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Yang C, Zhang X, Yan S, Yang S, Wu B, You F, Cui Y, Xie N, Wang Z, Jin L, Xu S, Zhang M. Large-scale lexical and genetic alignment supports a hybrid model of Han Chinese demic and cultural diffusions. Nat Hum Behav 2024; 8:1163-1176. [PMID: 38740988 DOI: 10.1038/s41562-024-01886-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 04/11/2024] [Indexed: 05/16/2024]
Abstract
The Han Chinese history is shaped by substantial demographic activities and sociocultural transmissions. However, it remains challenging to assess the contributions of demic and cultural diffusion to Han culture and language, primarily due to the lack of rigorous examination of genetic-linguistic congruence. Here we digitized a large-scale linguistic inventory comprising 1,018 lexical traits across 926 dialect varieties. Using phylogenetic analysis and admixture inference, we revealed a north-south gradient of lexical differences that probably resulted from historical migrations. Furthermore, we quantified extensive horizontal language transfers and pinpointed central China as a dialectal melting pot. Integrating genetic data from 30,408 Han Chinese individuals, we compared the lexical and genetic landscapes across 26 provinces. Our results support a hybrid model where demic diffusion predominantly impacts central China, while cultural diffusion and language assimilation occur in southwestern and coastal regions, respectively. This interdisciplinary study sheds light on the complex social-genetic history of the Han Chinese.
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Affiliation(s)
- Chengkun Yang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China
| | - Xiaoxi Zhang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Sizhe Yang
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China
| | - Baihui Wu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China
| | - Fengshuo You
- Department of Chinese Language and Literature, Fudan University, Shanghai, China
| | - Yue Cui
- Department of Cultural Heritage and Museology, Fudan University, Shanghai, China
| | - Ni Xie
- Department of Linguistics and Modern Languages, The Chinese University of Hong Kong, Hong Kong, China
| | - Zhiyi Wang
- Department of Chinese Language and Literature, Fudan University, Shanghai, China
| | - Li Jin
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China.
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, School of Life Science, Fudan University, Shanghai, China.
- School of Life Science and Technology, ShanghaiTech University, Shanghai, China.
- Key Laboratory of Computational Biology, Shanghai Institute of Nutrition and Health, University of Chinese Academy of Sciences, Chinese Academy of Sciences, Shanghai, China.
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai, China.
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai, China.
- Ministry of Education Key Laboratory of Contemporary Anthropology, Fudan University, Shanghai, China.
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2
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Herrscher E, Valentin F, Zinger W, Pradier B, André G. Life histories in Fiji as reconstructed from first millennium CE Sigatoka Sand Dune burials using isotopes. PLoS One 2024; 19:e0300749. [PMID: 38723036 PMCID: PMC11081393 DOI: 10.1371/journal.pone.0300749] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 03/04/2024] [Indexed: 05/13/2024] Open
Abstract
This paper aims to re-examine the dietary practices of individuals buried at Sigatoka Sand Dunes site (Fiji) in Burial Ground 1 excavated by Simon Best in 1987 and 1988 using two approaches and a reassessment of their archaeological, bioarchaeological and chronological frame. First, stable carbon and nitrogen isotope analysis was applied to document dietary changes between childhood and adulthood using an intra-individual approach on paired bone-tooth. Second, the potential adaptation of the individuals to their environment was evaluated through regional and temporal comparisons using inter-individual bone analysis. Ten AMS radiocarbon dates were measured directly on human bone collagen samples, placing the series in a range of approximately 600 years covering the middle of the first millennium CE (1,888 to 1,272 cal BP). δ13C and δ15N ratios were measured on bone and tooth collagen samples from 38 adult individuals. The results show that δ15N values from tooth are higher than those s from bone while bone and tooth δ13C values are similar, except for females. Fifteen individuals were included in an intra-individual analysis based on paired bone and tooth samples, which revealed six dietary patterns distinguished by a differential dietary intake of marine resources and resources at different trophic levels. These highlight sex-specific differences not related to mortuary practices but to daily life activities, supporting the hypothesis of a sexual division of labour. Compared to other Southwest Pacific series, Sigatoka diets show a specific trend towards marine food consumption that supports the hypothesis of a relative food self-sufficiency requiring no interactions with other groups.
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Affiliation(s)
- Estelle Herrscher
- Aix Marseille University, CNRS, Minist Culture, LAMPEA, Aix–en–Provence, France
| | | | - Wanda Zinger
- Institute for Archaeological Sciences, Archaeo–and Palaeogenetics Group, University of Tübingen, Tübingen, Germany
| | | | - Guy André
- Aix Marseille University, CNRS, Minist Culture, LAMPEA, Aix–en–Provence, France
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3
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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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4
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Zinger W, Valentin F, Spriggs M, Bedford S, Flexner JL, Willie E, Kuautonga T, Détroit F. "Feeling at home in Vanuatu": Integration of newcomers from the East during the last millennium. PLoS One 2024; 19:e0290465. [PMID: 38295041 PMCID: PMC10830024 DOI: 10.1371/journal.pone.0290465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 08/09/2023] [Indexed: 02/02/2024] Open
Abstract
Several localities across the Vanuatu archipelago (Melanesia), so-called 'Polynesian Outliers', are inhabited by communities that display Polynesian linguistic and cultural features although being located outside the Polynesian Triangle. Several introductions of Polynesian genetic components to Central and Southern Vanuatu during the last millenium have resulted in the cultural distinctiveness observed among the Polynesian Outliers in Vanuatu. However, social, political or economic process surrounding the exchange of genes between Polynesian and local individuals remain unidentified. Recent bioanthropological studies suggest the existence of female mobilities from neighboring regions to Vanuatu but also to the Polynesian Outliers of Taumako (Solomon Islands) within patrilocal societies. We aim to examine the hypothesis that Polynesian biological affinities observed in ancient individuals from Vanuatu are gendered or sex-specific, and that some of the Polynesian migrations during the last millennium may have involved practices of exogamy. By reconstructing phenotypes and biological identities from 13 archaeologically-recovered human skulls (400-300 years ago) from "Polynesian-related" regions of Vanuatu, we provide new insights to better contextualize the settlement patterns of Polynesian individuals. Eastern-Pacific associated phenotype are observable in 4 women from the Eretok burial complex (Efate region) and the Polynesian Outlier of Futuna, who were buried in close proximity to individuals with Western-Pacific associated phenotype. We suggest that close integration of individuals from the East into the local Vanuatu society, as well as the practice of exogamy, might have been key processes contributing to the preservation of Polynesian cultural features in Vanuatu over the past millennium. Our finding are cross-referenced with oral records from these two areas, as well as the known genetic makeup of the Vanuatu Polynesian Outliers.
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Affiliation(s)
- Wanda Zinger
- Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences, Tübingen University, Tübingen, Germany
| | - Frédérique Valentin
- UMR 8068 TEMPS/CNRS/ Université Paris1 Panthéon Sorbonne/ Université Paris Nanterre/ Ministère de la Culture, MSH Mondes, Nanterre, France
| | - Matthew Spriggs
- School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, ACT, Australia
| | - Stuart Bedford
- School of Culture, History & Language, College of Asia and the Pacific, The Australian National University, Canberra, ACT, Australia
- Max Planck Institute for Evolutionary Anthropology Department of Linguistic and Cultural Evolution, Leipzig, Germany
| | - James L. Flexner
- Department of Archaeology, School of Philosophical and Historical Inquiry, University of Sydney, Sydney, Australia
| | - Edson Willie
- Vanuatu Cultural Centre Port Vila, Port Vila, Vanuatu
| | | | - Florent Détroit
- Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences, Tübingen University, Tübingen, Germany
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5
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Heggarty P, Anderson C, Scarborough M, King B, Bouckaert R, Jocz L, Kümmel MJ, Jügel T, Irslinger B, Pooth R, Liljegren H, Strand RF, Haig G, Macák M, Kim RI, Anonby E, Pronk T, Belyaev O, Dewey-Findell TK, Boutilier M, Freiberg C, Tegethoff R, Serangeli M, Liosis N, Stroński K, Schulte K, Gupta GK, Haak W, Krause J, Atkinson QD, Greenhill SJ, Kühnert D, Gray RD. Language trees with sampled ancestors support a hybrid model for the origin of Indo-European languages. Science 2023; 381:eabg0818. [PMID: 37499002 DOI: 10.1126/science.abg0818] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 06/08/2023] [Indexed: 07/29/2023]
Abstract
The origins of the Indo-European language family are hotly disputed. Bayesian phylogenetic analyses of core vocabulary have produced conflicting results, with some supporting a farming expansion out of Anatolia ~9000 years before present (yr B.P.), while others support a spread with horse-based pastoralism out of the Pontic-Caspian Steppe ~6000 yr B.P. Here we present an extensive database of Indo-European core vocabulary that eliminates past inconsistencies in cognate coding. Ancestry-enabled phylogenetic analysis of this dataset indicates that few ancient languages are direct ancestors of modern clades and produces a root age of ~8120 yr B.P. for the family. Although this date is not consistent with the Steppe hypothesis, it does not rule out an initial homeland south of the Caucasus, with a subsequent branch northward onto the steppe and then across Europe. We reconcile this hybrid hypothesis with recently published ancient DNA evidence from the steppe and the northern Fertile Crescent.
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Affiliation(s)
- Paul Heggarty
- Departamento de Humanidades, Pontificia Universidad Católica del Perú, 15088 Lima, Peru
- Waves Group, Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cormac Anderson
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthew Scarborough
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Nordic Studies and Linguistics, University of Copenhagen, S 2300 København, Denmark
| | - Benedict King
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Remco Bouckaert
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand
| | - Lechosław Jocz
- Faculty of Humanities, Jacob of Paradies University, 66-400 Gorzów Wielkopolski, Poland
| | - Martin Joachim Kümmel
- Seminar for Indo-European Studies, Institut für Orientalistik, Indogermanistik, Ur- und Frühgeschichtliche Archäologie, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Thomas Jügel
- Center for Religious Studies (CERES), Ruhr University Bochum, 44789 Bochum, Germany
| | - Britta Irslinger
- Saxon Academy of Sciences and Humanities, 04107 Leipzig, Germany
| | - Roland Pooth
- Department of Linguistics, Ghent University, 9000 Ghent, Belgium
| | - Henrik Liljegren
- Department of Linguistics, Stockholm University, 10691 Stockholm, Sweden
| | | | - Geoffrey Haig
- Department of General Linguistics, University of Bamberg, 96047 Bamberg, Germany
| | | | - Ronald I Kim
- Department of Older Germanic Languages, Faculty of English, Adam Mickiewicz University in Poznań, 60-780 Poznań, Poland
| | - Erik Anonby
- School of Linguistics and Language Studies, Carleton University, Ottawa, ON K1S 5B6, Canada
- Leiden University Centre for Linguistics, 2300 RA Leiden, Netherlands
| | - Tijmen Pronk
- Leiden University Centre for Linguistics, 2300 RA Leiden, Netherlands
| | - Oleg Belyaev
- Department of Theoretical and Applied Linguistics, Lomonosov Moscow State University, 119991 GSP-1 Moscow, Russia
- Department of Iranian Languages, Institute of Linguistics RAS, Moscow 125009, Russia
| | - Tonya Kim Dewey-Findell
- Centre for the Study of the Viking Age, School of English, University of Nottingham NG7 2RD, UK
| | - Matthew Boutilier
- Department of German, Nordic, and Slavic, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Cassandra Freiberg
- Institut für deutsche Sprache und Linguistik, Sprach- und literaturwissenschaftliche Fakultät, Humboldt-Universität zu Berlin, 10099 Berlin, Germany
| | - Robert Tegethoff
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Seminar for Indo-European Studies, Institut für Orientalistik, Indogermanistik, Ur- und Frühgeschichtliche Archäologie, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Matilde Serangeli
- Seminar for Indo-European Studies, Institut für Orientalistik, Indogermanistik, Ur- und Frühgeschichtliche Archäologie, Friedrich-Schiller-Universität Jena, 07743 Jena, Germany
| | - Nikos Liosis
- Institute of Modern Greek Studies, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Krzysztof Stroński
- Faculty of Modern Languages, Adam Mickiewicz University in Poznań, 61-874 Poznań, Poland
| | - Kim Schulte
- Department of Translation and Communication, Jaume I University, 12006 Castelló de la Plana, Spain
| | - Ganesh Kumar Gupta
- Faculty of Modern Languages, Adam Mickiewicz University in Poznań, 61-874 Poznań, Poland
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Quentin D Atkinson
- School of Psychology, University of Auckland, Auckland 1010, New Zealand
- Centre for the Study of Social Cohesion, University of Oxford, Oxford OX2 6PN, UK
| | - Simon J Greenhill
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- ARC Center of Excellence for the Dynamics of Language, ANU College of Asia and the Pacific, The Australian National University, Canberra, ACT 2600, Australia
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute of Geoanthropology, 07745 Jena, Germany
| | - Russell D Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- School of Psychology, University of Auckland, Auckland 1010, New Zealand
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6
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Zidane M, Haber M, Truong T, Rachédi F, Ory C, Chevillard S, Blanché H, Olaso R, Boland A, Conte É, Karimi M, Ren Y, Xhaard C, Souchard V, Gardon J, Taquet M, Bouville A, Deleuze JF, Drozdovitch V, de Vathaire F, Cazier JB. Genetic factors for differentiated thyroid cancer in French Polynesia: new candidate loci. PRECISION CLINICAL MEDICINE 2023; 6:pbad015. [PMID: 37383672 PMCID: PMC10294640 DOI: 10.1093/pcmedi/pbad015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2023] [Accepted: 06/09/2023] [Indexed: 06/30/2023] Open
Abstract
Background Populations of French Polynesia (FP), where France performed atmospheric tests between 1966 and 1974, experience a high incidence of differentiated thyroid cancer (DTC). However, up to now, no sufficiently large study of DTC genetic factors in this population has been performed to reach definitive conclusion. This research aimed to analyze the genetic factors of DTC risk among the native FP populations. Methods We analyzed more than 300 000 single nucleotide polymorphisms (SNPs) genotyped in 283 DTC cases and 418 matched controls born in FP, most being younger than 15 years old at the time of the first nuclear tests. We analyzed the genetic profile of our cohort to identify population subgroups. We then completed a genome-wide analysis study on the whole population. Results We identified a specific genetic structure in the FP population reflecting admixture from Asian and European populations. We identified three regions associated with increased DTC risk at 6q24.3, 10p12.2, and 17q21.32. The lead SNPs at these loci showed respective p-values of 1.66 × 10-7, 2.39 × 10-7, and 7.19 × 10-7 and corresponding odds ratios of 2.02, 1.89, and 2.37. Conclusion Our study results suggest a role of the loci 6q24.3, 10p12.2 and 17q21.32 in DTC risk. However, a whole genome sequencing approach would be better suited to characterize these factors than genotyping with microarray chip designed for the Caucasian population. Moreover, the functional impact of these three new loci needs to be further explored and validated.
