1
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Simões LG, Peyroteo-Stjerna R, Marchand G, Bernhardsson C, Vialet A, Chetty D, Alaçamlı E, Edlund H, Bouquin D, Dina C, Garmond N, Günther T, Jakobsson M. Genomic ancestry and social dynamics of the last hunter-gatherers of Atlantic France. Proc Natl Acad Sci U S A 2024; 121:e2310545121. [PMID: 38408241 DOI: 10.1073/pnas.2310545121] [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: 07/03/2023] [Accepted: 11/13/2023] [Indexed: 02/28/2024] Open
Abstract
Since the early Holocene, western and central Europe was inhabited by a genetically distinct group of Western Hunter-Gatherers (WHGs). This group was eventually replaced and assimilated by the incoming Neolithic farmers. The western Atlantic façade was home to some of the last Mesolithic sites of mainland Europe, represented by the iconic open-air sites at Hoedic and Téviec in southern Brittany, France. These sites are known for the unusually well-preserved and rich burials. Genomic studies of Mesolithic European hunter-gatherers have been limited to single or a few individuals per site and our understanding of the social dynamics of the last Mesolithic hunter-gatherers of Europe and their interactions with incoming farmers is limited. We sequenced and analyzed the complete genomes of 10 individuals from the Late Mesolithic sites of Hoedic, Téviec, and Champigny, in France, four of which sequenced to between 23- and 8-times genome coverage. The analysis of genomic, chronological and dietary data revealed that the Late Mesolithic populations in Brittany maintained distinct social units within a network of exchanging mates. This resulted in low intra-group biological relatedness that prevented consanguineous mating, despite the small population size of the Late Mesolithic groups. We found no genetic ancestry from Neolithic farmers in the analyzed hunter-gatherers, even though some of them may have coexisted with the first farming groups in neighboring regions. Hence, contrary to previous conclusions based on stable isotope data from the same sites, the Late Mesolithic forager community was limited in mate-exchange to neighboring hunter-gatherer groups, to the exclusion of Neolithic farmers.
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Affiliation(s)
- Luciana G Simões
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Rita Peyroteo-Stjerna
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
- Department of Historical Studies, University of Gothenburg, 405 30 Gothenburg, Sweden
- Department of Cultural Sciences, Linnaeus University, 351 95 Växjö, Sweden
- Centre for Archaeology, School of Arts and Humanities, University of Lisbon, 1600-214 Lisbon, Portugal
| | - Grégor Marchand
- Centre de Recherche en Archéologie, Archéosciences, Histoire, Université de Rennes, Rennes, CNRS 35065, France
| | - Carolina Bernhardsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Amélie Vialet
- Muséum national d'Histoire naturelle, UMR7194, Université Perpignan Via Domitia, Department "Homme et Environnement", Paris 75013, France
| | - Darshan Chetty
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
- Department of Entomology, Texas A&M University, College Station, TX 77843
| | - Erkin Alaçamlı
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
- Forensic Section, Regional Investigation Unit, Swedish Police Authority, 753 32 Uppsala, Sweden
| | - Denis Bouquin
- UMR 6298, ARTEHIS, Université de Bourgogne-CNRS, Bâtiment Sciences Gabriel, 21000 Dijon, France
- Service Archéologique du Grand Reims, 51100 Reims, France
| | - Christian Dina
- Nantes Université, CNRS, INSERM, l'institut du thorax, F-44000 Nantes, France
| | | | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
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2
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Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. Proc Natl Acad Sci U S A 2024; 121:e2312377121. [PMID: 38363870 PMCID: PMC10907250 DOI: 10.1073/pnas.2312377121] [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: 07/19/2023] [Accepted: 01/09/2024] [Indexed: 02/18/2024] Open
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
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Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
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3
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Mallick S, Micco A, Mah M, Ringbauer H, Lazaridis I, Olalde I, Patterson N, Reich D. The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes. Sci Data 2024; 11:182. [PMID: 38341426 PMCID: PMC10858950 DOI: 10.1038/s41597-024-03031-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Accepted: 01/31/2024] [Indexed: 02/12/2024] Open
Abstract
More than two hundred papers have reported genome-wide data from ancient humans. While the raw data for the vast majority are fully publicly available testifying to the commitment of the paleogenomics community to open data, formats for both raw data and meta-data differ. There is thus a need for uniform curation and a centralized, version-controlled compendium that researchers can download, analyze, and reference. Since 2019, we have been maintaining the Allen Ancient DNA Resource (AADR), which aims to provide an up-to-date, curated version of the world's published ancient human DNA data, represented at more than a million single nucleotide polymorphisms (SNPs) at which almost all ancient individuals have been assayed. The AADR has gone through six public releases at the time of writing and review of this manuscript, and crossed the threshold of >10,000 individuals with published genome-wide ancient DNA data at the end of 2022. This note is intended as a citable descriptor of the AADR.
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Affiliation(s)
- Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Howard Hughes Medical Institute, Boston, MA, 02115, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany
| | - Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- BIOMICs Research Group, University of the Basque Country, 01006, Vitoria-Gasteiz, Spain
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
- Howard Hughes Medical Institute, Boston, MA, 02115, USA.
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.
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4
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Cox SL, Nicklisch N, Francken M, Wahl J, Meller H, Haak W, Alt KW, Rosenstock E, Mathieson I. Socio-cultural practices may have affected sex differences in stature in Early Neolithic Europe. Nat Hum Behav 2024; 8:243-255. [PMID: 38081999 DOI: 10.1038/s41562-023-01756-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 10/09/2023] [Indexed: 02/21/2024]
Abstract
The rules and structure of human culture impact health as much as genetics or environment. To study these relationships, we combine ancient DNA (n = 230), skeletal metrics (n = 391), palaeopathology (n = 606) and dietary stable isotopes (n = 873) to analyse stature variation in Early Neolithic Europeans from North Central, South Central, Balkan and Mediterranean regions. In North Central Europe, stable isotopes and linear enamel hypoplasias indicate high environmental stress across sexes, but female stature is low, despite polygenic scores identical to males, and suggests that cultural factors preferentially supported male recovery from stress. In Mediterranean populations, sexual dimorphism is reduced, indicating male vulnerability to stress and no strong cultural preference for males. Our analysis indicates that biological effects of sex-specific inequities can be linked to cultural influences at least as early as 7,000 yr ago, and culture, more than environment or genetics, drove height disparities in Early Neolithic Europe.
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Affiliation(s)
- Samantha L Cox
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
- Physical Anthropology Section, Penn Museum, University of Pennsylvania, Philadelphia, PA, USA.
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria
| | - Michael Francken
- State Office for Cultural Heritage Management Baden-Württemberg, Osteology, Konstanz, Germany
| | - Joachim Wahl
- Paleoanthropology Section, Institute of Archaeological Sciences, Eberhard Karls University, Tübingen, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt, State Museum of Prehistory, Halle, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria
| | - Eva Rosenstock
- Bonn Center for ArchaeoSciences, Universität Bonn, Bonn, Germany
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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5
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Antonio ML, Weiß CL, Gao Z, Sawyer S, Oberreiter V, Moots HM, Spence JP, Cheronet O, Zagorc B, Praxmarer E, Özdoğan KT, Demetz L, Gelabert P, Fernandes D, Lucci M, Alihodžić T, Amrani S, Avetisyan P, Baillif-Ducros C, Bedić Ž, Bertrand A, Bilić M, Bondioli L, Borówka P, Botte E, Burmaz J, Bužanić D, Candilio F, Cvetko M, De Angelis D, Drnić I, Elschek K, Fantar M, Gaspari A, Gasperetti G, Genchi F, Golubović S, Hukeľová Z, Jankauskas R, Vučković KJ, Jeremić G, Kaić I, Kazek K, Khachatryan H, Khudaverdyan A, Kirchengast S, Korać M, Kozlowski V, Krošláková M, Kušan Špalj D, La Pastina F, Laguardia M, Legrand S, Leleković T, Leskovar T, Lorkiewicz W, Los D, Silva AM, Masaryk R, Matijević V, Cherifi YMS, Meyer N, Mikić I, Miladinović-Radmilović N, Milošević Zakić B, Nacouzi L, Natuniewicz-Sekuła M, Nava A, Neugebauer-Maresch C, Nováček J, Osterholtz A, Paige J, Paraman L, Pieri D, Pieta K, Pop-Lazić S, Ruttkay M, Sanader M, Sołtysiak A, Sperduti A, Stankovic Pesterac T, Teschler-Nicola M, Teul I, Tončinić D, Trapp J, Vulović D, Waliszewski T, Walter D, Živanović M, Filah MEM, Čaušević-Bully M, Šlaus M, Borić D, Novak M, Coppa A, Pinhasi R, Pritchard JK. Stable population structure in Europe since the Iron Age, despite high mobility. eLife 2024; 13:e79714. [PMID: 38288729 PMCID: PMC10827293 DOI: 10.7554/elife.79714] [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: 04/23/2022] [Accepted: 12/12/2023] [Indexed: 02/01/2024] Open
Abstract
Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire's mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.
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Affiliation(s)
- Margaret L Antonio
- Biomedical Informatics Program, Stanford UniversityStanfordUnited States
| | - Clemens L Weiß
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Ziyue Gao
- Department of Genetics, University of Pennsylvania, Perelman School of MedicinePhiladelphiaUnited States
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Hannah M Moots
- Stanford Archaeology Center, Stanford UniversityStanfordUnited States
- University of Chicago, Department of Human GeneticsChicagoUnited States
| | - Jeffrey P Spence
- Department of Genetics, Stanford UniversityStanfordUnited States
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Elisa Praxmarer
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
| | | | - Lea Demetz
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
| | - Pere Gelabert
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
- CIAS, Department of Life Sciences, University of CoimbraCoimbraPortugal
| | - Michaela Lucci
- Dipartimento di Storia Antropologia Religioni Arte Spettacolo, Sapienza UniversityRomeItaly
| | | | - Selma Amrani
- LBEIG, Population Genetics & Conservation Unit, Department of Cellular and Molecular Biology – Faculty of Biological Sciences, University of Sciences and Technology Houari BoumedieneAlgiersAlgeria
| | - Pavel Avetisyan
- National Academy of Sciences of Armenia, Institute of Archaeology and EthnographyYerevanArmenia
| | - Christèle Baillif-Ducros
- French National Institute for Preventive Archaeological Research (INRAP)/CAGT UMR 5288ToulouseFrance
| | - Željka Bedić
- Centre for Applied Bioanthropology, Institute for Anthropological ResearchZagrebCroatia
| | | | | | - Luca Bondioli
- Dipartimento dei Beni Culturali, Archeologia, Storia dell'arte, del Cinema e della Musica, Università di PadovaPadovaItaly
| | - Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of LodzŁódźPoland
| | - Emmanuel Botte
- Aix Marseille Université, CNRS, Centre Camille JullianAix-en-ProvenceFrance
| | | | - Domagoj Bužanić
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | | | - Mirna Cvetko
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | - Daniela De Angelis
- Museo Archeologico Nazionale di Tarquinia, Direzione Regionale Musei LazioRomeItaly
| | - Ivan Drnić
- Archaeological Museum in ZagrebZagrebCroatia
| | - Kristián Elschek
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | - Mounir Fantar
- Département des Monuments et des Sites Antiques - Institut National du Patrimoine INPTunisTunisia
| | - Andrej Gaspari
- University of Ljubljana, Faculty of Arts, Department for ArchaeologyLjubljanaSlovenia
| | - Gabriella Gasperetti
- Soprintendenza Archeologia, belle arti e paesaggio per le province di Sassari e NuoroSassariItaly
| | - Francesco Genchi
- Department of Oriental Studies, Sapienza University of RomeRomeItaly
| | | | - Zuzana Hukeľová
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | | | | | | | - Iva Kaić
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | - Kevin Kazek
- Université de Lorraine, Centre de Recherche Universitaire Lorrain d' Histoire (CRULH)NancyFrance
| | - Hamazasp Khachatryan
- Department of Archaeologi, Shirak Centere of Armenological Studies, National Academy of Sciences Republic of ArmeniaGyumriArmenia
| | - Anahit Khudaverdyan
- Institute of Archaeology and Ethnography of the National Academy of Sciences of the Republic of ArmeniaYerevanArmenia
| | - Sylvia Kirchengast
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
| | | | | | - Mária Krošláková
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | | | | | - Marie Laguardia
- UMR 7041 ArScAn / French Institute of the Near EastBeirutLebanon
| | | | - Tino Leleković
- Archaeology Division, Croatian Academy of Sciences and ArtsZagrebCroatia
| | - Tamara Leskovar
- University of Ljubljana, Faculty of Arts, Department for ArchaeologyLjubljanaSlovenia
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of LodzŁódźPoland
| | | | - Ana Maria Silva
- CIAS, Department of Life Sciences, University of CoimbraCoimbraPortugal
- CEF - University of CoimbraCoimbraPortugal
- UNIARQ - University of LisbonLisbonPortugal
| | - Rene Masaryk
- Skupina STIK Zavod za preučevanje povezovalnih področij preteklosti in sedanjostiLjubljanaSlovenia
| | - Vinka Matijević
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | - Yahia Mehdi Seddik Cherifi
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Cardiolo-Oncology Research Collaborative Group (CORCG), Faculty of Medicine, Benyoucef Benkhedda UniversityAlgiersAlgeria
- Molecular Pathology, University Paul Sabatier Toulouse IIIToulouseFrance
| | - Nicolas Meyer
- French National Institute for Preventive Archaeological Research (INRAP)MetzFrance
| | - Ilija Mikić
- Institute of Archaeology BelgradeBelgradeSerbia
| | | | | | - Lina Nacouzi
- L’Institut français du Proche-OrientBeirutLebanon
| | - Magdalena Natuniewicz-Sekuła
- Institute of Archaeology and Ethnology Polish Academy of Sciences, Centre of Interdisciplinary Archaeological ResearchWarsawPoland
| | - Alessia Nava
- Department of Odontostomatological and Maxillofacial Sciences, Sapienza University of RomeRomeItaly
| | - Christine Neugebauer-Maresch
- Austrian Archaeological Institute, Austrian Academy of SciencesViennaAustria
- Institute of Prehistory and Early History, University of ViennaViennaAustria
| | - Jan Nováček
- Thuringia State Service for Cultural Heritage and Archaeology WeimarThuringiaGermany
- Institute of Anatomy and Cell Biology, University Medical Centre, Georg-August University of GöttingenGöttingenGermany
| | | | | | | | | | - Karol Pieta
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | | | - Matej Ruttkay
- Institute of Archaeology, Slovak Academy of SciencesNitraSlovakia
| | - Mirjana Sanader
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | | | - Alessandra Sperduti
- Bioarchaeology Service, Museum of CivilizationsRomeItaly
- Dipartimento Asia, Africa e Mediterraneo, Università degli Studi di Napoli “L’Orientale”NaplesItaly
| | | | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Department of Anthropology, Natural History Museum ViennaViennaAustria
| | - Iwona Teul
- Chair and Department of Normal Anatomy, Faculty of Medicine and Dentistry, Pomeranian Medical UniversitySzczecinPoland
| | - Domagoj Tončinić
- Faculty of Humanities and Social Sciences, University of ZagrebZagrebCroatia
| | - Julien Trapp
- Musée de La Cour d'Or, Eurométropole de MetzMetzFrance
| | | | | | - Diethard Walter
- Thuringia State Service for Cultural Heritage and Archaeology WeimarThuringiaGermany
| | - Miloš Živanović
- Department of Archeology, Center for Conservation and Archeology of MontenegroCetinjeMontenegro
| | | | | | - Mario Šlaus
- Anthropological Centre, Croatian Academy of Sciences and ArtsZagrebCroatia
| | - Dušan Borić
- Department of Environmental Biology, Sapienza University of RomeRomeItaly
- Department of Anthropology, New York UniversityNew YorkUnited States
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological ResearchZagrebCroatia
| | - Alfredo Coppa
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Department of Environmental Biology, Sapienza University of RomeRomeItaly
- Department of Genetics, Harvard Medical SchoolBostonUnited States
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of ViennaViennaAustria
- Human Evolution and Archaeological Sciences, University of ViennaViennaAustria
| | - Jonathan K Pritchard
- Department of Genetics, Stanford UniversityStanfordUnited States
- Department of Biology, Stanford UniversityStanfordUnited States
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6
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Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.11.548607. [PMID: 37503227 PMCID: PMC10370008 DOI: 10.1101/2023.07.11.548607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
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Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
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7
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Allentoft ME, Sikora M, Fischer A, Sjögren KG, Ingason A, Macleod R, Rosengren A, Schulz Paulsson B, Jørkov MLS, Novosolov M, Stenderup J, Price TD, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Sørensen L, Nielsen PO, Rasmussen P, Jensen TZT, Refoyo-Martínez A, Irving-Pease EK, Barrie W, Pearson A, Sousa da Mota B, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn A, Vinner L, Renaud G, Stern A, Johannsen NN, Ramsøe AD, Schork AJ, Ruter A, Gotfredsen AB, Henning Nielsen B, Brinch Petersen E, Kannegaard E, Hansen J, Buck Pedersen K, Pedersen L, Klassen L, Meldgaard M, Johansen M, Uldum OC, Lotz P, Lysdahl P, Bangsgaard P, Petersen PV, Maring R, Iversen R, Wåhlin S, Anker Sørensen S, Andersen SH, Jørgensen T, Lynnerup N, Lawson DJ, Rasmussen S, Korneliussen TS, Kjær KH, Durbin R, Nielsen R, Delaneau O, Werge T, Kristiansen K, Willerslev E. 100 ancient genomes show repeated population turnovers in Neolithic Denmark. Nature 2024; 625:329-337. [PMID: 38200294 PMCID: PMC10781617 DOI: 10.1038/s41586-023-06862-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024]
Abstract
Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
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Affiliation(s)
- 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.
