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Gao Y, Zhang X, Chen H, Lu Y, Ma S, Yang Y, Zhang M, Xu S. Reconstructing the ancestral gene pool to uncover the origins and genetic links of Hmong-Mien speakers. BMC Biol 2024; 22:59. [PMID: 38475771 PMCID: PMC10935854 DOI: 10.1186/s12915-024-01838-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 02/01/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND Hmong-Mien (HM) speakers are linguistically related and live primarily in China, but little is known about their ancestral origins or the evolutionary mechanism shaping their genomic diversity. In particular, the lack of whole-genome sequencing data on the Yao population has prevented a full investigation of the origins and evolutionary history of HM speakers. As such, their origins are debatable. RESULTS Here, we made a deep sequencing effort of 80 Yao genomes, and our analysis together with 28 East Asian populations and 968 ancient Asian genomes suggested that there is a strong genetic basis for the formation of the HM language family. We estimated that the most recent common ancestor dates to 5800 years ago, while the genetic divergence between the HM and Tai-Kadai speakers was estimated to be 8200 years ago. We proposed that HM speakers originated from the Yangtze River Basin and spread with agricultural civilization. We identified highly differentiated variants between HM and Han Chinese, in particular, a deafness-related missense variant (rs72474224) in the GJB2 gene is in a higher frequency in HM speakers than in others. CONCLUSIONS Our results indicated complex gene flow and medically relevant variants involved in the HM speakers' evolution history.
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Affiliation(s)
- Yang Gao
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Xiaoxi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Hao Chen
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yan Lu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China
| | - Sen Ma
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Yajun Yang
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, and Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, Department of Liver Surgery and Transplantation, Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai, 200032, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, 200031, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China.
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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3
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Buck LT, Menéndez LP, De Groote I, Hassett BR, Matsumura H, Stock JT. Factors influencing cranial variation between prehistoric Japanese forager populations. ARCHAEOLOGICAL AND ANTHROPOLOGICAL SCIENCES 2023; 16:3. [PMID: 38098511 PMCID: PMC10716076 DOI: 10.1007/s12520-023-01901-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 11/09/2023] [Indexed: 12/17/2023]
Abstract
Understanding the factors shaping human crania has long been a goal of biological anthropology, and climate, diet, and population history are three of the most well-established influences. The effects of these factors are, however, rarely compared within a single, variable population, limiting interpretations of their relative contribution to craniofacial form. Jomon prehistoric foragers inhabited Japan throughout its climatic and ecological range and developed correspondingly varied modes of subsistence. We have previously demonstrated that a large sample of Jomon crania showed no clear climatic pattern; here, we examine variation in Jomon crania in more detail to determine if dietary factors and/or population history influence human intrapopulation variation at this scale. Based on well-established archaeological differences, we divide the Jomon into dietary groups and use geometric morphometric methods to analyse relationships between cranial shape, diet, and population history. We find evidence for diet-related influences on the shape of the neurocranium, particularly in the temporalis region. These shape differences may be interpreted in the context of regional variation in the biomechanical requirements of different diets. More experimental biomechanical and nutritional evidence is needed, however, to move suggested links between dietary content and cranial shape from plausible to well-supported. In contrast with the global scale of human variation, where neutral processes are the strongest influence on cranial shape, we find no pattern of population history amongst individuals from these Jomon sites. The determinants of cranial morphology are complex and the effect of diet is likely mediated by factors including sex, social factors, and chronology. Our results underline the subtlety of the effects of dietary variation beyond the forager/farmer dichotomy on cranial morphology and contribute to our understanding of the complexity of selective pressures shaping human phenotypes on different geographic scales. Supplementary Information The online version contains supplementary material available at 10.1007/s12520-023-01901-6.
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Affiliation(s)
- L. T. Buck
- Research Centre for Evolutionary Anthropology and Palaeoecology, Liverpool John Moores University, Byrom Street, Liverpool, L3 3AF UK
| | - L. P. Menéndez
- Department of Anthropology of the Americas, University of Bonn, Oxfordstrasse 15, 53111 Bonn, Germany
- Department of Evolutionary Biology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - I. De Groote
- Department of Archaeology, Ghent University, Sint-Pietersnieuwstraat 35, 9000 Ghent, Belgium
| | - B. R. Hassett
- University of Central Lancashire, Fylde Rd, Preston, PR1 2HE Lancashire UK
- Natural History Museum London, Cromwell Road, London, SW7 5BD UK
| | - H. Matsumura
- School of Health Sciences, Sapporo Medical University, S1W17, Sapporo, 0608556 Japan
| | - J. T. Stock
- Department of Anthropology, Western University, London, ON N6A 3K7 Canada
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4
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Hodgins HP, Chen P, Lobb B, Wei X, Tremblay BJM, Mansfield MJ, Lee VCY, Lee PG, Coffin J, Duggan AT, Dolphin AE, Renaud G, Dong M, Doxey AC. Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains. Nat Commun 2023; 14:5475. [PMID: 37673908 PMCID: PMC10482840 DOI: 10.1038/s41467-023-41174-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/23/2023] [Indexed: 09/08/2023] Open
Abstract
The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.
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Affiliation(s)
- Harold P Hodgins
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Pengsheng Chen
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Briallen Lobb
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Xin Wei
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Benjamin J M Tremblay
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Michael J Mansfield
- Genomics and Regulatory Systems Unit, Okinawa Institute of Science and Technology Graduate University, Onna, Okinawa, Japan
| | - Victoria C Y Lee
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada
| | - Pyung-Gang Lee
- Department of Urology, Boston Children's Hospital, Boston, MA, USA
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA
| | - Jeffrey Coffin
- Department of Anthropology, University of Waterloo, Waterloo, ON, Canada
| | - Ana T Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Alexis E Dolphin
- Department of Anthropology, University of Waterloo, Waterloo, ON, Canada
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark.
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA, USA.
- Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA, USA.
| | - Andrew C Doxey
- Department of Biology and the Waterloo Centre for Microbial Research, University of Waterloo, Waterloo, ON, Canada.
