMCID: PMC10427457 DOI: 10.1017/ehs.2020.14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022] Open
Abstract
Over two decades ago, it was observed that the linguistic affinity of the language spoken by a particular population tended to correlate with the predominant paternal, i.e. Y-chromosomal, lineage found in that population. Such correlations were found to be ubiquitous but not universal, and the striking exceptions to such conspicuous patterns of correlation between linguistic and genetic phylogeography elicit particular interest and beg for clarification. Within the Austroasiatic language family, the Munda languages are a clear-cut case of father tongues, whereas Japanese and Korean are manifestly not. In this study, the cases of Munda and Japanese are juxtaposed. A holistic understanding of these contrasting cases of ethnolinguistic prehistory with respect to the father tongue correlation will first necessitate a brief exposition of the phylogeography of the Y chromosomal lineage O. Then triangulation discloses some contours and particulars of both long lost episodes of ethnolinguistic prehistory.
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Affiliation(s)
- Gyaneshwer Chaubey
- Department of Zoology, Benaras Hindu University, Varanasi, Uttar Pradesh221005, India
| | - George van Driem
- Linguistics Institute, University of Bern, Länggassstrasse 49, CH 3012Bern, Switzerland
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de Boer E, Yang MA, Kawagoe A, Barnes GL. Japan considered from the hypothesis of farmer/language spread. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e13. [PMID: 37588377 PMCID: PMC10427481 DOI: 10.1017/ehs.2020.7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of agriculture and spread of the Japanese language (between ca. 500 BC-AD 800). We review current data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases for these disciplines are drawn from different periods. Genetic data have primarily been sampled from present-day Japanese and prehistoric Jōmon peoples (14,000-300 BC), preceding the introduction of rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the Yayoi period (ca. 900 BC-AD 250), but little is known about northeastern Japan, which is a focal point here. And despite considerable hypothesizing about prehistoric language, the spread of historic languages/ dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricultural Jōmon peoples interacted with rice agriculturalists, our review of Jōmon genetics sets the stage for further research into their relationships. Modern linguistic research plays an unexpected role in bringing Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern Honshu by agriculturalists beyond the Kantō region.
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Affiliation(s)
- Elisabeth de Boer
- Faculty of East Asian Studies, Ruhr-Universität Bochum, Bochum, Germany
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, Virginia, USA
| | - Aileen Kawagoe
- Department of Social Studies, New International School of Japan, Tokyo, Japan
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Hudson MJ, Nakagome S, Whitman JB. The evolving Japanese: the dual structure hypothesis at 30. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e6. [PMID: 37588379 PMCID: PMC10427290 DOI: 10.1017/ehs.2020.6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The population history of Japan has been one of the most intensively studied anthropological questions anywhere in the world, with a huge literature dating back to the nineteenth century and before. A growing consensus over the 1980s that the modern Japanese comprise an admixture of a Neolithic population with Bronze Age migrants from the Korean peninsula was crystallised in Kazurō Hanihara's influential 'dual structure hypothesis' published in 1991. Here, we use recent research in biological anthropology, historical linguistics and archaeology to evaluate this hypothesis after three decades. Although the major assumptions of Hanihara's model have been supported by recent work, we discuss areas where new findings have led to a re-evaluation of aspects of the hypothesis and emphasise the need for further research in key areas including ancient DNA and archaeology.
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Affiliation(s)
- Mark J. Hudson
- Eurasia3angle Research Group, Max Planck Institute for the Science of Human History, Kahlaische straße 10, 07745Jena, Germany
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, 150-162 Pearse Street, Dublin, Ireland
| | - John B. Whitman
- Department of Linguistics, Cornell University, 203 Morrill Hall, Ithaca, NY14853, USA
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OMOTO KEIICHI, BABA HISAO, KANAZAWA EISAKU, YONEDA MINORU, SHINODA KENICHI, KANZAWA-KIRIYAMA HIDEAKI, KAKUDA TSUNEO, ADACHI NOBORU, SAKAUE KAZUHIRO, ALMEDA, JR. FERNANDOA, BAUZON LESLIEE. An integrated study of the human skeletal remains discovered in Escalon Cave, northeastern Mindanao, the Philippines. ANTHROPOL SCI 2020. [DOI: 10.1537/ase.200706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- KEIICHI OMOTO
- Department of Biological Science, Graduate School of Science, University of Tokyo, Tokyo
| | - HISAO BABA
- National Museum of Nature and Science, Tsukuba
| | | | | | | | | | - TSUNEO KAKUDA
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
| | - NOBORU ADACHI
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
| | | | | | - LESLIE E. BAUZON
- College of Social Sciences and Philosophy, University of the Philippines, Quezon
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15
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KANZAWA-KIRIYAMA HIDEAKI, JINAM TIMOTHYA, KAWAI YOSUKE, SATO TAKEHIRO, HOSOMICHI KAZUYOSHI, TAJIMA ATSUSHI, ADACHI NOBORU, MATSUMURA HIROFUMI, KRYUKOV KIRILL, SAITOU NARUYA, SHINODA KENICHI. Late Jomon male and female genome sequences from the Funadomari site in Hokkaido, Japan. ANTHROPOL SCI 2019. [DOI: 10.1537/ase.190415] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
| | - TIMOTHY A. JINAM
- Division of Population Genetics, National Institute of Genetics, Mishima
| | - YOSUKE KAWAI
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo
| | - TAKEHIRO SATO
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - KAZUYOSHI HOSOMICHI
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - ATSUSHI TAJIMA
- Department of Bioinformatics and Genomics, Graduate School of Medical Sciences, Kanazawa University, Kanazawa
| | - NOBORU ADACHI
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
| | - HIROFUMI MATSUMURA
