1
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Moreno-Mayar JV, Sousa da Mota B, Higham T, Klemm S, Gorman Edmunds M, Stenderup J, Iraeta-Orbegozo M, Laborde V, Heyer E, Torres Hochstetter F, Friess M, Allentoft ME, Schroeder H, Delaneau O, Malaspinas AS. Ancient Rapanui genomes reveal resilience and pre-European contact with the Americas. Nature 2024; 633:389-397. [PMID: 39261618 PMCID: PMC11390480 DOI: 10.1038/s41586-024-07881-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 07/26/2024] [Indexed: 09/13/2024]
Abstract
Rapa Nui (also known as Easter Island) is one of the most isolated inhabited places in the world. It has captured the imagination of many owing to its archaeological record, which includes iconic megalithic statues called moai1. Two prominent contentions have arisen from the extensive study of Rapa Nui. First, the history of the Rapanui has been presented as a warning tale of resource overexploitation that would have culminated in a major population collapse-the 'ecocide' theory2-4. Second, the possibility of trans-Pacific voyages to the Americas pre-dating European contact is still debated5-7. Here, to address these questions, we reconstructed the genomic history of the Rapanui on the basis of 15 ancient Rapanui individuals that we radiocarbon dated (1670-1950 CE) and whole-genome sequenced (0.4-25.6×). We find that these individuals are Polynesian in origin and most closely related to present-day Rapanui, a finding that will contribute to repatriation efforts. Through effective population size reconstructions and extensive population genetics simulations, we reject a scenario involving a severe population bottleneck during the 1600s, as proposed by the ecocide theory. Furthermore, the ancient and present-day Rapanui carry similar proportions of Native American admixture (about 10%). Using a Bayesian approach integrating genetic and radiocarbon dates, we estimate that this admixture event occurred about 1250-1430 CE.
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Affiliation(s)
- J Víctor Moreno-Mayar
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark.
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Tom Higham
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Science (HEAS) Network, University of Vienna, Vienna, Austria
| | - Signe Klemm
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper Stenderup
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Miren Iraeta-Orbegozo
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Véronique Laborde
- Direction Générale Déléguée aux Collections, Muséum national d'Histoire naturelle, Paris, France
| | - Evelyne Heyer
- Eco-anthropologie (EA), Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | | | - Martin Friess
- Eco-anthropologie (EA), Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Science, University of Copenhagen, Copenhagen, Denmark
| | | | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland.
- Swiss Institute of Bioinformatics, Lausanne, Switzerland.
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2
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Rodríguez-Varela R, Yaka R, Pochon Z, Sanchez-Pinto I, Solaun JL, Naidoo T, Guinet B, Pérez-Ramallo P, Lagerholm VK, de Anca Prado V, Valdiosera C, Krzewińska M, Herrasti L, Azkarate A, Götherström A. Five centuries of consanguinity, isolation, health, and conflict in Las Gobas: A Northern Medieval Iberian necropolis. SCIENCE ADVANCES 2024; 10:eadp8625. [PMID: 39196943 PMCID: PMC11352919 DOI: 10.1126/sciadv.adp8625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/15/2024] [Accepted: 07/19/2024] [Indexed: 08/30/2024]
Abstract
Between the 8th and 11th centuries CE, the Iberian Peninsula underwent profound upheaval due to the Umayyad invasion against the Visigoths, resulting in population shifts and lasting demographic impacts. Our understanding of this period is hindered by limited written sources and few archaeogenetic studies. We analyzed 33 individuals from Las Gobas, a necropolis in northern Spain, spanning the 7th to 11th centuries. By combining archaeological and osteological data with kinship, metagenomics, and ancestry analyses, we investigate conflicts, health, and demography of these individuals. We reveal intricate family relationships and genetic continuity within a consanguineous population while also identifying several zoonoses indicative of close interactions with animals. Notably, one individual was infected with a variola virus phylogenetically clustering with the northern European variola complex between ~885 and 1000 CE. Last, we did not detect a significant increase of North African or Middle East ancestries over time since the Islamic conquest of Iberia, possibly because this community remained relatively isolated.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Reyhan Yaka
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Zoé Pochon
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Iban Sanchez-Pinto
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - José Luis Solaun
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Thijessen Naidoo
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Ancient DNA Unit, Science for Life Laboratory, Stockholm, Sweden
| | - Benjamin Guinet
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute of Geoanthropology, Jena, Germany
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Cristina Valdiosera
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Lourdes Herrasti
- Departamento de Antropología, Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain
| | - Agustín Azkarate
- Departamento de Geografía, Prehistoria y Arqueología, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
- GPAC, C. I. Micaela Portilla, University of the Basque Country, UPV/EHU, Vitoria-Gasteiz, Spain
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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3
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Wang M, Huang Y, Liu K, Wang Z, Zhang M, Yuan H, Duan S, Wei L, Yao H, Sun Q, Zhong J, Tang R, Chen J, Sun Y, Li X, Su H, Yang Q, Hu L, Yun L, Yang J, Nie S, Cai Y, Yan J, Zhou K, Wang C, Zhu B, Liu C, He G. Multiple Human Population Movements and Cultural Dispersal Events Shaped the Landscape of Chinese Paternal Heritage. Mol Biol Evol 2024; 41:msae122. [PMID: 38885310 PMCID: PMC11232699 DOI: 10.1093/molbev/msae122] [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: 08/29/2023] [Revised: 05/30/2024] [Accepted: 06/13/2024] [Indexed: 06/20/2024] Open
Abstract
Large-scale genomic projects and ancient DNA innovations have ushered in a new paradigm for exploring human evolutionary history. However, the genetic legacy of spatiotemporally diverse ancient Eurasians within Chinese paternal lineages remains unresolved. Here, we report an integrated Y-chromosome genomic database encompassing 15,563 individuals from both modern and ancient Eurasians, including 919 newly reported individuals, to investigate the Chinese paternal genomic diversity. The high-resolution, time-stamped phylogeny reveals multiple diversification events and extensive expansions in the early and middle Neolithic. We identify four major ancient population movements, each associated with technological innovations that have shaped the Chinese paternal landscape. First, the expansion of early East Asians and millet farmers from the Yellow River Basin predominantly carrying O2/D subclades significantly influenced the formation of the Sino-Tibetan people and facilitated the permanent settlement of the Tibetan Plateau. Second, the dispersal of rice farmers from the Yangtze River Valley carrying O1 and certain O2 sublineages reshapes the genetic makeup of southern Han Chinese, as well as the Tai-Kadai, Austronesian, Hmong-Mien, and Austroasiatic people. Third, the Neolithic Siberian Q/C paternal lineages originated and proliferated among hunter-gatherers on the Mongolian Plateau and the Amur River Basin, leaving a significant imprint on the gene pools of northern China. Fourth, the J/G/R paternal lineages derived from western Eurasia, which were initially spread by Yamnaya-related steppe pastoralists, maintain their presence primarily in northwestern China. Overall, our research provides comprehensive genetic evidence elucidating the significant impact of interactions with culturally distinct ancient Eurasians on the patterns of paternal diversity in modern Chinese populations.