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5
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Watanabe Y, Ohashi J. Modern Japanese ancestry-derived variants reveal the formation process of the current Japanese regional gradations. iScience 2023; 26:106130. [PMID: 36879818 PMCID: PMC9984562 DOI: 10.1016/j.isci.2023.106130] [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: 09/26/2022] [Revised: 12/02/2022] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Modern Japanese people have two major ancestral populations: indigenous Jomon hunter-gatherers and continental East Asian farmers. To determine the formation process of the current Japanese population, we developed a detection method for variants derived from ancestral populations using a summary statistic, the ancestry marker index (AMI). We applied AMI to modern Japanese population samples and identified 208,648 single nucleotide polymorphisms (SNPs) that were likely derived from the Jomon people (Jomon-derived variants). Analysis of Jomon-derived variants in 10,842 modern Japanese individuals recruited from all over Japan revealed that the admixture proportions of the Jomon people varied between prefectures, probably owing to the prehistoric population size difference. The estimated allele frequencies of genome-wide SNPs in the ancestral populations of the modern Japanese suggested their adaptive phenotypic characteristics to their respective livelihoods. Based on our findings, we propose a formation model for the genotypic and phenotypic gradations of the current Japanese archipelago populations.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan.,Genome Medical Science Project Toyama Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo 113-0033, Japan
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6
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Suzuki R, Saitou N, Matsuari O, Shiota S, Matsumoto T, Akada J, Kinjo N, Kinjo F, Teruya K, Shimoji M, Shiroma A, Kato M, Satou K, Hirano T, Asaka M, Kryukov K, Moodley Y, Yamaoka Y. Helicobacter pylori genomes reveal Paleolithic human migration to the east end of Asia. iScience 2022; 25:104477. [PMID: 35720267 PMCID: PMC9204748 DOI: 10.1016/j.isci.2022.104477] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 09/29/2021] [Accepted: 04/28/2022] [Indexed: 11/25/2022] Open
Abstract
A virulence bacterium, Helicobacter pylori, evolved parallel to its host human, therefore, can work as a marker for tracing the human migration. We found H. pylori strains indigenous in the southernmost islands of Japanese Archipelago, Okinawa, and defined them as hspOkinawa and hpRyukyu. Genome data of the strains revealed that hspOkinawa diverged from other East Asian strains about 20,000 years ago, and that hpRyukyu diverged about 45,000 years ago. The closest strains of hpRyukyu were found from Afghanistan, Punjab, and Nepal, which suggest this strain originated in the central Asia and traveled across the Eurasian continent during Paleolithic era. The divergence date of hpRyukyu corresponds with human fossil records in Okinawa. Although it is controversial from human DNA analyses whether descendants of the Paleolithic migrants remain in the modern Japanese population, this study reveals that the bacterium of Paleolithic origin remains in the stomachs of current Japanese.
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Affiliation(s)
- Rumiko Suzuki
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita Prefecture 879-5593, Japan
| | - Naruya Saitou
- Population Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan
| | - Osamu Matsuari
- Department of Gastroenterology, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu 879-5593, Japan
| | - Seiji Shiota
- Department of General Medicine, OIta University Faculty of Medicine, Japan
| | - Takashi Matsumoto
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita Prefecture 879-5593, Japan
| | - Junko Akada
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita Prefecture 879-5593, Japan
| | | | - Fukunori Kinjo
- Center for Gastroenterology, Urasoe General Hospital, Urasoe 901-2132, Japan
| | - Kuniko Teruya
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma 904-2234, Japan
| | - Makiko Shimoji
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma 904-2234, Japan
| | - Akino Shiroma
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma 904-2234, Japan
| | - Mototsugu Kato
- Hakodate National Hospital, 18-16 Kawahara, Hakodate 041-8512, Japan
| | - Kazuhito Satou
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma 904-2234, Japan
| | - Takashi Hirano
- Okinawa Institute of Advanced Sciences, 5-1 Suzaki, Uruma 904-2234, Japan
| | - Masahiro Asaka
- Health Sciences University of Hokkaido, Ishikari-gun 061-0293, Japan
| | - Kirill Kryukov
- Population Genetics Laboratory, National Institute of Genetics, 1111 Yata, Mishima 411-8540, Japan
| | - Yoshan Moodley
- Department of Zoology, University of Venda, 2002 University Road, Thohoyandou 0950, Republic of South Africa
| | - Yoshio Yamaoka
- Department of Environmental and Preventive Medicine, Oita University Faculty of Medicine, 1-1 Idaigaoka, Hasama-machi, Yufu City, Oita Prefecture 879-5593, Japan
- Department of Medicine-Gastroenterology, Baylor College of Medicine and Michael E. Debakey Veterans Affairs Medical Center, 2002 Holcombe Blvd., Houston, TX 77030, USA
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7
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Genomic analyses of 10,376 individuals in the Westlake BioBank for Chinese (WBBC) pilot project. Nat Commun 2022; 13:2939. [PMID: 35618720 PMCID: PMC9135724 DOI: 10.1038/s41467-022-30526-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 05/05/2022] [Indexed: 01/04/2023] Open
Abstract
We initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole-genome sequencing (WGS) individuals and 5,841 high-density genotyping individuals, and identify 81.5 million SNPs and INDELs, of which 38.5% are absent in dbSNP Build 151. We provide a population-specific reference panel and an online imputation server (https://wbbc.westlake.edu.cn/) which could yield substantial improvement of imputation performance in Chinese population, especially for low-frequency and rare variants. By analyzing the singleton density of the WGS data, we find selection signatures in SNX29, DNAH1 and WDR1 genes, and the derived alleles of the alcohol metabolism genes (ADH1A and ADH1B) emerge around 7,000 years ago and tend to be more common from 4,000 years ago in East Asia. Genetic evidence supports the corresponding geographical boundaries of the Qinling-Huaihe Line and Nanling Mountains, which separate the Han Chinese into subgroups, and we reveal that North Han was more homogeneous than South Han. Biobanks of genetic data have been primarily in European populations, which gives us an incomplete understanding of complex traits across populations. Here, the authors initiate the Westlake BioBank for Chinese (WBBC) pilot project with 4,535 whole genome sequences and 5,841 high-density genotypes from China, characterizing large-scale genomic variation in Chinese populations.
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8
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Wohns AW, Wong Y, Jeffery B, Akbari A, Mallick S, Pinhasi R, Patterson N, Reich D, Kelleher J, McVean G. A unified genealogy of modern and ancient genomes. Science 2022; 375:eabi8264. [PMID: 35201891 PMCID: PMC10027547 DOI: 10.1126/science.abi8264] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
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Affiliation(s)
- Anthony Wilder Wohns
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ali Akbari
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Swapan Mallick
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; 1090 Vienna, Austria
| | - Nick Patterson
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - David Reich
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
- Corresponding author.
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9
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Tanaka K, Kogure G, Onuki M, Matsumoto K, Iwata T, Aoki D, Kukimoto I. Ancient Evolutionary History of Human Papillomavirus Type 16, 18 and 58 Variants Prevalent Exclusively in Japan. Viruses 2022; 14:v14030464. [PMID: 35336870 PMCID: PMC8953638 DOI: 10.3390/v14030464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/22/2022] [Accepted: 02/22/2022] [Indexed: 11/29/2022] Open
Abstract
Human papillomavirus (HPV) is a sexually transmitted virus with an approximately 8-kilo base DNA genome, which establishes long-term persistent infection in anogenital tissues. High levels of genetic variations, including viral genotypes and intra-type variants, have been described for HPV genomes, together with geographical differences in the distribution of genotypes and variants. Here, by employing a maximum likelihood method, we performed phylogenetic analyses of the complete genome sequences of HPV16, HPV18 and HPV58 available from GenBank (n = 627, 146 and 157, respectively). We found several characteristic clusters that exclusively contain HPV genomes from Japan: two for HPV16 (sublineages A4 and A5), one for HPV18 (sublineage A1) and two for HPV58 (sublineages A1 and A2). Bayesian phylogenetic analyses of concatenated viral gene sequences showed that divergence of the most recent common ancestor of these Japan-specific clades was estimated to have occurred ~98,000 years before present (YBP) for HPV16 A4, ~39,000 YBP for HPV16 A5, ~38,000 YBP for HPV18 A1, ~26,000 for HPV58 A1 and ~25,000 YBP for HPV58 A2. This estimated timeframe for the divergence of the Japan-specific clades suggests that the introduction of these HPV variants into the Japanese archipelago dates back to at least ~25,000 YBP and provides a scenario of virus co-migration with ancestral Japanese populations from continental Asia during the Upper Paleolithic period.