- Second Division of Physical Therapy, School of Health Sciences, Sapporo Medical University, Sapporo
| | - KIRILL KRYUKOV
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara
| | - NARUYA SAITOU
- Division of Population Genetics, National Institute of Genetics, Mishima
| | - KEN-ICHI SHINODA
- Department of Anthropology, National Museum of Nature and Science, Tsukuba
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TAKAHASHI RYOHEI, KOIBUCHI RYOKO, SAEKI FUMIKO, HAGIHARA YASUO, YONEDA MINORU, ADACHI NOBORU, NARA TAKASHI. Mitochondrial DNA analysis of the human skeletons excavated from the Shomyoji shell midden site, Kanagawa, Japan. ANTHROPOL SCI 2019. [DOI: 10.1537/ase.190307] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- RYOHEI TAKAHASHI
- Department of Legal Medicine, Graduate School of Medicine, University of Yamanashi, Chuo
| | - RYOKO KOIBUCHI
- Department of Rehabilitation, Department of Medical Technology, Niigata University of Health and Welfare, Niigata
| | - FUMIKO SAEKI
- Department of Rehabilitation, Department of Medical Technology, Niigata University of Health and Welfare, Niigata
| | - YASUO HAGIHARA
- Department of Rehabilitation, Department of Medical Technology, Niigata University of Health and Welfare, Niigata
| | - MINORU YONEDA
- The University Museum, The University of Tokyo, Tokyo
| | - NOBORU ADACHI
- Department of Legal Medicine, Graduate School of Medicine, University of Yamanashi, Chuo
| | - TAKASHI NARA
- Department of Rehabilitation, Department of Medical Technology, Niigata University of Health and Welfare, Niigata
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17
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Matsumura H, Shinoda KI, Shimanjuntak T, Oktaviana AA, Noerwidi S, Octavianus Sofian H, Prastiningtyas D, Nguyen LC, Kakuda T, Kanzawa-Kiriyama H, Adachi N, Hung HC, Fan X, Wu X, Willis A, Oxenham MF. Cranio-morphometric and aDNA corroboration of the Austronesian dispersal model in ancient Island Southeast Asia: Support from Gua Harimau, Indonesia. PLoS One 2018; 13:e0198689. [PMID: 29933384 PMCID: PMC6014653 DOI: 10.1371/journal.pone.0198689] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 05/23/2018] [Indexed: 12/23/2022] Open
Abstract
The Austronesian language is spread from Madagascar in the west, Island Southeast Asia (ISEA) in the east (e.g. the Philippines and Indonesian archipelagoes) and throughout the Pacific, as far east as Easter Island. While it seems clear that the remote ancestors of Austronesian speakers originated in Southern China, and migrated to Taiwan with the development of rice farming by c. 5500 BP and onto the northern Philippines by c. 4000 BP (the Austronesian Dispersal Hypothesis or ADH), we know very little about the origins and emergence of Austronesian speakers in the Indonesian Archipelago. Using a combination of cranial morphometric and ancient mtDNA analyses on a new dataset from Gua Hairmau, that spans the pre-Neolithic through to Metal Period (5712—5591cal BP to 1864—1719 cal BP), we rigorously test the validity of the ADH in ISEA. A morphometric analysis of 23 adult male crania, using 16 of Martin’s standard measurements, was carried out with results compared to an East and Southeast Asian dataset of 30 sample populations spanning the Late Pleistocene through to Metal Period, in addition to 39 modern samples from East and Southeast Asia, near Oceania and Australia. Further, 20 samples were analyzed for ancient mtDNA and assigned to identified haplogroups. We demonstrate that the archaeological human remains from Gua Harimau cave, Sumatra, Indonesia provide clear evidence for at least two (cranio-morphometrically defined) and perhaps even three (in the context of the ancient mtDNA results) distinct populations from two separate time periods. The results of these analyses provide substantive support for the ADH model in explaining the origins and population history of ISEA peoples.
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Affiliation(s)
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tokyo, Japan
| | | | | | - Sofwan Noerwidi
- The National Research Centre of Archaeology, Jakarta, Indonesia
| | | | | | - Lan Cuong Nguyen
- Institute of Archaeology, Vietnam Academy of Social Science, Hanoi, Vietnam
| | - Tsuneo Kakuda
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | | | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Kofu, Japan
| | - Hsiao-Chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, Australia
| | | | - Xiujie Wu
- Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Anna Willis
- College of Arts, Society and Education, James Cook University, Townsville, Australia
| | - Marc F Oxenham
- School of Archeology and Anthropology, Australian National University, Canberra, Australia
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18
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Nakazawa Y. On the Pleistocene Population History in the Japanese Archipelago. CURRENT ANTHROPOLOGY 2017. [DOI: 10.1086/694447] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Abstract
Homo sapiens phylogeography begins with the species' origin nearly 200 kya in Africa. First signs of the species outside Africa (in Arabia) are from 125 kya. Earliest dates elsewhere are now 100 kya in China, 45 kya in Australia and southern Europe (maybe even 60 kya in Australia), 32 kya in northeast Siberia, and maybe 20 kya in the Americas. Humans reached arctic regions and oceanic islands last-arctic North America about 5 kya, mid- and eastern Pacific islands about 2-1 kya, and New Zealand about 700 y ago. Initial routes along coasts seem the most likely given abundant and easily harvested shellfish there as indicated by huge ancient oyster shell middens on all continents. Nevertheless, the effect of geographic barriers-mountains and oceans-is clear. The phylogeographic pattern of diasporas from several single origins-northeast Africa to Eurasia, southeast Eurasia to Australia, and northeast Siberia to the Americas-allows the equivalent of a repeat experiment on the relation between geography and phylogenetic and cultural diversity. On all continents, cultural diversity is high in productive low latitudes, presumably because such regions can support populations of sustainable size in a small area, therefore allowing a high density of cultures. Of course, other factors operate. South America has an unusually low density of cultures in its tropical latitudes. A likely factor is the phylogeographic movement of peoples from the Old World bringing novel and hence, lethal diseases to the New World, a foretaste, perhaps, of present day global transport of tropical diseases.