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Affiliation(s)
- Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou 510275, China
| | - Yuguo Huang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
| | - Kaijun Liu
- School of International Tourism and Culture, Guizhou Normal University, Guiyang 550025, China
- MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Menghan Zhang
- Institute of Modern Languages and Linguistics, Fudan University, Shanghai 200433, China
- Research Institute of Intelligent Complex Systems, Fudan University, Shanghai 200433, China
| | - Haibing Yuan
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong 637100, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Institute of Humanities and Human Sciences, Inner Mongolia Normal University, Hohhot 010022, China
| | - Hongbing Yao
- Belt and Road Research Center for Forensic Molecular Anthropology Gansu University of Political Science and Law, Lanzhou 730000, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Jie Zhong
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
| | - Renkuan Tang
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing 400331, China
| | - Jing Chen
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030001, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Xiangping Li
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Haoran Su
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Laboratory Medicine and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Qingxin Yang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Libing Yun
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, China
| | - Junbao Yang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming 650500, China
| | - Yan Cai
- School of Laboratory Medicine and Center for Genetics and Prenatal Diagnosis, Affiliated Hospital of North Sichuan Medical College, Nanchong, Sichuan 637007, China
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Jinzhong 030001, China
| | - Kun Zhou
- MoFang Human Genome Research Institute, Tianfu Software Park, Chengdu, Sichuan 610042, China
| | - Chuanchao Wang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361005, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong 510515, China
| | - Chao Liu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou 510515, China
- Anti-Drug Technology Center of Guangdong Province, Guangzhou 510230, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu 610000, China
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4
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Sasso S, Saag L, Spros R, Beneker O, Molinaro L, Biagini SA, Lehouck A, Van De Vijver K, Hui R, D’Atanasio E, Kushniarevich A, Kabral H, Metspalu E, Guellil M, Ali MQA, Geypen J, Hoebreckx M, Berk B, De Winter N, Driesen P, Pijpelink A, Van Damme P, Scheib CL, Deschepper E, Deckers P, Snoeck C, Dewilde M, Ervynck A, Tambets K, Larmuseau MHD, Kivisild T. Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders. Proc Natl Acad Sci U S A 2024; 121:e2406734121. [PMID: 38913897 PMCID: PMC11228521 DOI: 10.1073/pnas.2406734121] [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: 04/03/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.
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Affiliation(s)
- Stefania Sasso
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Rachèl Spros
- Research Unit: Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, 1050Brussels, Belgium
- Research Unit: Social History of Capitalism, Vrije Universiteit Brussel, 1050Brussels, Belgium
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
| | | | - Simone A. Biagini
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
- Institut de Biologia Evolutiva, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003Barcelona, Spain
| | | | | | - Ruoyun Hui
- Alan Turing Institute, NW1 2DBLondon, United Kingdom
| | - Eugenia D’Atanasio
- Institute of Molecular Biology and Pathology, Italian National Research Council, Rome, Italy
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Helja Kabral
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Evolutionary Anthropology, University of Vienna, 1030Vienna, Austria
| | | | | | | | - Birgit Berk
- Birgit Berk Fysische Anthropologie, 6231ECMeerssen, Netherlands
| | | | | | - April Pijpelink
- Crematie en Inhumatie Analyse (CRINA) Fysische Antropologie, 5237JG 's-Hertogenbosch, Netherlands
| | - Philip Van Damme
- Department of Neurology, KU Leuven and Center for Brain & Disease Research Vlaamse Instituut voor Biotechnologie, 3000Leuven, Belgium
- Department of Neurosciences, KU Leuven and Center for Brain & Disease Research VIB, 3000Leuven, Belgium
| | - Christiana L. Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Zoology, University of Cambridge, CB2 3EJCambridge, United Kingdom
- Department of Archaeology, University of Cambridge, CB2 3DZCambridge, United Kingdom
- St John’s College, University of Cambridge, CB2 1TPCambridge, United Kingdom
| | - Ewoud Deschepper
- Historical Archaeology Research Group, Department of Archaeology, Ghent University, 9000Ghent, Belgium
| | | | - Christophe Snoeck
- Research Unit: Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, 1050Brussels, Belgium
| | | | | | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | | | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
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5
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Pathak AK, Simonian H, Ibrahim IAA, Hrechdakian P, Behar DM, Ayub Q, Arsanov P, Metspalu E, Yepiskoposyan L, Rootsi S, Endicott P, Villems R, Sahakyan H. Human Y chromosome haplogroup L1-M22 traces Neolithic expansion in West Asia and supports the Elamite and Dravidian connection. iScience 2024; 27:110016. [PMID: 38883810 PMCID: PMC11177204 DOI: 10.1016/j.isci.2024.110016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2024] [Revised: 04/06/2024] [Accepted: 05/14/2024] [Indexed: 06/18/2024] Open
Abstract
West and South Asian populations profoundly influenced Eurasian genetic and cultural diversity. We investigate the genetic history of the Y chromosome haplogroup L1-M22, which, while prevalent in these regions, lacks in-depth study. Robust Bayesian analyses of 165 high-coverage Y chromosomes favor a West Asian origin for L1-M22 ∼20.6 thousand years ago (kya). Moreover, this haplogroup parallels the genome-wide genetic ancestry of hunter-gatherers from the Iranian Plateau and the Caucasus. We characterized two L1-M22 harboring population groups during the Early Holocene. One expanded with the West Asian Neolithic transition. The other moved to South Asia ∼8-6 kya but showed no expansion. This group likely participated in the spread of Dravidian languages. These South Asian L1-M22 lineages expanded ∼4-3 kya, coinciding with the Steppe ancestry introduction. Our findings advance the current understanding of Eurasian historical dynamics, emphasizing L1-M22's West Asian origin, associated population movements, and possible linguistic impacts.
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Affiliation(s)
- Ajai Kumar Pathak
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Department of Human Genetics, KU Leuven, 3000 Leuven, Belgium
| | - Hovann Simonian
- Armenian DNA Project at Family Tree DNA, Houston, TX 77008, USA
| | - Ibrahim Abdel Aziz Ibrahim
- Department of Pharmacology and Toxicology, Faculty of Medicine, Umm Al-Qura University, Makkah 21955, Saudi Arabia
| | | | - Doron M Behar
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Qasim Ayub
- Monash University Malaysia Genomics Platform, School of Science, Monash University, Bandar Sunway, Selangor Darul Ehsan 47500, Malaysia
| | - Pakhrudin Arsanov
- Chechen-Noahcho DNA Project at Family Tree DNA, Kostanay 110008, Kazakhstan
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Levon Yepiskoposyan
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Phillip Endicott
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Department of Archaeology and Anthropology, Bournemouth University, Fern Barrow, Poole, Dorset BH12 5BB, UK
- Department of Linguistics, University of Hawai'i at Mānoa, Honolulu, Hawai'i 96822, USA
- DFG Center for Advanced Studies, University of Tübingen, 72074 Tübingen, Germany
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Institute of Genomics, University of Tartu, 51010 Tartu, Estonia
- Laboratory of Evolutionary Genomics, Institute of Molecular Biology of National Academy of Sciences of the Republic of Armenia, Yerevan 0014, Armenia
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6
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Bozlak E, Pokharel K, Weldenegodguad M, Paasivaara A, Stammler F, Røed KH, Kantanen J, Wallner B. Inferences about the population history of Rangifer tarandus from Y chromosome and mtDNA phylogenies. Ecol Evol 2024; 14:e11573. [PMID: 38863721 PMCID: PMC11164974 DOI: 10.1002/ece3.11573] [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: 01/30/2024] [Revised: 05/27/2024] [Accepted: 05/30/2024] [Indexed: 06/13/2024] Open
Abstract
Reindeer, called caribou in North America, has a circumpolar distribution and all extant populations belong to the same species (Rangifer tarandus). It has survived the Holocene thanks to its immense adaptability and successful coexistence with humans in different forms of hunting and herding cultures. Here, we examine the paternal and maternal history of Rangifer based on robust Y-chromosomal and mitochondrial DNA (mtDNA) trees representing Eurasian tundra reindeer, Finnish forest reindeer, Svalbard reindeer, Alaska tundra caribou, and woodland caribou. We first assembled Y-chromosomal contigs, representing 1.3 Mb of single-copy Y regions. Based on 545 Y-chromosomal and 458 mtDNA SNPs defined in 55 males, maximum parsimony trees were created. We observed two well separated clades in both phylogenies: the "EuroBeringian clade" formed by animals from Arctic Islands, Eurasia, and a few from North America and the "North American clade" formed only by caribou from North America. The time calibrated Y tree revealed an expansion and dispersal of lineages across continents after the Last Glacial Maximum. We show for the first time unique paternal lineages in Svalbard reindeer and Finnish forest reindeer and reveal a circumscribed Y haplogroup in Fennoscandian tundra reindeer. The Y chromosome in domesticated reindeer is markedly diverse indicating that several male lineages have undergone domestication and less intensive selection on males. This study places R. tarandus onto the list of species with resolved Y and mtDNA phylogenies and builds the basis for studies of the distribution and origin of paternal and maternal lineages in the future.