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Affiliation(s)
- Monia Zidane
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Radiations Epidemiology", Villejuif 94805, France
| | - Marc Haber
- Centre for Computational Biology, University of Birmingham, Birmingham B152TT, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
| | - Thérèse Truong
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif 94805, France
| | - Frédérique Rachédi
- Endocrinology Unit, Territorial Hospital Taaone, F-98713, Papeete, Tahiti 98713, French Polynesia
| | - Catherine Ory
- CEA, Laboratoire de Cancérologie Fondamentale, Institut de Biologie François Jacob, iRCM, SREIT, Laboratoire de Cancérologie Expérimentale (LCE), Université Paris-Saclay, Fontenay aux Roses 92265, France
| | - Sylvie Chevillard
- CEA, Laboratoire de Cancérologie Fondamentale, Institut de Biologie François Jacob, iRCM, SREIT, Laboratoire de Cancérologie Expérimentale (LCE), Université Paris-Saclay, Fontenay aux Roses 92265, France
| | - Hélène Blanché
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris 75010, France
| | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry 91057, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry 91057, France
| | - Éric Conte
- U.S.R. 2003 (CNRS / UPF), Faa'a, Tahiti 98702, France
| | - Mojgan Karimi
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Exposome and Heredity", Villejuif 94805, France
| | - Yan Ren
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Radiations Epidemiology", Villejuif 94805, France
| | - Constance Xhaard
- University of Lorraine, INSERM CIC 1433, Nancy CHRU, INSERM U1116, Nancy 54500, France
| | - Vincent Souchard
- University Paris-Saclay, UVSQ, Inserm, Gustave Roussy, CESP, Team "Radiations Epidemiology", Villejuif 94805, France
| | - Jacques Gardon
- Hydrosciences Montpellier, Research Institute for Development, CNRS, University of Montpellier, Montpellier 62307, France
| | - Marc Taquet
- Research Institute for Development, Center IRD on Tahiti, Arue, Tahiti 98713, French Polynesia
| | - André Bouville
- National Cancer Institute (retired), Bethesda, MD 20892, USA
| | - Jean-François Deleuze
- Fondation Jean Dausset-Centre d'Etude du Polymorphisme Humain, Paris 75010, France
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine, Evry 91057, France
| | - Vladimir Drozdovitch
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, NIH, DHHS, Bethesda, MD 20892, USA
| | | | - Jean-Baptiste Cazier
- Centre for Computational Biology, University of Birmingham, Birmingham B152TT, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B152TT, UK
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7
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Liu D, Ko AMS, Stoneking M. The genomic diversity of Taiwanese Austronesian groups: Implications for the "Into- and Out-of-Taiwan" models. PNAS NEXUS 2023; 2:pgad122. [PMID: 37200801 PMCID: PMC10187666 DOI: 10.1093/pnasnexus/pgad122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 03/29/2023] [Accepted: 03/30/2023] [Indexed: 05/20/2023]
Abstract
The origin and dispersal of the Austronesian language family, one of the largest and most widespread in the world, have long attracted the attention of linguists, archaeologists, and geneticists. Even though there is a growing consensus that Taiwan is the source of the spread of Austronesian languages, little is known about the migration patterns of the early Austronesians who settled in and left Taiwan, i.e. the "Into-Taiwan" and "out-of-Taiwan" events. In particular, the genetic diversity and structure within Taiwan and how this relates to the into-/out-of-Taiwan events are largely unexplored, primarily because most genomic studies have largely utilized data from just two of the 16 recognized Highland Austronesian groups in Taiwan. In this study, we generated the largest genome-wide data set of Taiwanese Austronesians to date, including six Highland groups and one Lowland group from across the island and two Taiwanese Han groups. We identified fine-scale genomic structure in Taiwan, inferred the ancestry profile of the ancestors of Austronesians, and found that the southern Taiwanese Austronesians show excess genetic affinities with the Austronesians outside of Taiwan. Our findings thus shed new light on the Into- and Out-of-Taiwan dispersals.
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Affiliation(s)
- Dang Liu
- To whom correspondence should be addressed: ;
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8
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Hermann A, Gutiérrez P, Chauvel C, Maury R, Liorzou C, Willie E, Phillip I, Forkel R, Rzymski C, Bedford S. Artifact geochemistry demonstrates long-distance voyaging in the Polynesian Outliers. SCIENCE ADVANCES 2023; 9:eadf4487. [PMID: 37083531 PMCID: PMC10121159 DOI: 10.1126/sciadv.adf4487] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Although the peopling of Remote Oceania is well-documented as a general process of eastward migrations from Island Southeast Asia and Near Oceania toward the archipelagos of Remote Oceania, the origin and the development of Polynesian societies in the Western Pacific (Polynesian Outliers), far away from the Polynesian triangle, remain unclear. Here, we present a large-scale geochemical sourcing study of stone artifacts excavated from archeological sites in central Vanuatu, the Solomon Islands, and the Caroline Islands and provide unambiguous evidence of multiple long-distance voyages, with exotic stone materials being transported up to 2500 kilometers from their source. Our results emphasize high mobility in the Western Pacific during the last millennium CE and offer insights on the scale and timing of contacts between the Polynesian Outliers, their neighbors in the Western Pacific, and societies of Western Polynesia.
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Affiliation(s)
- Aymeric Hermann
- UMR 8068 Temps, CNRS, F-92023 Nanterre, France
- Department of Linguistic and Cultural Evolution, MPI-EVA, D-04103 Leipzig, Germany
- Corresponding author.
| | - Pamela Gutiérrez
- Université Paris Cité, Institut de Physique du Globe de Paris, CNRS, F-75005 Paris, France
| | - Catherine Chauvel
- Université Paris Cité, Institut de Physique du Globe de Paris, CNRS, F-75005 Paris, France
| | - René Maury
- Université de Brest, UMR6538 Géosciences Océan, Institut Universitaire Européen de la Mer, CNRS, F-29280 Plouzané, France
| | - Céline Liorzou
- Université de Brest, UMR6538 Géosciences Océan, Institut Universitaire Européen de la Mer, CNRS, F-29280 Plouzané, France
| | - Edson Willie
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port-Vila, Vanuatu
| | - Iarawai Phillip
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port-Vila, Vanuatu
| | - Robert Forkel
- Department of Linguistic and Cultural Evolution, MPI-EVA, D-04103 Leipzig, Germany
| | - Christoph Rzymski
- Department of Linguistic and Cultural Evolution, MPI-EVA, D-04103 Leipzig, Germany
| | - Stuart Bedford
- Department of Linguistic and Cultural Evolution, MPI-EVA, D-04103 Leipzig, Germany
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port-Vila, Vanuatu
- Department of Archaeology and Natural History, College of Asia and the Pacific, The Australian National University, Canberra, ACT 2601, Australia
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9
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Teaching strategies are shaped by experience with formal education: Experimental evidence from caregiver-child dyads in two Tannese communities. Mem Cognit 2023; 51:792-806. [PMID: 35913535 DOI: 10.3758/s13421-022-01340-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/11/2022] [Indexed: 11/08/2022]
Abstract
Humans are extraordinary in the extent to which we rely on cumulative culture to act upon and make sense of our environment. Teaching is one social learning process thought to be fundamental to the evolution of cumulative culture as a means of adaptation in our species. However, the frequency of teaching and how we teach are known to vary across human sociocultural contexts. Understanding this variation adds to our understanding of the complex interplay between cognition and culture in shaping learning behavior but also contributes to theory around the costs and benefits of different social learning processes. Here, we examined how prior experience with formal education is related to the frequency and diversity of teaching behaviors in an experimental paradigm where caregivers were motivated (but not instructed) to teach a simple skill to a child (7-10 years old). We identified and coded a suite of subtle nonverbal behaviors that could be construed as facilitating learning. Dyads (n = 64) were recruited from two communities on Tanna Island that differ in their experience with formal schooling and their acceptance of Western institutions. We found evidence for parallel teaching strategies in both communities. However, the rate and diversity of teaching behaviors were positively associated with caregiver's experience with formal schooling and independently and negatively associated with being from a village that rejects Western-derived institutions. These results further our understanding of how multiple cultural processes influence social learning and highlights the powerful influence of formal schooling on the cultural evolution of teaching in humans.
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10
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Sibilsky A, Colleran H, Deffner D, Haun DBM. Copying fideliy of functional and non-functional features in ni-Vanuatu children: A transmission chain study. PLoS One 2023; 18:e0274061. [PMID: 36757970 PMCID: PMC9910636 DOI: 10.1371/journal.pone.0274061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 08/21/2022] [Indexed: 02/10/2023] Open
Abstract
Observational learning plays a key role in cultural transmission. Previous transmission chain experiments have shown that children are able to maintain information across multiple generations through observational learning. It still remains unclear how the transmission of functional vs. non-functional information and the effect of being observed unfold across age in different communities. Here, we examine children's copying fidelity in observational learning of 5- to 13-year-olds from five different communities in Vanuatu, both individually (n = 263, 144 boys) and throughout a transmission chain of five to six children (n = 324, 178 boys). We additionally varied the functionality of the feature being copied (shape vs. color) and the copying context (observed vs. unobserved). Further, we also study developmental and cultural variation in the interaction of features and conditions. We find that children transmit the functional feature shape more faithfully than the non-functional feature color, both in the dyadic transitions as well as the transmission chains with an increasing tendency to do so as they get older. The age patterns show greater variation between communities for color than for shape. Overall, we find that being observed shows no uniform effects but influences transmission differently across communities. Our study shows that children are prone to passing on a functional feature across multiple generations of peers. Children copy non-functional features as well, but with lower fidelity. In sum, our results show children's high propensity and developing abilities for observational learning, ultimately allowing for effective cultural transmission.