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Adachi N, Kakuda T, Takahashi R, Kanzawa-Kiriyama H, Shinoda KI. Ethnic derivation of the Ainu inferred from ancient mitochondrial DNA data. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 165:139-148. [PMID: 29023628 PMCID: PMC5765509 DOI: 10.1002/ajpa.23338] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Revised: 09/25/2017] [Accepted: 09/26/2017] [Indexed: 01/06/2023]
Abstract
Objectives The Ainu, the indigenous people living on the northernmost island of Japan, Hokkaido, have long been a focus of anthropological interest because of their cultural, linguistic, and physical identity. A major problem with genetic studies on the Ainu is that the previously published data stemmed almost exclusively from only 51 modern‐day individuals living in Biratori Town, central Hokkaido. To clarify the actual genetic characteristics of the Ainu, individuals who are less influenced by mainland Japanese, who started large‐scale immigration into Hokkaido about 150 years ago, should be examined. Moreover, the samples should be collected from all over Hokkaido. Materials and methods Mitochondrial DNA haplogroups of 94 Ainu individuals from the Edo era were successfully determined by analyzing haplogroup‐defining polymorphisms in the hypervariable and coding regions. Thereafter, their frequencies were compared to those of other populations. Results Our findings indicate that the Ainu still retain the matrilineage of the Hokkaido Jomon people. However, the Siberian influence on this population is far greater than previously recognized. Moreover, the influence of mainland Japanese is evident, especially in the southwestern part of Hokkaido that is adjacent to Honshu, the main island of Japan. Discussion Our results suggest that the Ainu were formed from the Hokkaido Jomon people, but subsequently underwent considerable admixture with adjacent populations. The present study strongly recommends revision of the widely accepted dual‐structure model for the population history of the Japanese, in which the Ainu are assumed to be the direct descendants of the Jomon people.
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Affiliation(s)
- Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Tsuneo Kakuda
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Ryohei Takahashi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi 409-3898, Japan
| | - Hideaki Kanzawa-Kiriyama
- Department of Anthropology, National Museum of Nature and Science, Tokyo Tsukuba, Ibaraki 305-0005, Japan
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tokyo Tsukuba, Ibaraki 305-0005, Japan
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Seguchi N, Quintyn CB, Yonemoto S, Takamuku H. An assessment of postcranial indices, ratios, and body mass versus eco-geographical variables of prehistoric Jomon, Yayoi agriculturalists, and Kumejima Islanders of Japan. Am J Hum Biol 2017; 29. [PMID: 28488767 DOI: 10.1002/ajhb.23015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Revised: 02/03/2017] [Accepted: 04/08/2017] [Indexed: 01/13/2023] Open
Abstract
OBJECTIVES We explore variations in body and limb proportions of the Jomon hunter-gatherers (14,000-2500 BP), the Yayoi agriculturalists (2500-1700 BP) of Japan, and the Kumejima Islanders of the Ryukyus (1600-1800 AD) with 11 geographically diverse skeletal postcranial samples from Africa, Europe, Asia, Australia, and North America using brachial-crural indices, femur head-breadth-to-femur length ratio, femur head-breadth-to-lower-limb-length ratio, and body mass as indicators of phenotypic climatic adaptation. Specifically, we test the hypothesis that variation in limb proportions seen in Jomon, Yayoi, and Kumejima is a complex interaction of genetic adaptation; development and allometric constraints; selection, gene flow and genetic drift with changing cultural factors (i.e., nutrition) and climate. METHODS The skeletal data (1127 individuals) were subjected to principle components analysis, Manly's permutation multiple regression tests, and Relethford-Blangero analysis. RESULTS The results of Manly's tests indicate that body proportions and body mass are significantly correlated with latitude, and minimum and maximum temperatures while limb proportions were not significantly correlated with these climatic variables. Principal components plots separated "climatic zones:" tropical, temperate, and arctic populations. The indigenous Jomon showed cold-adapted body proportions and warm-adapted limb proportions. Kumejima showed cold-adapted body proportions and limbs. The Yayoi adhered to the Allen-Bergmann expectation of cold-adapted body and limb proportions. Relethford-Blangero analysis showed that Kumejima experienced gene flow indicated by high observed variances while Jomon experienced genetic drift indicated by low observed variances. CONCLUSIONS The complex interaction of evolutionary forces and development/nutritional constraints are implicated in the mismatch of limb and body proportions.