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Affiliation(s)
- Kohsei Tanaka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.T.); (G.K.)
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (T.I.); (D.A.)
| | - Gota Kogure
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.T.); (G.K.)
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (M.O.); (K.M.)
| | - Mamiko Onuki
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (M.O.); (K.M.)
| | - Koji Matsumoto
- Department of Obstetrics and Gynecology, Showa University School of Medicine, Tokyo 142-8666, Japan; (M.O.); (K.M.)
| | - Takashi Iwata
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (T.I.); (D.A.)
| | - Daisuke Aoki
- Department of Obstetrics and Gynecology, Keio University School of Medicine, Tokyo 160-0016, Japan; (T.I.); (D.A.)
| | - Iwao Kukimoto
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo 208-0011, Japan; (K.T.); (G.K.)
- Correspondence: ; Tel.: +81-42-561-0771
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10
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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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11
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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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12
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Yu X, Li H. Origin of ethnic groups, linguistic families, and civilizations in China viewed from the Y chromosome. Mol Genet Genomics 2021; 296:783-797. [PMID: 34037863 DOI: 10.1007/s00438-021-01794-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 04/22/2021] [Indexed: 12/20/2022]
Abstract
East Asia, geographically extending to the Pamir Plateau in the west, to the Himalayan Mountains in the southwest, to Lake Baikal in the north and to the South China Sea in the south, harbors a variety of people, cultures, and languages. To reconstruct the natural history of East Asians is a mission of multiple disciplines, including genetics, archaeology, linguistics, and ethnology. Geneticists confirm the recent African origin of modern East Asians. Anatomically modern humans arose in Africa and immigrated into East Asia via a southern route approximately 50,000 years ago. Following the end of the Last Glacial Maximum approximately 12,000 years ago, rice and millet were domesticated in the south and north of East Asia, respectively, which allowed human populations to expand and linguistic families and ethnic groups to develop. These Neolithic populations produced a strong relation between the present genetic structures and linguistic families. The expansion of the Hongshan people from northeastern China relocated most of the ethnic populations on a large scale approximately 5300 years ago. Most of the ethnic groups migrated to remote regions, producing genetic structure differences between the edge and center of East Asia. In central China, pronounced population admixture occurred and accelerated over time, which subsequently formed the Han Chinese population and eventually the Chinese civilization. Population migration between the north and the south throughout history has left a smooth gradient in north-south changes in genetic structure. Observation of the process of shaping the genetic structure of East Asians may help in understanding the global natural history of modern humans.
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Affiliation(s)
- Xueer Yu
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China.,Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, Datong, 037006, China
| | - Hui Li
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, 200438, China. .,Shanxi Academy of Advanced Research and Innovation, Fudan-Datong Institute of Chinese Origin, Datong, 037006, China.
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13
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Koganebuchi K, Sato K, Fujii K, Kumabe T, Haneji K, Toma T, Ishida H, Joh K, Soejima H, Mano S, Ogawa M, Oota H. An analysis of the demographic history of the risk allele R4810K in RNF213 of moyamoya disease. Ann Hum Genet 2021; 85:166-177. [PMID: 34013582 PMCID: PMC8453937 DOI: 10.1111/ahg.12424] [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] [Received: 02/18/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 11/29/2022]
Abstract
BACKGROUND Ring finger protein 213 (RNF213) is a susceptibility gene of moyamoya disease (MMD). A previous case-control study and a family analysis demonstrated a strong association of the East Asian-specific variant, R4810K (rs112735431), with MMD. Our aim is to uncover evolutionary history of R4810K in East Asian populations. METHODS The RNF213 locus of 24 MMD patients in Japan were sequenced using targeted-capture sequencing. Based on the sequence data, we conducted population genetic analysis and estimated the age of R4810K using coalescent simulation. RESULTS The diversity of the RNF213 gene was higher in Africans than non-Africans, which can be explained by bottleneck effect of the out-of-Africa migration. Coalescent simulation showed that the risk variant was born in East Asia 14,500-5100 years ago and came to the Japanese archipelago afterward, probably in the period when the known migration based on archaeological evidences occurred. CONCLUSIONS Although clinical data show that the symptoms varies, all sequences harboring the risk allele are almost identical with a small number of exceptions, suggesting the MMD phenotypes are unaffected by the variants of this gene and rather would be more affected by environmental factors.
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Affiliation(s)
- Kae Koganebuchi
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan.,Faculty of Medicine, Advanced Medical Research Center, University of the Ryukyus, Nishihara, Okinawa, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
| | - Kimitoshi Sato
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kiyotaka Fujii
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Toshihiro Kumabe
- Department of Neurosurgery, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Kuniaki Haneji
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Takashi Toma
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Hajime Ishida
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, Japan
| | - Keiichiro Joh
- Division of Molecular Genetics and Epigenetics, Faculty of Medicine, Department of Biomolecular Sciences, Saga University, Saga, Saga, Japan
| | - Hidenobu Soejima
- Division of Molecular Genetics and Epigenetics, Faculty of Medicine, Department of Biomolecular Sciences, Saga University, Saga, Saga, Japan
| | - Shuhei Mano
- Department of Mathematical Analysis and Statistical Inference, The Institute of Statistical Mathematics, Tachikawa, Tokyo, Japan
| | - Motoyuki Ogawa
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan.,Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Hiroki Oota
- Department of Biological Structure, Kitasato University Graduate School of Medical Sciences, Sagamihara, Kanagawa, Japan.,Department of Anatomy, Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan.,Department of Biological Sciences, Graduate School of Science, University of Tokyo, Bunkyo-ku, Tokyo, Japan
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14
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Carlhoff S, Duli A, Nägele K, Nur M, Skov L, Sumantri I, Oktaviana AA, Hakim B, Burhan B, Syahdar FA, McGahan DP, Bulbeck D, Perston YL, Newman K, Saiful AM, Ririmasse M, Chia S, Hasanuddin, Pulubuhu DAT, Suryatman, Supriadi, Jeong C, Peter BM, Prüfer K, Powell A, Krause J, Posth C, Brumm A. Genome of a middle Holocene hunter-gatherer from Wallacea. Nature 2021; 596:543-547. [PMID: 34433944 PMCID: PMC8387238 DOI: 10.1038/s41586-021-03823-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/13/2021] [Indexed: 02/07/2023]
Abstract
Much remains unknown about the population history of early modern humans in southeast Asia, where the archaeological record is sparse and the tropical climate is inimical to the preservation of ancient human DNA1. So far, only two low-coverage pre-Neolithic human genomes have been sequenced from this region. Both are from mainland Hòabìnhian hunter-gatherer sites: Pha Faen in Laos, dated to 7939-7751 calibrated years before present (yr cal BP; present taken as AD 1950), and Gua Cha in Malaysia (4.4-4.2 kyr cal BP)1. Here we report, to our knowledge, the first ancient human genome from Wallacea, the oceanic island zone between the Sunda Shelf (comprising mainland southeast Asia and the continental islands of western Indonesia) and Pleistocene Sahul (Australia-New Guinea). We extracted DNA from the petrous bone of a young female hunter-gatherer buried 7.3-7.2 kyr cal BP at the limestone cave of Leang Panninge2 in South Sulawesi, Indonesia. Genetic analyses show that this pre-Neolithic forager, who is associated with the 'Toalean' technocomplex3,4, shares most genetic drift and morphological similarities with present-day Papuan and Indigenous Australian groups, yet represents a previously unknown divergent human lineage that branched off around the time of the split between these populations approximately 37,000 years ago5. We also describe Denisovan and deep Asian-related ancestries in the Leang Panninge genome, and infer their large-scale displacement from the region today.
