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Cooke NP, Murray M, Cassidy LM, Mattiangeli V, Okazaki K, Kasai K, Gakuhari T, Bradley DG, Nakagome S. Genomic imputation of ancient Asian populations contrasts local adaptation in pre- and post-agricultural Japan. iScience 2024; 27:110050. [PMID: 38883821 PMCID: PMC11176660 DOI: 10.1016/j.isci.2024.110050] [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] [Received: 10/07/2023] [Revised: 03/25/2024] [Accepted: 05/17/2024] [Indexed: 06/18/2024] Open
Abstract
Early modern humans lived as hunter-gatherers for millennia before agriculture, yet the genetic adaptations of these populations remain a mystery. Here, we investigate selection in the ancient hunter-gatherer-fisher Jomon and contrast pre- and post-agricultural adaptation in the Japanese archipelago. Building on the successful validation of imputation with ancient Asian genomes, we identify selection signatures in the Jomon, particularly robust signals from KITLG variants, which may have influenced dark pigmentation evolution. The Jomon lacks well-known adaptive variants (EDAR, ADH1B, and ALDH2), marking their emergence after the advent of farming in the archipelago. Notably, the EDAR and ADH1B variants were prevalent in the archipelago 1,300 years ago, whereas the ALDH2 variant could have emerged later due to its absence in other ancient genomes. Overall, our study underpins local adaptation unique to the Jomon population, which in turn sheds light on post-farming selection that continues to shape contemporary Asian populations.
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Affiliation(s)
- Niall P Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Yonago, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Institute for the Study of Ancient Civilizations and Cultural Resources, Kanazawa University, Kanazawa, Japan
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2
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Iasi LNM, Chintalapati M, Skov L, Mesa AB, Hajdinjak M, Peter BM, Moorjani P. Neandertal ancestry through time: Insights from genomes of ancient and present-day humans. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.13.593955. [PMID: 38798350 PMCID: PMC11118355 DOI: 10.1101/2024.05.13.593955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2024]
Abstract
Gene flow from Neandertals has shaped the landscape of genetic and phenotypic variation in modern humans. We identify the location and size of introgressed Neandertal ancestry segments in more than 300 genomes spanning the last 50,000 years. We study how Neandertal ancestry is shared among individuals to infer the time and duration of the Neandertal gene flow. We find the correlation of Neandertal segment locations across individuals and their divergence to sequenced Neandertals, both support a model of single major Neandertal gene flow. Our catalog of introgressed segments through time confirms that most natural selection-positive and negative-on Neandertal ancestry variants occurred immediately after the gene flow, and provides new insights into how the contact with Neandertals shaped human origins and adaptation.
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Affiliation(s)
- Leonardo N. M. Iasi
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
| | - Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
| | - Laurits Skov
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
| | - Alba Bossoms Mesa
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
| | - Mateja Hajdinjak
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
- The Francis Crick Institute; London, NW1 1AT, UK
| | - Benjamin M. Peter
- Department for Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology; Leipzig, 04301, Germany
- Department of Biology, University of Rochester; Rochester NY, 14620,USA
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California Berkeley; Berkeley, CA 94720, USA
- Center for Computational Biology, University of California Berkeley; Berkeley, CA 94720, USA
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3
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Caduff M, Eckel R, Leuenberger C, Wegmann D. Accurate Bayesian inference of sex chromosome karyotypes and sex-linked scaffolds from low-depth sequencing data. Mol Ecol Resour 2024; 24:e13913. [PMID: 38173222 DOI: 10.1111/1755-0998.13913] [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: 09/16/2023] [Revised: 11/27/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024]
Abstract
The identification of sex-linked scaffolds and the genetic sex of individuals, i.e. their sex karyotype, is a fundamental step in population genomic studies. If sex-linked scaffolds are known, single individuals may be sexed based on read counts of next-generation sequencing data. If both sex-linked scaffolds as well as sex karyotypes are unknown, as is often the case for non-model organisms, they have to be jointly inferred. For both cases, current methods rely on arbitrary thresholds, which limits their power for low-depth data. In addition, most current methods are limited to euploid sex karyotypes (XX and XY). Here we develop BeXY, a fully Bayesian method to jointly infer the posterior probabilities for each scaffold to be autosomal, X- or Y-linked and for each individual to be any of the sex karyotypes XX, XY, X0, XXX, XXY, XYY and XXYY. If the sex-linked scaffolds are known, it also identifies autosomal trisomies and estimates the sex karyotype posterior probabilities for single individuals. As we show with downsampling experiments, BeXY has higher power than all existing methods. It accurately infers the sex karyotype of ancient human samples with as few as 20,000 reads and accurately infers sex-linked scaffolds from data sets of just a handful of samples or with highly imbalanced sex ratios, also in the case of low-quality reference assemblies. We illustrate the power of BeXY by applying it to both whole-genome shotgun and target enrichment sequencing data of ancient and modern humans, as well as several non-model organisms.