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Affiliation(s)
- Elif Bozlak
- Department of Biomedical Sciences, Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
- Vienna Graduate School of Population GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
| | | | | | | | | | - Knut H. Røed
- Department of Preclinical Sciences and PathologyNorwegian University of Life SciencesÅsNorway
| | | | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and GeneticsUniversity of Veterinary Medicine ViennaViennaAustria
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7
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Wang Z, Wang M, Hu L, He G, Nie S. Evolutionary profiles and complex admixture landscape in East Asia: New insights from modern and ancient Y chromosome variation perspectives. Heliyon 2024; 10:e30067. [PMID: 38756579 PMCID: PMC11096704 DOI: 10.1016/j.heliyon.2024.e30067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2023] [Revised: 04/08/2024] [Accepted: 04/18/2024] [Indexed: 05/18/2024] Open
Abstract
Human Y-chromosomes are characterized by nonrecombination and uniparental inheritance, carrying traces of human history evolution and admixture. Large-scale population-specific genomic sources based on advanced sequencing technologies have revolutionized our understanding of human Y chromosome diversity and its anthropological and forensic applications. Here, we reviewed and meta-analyzed the Y chromosome genetic diversity of modern and ancient people from China and summarized the patterns of founding lineages of spatiotemporally different populations associated with their origin, expansion, and admixture. We emphasized the strong association between our identified founding lineages and language-related human dispersal events correlated with the Sino-Tibetan, Altaic, and southern Chinese multiple-language families related to the Hmong-Mien, Tai-Kadai, Austronesian, and Austro-Asiatic languages. We subsequently summarize the recent advances in translational applications in forensic and anthropological science, including paternal biogeographical ancestry inference (PBGAI), surname investigation, and paternal history reconstruction. Whole-Y sequencing or high-resolution panels with high coverage of terminal Y chromosome lineages are essential for capturing the genomic diversity of ethnolinguistically diverse East Asians. Generally, we emphasized the importance of including more ethnolinguistically diverse, underrepresented modern and spatiotemporally different ancient East Asians in human genetic research for a comprehensive understanding of the paternal genetic landscape of East Asians with a detailed time series and for the reconstruction of a reference database in the PBGAI, even including new technology innovations of Telomere-to-Telomere (T2T) for new genetic variation discovery.
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Affiliation(s)
- Zhiyong Wang
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Mengge Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-sen University, Guangzhou, 510275, China
| | - Liping Hu
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
| | - Shengjie Nie
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
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8
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Gnecchi-Ruscone GA, Rácz Z, Samu L, Szeniczey T, Faragó N, Knipper C, Friedrich R, Zlámalová D, Traverso L, Liccardo S, Wabnitz S, Popli D, Wang K, Radzeviciute R, Gulyás B, Koncz I, Balogh C, Lezsák GM, Mácsai V, Bunbury MME, Spekker O, le Roux P, Szécsényi-Nagy A, Mende BG, Colleran H, Hajdu T, Geary P, Pohl W, Vida T, Krause J, Hofmanová Z. Network of large pedigrees reveals social practices of Avar communities. Nature 2024; 629:376-383. [PMID: 38658749 PMCID: PMC11078744 DOI: 10.1038/s41586-024-07312-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 03/13/2024] [Indexed: 04/26/2024]
Abstract
From AD 567-568, at the onset of the Avar period, populations from the Eurasian Steppe settled in the Carpathian Basin for approximately 250 years1. Extensive sampling for archaeogenomics (424 individuals) and isotopes, combined with archaeological, anthropological and historical contextualization of four Avar-period cemeteries, allowed for a detailed description of the genomic structure of these communities and their kinship and social practices. We present a set of large pedigrees, reconstructed using ancient DNA, spanning nine generations and comprising around 300 individuals. We uncover a strict patrilineal kinship system, in which patrilocality and female exogamy were the norm and multiple reproductive partnering and levirate unions were common. The absence of consanguinity indicates that this society maintained a detailed memory of ancestry over generations. These kinship practices correspond with previous evidence from historical sources and anthropological research on Eurasian Steppe societies2. Network analyses of identity-by-descent DNA connections suggest that social cohesion between communities was maintained via female exogamy. Finally, despite the absence of major ancestry shifts, the level of resolution of our analyses allowed us to detect genetic discontinuity caused by the replacement of a community at one of the sites. This was paralleled with changes in the archaeological record and was probably a result of local political realignment.
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Affiliation(s)
| | - Zsófia Rácz
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Levente Samu
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Norbert Faragó
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Corina Knipper
- Curt Engelhorn Center for Archaeometry gGmbH, Mannheim, Germany
| | - Ronny Friedrich
- Curt Engelhorn Center for Archaeometry gGmbH, Mannheim, Germany
| | - Denisa Zlámalová
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czechia
| | - Luca Traverso
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Salvatore Liccardo
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Sandra Wabnitz
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Divyaratan Popli
- Department of Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ke Wang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Sciences, Fudan University, Shanghai, China
| | - Rita Radzeviciute
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - István Koncz
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Csilla Balogh
- Department of Art History, Istanbul Medeniyet University, Istanbul, Turkey
| | - Gabriella M Lezsák
- Institute of History, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Viktor Mácsai
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
| | - Magdalena M E Bunbury
- ARC Centre of Excellence for Australian Biodiversity and Heritage, College of Arts, Society and Education, James Cook University, Cairns, Queensland, Australia
| | - Olga Spekker
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary
- Department of Biological Anthropology, University of Szeged, Szeged, Hungary
| | - Petrus le Roux
- Department of Geological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Budapest, Hungary
| | - Heidi Colleran
- BirthRites Lise Meitner 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
| | - Tamás Hajdu
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Budapest, Hungary
| | | | - Walter Pohl
- Department of History, University of Vienna, Vienna, Austria
- Institute for Medieval Research, Austrian Academy of Sciences, Vienna, Austria
| | - Tivadar Vida
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Budapest, Hungary.
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Budapest, Hungary.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Brno, Czechia.