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Affiliation(s)
- Selina Carlhoff
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Akin Duli
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Kathrin Nägele
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Muhammad Nur
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Laurits Skov
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Iwan Sumantri
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Adhi Agus Oktaviana
- grid.512005.30000 0001 2178 7840Pusat Penelitian Arkeologi Nasional (ARKENAS), Jakarta, Indonesia ,grid.1022.10000 0004 0437 5432Place, Evolution and Rock Art Heritage Unit, Griffith Centre for Social and Cultural Research, Griffith University, Gold Coast, Queensland Australia
| | - Budianto Hakim
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Basran Burhan
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | | | - David P. McGahan
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | - David Bulbeck
- grid.1001.00000 0001 2180 7477Archaeology and Natural History, School of Culture, History and Language, College of Asia and the Pacific, Australian National University, Canberra, Australian Capital Territory Australia
| | - Yinika L. Perston
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | - Kim Newman
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
| | | | - Marlon Ririmasse
- grid.512005.30000 0001 2178 7840Pusat Penelitian Arkeologi Nasional (ARKENAS), Jakarta, Indonesia
| | - Stephen Chia
- grid.11875.3a0000 0001 2294 3534Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Hasanuddin
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Dwia Aries Tina Pulubuhu
- grid.412001.60000 0000 8544 230XDepartemen Sosiologi, Fakultas Ilmu Sosial, Universitas Hasanuddin, Makassar, Indonesia
| | - Suryatman
- grid.511616.4Balai Arkeologi Sulawesi Selatan, Makassar, Indonesia
| | - Supriadi
- grid.412001.60000 0000 8544 230XDepartemen Arkeologi, Fakultas Ilmu Budaya, Universitas Hasanuddin, Makassar, Indonesia
| | - Choongwon Jeong
- grid.31501.360000 0004 0470 5905School of Biological Sciences, Seoul National University, Seoul, Republic of Korea
| | - Benjamin M. Peter
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kay Prüfer
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam Powell
- grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.419518.00000 0001 2159 1813Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- grid.469873.70000 0004 4914 1197Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany ,grid.10392.390000 0001 2190 1447Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany ,grid.10392.390000 0001 2190 1447Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Adam Brumm
- grid.1022.10000 0004 0437 5432Australian Research Centre for Human Evolution, Griffith University, Brisbane, Queensland Australia
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15
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OSADA NAOKI, KAWAI YOSUKE. Exploring models of human migration to the Japanese archipelago using genome-wide genetic data. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.201215] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- NAOKI OSADA
- Faculty of Information Science and Technology, Hokkaido University, Sapporo
| | - YOSUKE KAWAI
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo
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16
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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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17
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KOGANEBUCHI KAE, OOTA HIROKI. Paleogenomics of human remains in East Asia and Yaponesia focusing on current advances and future directions. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.2011302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- KAE KOGANEBUCHI
- Laboratory of Genome Anthropology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
| | - HIROKI OOTA
- Laboratory of Genome Anthropology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
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18
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Watanabe Y, Isshiki M, Ohashi J. Prefecture-level population structure of the Japanese based on SNP genotypes of 11,069 individuals. J Hum Genet 2020; 66:431-437. [PMID: 33051579 DOI: 10.1038/s10038-020-00847-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2020] [Revised: 09/10/2020] [Accepted: 09/11/2020] [Indexed: 11/09/2022]
Abstract
We analyzed genome-wide single-nucleotide polymorphism data of 11,069 Japanese individuals recruited from all 47 prefectures of Japan to clarify their genetic structure. The principal component analysis at the prefectural level enabled us to study the relationship between geographical location and genetic differentiation. The results revealed that the mainland Japanese were not genetically homogeneous, and the genetic structure could be explained mainly by the degree of Jomon ancestry and the geographical location. One of the interesting findings was that individuals in the Shikoku region (i.e., Tokushima Prefecture, Kagawa Prefecture, Ehime Prefecture, and Kochi Prefecture) were genetically close to Han Chinese. Therefore, the genetic components of immigrants from continental East Asia in the Yayoi period may have been well maintained in Shikoku. The present results will be useful for understanding the peopling of Japan, and also provide suggestions for recruiting subjects in genetic association studies.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.,Genome Medical Science Project Toyama Project, National Center for Global Health and Medicine, Tokyo, 162-8655, Japan
| | - Mariko Isshiki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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19
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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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20
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Identification of ancient viruses from metagenomic data of the Jomon people. J Hum Genet 2020; 66:287-296. [PMID: 32994538 DOI: 10.1038/s10038-020-00841-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/20/2020] [Accepted: 09/05/2020] [Indexed: 11/08/2022]
Abstract
Ancient DNA studies provide genomic information about the origins, population structures, and physical characteristics of ancient humans that cannot be solely examined by archeological studies. The DNAs extracted from ancient human bones, teeth, or tissues are often contaminated with coexisting bacterial and viral genomes that contain DNA from ancient microbes infecting those of ancient humans. Information on ancient viral genomes is useful in making inferences about the viral evolution. Here, we have utilized metagenomic sequencing data from the dental pulp of five Jomon individuals, who lived on the Japanese archipelago more than 3000 years ago; this is to detect ancient viral genomes. We conducted de novo assembly of the non-human reads where we have obtained 277,387 contigs that were longer than 1000 bp. These contigs were subjected to homology searches against a collection of modern viral genome sequences. We were able to detect eleven putative ancient viral genomes. Among them, we reconstructed the complete sequence of the Siphovirus contig89 (CT89) viral genome. The Jomon CT89-like sequence was determined to contain 59 open reading frames, among which five genes known to encode phage proteins were under strong purifying selection. The host of CT89 was predicted to be Schaalia meyeri, a bacterium residing in the human oral cavity. Finally, the CT89 phylogenetic tree showed two clusters, from both of which the Jomon sequence was separated. Our results suggest that metagenomic information from the dental pulp of the Jomon people is essential in retrieving ancient viral genomes used to examine their evolution.
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21
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Gakuhari T, Nakagome S, Rasmussen S, Allentoft ME, Sato T, Korneliussen T, Chuinneagáin BN, Matsumae H, Koganebuchi K, Schmidt R, Mizushima S, Kondo O, Shigehara N, Yoneda M, Kimura R, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Tsurumoto T, Wakebe T, Shitara H, Hanihara T, Willerslev E, Sikora M, Oota H. Ancient Jomon genome sequence analysis sheds light on migration patterns of early East Asian populations. Commun Biol 2020; 3:437. [PMID: 32843717 PMCID: PMC7447786 DOI: 10.1038/s42003-020-01162-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Accepted: 07/16/2020] [Indexed: 12/28/2022] Open
Abstract
Anatomically modern humans reached East Asia more than 40,000 years ago. However, key questions still remain unanswered with regard to the route(s) and the number of wave(s) in the dispersal into East Eurasia. Ancient genomes at the edge of the region may elucidate a more detailed picture of the peopling of East Eurasia. Here, we analyze the whole-genome sequence of a 2,500-year-old individual (IK002) from the main-island of Japan that is characterized with a typical Jomon culture. The phylogenetic analyses support multiple waves of migration, with IK002 forming a basal lineage to the East and Northeast Asian genomes examined, likely representing some of the earliest-wave migrants who went north from Southeast Asia to East Asia. Furthermore, IK002 shows strong genetic affinity with the indigenous Taiwan aborigines, which may support a coastal route of the Jomon-ancestry migration. This study highlights the power of ancient genomics to provide new insights into the complex history of human migration into East Eurasia. Takashi Gakuhari, Shigeki Nakagome et al. report the genomic analysis on a 2.5 kya individual from the ancient Jomon culture in present-day Japan. Phylogenetic analysis with comparison to other Eurasian sequences suggests early migration patterns in Asia and provides insight into the genetic affinities between peoples of the region.