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Affiliation(s)
- Madleina Caduff
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Raphael Eckel
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Christoph Leuenberger
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, Fribourg, Switzerland
- Swiss Institute of Bioinformatics, Fribourg, Switzerland
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4
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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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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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Irving-Pease EK, Refoyo-Martínez A, Barrie W, Ingason A, Pearson A, Fischer A, Sjögren KG, Halgren AS, Macleod R, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn AH, Speidel L, Stern AJ, Scorrano G, Ramsøe A, Schork AJ, Rosengren A, Zhao L, Kristiansen K, Iversen AKN, Fugger L, Sudmant PH, Lawson DJ, Durbin R, Korneliussen T, Werge T, Allentoft ME, Sikora M, Nielsen R, Racimo F, Willerslev E. The selection landscape and genetic legacy of ancient Eurasians. Nature 2024; 625:312-320. [PMID: 38200293 PMCID: PMC10781624 DOI: 10.1038/s41586-023-06705-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/03/2023] [Indexed: 01/12/2024]
Abstract
The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
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Affiliation(s)
- Evan K Irving-Pease
- 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
| | - William Barrie
- GeoGenetics Group, Department of Zoology, 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
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - 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
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Alma S Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Ruairidh Macleod
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- UCL Genetics Institute, University College London, London, UK
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie, 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 H Vaughn
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Leo Speidel
- UCL Genetics Institute, University College London, London, UK
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Aaron J Stern
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Abigail Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Lei Zhao
- 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
| | - Astrid K N Iversen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
- MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Perth, Western Australia, Australia
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - 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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7
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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: 11] [Impact Index Per Article: 11.0] [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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8
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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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9
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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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10
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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: 18] [Impact Index Per Article: 18.0] [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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11
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Abstract
Nearly 20 y ago, Jared Diamond and Peter Bellwood reviewed the evidence for the associated spread of farming and large language families by the demographic expansions of farmers. Since then, advances in obtaining and analyzing genomic data from modern and ancient populations have transformed our knowledge of human dispersals during the Holocene. Here, we provide an overview of Holocene dispersals in the light of genomic evidence and conclude that they have a complex history. Even when there is a demonstrated connection between a demographic expansion of people, the spread of agriculture, and the spread of a particular language family, the outcome in the results of contact between expanding and resident groups is highly variable. Further research is needed to identify the factors and social circumstances that have influenced this variation and complex history.