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Anders Fischer
- Cluster of Excellence ROOTS, Kiel University, Kiel, Germany
- Sealand Archaeology, Kalundborg, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, Gothenburg University, Göteborg, Sweden
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ruairidh Macleod
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Maria Novosolov
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | | | | | | | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alice Pearson
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), Dpt ABBA, Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Vaughn
- Center for Computational Biology, University of California, Berkeley, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aaron Stern
- Center for Computational Biology, University of California, Berkeley, USA
| | | | - Abigail Daisy Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Joseph Schork
- Laboratory of Biological Anthropology, University of Copenhagen, Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anthony Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anne Birgitte Gotfredsen
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | | | - Morten Meldgaard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Health and Nature, University of Greenland, Nuuk, Greenland
| | | | | | - Per Lotz
- Museum Nordsjælland, Hillerød, Denmark
- Museum Vestsjælland, Holbæk, Denmark
| | - Per Lysdahl
- Vendsyssel Historiske Museum, Hjørring, Denmark
| | - Pernille Bangsgaard
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rikke Maring
- Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark
- Museum Østjylland, Randers, Denmark
| | - Rune Iversen
- The Saxo Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Niels Lynnerup
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Simon Rasmussen
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | | | - Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, Gothenburg University, Göteborg, Sweden
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
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8
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Allentoft ME, Sikora M, Refoyo-Martínez A, Irving-Pease EK, Fischer A, Barrie W, Ingason A, Stenderup J, Sjögren KG, Pearson A, Sousa da Mota B, Schulz Paulsson B, Halgren A, Macleod R, Jørkov MLS, Demeter F, Sørensen L, Nielsen PO, Henriksen RA, Vimala T, McColl H, Margaryan A, Ilardo M, Vaughn A, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Johannsen NN, Rasmussen P, Vinner L, Renaud G, Stern A, Jensen TZT, Scorrano G, Schroeder H, Lysdahl P, Ramsøe AD, Skorobogatov A, Schork AJ, Rosengren A, Ruter A, Outram A, Timoshenko AA, Buzhilova A, Coppa A, Zubova A, Silva AM, Hansen AJ, Gromov A, Logvin A, Gotfredsen AB, Henning Nielsen B, González-Rabanal B, Lalueza-Fox C, McKenzie CJ, Gaunitz C, Blasco C, Liesau C, Martinez-Labarga C, Pozdnyakov DV, Cuenca-Solana D, Lordkipanidze DO, En'shin D, Salazar-García DC, Price TD, Borić D, Kostyleva E, Veselovskaya EV, Usmanova ER, Cappellini E, Brinch Petersen E, Kannegaard E, Radina F, Eylem Yediay F, Duday H, Gutiérrez-Zugasti I, Merts I, Potekhina I, Shevnina I, Altinkaya I, Guilaine J, Hansen J, Aura Tortosa JE, Zilhão J, Vega J, Buck Pedersen K, Tunia K, Zhao L, Mylnikova LN, Larsson L, Metz L, Yepiskoposyan L, Pedersen L, Sarti L, Orlando L, Slimak L, Klassen L, Blank M, González-Morales M, Silvestrini M, Vretemark M, Nesterova MS, Rykun M, Rolfo MF, Szmyt M, Przybyła M, Calattini M, Sablin M, Dobisíková M, Meldgaard M, Johansen M, Berezina N, Card N, Saveliev NA, Poshekhonova O, Rickards O, Lozovskaya OV, Gábor O, Uldum OC, Aurino P, Kosintsev P, Courtaud P, Ríos P, Mortensen P, Lotz P, Persson P, Bangsgaard P, de Barros Damgaard P, Vang Petersen P, Martinez PP, Włodarczak P, Smolyaninov RV, Maring R, Menduiña R, Badalyan R, Iversen R, Turin R, Vasilyev S, Wåhlin S, Borutskaya S, Skochina S, Sørensen SA, Andersen SH, Jørgensen T, Serikov YB, Molodin VI, Smrcka V, Merts V, Appadurai V, Moiseyev V, Magnusson Y, Kjær KH, Lynnerup N, Lawson DJ, Sudmant PH, Rasmussen S, Korneliussen TS, Durbin R, Nielsen R, Delaneau O, Werge T, Racimo F, Kristiansen K, Willerslev E. Population genomics of post-glacial western Eurasia. Nature 2024; 625:301-311. [PMID: 38200295 PMCID: PMC10781627 DOI: 10.1038/s41586-023-06865-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/14/2023] [Indexed: 01/12/2024]
Abstract
Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
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Affiliation(s)
- 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.
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anders Fischer
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Alma Halgren
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Ruairidh Macleod
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Musée de l'Homme, Paris, France
| | | | | | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Melissa Ilardo
- Anthropology Department, University of Utah, Salt Lake City, UT, USA
| | - Andrew Vaughn
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aaron Stern
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | | | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Per Lysdahl
- Vendsyssel Historiske Museum, Hjørring, Denmark
| | - Abigail Daisy Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Andrew Joseph Schork
- Department of Genetics, University of Cambridge, Cambridge, UK
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Anthony Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Aleksey A Timoshenko
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexandra Buzhilova
- Department of Anthropology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Alisa Zubova
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Ana Maria Silva
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- UNIARQ, University of Lisbon, Lisbon, Portugal
| | - Anders J Hansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrey Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Andrey Logvin
- Kostanay Regional University A. Baitursynov, Kostanay, Kazakhstan
| | - Anne Birgitte Gotfredsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Borja González-Rabanal
- Grupo EvoAdapta, Departamento de Ciencias Históricas, Universidad de Cantabria, Santander, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Natural Sciences Museum of Barcelona (MCNB), Barcelona, Spain
| | | | - Charleen Gaunitz
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Dmitri V Pozdnyakov
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - David Cuenca-Solana
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Banco Santander, Gobierno de Cantabria, Santander, Spain
- Centre de Recherche en Archéologie, Archeosciences, Histoire (CReAAH), UMR-6869 CNRS, Rennes, France
| | - David O Lordkipanidze
- Georgian National Museum, Tbilisi, Georgia
- Tbilisi State University, Tbilisi, Georgia
| | - Dmitri En'shin
- IPND, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences, Tyumen, Russian Federation
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - T Douglas Price
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Laboratory for Archaeological Chemistry, Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA
| | - Dušan Borić
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- Department of Anthropology, New York University, New York, NY, USA
| | - Elena Kostyleva
- Institute of Humanities, Ivanovo State University, Ivanovo, Russian Federation
| | - Elizaveta V Veselovskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Emma R Usmanova
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
- South Ural State University, Chelyabinsk, Russia
- A. Kh. Khalikov Institute of Archeology of the Academy of Sciences of the Republic of Tatarstan, Kazan, Russia
- Margulan Institute of Archaeology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Enrico Cappellini
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Francesca Radina
- Soprintendenza Archeologia Belle Arti e Paesaggio per la Città Metropolitana di Bari, Bari, Italy
| | - Fulya Eylem Yediay
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Henri Duday
- UMR 5199 PACEA, CNRS, Université de Bordeaux, Pessac, France
| | - Igor Gutiérrez-Zugasti
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Banco Santander, Gobierno de Cantabria, Santander, Spain
| | - Ilya Merts
- A.Kh. Margulan Institute of Archaeology, Almaty, Kazakhstan
| | - Inna Potekhina
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- National University of Kyiv-Mohyla Academy, Kyiv, Ukraine
| | - Irina Shevnina
- Kostanay Regional University A. Baitursynov, Kostanay, Kazakhstan
| | - Isin Altinkaya
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Joan Emili Aura Tortosa
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - João Zilhão
- UNIARQ, University of Lisbon, Lisbon, Portugal
- ICREA, University of Barcelona, Barcelona, Spain
| | | | | | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Lei Zhao
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Liudmila N Mylnikova
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Lars Larsson
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Laure Metz
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, Aix-en-Provence, France
| | - Levon Yepiskoposyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
- Russian-Armenian University, Yerevan, Armenia
| | | | - Lucia Sarti
- Department of History and Cultural Heritage, University of Siena, Siena, Italy
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5500, Université Paul Sabatier, Toulouse, France
| | - Ludovic Slimak
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5500, Université Paul Sabatier, Toulouse, France
| | | | - Malou Blank
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Manuel González-Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Banco Santander, Gobierno de Cantabria, Santander, Spain
| | - Mara Silvestrini
- Soprintendenza per i Beni Archeologici delle Marche, Ancona, Italy
| | | | - Marina S Nesterova
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Marina Rykun
- Cabinet of Anthropology, Tomsk State University, Tomsk, Russian Federation
| | - Mario Federico Rolfo
- Department of History, Humanities and Society, University of Rome Tor Vergata, Rome, Italy
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Marcin Przybyła
- Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | - Mauro Calattini
- Department of History and Cultural Heritage, University of Siena, Siena, Italy
| | - Mikhail Sablin
- Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Miluše Dobisíková
- Department of Anthropology, Czech National Museum, Prague, Czech Republic
| | - Morten Meldgaard
- Department of Health and Nature, University of Greenland, Nuuk, Greenland
| | | | - Natalia Berezina
- Department of Anthropology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Nick Card
- Archaeology Institute, University of Highlands and Islands, Orkney, UK
| | - Nikolai A Saveliev
- Scientific Research Center "Baikal region", Irkutsk State University, Irkutsk, Russian Federation
| | - Olga Poshekhonova
- IPND, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences, Tyumen, Russian Federation
| | - Olga Rickards
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Olga V Lozovskaya
- Laboratory for Experimental Traceology, Institute for the History of Material Culture of the Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | | | | | - Paola Aurino
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la provincia di Cosenza, Cosenza, Italy
| | - Pavel Kosintsev
- Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russian Federation
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russian Federation
| | | | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Peder Mortensen
- Centre for the Study of Early Agricultural Societies, Department of Cross-Cultural and Regional Studies, University of Copenhagen, Copenhagen, Denmark
| | - Per Lotz
- Museum Nordsjælland, Hillerød, Denmark
- Museum Vestsjælland, Holbæk, Denmark
| | - Per Persson
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Pernille Bangsgaard
- ArchaeoScience, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Pilar Prieto Martinez
- Department of History, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Roman V Smolyaninov
- Lipetsk Regional Scientific Public Organisation "Archaeological Research", Lipetsk, Russian Federation
| | - Rikke Maring
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
- Museum Østjylland, Randers, Denmark
| | | | - Ruben Badalyan
- Institute of Archaeology and Ethnography, National Academy of Sciences, Yerevan, Armenia
| | - Rune Iversen
- The Saxo Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russian Federation
- Center for Egyptological Studies, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Svetlana Borutskaya
- Department of Anthropology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Svetlana Skochina
- IPND, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences, Tyumen, Russian Federation
| | | | | | | | - Yuri B Serikov
- Nizhny Tagil State Socio-Pedagogical Institute, Nizhny Tagil, Russia
| | - Vyacheslav I Molodin
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Vaclav Smrcka
- Institute for History of Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Victor Merts
- Centre for Archaeological Research, Toraighyrov University, Pavlodar, Kazakhstan
| | - Vivek Appadurai
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | | | - Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Niels Lynnerup
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Simon Rasmussen
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
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9
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Davidson R, Williams MP, Roca-Rada X, Kassadjikova K, Tobler R, Fehren-Schmitz L, Llamas B. Allelic bias when performing in-solution enrichment of ancient human DNA. Mol Ecol Resour 2023; 23:1823-1840. [PMID: 37712846 DOI: 10.1111/1755-0998.13869] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 08/11/2023] [Indexed: 09/16/2023]
Abstract
In-solution hybridisation enrichment of genetic variation is a valuable methodology in human paleogenomics. It allows enrichment of endogenous DNA by targeting genetic markers that are comparable between sequencing libraries. Many studies have used the 1240k reagent-which enriches 1,237,207 genome-wide SNPs-since 2015, though access was restricted. In 2021, Twist Biosciences and Daicel Arbor Biosciences independently released commercial kits that enabled all researchers to perform enrichments for the same 1240 k SNPs. We used the Daicel Arbor Biosciences Prime Plus kit to enrich 132 ancient samples from three continents. We identified a systematic assay bias that increases genetic similarity between enriched samples and that cannot be explained by batch effects. We present the impact of the bias on population genetics inferences (e.g. Principal Components Analysis, ƒ-statistics) and genetic relatedness (READ). We compare the Prime Plus bias to that previously reported of the legacy 1240k enrichment assay. In ƒ-statistics, we find that all Prime-Plus-generated data exhibit artefactual excess shared drift, such that within-continent relationships cannot be correctly determined. The bias is more subtle in READ, though interpretation of the results can still be misleading in specific contexts. We expect the bias may affect analyses we have not yet tested. Our observations support previously reported concerns for the integration of different data types in paleogenomics. We also caution that technological solutions to generate 1240k data necessitate a thorough validation process before their adoption in the paleogenomic community.