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9
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Martiniano R, Haber M, Almarri MA, Mattiangeli V, Kuijpers MCM, Chamel B, Breslin EM, Littleton J, Almahari S, Aloraifi F, Bradley DG, Lombard P, Durbin R. Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. CELL GENOMICS 2024; 4:100507. [PMID: 38417441 PMCID: PMC10943591 DOI: 10.1016/j.xgen.2024.100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/01/2024]
Abstract
The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.
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Affiliation(s)
- Rui Martiniano
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK.
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham Dubai, Dubai, United Arab Emirates
| | - Mohamed A Almarri
- Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Berenice Chamel
- Institut Français du Proche-Orient (MEAE/CNRS), Beirut, Lebanon
| | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Judith Littleton
- School of Social Sciences, University of Auckland, Auckland, New Zealand
| | - Salman Almahari
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain
| | - Fatima Aloraifi
- Mersey and West Lancashire Teaching Hospitals NHS Trust, Whiston Hospital, Warrington Road, Prescot, L35 5DR Liverpool, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierre Lombard
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain; Archéorient UMR 5133, CNRS, Université Lyon 2, Maison de l'Orient et de la Méditerranée - Jean Pouilloux, Lyon, France
| | - Richard Durbin
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK.
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10
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Hui R, Scheib CL, D’Atanasio E, Inskip SA, Cessford C, Biagini SA, Wohns AW, Ali MQ, Griffith SJ, Solnik A, Niinemäe H, Ge XJ, Rose AK, Beneker O, O’Connell TC, Robb JE, Kivisild T. Genetic history of Cambridgeshire before and after the Black Death. SCIENCE ADVANCES 2024; 10:eadi5903. [PMID: 38232165 PMCID: PMC10793959 DOI: 10.1126/sciadv.adi5903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.
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Affiliation(s)
- Ruoyun Hui
- Alan Turing Institute, London, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Christiana L. Scheib
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John’s College, University of Cambridge, Cambridge, UK
| | | | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Craig Cessford
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Anthony W. Wohns
- School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics and Biology, Stanford University, Stanford, CA, USA
| | | | - Samuel J. Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Niinemäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, UK
| | - Alice K. Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Durham, Durham, UK
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tamsin C. O’Connell
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Toomas Kivisild
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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11
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Bennett EA, Parasayan O, Prat S, Péan S, Crépin L, Yanevich A, Grange T, Geigl EM. Genome sequences of 36,000- to 37,000-year-old modern humans at Buran-Kaya III in Crimea. Nat Ecol Evol 2023; 7:2160-2172. [PMID: 37872416 DOI: 10.1038/s41559-023-02211-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 09/06/2023] [Indexed: 10/25/2023]
Abstract
Populations genetically related to present-day Europeans first appeared in Europe at some point after 38,000-40,000 years ago, following a cold period of severe climatic disruption. These new migrants would eventually replace the pre-existing modern human ancestries in Europe, but initial interactions between these groups are unclear due to the lack of genomic evidence from the earliest periods of the migration. Here we describe the genomes of two 36,000-37,000-year-old individuals from Buran-Kaya III in Crimea as belonging to this newer migration. Both genomes share the highest similarity to Gravettian-associated individuals found several thousand years later in southwestern Europe. These genomes also revealed that the population turnover in Europe after 40,000 years ago was accompanied by admixture with pre-existing modern human populations. European ancestry before 40,000 years ago persisted not only at Buran-Kaya III but is also found in later Gravettian-associated populations of western Europe and Mesolithic Caucasus populations.
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Affiliation(s)
- E Andrew Bennett
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing, China
| | - Oğuzhan Parasayan
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR2000, Human Evolutionary Genetics Unit, Paris, France
| | - Sandrine Prat
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Alliance Sorbonne Université, Musée de l'Homme, Palais de Chaillot, Paris, France
| | - Stéphane Péan
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Muséum national d'Histoire naturelle, Alliance Sorbonne Université, Institut de Paléontologie Humaine, Paris, France
| | - Laurent Crépin
- UMR 7194 (HNHP), MNHN/CNRS/UPVD, Muséum national d'Histoire naturelle, Alliance Sorbonne Université, Institut de Paléontologie Humaine, Paris, France
| | - Alexandr Yanevich
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Thierry Grange
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France.
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, Université Paris Cité, Paris, France.
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12
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García-Olivares V, Muñoz-Barrera A, Rubio-Rodríguez LA, Jáspez D, Díaz-de Usera A, Iñigo-Campos A, Veeramah KR, Alonso S, Thomas MG, Lorenzo-Salazar JM, González-Montelongo R, Flores C. Benchmarking of human Y-chromosomal haplogroup classifiers with whole-genome and whole-exome sequence data. Comput Struct Biotechnol J 2023; 21:4613-4618. [PMID: 37817776 PMCID: PMC10560978 DOI: 10.1016/j.csbj.2023.09.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 09/12/2023] [Accepted: 09/12/2023] [Indexed: 10/12/2023] Open
Abstract
In anthropological, medical, and forensic studies, the nonrecombinant region of the human Y chromosome (NRY) enables accurate reconstruction of pedigree relationships and retrieval of ancestral information. Using high-throughput sequencing (HTS) data, we present a benchmarking analysis of command-line tools for NRY haplogroup classification. The evaluation was performed using paired Illumina data from whole-genome sequencing (WGS) and whole-exome sequencing (WES) experiments from 50 unrelated donors. Additionally, as a validation, we also used paired WGS/WES datasets of 54 individuals from the 1000 Genomes Project. Finally, we evaluated the tools on data from third-generation HTS obtained from a subset of donors and one reference sample. Our results show that WES, despite typically offering less genealogical resolution than WGS, is an effective method for determining the NRY haplogroup. Y-LineageTracker and Yleaf showed the highest accuracy for WGS data, classifying precisely 98% and 96% of the samples, respectively. Yleaf outperforms all benchmarked tools in the WES data, classifying approximately 90% of the samples. Yleaf, Y-LineageTracker, and pathPhynder can correctly classify most samples (88%) sequenced with third-generation HTS. As a result, Yleaf provides the best performance for applications that use WGS and WES. Overall, our study offers researchers with a guide that allows them to select the most appropriate tool to analyze the NRY region using both second- and third-generation HTS data.
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Affiliation(s)
- Víctor García-Olivares
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Adrián Muñoz-Barrera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Luis A. Rubio-Rodríguez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - David Jáspez
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Ana Díaz-de Usera
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Antonio Iñigo-Campos
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Krishna R. Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY 11794-5245, United States
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Leioa, Bizkaia, Spain
- María Goyri Building, Biotechnology Center, Human Molecular Evolution Lab 2.08 UPV/EHU Science Park, 48940 Leioa, Bizkaia, Spain
| | - Mark G. Thomas
- UCL Genetics Institute, University College London (UCL), Gower Street, London WC1E 6BT, United Kingdom
- Research Department of Genetics, Evolution & Environment, University College London (UCL), Darwin Building, Gower Street, London WC1E 6BT, United Kingdom
| | - José M. Lorenzo-Salazar
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
| | - Rafaela González-Montelongo
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
| | - Carlos Flores
- Genomics Division, Instituto Tecnológico y de Energías Renovables (ITER), Santa Cruz de Tenerife, Spain
- Plataforma Genómica de Alto Rendimiento para el Estudio de la Biodiversidad, Instituto de Productos Naturales y Agrobiología (IPNA), Consejo Superior de Investigaciones Científicas, San Cristóbal de La Laguna, Spain
- Research Unit, Hospital Universitario Nuestra Señora de Candelaria, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias (CIBERES), Instituto de Salud Carlos III, Madrid, Spain
- Facultad de Ciencias de la Salud, Universidad Fernando de Pessoa Canarias, Las Palmas de Gran Canaria, Spain
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13
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Mutti G, Oteo-Garcia G, Caldon M, da Silva MJF, Minhós T, Cowlishaw G, Gottelli D, Huchard E, Carter A, Martinez FI, Raveane A, Capelli C. Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes. Sci Rep 2023; 13:13839. [PMID: 37620368 PMCID: PMC10449864 DOI: 10.1038/s41598-023-40931-x] [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: 04/03/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.