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Affiliation(s)
- Takashi Gakuhari
- Center for Cultural Resource Studies, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan.,Institute for Frontier Science Initiative, Kanazawa University, Kanazawa, Japan.,Kitasato University School of Medicine, Sagamihara, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, the University of Dublin, Dublin, Ireland
| | - Simon Rasmussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) laboratory, School of Molecular and Life Sciences, Curtin University, Perth, WA, Australia
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | - Ryan Schmidt
- Kitasato University School of Medicine, Sagamihara, Japan
| | - Souichiro Mizushima
- Department of Anatomy, St. Marianna University School of Medicine, Kawasaki, Japan
| | - Osamu Kondo
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- The University Museum, The University of Tokyo, Tokyo, Japan
| | - Ryosuke Kimura
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Japan
| | | | | | - Atsushi Tajima
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Hiroki Shibata
- Division of Genomics, Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
| | | | - Toshiyuki Tsurumoto
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Tetsuaki Wakebe
- Department of Macroscopic Anatomy, Nagasaki University Graduate School of Biomedical Science, Nagasaki, Japan
| | - Hiromi Shitara
- Department of Archaeology, The University of Tokyo, Tokyo, Japan
| | | | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,GeoGenetics Groups, Department of Zoology, University of Cambridge, Cambridge, UK.,Wellcome Trust Sanger Institute, Hinxton, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Japan. .,Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, Japan.
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22
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Zhang M, Fu Q. Human evolutionary history in Eastern Eurasia using insights from ancient DNA. Curr Opin Genet Dev 2020; 62:78-84. [PMID: 32688244 DOI: 10.1016/j.gde.2020.06.009] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Revised: 05/22/2020] [Accepted: 06/17/2020] [Indexed: 12/12/2022]
Abstract
Advances in ancient genomics are providing unprecedented insight into modern human history. Here, we review recent progress uncovering prehistoric populations in Eastern Eurasia based on ancient DNA studies from the Upper Pleistocene to the Holocene. Many ancient populations existed during the Upper Pleistocene of Eastern Eurasia-some with no substantial ancestry related to present-day populations, some with an affinity to East Asians, and some who contributed to Native Americans. By the Holocene, the genetic composition across East Asia greatly shifted, with several substantial migrations. Three are southward: an increase in northern East Asian-related ancestry in southern East Asia; movement of East Asian-related ancestry into Southeast Asia, mixing with Basal Asian ancestry; and movement of southern East Asian ancestry to islands of Southeast Asia and the Southwest Pacific through the expansion of Austronesians. We anticipate that additional ancient DNA will magnify our understanding of the genetic history in Eastern Eurasia.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China; Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China.
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23
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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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24
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Pureepatpong Kongkasuriyachai N, Prasitwattanaseree S, Case DT, Mahakkanukrauh P. Craniometric estimation of ancestry in Thai and Japanese individuals. AUST J FORENSIC SCI 2020. [DOI: 10.1080/00450618.2020.1789219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- Natthamon Pureepatpong Kongkasuriyachai
- Forensic Osteology, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Forensic Osteology Research Center, Faculty of Medicine and Graduate School, Chiang Mai University, Chiang Mai, Thailand
| | | | - D. Troy Case
- Department of Sociology & Anthropology, North Carolina State University, Raleigh, NC, USA
| | - Pasuk Mahakkanukrauh
- Forensic Osteology Research Center, Faculty of Medicine and Graduate School, Chiang Mai University, Chiang Mai, Thailand
- Department of Anatomy, Faculty of Medicine, Chiang Mai University, Chiang Mai, Thailand
- Excellence Center in Osteology Research and Training Center (ORTC), Chiang Mai University, Chiang Mai, Thailand
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25
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Iwasaki RL, Ishiya K, Kanzawa-Kiriyama H, Kawai Y, Gojobori J, Satta Y. Evolutionary History of the Risk of SNPs for Diffuse-Type Gastric Cancer in the Japanese Population. Genes (Basel) 2020; 11:genes11070775. [PMID: 32664326 PMCID: PMC7396988 DOI: 10.3390/genes11070775] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/02/2020] [Accepted: 07/08/2020] [Indexed: 12/24/2022] Open
Abstract
A genome wide association study reported that the T allele of rs2294008 in a cancer-related gene, PSCA, is a risk allele for diffuse-type gastric cancer. This allele has the highest frequency (0.63) in Japanese in Tokyo (JPT) among 26 populations in the 1000 Genomes Project database. FST ≈ 0.26 at this single nucleotide polymorphism is one of the highest between JPT and the genetically close Han Chinese in Beijing (CHB). To understand the evolutionary history of the alleles in PSCA, we addressed: (i) whether the C non-risk allele at rs2294008 is under positive selection, and (ii) why the mainland Japanese population has a higher T allele frequency than other populations. We found that haplotypes harboring the C allele are composed of two subhaplotypes. We detected that positive selection on both subhaplotypes has occurred in the East Asian lineage. However, the selection on one of the subhaplotypes in JPT seems to have been relaxed or ceased after divergence from the continental population; this may have caused the elevation of T allele frequency. Based on simulations under the dual structure model (a specific demography for the Japanese) and phylogenetic analysis with ancient DNA, the T allele at rs2294008 might have had high frequency in the Jomon people (one of the ancestral populations of the modern Japanese); this may explain the high T allele frequency in the extant Japanese.
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Affiliation(s)
- Risa L. Iwasaki
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan; (R.L.I.); (J.G.)
| | - Koji Ishiya
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Sapporo 062-8517, Japan;
| | | | - Yosuke Kawai
- Genome Medical Science Project, National Center for Global Health and Medicine, Tokyo 162-8655, Japan;
| | - Jun Gojobori
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan; (R.L.I.); (J.G.)
| | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (The Graduate University for Advanced Studies), Kanagawa 240-0193, Japan; (R.L.I.); (J.G.)
- Correspondence: ; Tel.: +81-46-858-1574
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26
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Mathieson I. Human adaptation over the past 40,000 years. Curr Opin Genet Dev 2020; 62:97-104. [PMID: 32745952 PMCID: PMC7484260 DOI: 10.1016/j.gde.2020.06.003] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/10/2020] [Accepted: 06/01/2020] [Indexed: 02/07/2023]
Abstract
Over the past few years several methodological and data-driven advances have greatly improved our ability to robustly detect genomic signatures of selection in humans. New methods applied to large samples of present-day genomes provide increased power, while ancient DNA allows precise estimation of timing and tempo. However, despite these advances, we are still limited in our ability to translate these signatures into understanding about which traits were actually under selection, and why. Combining information from different populations and timescales may allow interpretation of selective sweeps. Other modes of selection have proved more difficult to detect. In particular, despite strong evidence of the polygenicity of most human traits, evidence for polygenic selection is weak, and its importance in recent human evolution remains unclear. Balancing selection and archaic introgression seem important for the maintenance of potentially adaptive immune diversity, but perhaps less so for other traits.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, United States.