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Affiliation(s)
- Noriko Seguchi
- Department of Environmental Changes, Faculty of Social and Cultural Studies, Kyushu University, 744 Motooka, Nishi-Ku, Fukuoka City, Fukuoka, 819-0395, Japan.,Department of Anthropology, The University of Montana, 32 Campus Drive, Missoula, Montana, 59812
| | - Conrad B Quintyn
- Department of Anthropology, Bloomsburg University, Centennial Hall 154, 400 East Second Street, Bloomsburg, Pennsylvania, 17815
| | - Shiori Yonemoto
- The Kyushu University Museum, Kyushu University, 6-10-1 Hakozaki, Higashi-ku, Fukuoka City, Fukuoka, 812-8581, Japan
| | - Hirofumi Takamuku
- Department of Anthropology, Doigahama Site Anthropological Museum, 891-8 Kandakami, Houhoku-cho, Shimonoseki City, Yamaguchi, 759-6121, Japan
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Leipe C, Sergusheva EA, Müller S, Spengler RN, Goslar T, Kato H, Wagner M, Weber AW, Tarasov PE. Barley (Hordeum vulgare) in the Okhotsk culture (5th-10th century AD) of northern Japan and the role of cultivated plants in hunter-gatherer economies. PLoS One 2017; 12:e0174397. [PMID: 28355249 PMCID: PMC5371317 DOI: 10.1371/journal.pone.0174397] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 03/08/2017] [Indexed: 11/19/2022] Open
Abstract
This paper discusses archaeobotanical remains of naked barley recovered from the Okhotsk cultural layers of the Hamanaka 2 archaeological site on Rebun Island, northern Japan. Calibrated ages (68% confidence interval) of the directly dated barley remains suggest that the crop was used at the site ca. 440–890 cal yr AD. Together with the finds from the Oumu site (north-eastern Hokkaido Island), the recovered seed assemblage marks the oldest well-documented evidence for the use of barley in the Hokkaido Region. The archaeobotanical data together with the results of a detailed pollen analysis of contemporaneous sediment layers from the bottom of nearby Lake Kushu point to low-level food production, including cultivation of barley and possible management of wild plants that complemented a wide range of foods derived from hunting, fishing, and gathering. This qualifies the people of the Okhotsk culture as one element of the long-term and spatially broader Holocene hunter–gatherer cultural complex (including also Jomon, Epi-Jomon, Satsumon, and Ainu cultures) of the Japanese archipelago, which may be placed somewhere between the traditionally accepted boundaries between foraging and agriculture. To our knowledge, the archaeobotanical assemblages from the Hokkaido Okhotsk culture sites highlight the north-eastern limit of prehistoric barley dispersal. Seed morphological characteristics identify two different barley phenotypes in the Hokkaido Region. One compact type (naked barley) associated with the Okhotsk culture and a less compact type (hulled barley) associated with Early–Middle Satsumon culture sites. This supports earlier suggestions that the “Satsumon type” barley was likely propagated by the expansion of the Yayoi culture via south-western Japan, while the “Okhotsk type” spread from the continental Russian Far East region, across the Sea of Japan. After the two phenotypes were independently introduced to Hokkaido, the boundary between both barley domains possibly existed ca. 600–1000 cal yr AD across the island region. Despite a large body of studies and numerous theoretical and conceptual debates, the question of how to differentiate between hunter–gatherer and farming economies persists reflecting the wide range of dynamic subsistence strategies used by humans through the Holocene. Our current study contributes to the ongoing discussion of this important issue.
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Affiliation(s)
- Christian Leipe
- Institute of Geological Sciences, Section Paleontology, Freie Universität Berlin, Malteserstr. 74–100, Building D, Berlin, Germany
- * E-mail:
| | - Elena A. Sergusheva
- Institute of History, Archaeology and Ethnography, Far Eastern Branch of the Russian Academy of Sciences, Pushkinskaya 89, Vladivostok, Russia
| | - Stefanie Müller
- Institute of Geological Sciences, Section Paleontology, Freie Universität Berlin, Malteserstr. 74–100, Building D, Berlin, Germany
- Eurasia Department and Beijing Branch Office, German Archaeological Institute, Im Dol 2–6, Building II, Berlin, Germany
| | - Robert N. Spengler
- Institute for the Study of the Ancient World, New York University, New York, NY, United States of America
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Tomasz Goslar
- Faculty of Physics, Adam Mickiewicz University, Umultowska 85, Poznan, Poland
- Poznan Radiocarbon Laboratory, Foundation of the A. Mickiewicz University, Rubiez 46, Poznan, Poland
| | - Hirofumi Kato
- Center for Ainu and Indigenous Studies, Hokkaido University, Kita 8, Nishi 6, Kita-ku Sapporo, Hokkaido, Japan
| | - Mayke Wagner
- Eurasia Department and Beijing Branch Office, German Archaeological Institute, Im Dol 2–6, Building II, Berlin, Germany
| | - Andrzej W. Weber
- Department of Anthropology, University of Alberta, Tory Bldg. 13–15, Edmonton, Alberta, Canada
- Aix Marseille Univ, CNRS, Minist Culture & Com, LAMPEA, Aix-en-Provence, France
| | - Pavel E. Tarasov
- Institute of Geological Sciences, Section Paleontology, Freie Universität Berlin, Malteserstr. 74–100, Building D, Berlin, Germany
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Siska V, Jones ER, Jeon S, Bhak Y, Kim HM, Cho YS, Kim H, Lee K, Veselovskaya E, Balueva T, Gallego-Llorente M, Hofreiter M, Bradley DG, Eriksson A, Pinhasi R, Bhak J, Manica A. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. SCIENCE ADVANCES 2017; 3:e1601877. [PMID: 28164156 PMCID: PMC5287702 DOI: 10.1126/sciadv.1601877] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Accepted: 12/21/2016] [Indexed: 05/06/2023]
Abstract
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
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Affiliation(s)
- Veronika Siska
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Eppie Ruth Jones
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Sungwon Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Youngjune Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hak-Min Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Yun Sung Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyunho Kim
- Geromics, Ulsan 44919, Republic of Korea
| | - Kyusang Lee
- Clinomics Inc., Ulsan 4919, Republic of Korea
| | | | - Tatiana Balueva
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Michael Hofreiter
- Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Geromics, Ulsan 44919, Republic of Korea
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
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24
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Masuyama K, Shojo H, Nakanishi H, Inokuchi S, Adachi N. Sex Determination from Fragmented and Degenerated DNA by Amplified Product-Length Polymorphism Bidirectional SNP Analysis of Amelogenin and SRY Genes. PLoS One 2017; 12:e0169348. [PMID: 28052096 PMCID: PMC5214517 DOI: 10.1371/journal.pone.0169348] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 12/15/2016] [Indexed: 11/23/2022] Open
Abstract