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Affiliation(s)
- Giacomo Mutti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Gonzalo Oteo-Garcia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
| | - Matteo Caldon
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
| | - Maria Joana Ferreira da Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Centro de Investigação Em Biodiversidade E Recursos Genéticos, CIBIOInBIO Laboratório AssociadoUniversidade Do Porto, Campus de Vairão, Vairão, Portugal
- ONE ‑ Organisms and Environment Group, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, UK
| | - Tânia Minhós
- Centre for Research in Anthropology (CRIA-NOVA FCSH), Av. Forças Armadas, Edifício ISCTE, Sala 2w2, 1649-026, Lisboa, Portugal
- Anthropology Department, School of Social Sciences and Humanities, Universidade Nova de Lisboa (NOVA FCSH), Av. de Berna, 26-C, 1069-061, Lisboa, Portugal
| | - Guy Cowlishaw
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Dada Gottelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Elise Huchard
- Institut Des Sciences de L'Evolution, CNRS, Universite de Montpellier, CC 065, 34095, Montpellier 05, France
| | - Alecia Carter
- Department of Anthropology, University College London, 14 Taviton Street, London, WC1H 0BW, UK
| | - Felipe I Martinez
- Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy.
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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14
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Serrano JG, Ordóñez AC, Santana J, Sánchez-Cañadillas E, Arnay M, Rodríguez-Rodríguez A, Morales J, Velasco-Vázquez J, Alberto-Barroso V, Delgado-Darias T, de Mercadal MCC, Hernández JC, Moreno-Benítez MA, Pais J, Ringbauer H, Sikora M, McColl H, Pino-Yanes M, Ferrer MH, Bustamante CD, Fregel R. The genomic history of the indigenous people of the Canary Islands. Nat Commun 2023; 14:4641. [PMID: 37582830 PMCID: PMC10427657 DOI: 10.1038/s41467-023-40198-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
The indigenous population of the Canary Islands, which colonized the archipelago around the 3rd century CE, provides both a window into the past of North Africa and a unique model to explore the effects of insularity. We generate genome-wide data from 40 individuals from the seven islands, dated between the 3rd-16rd centuries CE. Along with components already present in Moroccan Neolithic populations, the Canarian natives show signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations. The lack of gene flow between islands and constant or decreasing effective population sizes suggest that populations were isolated. While some island populations maintained relatively high genetic diversity, with the only detected bottleneck coinciding with the colonization time, other islands with fewer natural resources show the effects of insularity and isolation. Finally, consistent genetic differentiation between eastern and western islands points to a more complex colonization process than previously thought.
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Affiliation(s)
- Javier G Serrano
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Alejandra C Ordóñez
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Jonathan Santana
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Elías Sánchez-Cañadillas
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Matilde Arnay
- Bioanthropology: Paleopathology, Diet and Nutrition in Ancient Populations Group, Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Amelia Rodríguez-Rodríguez
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Jacob Morales
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Javier Velasco-Vázquez
- Servicio de Patrimonio Histórico, Cabildo de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | | | | | - Juan Carlos Hernández
- Museo Arqueológico de La Gomera, San Sebastián de La Gomera, Santa Cruz de Tenerife, Spain
| | | | - Jorge Pais
- Museo Arqueológico Benahoarita, Los Llanos de Aridane, Santa Cruz de Tenerife, Spain
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Mariano Hernández Ferrer
- Molecular Genetics and Biodiversity Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Rosa Fregel
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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15
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Hajiesmaeil M, Ravasini F, Risi F, Magnarini G, Olivieri A, D'Atanasio E, Galehdari H, Trombetta B, Cruciani F. High incidence of AZF duplications in clan-structured Iranian populations detected through Y chromosome sequencing read depth analysis. Sci Rep 2023; 13:11857. [PMID: 37481605 PMCID: PMC10363161 DOI: 10.1038/s41598-023-39069-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Accepted: 07/19/2023] [Indexed: 07/24/2023] Open
Abstract
The ampliconic region of the human Y chromosome consists of large duplicated sequences that can undergo non-allelic homologous recombination (NAHR), resulting in structural rearrangements that may cause infertility, especially when they occur in the azoospermia factor b/c (AZFb/c) region. Although AZF duplications have long been neglected due to the technical limitations of STS-based studies that focused mainly on deletions, recent next generation sequencing (NGS) technologies provided evidence for their importance in fertility. In this study, a NGS read depth approach was used to detect AZFb/c rearrangements in 87 Iranians from different ethnic groups. The duplication frequency in Iran proved to be twice as high as in the "1000 Genomes" dataset. Interestingly, most duplications were found in patrilineal ethnic groups, possibly as a consequence of their lower male effective population size which can counteract negative selection. Moreover, we found a large 8.0 Mb duplication, resulting in a fourfold increase in the copy number of AZFc genes, which to our knowledge is the largest duplication ever reported in this region. Overall, our results suggest that it is important to consider not only AZF deletions but also duplications to investigate the causes of male infertility, especially in patrilineal clan-based populations.
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Affiliation(s)
- Mogge Hajiesmaeil
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Francesco Ravasini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Flavia Risi
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Giorgia Magnarini
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Anna Olivieri
- Department of Biology and Biotechnology 'Lazzaro Spallanzani', Pavia University, Pavia, Italy
- NBFC, National Biodiversity Future Center, 90133, Palermo, Italy
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy
| | - Hamid Galehdari
- Department of Biology, Faculty of Sciences, Shahid Chamran University of Ahvaz, Ahvaz, Iran
| | - Beniamino Trombetta
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy
| | - Fulvio Cruciani
- Department of Biology and Biotechnologies 'Charles Darwin', Sapienza University of Rome, P.le Aldo Moro 5, 00185, Rome, Italy.
- Institute of Molecular Biology and Pathology (IBPM), CNR, 00185, Rome, Italy.