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27
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Uchiyama J, Gillam JC, Savelyev A, Ning C. Populations dynamics in Northern Eurasian forests: a long-term perspective from Northeast Asia. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e16. [PMID: 37588381 PMCID: PMC10427466 DOI: 10.1017/ehs.2020.11] [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: 12/14/2022] Open
Abstract
The 'Northern Eurasian Greenbelt' (NEG) is the northern forest zone stretching from the Japanese Archipelago to Northern Europe. The NEG has created highly productive biomes for humanity to exploit since the end of the Pleistocene. This research explores how the ecological conditions in northern Eurasia contributed to and affected human migrations and cultural trajectories by synthesizing the complimentary viewpoints of environmental archaeology, Geographic Information Science (GIS), genetics and linguistics. First, the environmental archaeology perspective raises the possibility that the NEG functioned as a vessel fostering people to develop diverse cultures and engage in extensive cross-cultural exchanges. Second, geographical analysis of genomic data on mitochondrial DNA using GIS reveals the high probability that population dynamics in the southeastern NEG promoted the peopling of the Americas at the end of the Pleistocene. Finally, a linguistic examination of environmental- and landscape-related vocabulary of the proto-Turkic language groups enables the outline of their original cultural landscape and natural conditions, demonstrating significant cultural spheres, i.e. from southern Siberia to eastern Inner Mongolia during Neolithization. All of these results combine to suggest that the ecological complex in the southern edge of the NEG in northeast Asia played a significant role in peopling across the continents during prehistory.
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Affiliation(s)
- Junzo Uchiyama
- The Sainsbury Institute for the Study of Japanese Arts and Cultures, University of East Anglia, 64 The Close, NorwichNR1 4DH, UK
- Center for Cultural Resource Studies, Kanazawa University, Kakuma-machi, Kanazawa-shi, 920-1192, Japan
| | - J. Christopher Gillam
- Department of Sociology, Criminology and Anthropology, Winthrop University, 319 Kinard Hall, Rock Hill, SC29733, USA
| | - Alexander Savelyev
- Max Planck Institute for the Science of Human History, 07745Jena, Germany
- Institute of Linguistics, Russian Academy of Sciences, Bolshoy Kislovsky Pereulok 1/1, 125009Moscow, Russia
| | - Chao Ning
- Max Planck Institute for the Science of Human History, 07745Jena, Germany
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28
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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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29
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Wang CC, Robbeets M. The homeland of Proto-Tungusic inferred from contemporary words and ancient genomes. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e8. [PMID: 37588383 PMCID: PMC10427446 DOI: 10.1017/ehs.2020.8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
The Tungusic languages form a language family spoken in Xinjiang, Siberia, Manchuria and the Russian Far East. There is a general consensus that these languages are genealogically related and descend from a common ancestral language, conventionally called 'Proto-Tungusic'. However, the exact geographical location where the ancestral speakers of Proto-Tungusic originated from is subject to debate. Here we take an unprecedented approach to this problem, by integrating linguistic, archaeological and genetic evidence in a single study. Our analysis of ancient DNA suggests genetic continuity between an ancient Amur genetic lineage and the contemporary speakers of the Tungusic languages. Adding an archaeolinguistic perspective, we infer that the most plausible homeland for the speakers of Proto-Tungusic is the region around Lake Khanka in the Russian Far East. Our study pushes the field forward in answering the tantalizing question about the location of the Tungusic homeland and in illustrating how these three disciplines can converge into a holistic approach to the human past.
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Affiliation(s)
- Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, National Institute for Data Science in Health and Medicine, and School of Life Sciences, Xiamen University, Xiamen361005, China
| | - Martine Robbeets
- Eurasia3angle Research Group, Max Planck Institute for the Science of Human History, Jena, Germany
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30
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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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31
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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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32
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Buck LT, De Groote I, Hamada Y, Hassett BR, Ito T, Stock JT. Evidence of different climatic adaptation strategies in humans and non-human primates. Sci Rep 2019; 9:11025. [PMID: 31363121 PMCID: PMC6667491 DOI: 10.1038/s41598-019-47202-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 07/05/2019] [Indexed: 12/17/2022] Open
Abstract
To understand human evolution it is critical to clarify which adaptations enabled our colonisation of novel ecological niches. For any species climate is a fundamental source of environmental stress during range expansion. Mammalian climatic adaptations include changes in size and shape reflected in skeletal dimensions and humans fit general primate ecogeographic patterns. It remains unclear however, whether there are also comparable amounts of adaptation in humans, which has implications for understanding the relative importance of biological/behavioural mechanisms in human evolution. We compare cranial variation between prehistoric human populations from throughout Japan and ecologically comparable groups of macaques. We compare amounts of intraspecific variation and covariation between cranial shape and ecological variables. Given equal rates and sufficient time for adaptation for both groups, human conservation of non-human primate adaptation should result in comparable variation and patterns of covariation in both species. In fact, we find similar amounts of intraspecific variation in both species, but no covariation between shape and climate in humans, contrasting with strong covariation in macaques. The lack of covariation in humans may suggest a disconnect in climatic adaptation strategies from other primates. We suggest this is due to the importance of human behavioural adaptations, which act as a buffer from climatic stress and were likely key to our evolutionary success.
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Affiliation(s)
- L T Buck
- PAVE research group, Department of Archaeology, University of Cambridge, Pembroke Street, Cambridge, CB2 3QG, UK. .,Human Origins Research Group, Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK. .,Department of Anthropology, University of California Davis, 1 Shields Avenue, Davis, 95616, CA, USA.