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Affiliation(s)
- Roberta Davidson
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Matthew P Williams
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Biology Department, The Pennsylvania State University, Pennsylvania, USA
| | - Xavier Roca-Rada
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
| | - Kalina Kassadjikova
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
| | - Raymond Tobler
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Evolution of Cultural Diversity Initiative, Australian National University, Canberra, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics, Department of Anthropology, University of California, California, USA
- UCSC Genomics Institute, University of California, California, USA
| | - Bastien Llamas
- The Australian Centre for Ancient DNA and the Environment Institute, School of Biological Sciences, The University of Adelaide, Adelaide, South Australia, Australia
- Centre of Excellence for Australian Biodiversity and Heritage, The University of Adelaide, Adelaide, South Australia, Australia
- National Centre for Indigenous Genomics, Australian National University, Canberra, Australia
- Indigenous Genomics, Telethon Kids Institute, Adelaide, South Australia, Australia
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10
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Godinho RM, Umbelino C, Valera AC, Carvalho AF, Bicho N, Cascalheira J, Gonçalves C, Smith P. Mandibular morphology and the Mesolithic-Neolithic transition in Westernmost Iberia. Sci Rep 2023; 13:16648. [PMID: 37789074 PMCID: PMC10547775 DOI: 10.1038/s41598-023-42846-z] [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: 05/21/2023] [Accepted: 09/15/2023] [Indexed: 10/05/2023] Open
Abstract
Neolithic farming and animal husbandry were first developed in the Near East ~ 10,000 BCE and expanded westwards, reaching westernmost Iberia no later than 5500 BCE. It resulted in major social, cultural, economic and dietary changes. Yet, the impact of this change on human mandibular morphology in Iberia is yet to be assessed, which is regrettable because mandible form is impacted by population history and diet. In this study we used Mesolithic to Chalcolithic Iberian samples to examine the impact of this transition on mandibular morphology. We also compared these samples with a Southern Levantine Chalcolithic population to assess their relationship. Lastly, we assessed dental wear to determine if the morphological differences identified were related to the material properties of the diet. We found differences between samples in mandibular shape but not size, which we attribute to contrasting population histories between Mesolithic and later populations. Some differences in the severity of dental wear were also found between Mesolithic and later Iberian samples, and smaller between the Mesolithic Iberians and southern Levantines. Little relationship was found between wear magnitude and mandibular shape. Altogether, our results show that the Mesolithic-Neolithic Iberian transition resulted in a meaningful change in mandibular morphology, which was likely driven more by population history than by dietary change.
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Affiliation(s)
- Ricardo Miguel Godinho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), Faculdade das Ciências Humanas e Sociais, University of Algarve, Campus Gambelas, 8005-139, Faro, Portugal.
| | - Cláudia Umbelino
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), Faculdade das Ciências Humanas e Sociais, University of Algarve, Campus Gambelas, 8005-139, Faro, Portugal
- Department of Life Sciences, Research Centre for Anthropology and Health, University of Coimbra, Coimbra, Portugal
| | - António Carlos Valera
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), Faculdade das Ciências Humanas e Sociais, University of Algarve, Campus Gambelas, 8005-139, Faro, Portugal
- Era Arqueologia, S.A., Calçada de Santa Catarina, 9C, 1495-705, Cruz Quebrada, Portugal
| | - António Faustino Carvalho
- Centro de Estudos de Arqueologia, Artes e Ciências do Património (CEAACP), F.C.H.S., University of Algarve, Campus de Gambelas, 8000-117, Faro, Portugal
| | - Nuno Bicho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), Faculdade das Ciências Humanas e Sociais, University of Algarve, Campus Gambelas, 8005-139, Faro, Portugal
| | - João Cascalheira
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), Faculdade das Ciências Humanas e Sociais, University of Algarve, Campus Gambelas, 8005-139, Faro, Portugal
| | - Célia Gonçalves
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), Faculdade das Ciências Humanas e Sociais, University of Algarve, Campus Gambelas, 8005-139, Faro, Portugal
| | - Patricia Smith
- Faculties of Medicine and Dental Medicine and National Natural History Collections, The Hebrew University, Jerusalem, Israel
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11
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Wang K, Prüfer K, Krause-Kyora B, Childebayeva A, Schuenemann VJ, Coia V, Maixner F, Zink A, Schiffels S, Krause J. High-coverage genome of the Tyrolean Iceman reveals unusually high Anatolian farmer ancestry. CELL GENOMICS 2023; 3:100377. [PMID: 37719142 PMCID: PMC10504632 DOI: 10.1016/j.xgen.2023.100377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 05/10/2023] [Accepted: 07/13/2023] [Indexed: 09/19/2023]
Abstract
The Tyrolean Iceman is known as one of the oldest human glacier mummies, directly dated to 3350-3120 calibrated BCE. A previously published low-coverage genome provided novel insights into European prehistory, despite high present-day DNA contamination. Here, we generate a high-coverage genome with low contamination (15.3×) to gain further insights into the genetic history and phenotype of this individual. Contrary to previous studies, we found no detectable Steppe-related ancestry in the Iceman. Instead, he retained the highest Anatolian-farmer-related ancestry among contemporaneous European populations, indicating a rather isolated Alpine population with limited gene flow from hunter-gatherer-ancestry-related populations. Phenotypic analysis revealed that the Iceman likely had darker skin than present-day Europeans and carried risk alleles associated with male-pattern baldness, type 2 diabetes, and obesity-related metabolic syndrome. These results corroborate phenotypic observations of the preserved mummified body, such as high pigmentation of his skin and the absence of hair on his head.
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Affiliation(s)
- Ke Wang
- MOE Key Laboratory of Contemporary Anthropology, Department of Anthropology and Human Genetics, School of Life Science, Fudan University, Shanghai 200438, China
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Center of Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, 24118 Kiel, Germany
| | | | - Verena J. Schuenemann
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Institute of Evolutionary Medicine, University of Zurich, 8057 Zurich, Switzerland
- Human Evolution and Archaeological Sciences, University of Vienna, 1030 Vienna, Austria
| | - Valentina Coia
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Frank Maixner
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Albert Zink
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
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12
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Mattila TM, Svensson EM, Juras A, Günther T, Kashuba N, Ala-Hulkko T, Chyleński M, McKenna J, Pospieszny Ł, Constantinescu M, Rotea M, Palincaș N, Wilk S, Czerniak L, Kruk J, Łapo J, Makarowicz P, Potekhina I, Soficaru A, Szmyt M, Szostek K, Götherström A, Storå J, Netea MG, Nikitin AG, Persson P, Malmström H, Jakobsson M. Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe. Commun Biol 2023; 6:793. [PMID: 37558731 PMCID: PMC10412644 DOI: 10.1038/s42003-023-05131-3] [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: 09/01/2022] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.
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Affiliation(s)
- Tiina M Mattila
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden.
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Natalija Kashuba
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Department of Archaeology and Ancient History, Uppsala University, 75126, Uppsala, Sweden
| | - Terhi Ala-Hulkko
- Geography Research Unit, University of Oulu, 90014, Oulu, Finland
- Kerttu Saalasti Institute, University of Oulu, 90014, Oulu, Finland
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
- Institute of Archaeology, University of Gdańsk, 80-851, Gdańsk, Poland
| | - Mihai Constantinescu
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, 050711, Bucharest, Romania
- Faculty of History, University of Bucharest, 030167, Bucharest, Romania
| | - Mihai Rotea
- National History Museum of Transylvania, Cluj-Napoca, Romania
| | - Nona Palincaș
- Vasile Pârvan Institute of Archaeology, Bucharest, Romania
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, 31-007, Kraków, Poland
- Karkonosze Museum, 58-500, Jelenia Góra, Poland
| | - Lech Czerniak
- Institute of Archaeology, University of Gdańsk, 80-851, Gdańsk, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, 31-016, Kraków, Poland
| | - Jerzy Łapo
- Museum of Folk Culture, 11-600, Węgorzewo, Poland
| | - Przemysław Makarowicz
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210, Kyiv, Ukraine
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, 3008, Bern, Switzerland
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, 050711, Bucharest, Romania
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
- Archaeological Museum, 61-781, Poznań, Poland
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, 01-938, Warszawa, Poland
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University and the Swedish Museum of Natural History, 106 91, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91, Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 106 91, Stockholm, Sweden
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - Alexey G Nikitin
- Grand Valley State University, Department of Biology, Allendale, MI, 49401, USA
| | - Per Persson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Museum of Cultural History, University of Oslo, 0130, Oslo, Norway
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden.
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa.
- SciLifeLab, Uppsala University, 75105, Uppsala, Sweden.
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13
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Rivollat M, Rohrlach AB, Ringbauer H, Childebayeva A, Mendisco F, Barquera R, Szolek A, Le Roy M, Colleran H, Tuke J, Aron F, Pemonge MH, Späth E, Télouk P, Rey L, Goude G, Balter V, Krause J, Rottier S, Deguilloux MF, Haak W. Extensive pedigrees reveal the social organization of a Neolithic community. Nature 2023; 620:600-606. [PMID: 37495691 PMCID: PMC10432279 DOI: 10.1038/s41586-023-06350-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 06/21/2023] [Indexed: 07/28/2023]
Abstract
Social anthropology and ethnographic studies have described kinship systems and networks of contact and exchange in extant populations1-4. However, for prehistoric societies, these systems can be studied only indirectly from biological and cultural remains. Stable isotope data, sex and age at death can provide insights into the demographic structure of a burial community and identify local versus non-local childhood signatures, archaeogenetic data can reconstruct the biological relationships between individuals, which enables the reconstruction of pedigrees, and combined evidence informs on kinship practices and residence patterns in prehistoric societies. Here we report ancient DNA, strontium isotope and contextual data from more than 100 individuals from the site Gurgy 'les Noisats' (France), dated to the western European Neolithic around 4850-4500 BC. We find that this burial community was genetically connected by two main pedigrees, spanning seven generations, that were patrilocal and patrilineal, with evidence for female exogamy and exchange with genetically close neighbouring groups. The microdemographic structure of individuals linked and unlinked to the pedigrees reveals additional information about the social structure, living conditions and site occupation. The absence of half-siblings and the high number of adult full siblings suggest that there were stable health conditions and a supportive social network, facilitating high fertility and low mortality5. Age-structure differences and strontium isotope results by generation indicate that the site was used for just a few decades, providing new insights into shifting sedentary farming practices during the European Neolithic.
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Affiliation(s)
- Maïté Rivollat
- University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France.
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
- Department of Archaeology, Durham University, Durham, UK.
- Department of Archaeology, Ghent University, Ghent, Belgium.
| | - Adam Benjamin Rohrlach
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fanny Mendisco
- University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - András Szolek
- Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
- Applied Bioinformatics, Department of Computer Science, University of Tübingen, Tübingen, Germany
| | - Mélie Le Roy
- Department of Archaeology & Anthropology, Bournemouth University, Bournemouth, UK
| | - Heidi Colleran
- Department of Human Behavior, Ecology and Culture, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- BirthRites Lise Meitner Research Group, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Jonathan Tuke
- School of Computer and Mathematical Sciences, University of Adelaide, Adelaide, South Australia, Australia
| | - Franziska Aron
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
- RNA Bioinformatics and High Throughput Analysis, Friedrich Schiller University, Jena, Germany
| | - Marie-Hélène Pemonge
- University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France
| | - Ellen Späth
- Leibniz Institute on Aging-Fritz Lipmann Institute (FLI), Jena, Germany
| | - Philippe Télouk
- Ecole Normale Supérieure de Lyon, CNRS, UCBL, LGL-TPE, Lyon, France
| | - Léonie Rey
- University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France
| | - Gwenaëlle Goude
- CNRS, Aix Marseille University, Ministry of Culture, LAMPEA, Aix-en-Provence, France
| | - Vincent Balter
- Ecole Normale Supérieure de Lyon, CNRS, UCBL, LGL-TPE, Lyon, France
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stéphane Rottier
- University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France.
| | - Marie-France Deguilloux
- University of Bordeaux, CNRS, PACEA - UMR 5199, Allée Geoffroy Saint-Hilaire, Pessac, France
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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14
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Simões LG, Günther T, Martínez-Sánchez RM, Vera-Rodríguez JC, Iriarte E, Rodríguez-Varela R, Bokbot Y, Valdiosera C, Jakobsson M. Northwest African Neolithic initiated by migrants from Iberia and Levant. Nature 2023:10.1038/s41586-023-06166-6. [PMID: 37286608 DOI: 10.1038/s41586-023-06166-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 05/03/2023] [Indexed: 06/09/2023]
Abstract
In northwestern Africa, lifestyle transitioned from foraging to food production around 7,400 years ago but what sparked that change remains unclear. Archaeological data support conflicting views: (1) that migrant European Neolithic farmers brought the new way of life to North Africa1-3 or (2) that local hunter-gatherers adopted technological innovations4,5. The latter view is also supported by archaeogenetic data6. Here we fill key chronological and archaeogenetic gaps for the Maghreb, from Epipalaeolithic to Middle Neolithic, by sequencing the genomes of nine individuals (to between 45.8- and 0.2-fold genome coverage). Notably, we trace 8,000 years of population continuity and isolation from the Upper Palaeolithic, via the Epipaleolithic, to some Maghrebi Neolithic farming groups. However, remains from the earliest Neolithic contexts showed mostly European Neolithic ancestry. We suggest that farming was introduced by European migrants and was then rapidly adopted by local groups. During the Middle Neolithic a new ancestry from the Levant appears in the Maghreb, coinciding with the arrival of pastoralism in the region, and all three ancestries blend together during the Late Neolithic. Our results show ancestry shifts in the Neolithization of northwestern Africa that probably mirrored a heterogeneous economic and cultural landscape, in a more multifaceted process than observed in other regions.
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Affiliation(s)
- Luciana G Simões
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden
| | | | - Juan Carlos Vera-Rodríguez
- Área de Prehistoria, Departamento de Historia, Geografía y Antropología, Centro de Investigación en Patrimonio Histórico, Cultural y Natural, Facultad de Humanidades, Universidad de Huelva, Huelva, Spain
| | - Eneko Iriarte
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain
| | - Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Youssef Bokbot
- Institut National des Sciences de l'Archéologie et du Patrimoine, Rabat, Morocco
| | - Cristina Valdiosera
- Universidad de Burgos, Departamento de Historia, Geografía y Comunicaciones, Burgos, Spain.
- Department of History and Archaeology, La Trobe University, Melbourne, Victoria, Australia.
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.
- Palaeo-Research Institute, University of Johannesburg, Auckland Park, South Africa.
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15
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Pandey D, Harris M, Garud NR, Narasimhan VM. Understanding natural selection in Holocene Europe using multi-locus genotype identity scans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.24.538113. [PMID: 37163039 PMCID: PMC10168228 DOI: 10.1101/2023.04.24.538113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Ancient DNA (aDNA) has been a revolutionary technology in understanding human history but has not been used extensively to study natural selection as large sample sizes to study allele frequency changes over time have thus far not been available. Here, we examined a time transect of 708 published samples over the past 7,000 years of European history using multi-locus genotype-based selection scans. As aDNA data is affected by high missingness, ascertainment bias, DNA damage, random allele calling, and is unphased, we first validated our selection scan, G 12 a n c i e n t , on simulated data resembling aDNA under a demographic model that captures broad features of the allele frequency spectrum of European genomes as well as positive controls that have been previously identified and functionally validated in modern European datasets on data from ancient individuals from time periods very close to the present time. We then applied our statistic to the aDNA time transect to detect and resolve the timing of natural selection occurring genome wide and found several candidates of selection across the different time periods that had not been picked up by selection scans using single SNP allele frequency approaches. In addition, enrichment analysis discovered multiple categories of complex traits that might be under adaptation across these periods. Our results demonstrate the utility of applying different types of selection scans to aDNA to uncover putative selection signals at loci in the ancient past that might have been masked in modern samples.