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Affiliation(s)
- Anne Sibilsky
- Department of Comparative Cultural Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Leipzig Research Center for Early Child Development, Leipzig University, Leipzig, Germany
| | - Heidi Colleran
- BirthRites Independent Max Planck Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Dominik Deffner
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Science of Intelligence Excellence Cluster, Technical University Berlin, Berlin, Germany
- Center for Adaptive Rationality, Max Planck Institute for Human Development, Berlin, Germany
| | - Daniel B. M. Haun
- Department of Comparative Cultural Psychology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Leipzig Research Center for Early Child Development, Leipzig University, Leipzig, Germany
- * E-mail:
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11
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Arias L, Emlen NQ, Norder S, Julmi N, Lemus Serrano M, Chacon T, Wiegertjes J, Howard A, Azevedo MCBC, Caine A, Dunn S, Stoneking M, Van Gijn R. Interpreting mismatches between linguistic and genetic patterns among speakers of Tanimuka (Eastern Tukanoan) and Yukuna (Arawakan). Interface Focus 2023; 13:20220056. [PMID: 36655193 PMCID: PMC9732642 DOI: 10.1098/rsfs.2022.0056] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022] Open
Abstract
Northwestern Amazonia is home to a great degree of linguistic diversity, and the human societies in that region are part of complex networks of interaction that predate the arrival of Europeans. This study investigates the population and language contact dynamics between two languages found within this region, Yukuna and Tanimuka, which belong to the Arawakan and Tukanoan language families, respectively. We use evidence from linguistics, ethnohistory, ethnography and population genetics to provide new insights into the contact dynamics between these and other human groups in NWA. Our results show that the interaction between these groups intensified in the last 500 years, to the point that it is difficult to differentiate between them genetically. However, this close interaction has led to more substantial contact-induced language changes in Tanimuka than in Yukuna, consistent with a scenario of language shift and asymmetrical power relations.
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Affiliation(s)
- Leonardo Arias
- Leiden University Centre for Linguistics, Leiden, The Netherlands
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nicholas Q. Emlen
- Leiden University Centre for Linguistics, Leiden, The Netherlands
- University of Groningen (Campus Fryslân), Groningen, The Netherlands
| | - Sietze Norder
- Leiden University Centre for Linguistics, Leiden, The Netherlands
- Copernicus Institute of Sustainable Development, Environmental Science Group, Utrecht University, Princetonlaan 8a, 3584 CB Utrecht, The Netherlands
| | - Nora Julmi
- Leiden University Centre for Linguistics, Leiden, The Netherlands
| | | | | | | | - Austin Howard
- Leiden University Centre for Linguistics, Leiden, The Netherlands
| | | | - Allison Caine
- Leiden University Centre for Linguistics, Leiden, The Netherlands
- University of Wyoming, Laramie, WY, USA
| | - Saskia Dunn
- Leiden University Centre for Linguistics, Leiden, The Netherlands
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Laboratoire de Biométrie et Biologie Evolutive, Université Lyon 1, CNRS, UMR 5558, Villeurbanne, France
| | - Rik Van Gijn
- Leiden University Centre for Linguistics, Leiden, The Netherlands
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12
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Abstract
Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. Here, we provide an overview of Holocene dispersals in the light of genomic evidence and conclude that they have a complex history. Even when there is a demonstrated connection between a demographic expansion of people, the spread of agriculture, and the spread of a particular language family, the outcome in the results of contact between expanding and resident groups is highly variable. Further research is needed to identify the factors and social circumstances that have influenced this variation and complex history.
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13
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Taufik L, Teixeira JC, Llamas B, Sudoyo H, Tobler R, Purnomo GA. Human Genetic Research in Wallacea and Sahul: Recent Findings and Future Prospects. Genes (Basel) 2022; 13:genes13122373. [PMID: 36553640 PMCID: PMC9778601 DOI: 10.3390/genes13122373] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/08/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Genomic sequence data from worldwide human populations have provided a range of novel insights into our shared ancestry and the historical migrations that have shaped our global genetic diversity. However, a comprehensive understanding of these fundamental questions has been impeded by the lack of inclusion of many Indigenous populations in genomic surveys, including those from the Wallacean archipelago (which comprises islands of present-day Indonesia located east and west of Wallace's and Lydekker's Lines, respectively) and the former continent of Sahul (which once combined New Guinea and Australia during lower sea levels in the Pleistocene). Notably, these regions have been important areas of human evolution throughout the Late Pleistocene, as documented by diverse fossil and archaeological records which attest to the regional presence of multiple hominin species prior to the arrival of anatomically modern human (AMH) migrants. In this review, we collate and discuss key findings from the past decade of population genetic and phylogeographic literature focussed on the hominin history in Wallacea and Sahul. Specifically, we examine the evidence for the timing and direction of the ancient AMH migratory movements and subsequent hominin mixing events, emphasising several novel but consistent results that have important implications for addressing these questions. Finally, we suggest potentially lucrative directions for future genetic research in this key region of human evolution.
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Affiliation(s)
- Leonard Taufik
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
- Correspondence: (L.T.); (G.A.P.)
| | - João C. Teixeira
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
- Centre for Interdisciplinary Studies, University of Coimbra, 3004-531 Coimbra, Portugal
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Environment Institute, University of Adelaide, Adelaide, SA 5005, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 2601, Australia
- Indigenous Genomics Research Group, Telethon Kids Institute, Adelaide, SA 5001, Australia
| | - Herawati Sudoyo
- Mochtar Riady Institute for Nanotechnology, Tangerang 15810, Indonesia
| | - Raymond Tobler
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, ACT 2601, Australia
| | - Gludhug A. Purnomo
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, SA 5005, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, University of Adelaide, Adelaide, SA 5005, Australia
- Correspondence: (L.T.); (G.A.P.)
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14
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Barbieri C, Blasi DE, Arango-Isaza E, Sotiropoulos AG, Hammarström H, Wichmann S, Greenhill SJ, Gray RD, Forkel R, Bickel B, Shimizu KK. A global analysis of matches and mismatches between human genetic and linguistic histories. Proc Natl Acad Sci U S A 2022; 119:e2122084119. [PMID: 36399547 PMCID: PMC9704691 DOI: 10.1073/pnas.2122084119] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 10/10/2022] [Indexed: 10/14/2023] Open
Abstract
Human history is written in both our genes and our languages. The extent to which our biological and linguistic histories are congruent has been the subject of considerable debate, with clear examples of both matches and mismatches. To disentangle the patterns of demographic and cultural transmission, we need a global systematic assessment of matches and mismatches. Here, we assemble a genomic database (GeLaTo, or Genes and Languages Together) specifically curated to investigate genetic and linguistic diversity worldwide. We find that most populations in GeLaTo that speak languages of the same language family (i.e., that descend from the same ancestor language) are also genetically highly similar. However, we also identify nearly 20% mismatches in populations genetically close to linguistically unrelated groups. These mismatches, which occur within the time depth of known linguistic relatedness up to about 10,000 y, are scattered around the world, suggesting that they are a regular outcome in human history. Most mismatches result from populations shifting to the language of a neighboring population that is genetically different because of independent demographic histories. In line with the regularity of such shifts, we find that only half of the language families in GeLaTo are genetically more cohesive than expected under spatial autocorrelations. Moreover, the genetic and linguistic divergence times of population pairs match only rarely, with Indo-European standing out as the family with most matches in our sample. Together, our database and findings pave the way for systematically disentangling demographic and cultural history and for quantifying processes of shifts in language and social identities on a global scale.
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Affiliation(s)
- Chiara Barbieri
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
- Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Damián E. Blasi
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02134
- Human Relations Area Files, Yale University, New Haven, CT 06511-1225
| | - Epifanía Arango-Isaza
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
- Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland
| | | | - Harald Hammarström
- Department of Linguistics and Philology, University of Uppsala, Uppsala 75126, Sweden
| | - Søren Wichmann
- Cluster of Excellence ROOTS, Kiel University, Kiel 24118, Germany
| | - Simon J. Greenhill
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Russell D. Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Robert Forkel
- Department of Linguistic and Cultural Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Balthasar Bickel
- Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland
- Department of Comparative Language Science, University of Zurich, Zurich 8050, Switzerland
| | - Kentaro K. Shimizu
- Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich 8057, Switzerland
- Center for the Interdisciplinary Study of Language Evolution, University of Zurich, Zurich 8050, Switzerland
- Kihara Institute for Biological Research, Yokohama City University, 244-0813, Yokohama, Japan
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15
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Kyritsis T, Matthews LJ, Welch D, Atkinson QD. Shared cultural ancestry predicts the global diffusion of democracy. EVOLUTIONARY HUMAN SCIENCES 2022; 4:e42. [PMID: 37588939 PMCID: PMC10426017 DOI: 10.1017/ehs.2022.40] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 07/07/2022] [Accepted: 08/17/2022] [Indexed: 11/07/2022] Open
Abstract
Understanding global variation in democratic outcomes is critical to efforts to promote and sustain democracy today. Here, we use data on the democratic status of 221 modern and historical nations stretching back up to 200 years to show that, particularly over the last 50 years, nations with shared linguistic and, more recently, religious ancestry have more similar democratic outcomes. We also find evidence that for most of the last 50 years the democratic trajectory of a nation can be predicted by the democratic status of its linguistic and, less clearly, religious relatives, years and even decades earlier. These results are broadly consistent across three democracy indicators (Polity 5, Vanhanen's Index of Democracy, and Freedom in the World) and are not explained by geographical proximity or current shared language or religion. Our findings suggest that deep cultural ancestry remains an important force shaping the fortunes of modern nations, at least in part because democratic norms, institutions, and the factors that support them are more likely to diffuse between close cultural relatives.
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Affiliation(s)
| | - Luke J. Matthews
- RAND Corporation, Boston, Massachusetts, USA
- Faculty, Pardee RAND Graduate School, Santa Monica, California, USA
| | - David Welch
- Centre for Computational Evolution, University of Auckland, New Zealand
- School of Computer Science, University of Auckland, Auckland, New Zealand
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16
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Arauna LR, Bergstedt J, Choin J, Mendoza-Revilla J, Harmant C, Roux M, Mas-Sandoval A, Lémée L, Colleran H, François A, Valentin F, Cassar O, Gessain A, Quintana-Murci L, Patin E. The genomic landscape of contemporary western Remote Oceanians. Curr Biol 2022; 32:4565-4575.e6. [PMID: 36108636 DOI: 10.1016/j.cub.2022.08.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 07/01/2022] [Accepted: 08/18/2022] [Indexed: 11/25/2022]
Abstract
The Vanuatu archipelago served as a gateway to Remote Oceania during one of the most extensive human migrations to uninhabited lands ∼3,000 years ago. Ancient DNA studies suggest an initial settlement by East Asian-related peoples that was quickly followed by the arrival of Papuan-related populations, leading to a major population turnover. Yet there is uncertainty over the population processes and the sociocultural factors that have shaped the genomic diversity of ni-Vanuatu, who present nowadays among the world's highest linguistic and cultural diversity. Here, we report new genome-wide data for 1,433 contemporary ni-Vanuatu from 29 different islands, including 287 couples. We find that ni-Vanuatu derive their East Asian- and Papuan-related ancestry from the same source populations and descend from relatively synchronous, sex-biased admixture events that occurred ∼1,700-2,300 years ago, indicating a peopling history common to the whole archipelago. However, East Asian-related ancestry proportions differ markedly across islands, suggesting that the Papuan-related population turnover was geographically uneven. Furthermore, we detect Polynesian ancestry arriving ∼600-1,000 years ago to Central and South Vanuatu in both Polynesian-speaking and non-Polynesian-speaking populations. Last, we provide evidence for a tendency of spouses to carry similar genetic ancestry, when accounting for relatedness avoidance. The signal is not driven by strong genetic effects of specific loci or trait-associated variants, suggesting that it results instead from social assortative mating. Altogether, our findings provide an insight into both the genetic history of ni-Vanuatu populations and how sociocultural processes have shaped the diversity of their genomes.
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Affiliation(s)
- Lara R Arauna
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris 75015, France.
| | - Jacob Bergstedt
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris 75015, France; Institute of Environmental Medicine, Karolinska Institutet, Stockholm 171 77, Sweden; Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Jeremy Choin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris 75015, France; Chair Human Genomics and Evolution, Collège de France, Paris 75005, France
| | - Javier Mendoza-Revilla
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris 75015, France; Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Christine Harmant
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris 75015, France
| | - Maguelonne Roux
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris 75015, France; Bioinformatics and Biostatistics Hub, Institut Pasteur, Université Paris Cité, Paris 75015, France
| | - Alex Mas-Sandoval
- Department of Life Sciences, Imperial College London, Ascot SL5 7PY, UK
| | - Laure Lémée
- Institut Pasteur, Biomics Platform, Paris 75015, France
| | - Heidi Colleran
- BirthRites Independent Max Planck Research Group, Department of Human Behavior, Ecology, and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Alexandre François
- Langues, Textes, Traitements Informatiques, Cognition (LaTTiCe), UMR 8094, CNRS, Paris 75015, France
| | | | - Olivier Cassar
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Oncogenic Virus Epidemiology and Pathophysiology Unit, Paris 75015, France
| | - Antoine Gessain
- Institut Pasteur, Université Paris Cité, CNRS UMR 3569, Oncogenic Virus Epidemiology and Pathophysiology Unit, Paris 75015, France
| | - Lluis Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris 75015, France; Chair Human Genomics and Evolution, Collège de France, Paris 75005, France.
| | - Etienne Patin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris 75015, France.