| | - I De Groote
- School of Natural Science and Psychology, Liverpool John Moores University, James Parsons Building, Byrom Street, Liverpool, L3 3AF, UK
| | - Y Hamada
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - B R Hassett
- Human Origins Research Group, Department of Earth Sciences, Natural History Museum, Cromwell Road, London, SW7 5BD, UK.,Institute of Archaeology, University College London, 31-4 Gordon Square, London, WC1H 0PY, UK
| | - T Ito
- Primate Research Institute, Kyoto University, Inuyama, Aichi, 484-8506, Japan
| | - J T Stock
- PAVE research group, Department of Archaeology, University of Cambridge, Pembroke Street, Cambridge, CB2 3QG, UK.,Department of Anthropology, Western University, London, Ontario, N6A 3K7, Canada.,Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07745, Jena, Germany
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Park J, Park J, Yi S, Cheul Kim J, Lee E, Choi J. Abrupt Holocene climate shifts in coastal East Asia, including the 8.2 ka, 4.2 ka, and 2.8 ka BP events, and societal responses on the Korean peninsula. Sci Rep 2019; 9:10806. [PMID: 31346228 PMCID: PMC6658530 DOI: 10.1038/s41598-019-47264-8] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 07/08/2019] [Indexed: 11/09/2022] Open
Abstract
Holocene abrupt cooling events have long attracted attention in academia due to public concern that similar rapid changes may reappear in the near future. Thus, considerable progress has been made toward understanding these short-term cooling events in the Northern Hemisphere, particularly in Europe and North America. However, few relevant studies have been conducted in coastal East Asia due to a lack of undisturbed sample materials appropriate for paleoclimate studies. In this study, we examined Holocene abrupt drying events and the Holocene climate optimum (HCO) based on a new high-resolution multi-proxy record (pollen, mean grain size, total organic carbon, carbon/nitrogen ratio) from the south coast of Korea. Possible cultural impacts of the events were also explored using summed probability distributions (SPDs) of archaeological radiocarbon dates. Our arboreal pollen percentage (AP) data clearly indicated drying events centered at 9.8 ka, 9.2 ka, 8.2 ka, 4.7 ka, 4.2 ka, 3.7 ka, 3.2 ka, 2.8 ka, and 2.4 ka BP. The AP data also indicated that forests were severely damaged by a two-step successive drying event during the period from 8.4 ka to 8 ka BP and that the HCO lasted from ca. 7.6 ka to ca. 4.8 ka BP. According to the results of a correlation analysis, climate variations on the Korean peninsula were possibly controlled by shifts in western tropical Pacific (WTP) sea surface temperatures during the past ~5500 years. Simultaneous declines in the SPDs and AP from 2.8 ka to 2.3 ka BP may reflect a demographic reduction attributable to rapid climate deterioration on the peninsula. Refugee agriculturalists might have immigrated to Japan and developed the Yayoi culture. In this study, the 2.8 ka event and its societal impact are recognized clearly for the first time in coastal East Asia.
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Affiliation(s)
- Jungjae Park
- Department of Geography, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea. .,Institute for Korean Regional Studies, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea.
| | - Jinheum Park
- Department of Geography, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
| | - Sangheon Yi
- Geology Division, Korea Institute of Geoscience and Mineral Resources, 124 Gwahak-ro, Yuseong-gu, Daejon, 34132, Republic of Korea. .,Department of Petroleum Resources Technology, University of Science and Technology, 217 Gajeong-ro, Yuseong-gu, Daejeon, 34113, Republic of Korea.
| | - Jin Cheul Kim
- Geology Division, Korea Institute of Geoscience and Mineral Resources, 124 Gwahak-ro, Yuseong-gu, Daejon, 34132, Republic of Korea
| | - Eunmi Lee
- Geology Division, Korea Institute of Geoscience and Mineral Resources, 124 Gwahak-ro, Yuseong-gu, Daejon, 34132, Republic of Korea
| | - Jieun Choi
- Department of Geography, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul, 08826, Republic of Korea
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Watanabe Y, Naka I, Khor SS, Sawai H, Hitomi Y, Tokunaga K, Ohashi J. Analysis of whole Y-chromosome sequences reveals the Japanese population history in the Jomon period. Sci Rep 2019; 9:8556. [PMID: 31209235 PMCID: PMC6572846 DOI: 10.1038/s41598-019-44473-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Accepted: 05/17/2019] [Indexed: 01/06/2023] Open
Abstract
The Jomon and the Yayoi are considered to be the two major ancestral populations of the modern mainland Japanese. The Jomon people, who inhabited mainland Japan, admixed with Yayoi immigrants from the Asian continent. To investigate the population history in the Jomon period (14,500–2,300 years before present [YBP]), we analyzed whole Y-chromosome sequences of 345 Japanese males living in mainland Japan. A phylogenetic analysis of East Asian Y chromosomes identified a major clade (35.4% of mainland Japanese) consisting of only Japanese Y chromosomes, which seem to have originated from indigenous Jomon people. A Monte Carlo simulation indicated that ~70% of Jomon males had Y chromosomes in this clade. The Bayesian skyline plots of 122 Japanese Y chromosomes in the clade detected a marked decrease followed by a subsequent increase in the male population size from around the end of the Jomon period to the beginning of the Yayoi period (2,300 YBP). The colder climate in the Late to Final Jomon period may have resulted in critical shortages of food for the Jomon people, who were hunter-gatherers, and the rice farming introduced by Yayoi immigrants may have helped the population size of the Jomon people to recover.
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Affiliation(s)
- Yusuke Watanabe
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Izumi Naka
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Seik-Soon Khor
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Yuki Hitomi
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Tokyo, 113-0033, Japan
| | - Jun Ohashi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, Tokyo, 113-0033, Japan.
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Craniometrics Reveal "Two Layers" of Prehistoric Human Dispersal in Eastern Eurasia. Sci Rep 2019; 9:1451. [PMID: 30723215 PMCID: PMC6363732 DOI: 10.1038/s41598-018-35426-z] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 10/31/2018] [Indexed: 12/22/2022] Open
Abstract
This cranio-morphometric study emphasizes a “two-layer model” for eastern Eurasian anatomically modern human (AMH) populations, based on large datasets of 89 population samples including findings directly from ancient archaeological contexts. Results suggest that an initial “first layer” of AMH had related closely to ancestral Andaman, Australian, Papuan, and Jomon groups who likely entered this region via the Southeast Asian landmass, prior to 65–50 kya. A later “second layer” shared strong cranial affinities with Siberians, implying a Northeast Asian source, evidenced by 9 kya in central China and then followed by expansions of descendant groups into Southeast Asia after 4 kya. These two populations shared limited initial exchange, and the second layer grew at a faster rate and in greater numbers, linked with contexts of farming that may have supported increased population densities. Clear dichotomization between the two layers implies a temporally deep divergence of distinct migration routes for AMH through both southern and northern Eurasia.
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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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Abstract
The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent—in particular the effect of agricultural expansions in Africa, Europe, and Oceania—and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.
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Affiliation(s)
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
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38
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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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39
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Jinam TA, Phipps ME, Aghakhanian F, Majumder PP, Datar F, Stoneking M, Sawai H, Nishida N, Tokunaga K, Kawamura S, Omoto K, Saitou N. Discerning the Origins of the Negritos, First Sundaland People: Deep Divergence and Archaic Admixture. Genome Biol Evol 2018; 9:2013-2022. [PMID: 28854687 PMCID: PMC5597900 DOI: 10.1093/gbe/evx118] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/09/2017] [Indexed: 12/26/2022] Open
Abstract
Human presence in Southeast Asia dates back to at least 40,000 years ago, when the current islands formed a continental shelf called Sundaland. In the Philippine Islands, Peninsular Malaysia, and Andaman Islands, there exist indigenous groups collectively called Negritos whose ancestry can be traced to the "First Sundaland People." To understand the relationship between these Negrito groups and their demographic histories, we generated genome-wide single nucleotide polymorphism data in the Philippine Negritos and compared them with existing data from other populations. Phylogenetic tree analyses show that Negritos are basal to other East and Southeast Asians, and that they diverged from West Eurasians at least 38,000 years ago. We also found relatively high traces of Denisovan admixture in the Philippine Negritos, but not in the Malaysian and Andamanese groups, suggesting independent introgression and/or parallel losses involving Denisovan introgressed regions. Shared genetic loci between all three Negrito groups could be related to skin pigmentation, height, facial morphology and malarial resistance. These results show the unique status of Negrito groups as descended from the First Sundaland People.