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16
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Posth C, Yu H, Ghalichi A, Rougier H, Crevecoeur I, Huang Y, Ringbauer H, Rohrlach AB, Nägele K, Villalba-Mouco V, Radzeviciute R, Ferraz T, Stoessel A, Tukhbatova R, Drucker DG, Lari M, Modi A, Vai S, Saupe T, Scheib CL, Catalano G, Pagani L, Talamo S, Fewlass H, Klaric L, Morala A, Rué M, Madelaine S, Crépin L, Caverne JB, Bocaege E, Ricci S, Boschin F, Bayle P, Maureille B, Le Brun-Ricalens F, Bordes JG, Oxilia G, Bortolini E, Bignon-Lau O, Debout G, Orliac M, Zazzo A, Sparacello V, Starnini E, Sineo L, van der Plicht J, Pecqueur L, Merceron G, Garcia G, Leuvrey JM, Garcia CB, Gómez-Olivencia A, Połtowicz-Bobak M, Bobak D, Le Luyer M, Storm P, Hoffmann C, Kabaciński J, Filimonova T, Shnaider S, Berezina N, González-Rabanal B, González Morales MR, Marín-Arroyo AB, López B, Alonso-Llamazares C, Ronchitelli A, Polet C, Jadin I, Cauwe N, Soler J, Coromina N, Rufí I, Cottiaux R, Clark G, Straus LG, Julien MA, Renhart S, Talaa D, Benazzi S, Romandini M, Amkreutz L, Bocherens H, Wißing C, Villotte S, de Pablo JFL, Gómez-Puche M, Esquembre-Bebia MA, Bodu P, Smits L, Souffi B, Jankauskas R, Kozakaitė J, Cupillard C, Benthien H, Wehrberger K, Schmitz RW, Feine SC, Schüler T, Thevenet C, Grigorescu D, Lüth F, Kotula A, Piezonka H, Schopper F, Svoboda J, Sázelová S, Chizhevsky A, Khokhlov A, Conard NJ, Valentin F, Harvati K, Semal P, Jungklaus B, Suvorov A, Schulting R, Moiseyev V, Mannermaa K, Buzhilova A, Terberger T, Caramelli D, Altena E, Haak W, Krause J. Palaeogenomics of Upper Palaeolithic to Neolithic European hunter-gatherers. Nature 2023; 615:117-126. [PMID: 36859578 PMCID: PMC9977688 DOI: 10.1038/s41586-023-05726-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 01/12/2023] [Indexed: 03/03/2023]
Abstract
Modern humans have populated Europe for more than 45,000 years1,2. Our knowledge of the genetic relatedness and structure of ancient hunter-gatherers is however limited, owing to the scarceness and poor molecular preservation of human remains from that period3. Here we analyse 356 ancient hunter-gatherer genomes, including new genomic data for 116 individuals from 14 countries in western and central Eurasia, spanning between 35,000 and 5,000 years ago. We identify a genetic ancestry profile in individuals associated with Upper Palaeolithic Gravettian assemblages from western Europe that is distinct from contemporaneous groups related to this archaeological culture in central and southern Europe4, but resembles that of preceding individuals associated with the Aurignacian culture. This ancestry profile survived during the Last Glacial Maximum (25,000 to 19,000 years ago) in human populations from southwestern Europe associated with the Solutrean culture, and with the following Magdalenian culture that re-expanded northeastward after the Last Glacial Maximum. Conversely, we reveal a genetic turnover in southern Europe suggesting a local replacement of human groups around the time of the Last Glacial Maximum, accompanied by a north-to-south dispersal of populations associated with the Epigravettian culture. From at least 14,000 years ago, an ancestry related to this culture spread from the south across the rest of Europe, largely replacing the Magdalenian-associated gene pool. After a period of limited admixture that spanned the beginning of the Mesolithic, we find genetic interactions between western and eastern European hunter-gatherers, who were also characterized by marked differences in phenotypically relevant variants.
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Affiliation(s)
- Cosimo Posth
- Archaeo- and Palaeogenetics, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany.
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - He Yu
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, China.
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Hélène Rougier
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Anthropology, California State University Northridge, Northridge, CA, USA
| | | | - Yilei Huang
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Instituto Universitario de Investigación en Ciencias Ambientales de Aragón, IUCA-Aragosaurus, Zaragoza, Spain
| | - Rita Radzeviciute
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alexander Stoessel
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute of Zoology and Evolutionary Research, University of Jena, Jena, Germany
| | - Rezeda Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Center of Excellence 'Archaeometry', Kazan Federal University, Kazan, Russia
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John's College, University of Cambridge, Cambridge, UK
| | - Giulio Catalano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biology, University of Padova, Padova, Italy
| | - Sahra Talamo
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Laurent Klaric
- UMR 8068 CNRS, TEMPS-Technologie et Ethnologie des Mondes Préhistoriques, Nanterre Cedex, France
| | - André Morala
- Université de Bordeaux, CNRS, MC, PACEA UMR 5199, Pessac, France
- Musée National de Préhistoire, Les Eyzies de Tayac, France
| | - Mathieu Rué
- Paléotime, Villard-de-Lans, France
- UMR 5140 CNRS, Archéologie des Sociétés Méditerranéennes, Université Paul-Valéry, Montpellier, France
| | - Stéphane Madelaine
- Université de Bordeaux, CNRS, MC, PACEA UMR 5199, Pessac, France
- Musée National de Préhistoire, Les Eyzies de Tayac, France
| | - Laurent Crépin
- UMR 7194, Histoire Naturelle de l'Homme Préhistorique (HNHP), Département Homme et Environnement, Muséum National d'Histoire Naturelle, CNRS, UPVD, Paris, France
| | - Jean-Baptiste Caverne
- Association APRAGE (Approches pluridisciplinaires de recherche archéologique du Grand-Est), Besançon, France
- Inrap GE, Metz, France
| | - Emmy Bocaege
- Skeletal Biology Research Centre, School of Anthropology and Conservation, University of Kent, Canterbury, UK
| | - Stefano Ricci
- Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, U.R. Preistoria e Antropologia, Università degli Studi di Siena, Siena, Italy
- Accademia dei Fisiocritici, Siena, Italy
| | - Francesco Boschin
- Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, U.R. Preistoria e Antropologia, Università degli Studi di Siena, Siena, Italy
- Accademia dei Fisiocritici, Siena, Italy
- Centro Studi sul Quaternario ODV, Sansepolcro, Italy
| | - Priscilla Bayle
- Université de Bordeaux, CNRS, MC, PACEA UMR 5199, Pessac, France
| | - Bruno Maureille
- Université de Bordeaux, CNRS, MC, PACEA UMR 5199, Pessac, France
| | | | | | - Gregorio Oxilia
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Human Ecology and Archaeology (HUMANE), Department of Archaeology and Anthropology, Institució Milà i Fontanals de Investigación en Humanidades, Consejo Superior de Investigaciones Científicas (IMF - CSIC), Barcelona, Spain
| | - Olivier Bignon-Lau
- UMR 8068 CNRS, TEMPS-Technologie et Ethnologie des Mondes Préhistoriques, Nanterre Cedex, France
| | - Grégory Debout
- UMR 8068 CNRS, TEMPS-Technologie et Ethnologie des Mondes Préhistoriques, Nanterre Cedex, France
| | - Michel Orliac
- UMR 8068 CNRS, TEMPS-Technologie et Ethnologie des Mondes Préhistoriques, Nanterre Cedex, France
| | - Antoine Zazzo
- UMR 7209-Archéozoologie et Archéobotanique-Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris, France
| | - Vitale Sparacello
- Dipartimento di Scienze Della Vita e Dell'Ambiente, Sezione di Neuroscienze e Antropologia, Università Degli Studi di Cagliari, Cittadella Monserrato, Cagliari, Italy
| | | | - Luca Sineo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | | | - Laure Pecqueur
- Inrap CIF, Croissy-Beaubourg, France
- UMR 7206 Éco-Anthropologie, Équipe ABBA. CNRS, MNHN, Université de Paris Cité, Musée de l'Homme, Paris, France
| | - Gildas Merceron
- PALEVOPRIM Lab UMR 7262 CNRS-INEE, University of Poitiers, Poitiers, France
| | - Géraldine Garcia
- PALEVOPRIM Lab UMR 7262 CNRS-INEE, University of Poitiers, Poitiers, France
- Centre de Valorisation des Collections Scientifiques, Université de Poitiers, Mignaloux Beauvoir, France
| | | | | | - Asier Gómez-Olivencia
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain
- Sociedad de Ciencias Aranzadi, Donostia-San Sebastian, Spain
- Centro UCM-ISCIII de Investigación sobre Evolución y Comportamiento Humanos, Madrid, Spain
| | | | - Dariusz Bobak
- Foundation for Rzeszów Archaeological Centre, Rzeszów, Poland
| | - Mona Le Luyer
- Université de Bordeaux, CNRS, MC, PACEA UMR 5199, Pessac, France
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Paul Storm
- Groninger Instituut voor Archeologie, Groningen University, Groningen, The Netherlands
| | | | - Jacek Kabaciński
- Institute of Archaeology and Ethnology, Polish Academy of Science, Poznań, Poland
| | | | - Svetlana Shnaider