Sex determination is important in archeology and anthropology for the study of past societies, cultures, and human activities. Sex determination is also one of the most important components of individual identification in criminal investigations. We developed a new method of sex determination by detecting a single-nucleotide polymorphism in the amelogenin gene using amplified product-length polymorphisms in combination with sex-determining region Y analysis. We particularly focused on the most common types of postmortem DNA damage in ancient and forensic samples: fragmentation and nucleotide modification resulting from deamination. Amplicon size was designed to be less than 60 bp to make the method more useful for analyzing degraded DNA samples. All DNA samples collected from eight Japanese individuals (four male, four female) were evaluated correctly using our method. The detection limit for accurate sex determination was determined to be 20 pg of DNA. We compared our new method with commercial short tandem repeat analysis kits using DNA samples artificially fragmented by ultraviolet irradiation. Our novel method was the most robust for highly fragmented DNA samples. To deal with allelic dropout resulting from deamination, we adopted “bidirectional analysis,” which analyzed samples from both sense and antisense strands. This new method was applied to 14 Jomon individuals (3500-year-old bone samples) whose sex had been identified morphologically. We could correctly identify the sex of 11 out of 14 individuals. These results show that our method is reliable for the sex determination of highly degenerated samples.
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Affiliation(s)
- Kotoka Masuyama
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
| | - Hideki Shojo
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
- * E-mail: (NA); (HS)
| | - Hiroaki Nakanishi
- Department of Forensic Medicine, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Shota Inokuchi
- Department of Forensic Medicine, Juntendo University School of Medicine, Bunkyo-ku, Tokyo, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo, Yamanashi, Japan
- * E-mail: (NA); (HS)
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25
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Kanzawa-Kiriyama H, Kryukov K, Jinam TA, Hosomichi K, Saso A, Suwa G, Ueda S, Yoneda M, Tajima A, Shinoda KI, Inoue I, Saitou N. A partial nuclear genome of the Jomons who lived 3000 years ago in Fukushima, Japan. J Hum Genet 2016; 62:213-221. [PMID: 27581845 PMCID: PMC5285490 DOI: 10.1038/jhg.2016.110] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2016] [Revised: 07/22/2016] [Accepted: 07/26/2016] [Indexed: 12/11/2022]
Abstract
The Jomon period of the Japanese Archipelago, characterized by cord-marked ‘jomon' potteries, has yielded abundant human skeletal remains. However, the genetic origins of the Jomon people and their relationships with modern populations have not been clarified. We determined a total of 115 million base pair nuclear genome sequences from two Jomon individuals (male and female each) from the Sanganji Shell Mound (dated 3000 years before present) with the Jomon-characteristic mitochondrial DNA haplogroup N9b, and compared these nuclear genome sequences with those of worldwide populations. We found that the Jomon population lineage is best considered to have diverged before diversification of present-day East Eurasian populations, with no evidence of gene flow events between the Jomon and other continental populations. This suggests that the Sanganji Jomon people descended from an early phase of population dispersals in East Asia. We also estimated that the modern mainland Japanese inherited <20% of Jomon peoples' genomes. Our findings, based on the first analysis of Jomon nuclear genome sequence data, firmly demonstrate that the modern mainland Japanese resulted from genetic admixture of the indigenous Jomon people and later migrants.
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Affiliation(s)
- Hideaki Kanzawa-Kiriyama
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kirill Kryukov
- Department of Molecular Life Science, School of Medicine, Tokai University, Isehara, Japan
| | - Timothy A Jinam
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Kazuyoshi Hosomichi
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Aiko Saso
- The University Museum, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Gen Suwa
- The University Museum, The University of Tokyo, Tokyo, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Shintaroh Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Ken-Ichi Shinoda
- Department of Anthropology, National Museum of Nature and Science, Tsukuba, Japan
| | - Ituro Inoue
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Human Genetics, National Institute of Genetics, Mishima, Japan
| | - Naruya Saitou
- Department of Genetics, School of Life Science, SOKENDAI (Graduate University for Advanced Studies), Mishima, Japan.,Division of Population Genetics, National Institute of Genetics, Mishima, Japan.,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
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26
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Kakuda T, Shojo H, Tanaka M, Nambiar P, Minaguchi K, Umetsu K, Adachi N. Multiplex APLP System for High-Resolution Haplogrouping of Extremely Degraded East-Asian Mitochondrial DNAs. PLoS One 2016; 11:e0158463. [PMID: 27355212 PMCID: PMC4927117 DOI: 10.1371/journal.pone.0158463] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 06/16/2016] [Indexed: 12/26/2022] Open
Abstract
Mitochondrial DNA (mtDNA) serves as a powerful tool for exploring matrilineal phylogeographic ancestry, as well as for analyzing highly degraded samples, because of its polymorphic nature and high copy numbers per cell. The recent advent of complete mitochondrial genome sequencing has led to improved techniques for phylogenetic analyses based on mtDNA, and many multiplex genotyping methods have been developed for the hierarchical analysis of phylogenetically important mutations. However, few high-resolution multiplex genotyping systems for analyzing East-Asian mtDNA can be applied to extremely degraded samples. Here, we present a multiplex system for analyzing mitochondrial single nucleotide polymorphisms (mtSNPs), which relies on a novel amplified product-length polymorphisms (APLP) method that uses inosine-flapped primers and is specifically designed for the detailed haplogrouping of extremely degraded East-Asian mtDNAs. We used fourteen 6-plex polymerase chain reactions (PCRs) and subsequent electrophoresis to examine 81 haplogroup-defining SNPs and 3 insertion/deletion sites, and we were able to securely assign the studied mtDNAs to relevant haplogroups. Our system requires only 1×10-13 g (100 fg) of crude DNA to obtain a full profile. Owing to its small amplicon size (<110 bp), this new APLP system was successfully applied to extremely degraded samples for which direct sequencing of hypervariable segments using mini-primer sets was unsuccessful, and proved to be more robust than conventional APLP analysis. Thus, our new APLP system is effective for retrieving reliable data from extremely degraded East-Asian mtDNAs.