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Affiliation(s)
- Devansh Pandey
- Department of Integrative Biology, The University of Texas at Austin
| | - Mariana Harris
- Department of Computational Medicine, University of California, Los Angeles
| | - Nandita R Garud
- Department of Ecology and Evolutionary Biology, University of California, Los Angeles
- Department of Human Genetics, University of California, Los Angeles
| | - Vagheesh M Narasimhan
- Department of Integrative Biology, The University of Texas at Austin
- Department of Statistics and Data Science, The University of Texas at Austin
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16
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Villalba-Mouco V, van de Loosdrecht MS, Rohrlach AB, Fewlass H, Talamo S, Yu H, Aron F, Lalueza-Fox C, Cabello L, Cantalejo Duarte P, Ramos-Muñoz J, Posth C, Krause J, Weniger GC, Haak W. A 23,000-year-old southern Iberian individual links human groups that lived in Western Europe before and after the Last Glacial Maximum. Nat Ecol Evol 2023; 7:597-609. [PMID: 36859553 PMCID: PMC10089921 DOI: 10.1038/s41559-023-01987-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 01/03/2023] [Indexed: 03/03/2023]
Abstract
Human populations underwent range contractions during the Last Glacial Maximum (LGM) which had lasting and dramatic effects on their genetic variation. The genetic ancestry of individuals associated with the post-LGM Magdalenian technocomplex has been interpreted as being derived from groups associated with the pre-LGM Aurignacian. However, both these ancestries differ from that of central European individuals associated with the chronologically intermediate Gravettian. Thus, the genomic transition from pre- to post-LGM remains unclear also in western Europe, where we lack genomic data associated with the intermediate Solutrean, which spans the height of the LGM. Here we present genome-wide data from sites in Andalusia in southern Spain, including from a Solutrean-associated individual from Cueva del Malalmuerzo, directly dated to ~23,000 cal yr BP. The Malalmuerzo individual carried genetic ancestry that directly connects earlier Aurignacian-associated individuals with post-LGM Magdalenian-associated ancestry in western Europe. This scenario differs from Italy, where individuals associated with the transition from pre- and post-LGM carry different genetic ancestries. This suggests different dynamics in the proposed southern refugia of Ice Age Europe and posits Iberia as a potential refugium for western European pre-LGM ancestry. More, individuals from Cueva Ardales, which were thought to be of Palaeolithic origin, date younger than expected and, together with individuals from the Andalusian sites Caserones and Aguilillas, fall within the genetic variation of the Neolithic, Chalcolithic and Bronze Age individuals from southern Iberia.
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Affiliation(s)
- 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.
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
| | - Marieke S van de Loosdrecht
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Biosystematics Group, Wageningen University, Wageningen, the Netherlands
| | - 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
| | - Helen Fewlass
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry G. Ciamician, Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - 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
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Natural Sciences Museum of Barcelona (MCNB), Barcelona, Spain
| | - Lidia Cabello
- University of Málaga and Grupo HUM-440 University of Cádiz, Cádiz, Spain
| | | | - José Ramos-Muñoz
- Departamento de Historia, Geografía y Filosofía, Universidad de Cádiz, Cádiz, Spain
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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17
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Carlberg C. Nutrigenomics in the context of evolution. Redox Biol 2023; 62:102656. [PMID: 36933390 PMCID: PMC10036735 DOI: 10.1016/j.redox.2023.102656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/13/2023] Open
Abstract
Nutrigenomics describes the interaction between nutrients and our genome. Since the origin of our species most of these nutrient-gene communication pathways have not changed. However, our genome experienced over the past 50,000 years a number of evolutionary pressures, which are based on the migration to new environments concerning geography and climate, the transition from hunter-gatherers to farmers including the zoonotic transfer of many pathogenic microbes and the rather recent change of societies to a preferentially sedentary lifestyle and the dominance of Western diet. Human populations responded to these challenges not only by specific anthropometric adaptations, such as skin color and body stature, but also through diversity in dietary intake and different resistance to complex diseases like the metabolic syndrome, cancer and immune disorders. The genetic basis of this adaptation process has been investigated by whole genome genotyping and sequencing including that of DNA extracted from ancient bones. In addition to genomic changes, also the programming of epigenomes in pre- and postnatal phases of life has an important contribution to the response to environmental changes. Thus, insight into the variation of our (epi)genome in the context of our individual's risk for developing complex diseases, helps to understand the evolutionary basis how and why we become ill. This review will discuss the relation of diet, modern environment and our (epi)genome including aspects of redox biology. This has numerous implications for the interpretation of the risks for disease and their prevention.
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Affiliation(s)
- Carsten Carlberg
- Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, ul. Juliana Tuwima 10, PL-10748, Olsztyn, Poland; School of Medicine, Institute of Biomedicine, University of Eastern Finland, FI-70211, Kuopio, Finland.
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18
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Davy T, Ju D, Mathieson I, Skoglund P. Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers. Curr Biol 2023; 33:1365-1371.e3. [PMID: 36963383 PMCID: PMC10153476 DOI: 10.1016/j.cub.2023.02.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 02/15/2023] [Indexed: 03/26/2023]
Abstract
Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.1,2,3,4 Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10-56). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.
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Affiliation(s)
- Tom Davy
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
| | - Dan Ju
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
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19
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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: 13] [Impact Index Per Article: 13.0] [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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20
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Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave. Commun Biol 2022; 5:1262. [DOI: 10.1038/s42003-022-04190-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
AbstractRecent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.
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21
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Arzelier A, Rivollat M, De Belvalet H, Pemonge MH, Binder D, Convertini F, Duday H, Gandelin M, Guilaine J, Haak W, Deguilloux MF, Pruvost M. Neolithic genomic data from southern France showcase intensified interactions with hunter-gatherer communities. iScience 2022; 25:105387. [PMID: 36405775 PMCID: PMC9667241 DOI: 10.1016/j.isci.2022.105387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Revised: 07/06/2022] [Accepted: 10/14/2022] [Indexed: 11/15/2022] Open
Abstract
Archaeological research shows that the dispersal of the Neolithic took a more complex turn when reaching western Europe, painting a contrasted picture of interactions between autochthonous hunter-gatherers (HGs) and incoming farmers. In order to clarify the mode, the intensity, and the regional variability of biological exchanges implied in these processes, we report new palaeogenomic data from Occitanie, a key region in Southern France. Genomic data from 28 individuals originating from six sites spanning from c. 5,500 to c. 2,500 BCE allow us to characterize regional patterns of ancestries throughout the Neolithic period. Results highlight major differences between the Mediterranean and Continental Neolithic expansion routes regarding both migration and interaction processes. High proportions of HG ancestry in both Early and Late Neolithic groups in Southern France support multiple pulses of inter-group gene flow throughout time and space and confirm the need for regional studies to address the complexity of the processes involved. Genome-wide data from 28 individuals from Southern France (∼5,500–∼2,500 BCE) Small groups associated with the Neolithic expansion along the Mediterranean Early admixture between hunter-gatherers and Neolithic farmers in Southern France Multiple pulses of HG legacy introgression in Western Europe throughout Neolithic
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22
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Charlton S, Brace S, Hajdinjak M, Kearney R, Booth T, Reade H, Tripp JA, Sayle KL, Grimm SB, Bello SM, Walker EA, Gilardet A, East P, Glocke I, Larson G, Higham T, Stringer C, Skoglund P, Barnes I, Stevens RE. Dual ancestries and ecologies of the Late Glacial Palaeolithic in Britain. Nat Ecol Evol 2022; 6:1658-1668. [PMID: 36280785 PMCID: PMC9630104 DOI: 10.1038/s41559-022-01883-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 08/16/2022] [Indexed: 11/09/2022]
Abstract
Genetic investigations of Upper Palaeolithic Europe have revealed a complex and transformative history of human population movements and ancestries, with evidence of several instances of genetic change across the European continent in the period following the Last Glacial Maximum (LGM). Concurrent with these genetic shifts, the post-LGM period is characterized by a series of significant climatic changes, population expansions and cultural diversification. Britain lies at the extreme northwest corner of post-LGM expansion and its earliest Late Glacial human occupation remains unclear. Here we present genetic data from Palaeolithic human individuals in the United Kingdom and the oldest human DNA thus far obtained from Britain or Ireland. We determine that a Late Upper Palaeolithic individual from Gough's Cave probably traced all its ancestry to Magdalenian-associated individuals closely related to those from sites such as El Mirón Cave, Spain, and Troisième Caverne in Goyet, Belgium. However, an individual from Kendrick's Cave shows no evidence of having ancestry related to the Gough’s Cave individual. Instead, the Kendrick’s Cave individual traces its ancestry to groups who expanded across Europe during the Late Glacial and are represented at sites such as Villabruna, Italy. Furthermore, the individuals differ not only in their genetic ancestry profiles but also in their mortuary practices and their diets and ecologies, as evidenced through stable isotope analyses. This finding mirrors patterns of dual genetic ancestry and admixture previously detected in Iberia but may suggest a more drastic genetic turnover in northwestern Europe than in the southwest. The authors report genetic, archaeological and stable isotopic data from two late Palaeolithic individuals in Britain, from Gough's Cave and Kendrick's Cave. The individuals differ not only in their ancestry but also their diets, ecologies and mortuary practices, revealing diverse origins and lifeways among inhabitants of late Pleistocene Britain.
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23
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Modi A, Vizzari MT, Catalano G, Boscolo Agostini R, Vai S, Lari M, Vergata C, Zaro V, Liccioli L, Fedi M, Barone S, Nigro L, Lancioni H, Achilli A, Sineo L, Caramelli D, Ghirotto S. Genetic structure and differentiation from early bronze age in the mediterranean island of sicily: Insights from ancient mitochondrial genomes. Front Genet 2022; 13:945227. [PMID: 36159977 PMCID: PMC9500526 DOI: 10.3389/fgene.2022.945227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
Sicily is one of the main islands of the Mediterranean Sea, and it is characterized by a variety of archaeological records, material culture and traditions, reflecting the history of migrations and populations’ interaction since its first colonization, during the Paleolithic. These deep and complex demographic and cultural dynamics should have affected the genomic landscape of Sicily at different levels; however, the relative impact of these migrations on the genomic structure and differentiation within the island remains largely unknown. The available Sicilian modern genetic data gave a picture of the current genetic structure, but the paucity of ancient data did not allow so far to make predictions about the level of historical variation. In this work, we sequenced and analyzed the complete mitochondrial genomes of 36 individuals from five different locations in Sicily, spanning from Early Bronze Age to Iron Age, and with different cultural backgrounds. The comparison with coeval groups from the Mediterranean Basin highlighted structured genetic variation in Sicily since Early Bronze Age, thus supporting a demic impact of the cultural transitions within the Island. Explicit model testing through Approximate Bayesian Computation allowed us to make predictions about the origin of Sicanians, one of the three indigenous peoples of Sicily, whose foreign origin from Spain, historically attributed, was not confirmed by our analysis of genetic data. Sicilian modern mitochondrial data show a different, more homogeneous, genetic composition, calling for a recent genetic replacement in the Island of pre-Iron Age populations, that should be further investigated.
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Affiliation(s)
- Alessandra Modi
- Department of Biology, University of Florence, Firenze, Italy
- *Correspondence: Alessandra Modi, ; Silvia Ghirotto,
| | - Maria Teresa Vizzari
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Giulio Catalano
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | | | - Stefania Vai
- Department of Biology, University of Florence, Firenze, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Firenze, Italy
| | - Chiara Vergata
- Department of Biology, University of Florence, Firenze, Italy
| | - Valentina Zaro
- Department of Biology, University of Florence, Firenze, Italy
| | - Lucia Liccioli
- INFN (Istituto Nazionale di Fisica Nucleare) Sezione di Firenze, Firenze, Italy
| | - Mariaelena Fedi
- INFN (Istituto Nazionale di Fisica Nucleare) Sezione di Firenze, Firenze, Italy
| | - Serena Barone
- INFN (Istituto Nazionale di Fisica Nucleare) Sezione di Firenze, Firenze, Italy
- Department of Physics and Astronomy, University of Florence, Florence, Italy
| | - Lorenzo Nigro
- Department “Italian Institute of Oriental Studies—ISO”, Sapienza University of Rome, Rome, Italy
| | - Hovirag Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - Alessandro Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - Luca Sineo
- Department of Biological, Chemical and Pharmaceutical Sciences and Technologies, University of Palermo, Palermo, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Firenze, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
- *Correspondence: Alessandra Modi, ; Silvia Ghirotto,
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24
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Lazaridis I, Alpaslan-Roodenberg S, Acar A, Açıkkol A, Agelarakis A, Aghikyan L, Akyüz U, Andreeva D, Andrijašević G, Antonović D, Armit I, Atmaca A, Avetisyan P, Aytek Aİ, Bacvarov K, Badalyan R, Bakardzhiev S, Balen J, Bejko L, Bernardos R, Bertsatos A, Biber H, Bilir A, Bodružić M, Bonogofsky M, Bonsall C, Borić D, Borovinić N, Bravo Morante G, Buttinger K, Callan K, Candilio F, Carić M, Cheronet O, Chohadzhiev S, Chovalopoulou ME, Chryssoulaki S, Ciobanu I, Čondić N, Constantinescu M, Cristiani E, Culleton BJ, Curtis E, Davis J, Demcenco TI, Dergachev V, Derin Z, Deskaj S, Devejyan S, Djordjević V, Duffett Carlson KS, Eccles LR, Elenski N, Engin A, Erdoğan N, Erir-Pazarcı S, Fernandes DM, Ferry M, Freilich S, Frînculeasa A, Galaty ML, Gamarra B, Gasparyan B, Gaydarska B, Genç E, Gültekin T, Gündüz S, Hajdu T, Heyd V, Hobosyan S, Hovhannisyan N, Iliev I, Iliev L, Iliev S, İvgin İ, Janković I, Jovanova L, Karkanas P, Kavaz-Kındığılı B, Kaya EH, Keating D, Kennett DJ, Deniz Kesici S, Khudaverdyan A, Kiss K, Kılıç S, Klostermann P, Kostak Boca Negra Valdes S, Kovačević S, Krenz-Niedbała M, Krznarić Škrivanko M, Kurti R, Kuzman P, Lawson AM, Lazar C, Leshtakov K, Levy TE, Liritzis I, Lorentz KO, Łukasik S, Mah M, Mallick S, Mandl K, Martirosyan-Olshansky K, Matthews R, Matthews W, McSweeney K, Melikyan V, Micco A, Michel M, Milašinović L, Mittnik A, Monge JM, Nekhrizov G, Nicholls R, Nikitin AG, Nikolov V, Novak M, Olalde I, Oppenheimer J, Osterholtz A, Özdemir C, Özdoğan KT, Öztürk N, Papadimitriou N, Papakonstantinou N, Papathanasiou A, Paraman L, Paskary EG, Patterson N, Petrakiev I, Petrosyan L, Petrova V, Philippa-Touchais A, Piliposyan A, Pocuca Kuzman N, Potrebica H, Preda-Bălănică B, Premužić Z, Price TD, Qiu L, Radović S, Raeuf Aziz K, Rajić Šikanjić P, Rasheed Raheem K, Razumov S, Richardson A, Roodenberg J, Ruka R, Russeva V, Şahin M, Şarbak A, Savaş E, Schattke C, Schepartz L, Selçuk T, Sevim-Erol A, Shamoon-Pour M, Shephard HM, Sideris A, Simalcsik A, Simonyan H, Sinika V, Sirak K, Sirbu G, Šlaus M, Soficaru A, Söğüt B, Sołtysiak A, Sönmez-Sözer Ç, Stathi M, Steskal M, Stewardson K, Stocker S, Suata-Alpaslan F, Suvorov A, Szécsényi-Nagy A, Szeniczey T, Telnov N, Temov S, Todorova N, Tota U, Touchais G, Triantaphyllou S, Türker A, Ugarković M, Valchev T, Veljanovska F, Videvski Z, Virag C, Wagner A, Walsh S, Włodarczak P, Workman JN, Yardumian A, Yarovoy E, Yavuz AY, Yılmaz H, Zalzala F, Zettl A, Zhang Z, Çavuşoğlu R, Rohland N, Pinhasi R, Reich D. The genetic history of the Southern Arc: A bridge between West Asia and Europe. Science 2022; 377:eabm4247. [PMID: 36007055 PMCID: PMC10064553 DOI: 10.1126/science.abm4247] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.