- ArchaeoZOOlogy in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Institute of Archaeology SB RAS, Novosibirsk, Russia
| | - Natalia Berezina
- Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Borja González-Rabanal
- Grupo de I+D+i EVOADAPTA (Evolución Humana y Adaptaciones durante la Prehistoria) Departamento de Ciencias Históricas, Universidad de Cantabria, Santander, Spain
| | - Manuel R González Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria (IIIPC), Universidad de Cantabria-Gobierno de Cantabria-Banco Santander, Santander, Spain
| | - Ana B Marín-Arroyo
- Grupo de I+D+i EVOADAPTA (Evolución Humana y Adaptaciones durante la Prehistoria) Departamento de Ciencias Históricas, Universidad de Cantabria, Santander, Spain
| | - Belén López
- Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain
| | | | - Annamaria Ronchitelli
- Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, U.R. Preistoria e Antropologia, Università degli Studi di Siena, Siena, Italy
| | - Caroline Polet
- Quaternary Environments and Humans, OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Ivan Jadin
- Quaternary Environments and Humans, OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Nicolas Cauwe
- Musées Royaux d'Art et d'Histoire, Bruxelles, Belgium
| | - Joaquim Soler
- Institute of Historical Research, University of Girona, Catalonia, Spain
| | - Neus Coromina
- Institute of Historical Research, University of Girona, Catalonia, Spain
| | - Isaac Rufí
- Institute of Historical Research, University of Girona, Catalonia, Spain
| | | | - Geoffrey Clark
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA
| | - Lawrence G Straus
- Grupo de I+D+i EVOADAPTA (Evolución Humana y Adaptaciones durante la Prehistoria) Departamento de Ciencias Históricas, Universidad de Cantabria, Santander, Spain
- Department of Anthropology, University of New Mexico, Albuquerque, NM, USA
| | - Marie-Anne Julien
- UMR 7194, Histoire Naturelle de l'Homme Préhistorique (HNHP), Département Homme et Environnement, Muséum National d'Histoire Naturelle, CNRS, UPVD, Paris, France
- GéoArchPal-GéoArchÉon, Viéville sous-les-Cotes, France
| | - Silvia Renhart
- Archäologie & Münzkabinett, Universalmuseum Joanneum, Graz, Austria
| | - Dorothea Talaa
- Museum 'Das Dorf des Welan', Wöllersdorf-Steinabrückl, Austria
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Matteo Romandini
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
- Pradis Cave Museum, Clauzetto, Italy
- Department of Humanities, University of Ferrara, Ferrara, Italy
| | - Luc Amkreutz
- National Museum of Antiquities, Leiden, The Netherlands
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Hervé Bocherens
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany
- Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Christoph Wißing
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany
- Biogeology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Sébastien Villotte
- UMR 7206 Éco-Anthropologie, Équipe ABBA. CNRS, MNHN, Université de Paris Cité, Musée de l'Homme, Paris, France
- Quaternary Environments and Humans, OD Earth and History of Life, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Unité de Recherches Art, Archéologie Patrimoine, Université de Liège, Liège, Belgium
| | - Javier Fernández-López de Pablo
- I.U. de Investigación en Arqueología y Patrimonio Histórico, University of Alicante, Sant Vicent del Raspeig, Alicante, Spain
| | - Magdalena Gómez-Puche
- I.U. de Investigación en Arqueología y Patrimonio Histórico, University of Alicante, Sant Vicent del Raspeig, Alicante, Spain
| | | | - Pierre Bodu
- UMR 8068 CNRS, TEMPS-Technologie et Ethnologie des Mondes Préhistoriques, Nanterre Cedex, France
| | - Liesbeth Smits
- Amsterdam Centre of Ancient Studies and Archaeology, University of Amsterdam, Amsterdam, The Netherlands
| | - Bénédicte Souffi
- UMR 8068 CNRS, TEMPS-Technologie et Ethnologie des Mondes Préhistoriques, Nanterre Cedex, France
- Inrap CIF, Croissy-Beaubourg, France
| | - Rimantas Jankauskas
- Department of Anatomy, Histology and Anthropology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Justina Kozakaitė
- Department of Anatomy, Histology and Anthropology, Faculty of Medicine, Vilnius University, Vilnius, Lithuania
| | - Christophe Cupillard
- Service Régional de l'Archéologie de Bourgogne-Franche-Comté, Besançon Cedex, France
- Laboratoire de Chrono-Environnement, UMR 6249 du CNRS, UFR des Sciences et Techniques, Besançon Cedex, France
| | | | | | | | - Susanne C Feine
- LVR-LandesMuseum Bonn, Bonn, Germany
- Institute of Pre- and Protohistory, University of Tübingen, Tübingen, Germany
| | - Tim Schüler
- Department of Archeological Sciences, Thuringian State Office for Monuments Preservation and Archeology, Weimar, Germany
| | | | - Dan Grigorescu
- University of Bucharest, Faculty of Geology and Geophysics, Department of Geology, Bucharest, Romania
- Institute for Advanced Studies in Levant Culture and Civilization, Bucharest, Romania
| | | | - Andreas Kotula
- Brandenburg Authorities for Heritage Management and Archaeological State Museum, Zossen, Germany
| | - Henny Piezonka
- Institute for Pre- and Protohistory, Kiel University, Kiel, Germany
| | - Franz Schopper
- Brandenburg Authorities for Heritage Management and Archaeological State Museum, Zossen, Germany
| | - Jiří Svoboda
- Institute of Archeology at Brno, Czech Academy of Sciences, Centre for Palaeolithic and Paleoanthropology, Brno, Czechia
| | - Sandra Sázelová
- Institute of Archeology at Brno, Czech Academy of Sciences, Centre for Palaeolithic and Paleoanthropology, Brno, Czechia
| | - Andrey Chizhevsky
- Institute of Archaeology, Academy of Sciences of the Republic of Tatarstan, Kazan, Russia
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara, Russia
| | - Nicholas J Conard
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany
- Early Prehistory and Quaternary Ecology, Department of Geosciences, University of Tübingen, Tübingen, Germany
| | - Frédérique Valentin
- UMR 8068 CNRS, TEMPS-Technologie et Ethnologie des Mondes Préhistoriques, Nanterre Cedex, France
| | - Katerina Harvati
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, Tübingen, Germany
- Paleoanthropology, Institute for Archaeological Sciences, Department of Geosciences, University of Tübingen, Tübingen, Germany
- DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools', University of Tübingen, Tübingen, Germany
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | | | - Alexander Suvorov
- Institute of Archaeology Russian, Academy of Sciences, Moscow, Russia
| | | | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Saint Petersburg, Russia
| | | | - Alexandra Buzhilova
- Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Thomas Terberger
- Seminar for Pre- and Protohistory, Göttingen University, Göttingen, Germany
- Lower Saxony State Service for Cultural Heritage, Hannover, Germany
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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17
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Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AMA, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E. A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA. Nature 2022; 612:283-291. [PMID: 36477129 PMCID: PMC9729109 DOI: 10.1038/s41586-022-05453-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 10/18/2022] [Indexed: 12/12/2022]
Abstract
Late Pliocene and Early Pleistocene epochs 3.6 to 0.8 million years ago1 had climates resembling those forecasted under future warming2. Palaeoclimatic records show strong polar amplification with mean annual temperatures of 11-19 °C above contemporary values3,4. The biological communities inhabiting the Arctic during this time remain poorly known because fossils are rare5. Here we report an ancient environmental DNA6 (eDNA) record describing the rich plant and animal assemblages of the Kap København Formation in North Greenland, dated to around two million years ago. The record shows an open boreal forest ecosystem with mixed vegetation of poplar, birch and thuja trees, as well as a variety of Arctic and boreal shrubs and herbs, many of which had not previously been detected at the site from macrofossil and pollen records. The DNA record confirms the presence of hare and mitochondrial DNA from animals including mastodons, reindeer, rodents and geese, all ancestral to their present-day and late Pleistocene relatives. The presence of marine species including horseshoe crab and green algae support a warmer climate than today. The reconstructed ecosystem has no modern analogue. The survival of such ancient eDNA probably relates to its binding to mineral surfaces. Our findings open new areas of genetic research, demonstrating that it is possible to track the ecology and evolution of biological communities from two million years ago using ancient eDNA.