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17
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Liu YC, Hunter-Anderson R, Cheronet O, Eakin J, Camacho F, Pietrusewsky M, Rohland N, Ioannidis A, Athens JS, Douglas MT, Ikehara-Quebral RM, Bernardos R, Culleton BJ, Mah M, Adamski N, Broomandkhoshbacht N, Callan K, Lawson AM, Mandl K, Michel M, Oppenheimer J, Stewardson K, Zalzala F, Kidd K, Kidd J, Schurr TG, Auckland K, Hill AVS, Mentzer AJ, Quinto-Cortés CD, Robson K, Kennett DJ, Patterson N, Bustamante CD, Moreno-Estrada A, Spriggs M, Vilar M, Lipson M, Pinhasi R, Reich D. Ancient DNA reveals five streams of migration into Micronesia and matrilocality in early Pacific seafarers. Science 2022; 377:72-79. [PMID: 35771911 PMCID: PMC9983687 DOI: 10.1126/science.abm6536] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Micronesia began to be peopled earlier than other parts of Remote Oceania, but the origins of its inhabitants remain unclear. We generated genome-wide data from 164 ancient and 112 modern individuals. Analysis reveals five migratory streams into Micronesia. Three are East Asian related, one is Polynesian, and a fifth is a Papuan source related to mainland New Guineans that is different from the New Britain-related Papuan source for southwest Pacific populations but is similarly derived from male migrants ~2500 to 2000 years ago. People of the Mariana Archipelago may derive all of their precolonial ancestry from East Asian sources, making them the only Remote Oceanians without Papuan ancestry. Female-inherited mitochondrial DNA was highly differentiated across early Remote Oceanian communities but homogeneous within, implying matrilocal practices whereby women almost never raised their children in communities different from the ones in which they grew up.
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Affiliation(s)
- Yue-Chen Liu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Joanne Eakin
- Independent Researcher, Albuquerque, NM 87107, USA
| | - Frank Camacho
- Department of Biology, University of Guam, Mangilao 96923, Guam
| | - Michael Pietrusewsky
- Department of Anthropology, University of Hawaiʻi at Mānoa, Honolulu, HI 96822, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Alexander Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA.,Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA
| | - J. Stephen Athens
- International Archaeological Research Institute, Inc., Honolulu, HI 96826, USA
| | | | | | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Brendan J. Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kenneth Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Judith Kidd
- Department of Genetics, Yale Medical School, New Haven, CT 06520, USA
| | - Theodore G. Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V. S. Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford OX3 7DQ, UK
| | - Alexander J. Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK,Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7LF, UK
| | - Consuelo D. Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Douglas J. Kennett
- Department of Anthropology, University of California, Santa Barbara, CA 93106, USA
| | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carlos D. Bustamante
- Department of Biomedical Data Science, Stanford University, Stanford, CA 94305, USA.,Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA 94305, USA,Current Address: Galatea Bio, Inc. 975 W 22nd St. Hialeah, FL 33010, USA
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), Unit of Advanced Genomics, CINVESTAV, Irapuato 36821, Mexico
| | - Matthew Spriggs
- School of Archaeology and Anthropology, The Australian National University, Canberra, ACT 2601, Australia,Vanuatu National Museum, Vanuatu Culture Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Miguel Vilar
- Department of Anthropology, University of Maryland, College Park, MD 20742, USA
| | - Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria,Human Evolution and Archaeological Sciences, University of Vienna, Vienna 1030, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
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18
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Ancient genomes from the last three millennia support multiple human dispersals into Wallacea. Nat Ecol Evol 2022; 6:1024-1034. [PMID: 35681000 PMCID: PMC9262713 DOI: 10.1038/s41559-022-01775-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 04/13/2022] [Indexed: 12/27/2022]
Abstract
Previous research indicates that human genetic diversity in Wallacea-islands in present-day Eastern Indonesia and Timor-Leste that were never part of the Sunda or Sahul continental shelves-has been shaped by complex interactions between migrating Austronesian farmers and indigenous hunter-gatherer communities. Yet, inferences based on present-day groups proved insufficient to disentangle this region's demographic movements and admixture timings. Here, we investigate the spatio-temporal patterns of variation in Wallacea based on genome-wide data from 16 ancient individuals (2600-250 years BP) from the North Moluccas, Sulawesi and East Nusa Tenggara. While ancestry in the northern islands primarily reflects contact between Austronesian- and Papuan-related groups, ancestry in the southern islands reveals additional contributions from Mainland Southeast Asia that seem to predate the arrival of Austronesians. Admixture time estimates further support multiple and/or continuous admixture involving Papuan- and Asian-related groups throughout Wallacea. Our results clarify previously debated times of admixture and suggest that the Neolithic dispersals into Island Southeast Asia are associated with the spread of multiple genetic ancestries.
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19
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Choin J, Quintana-Murci L. Paleogenomics: The demographic past of prehistoric Europeans. Curr Biol 2022; 32:R535-R538. [PMID: 35671731 DOI: 10.1016/j.cub.2022.04.081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Ancient DNA provides answers to long-standing debates about past human history. New work using demographic modeling on ancient genomes documents the nature and timing of the demographic processes - population size changes, divergences and admixture - that took place in prehistoric Europe.
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Affiliation(s)
- Jeremy Choin
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Unit of Human Evolutionary Genetics, F-75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, F-75005 Paris, France
| | - Lluis Quintana-Murci
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Unit of Human Evolutionary Genetics, F-75015 Paris, France; Chair of Human Genomics and Evolution, Collège de France, F-75005 Paris, France.
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20
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Brand CM, Colbran LL, Capra JA. Predicting Archaic Hominin Phenotypes from Genomic Data. Annu Rev Genomics Hum Genet 2022; 23:591-612. [PMID: 35440148 DOI: 10.1146/annurev-genom-111521-121903] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Ancient DNA provides a powerful window into the biology of extant and extinct species, including humans' closest relatives: Denisovans and Neanderthals. Here, we review what is known about archaic hominin phenotypes from genomic data and how those inferences have been made. We contend that understanding the influence of variants on lower-level molecular phenotypes-such as gene expression and protein function-is a promising approach to using ancient DNA to learn about archaic hominin traits. Molecular phenotypes have simpler genetic architectures than organism-level complex phenotypes, and this approach enables moving beyond association studies by proposing hypotheses about the effects of archaic variants that are testable in model systems. The major challenge to understanding archaic hominin phenotypes is broadening our ability to accurately map genotypes to phenotypes, but ongoing advances ensure that there will be much more to learn about archaic hominin phenotypes from their genomes. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 23 is October 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Colin M Brand
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John A Capra
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California, USA; , .,Bakar Computational Health Sciences Institute, University of California, San Francisco, California, USA
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21
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Kumar V, Wang W, Zhang J, Wang Y, Ruan Q, Yu J, Wu X, Hu X, Wu X, Guo W, Wang B, Niyazi A, Lv E, Tang Z, Cao P, Liu F, Dai Q, Yang R, Feng X, Ping W, Zhang L, Zhang M, Hou W, Liu Y, Bennett EA, Fu Q. Bronze and Iron Age population movements underlie Xinjiang population history. Science 2022; 376:62-69. [PMID: 35357918 DOI: 10.1126/science.abk1534] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The Xinjiang region in northwest China is a historically important geographical passage between East and West Eurasia. By sequencing 201 ancient genomes from 39 archaeological sites, we clarify the complex demographic history of this region. Bronze Age Xinjiang populations are characterized by four major ancestries related to Early Bronze Age cultures from the central and eastern Steppe, Central Asian, and Tarim Basin regions. Admixtures between Middle and Late Bronze Age Steppe cultures continued during the Late Bronze and Iron Ages, along with an inflow of East and Central Asian ancestry. Historical era populations show similar admixed and diverse ancestries as those of present-day Xinjiang populations. These results document the influence that East and West Eurasian populations have had over time in the different regions of Xinjiang.
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Affiliation(s)
- Vikas Kumar
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.,Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - Wenjun Wang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.,National Centre for Archaeology, Beijing 100013, China
| | - Jie Zhang
- Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi 830011, China
| | - Yongqiang Wang
- Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi 830011, China
| | - Qiurong Ruan
- Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi 830011, China
| | - Jianjun Yu
- Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi 830011, China
| | - Xiaohong Wu
- School of Archaeology and Museology, Peking University, Beijing 100871, China
| | - Xingjun Hu
- Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi 830011, China
| | - Xinhua Wu
- Institute of Archaeology, Chinese Academy of Social Science, Beijing 100710, China
| | - Wu Guo
- Institute of Archaeology, Chinese Academy of Social Science, Beijing 100710, China
| | - Bo Wang
- Xinjiang Uygur Autonomous Region Museum, Urumqi 830002, China
| | - Alipujiang Niyazi
- Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi 830011, China
| | - Enguo Lv
- Institute of Cultural Relics and Archaeology in Xinjiang, Urumqi 830011, China
| | - Zihua Tang
- Institute of Geology and Geophysics, Chinese Academy of Science, Beijing 100020, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qingyan Dai
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Ruowei Yang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Xiaotian Feng
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Wanjing Ping
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Weihong Hou
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.,Shanghai Qi Zhi Institute, Shanghai 200232, China
| | - E Andrew Bennett
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing 100044, China.,Shanghai Qi Zhi Institute, Shanghai 200232, China.,University of Chinese Academy of Sciences, Beijing 100049, China
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22
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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: 40] [Impact Index Per Article: 20.0] [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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23
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Chiang CWK. The Opportunities and Challenges of Integrating Population Histories Into Genetic Studies for Diverse Populations: A Motivating Example From Native Hawaiians. Front Genet 2021; 12:643883. [PMID: 34646295 PMCID: PMC8503554 DOI: 10.3389/fgene.2021.643883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
There is a well-recognized need to include diverse populations in genetic studies, but several obstacles continue to be prohibitive, including (but are not limited to) the difficulty of recruiting individuals from diverse populations in large numbers and the lack of representation in available genomic references. These obstacles notwithstanding, studying multiple diverse populations would provide informative, population-specific insights. Using Native Hawaiians as an example of an understudied population with a unique evolutionary history, I will argue that by developing key genomic resources and integrating evolutionary thinking into genetic epidemiology, we will have the opportunity to efficiently advance our knowledge of the genetic risk factors, ameliorate health disparity, and improve healthcare in this underserved population.
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Affiliation(s)
- Charleston W K Chiang
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, United States
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24
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Posth C, Zaro V, Spyrou MA, Vai S, Gnecchi-Ruscone GA, Modi A, Peltzer A, Mötsch A, Nägele K, Vågene ÅJ, Nelson EA, Radzevičiūtė R, Freund C, Bondioli LM, Cappuccini L, Frenzel H, Pacciani E, Boschin F, Capecchi G, Martini I, Moroni A, Ricci S, Sperduti A, Turchetti MA, Riga A, Zavattaro M, Zifferero A, Heyne HO, Fernández-Domínguez E, Kroonen GJ, McCormick M, Haak W, Lari M, Barbujani G, Bondioli L, Bos KI, Caramelli D, Krause J. The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect. SCIENCE ADVANCES 2021; 7:eabi7673. [PMID: 34559560 PMCID: PMC8462907 DOI: 10.1126/sciadv.abi7673] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.