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Affiliation(s)
- Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Songül Alpaslan-Roodenberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Ayşe Acar
- Department of Anthropology, Faculty of Letters, Mardin Artuklu University, 47510 Artuklu, Mardin, Turkey
| | - Ayşen Açıkkol
- Department of Anthropology, Faculty of Letters, Sivas Cumhuriyet University, 58140 Sivas, Turkey
| | | | - Levon Aghikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Uğur Akyüz
- Samsun Museum of Archeology and Ethnography, Kale Mahallesi, Merkez, İlkadım, 55030 Samsun, Turkey
| | | | | | | | - Ian Armit
- Department of Archaeology, University of York, York YO1 7EP, UK
| | - Alper Atmaca
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Pavel Avetisyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Ahmet İhsan Aytek
- Department of Anthropology, Faculty of Arts and Science, Burdur Mehmet Akif University, 15100 Burdur, Turkey
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Ruben Badalyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Lorenc Bejko
- Department of Archaeology and Heritage Studies, University of Tirana, 1010 Tirana, Albania
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andreas Bertsatos
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Hanifi Biber
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Ahmet Bilir
- Department of Archaeology, Faculty of Science and Letters, Düzce University, 81620 Düzce, Turkey
| | | | | | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027, USA
| | - Nikola Borovinić
- Center for Conservation and Archaeology of Montenegro, 81250 Cetinje, Montenegro
| | | | - Katharina Buttinger
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Stefan Chohadzhiev
- Department of Archaeology, University of Veliko Tarnovo "St. Cyril and St. Methodius," 5003 Veliko Tarnovo, Bulgaria
| | - Maria-Eleni Chovalopoulou
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Stella Chryssoulaki
- Hellenic Ministry of Culture and Sports, Ephorate of Antiquities of Piraeus and the Islands, 10682 Piraeus, Greece
| | - Ion Ciobanu
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,National Archaeological Agency, 2012 Chișinău, Moldova
| | | | | | - Emanuela Cristiani
- Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jack Davis
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Valentin Dergachev
- Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, 2001 Chișinău, Moldova
| | - Zafer Derin
- Department of Archaeology, Faculty of Letters, Ege University, 35100 Bornova-Izmir, Turkey
| | - Sylvia Deskaj
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seda Devejyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Laurie R Eccles
- Human Paleoecology and Isotope Geochemistry Lab, Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nedko Elenski
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Atilla Engin
- Department of Archaeology, Faculty of Science and Letters, Gaziantep University, 27310 Gaziantep, Turkey
| | - Nihat Erdoğan
- Mardin Archaeological Museum, Şar, Cumhuriyet Meydanı üstü, 47100 Artuklu, Mardin, Turkey
| | | | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, 100042 Ploiești, Romania
| | - Michael L Galaty
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, 43007 Tarragona, Spain.,Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, 43002 Tarragona, Spain.,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | - Elif Genç
- Department of Archaeology, Faculty of Science and Letters, Çukurova University, 01330 Balçalı-Sarıçam-Adana, Turkey
| | - Timur Gültekin
- Department of Anthropology, Faculty of Humanities, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Serkan Gündüz
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Volker Heyd
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Suren Hobosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Nelli Hovhannisyan
- Department of Ecology and Nature Protection, Yerevan State University, 0025 Yerevan, Armenia
| | - Iliya Iliev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - İlkay İvgin
- Ministry of Culture and Tourism, İsmet İnönü Bulvarı, 06100 Emek, Ankara, Turkey
| | - Ivor Janković
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Lence Jovanova
- Museum of the City of Skopje, 1000 Skopje, North Macedonia
| | - Panagiotis Karkanas
- Malcolm H. Wiener Laboratory, American School of Classical Studies at Athens, 10676 Athens, Greece
| | - Berna Kavaz-Kındığılı
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | - Esra Hilal Kaya
- Muğla Archaeological Museum and Yatağan Thermal Power Generation Company, Rescue Excavations, 48000 Muğla, Turkey
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Douglas J Kennett
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Seda Deniz Kesici
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | | | - Krisztián Kiss
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary.,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Sinan Kılıç
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Paul Klostermann
- Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | | | | | | | | | - Rovena Kurti
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Pasko Kuzman
- National Museum in Ohrid, 6000 Ohrid, North Macedonia
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Catalin Lazar
- ArchaeoSciences Division, Research Institute of the University of Bucharest, University of Bucharest, 050663 Bucharest, Romania
| | - Krassimir Leshtakov
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Thomas E Levy
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ioannis Liritzis
- Key Research Institute of Yellow River Civilization and Sustainable Development and the Collaborative Innovation Center on Yellow River Civilization of Henan Province, Laboratory of Yellow River Cultural Heritage, Henan University, 475001 Kaifeng, China.,European Academy of Sciences and Arts, 5020 Salzburg, Austria
| | - Kirsi O Lorentz
- Science and Technology in Archaeology and Culture Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
| | - Sylwia Łukasik
- Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | | | - Roger Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Wendy Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Varduhi Melikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Megan Michel
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alissa Mittnik
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet M Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Georgi Nekhrizov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Rebecca Nicholls
- School of Archaeological and Forensic Sciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Alexey G Nikitin
- Department of Biology, Grand Valley State University, Allendale, MI 49401, USA
| | - Vassil Nikolov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Osterholtz
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS 39762, USA
| | - Celal Özdemir
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Kadir Toykan Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Nurettin Öztürk
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | | | - Niki Papakonstantinou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoantropology and Speleology, Greek Ministry of Culture, 11636 Athens, Greece
| | | | | | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ilian Petrakiev
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Levon Petrosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Vanya Petrova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | | | - Ashot Piliposyan
- Department of Armenian History, Armenian State Pedagogical University After Khachatur Abovyan, 0010 Yerevan, Armenia
| | | | - Hrvoje Potrebica
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | | | | | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Siniša Radović
- Institute for Quaternary Paleontology and Geology, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Kamal Raeuf Aziz
- Sulaymaniyah Directorate of Antiquities and Heritage, 46010 Sulaymaniyah, Iraq
| | - Petra Rajić Šikanjić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | | | - Sergei Razumov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Amy Richardson
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Jacob Roodenberg
- The Netherlands Institute for the Near East, 2311 Leiden, Netherlands
| | - Rudenc Ruka
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Victoria Russeva
- Institute of Experimental Morphology, Pathology and Archeology with Museum, Bulgarian Academy of Science, 1113 Sofia, Bulgaria
| | - Mustafa Şahin
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Ayşegül Şarbak
- Department of Anthropology, Faculty of Science and Letters, Hitit University, 19040 Çorum, Turkey
| | - Emre Savaş
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Lynne Schepartz
- School of Anatomical Sciences, The University of the Witwatersrand, 2193 Johannesburg, South Africa
| | - Tayfun Selçuk
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Ayla Sevim-Erol
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Michel Shamoon-Pour
- Department of Anthropology, Binghamton University, Binghamton, NY 13902, USA
| | | | - Athanasios Sideris
- Institute of Classical Archaeology, Charles University, 11636 Prague, Czechia
| | - Angela Simalcsik
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,"Olga Necrasov" Centre of Anthropological Research, Romanian Academy Iași Branch, 2012 Iaşi Romania
| | - Hakob Simonyan
- Scientific Research Center of the Historical and Cultural Heritage, 0010 Yerevan, Armenia
| | - Vitalij Sinika
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ghenadie Sirbu
- Thracology Scientific Research Laboratory of the State University of Moldova, Department of Academic Management, Academy of Science of Moldova, 2009 Chișinău, Moldova
| | - Mario Šlaus
- Anthropological Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, 050711 Bucharest, Romania
| | - Bilal Söğüt
- Department of Archaeology, Faculty of Science and Arts, Pamukkale University, 20070 Denizli, Turkey
| | | | - Çilem Sönmez-Sözer
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Maria Stathi
- Ephorate of Antiquities of East Attica, Ministry of Culture and Sports, 10682 Athens, Greece
| | - Martin Steskal
- Austrian Archaeological Institute at the Austrian Academy of Sciences, 1190 Vienna, Austria
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sharon Stocker
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Fadime Suata-Alpaslan
- Department of Anthropology, Faculty of Letters, Istanbul University, 34134 Istanbul, Turkey
| | - Alexander Suvorov
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Nikolai Telnov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Strahil Temov
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | - Nadezhda Todorova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Ulsi Tota
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania.,Culture and Patrimony Department, University of Avignon, F-84029 Avignon, France
| | - Gilles Touchais
- Department of the History of Art and Archaeology, Université Paris 1 Panthéon-Sorbonne, 75006 Paris, France
| | - Sevi Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Atila Türker
- Department of Archaeology, Faculty of Science and Letters, Ondokuz Mayıs University, 55139 Atakum-Samsun, Turkey
| | | | - Todor Valchev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | | | - Zlatko Videvski
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | | | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Sam Walsh
- School of Natural Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, 31-016 Kraków, Poland
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Bryn Athyn, PA 19009, USA.,Penn Museum, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evgenii Yarovoy
- History of the Ancient World and Middle Ages Department, Moscow Region State University, Moscow Region, 141014 Mytishi, Russia
| | - Alper Yener Yavuz
- Department of Anthropology, Burdur Mehmet Akif Ersoy University, Istiklal Campus, 15100 Burdur, Turkey
| | - Hakan Yılmaz
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rafet Çavuşoğlu
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, 1030 Vienna, Austria
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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25
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Evershed RP, Davey Smith G, Roffet-Salque M, Timpson A, Diekmann Y, Lyon MS, Cramp LJE, Casanova E, Smyth J, Whelton HL, Dunne J, Brychova V, Šoberl L, Gerbault P, Gillis RE, Heyd V, Johnson E, Kendall I, Manning K, Marciniak A, Outram AK, Vigne JD, Shennan S, Bevan A, Colledge S, Allason-Jones L, Amkreutz L, Anders A, Arbogast RM, Bălăşescu A, Bánffy E, Barclay A, Behrens A, Bogucki P, Carrancho Alonso Á, Carretero JM, Cavanagh N, Claßen E, Collado Giraldo H, Conrad M, Csengeri P, Czerniak L, Dębiec M, Denaire A, Domboróczki L, Donald C, Ebert J, Evans C, Francés-Negro M, Gronenborn D, Haack F, Halle M, Hamon C, Hülshoff R, Ilett M, Iriarte E, Jakucs J, Jeunesse C, Johnson M, Jones AM, Karul N, Kiosak D, Kotova N, Krause R, Kretschmer S, Krüger M, Lefranc P, Lelong O, Lenneis E, Logvin A, Lüth F, Marton T, Marley J, Mortimer R, Oosterbeek L, Oross K, Pavúk J, Pechtl J, Pétrequin P, Pollard J, Pollard R, Powlesland D, Pyzel J, Raczky P, Richardson A, Rowe P, Rowland S, Rowlandson I, Saile T, Sebők K, Schier W, Schmalfuß G, Sharapova S, Sharp H, Sheridan A, Shevnina I, Sobkowiak-Tabaka I, Stadler P, Stäuble H, Stobbe A, Stojanovski D, Tasić N, van Wijk I, Vostrovská I, Vuković J, Wolfram S, Zeeb-Lanz A, Thomas MG. Dairying, diseases and the evolution of lactase persistence in Europe. Nature 2022; 608:336-345. [PMID: 35896751 PMCID: PMC7615474 DOI: 10.1038/s41586-022-05010-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/22/2022] [Indexed: 12/22/2022]
Abstract
In European and many African, Middle Eastern and southern Asian populations, lactase persistence (LP) is the most strongly selected monogenic trait to have evolved over the past 10,000 years1. Although the selection of LP and the consumption of prehistoric milk must be linked, considerable uncertainty remains concerning their spatiotemporal configuration and specific interactions2,3. Here we provide detailed distributions of milk exploitation across Europe over the past 9,000 years using around 7,000 pottery fat residues from more than 550 archaeological sites. European milk use was widespread from the Neolithic period onwards but varied spatially and temporally in intensity. Notably, LP selection varying with levels of prehistoric milk exploitation is no better at explaining LP allele frequency trajectories than uniform selection since the Neolithic period. In the UK Biobank4,5 cohort of 500,000 contemporary Europeans, LP genotype was only weakly associated with milk consumption and did not show consistent associations with improved fitness or health indicators. This suggests that other reasons for the beneficial effects of LP should be considered for its rapid frequency increase. We propose that lactase non-persistent individuals consumed milk when it became available but, under conditions of famine and/or increased pathogen exposure, this was disadvantageous, driving LP selection in prehistoric Europe. Comparison of model likelihoods indicates that population fluctuations, settlement density and wild animal exploitation-proxies for these drivers-provide better explanations of LP selection than the extent of milk exploitation. These findings offer new perspectives on prehistoric milk exploitation and LP evolution.
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Affiliation(s)
- Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK.
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.
- NIHR Bristol Biomedical Research Centre, University of Bristol, Bristol, UK.