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Affiliation(s)
- Tsuneo Kakuda
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi 409–3898, Japan
| | - Hideki Shojo
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi 409–3898, Japan
| | - Mayumi Tanaka
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi 409–3898, Japan
| | - Phrabhakaran Nambiar
- Department of General Dental Practice and Oral & Maxillofacial Imaging, Faculty of Dentistry, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kiyoshi Minaguchi
- Department of Forensic Medicine, Tokai University School of Medicine, 143 Shimokasuya, Kanagawa 259–1193, Japan
| | - Kazuo Umetsu
- Department of Forensic Medicine, Faculty of Medicine, Yamagata University, 2-2-2 Iida-nishi, Yamagata 990–2331, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi 409–3898, Japan
- * E-mail:
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27
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The art of traditional native PAGE: The APLP 48-ID assay for human identification. Leg Med (Tokyo) 2016; 19:28-31. [PMID: 26980250 DOI: 10.1016/j.legalmed.2015.12.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 12/07/2015] [Accepted: 12/09/2015] [Indexed: 11/24/2022]
Abstract
When full STR profiles cannot be obtained, further DNA analyses targeting single nucleotide polymorphisms (SNPs) may occasionally yield valuable information. Although the discrimination power of each SNP is relatively low, combined analysis of many SNPs can improve the personal identification ability to a level as high as that of commercial STR typing kits. In this study, we developed a new SNP typing method, named the amplified-product length polymorphism (APLP) 48-ID assay, for genotyping of 47 autosomal SNPs and two X and Y chromosomal markers for sex typing. Forty-seven SNPs were selected from all 22 autosomes, showing high diversity in European, Nigerian, Han Chinese, and Japanese population in the HapMap data. PCR primers were designed to generate amplicons 40-100 bp in length to increase the robustness of the PCR. The APLP 48-ID assay consisted of four independent PCR reactions followed by electrophoretic run on four lanes in a polyacrylamide gel. Complete profiles were obtained when more than 1.2 ng of DNA was used. We applied this assay for genotyping of 236 Japanese individuals. The random matching probability was 3.3E-20, and the power of exclusion was greater than 0.9999999. This method is a rapid, robust, and cost-effective approach for human identification and paternity testing.
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28
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Shojo H, Tanaka M, Takahashi R, Kakuda T, Adachi N. A Unique Primer with an Inosine Chain at the 5'-Terminus Improves the Reliability of SNP Analysis Using the PCR-Amplified Product Length Polymorphism Method. PLoS One 2015; 10:e0136995. [PMID: 26381262 PMCID: PMC4575067 DOI: 10.1371/journal.pone.0136995] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 08/11/2015] [Indexed: 12/30/2022] Open
Abstract
Polymerase chain reaction-amplified product length polymorphism (PCR-APLP) is one of the most convenient and reliable methods for single nucleotide polymorphism (SNP) analysis. This method is based on PCR, but uses allele-specific primers containing SNP sites at the 3′-terminus of each primer. To use this method at least two allele-specific primers and one “counter-primer”, which serves as a common forward or reverse primer of the allele-specific primers, are required. The allele-specific primers have SNP sites at the 3′-terminus, and another primer should have a few non-complementary flaps at the 5′-terminus to detect SNPs by determining the difference of amplicon length by PCR and subsequent electrophoresis. A major disadvantage of the addition of a non-complementary flap is the non-specific annealing of the primer with non-complementary flaps. However, a design principle for avoiding this undesired annealing has not been fully established, therefore, it is often difficult to design effective APLP primers. Here, we report allele-specific primers with an inosine chain at the 5′-terminus for PCR-APLP analysis. This unique design improves the competitiveness of allele-specific primers and the reliability of SNP analysis when using the PCR-APLP method.