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Affiliation(s)
- Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen 72074, Germany
| | - Valentina Zaro
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Maria A. Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72074, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Guido A. Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Alexander Peltzer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Angela Mötsch
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Åshild J. Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Section for Evolutionary Genomics, The GLOBE Institute, University of Copenhagen, Copenhagen 1350, Denmark
| | - Elizabeth A. Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Cäcilia Freund
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | | | - Luca Cappuccini
- Department of History, Archeology, Geography, Art and Entertainment, University of Florence, Firenze 50121, Italy
| | - Hannah Frenzel
- Anatomy Institute, University of Leipzig, Leipzig 04103, Germany
| | - Elsa Pacciani
- Superintendence of Archaeology, Fine Arts and Landscape for Firenze, Pistoia and Prato, Italy
| | - Francesco Boschin
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Giulia Capecchi
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Ivan Martini
- Department of Physical Sciences, Earth and Environment, University of Siena, Siena 53100, Italy
| | - Adriana Moroni
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Stefano Ricci
- Department of Physical Sciences, Earth and Environment, Research Unit Prehistory and Anthropology, University of Siena, Siena 53100, Italy
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome 00144, Italy
- Asia, Africa and Mediterranean Department, University of Naples, Naples 80134, Italy
| | | | - Alessandro Riga
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Monica Zavattaro
- Museum of Anthropology and Ethnology, Museum System of the University of Florence, Florence 50122, Italy
| | - Andrea Zifferero
- Department of History and Cultural Heritage, University of Siena, Siena 53100, Italy
| | - Henrike O. Heyne
- Institute for Molecular Medicine Finland (FIMM), Helsinki, Finland
- Program for Medical and Population Genetics/Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Guus J. Kroonen
- Department of Nordic Studies and Linguistics, University of Copenhagen, Copenhagen 2300, Denmark
- Leiden University Center for Linguistics, Leiden 2311 BE, Netherlands
| | - Michael McCormick
- Initiative for the Science of the Human Past, Department of History-Max Planck Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Harvard University, Cambridge, MA 02138, USA
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Martina Lari
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44121, Italy
| | - Luca Bondioli
- Bioarchaeology Service, Museum of Civilizations, Rome 00144, Italy
- Department of Cultural Heritage, University of Padua, Padua 35139, Italy
| | - Kirsten I. Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
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25
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Liu Y, Mao X, Krause J, Fu Q. Insights into human history from the first decade of ancient human genomics. Science 2021; 373:1479-1484. [PMID: 34554811 DOI: 10.1126/science.abi8202] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
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26
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Ioannidis AG, Blanco-Portillo J, Sandoval K, Hagelberg E, Barberena-Jonas C, Hill AVS, Rodríguez-Rodríguez JE, Fox K, Robson K, Haoa-Cardinali S, Quinto-Cortés CD, Miquel-Poblete JF, Auckland K, Parks T, Sofro ASM, Ávila-Arcos MC, Sockell A, Homburger JR, Eng C, Huntsman S, Burchard EG, Gignoux CR, Verdugo RA, Moraga M, Bustamante CD, Mentzer AJ, Moreno-Estrada A. Paths and timings of the peopling of Polynesia inferred from genomic networks. Nature 2021; 597:522-526. [PMID: 34552258 PMCID: PMC9710236 DOI: 10.1038/s41586-021-03902-8] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 08/12/2021] [Indexed: 02/08/2023]
Abstract
Polynesia was settled in a series of extraordinary voyages across an ocean spanning one third of the Earth1, but the sequences of islands settled remain unknown and their timings disputed. Currently, several centuries separate the dates suggested by different archaeological surveys2-4. Here, using genome-wide data from merely 430 modern individuals from 21 key Pacific island populations and novel ancestry-specific computational analyses, we unravel the detailed genetic history of this vast, dispersed island network. Our reconstruction of the branching Polynesian migration sequence reveals a serial founder expansion, characterized by directional loss of variants, that originated in Samoa and spread first through the Cook Islands (Rarotonga), then to the Society (Tōtaiete mā) Islands (11th century), the western Austral (Tuha'a Pae) Islands and Tuāmotu Archipelago (12th century), and finally to the widely separated, but genetically connected, megalithic statue-building cultures of the Marquesas (Te Henua 'Enana) Islands in the north, Raivavae in the south, and Easter Island (Rapa Nui), the easternmost of the Polynesian islands, settled in approximately AD 1200 via Mangareva.
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Affiliation(s)
- Alexander G Ioannidis
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA, USA.
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
| | - Javier Blanco-Portillo
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Carmina Barberena-Jonas
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Juan Esteban Rodríguez-Rodríguez
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Keolu Fox
- Department of Anthropology, University of California San Diego, La Jolla, CA, USA
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | | | - Consuelo D Quinto-Cortés
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico
| | | | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Abdul Salam M Sofro
- Department of Biochemistry, Faculty of Medicine, Yayasan Rumah Sakit Islam (YARSI) University, Cempaka Putih, Jakarta, Indonesia
| | - María C Ávila-Arcos
- International Laboratory for Human Genome Research (LIIGH), UNAM Juriquilla, Queretaro, Mexico
| | - Alexandra Sockell
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Julian R Homburger
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
| | - Celeste Eng
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Scott Huntsman
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Program in Pharmaceutical Sciences and Pharmacogenomics, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Christopher R Gignoux
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Denver, CO, USA
| | - Ricardo A Verdugo
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Translational Oncology Department, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Mauricio Moraga
- Human Genetics Program, Institute of Biomedical Sciences, Faculty of Medicine, University of Chile, Santiago, Chile
- Department of Anthropology, Faculty of Social Sciences, University of Chile, Santiago, Chile
| | - Carlos D Bustamante
- Center for Computational, Evolutionary and Human Genomics (CEHG), Stanford University, Stanford, CA, USA
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, UK
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| | - Andrés Moreno-Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO)-Advanced Genomics Unit (UGA), CINVESTAV, Irapuato, Guanajuato, Mexico.
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27
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Evans CL, Greenhill SJ, Watts J, List JM, Botero CA, Gray RD, Kirby KR. The uses and abuses of tree thinking in cultural evolution. Philos Trans R Soc Lond B Biol Sci 2021; 376:20200056. [PMID: 33993767 PMCID: PMC8126464 DOI: 10.1098/rstb.2020.0056] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2021] [Indexed: 11/13/2022] Open
Abstract
Modern phylogenetic methods are increasingly being used to address questions about macro-level patterns in cultural evolution. These methods can illuminate the unobservable histories of cultural traits and identify the evolutionary drivers of trait change over time, but their application is not without pitfalls. Here, we outline the current scope of research in cultural tree thinking, highlighting a toolkit of best practices to navigate and avoid the pitfalls and 'abuses' associated with their application. We emphasize two principles that support the appropriate application of phylogenetic methodologies in cross-cultural research: researchers should (1) draw on multiple lines of evidence when deciding if and which types of phylogenetic methods and models are suitable for their cross-cultural data, and (2) carefully consider how different cultural traits might have different evolutionary histories across space and time. When used appropriately phylogenetic methods can provide powerful insights into the processes of evolutionary change that have shaped the broad patterns of human history. This article is part of the theme issue 'Foundations of cultural evolution'.
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Affiliation(s)
- Cara L. Evans
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Simon J. Greenhill
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- ARC Centre of Excellence for the Dynamics of Language, ANU College of Asia and the Pacific, Australian National University, Canberra 2700, Australia
| | - Joseph Watts
- Religion Programme, University of Otago, Dunedin 9016, New Zealand
- Centre for Research on Evolution, Belief and Behaviour, University of Otago, Dunedin 9016, New Zealand
| | - Johann-Mattis List
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Carlos A. Botero
- Department of Biology, Washington University in St Louis, St Louis, MO 63130, USA
| | - Russell D. Gray
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- School of Psychology, University of Auckland, Auckland 1010, New Zealand
| | - Kathryn R. Kirby
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Department of Ecology and Evolutionary Biology, University of Toronto, Toronto, ON, Canada M5S 3B2
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28
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Abstract
Cultural diversity is disappearing quickly. Whilst a phylogenetic approach makes explicit the continuous extinction of cultures, and the generation of new ones, cultural evolutionary changes such as the rise of agriculture or more recently colonisation can cause periods of mass cultural extinction. At the current rate, 90% of languages will become extinct or moribund by the end of this century. Unlike biological extinction, cultural extinction does not necessarily involve genetic extinction or even deaths, but results from the disintegration of a social entity and discontinuation of culture-specific behaviours. Here we propose an analytical framework to examine the phenomenon of cultural extinction. When examined over millennia, extinctions of cultural traits or institutions can be studied in a phylogenetic comparative framework that incorporates archaeological data on ancestral states. Over decades or centuries, cultural extinction can be studied in a behavioural ecology framework to investigate how the fitness consequences of cultural behaviours and population dynamics shift individual behaviours away from the traditional norms. Frequency-dependent costs and benefits are key to understanding both the origin and the loss of cultural diversity. We review recent evolutionary studies that have informed cultural extinction processes and discuss avenues of future studies.
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Affiliation(s)
- Hanzhi Zhang
- Department of Anthropology, University College London, LondonWC1H 0BW, UK
| | - Ruth Mace
- Department of Anthropology, University College London, LondonWC1H 0BW, UK
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29
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Choin J, Mendoza-Revilla J, Arauna LR, Cuadros-Espinoza S, Cassar O, Larena M, Ko AMS, Harmant C, Laurent R, Verdu P, Laval G, Boland A, Olaso R, Deleuze JF, Valentin F, Ko YC, Jakobsson M, Gessain A, Excoffier L, Stoneking M, Patin E, Quintana-Murci L. Genomic insights into population history and biological adaptation in Oceania. Nature 2021; 592:583-589. [PMID: 33854233 DOI: 10.1038/s41586-021-03236-5] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 01/13/2021] [Indexed: 12/27/2022]
Abstract
The Pacific region is of major importance for addressing questions regarding human dispersals, interactions with archaic hominins and natural selection processes1. However, the demographic and adaptive history of Oceanian populations remains largely uncharacterized. Here we report high-coverage genomes of 317 individuals from 20 populations from the Pacific region. We find that the ancestors of Papuan-related ('Near Oceanian') groups underwent a strong bottleneck before the settlement of the region, and separated around 20,000-40,000 years ago. We infer that the East Asian ancestors of Pacific populations may have diverged from Taiwanese Indigenous peoples before the Neolithic expansion, which is thought to have started from Taiwan around 5,000 years ago2-4. Additionally, this dispersal was not followed by an immediate, single admixture event with Near Oceanian populations, but involved recurrent episodes of genetic interactions. Our analyses reveal marked differences in the proportion and nature of Denisovan heritage among Pacific groups, suggesting that independent interbreeding with highly structured archaic populations occurred. Furthermore, whereas introgression of Neanderthal genetic information facilitated the adaptation of modern humans related to multiple phenotypes (for example, metabolism, pigmentation and neuronal development), Denisovan introgression was primarily beneficial for immune-related functions. Finally, we report evidence of selective sweeps and polygenic adaptation associated with pathogen exposure and lipid metabolism in the Pacific region, increasing our understanding of the mechanisms of biological adaptation to island environments.
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Affiliation(s)
- Jeremy Choin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | | | - Lara R Arauna
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France
| | - Sebastian Cuadros-Espinoza
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France.,Sorbonne Université, Collège doctoral, Paris, France
| | - Olivier Cassar
- Oncogenic Virus Epidemiology and Pathophysiology, Institut Pasteur, UMR 3569, CNRS, Paris, France
| | - Maximilian Larena
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Christine Harmant
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France
| | - Romain Laurent
- Muséum National d'Histoire Naturelle, UMR7206, CNRS, Université de Paris, Paris, France
| | - Paul Verdu
- Muséum National d'Histoire Naturelle, UMR7206, CNRS, Université de Paris, Paris, France
| | - Guillaume Laval
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France
| | - Anne Boland
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Robert Olaso
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Jean-François Deleuze
- Centre National de Recherche en Génomique Humaine (CNRGH), Institut de Biologie François Jacob, CEA, Université Paris-Saclay, Evry, France
| | - Frédérique Valentin
- Maison de l'Archéologie et de l'Ethnologie, UMR 7041, CNRS, Nanterre, France
| | - Ying-Chin Ko
- Environment-Omics-Disease Research Center, China Medical University and Hospital, Taichung, Taiwan
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Antoine Gessain
- Oncogenic Virus Epidemiology and Pathophysiology, Institut Pasteur, UMR 3569, CNRS, Paris, France
| | - Laurent Excoffier
- Institute of Ecology and Evolution, University of Bern, Bern, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Mark Stoneking
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Etienne Patin
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France.
| | - Lluis Quintana-Murci
- Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris, France. .,Collège de France, Paris, France.