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Affiliation(s)
- Timothy A Jinam
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
| | - Maude E Phipps
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Sunway City, Selangor, Malaysia
| | - Farhang Aghakhanian
- Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia, Sunway City, Selangor, Malaysia
| | - Partha P Majumder
- National Institute of Biomedical Genomics, Kalyani, West Bengal, India
| | - Francisco Datar
- Department of Anthropology, University of the Philippines, Diliman, Quezon City, The Philippines
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hiromi Sawai
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Nao Nishida
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan.,Department of Hepatic Disease, Research Center for Hepatitis and Immunology, National Center for Global Health and Medicine, Chiba, Japan
| | - Katsushi Tokunaga
- Department of Human Genetics, Graduate School of Medicine, The University of Tokyo, Japan
| | - Shoji Kawamura
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, Japan
| | - Keiichi Omoto
- Department of Anthropology, Faculty of Science, The University of Tokyo, Japan
| | - Naruya Saitou
- Division of Population Genetics, National Institute of Genetics, Mishima, Japan
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40
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Loreille O, Ratnayake S, Bazinet AL, Stockwell TB, Sommer DD, Rohland N, Mallick S, Johnson PLF, Skoglund P, Onorato AJ, Bergman NH, Reich D, Irwin JA. Biological Sexing of a 4000-Year-Old Egyptian Mummy Head to Assess the Potential of Nuclear DNA Recovery from the Most Damaged and Limited Forensic Specimens. Genes (Basel) 2018; 9:genes9030135. [PMID: 29494531 PMCID: PMC5867856 DOI: 10.3390/genes9030135] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Revised: 02/06/2018] [Accepted: 02/06/2018] [Indexed: 12/17/2022] Open
Abstract
High throughput sequencing (HTS) has been used for a number of years in the field of paleogenomics to facilitate the recovery of small DNA fragments from ancient specimens. Recently, these techniques have also been applied in forensics, where they have been used for the recovery of mitochondrial DNA sequences from samples where traditional PCR-based assays fail because of the very short length of endogenous DNA molecules. Here, we describe the biological sexing of a ~4000-year-old Egyptian mummy using shotgun sequencing and two established methods of biological sex determination (RX and RY), by way of mitochondrial genome analysis as a means of sequence data authentication. This particular case of historical interest increases the potential utility of HTS techniques for forensic purposes by demonstrating that data from the more discriminatory nuclear genome can be recovered from the most damaged specimens, even in cases where mitochondrial DNA cannot be recovered with current PCR-based forensic technologies. Although additional work remains to be done before nuclear DNA recovered via these methods can be used routinely in operational casework for individual identification purposes, these results indicate substantial promise for the retrieval of probative individually identifying DNA data from the most limited and degraded forensic specimens.
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Affiliation(s)
- Odile Loreille
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Shashikala Ratnayake
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Adam L Bazinet
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Timothy B Stockwell
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Daniel D Sommer
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - Nadin Rohland
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Swapan Mallick
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
| | - Philip L F Johnson
- Department of Biology, University of Maryland, 1210 Biology-Psychology Building, 4094 Campus Drive, College Park, MD 20742, USA.
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Rd, London NW1 1AT, UK.
| | - Anthony J Onorato
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
| | - Nicholas H Bergman
- National Biodefense Analysis and Countermeasures Center, 8300 Research Plaza, Fort Detrick, MD 21702, USA.
| | - David Reich
- Department of Genetics Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA.
- Broad Institute of MIT and Harvard, 415 Main Street, Cambridge, MA 02142, USA.
| | - Jodi A Irwin
- DNA Support Unit, FBI Laboratory, 2501 Investigation Parkway, Quantico, VA 22135, USA.
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41
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Takeuchi F, Katsuya T, Kimura R, Nabika T, Isomura M, Ohkubo T, Tabara Y, Yamamoto K, Yokota M, Liu X, Saw WY, Mamatyusupu D, Yang W, Xu S, Teo YY, Kato N. The fine-scale genetic structure and evolution of the Japanese population. PLoS One 2017; 12:e0185487. [PMID: 29091727 PMCID: PMC5665431 DOI: 10.1371/journal.pone.0185487] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 09/13/2017] [Indexed: 11/21/2022] Open
Abstract
The contemporary Japanese populations largely consist of three genetically distinct groups—Hondo, Ryukyu and Ainu. By principal-component analysis, while the three groups can be clearly separated, the Hondo people, comprising 99% of the Japanese, form one almost indistinguishable cluster. To understand fine-scale genetic structure, we applied powerful haplotype-based statistical methods to genome-wide single nucleotide polymorphism data from 1600 Japanese individuals, sampled from eight distinct regions in Japan. We then combined the Japanese data with 26 other Asian populations data to analyze the shared ancestry and genetic differentiation. We found that the Japanese could be separated into nine genetic clusters in our dataset, showing a marked concordance with geography; and that major components of ancestry profile of Japanese were from the Korean and Han Chinese clusters. We also detected and dated admixture in the Japanese. While genetic differentiation between Ryukyu and Hondo was suggested to be caused in part by positive selection, genetic differentiation among the Hondo clusters appeared to result principally from genetic drift. Notably, in Asians, we found the possibility that positive selection accentuated genetic differentiation among distant populations but attenuated genetic differentiation among close populations. These findings are significant for studies of human evolution and medical genetics.
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Affiliation(s)
- Fumihiko Takeuchi
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- * E-mail: (FT); (NK)
| | - Tomohiro Katsuya
- Department of Clinical Gene Therapy, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara-cho, Japan
| | - Toru Nabika
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Minoru Isomura
- Department of Functional Pathology, Shimane University School of Medicine, Izumo, Japan
| | - Takayoshi Ohkubo
- Department of Hygiene and Public Health, Teikyo University School of Medicine, Tokyo, Japan
| | - Yasuharu Tabara
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Ken Yamamoto
- Department of Medical Chemistry, Kurume University School of Medicine, Kurume, Japan
| | - Mitsuhiro Yokota
- Department of Genome Science, School of Dentistry, Aichi Gakuin University, Nagoya, Japan
| | - Xuanyao Liu
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Dolikun Mamatyusupu
- College of the Life Sciences and Technology, Xinjiang University, Urumqi, China
| | - Wenjun Yang
- Key Laboratory of Reproduction and Heredity of Ningxia Region, Ningxia Medical University, Yinchuan, Ningxia, China
| | - Shuhua Xu
- Max Planck Independent Research Group on Population Genomics, Chinese Academy of Sciences and Max Planck Society Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences Shanghai, China
- School of Life Sciences and Technology, ShanghaiTech University, Shanghai, China
- Collaborative Innovation Center of Genetics and Development, Shanghai, China
| | | | - Yik-Ying Teo
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore
- Life Sciences Institute, National University of Singapore, Singapore, Singapore
- Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore, Singapore
- Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Norihiro Kato
- Department of Gene Diagnostics and Therapeutics, National Center for Global Health and Medicine, Tokyo, Japan
- * E-mail: (FT); (NK)
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42
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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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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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KONDO OSAMU, FUKASE HITOSHI, FUKUMOTO TAKASHI. Regional variations in the Jomon population revisited on craniofacial morphology. ANTHROPOL SCI 2017. [DOI: 10.1537/ase.170428] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- OSAMU KONDO
- Department of Biological Sciences (Anthropology), Graduate School of Science, The University of Tokyo, Tokyo
| | - HITOSHI FUKASE
- Department of Medicine, Kagoshima University School of Medicine, Kagoshima
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