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Affiliation(s)
- Hideki Shojo
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi, 409–3898, Japan
| | - Mayumi Tanaka
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi, 409–3898, Japan
| | - Ryohei Takahashi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi, 409–3898, Japan
| | - Tsuneo Kakuda
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi, 409–3898, Japan
| | - Noboru Adachi
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, 1110 Shimokato, Yamanashi, 409–3898, Japan
- * E-mail:
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29
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Tsutaya T, Ishida H, Yoneda M. Weaning age in an expanding population: stable carbon and nitrogen isotope analysis of infant feeding practices in the Okhotsk culture (5th-13th centuries AD) in Northern Japan. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:544-55. [DOI: 10.1002/ajpa.22740] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Revised: 02/24/2015] [Accepted: 02/25/2015] [Indexed: 11/11/2022]
Affiliation(s)
- Takumi Tsutaya
- Department of Integrated Biosciences; Graduate School of Frontier Sciences, the University of Tokyo; Kashiwanoha 5-1-5 Kashiwa Chiba 277-8561 Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy; Graduate School of Medicine, University of the Ryukyus; 207 Uehara Nishihara Okinawa 903-0215 Japan
| | - Minoru Yoneda
- Department of Integrated Biosciences; Graduate School of Frontier Sciences, the University of Tokyo; Kashiwanoha 5-1-5 Kashiwa Chiba 277-8561 Japan
- The University Museum, the University of Tokyo; Hongo 7-3-1 Bunkyo Tokyo 113-0033 Japan
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30
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Yuasa I, Umetsu K, Adachi N, Matsusue A, Nakayashiki N, Fujihara J, Akane A, Harihara S, Jin F, Ishikawa T. Investigation of Japanese-specific alleles: Most are of Jomon lineage. Leg Med (Tokyo) 2015; 17:52-5. [DOI: 10.1016/j.legalmed.2014.08.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 08/25/2014] [Accepted: 08/28/2014] [Indexed: 11/26/2022]
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31
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Jinam TA, Kanzawa-Kiriyama H, Saitou N. Human genetic diversity in the Japanese Archipelago: dual structure and beyond. Genes Genet Syst 2015; 90:147-52. [DOI: 10.1266/ggs.90.147] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Affiliation(s)
| | | | - Naruya Saitou
- Division of Population Genetics, National Institute of Genetics
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32
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Tooth size in Chinese Oroqen ethnic minority of Inner Mongolia Autonomous Region. Odontology 2014; 103:264-73. [PMID: 24996929 DOI: 10.1007/s10266-014-0161-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Accepted: 05/27/2014] [Indexed: 10/25/2022]
Abstract
The Oroqen are Tungusic hunters of the Amur River basin. We analyzed dental crown measurements from their dental impression models for anthropological characteristics. Sex difference was comparatively larger in the mesiodistal diameters. To examine the Mongoloids' distribution in the Northeast Asia, the data were compared with the results from the previous studies on other Northeast Asian races, using deviation diagrams, cluster analysis, and Multidimensional Scaling from Q-mode correlation coefficients. The Oroqen dentition is classified as Sinodont by the large surface area of their crowns. In the deviation diagram, the Oroqen beared an inverse proportion to the Aleutian Islanders, while showing little difference from the Okhotsk culture people, which suggested a close relation between the two races. The Q-mode correlation coefficients clustered the Oroqen into the Central Asian group with the Buriats and Mongolians. In the analysis of the distances transformed from Q-mode correlation coefficients, the Oroqen was delineated in the neighboring cluster to the Epi-Jomon/Satsumon and the Okhotsk people. It is inferred that the Central Asian group, spreading from Lake Baikal to the Amur basin have gradually mixed with the Baikal group, which later moved into the Amur region from the south. The mixing of the two groups could have been influenced by the geographical features of this area. It would be valuable to gather more data on the groups around the lower Amur region and to evaluate the distribution of the Mongoloids in Eastern Asia.
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33
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Forensic strategy to ensure the quality of sequencing data of mitochondrial DNA in highly degraded samples. Leg Med (Tokyo) 2014; 16:52-5. [DOI: 10.1016/j.legalmed.2013.10.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2013] [Revised: 09/18/2013] [Accepted: 10/04/2013] [Indexed: 11/23/2022]
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34
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Abstract
Languages evolve over space and time. Illuminating the evolutionary history of language is important because it provides a unique opportunity to shed light on the population history of the speakers. Spatial and temporal aspects of language evolution are particularly crucial for understanding demographic history, as they allow us to identify when and where the languages originated, as well as how they spread across the globe. Here we apply Bayesian phylogeographic methods to reconstruct spatiotemporal evolution of the Ainu language: an endangered language spoken by an indigenous group that once thrived in northern Japan. The conventional dual-structure model has long argued that modern Ainu are direct descendants of a single, Pleistocene human lineage from Southeast Asia, namely the Jomon people. In contrast, recent evidence from archaeological, anthropological and genetic evidence suggest that the Ainu are an outcome of significant genetic and cultural contributions from Siberian hunter-gatherers, the Okhotsk, who migrated into northern Hokkaido around 900-1600 years ago. Estimating from 19 Ainu language varieties preserved five decades ago, our analysis shows that they are descendants of a common ancestor who spread from northern Hokkaido around 1300 years ago. In addition to several lines of emerging evidence, our phylogeographic analysis strongly supports the hypothesis that recent expansion of the Okhotsk to northern Hokkaido had a profound impact on the origins of the Ainu people and their culture, and hence calls for a refinement to the dual-structure model.
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Affiliation(s)
- Sean Lee
- Department of Cognitive and Behavioral Science, Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.