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30
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Zhang M, Sun G, Ren L, Yuan H, Dong G, Zhang L, Liu F, Cao P, Ko AMS, Yang MA, Hu S, Wang GD, Fu Q. Ancient DNA Evidence from China Reveals the Expansion of Pacific Dogs. Mol Biol Evol 2021; 37:1462-1469. [PMID: 31913480 DOI: 10.1093/molbev/msz311] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
The ancestral homeland of Australian dingoes and Pacific dogs is proposed to be in South China. However, the location and timing of their dispersal and relationship to dog domestication is unclear. Here, we sequenced 7,000- to 2,000-year-old complete mitochondrial DNA (mtDNA) genomes of 27 ancient canids (one gray wolf and 26 domestic dogs) from the Yellow River and Yangtze River basins (YYRB). These are the first complete ancient mtDNA of Chinese dogs from the cradle of early Chinese civilization. We found that most ancient dogs (18/26) belong to the haplogroup A1b lineage that is found in high frequency in present-day Australian dingoes and precolonial Pacific Island dogs but low frequency in present-day China. Particularly, a 7,000-year-old dog from the Tianluoshan site in Zhejiang province possesses a haplotype basal to the entire haplogroup A1b lineage. We propose that A1b lineage dogs were once widely distributed in the YYRB area. Following their dispersal to South China, and then into Southeast Asia, New Guinea and remote Oceania, they were largely replaced by dogs belonging to other lineages in the last 2,000 years in present-day China, especially North China.
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Affiliation(s)
- Ming Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Guoping Sun
- Zhejiang Provincial Institute of Relics and Archaeology, Hangzhou, China
| | - Lele Ren
- School of History and Culture, Lanzhou University, Lanzhou, China
| | - Haibing Yuan
- National Demonstration Center for Experimental Archaeology Education, Department of Archaeology, Sichuan University, Chengdu, China
| | - Guanghui Dong
- Key Laboratory of Western China's Environmental Systems (Ministry of Education), College of Earth and Environmental Sciences, Lanzhou University, Lanzhou, China
| | - Lizhao Zhang
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Feng Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Peng Cao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Albert Min-Shan Ko
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Melinda A Yang
- Department of Biology, University of Richmond, Richmond, VA
| | - Songmei Hu
- Shaanxi Academy of Archaeology, Xi'an, China
| | - Guo-Dong Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
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31
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Sun J, Li YX, Ma PC, Yan S, Cheng HZ, Fan ZQ, Deng XH, Ru K, Wang CC, Chen G, Wei LH. Shared paternal ancestry of Han, Tai-Kadai-speaking, and Austronesian-speaking populations as revealed by the high resolution phylogeny of O1a-M119 and distribution of its sub-lineages within China. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 174:686-700. [PMID: 33555039 DOI: 10.1002/ajpa.24240] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 01/06/2021] [Accepted: 01/12/2021] [Indexed: 12/27/2022]
Abstract
OBJECTIVES The aim of this research was to explore the origin, diversification, and demographic history of O1a-M119 over the past 10,000 years, as well as its role during the formation of East Asian and Southeast Asian populations, particularly the Han, Tai-Kadai-speaking, and Austronesian-speaking populations. MATERIALS AND METHODS Y-chromosome sequences (n = 141) of the O1a-M119 lineage, including 17 newly generated in this study, were used to reconstruct a revised phylogenetic tree with age estimates, and identify sub-lineages. The geographic distribution of 12 O1a-M119 sub-lineages was summarized, based on 7325 O1a-M119 individuals identified among 60,009 Chinese males. RESULTS A revised phylogenetic tree, age estimation, and distribution maps indicated continuous expansion of haplogroup O1a-M119 over the past 10,000 years, and differences in demographic history across geographic regions. We propose several sub-lineages of O1a-M119 as founding paternal lineages of Han, Tai-Kadai-speaking, and Austronesian-speaking populations. The sharing of several young O1a-M119 sub-lineages with expansion times less than 6000 years between these three population groups supports a partial common ancestry for them in the Neolithic Age; however, the paternal genetic divergence pattern is much more complex than previous hypotheses based on ethnology, archeology, and linguistics. DISCUSSION Our analyses contribute to a better understanding of the demographic history of O1a-M119 sub-lineages over the past 10,000 years during the emergence of Han, Austronesians, Tai-Kadai-speaking populations. The data described in this study will assist in understanding of the history of Han, Tai-Kadai-speaking, and Austronesian-speaking populations from ethnology, archeology, and linguistic perspectives in the future.
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Affiliation(s)
- Jin Sun
- Xingyi Normal University for Nationalities, Xingyi, China
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Ying-Xiang Li
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Peng-Cheng Ma
- School of Life Sciences, Jilin University, Changchun, China
| | - Shi Yan
- School of Ethnology and Sociology, Minzu University of China, Beijing, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Kai Ru
- Enlighten Co., Ltd., Shanghai, China
| | - Chuan-Chao Wang
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
| | - Gang Chen
- Hunan Key Lab of Bioinformatics, School of Computer Science and Engineering, Central South University, Changsha, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, School of Sociology and Anthropology, Xiamen University, Xiamen, China
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
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32
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Abstract
Humans reached the Mariana Islands in the western Pacific by ∼3,500 y ago, contemporaneous with or even earlier than the initial peopling of Polynesia. They crossed more than 2,000 km of open ocean to get there, whereas voyages of similar length did not occur anywhere else until more than 2,000 y later. Yet, the settlement of Polynesia has received far more attention than the settlement of the Marianas. There is uncertainty over both the origin of the first colonizers of the Marianas (with different lines of evidence suggesting variously the Philippines, Indonesia, New Guinea, or the Bismarck Archipelago) as well as what, if any, relationship they might have had with the first colonizers of Polynesia. To address these questions, we obtained ancient DNA data from two skeletons from the Ritidian Beach Cave Site in northern Guam, dating to ∼2,200 y ago. Analyses of complete mitochondrial DNA genome sequences and genome-wide SNP data strongly support ancestry from the Philippines, in agreement with some interpretations of the linguistic and archaeological evidence, but in contradiction to results based on computer simulations of sea voyaging. We also find a close link between the ancient Guam skeletons and early Lapita individuals from Vanuatu and Tonga, suggesting that the Marianas and Polynesia were colonized from the same source population, and raising the possibility that the Marianas played a role in the eventual settlement of Polynesia.
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33
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Lipson M, Spriggs M, Valentin F, Bedford S, Shing R, Zinger W, Buckley H, Petchey F, Matanik R, Cheronet O, Rohland N, Pinhasi R, Reich D. Three Phases of Ancient Migration Shaped the Ancestry of Human Populations in Vanuatu. Curr Biol 2020; 30:4846-4856.e6. [PMID: 33065004 DOI: 10.1016/j.cub.2020.09.035] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 07/14/2020] [Accepted: 09/10/2020] [Indexed: 12/13/2022]
Abstract
The archipelago of Vanuatu has been at the crossroads of human population movements in the Pacific for the past three millennia. To help address several open questions regarding the history of these movements, we generated genome-wide data for 11 ancient individuals from the island of Efate dating from its earliest settlement to the recent past, including five associated with the Chief Roi Mata's Domain World Heritage Area, and analyzed them in conjunction with 34 published ancient individuals from Vanuatu and elsewhere in Oceania, as well as present-day populations. Our results outline three distinct periods of population transformations. First, the four earliest individuals, from the Lapita-period site of Teouma, are concordant with eight previously described Lapita-associated individuals from Vanuatu and Tonga in having almost all of their ancestry from a "First Remote Oceanian" source related to East and Southeast Asians. Second, both the Papuan ancestry predominating in Vanuatu for the past 2,500 years and the smaller component of Papuan ancestry found in Polynesians can be modeled as deriving from a single source most likely originating in New Britain, suggesting that the movement of people carrying this ancestry to Remote Oceania closely followed that of the First Remote Oceanians in time and space. Third, the Chief Roi Mata's Domain individuals descend from a mixture of Vanuatu- and Polynesian-derived ancestry and are related to Polynesian-influenced communities today in central, but not southern, Vanuatu, demonstrating Polynesian genetic input in multiple groups with independent histories.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
| | - Matthew Spriggs
- School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, ACT 2601, Australia; Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu.
| | | | - Stuart Bedford
- Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu; Department of Archaeology and Natural History, College of Asia-Pacific, The Australian National University, Canberra, ACT 2601, Australia; Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Richard Shing
- Vanuatu National Museum, Vanuatu Cultural Centre, Port Vila, Vanuatu
| | - Wanda Zinger
- Muséum national d'Histoire naturelle, UMR 7194 (HNHP), MNHN/CNRS/UPVD, Sorbonne Université, Musée de l'Homme, 75016 Paris, France
| | - Hallie Buckley
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Fiona Petchey
- Radiocarbon Dating Laboratory, Division of Health, Engineering, Computing and Science, University of Waikato, Hamilton 3240, New Zealand; ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society and Education, James Cook University, Cairns, QLD 4878, Australia
| | - Richard Matanik
- Lelema World Heritage Committee and Vanuatu Cultural Centre, Port Vila, Vanuatu
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria.
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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34
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Friedlaender JS, Tucci S. Human Migrations: Tales of the Pacific. Curr Biol 2020; 30:R1478-R1481. [DOI: 10.1016/j.cub.2020.11.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Parker C, Rohrlach AB, Friederich S, Nagel S, Meyer M, Krause J, Bos KI, Haak W. A systematic investigation of human DNA preservation in medieval skeletons. Sci Rep 2020; 10:18225. [PMID: 33106554 PMCID: PMC7588426 DOI: 10.1038/s41598-020-75163-w] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2020] [Accepted: 10/07/2020] [Indexed: 12/14/2022] Open
Abstract
Ancient DNA (aDNA) analyses necessitate the destructive sampling of archaeological material. Currently, the cochlea, part of the osseous inner ear located inside the petrous pyramid, is the most sought after skeletal element for molecular analyses of ancient humans as it has been shown to yield high amounts of endogenous DNA. However, destructive sampling of the petrous pyramid may not always be possible, particularly in cases where preservation of skeletal morphology is of top priority. To investigate alternatives, we present a survey of human aDNA preservation for each of ten skeletal elements in a skeletal collection from Medieval Germany. Through comparison of human DNA content and quality we confirm best performance of the petrous pyramid and identify seven additional sampling locations across four skeletal elements that yield adequate aDNA for most applications in human palaeogenetics. Our study provides a better perspective on DNA preservation across the human skeleton and takes a further step toward the more responsible use of ancient materials in human aDNA studies.
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Affiliation(s)
- Cody Parker
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Adam B Rohrlach
- Max Planck Institute for the Science of Human History, Jena, Germany
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA, Australia
| | - Susanne Friederich
- Landesamt für Denkmalpflege und Archäologie, Sachsen-Anhalt, Halle (Saale), Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany.
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36
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Blevins KE, Crane AE, Lum C, Furuta K, Fox K, Stone AC. Evolutionary history of Mycobacterium leprae in the Pacific Islands. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190582. [PMID: 33012236 PMCID: PMC7702798 DOI: 10.1098/rstb.2019.0582] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
As one of the oldest known human diseases, leprosy or Hansen's disease remains a public health concern around the world with over 200 000 new cases in 2018. Most human leprosy cases are caused by Mycobacterium leprae, but a small number of cases are now known to be caused by Mycobacterium lepromatosis, a sister taxon of M. leprae. The global pattern of genomic variation in M. leprae is not well defined. Particularly, in the Pacific Islands, the origins of leprosy are disputed. Historically, it has been argued that leprosy arrived on the islands during nineteenth century colonialism, but some oral traditions and palaeopathological evidence suggest an older introduction. To address this, as well as investigate patterns of pathogen exchange across the Pacific Islands, we extracted DNA from 39 formalin-fixed paraffin-embedded biopsy blocks dating to 1992-2016. Using whole-genome enrichment and next-generation sequencing, we produced nine M. leprae genomes dating to 1998-2015 and ranging from 4-63× depth of coverage. Phylogenetic analyses indicate that these strains belong to basal lineages within the M. leprae phylogeny, specifically falling in branches 0 and 5. The phylogeographical patterning and evolutionary dating analysis of these strains support a pre-modern introduction of M. leprae into the Pacific Islands. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Kelly E Blevins
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Adele E Crane
- School of Life Sciences, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Christopher Lum
- Department of Pathology, John A Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Kanako Furuta
- Hawaii Pathologists Laboratory, Honolulu, HI 96813, USA
| | - Keolu Fox
- Departments of Anthropology and Global Health, University of California, San Diego, CA, USA
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
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Broesch T, Crittenden AN, Beheim BA, Blackwell AD, Bunce JA, Colleran H, Hagel K, Kline M, McElreath R, Nelson RG, Pisor AC, Prall S, Pretelli I, Purzycki B, Quinn EA, Ross C, Scelza B, Starkweather K, Stieglitz J, Mulder MB. Navigating cross-cultural research: methodological and ethical considerations. Proc Biol Sci 2020; 287:20201245. [PMID: 32962541 PMCID: PMC7542829 DOI: 10.1098/rspb.2020.1245] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Accepted: 09/01/2020] [Indexed: 01/03/2023] Open
Abstract
The intensifying pace of research based on cross-cultural studies in the social sciences necessitates a discussion of the unique challenges of multi-sited research. Given an increasing demand for social scientists to expand their data collection beyond WEIRD (Western, educated, industrialized, rich and democratic) populations, there is an urgent need for transdisciplinary conversations on the logistical, scientific and ethical considerations inherent to this type of scholarship. As a group of social scientists engaged in cross-cultural research in psychology and anthropology, we hope to guide prospective cross-cultural researchers through some of the complex scientific and ethical challenges involved in such work: (a) study site selection, (b) community involvement and (c) culturally appropriate research methods. We aim to shed light on some of the difficult ethical quandaries of this type of research. Our recommendation emphasizes a community-centred approach, in which the desires of the community regarding research approach and methodology, community involvement, results communication and distribution, and data sharing are held in the highest regard by the researchers. We argue that such considerations are central to scientific rigour and the foundation of the study of human behaviour.