| | | | - Adrian Timpson
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Yoan Diekmann
- Department of Genetics, Evolution and Environment, University College London, London, UK
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, Mainz, Germany
| | - Matthew S Lyon
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK
- NIHR Bristol Biomedical Research Centre, University of Bristol, Bristol, UK
| | - Lucy J E Cramp
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
| | - Emmanuelle Casanova
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Jessica Smyth
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
- School of Archaeology, University College Dublin, Dublin, Ireland
| | - Helen L Whelton
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Julie Dunne
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Veronika Brychova
- Department of Dairy, Fat and Cosmetics, University of Chemistry and Technology Prague, Prague, Czech Republic
- Nuclear Dosimetry Department, Institute of Nuclear Physics of the Czech Academy of Sciences, Prague, Czech Republic
| | - Lucija Šoberl
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Pascale Gerbault
- Department of Genetics, Evolution and Environment, University College London, London, UK
- School of Life Sciences, University of Westminster, London, UK
| | - Rosalind E Gillis
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CNRS-Muséum National d'Histoire Naturelle-Sorbonne Universités, Paris, France
- ICArEHB, Faculdade de Ciências Humanas e Sociais, Universidade do Algarve, Faro, Portugal
| | - Volker Heyd
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
- Department of Cultures, Section of Archaeology, University of Helsinki, Helsinki, Finland
| | - Emily Johnson
- Department of Archaeology, University of Exeter, Exeter, UK
- Archaeology South-East, UCL Institute of Archaeology, University College London, London, UK
| | - Iain Kendall
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Bristol, UK
| | - Katie Manning
- Department of Geography, King's College London, London, UK
| | | | - Alan K Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Jean-Denis Vigne
- Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CNRS-Muséum National d'Histoire Naturelle-Sorbonne Universités, Paris, France
| | - Stephen Shennan
- UCL Institute of Archaeology, University College London, London, UK
| | - Andrew Bevan
- UCL Institute of Archaeology, University College London, London, UK
| | - Sue Colledge
- UCL Institute of Archaeology, University College London, London, UK
| | | | - Luc Amkreutz
- National Museum of Antiquities, Leiden, the Netherlands
| | - Alexandra Anders
- Institute of Archaeological Sciences, Eötvös Loránd University, Budapest, Hungary
| | | | - Adrian Bălăşescu
- Department of Bioarchaeology, 'Vasile Pârvan' Institute of Archaeology, Romanian Academy, Bucharest, Romania
| | - Eszter Bánffy
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Centre of Excellence of the Hungarian Academy of Sciences, Budapest, Hungary
- Römisch-Germanische Kommission, Frankfurt, Germany
| | | | - Anja Behrens
- German Archaeological Institute, Berlin, Germany
| | - Peter Bogucki
- School of Engineering and Applied Science, Princeton University, Princeton, NJ, USA
| | - Ángel Carrancho Alonso
- Área de Prehistoria, Departamento de Historia, Geografía y Comunicación, University of Burgos, Burgos, Spain
| | - José Miguel Carretero
- Laboratorio Evolución Humana, University of Burgos, Burgos, Spain
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humana, Madrid, Spain
| | | | - Erich Claßen
- LVR-State Service for Archaeological Heritage, Bonn, Germany
| | - Hipolito Collado Giraldo
- Patrimonio & Arte Research Group, Extremadura University, Badajoz and Cáceres, Badajoz, Spain
- Geosciences Centre, Coimbra University, Coimbra, Portugal
| | | | | | - Lech Czerniak
- Institute of Archaeology and Ethnology, University of Gdańsk, Gdańsk, Poland
| | - Maciej Dębiec
- Institute of Archaeology, University Rzeszów, Rzeszów, Poland
| | | | | | | | - Julia Ebert
- Institute of Prehistoric Archaeology, Free University of Berlin, Berlin, Germany
| | - Christopher Evans
- Cambridge Archaeological Unit, University of Cambridge, Cambridge, UK
| | | | - Detlef Gronenborn
- Römisch-Germanisches Zentralmuseum, Leibniz Research Institute for Archaeology, Mainz, Germany
| | - Fabian Haack
- Archaeological Department, Landesmuseum Württemberg, Stuttgart, Germany
| | | | - Caroline Hamon
- UMR 8215, Trajectoires, Université Paris 1 Panthéon-Sorbonne, Paris, France
| | - Roman Hülshoff
- State Office for Heritage Management and Archaeology, Saxony Anhalt/State Museum of Prehistory, Halle/Saale, Germany
| | - Michael Ilett
- UMR 8215, Trajectoires, Université Paris 1 Panthéon-Sorbonne, Paris, France
| | - Eneko Iriarte
- Laboratorio Evolución Humana, University of Burgos, Burgos, Spain
| | - János Jakucs
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Centre of Excellence of the Hungarian Academy of Sciences, Budapest, Hungary
| | | | | | - Andy M Jones
- Cornwall Archaeological Unit, Cornwall Council, Truro, UK
| | | | - Dmytro Kiosak
- 'I.I. Mechnikov', Odessa National University, Odessa, Ukraine
- Ca' Foscari, University of Venice, Venice, Italy
| | - Nadezhda Kotova
- Institute of Archaeology of Academy of Science of Ukraine, Kiev, Ukraine
| | - Rüdiger Krause
- Prehistory Department, Institut of Archaeology, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | | | - Marta Krüger
- Department of Archaeology, Adam Mickiewicz University, Poznań, Poland
| | - Philippe Lefranc
- UMR 7044, INRAP Grand-Est Sud, University of Strasbourg, Strasbourg, France
| | - Olivia Lelong
- GUARD Glasgow, Glasgow, UK
- Eunomia Research & Consulting, Bristol, UK
| | - Eva Lenneis
- Department of Prehistoric and Historical Archaeology, University of Vienna, Vienna, Austria
| | | | | | - Tibor Marton
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Centre of Excellence of the Hungarian Academy of Sciences, Budapest, Hungary
| | | | | | - Luiz Oosterbeek
- Geosciences Centre, Coimbra University, Coimbra, Portugal
- Polytechnic Institute of Tomar, Tomar, Portugal
- Terra e Memória Institute, Mação, Portugal
| | - Krisztián Oross
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Centre of Excellence of the Hungarian Academy of Sciences, Budapest, Hungary
| | | | - Joachim Pechtl
- Kelten Römer Museum Manching, Manching, Germany
- Department of Archaeology, University of Innsbruck, Innsbruck, Austria
| | - Pierre Pétrequin
- MSHE C.N. Ledoux, CNRS & University of Franche-Comté, Besançon, France
| | - Joshua Pollard
- Department of Archaeology, University of Southampton, Southampton, UK
| | | | | | - Joanna Pyzel
- Institute of Archaeology and Ethnology, University of Gdańsk, Gdańsk, Poland
| | - Pál Raczky
- Institute of Archaeological Sciences, Eötvös Loránd University, Budapest, Hungary
| | | | - Peter Rowe
- Tees Archaeology, Hartlepool, UK
- North Yorkshire County Council HER, Northallerton, UK
| | | | | | - Thomas Saile
- Institute of History, University of Regensburg, Regensburg, Germany
| | - Katalin Sebők
- Institute of Archaeological Sciences, Eötvös Loránd University, Budapest, Hungary
| | - Wolfram Schier
- Institute of Prehistoric Archaeology, Free University of Berlin, Berlin, Germany
| | | | | | - Helen Sharp
- Leicestershire County Council Museums, Leicestershire, UK
| | | | | | - Iwona Sobkowiak-Tabaka
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
- Faculty of Archaeology, Adam Mickiewicz University, Poznań, Poland
| | - Peter Stadler
- Department of Prehistoric and Historical Archaeology, University of Vienna, Vienna, Austria
| | | | - Astrid Stobbe
- Prehistory Department, Institut of Archaeology, Johann Wolfgang Goethe-Universität, Frankfurt, Germany
| | - Darko Stojanovski
- Geology Department, University of Trás-os-Montes and Alto Douro, Vila Real, Portugal
- Department of Humanistic Studies, University of Ferrara, Ferrara, Italy
| | | | - Ivo van Wijk
- Faculty of Archaeology, Leiden University, Leiden, the Netherlands
| | - Ivana Vostrovská
- Institute of Archaeology and Museology, Masaryk University, Brno, Czech Republic
- Department of History, Palacký University, Olomouc, Czech Republic
| | | | | | - Andrea Zeeb-Lanz
- Generaldirektion Kulturelles Erbe Rheinland-Pfalz, Dir. Landesarchäologie, Speyer, Germany
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London, UK.
- UCL Genetics Institute, University College London, London, UK.
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26
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Vitamin D in the Context of Evolution. Nutrients 2022; 14:nu14153018. [PMID: 35893872 PMCID: PMC9332464 DOI: 10.3390/nu14153018] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2022] [Revised: 07/18/2022] [Accepted: 07/21/2022] [Indexed: 12/12/2022] Open
Abstract
For at least 1.2 billion years, eukaryotes have been able to synthesize sterols and, therefore, can produce vitamin D when exposed to UV-B. Vitamin D endocrinology was established some 550 million years ago in animals, when the high-affinity nuclear receptor VDR (vitamin D receptor), transport proteins and enzymes for vitamin D metabolism evolved. This enabled vitamin D to regulate, via its target genes, physiological process, the first of which were detoxification and energy metabolism. In this way, vitamin D was enabled to modulate the energy-consuming processes of the innate immune system in its fight against microbes. In the evolving adaptive immune system, vitamin D started to act as a negative regulator of growth, which prevents overboarding reactions of T cells in the context of autoimmune diseases. When, some 400 million years ago, species left the ocean and were exposed to gravitation, vitamin D endocrinology took over the additional role as a major regulator of calcium homeostasis, being important for a stable skeleton. Homo sapiens evolved approximately 300,000 years ago in East Africa and had adapted vitamin D endocrinology to the intensive exposure of the equatorial sun. However, when some 75,000 years ago, when anatomically modern humans started to populate all continents, they also reached regions with seasonally low or no UV-B, i.e., and under these conditions vitamin D became a vitamin.
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Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy. Genomics 2022; 114:110405. [PMID: 35709925 DOI: 10.1016/j.ygeno.2022.110405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022]
Abstract
Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.
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Ancient DNA gives new insights into a Norman Neolithic monumental cemetery dedicated to male elites. Proc Natl Acad Sci U S A 2022; 119:e2120786119. [PMID: 35446690 PMCID: PMC9170172 DOI: 10.1073/pnas.2120786119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
By integrating genomic and archaeological data, we provide new insights into the Neolithic French monumental site of Fleury-sur-Orne in Normandy, where a group of selected individuals was buried in impressively long monuments. The earliest individuals buried at Fleury-sur-Orne match the expected western European Neolithic genetic diversity, while three individuals, designated as genetic outliers, were buried after 4,000 calibrated BCE. We hypothesize that different, unrelated families or clans used the site over several centuries. Thirteen of 14 of the analyzed individuals were male, indicating an overarching patrilineal system. However, one exception, a female buried with a symbolically male artifact, suggests that the embodiment of the male gender in death was required to access burial at the monumental structures. The Middle Neolithic in western Europe is characterized by monumental funerary structures, known as megaliths, along the Atlantic façade. The first manifestations of this phenomenon occurred in modern-day France with the long mounds of the Cerny culture. Here, we present genome-wide data from the fifth-millennium BCE site of Fleury-sur-Orne in Normandy (France), famous for its impressively long monuments built for selected individuals. The site encompasses 32 monuments of variable sizes, containing the burials of 19 individuals from the Neolithic period. To address who was buried at the site, we generated genome-wide data for 14 individuals, of whom 13 are males, completing previously published data [M. Rivollat et al., Sci. Adv. 6, eaaz5344 (2020)]. Population genetic and Y chromosome analyses show that the Fleury-sur-Orne group fits within western European Neolithic genetic diversity and that the arrival of a new group is detected after 4,000 calibrated BCE. The results of analyzing uniparentally inherited markers and an overall low number of long runs of homozygosity suggest a patrilineal group practicing female exogamy. We find two pairs of individuals to be father and son, buried together in the same monument/grave. No other biological relationship can link monuments together, suggesting that each monument was dedicated to a genetically independent lineage. The combined data and documented father–son line of descent suggest a male-mediated transmission of sociopolitical authority. However, a single female buried with an arrowhead, otherwise considered a symbol of power of the male elite of the Cerny culture, questions a strictly biological sex bias in the burial rites of this otherwise “masculine” monumental cemetery.
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Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily. iScience 2022; 25:104244. [PMID: 35494246 PMCID: PMC9051636 DOI: 10.1016/j.isci.2022.104244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 11/23/2022] Open
Abstract
Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700–4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell’Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition. Genetic transition between Early Mesolithic and Late Mesolithic hunter-gatherers A near-complete genetic turnover during the Mesolithic-Neolithic transition Exchange of subsistence practices between hunter-gatherers and early farmers
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Aneli S, Saupe T, Montinaro F, Solnik A, Molinaro L, Scaggion C, Carrara N, Raveane A, Kivisild T, Metspalu M, Scheib CL, Pagani L. The genetic origin of Daunians and the Pan-Mediterranean southern Italian Iron Age context. Mol Biol Evol 2022; 39:6509524. [PMID: 35038748 PMCID: PMC8826970 DOI: 10.1093/molbev/msac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at the beginning of the Iron Age with the Iapygian civilization which consisted of three cultures: Peucetians, Messapians, and Daunians. Among them, the Daunians left a peculiar cultural heritage, with one-of-a-kind stelae and pottery, but, despite the extensive archaeological literature, their origin has been lost to time. In order to shed light on this and to provide a genetic picture of Iron Age Southern Italy, we collected and sequenced human remains from three archaeological sites geographically located in Northern Apulia (the area historically inhabited by Daunians) and radiocarbon dated between 1157 and 275 calBCE. We find that Iron Age Apulian samples are still distant from the genetic variability of modern-day Apulians, they show a degree of genetic heterogeneity comparable with the cosmopolitan Republican and Imperial Roman civilization, even though a few kilometers and centuries separate them, and they are well inserted into the Iron Age Pan-Mediterranean genetic landscape. Our study provides for the first time a window on the genetic make-up of pre-Roman Apulia, whose increasing connectivity within the Mediterranean landscape, would have contributed to laying the foundation for modern genetic variability. In this light, the genetic profile of Daunians may be compatible with an at least partial autochthonous origin, with plausible contributions from the Balkan peninsula.
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Affiliation(s)
- Serena Aneli
- Department of Biology, University of Padua, Via Ugo Bassi, 58b, Padova 35121, Italy
| | - Tina Saupe
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Anu Solnik
- Core Facility,Institute of Genomics,University of Tartu, Riia 23B, Tartu, 51010 Estonia
| | - Ludovica Molinaro
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Cinzia Scaggion
- Department of Geosciences, University of Padua, Via Giovanni Gradenigo, 6, Padova 35131, Italy
| | - Nicola Carrara
- Anthropology Museum,University of Padova,Via Giotto, 1, Padova 35121, Italy
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Toomas Kivisild
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia.,Department of Human Genetics, KU Leuven, Leuven, Herestraat 49, B-3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Christiana L Scheib
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia.,St John's College, Cambridge, CB2 1TP, United Kingdom
| | - Luca Pagani
- Department of Biology, University of Padua, Via Ugo Bassi, 58b, Padova 35121, Italy.,Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
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31
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López-Onaindia D, Schmitt A, Gibaja JF, Subirà ME. Non-metric dental analysis of human interactions around the Pyrenees during the Neolithic and their biological impact. Ann Anat 2022; 242:151895. [DOI: 10.1016/j.aanat.2022.151895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 09/10/2021] [Accepted: 01/17/2022] [Indexed: 12/26/2022]
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32
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Cortell-Nicolau A, García-Puchol O, Barrera-Cruz M, García-Rivero D. The spread of agriculture in Iberia through Approximate Bayesian Computation and Neolithic projectile tools. PLoS One 2021; 16:e0261813. [PMID: 34962962 PMCID: PMC8714124 DOI: 10.1371/journal.pone.0261813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 12/13/2021] [Indexed: 11/18/2022] Open
Abstract
In the present article we use geometric microliths (a specific type of arrowhead) and Approximate Bayesian Computation (ABC) in order to evaluate possible origin points and expansion routes for the Neolithic in the Iberian Peninsula. In order to do so, we divide the Iberian Peninsula in four areas (Ebro river, Catalan shores, Xúquer river and Guadalquivir river) and we sample the geometric microliths existing in the sites with the oldest radiocarbon dates for each zone. On this data, we perform a partial Mantel test with three matrices: geographic distance matrix, cultural distance matrix and chronological distance matrix. After this is done, we simulate a series of partial Mantel tests where we alter the chronological matrix by using an expansion model with randomised origin points, and using the distribution of the observed partial Mantel test’s results as a summary statistic within an Approximate Bayesian Computation-Sequential Monte-Carlo (ABC-SMC) algorithm framework. Our results point clearly to a Neolithic expansion route following the Northern Mediterranean, whilst the Southern Mediterranean route could also find support and should be further discussed. The most probable origin points focus on the Xúquer river area.
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Affiliation(s)
- Alfredo Cortell-Nicolau
- Departament de Prehistòria, Arqueologia i Història Antiga, Facultat de Geografia i Història, Universitat de València, València, Spain
- Department of Archaeology, McDonald Institute for Archaeological Research, Faculty of Human, Social, and Political Science, University of Cambridge, Cambridge, United Kingdom
- * E-mail: (OGP); (ACN)
| | - Oreto García-Puchol
- Departament de Prehistòria, Arqueologia i Història Antiga, Facultat de Geografia i Història, Universitat de València, València, Spain
- * E-mail: (OGP); (ACN)
| | - María Barrera-Cruz
- Departament de Prehistòria, Arqueologia i Història Antiga, Facultat de Geografia i Història, Universitat de València, València, Spain
| | - Daniel García-Rivero
- Department of Prehistory and Archaeology, Faculty of Geography and History, University of Seville, Seville, Spain
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33
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Villalba-Mouco V, Oliart C, Rihuete-Herrada C, Childebayeva A, Rohrlach AB, Fregeiro MI, Celdrán Beltrán E, Velasco-Felipe C, Aron F, Himmel M, Freund C, Alt KW, Salazar-García DC, García Atiénzar G, de Miguel Ibáñez MP, Hernández Pérez MS, Barciela V, Romero A, Ponce J, Martínez A, Lomba J, Soler J, Martínez AP, Avilés Fernández A, Haber-Uriarte M, Roca de Togores Muñoz C, Olalde I, Lalueza-Fox C, Reich D, Krause J, García Sanjuán L, Lull V, Micó R, Risch R, Haak W. Genomic transformation and social organization during the Copper Age-Bronze Age transition in southern Iberia. SCIENCE ADVANCES 2021; 7:eabi7038. [PMID: 34788096 PMCID: PMC8597998 DOI: 10.1126/sciadv.abi7038] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 09/28/2021] [Indexed: 06/13/2023]
Abstract
The emerging Bronze Age (BA) of southeastern Iberia saw marked social changes. Late Copper Age (CA) settlements were abandoned in favor of hilltop sites, and collective graves were largely replaced by single or double burials with often distinctive grave goods indirectly reflecting a hierarchical social organization, as exemplified by the BA El Argar group. We explored this transition from a genomic viewpoint by tripling the amount of data available for this period. Concomitant with the rise of El Argar starting ~2200 cal BCE, we observe a complete turnover of Y-chromosome lineages along with the arrival of steppe-related ancestry. This pattern is consistent with a founder effect in male lineages, supported by our finding that males shared more relatives at sites than females. However, simple two-source models do not find support in some El Argar groups, suggesting additional genetic contributions from the Mediterranean that could predate the BA.