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35
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KUDAKA MASATOMI, FUKASE HITOSHI, KIMURA RYOSUKE, HANIHARA TSUNEHIKO, MATSUMURA HIROFUMI, SASO AIKO, FUKUMINE TADAHIKO, ISHIDA HAJIME. Metric characteristics of human limb bones in Asian and Japanese populations. ANTHROPOL SCI 2013. [DOI: 10.1537/ase.121125] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- MASATOMI KUDAKA
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
| | - HITOSHI FUKASE
- Division of Human Evolution Studies, Graduate School of Medicine, Hokkaido University, Sapporo
| | - RYOSUKE KIMURA
- Transdisciplinary Research Organization for Subtropics and Island Studies, University of the Ryukyus, Nishihara
| | - TSUNEHIKO HANIHARA
- Department of Anatomy, Kitasato University School of Medicine, Sagamihara
| | | | - AIKO SASO
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo
| | - TADAHIKO FUKUMINE
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
| | - HAJIME ISHIDA
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
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36
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ADACHI NOBORU, SAWADA JUNMEI, YONEDA MINORU, KOBAYASHI KOICHI, ITOH SHIGERU. Mitochondrial DNA analysis of the human skeleton of the initial Jomon phase excavated at the Yugura cave site, Nagano, Japan. ANTHROPOL SCI 2013. [DOI: 10.1537/ase.130313] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NOBORU ADACHI
- Department of Legal Medicine, Interdisciplinary Graduate School of Medicine and Engineering, University of Yamanashi, Chuo
| | - JUNMEI SAWADA
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki
| | - MINORU YONEDA
- The University Museum, The University of Tokyo, Tokyo
| | | | - SHIGERU ITOH
- AMS Dating Facility, Paleo Labo Co., Ltd., Kiryu
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37
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KANZAWA-KIRIYAMA HIDEAKI, SASO AIKO, SUWA GEN, SAITOU NARUYA. Ancient mitochondrial DNA sequences of Jomon teeth samples from Sanganji, Tohoku district, Japan. ANTHROPOL SCI 2013. [DOI: 10.1537/ase.121113] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- HIDEAKI KANZAWA-KIRIYAMA
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima
- Division of Population Genetics, National Institute of Genetics, Mishima
| | - AIKO SASO
- Department of Biological Sciences, The University of Tokyo, Tokyo
- The University Museum, The University of Tokyo, Tokyo
| | - GEN SUWA
- The University Museum, The University of Tokyo, Tokyo
| | - NARUYA SAITOU
- Department of Genetics, School of Life Science, Graduate University for Advanced Studies, Mishima
- Division of Population Genetics, National Institute of Genetics, Mishima
- Department of Biological Sciences, The University of Tokyo, Tokyo
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38
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Jinam T, Nishida N, Hirai M, Kawamura S, Oota H, Umetsu K, Kimura R, Ohashi J, Tajima A, Yamamoto T, Tanabe H, Mano S, Suto Y, Kaname T, Naritomi K, Yanagi K, Niikawa N, Omoto K, Tokunaga K, Saitou N. 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. J Hum Genet 2012; 57:787-95. [PMID: 23135232 DOI: 10.1038/jhg.2012.114] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
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 and root populations have been proposed. Here, we determined close to one million single-nucleotide polymorphisms (SNPs) for the Ainu and the Ryukyuan, and compared these with existing data sets. This is the first report of these genome-wide SNP data. Major findings are: (1) Recent admixture with the Mainland Japanese was observed for more than one third of the Ainu individuals from principal component analysis and frappe analyses; (2) The Ainu population seems to have experienced admixture with another population, and a combination of two types of admixtures is the unique characteristics of this population; (3) The Ainu and the Ryukyuan are tightly clustered with 100% bootstrap probability followed by the Mainland Japanese in the phylogenetic trees of East Eurasian populations. These results clearly support the dual structure model on the Japanese Archipelago populations, though the origins of the Jomon and the Yayoi people still remain to be solved.
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Fukase H, Wakebe T, Tsurumoto T, Saiki K, Fujita M, Ishida H. Geographic variation in body form of prehistoric Jomon males in the Japanese archipelago: its ecogeographic implications. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2012; 149:125-35. [PMID: 22791466 DOI: 10.1002/ajpa.22112] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2012] [Accepted: 06/05/2012] [Indexed: 11/10/2022]
Abstract
Diversity of human body size and shape is often biogeographically interpreted in association with climatic conditions. According to Bergmann's and Allen's rules, populations in regions with a cold climate are expected to display an overall larger body and smaller/shorter extremities than those in warm/hot environments. In the present study, the skeletal limb size and proportions of prehistoric Jomon hunter-gatherers, who extensively inhabited subarctic to subtropical areas in the ancient Japanese archipelago, were examined to evaluate whether or not the inter-regional differences follow such ecogeographic patterns. Results showed that the Jomon intralimb proportions including relative distal limb lengths did not differ significantly among five regions from northern Hokkaido to the southern Okinawa Islands. This suggests a limited co-variability of the intralimb proportions with climate, particularly within genealogically close populations. In contrast, femoral head breadth (associated with body mass) and skeletal limb lengths were found to be significantly and positively correlated with latitude, suggesting a north-south geographical cline in the body size. This gradient therefore comprehensively conforms to Bergmann's rule, and may stem from multiple potential factors such as phylogenetic constraints, microevolutionary adaptation to climatic/geographic conditions during the Jomon period, and nutritional and physiological response during ontogeny. Specifically, the remarkably small-bodied Jomon in the Okinawa Islands can also be explained as an adjustment to subtropical and insular environments. Thus, the findings obtained in this study indicate that Jomon people, while maintaining fundamental intralimb proportions, displayed body size variation in concert with ambient surroundings.
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Affiliation(s)
- Hitoshi Fukase
- Division of Human Evolution Studies, Graduate School of Medicine, Hokkaido University, Japan.
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