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Affiliation(s)
- Tanya Broesch
- Department of Psychology, Simon Fraser University, BC, Canada
| | | | - Bret A. Beheim
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Aaron D. Blackwell
- Department of Anthropology, Washington State University, Pullman, WA, USA
| | - John A. Bunce
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Heidi Colleran
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- BirthRites Independent Max Planck Research Group, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kristin Hagel
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michelle Kline
- Centre for Culture and Evolution, Brunel University, London, UK
| | - Richard McElreath
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Anne C. Pisor
- Department of Anthropology, Washington State University, Pullman, WA, USA
| | - Sean Prall
- Department of Anthropology, University of Missouri, MO, USA
| | - Ilaria Pretelli
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Purzycki
- Department of the Study of Religion, Aarhus University, Aarhus, Denmark
| | | | - Cody Ross
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Brooke Scelza
- Department of Anthropology, UCLA, Los Angeles, CA, USA
| | - Kathrine Starkweather
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of Illinois, Chicago, USA
| | | | - Monique Borgerhoff Mulder
- Department of Human Behavior, Ecology and Culture, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, University of California, Davis, CA, USA
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38
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Sun J, Wei LH, Wang LX, Huang YZ, Yan S, Cheng HZ, Ong RTH, Saw WY, Fan ZQ, Deng XH, Lu Y, Zhang C, Xu SH, Jin L, Teo YY, Li H. Paternal gene pool of Malays in Southeast Asia and its applications for the early expansion of Austronesians. Am J Hum Biol 2020; 33:e23486. [PMID: 32851723 DOI: 10.1002/ajhb.23486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Revised: 06/16/2020] [Accepted: 07/10/2020] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVES The origin and differentiation of Austronesian populations and their languages have long fascinated linguists, archeologists, and geneticists. However, the founding process of Austronesians and when they separated from their close relatives, such as the Daic and Austro-Asiatic populations in the mainland of Asia, remain unclear. In this study, we explored the paternal origin of Malays in Southeast Asia and the early differentiation of Austronesians. MATERIALS AND METHODS We generated whole Y-chromosome sequences of 50 Malays and co-analyzed 200 sequences from other Austronesians and related populations. We generated a revised phylogenetic tree with time estimation. RESULTS We identified six founding paternal lineages among the studied Malays samples. These founding lineages showed a surprisingly coincident expansion age at 5000 to 6000 years ago. We also found numerous mostly close related samples of the founding lineages of Malays among populations from Mainland of Asia. CONCLUSION Our analyses provided a refined phylogenetic resolution for the dominant paternal lineages of Austronesians found by previous studies. We suggested that the co-expansion of numerous founding paternal lineages corresponds to the initial differentiation of the most recent common ancestor of modern Austronesians. The splitting time and divergence pattern in perspective of paternal Y-chromosome evidence are highly consistent with the previous theories of ethnologists, linguists, and archeologists.
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Affiliation(s)
- Jin Sun
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Lan-Hai Wei
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China
| | | | - Yun-Zhi Huang
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China
| | - Shi Yan
- Human Phenome Institute, Fudan University, Shanghai, China
| | - Hui-Zhen Cheng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Rick Twee-Hee Ong
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
| | - Woei-Yuh Saw
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore.,Life Sciences Institute, National University of Singapore, Singapore, Singapore
| | - Zhi-Quan Fan
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China
| | - Xiao-Hua Deng
- Department of Anthropology and Ethnology, Institute of Anthropology, Xiamen University, Xiamen, China.,Center for collation and studies of Fujian local literature, Fujian University of Technology, Fuzhou, China
| | - Yan Lu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China
| | - Chao Zhang
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China
| | - Shu-Hua Xu
- Chinese Academy of Sciences (CAS) Key Laboratory of Computational Biology, Max Planck Independent Research Group on Population Genomics, CAS-MPG Partner Institute for Computational Biology (PICB), Shanghai Institute of Nutrition and Health, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, CAS, Shanghai, China.,School of Life Science and Technology, Shanghai Tech University, Shanghai, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Li Jin
- MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
| | - Yik-Ying Teo
- Saw Swee Hock School of Public Health, 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.,NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore, Singapore.,Department of Statistics and Applied Probability, National University of Singapore, Singapore, Singapore
| | - Hui Li
- B&R International Joint Laboratory for Eurasian Anthropology, Fudan University, Shanghai, China.,MOE Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai, China.,Human Phenome Institute, Fudan University, Shanghai, China
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39
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Callaway E. Ancient voyage carried Native Americans' DNA to remote Pacific islands. Nature 2020:10.1038/d41586-020-02055-4. [PMID: 32641794 DOI: 10.1038/d41586-020-02055-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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40
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Abstract
In this special collection, we address the origin and dispersal of the Transeurasian languages, i.e. Japonic, Koreanic, Tungusic, Mongolic and Turkic, from an interdisciplinary perspective. Our key objective is to effectively synthesize linguistic, archaeological and genetic evidence in a single approach, for which we use the term 'triangulation'. The 10 articles collected in this volume contribute to the question of whether and to what extent the early spread of Transeurasian languages was driven by agriculture in general, and by economic reliance on millet cultivation in particular.
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Affiliation(s)
- Martine Robbeets
- Eurasia3angle Research group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - 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
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41
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Nägele K, Posth C, Iraeta Orbegozo M, Chinique de Armas Y, Hernández Godoy ST, González Herrera UM, Nieves-Colón MA, Sandoval-Velasco M, Mylopotamitaki D, Radzeviciute R, Laffoon J, Pestle WJ, Ramos-Madrigal J, Lamnidis TC, Schaffer WC, Carr RS, Day JS, Arredondo Antúnez C, Rangel Rivero A, Martínez-Fuentes AJ, Crespo-Torres E, Roksandic I, Stone AC, Lalueza-Fox C, Hoogland M, Roksandic M, Hofman CL, Krause J, Schroeder H. Genomic insights into the early peopling of the Caribbean. Science 2020; 369:456-460. [PMID: 32499399 DOI: 10.1126/science.aba8697] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Accepted: 05/18/2020] [Indexed: 12/31/2022]
Abstract
The Caribbean was one of the last regions of the Americas to be settled by humans, but where they came from and how and when they reached the islands remain unclear. We generated genome-wide data for 93 ancient Caribbean islanders dating between 3200 and 400 calibrated years before the present and found evidence of at least three separate dispersals into the region, including two early dispersals into the Western Caribbean, one of which seems connected to radiation events in North America. This was followed by a later expansion from South America. We also detected genetic differences between the early settlers and the newcomers from South America, with almost no evidence of admixture. Our results add to our understanding of the initial peopling of the Caribbean and the movements of Archaic Age peoples in the Americas.
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Affiliation(s)
- Kathrin Nägele
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Miren Iraeta Orbegozo
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Silvia Teresita Hernández Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | | | - Maria A Nieves-Colón
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Marcela Sandoval-Velasco
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Dorothea Mylopotamitaki
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Rita Radzeviciute
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Jason Laffoon
- Faculty of Archaeology, Leiden University, Leiden, Netherlands
| | | | - Jazmin Ramos-Madrigal
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - William C Schaffer
- Liberal Arts Department, Phoenix College, Phoenix, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Robert S Carr
- Archaeological and Historical Conservancy Inc., Davie, FL, USA
| | - Jane S Day
- Research Atlantica Inc., Boca Raton, FL, USA
| | | | - Armando Rangel Rivero
- Museo Antropológico Montané, Facultad de Biología, Universidad de La Habana, Havana, Cuba
| | | | - Edwin Crespo-Torres
- Departamento de Sociología y Antropología, Universidad de Puerto Rico Rio Piedras, San Juan, Puerto Rico
| | - Ivan Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Anne C Stone
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Center for Bioarchaeological Research, Arizona State University, Tempe, AZ, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, Spanish National Research Council (CSIC)-Universitat Pompeu Fabra, Barcelona, Spain
| | - Menno Hoogland
- Faculty of Archaeology, Leiden University, Leiden, Netherlands.,Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Corinne L Hofman
- Faculty of Archaeology, Leiden University, Leiden, Netherlands.,Royal Netherlands Institute of Southeast Asian and Caribbean Studies, Leiden, Netherlands
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark. .,Faculty of Archaeology, Leiden University, Leiden, Netherlands
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Abstract
Over the past decade, a genomics revolution, made possible through the development of high-throughput sequencing, has triggered considerable progress in the study of ancient DNA, enabling complete genomes of past organisms to be reconstructed. A newly established branch of this field, ancient pathogen genomics, affords an in-depth view of microbial evolution by providing a molecular fossil record for a number of human-associated pathogens. Recent accomplishments include the confident identification of causative agents from past pandemics, the discovery of microbial lineages that are now extinct, the extrapolation of past emergence events on a chronological scale and the characterization of long-term evolutionary history of microorganisms that remain relevant to public health today. In this Review, we discuss methodological advancements, persistent challenges and novel revelations gained through the study of ancient pathogen genomes.
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43
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Gutiérrez Rico EM, Kikuchi A, Saito T, Kumondai M, Hishinuma E, Kaneko A, Chan CW, Gitaka J, Nakayoshi T, Oda A, Saito S, Hirasawa N, Hiratsuka M. CYP2D6 genotyping analysis and functional characterization of novel allelic variants in a Ni-Vanuatu and Kenyan population by assessing dextromethorphan O-demethylation activity. Drug Metab Pharmacokinet 2019; 35:89-101. [PMID: 32037159 DOI: 10.1016/j.dmpk.2019.07.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 07/03/2019] [Accepted: 07/16/2019] [Indexed: 12/11/2022]
Abstract
While CYP2D6 allele and phenotype frequencies have been extensively studied, currently, very little ethnically specific data is available regarding the East African and South Pacific region, including Kenya and Vanuatu. The absence of information regarding gene polymorphisms and their resulting clinical effects in these populations may hinder treatment strategies and patient outcome. Given the scarceness of CYP2D6 related data in these populations, the purpose of this study was to perform a pharmacogenomic analysis of the Kenyan and Ni-Vanuatu population and ultimately characterize the enzymatic properties of eight novel CYP2D6 variant proteins expressed in 293FT cells in vitro using dextromethorphan as a substrate. Our study revealed a prevalence of functional alleles in both populations a low frequency for decreased function defining genotypes in the Ni-Vanuatu population, with approximately 36% of our Kenyan subjects presenting substrate-dependent decreased function alleles. Additionally, 6 variants (P171L, G306R, V402L, K1, K2, and K3) showed significantly reduced intrinsic clearance compared to wild-type CYP2D6.1. Our findings aid in efforts to bridge the gap between pharmacogenomic analysis and clinical application, by providing useful information in the development of ethnic-specific strategies as well as stressing the importance of population-specific genotyping when conducting multi-regional clinical trials and designing therapeutic strategies.