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Affiliation(s)
- Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Mikkel Winther Pedersen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Bianca De Sanctis
- Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Binia De Cahsan
- Section for Molecular Ecology and Evolution, The Globe Institute, Faculty of Health and Medical Sciences, Copenhagen, Denmark
| | - Thorfinn S Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Christian S Michelsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Niels Bohr Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karina K Sand
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, IRD, Université Gustave Eiffel, ISTerre, Grenoble, France
| | - Anthony H Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Astrid M A Schmidt
- Nordic Foundation for Development and Ecology (NORDECO), Copenhagen, Denmark
- DIS Study Abroad in Scandinavia, University of Copenhagen, Copenhagen, Denmark
| | - Kristian K Kjeldsen
- Department of Glaciology and Climate, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Alexey S Tesakov
- Geological Institute, Russian Academy of Sciences, Moscow, Russia
| | - Ian Snowball
- Department of Earth Sciences, Uppsala University, Uppsala, Sweden
| | - John C Gosse
- Department of Earth and Environmental Sciences, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Inger G Alsos
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
| | - Yucheng Wang
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | | | | | | | | | - Ana Prohaska
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Jeppe Å Kristensen
- Environmental Change Institute, School of Geography and the Environment, University of Oxford, Oxford, UK
- Geological Survey of Denmark and Greenland, (GEUS), Copenhagen, Denmark
| | - Morten Bjerager
- Department of Geophysics and Sedimentary Basins, Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Eric Coissac
- The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromsø, Norway
- University of Grenoble-Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | - Alexandra Rouillard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Geosciences, UiT-The Arctic University of Norway, Tromsø, Norway
| | | | - Antonio Fernandez-Guerra
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM Université PSL, Paris, France
| | - Marc Macias-Fauria
- School of Geography and the Environment, University of Oxford, Oxford, UK
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - John J Welch
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alan J Hidy
- Center for Accelerator Mass Spectrometry, Lawrence Livermore National Laboratory, Livermore, CA, USA
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew J Collins
- Department of Archaeology, University of Cambridge, Cambridge, UK
- Section for GeoBiology, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Nicolaj K Larsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM, University of Bremen, Bremen, Germany.
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18
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Castaneda C, Radović L, Felkel S, Juras R, Davis BW, Cothran EG, Wallner B, Raudsepp T. Copy number variation of horse Y chromosome genes in normal equine populations and in horses with abnormal sex development and subfertility: relationship of copy number variations with Y haplogroups. G3 (BETHESDA, MD.) 2022; 12:jkac278. [PMID: 36227030 PMCID: PMC9713435 DOI: 10.1093/g3journal/jkac278] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 10/08/2022] [Indexed: 11/03/2023]
Abstract
Structural rearrangements like copy number variations in the male-specific Y chromosome have been associated with male fertility phenotypes in human and mouse but have been sparsely studied in other mammalian species. Here, we designed digital droplet PCR assays for 7 horse male-specific Y chromosome multicopy genes and SRY and evaluated their absolute copy numbers in 209 normal male horses of 22 breeds, 73 XY horses with disorders of sex development and/or infertility, 5 Przewalski's horses and 2 kulans. This established baseline copy number for these genes in horses. The TSPY gene showed the highest copy number and was the most copy number variable between individuals and breeds. SRY was a single-copy gene in most horses but had 2-3 copies in some indigenous breeds. Since SRY is flanked by 2 copies of RBMY, their copy number variations were interrelated and may lead to SRY-negative XY disorders of sex development. The Przewalski's horse and kulan had 1 copy of SRY and RBMY. TSPY and ETSTY2 showed significant copy number variations between cryptorchid and normal males (P < 0.05). No significant copy number variations were observed in subfertile/infertile males. Notably, copy number of TSPY and ETSTY5 differed between successive male generations and between cloned horses, indicating germline and somatic mechanisms for copy number variations. We observed no correlation between male-specific Y chromosome gene copy number variations and male-specific Y chromosome haplotypes. We conclude that the ampliconic male-specific Y chromosome reference assembly has deficiencies and further studies with an improved male-specific Y chromosome assembly are needed to determine selective constraints over horse male-specific Y chromosome gene copy number and their relation to stallion reproduction and male biology.
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Affiliation(s)
- Caitlin Castaneda
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Lara Radović
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Sabine Felkel
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Vienna Graduate School of Population Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
- Department of Biotechnology, Institute of Computational Biology, BOKU University of Life Sciences and Natural Resources, Vienna 1190, Austria
| | - Rytis Juras
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Brian W Davis
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Ernest Gus Cothran
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
| | - Barbara Wallner
- Department of Biomedical Sciences, Institute of Animal Breeding and Genetics, University of Veterinary Medicine Vienna, Vienna 1210, Austria
| | - Terje Raudsepp
- Department of Veterinary Integrative Biosciences, School of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, TX 7784-4458, USA
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19
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Altınışık NE, Kazancı DD, Aydoğan A, Gemici HC, Erdal ÖD, Sarıaltun S, Vural KB, Koptekin D, Gürün K, Sağlıcan E, Fernandes D, Çakan G, Koruyucu MM, Lagerholm VK, Karamurat C, Özkan M, Kılınç GM, Sevkar A, Sürer E, Götherström A, Atakuman Ç, Erdal YS, Özer F, Erim Özdoğan A, Somel M. A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition. SCIENCE ADVANCES 2022; 8:eabo3609. [PMID: 36332018 PMCID: PMC9635823 DOI: 10.1126/sciadv.abo3609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.
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Affiliation(s)
- N. Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Duygu Deniz Kazancı
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayça Aydoğan
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Hasan Can Gemici
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Ömür Dilek Erdal
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Savaş Sarıaltun
- Department of Museology and Cultural Heritage Management, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Dilek Koptekin
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Gökhan Çakan
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Meliha Melis Koruyucu
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Cansu Karamurat
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey
| | - Arda Sevkar
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Yılmaz Selim Erdal
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Füsun Özer
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Aslı Erim Özdoğan
- Department of Archaeology, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
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