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Affiliation(s)
- Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Institute of Evolutionary Biology, CSIC–Universitat Pompeu Fabra, Barcelona, Spain
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Camila Oliart
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Adam B. Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide SA-5005, Australia
| | - María Inés Fregeiro
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Eva Celdrán Beltrán
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | | | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Marie Himmel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Caecilia Freund
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
| | - Kurt W. Alt
- Center of Natural and Cultural Human History, Danube Private University, Steiner Landstr. 124, A-3500 Krems, Austria
- Department of Biomedical Engineering, University of Basel, Gewerbestrasse 14-16, CH-4123 Allschwil, Switzerland
| | - Domingo C. Salazar-García
- Grupo de investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE—Basque Foundation for Science, Vitoria, Spain
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
| | - Ma. Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
| | - Mauro S. Hernández Pérez
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
| | - Virginia Barciela
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), Universidad de Alicante, 03690 Alicante, Spain
- Departamento de Biotecnología, Universidad de Alicante, 03690 Alicante, Spain
| | - Juana Ponce
- Museo Arqueológico Municipal de Lorca, Murcia, Spain
| | | | - Joaquín Lomba
- Department of Prehistory, Universidad de Murcia, Murcia, Spain
| | | | | | - Azucena Avilés Fernández
- Arqueología y Diseño Web S.L. (Grupo Entorno), Floridablanca 14, 1.°D, 30800 Lorca, Murcia, Spain
| | | | | | - Iñigo Olalde
- Institute of Evolutionary Biology, CSIC–Universitat Pompeu Fabra, Barcelona, Spain
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC–Universitat Pompeu Fabra, Barcelona, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | | | - Vicente Lull
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Rafael Micó
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Roberto Risch
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Prehistory, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
- School of Biological Sciences, The University of Adelaide, Adelaide SA-5005, Australia
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34
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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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Liu Y, Mao X, Krause J, Fu Q. Insights into human history from the first decade of ancient human genomics. Science 2021; 373:1479-1484. [PMID: 34554811 DOI: 10.1126/science.abi8202] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Yichen Liu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Xiaowei Mao
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins, Institute of Vertebrate Paleontology and Paleoanthropology, Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Beijing, 100044, China.,University of the Chinese Academy of Sciences, Beijing, 100049, China
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36
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Serrano JG, Ordóñez AC, Fregel R. Paleogenomics of the prehistory of Europe: human migrations, domestication and disease. Ann Hum Biol 2021; 48:179-190. [PMID: 34459342 DOI: 10.1080/03014460.2021.1942205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.
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Affiliation(s)
- Javier G Serrano
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
| | - Alejandra C Ordóñez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain.,Departamento Geografía e Historia, Facultad de Humanidades, Universidad de La Laguna, La Laguna, Spain
| | - Rosa Fregel
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
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37
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Modi A, Vai S, Posth C, Vergata C, Zaro V, Diroma MA, Boschin F, Capecchi G, Ricci S, Ronchitelli A, Catalano G, Lauria G, D'Amore G, Sineo L, Caramelli D, Lari M. More data on ancient human mitogenome variability in Italy: new mitochondrial genome sequences from three Upper Palaeolithic burials. Ann Hum Biol 2021; 48:213-222. [PMID: 34459344 DOI: 10.1080/03014460.2021.1942549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Recently, the study of mitochondrial variability in ancient humans has allowed the definition of population dynamics that characterised Europe in the Late Pleistocene and Early Holocene. Despite the abundance of sites and skeletal remains few data are available for Italy. AIM We reconstructed the mitochondrial genomes of three Upper Palaeolithic individuals for some of the most important Italian archaeological contexts: Paglicci (South-Eastern Italy), San Teodoro (South-Western Italy) and Arene Candide (North-Western Italy) caves. SUBJECTS AND METHODS We explored the phylogenetic relationships of the three mitogenomes in the context of Western Eurasian ancient and modern variability. RESULTS Paglicci 12 belongs to sub-haplogroup U8c, described in only two other Gravettian individuals; San Teodoro 2 harbours a U2'3'4'7'8'9 sequence, the only lineage found in Sicily during the Late Pleistocene and Early Holocene; Arene Candide 16 displays an ancestral U5b1 haplotype already detected in other Late Pleistocene hunter-gatherers from Central Europe. CONCLUSION Regional genetic continuity is highlighted in the Gravettian groups that succeeded in Paglicci. Data from one of the oldest human remains from Sicily reinforce the hypothesis that Epigravettian groups carrying U2'3'4'7'8'9 could be the first inhabitants of the island. The first pre-Neolithic mitogenome from North-Western Italy, sequenced here, shows more affinity with continental Europe than with the Italian peninsula.
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Affiliation(s)
- Alessandra Modi
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Chiara Vergata
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | - Valentina Zaro
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | | | - Francesco Boschin
- Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Siena, Italy
| | - Giulia Capecchi
- Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Siena, Italy
| | - Stefano Ricci
- Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Siena, Italy
| | - Annamaria Ronchitelli
- Dipartimento di Scienze Fisiche, della Terra e dell'Ambiente, Università degli Studi di Siena, Siena, Italy
| | - Giulio Catalano
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy
| | - Gabriele Lauria
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy.,Departamento de Ciencia Animal, Universitat Politecnica de Valencia, Valencia, Spain
| | - Giuseppe D'Amore
- Istituto di Studi Archeo-antropologici - I.S.A, Scandicci, Italy
| | - Luca Sineo
- Dipartimento di Scienze e Tecnologie Biologiche, Chimiche e Farmaceutiche, Università degli Studi di Palermo, Palermo, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, Firenze, Italy
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38
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Aneli S, Caldon M, Saupe T, Montinaro F, Pagani L. Through 40,000 years of human presence in Southern Europe: the Italian case study. Hum Genet 2021; 140:1417-1431. [PMID: 34410492 PMCID: PMC8460580 DOI: 10.1007/s00439-021-02328-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 07/29/2021] [Indexed: 12/16/2022]
Abstract
The Italian Peninsula, a natural pier across the Mediterranean Sea, witnessed intricate population events since the very beginning of the human occupation in Europe. In the last few years, an increasing number of modern and ancient genomes from the area have been published by the international research community. This genomic perspective started unveiling the relevance of Italy to understand the post-Last Glacial Maximum (LGM) re-peopling of Europe, the earlier phase of the Neolithic westward migrations, and its linking role between Eastern and Western Mediterranean areas after the Iron Age. However, many open questions are still waiting for more data to be addressed in full. With this review, we summarize the current knowledge emerging from the available ancient Italian individuals and, by re-analysing them all at once, we try to shed light on the avenues future research in the area should cover. In particular, open questions concern (1) the fate of pre-Villabruna Europeans and to what extent their genomic components were absorbed by the post-LGM hunter-gatherers; (2) the role of Sicily and Sardinia before LGM; (3) to what degree the documented genetic structure within the Early Neolithic settlers can be described as two separate migrations; (4) what are the population events behind the marked presence of an Iranian Neolithic-like component in Bronze Age and Iron Age Italian and Southern European samples.
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Affiliation(s)
- Serena Aneli
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.
| | - Matteo Caldon
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.,Department of Biology-Genetics, University of Bari, Via Edoardo Orabona 4, 70125, Bari, Italy
| | - Luca Pagani
- Department of Biology, University of Padova, Via Ugo Bassi, 58/B, 35131, Padova, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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39
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Almarri MA, Haber M, Lootah RA, Hallast P, Al Turki S, Martin HC, Xue Y, Tyler-Smith C. The genomic history of the Middle East. Cell 2021; 184:4612-4625.e14. [PMID: 34352227 PMCID: PMC8445022 DOI: 10.1016/j.cell.2021.07.013] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 05/17/2021] [Accepted: 07/09/2021] [Indexed: 11/22/2022]
Abstract
The Middle East region is important to understand human evolution and migrations but is underrepresented in genomic studies. Here, we generated 137 high-coverage physically phased genome sequences from eight Middle Eastern populations using linked-read sequencing. We found no genetic traces of early expansions out-of-Africa in present-day populations but found Arabians have elevated Basal Eurasian ancestry that dilutes their Neanderthal ancestry. Population sizes within the region started diverging 15–20 kya, when Levantines expanded while Arabians maintained smaller populations that derived ancestry from local hunter-gatherers. Arabians suffered a population bottleneck around the aridification of Arabia 6 kya, while Levantines had a distinct bottleneck overlapping the 4.2 kya aridification event. We found an association between movement and admixture of populations in the region and the spread of Semitic languages. Finally, we identify variants that show evidence of selection, including polygenic selection. Our results provide detailed insights into the genomic and selective histories of the Middle East. Middle Easterners do not have ancestry from an early out-of-Africa expansion Basal Eurasian and African ancestry in Arabians deplete their Neanderthal ancestry Populations experienced bottlenecks overlapping aridification events Identification of recent single and polygenic signals of selection in Arabia
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Affiliation(s)
- Mohamed A Almarri
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates.
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham B15 2TT, UK; Centre for Computational Biology, University of Birmingham, Birmingham B15 2TT, UK.
| | - Reem A Lootah
- Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates
| | - Pille Hallast
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK; Institute of Biomedicine and Translational Medicine, University of Tartu, Tartu 50411, Estonia
| | - Saeed Al Turki
- Translational Pathology, Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City, Ministry of National Guard-Health Affairs, Riyadh, Saudi Arabia; Department of Genetics & Genomics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Hilary C Martin
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Yali Xue
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
| | - Chris Tyler-Smith
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK
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Bortolini E, Pagani L, Oxilia G, Posth C, Fontana F, Badino F, Saupe T, Montinaro F, Margaritora D, Romandini M, Lugli F, Papini A, Boggioni M, Perrini N, Oxilia A, Cigliano RA, Barcelona R, Visentin D, Fasser N, Arrighi S, Figus C, Marciani G, Silvestrini S, Bernardini F, Menghi Sartorio JC, Fiorenza L, Cecchi JM, Tuniz C, Kivisild T, Gianfrancesco F, Peresani M, Scheib CL, Talamo S, D'Esposito M, Benazzi S. Early Alpine occupation backdates westward human migration in Late Glacial Europe. Curr Biol 2021; 31:2484-2493.e7. [PMID: 33887180 DOI: 10.1016/j.cub.2021.03.078] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 01/07/2021] [Accepted: 03/22/2021] [Indexed: 02/07/2023]
Abstract
Before the end of the Last Glacial Maximum (LGM, ∼16.5 ka ago)1 set in motion major shifts in human culture and population structure,2 a consistent change in lithic technology, material culture, settlement pattern, and adaptive strategies is recorded in Southern Europe at ∼18-17 ka ago. In this time frame, the landscape of Northeastern Italy changed considerably, and the retreat of glaciers allowed hunter-gatherers to gradually recolonize the Alps.3-6 Change within this renewed cultural frame (i.e., during the Late Epigravettian phase) is currently associated with migrations favored by warmer climate linked to the Bølling-Allerød onset (14.7 ka ago),7-11 which replaced earlier genetic lineages with ancestry found in an individual who lived ∼14 ka ago at Riparo Villabruna, Italy, and shared among different contexts (Villabruna Cluster).9 Nevertheless, these dynamics and their chronology are still far from being disentangled due to fragmentary evidence for long-distance interactions across Europe.12 Here, we generate new genomic data from a human mandible uncovered at Riparo Tagliente (Veneto, Italy), which we directly dated to 16,980-16,510 cal BP (2σ). This individual, affected by focal osseous dysplasia, is genetically affine to the Villabruna Cluster. Our results therefore backdate by at least 3 ka the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bølling/Allerød event. In light of the new genetic evidence, this population replacement chronologically coincides with the very emergence of major cultural transitions in Southern and Western Europe.
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Affiliation(s)
- Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy; CaSEs (Culture and Socio-Ecological Dynamics) Department of Humanities, Universitat Pompeu Fabra, Ramon Trias Fargas, 25-27, 08005 Barcelona, Spain.
| | - Luca Pagani
- Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy; Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia.