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Affiliation(s)
- Evelyn Marie Gutiérrez Rico
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Aoi Kikuchi
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Takahiro Saito
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Masaki Kumondai
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan
| | - Eiji Hishinuma
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8575, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8575, Japan
| | - Akira Kaneko
- Department of Parasitology and Research Center for Infectious Disease Sciences, Graduate School of Medicine, Osaka City University, Osaka 545-8585, Japan; Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | - Chim Wai Chan
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 17177 Stockholm, Sweden
| | | | | | - Akifumi Oda
- Faculty of Pharmacy, Meijo University, Nagoya 468-8503, Japan
| | - Sakae Saito
- Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8575, Japan
| | - Noriyasu Hirasawa
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8575, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan
| | - Masahiro Hiratsuka
- Laboratory of Pharmacotherapy of Life-Style Related Diseases, Graduate School of Pharmaceutical Sciences, Tohoku University, Sendai 980-8578, Japan; Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, Sendai, 980-8575, Japan; Tohoku Medical Megabank Organization, Tohoku University, Sendai, 980-8575, Japan; Department of Pharmaceutical Sciences, Tohoku University Hospital, Sendai 980-8574, Japan.
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44
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Affiliation(s)
- Hao-Li Lin
- Institute of Anthropology, National Tsing Hua University, Hsinchu, Taiwan
| | - Richard Scaglion
- Department of Anthropology, University of Pittsburgh, Pittsburgh, PA, USA
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45
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Villalba-Mouco V, van de Loosdrecht MS, Posth C, Mora R, Martínez-Moreno J, Rojo-Guerra M, Salazar-García DC, Royo-Guillén JI, Kunst M, Rougier H, Crevecoeur I, Arcusa-Magallón H, Tejedor-Rodríguez C, García-Martínez de Lagrán I, Garrido-Pena R, Alt KW, Jeong C, Schiffels S, Utrilla P, Krause J, Haak W. Survival of Late Pleistocene Hunter-Gatherer Ancestry in the Iberian Peninsula. Curr Biol 2019; 29:1169-1177.e7. [DOI: 10.1016/j.cub.2019.02.006] [Citation(s) in RCA: 60] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2018] [Revised: 01/04/2019] [Accepted: 02/01/2019] [Indexed: 12/18/2022]
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46
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Palencia-Madrid L, Baeta M, Villaescusa P, Nuñez C, de Pancorbo MM, Luis JR, Fadhlaoui-Zid K, Somarelli J, Garcia-Bertrand R, Herrera RJ. The Marquesans at the fringes of the Austronesian expansion. Eur J Hum Genet 2019; 27:801-810. [PMID: 30683925 DOI: 10.1038/s41431-019-0336-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 12/19/2018] [Accepted: 12/25/2018] [Indexed: 11/09/2022] Open
Abstract
In the present study, 87 unrelated individuals from the Marquesas Archipelago in French Polynesia were typed using mtDNA, Y-chromosome and autosomal (STRs) markers and compared to key target populations from Island South East Asia (ISEA), Taiwan, and West and East Polynesia to investigate their genetic relationships. The Marquesas, located at the eastern-most fringes of the Austronesian expansion, offer a unique opportunity to examine the effects of a protracted population expansion wave on population structure. We explore the contribution of Melanesian, Asian and European heritage to the Marquesan islands of Nuku-Hiva, Hiva-Oa and Tahuata. Overall, the Marquesas Islands are genetically homogeneous. In the Marquesan Archipelago all of the mtDNA haplogroups are of Austronesian origin belonging to the B4a1 subhaplogroup as the region marks the end of a west to east decreasing cline of Melanesian mtDNA starting with the West Polynesian population of Tonga. Genetic discrepancies are less pronounced between the Marquesan and Society islands, and among the Marquesan islands. Interestingly, a number of Melanesian, Polynesian and European Y-chromosome haplogroups exhibit very different distribution between the Marquesan islands of Nuku Hiva and Hiva Oa, likely resulting from drift, differential migration involving various source populations and/or unique trading routes.
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Affiliation(s)
- Leire Palencia-Madrid
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Miriam Baeta
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Patricia Villaescusa
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Carolina Nuñez
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Marian M de Pancorbo
- BIOMICs Research Group, Dpto. Z. y Biologia Celular A., Lascaray Research Centre, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Javier Rodriguez Luis
- Area de Antropología, Facultad de Biología, Universidad de Santiago de Compostela, Campus Sur s/n, 15782, Santiago de Compostela, Spain
| | - Karima Fadhlaoui-Zid
- Faculty of Science of Tunis, Laboratory of Genetics, Immunology, and Human Pathologies, University Tunis, El Manar, Tunis, Tunisia
| | - Jason Somarelli
- Department of Medicine, Duke University Medical Center, Duke Cancer Institute, Durham, NC, 27710, USA
| | | | - Rene J Herrera
- Department of Molecular Biology, Colorado College, Colorado Springs, CO, 80903, USA.
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47
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The evolutionary history and human settlement of Australia and the Pacific. Curr Opin Genet Dev 2018; 53:53-59. [PMID: 30029008 DOI: 10.1016/j.gde.2018.06.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Revised: 06/09/2018] [Accepted: 06/26/2018] [Indexed: 11/21/2022]
Abstract
Understanding the timing and processes involved in the human settlement of Australia and the Pacific has significance for addressing some key debates relating to human origins and population expansions worldwide. Despite this, for many years, Pacific populations were seriously under-represented in genetic studies of human origins. The last 15 years, however, have seen some major genetic studies involving Australian and Pacific populations which have shed light on their origins and interactions, and the last five years have seen some major developments that are challenging long-held concepts of Pacific settlement.
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48
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McColl H, Racimo F, Vinner L, Demeter F, Gakuhari T, Moreno-Mayar JV, van Driem G, Gram Wilken U, Seguin-Orlando A, de la Fuente Castro C, Wasef S, Shoocongdej R, Souksavatdy V, Sayavongkhamdy T, Saidin MM, Allentoft ME, Sato T, Malaspinas AS, Aghakhanian FA, Korneliussen T, Prohaska A, Margaryan A, de Barros Damgaard P, Kaewsutthi S, Lertrit P, Nguyen TMH, Hung HC, Minh Tran T, Nghia Truong H, Nguyen GH, Shahidan S, Wiradnyana K, Matsumae H, Shigehara N, Yoneda M, Ishida H, Masuyama T, Yamada Y, Tajima A, Shibata H, Toyoda A, Hanihara T, Nakagome S, Deviese T, Bacon AM, Duringer P, Ponche JL, Shackelford L, Patole-Edoumba E, Nguyen AT, Bellina-Pryce B, Galipaud JC, Kinaston R, Buckley H, Pottier C, Rasmussen S, Higham T, Foley RA, Lahr MM, Orlando L, Sikora M, Phipps ME, Oota H, Higham C, Lambert DM, Willerslev E. The prehistoric peopling of Southeast Asia. Science 2018; 361:88-92. [DOI: 10.1126/science.aat3628] [Citation(s) in RCA: 216] [Impact Index Per Article: 36.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/29/2018] [Indexed: 12/11/2022]
Abstract
The human occupation history of Southeast Asia (SEA) remains heavily debated. Current evidence suggests that SEA was occupied by Hòabìnhian hunter-gatherers until ~4000 years ago, when farming economies developed and expanded, restricting foraging groups to remote habitats. Some argue that agricultural development was indigenous; others favor the “two-layer” hypothesis that posits a southward expansion of farmers giving rise to present-day Southeast Asian genetic diversity. By sequencing 26 ancient human genomes (25 from SEA, 1 Japanese Jōmon), we show that neither interpretation fits the complexity of Southeast Asian history: Both Hòabìnhian hunter-gatherers and East Asian farmers contributed to current Southeast Asian diversity, with further migrations affecting island SEA and Vietnam. Our results help resolve one of the long-standing controversies in Southeast Asian prehistory.
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Affiliation(s)
- Hugh McColl
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fernando Racimo
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Fabrice Demeter
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- National Museum of Natural History, Ecoanthropology and Ethnobiology, Musée de l’Homme, Paris, France
| | - Takashi Gakuhari
- Center for Cultural Resource Studies, Kanazawa University, Kanazawa, Japan
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | | | - George van Driem
- Institut für Sprachwissenschaft, Universität Bern, Bern, Switzerland
- University of New England, Armidale, NSW, Australia
| | - Uffe Gram Wilken
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | | | - Sally Wasef
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Rasmi Shoocongdej
- Department of Archaeology, Faculty of Archaeology, Silpakorn University, Bangkok, Thailand
| | - Viengkeo Souksavatdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Thongsa Sayavongkhamdy
- Department of Heritage, Ministry of Information, Culture and Tourism, Vientiane, Lao People’s Democratic Republic
| | - Mohd Mokhtar Saidin
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | - Morten E. Allentoft
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Takehiro Sato
- Department of Bioinformatics and Genomics, Graduate School of Advanced Preventive Medical Sciences, Kanazawa University, Kanazawa, Japan
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne and SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Farhang A. Aghakhanian
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | | | - Ana Prohaska
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Ashot Margaryan
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
| | | | - Supannee Kaewsutthi
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Patcharee Lertrit
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Thi Mai Huong Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Hsiao-chun Hung
- Department of Archaeology and Natural History, Australian National University, Canberra, ACT, Australia
| | - Thi Minh Tran
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Huu Nghia Truong
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Giang Hai Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Shaiful Shahidan
- Centre for Global Archaeological Research, Universiti Sains Malaysia, Penang, Malaysia
| | | | - Hiromi Matsumae
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Nobuo Shigehara
- Nara National Research Institute for Cultural Properties, Nara, Japan
| | - Minoru Yoneda
- University Museum, University of Tokyo, Tokyo, Japan
| | - Hajime Ishida
- Graduate School of Medicine, University of the Ryukyus, Nishihara, Okinawa, 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
| | - Atsushi Toyoda
- Center for Information Biology, National Institute of Genetics, Mishima, Japan
| | | | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, University of Dublin, Dublin, Ireland
| | - Thibaut Deviese
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Anne-Marie Bacon
- Laboratoire AMIS, Université Paris Descartes, Faculté de Chirurgie Dentaire, Montrouge, France
| | - Philippe Duringer
- École et Observatoire des Sciences de la Terre, Université de Strasbourg, Strasbourg, France
- Institut de Physique du Globe de Strasbourg (IPGS) (CNRS/UDS UMR 7516), Strasbourg, France
| | - Jean-Luc Ponche
- Laboratory “Image Ville et Environnement LIVE,” UMR7362, CNRS and Université de Strasbourg, Strasbourg, France
| | - Laura Shackelford
- Department of Anthropology, University of Illinois at Urbana-Champaign, Champaign, IL, USA
| | | | - Anh Tuan Nguyen
- Anthropological and Paleoenvironmental Department, Institute of Archaeology, Hanoi, Vietnam
| | - Bérénice Bellina-Pryce
- CNRS, UMR7055 “Préhistoire et Technologie,” Maison Archéologie et Ethnologie, Nanterre, France
| | - Jean-Christophe Galipaud
- Research Institute for Development, National Museum of Natural History, UMR Paloc, Paris, France
| | - Rebecca Kinaston
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hallie Buckley
- Department of Anatomy, School of Biomedical Sciences, University of Otago, Dunedin, New Zealand
| | | | - Simon Rasmussen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit (ORAU), University of Oxford, Oxford, UK
| | - Robert A. Foley
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Marta Mirazón Lahr
- Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Laboratoire AMIS, Université Paul Sabatier (UPS), Toulouse, France
| | - Martin Sikora
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
| | - Maude E. Phipps
- Jeffrey Cheah School of Medicine & Health Sciences, Monash University Malaysia, Jalan Lagoon Selatan, Sunway City, Selangor, Malaysia
| | - Hiroki Oota
- Kitasato University School of Medicine, Sagamihara, Kanagawa, Japan
| | - Charles Higham
- Department of Anthropology and Archaeology, University of Otago, Dunedin, New Zealand
- St. Catharine’s College, University of Cambridge, Cambridge, UK
| | - David M. Lambert
- Australian Research Centre for Human Evolution, Griffith University, Nathan, QLD, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
- Wellcome Trust Sanger Institute, Hinxton, UK
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Bergström A, Tyler-Smith C. Human Genetics: Busy Subway Networks in Remote Oceania? Curr Biol 2018; 28:R549-R551. [PMID: 29738726 DOI: 10.1016/j.cub.2018.03.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ancient human DNA from the Oceanian islands of Vanuatu reveals a surprisingly complex history of human settlement, featuring almost complete replacement shortly after initial colonisation, followed by mixing and a puzzling disconnect between genetic ancestry and language.
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Affiliation(s)
- Anders Bergström
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK.
| | - Chris Tyler-Smith
- The Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, CB10 1SA, UK
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50
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Ancient DNA offers clues to remote Pacific islands’ population puzzle. Nature 2018. [DOI: 10.1038/d41586-018-02620-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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