| | - Gregorio Oxilia
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Rümelinstrasse 19-23, 72070 Tübingen, Germany
| | - Federica Fontana
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Federica Badino
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy; Research Group on Vegetation, Climate and Human Stratigraphy, Lab of Palynology and Palaeoecology, CNR - Institute of Environmental Geology and Geoengineering (IGAG), 20126 Milano, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia
| | - Davide Margaritora
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Matteo Romandini
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Federico Lugli
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Andrea Papini
- Dentist surgeon, via Walter Tobagi 35, 59100 Prato, Italy
| | - Marco Boggioni
- Dentist surgeon, via D'Andrade 34/207, 16154 Genova Sestri Ponente, Italy
| | - Nicola Perrini
- Dentist surgeon, Centro di Odontoiatria e Stomatologia, Via Luca Signorelli, 5, 51100 Pistoia PT, Italy
| | - Antonio Oxilia
- General surgeon, via Marcantonio Della Torre, 7, 37131 Verona, Italy
| | | | - Rosa Barcelona
- Sequentia Biotech, Calle Comte D'Urgell 240, 08036 Barcelona, Spain; Institute of Genetics and Biophysics "Adriano Buzzati-Traverso," National Research Council of Italy, Via P.Castellino 111, 80131 Naples, Italy; Departamento de Matemáticas, Escuela Técnica Superior de Ingeniería Industrial de Barcelona (ETSEIB), Universitat Politècnica de Catalunya (UPC), Diagonal 647, 08028 Barcelona, Spain
| | - Davide Visentin
- Archaeology of Social Dynamics, Institució Milà i Fontanals, Spanish National Research Council (IMF-CSIC), C/Egipcíaques 15, 08001 Barcelona, Spain
| | - Nicolò Fasser
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Simona Arrighi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Carla Figus
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Sara Silvestrini
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy
| | - Federico Bernardini
- Department of Humanities, Università Ca' Foscari Venezia, Dorsoduro, 3484/D, 30123 Venezia, Italy; Multidisciplinary Laboratory, The "Abdus Salam" International Centre for Theoretical Physics (ICTP), Strada Costiera, 11 - 34151 Trieste, Italy
| | - Jessica C Menghi Sartorio
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Luca Fiorenza
- Monash Biomedicine Discovery Institute, Department of Anatomy and Developmental Biology, Monash University, Melbourne, VIC 3800, Australia; Earth Sciences, University of New England, Armidale, NSW 2351, Australia
| | - Jacopo Moggi Cecchi
- Department of Biology, University of Florence, Via del Proconsolo, 12, Firenze 50122, Italy
| | - Claudio Tuniz
- Multidisciplinary Laboratory, The "Abdus Salam" International Centre for Theoretical Physics (ICTP), Strada Costiera, 11 - 34151 Trieste, Italy; Centre for Archaeological Science, University of Wollongong, Northfields Avenue, Wollongong, NSW 2522, Australia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia; Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Fernando Gianfrancesco
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso," National Research Council of Italy, Via P.Castellino 111, 80131 Naples, Italy
| | - Marco Peresani
- Department of Humanities - Section of Prehistoric and Anthropological Sciences, University of Ferrara, Corso Ercole I d'Este 32, 44121 Ferrara, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b 51010 Tartu, Estonia
| | - Sahra Talamo
- Department of Chemistry "G. Ciamician," University of Bologna, Via Selmi, 2, 40126 Bologna, Italy; Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Maurizio D'Esposito
- Institute of Genetics and Biophysics "Adriano Buzzati-Traverso," National Research Council of Italy, Via P.Castellino 111, 80131 Naples, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1 48121 Ravenna, Italy; Max Planck Institute for Evolutionary Anthropology, Department of Human Evolution, Deutscher Platz 6, 04103 Leipzig, Germany
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Abstract
Some of the genes responsible for the evolution of light skin pigmentation in Europeans show signals of positive selection in present-day populations. Recently, genome-wide association studies have highlighted the highly polygenic nature of skin pigmentation. It is unclear whether selection has operated on all of these genetic variants or just a subset. By studying variation in over a thousand ancient genomes from West Eurasia covering 40,000 y, we are able to study both the aggregate behavior of pigmentation-associated variants and the evolutionary history of individual variants. We find that the evolution of light skin pigmentation in Europeans was driven by frequency changes in a relatively small fraction of the genetic variants that are associated with variation in the trait today. Skin pigmentation is a classic example of a polygenic trait that has experienced directional selection in humans. Genome-wide association studies have identified well over a hundred pigmentation-associated loci, and genomic scans in present-day and ancient populations have identified selective sweeps for a small number of light pigmentation-associated alleles in Europeans. It is unclear whether selection has operated on all of the genetic variation associated with skin pigmentation as opposed to just a small number of large-effect variants. Here, we address this question using ancient DNA from 1,158 individuals from West Eurasia covering a period of 40,000 y combined with genome-wide association summary statistics from the UK Biobank. We find a robust signal of directional selection in ancient West Eurasians on 170 skin pigmentation-associated variants ascertained in the UK Biobank. However, we also show that this signal is driven by a limited number of large-effect variants. Consistent with this observation, we find that a polygenic selection test in present-day populations fails to detect selection with the full set of variants. Our data allow us to disentangle the effects of admixture and selection. Most notably, a large-effect variant at SLC24A5 was introduced to Western Europe by migrations of Neolithic farming populations but continued to be under selection post-admixture. This study shows that the response to selection for light skin pigmentation in West Eurasia was driven by a relatively small proportion of the variants that are associated with present-day phenotypic variation.
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Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France. Curr Biol 2021; 31:1072-1083.e10. [PMID: 33434506 DOI: 10.1016/j.cub.2020.12.015] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022]
Abstract
The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.
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KOGANEBUCHI KAE, OOTA HIROKI. Paleogenomics of human remains in East Asia and Yaponesia focusing on current advances and future directions. ANTHROPOL SCI 2021. [DOI: 10.1537/ase.2011302] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- KAE KOGANEBUCHI
- Laboratory of Genome Anthropology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
- Advanced Medical Research Center, Faculty of Medicine, University of the Ryukyus, Nishihara
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, Nishihara
| | - HIROKI OOTA
- Laboratory of Genome Anthropology, Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
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Mounier A, Heuzé Y, Samsel M, Vasilyev S, Klaric L, Villotte S. Gravettian cranial morphology and human group affinities during the European Upper Palaeolithic. Sci Rep 2020; 10:21931. [PMID: 33318530 PMCID: PMC7736346 DOI: 10.1038/s41598-020-78841-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 11/23/2020] [Indexed: 11/09/2022] Open
Abstract
Archaeologically defined Upper Palaeolithic (UP, 45,000-10,000 years ago) "cultures" are often used as proxies to designate fossil populations. While recent genomic studies have partly clarified the complex relationship between European UP "cultures" and past population dynamics, they leave open numerous questions regarding the biological characterization of these human groups, especially regarding the Mid-UP period (MUP, 33,000-24,000 years ago), which encompasses a pan-European cultural mosaic (Gravettian) with several regional facies. Here, we analyse a large database of well-dated and well-preserved UP crania, including MUP specimens from South-West France (SWF) and Moravia, using 3D geometric morphometrics to test for human group affinities. Our results show that the Gravettian makers from these two regions form a remarkably phenetically homogeneous sample which is different from, and more homogeneous than, the Late UP sample. Those results are congruent with genomic studies indicating a genetic continuity within the Gravettian manufacturers and a discontinuity marked by the Last Glacial Maximum (LGM). Moreover, our study expands the geographical range of the MUP phenetic continuity to SWF, for which aDNA data are scarce, and clarifies the post-LGM European population structure in SWF, with a possible dual ancestry stemming from different LGM refugia.
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Affiliation(s)
- Aurélien Mounier
- Histoire Naturelle de l'Homme Préhistorique (HNHP, UMR 7194), MNHN/CNRS/UPVD, Musée de l'Homme, 17 place du Trocadéro et du 11 novembre, 75016, Paris, France. .,Leverhulme Centre for Human Evolutionary Studies, Department of Archaeology, University of Cambridge, Fitzwilliam Street, Cambridge, CB2 1QH, United Kingdom.
| | - Yann Heuzé
- UMR 5199 PACEA, CNRS-Université de Bordeaux, Bâtiment B8, Allée Geoffroy Saint Hilaire, Pessac, 33615, France
| | - Mathilde Samsel
- UMR 5199 PACEA, CNRS-Université de Bordeaux, Bâtiment B8, Allée Geoffroy Saint Hilaire, Pessac, 33615, France
| | - Sergey Vasilyev
- Institute of Ethnology and Anthropology RAS, Leninsky pr. 32a, Moscow, Russian Federation, 119991
| | - Laurent Klaric
- CNRS, UMR-7055 PréTech, MSH Mondes, 21 allée de l'Université, 92023, Nanterre, France
| | - Sébastien Villotte
- UMR 5199 PACEA, CNRS-Université de Bordeaux, Bâtiment B8, Allée Geoffroy Saint Hilaire, Pessac, 33615, France.
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McLaughlin TR, Gómez-Puche M, Cascalheira J, Bicho N, Fernández-López de Pablo J. Late Glacial and Early Holocene human demographic responses to climatic and environmental change in Atlantic Iberia. Philos Trans R Soc Lond B Biol Sci 2020; 376:20190724. [PMID: 33250026 PMCID: PMC7741096 DOI: 10.1098/rstb.2019.0724] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Successive generations of hunter-gatherers of the Late Glacial and Early Holocene in Iberia had to contend with rapidly changing environments and climatic conditions. This constrained their economic resources and capacity for demographic growth. The Atlantic façade of Iberia was occupied throughout these times and witnessed very significant environmental transformations. Archaeology offers a perspective on how past human population ecologies changed in response to this scenario. Archaeological radiocarbon data are used here to reconstruct demographics of the region over the long term. We introduce various quantitative methods that allow us to develop palaeodemographic and spatio-temporal models of population growth and density, and compare our results to independent records of palaeoenvironmental and palaeodietary change, and growth rates derived from skeletal data. Our results demonstrate that late glacial population growth was stifled by the Younger Dryas stadial, but populations grew in size and density during the Early to Middle Holocene transition. This growth was fuelled in part by an increased dependence on marine and estuarine food sources, demonstrating how the environment was linked to demographic change via the resource base, and ultimately the carrying capacity of the environment. This article is part of the theme issue 'Cross-disciplinary approaches to prehistoric demography'.
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Affiliation(s)
- T Rowan McLaughlin
- I.U. de Investigación en Arqueología y Patrimonio Histórico (INAPH), University of Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - Magdalena Gómez-Puche
- I.U. de Investigación en Arqueología y Patrimonio Histórico (INAPH), University of Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain
| | - João Cascalheira
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Nuno Bicho
- Interdisciplinary Center for Archaeology and Evolution of Human Behaviour (ICArEHB), Universidade do Algarve, Campus de Gambelas, 8005-139 Faro, Portugal
| | - Javier Fernández-López de Pablo
- I.U. de Investigación en Arqueología y Patrimonio Histórico (INAPH), University of Alicante, Carr. de San Vicente del Raspeig, s/n, 03690 San Vicente del Raspeig, Alicante, Spain
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Hui R, D'Atanasio E, Cassidy LM, Scheib CL, Kivisild T. Evaluating genotype imputation pipeline for ultra-low coverage ancient genomes. Sci Rep 2020; 10:18542. [PMID: 33122697 PMCID: PMC7596702 DOI: 10.1038/s41598-020-75387-w] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/12/2020] [Indexed: 01/12/2023] Open
Abstract
Although ancient DNA data have become increasingly more important in studies about past populations, it is often not feasible or practical to obtain high coverage genomes from poorly preserved samples. While methods of accurate genotype imputation from > 1 × coverage data have recently become a routine, a large proportion of ancient samples remain unusable for downstream analyses due to their low coverage. Here, we evaluate a two-step pipeline for the imputation of common variants in ancient genomes at 0.05-1 × coverage. We use the genotype likelihood input mode in Beagle and filter for confident genotypes as the input to impute missing genotypes. This procedure, when tested on ancient genomes, outperforms a single-step imputation from genotype likelihoods, suggesting that current genotype callers do not fully account for errors in ancient sequences and additional quality controls can be beneficial. We compared the effect of various genotype likelihood calling methods, post-calling, pre-imputation and post-imputation filters, different reference panels, as well as different imputation tools. In a Neolithic Hungarian genome, we obtain ~ 90% imputation accuracy for heterozygous common variants at coverage 0.05 × and > 97% accuracy at coverage 0.5 ×. We show that imputation can mitigate, though not eliminate reference bias in ultra-low coverage ancient genomes.
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Affiliation(s)
- Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Eugenia D'Atanasio
- Department of Human Genetics, Katholieke Universiteit Leuven, Herestraat 49 - box 602, 3000, Leuven, Belgium
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, Rome, Italy
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John's College, St John's Street, Cambridge, CB2 1TP, UK
| | - Toomas Kivisild
- Department of Human Genetics, Katholieke Universiteit Leuven, Herestraat 49 - box 602, 3000, Leuven, Belgium.
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia.
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47
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Hanel A, Carlberg C. Skin colour and vitamin D: An update. Exp Dermatol 2020; 29:864-875. [PMID: 32621306 DOI: 10.1111/exd.14142] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/14/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
Homo sapiens evolved in East Africa and had dark skin, hair, and eyes, in order to protect against deleterious consequences of intensive UV radiation at equatorial latitudes. Intensive skin pigmentation was thought to bear the risk of inefficient vitamin D3 synthesis in the skin. This initiated the hypothesis that within the past 75 000 years, in which humans migrated to higher latitudes in Asia and Europe, the need for vitamin D3 synthesis served as an evolutionary driver for skin lightening. In this review, we summarize the recent archeogenomic reconstruction of population admixture in Europe and demonstrate that skin lightening happened as late as 5000 years ago through immigration of lighter pigmented populations from western Anatolia and the Russian steppe but not primarily via evolutionary pressure for vitamin D3 synthesis. We show that variations in genes encoding for proteins being responsible for the transport, metabolism and signalling of vitamin D provide alternative mechanisms of adaptation to a life in northern latitudes without suffering from consequences of vitamin D deficiency. This includes hypotheses explaining differences in the vitamin D status and response index of European populations.
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Affiliation(s)
- Andrea Hanel
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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A Genetic History of the Near East from an aDNA Time Course Sampling Eight Points in the Past 4,000 Years. Am J Hum Genet 2020; 107:149-157. [PMID: 32470374 PMCID: PMC7332655 DOI: 10.1016/j.ajhg.2020.05.008] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 05/11/2020] [Indexed: 01/12/2023] Open
Abstract
The Iron and Classical Ages in the Near East were marked by population expansions carrying cultural transformations that shaped human history, but the genetic impact of these events on the people who lived through them is little-known. Here, we sequenced the whole genomes of 19 individuals who each lived during one of four time periods between 800 BCE and 200 CE in Beirut on the Eastern Mediterranean coast at the center of the ancient world’s great civilizations. We combined these data with published data to traverse eight archaeological periods and observed any genetic changes as they arose. During the Iron Age (∼1000 BCE), people with Anatolian and South-East European ancestry admixed with people in the Near East. The region was then conquered by the Persians (539 BCE), who facilitated movement exemplified in Beirut by an ancient family with Egyptian-Lebanese admixed members. But the genetic impact at a population level does not appear until the time of Alexander the Great (beginning 330 BCE), when a fusion of Asian and Near Easterner ancestry can be seen, paralleling the cultural fusion that appears in the archaeological records from this period. The Romans then conquered the region (31 BCE) but had little genetic impact over their 600 years of rule. Finally, during the Ottoman rule (beginning 1516 CE), Caucasus-related ancestry penetrated the Near East. Thus, in the past 4,000 years, three limited admixture events detectably impacted the population, complementing the historical records of this culturally complex region dominated by the elite with genetic insights from the general population.
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Olalde I, Posth C. Latest trends in archaeogenetic research of west Eurasians. Curr Opin Genet Dev 2020; 62:36-43. [PMID: 32610222 DOI: 10.1016/j.gde.2020.05.021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2020] [Revised: 05/11/2020] [Accepted: 05/22/2020] [Indexed: 11/26/2022]
Abstract
During the past ten years, archaeogenetic research has exponentially grown to study the genetic history of human populations, using genome-wide data from large numbers of ancient individuals. Of the entire globe, Europe and the Near East are the regions where ancient DNA data is by far most abundant with over 2500 genomes published at present. In this review, we focus on archaeological contexts that have received less attention in the literature, specifically those associated with west Eurasian hunter-gatherers as well as populations from the Iron Age and later historical periods. In addition, we emphasize a recent shift from continent-wide to regional and even site-specific studies, which is starting to provide novel insights into sociocultural aspects of past societies.
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Affiliation(s)
- Iñigo Olalde
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen 72070, Germany.
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Abstract
The nature and distribution of political power in Europe during the Neolithic era remains poorly understood1. During this period, many societies began to invest heavily in building monuments, which suggests an increase in social organization. The scale and sophistication of megalithic architecture along the Atlantic seaboard, culminating in the great passage tomb complexes, is particularly impressive2. Although co-operative ideology has often been emphasised as a driver of megalith construction1, the human expenditure required to erect the largest monuments has led some researchers to emphasize hierarchy3—of which the most extreme case is a small elite marshalling the labour of the masses. Here we present evidence that a social stratum of this type was established during the Neolithic period in Ireland. We sampled 44 whole genomes, among which we identify the adult son of a first-degree incestuous union from remains that were discovered within the most elaborate recess of the Newgrange passage tomb. Socially sanctioned matings of this nature are very rare, and are documented almost exclusively among politico-religious elites4—specifically within polygynous and patrilineal royal families that are headed by god-kings5,6. We identify relatives of this individual within two other major complexes of passage tombs 150 km to the west of Newgrange, as well as dietary differences and fine-scale haplotypic structure (which is unprecedented in resolution for a prehistoric population) between passage tomb samples and the larger dataset, which together imply hierarchy. This elite emerged against a backdrop of rapid maritime colonization that displaced a unique Mesolithic isolate population, although we also detected rare Irish hunter-gatherer introgression within the Neolithic population.
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