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12
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Long-term trends in human body size track regional variation in subsistence transitions and growth acceleration linked to dairying. Proc Natl Acad Sci U S A 2023; 120:e2209482119. [PMID: 36649422 PMCID: PMC9942808 DOI: 10.1073/pnas.2209482119] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Evidence for a reduction in stature between Mesolithic foragers and Neolithic farmers has been interpreted as reflective of declines in health, however, our current understanding of this trend fails to account for the complexity of cultural and dietary transitions or the possible causes of phenotypic change. The agricultural transition was extended in primary centers of domestication and abrupt in regions characterized by demic diffusion. In regions such as Northern Europe where foreign domesticates were difficult to establish, there is strong evidence for natural selection for lactase persistence in relation to dairying. We employ broad-scale analyses of diachronic variation in stature and body mass in the Levant, Europe, the Nile Valley, South Asia, and China, to test three hypotheses about the timing of subsistence shifts and human body size, that: 1) the adoption of agriculture led to a decrease in stature, 2) there were different trajectories in regions of in situ domestication or cultural diffusion of agriculture; and 3) increases in stature and body mass are observed in regions with evidence for selection for lactase persistence. Our results demonstrate that 1) decreases in stature preceded the origins of agriculture in some regions; 2) the Levant and China, regions of in situ domestication of species and an extended period of mixed foraging and agricultural subsistence, had stable stature and body mass over time; and 3) stature and body mass increases in Central and Northern Europe coincide with the timing of selective sweeps for lactase persistence, providing support for the "Lactase Growth Hypothesis."
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13
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Söylev A, Çokoglu SS, Koptekin D, Alkan C, Somel M. CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. PLoS Comput Biol 2022; 18:e1010788. [PMID: 36516232 PMCID: PMC9873172 DOI: 10.1371/journal.pcbi.1010788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/24/2023] [Accepted: 12/03/2022] [Indexed: 12/15/2022] Open
Abstract
To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.
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Affiliation(s)
- Arda Söylev
- Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- * E-mail: (AS); (MS)
| | | | - Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biology, Middle East Technical University, Ankara, Turkey
- * E-mail: (AS); (MS)
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14
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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: 32] [Impact Index Per Article: 16.0] [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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15
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Ariano B, Mattiangeli V, Breslin EM, Parkinson EW, McLaughlin TR, Thompson JE, Power RK, Stock JT, Mercieca-Spiteri B, Stoddart S, Malone C, Gopalakrishnan S, Cassidy LM, Bradley DG. Ancient Maltese genomes and the genetic geography of Neolithic Europe. Curr Biol 2022; 32:2668-2680.e6. [PMID: 35588742 PMCID: PMC9245899 DOI: 10.1016/j.cub.2022.04.069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/07/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans.
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Affiliation(s)
- Bruno Ariano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eóin W Parkinson
- Department of Classics and Archaeology, University of Malta, Msida 2080, Malta
| | - T Rowan McLaughlin
- Department of Scientific Research, The British Museum, Great Russell Street, London WC1B 3DG, UK
| | - Jess E Thompson
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ronika K Power
- Department of History and Archaeology, Macquarie University, 25B Wally's Walk, Sydney, NSW, Australia
| | - Jay T Stock
- Department of Anthropology, Western University, 1151 Richmond St, London, ON N6G 2V4, Canada
| | | | - Simon Stoddart
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Caroline Malone
- School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, UK
| | - Shyam Gopalakrishnan
- GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark.
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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16
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Gelabert P, Schmidt RW, Fernandes DM, Karsten JK, Harper TK, Madden GD, Ledogar SH, Sokhatsky M, Oota H, Kennett DJ, Pinhasi R. Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine. Sci Rep 2022; 12:7242. [PMID: 35508651 PMCID: PMC9068698 DOI: 10.1038/s41598-022-11117-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000–3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935–825 cal BCE). Results reveal that the CTCC individuals’ ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980–825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
| | - Ryan W Schmidt
- University of Porto, CIBIO-InBIO, Rua Padre Armando Quintas, nº 7, 4485-661, Vairão, Portugal. .,School of Archaeology & Earth Institute, University College, Dublin, Belfield, Dublin 4, Ireland.
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Jordan K Karsten
- Department of Anthropology, Global Religions, and Cultures, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI, 54901, USA
| | - Thomas K Harper
- Institute for European and Mediterranean Archaeology, State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Gwyn D Madden
- Department of Anthropology, Grand Valley State University, 1 Campus Dr., Allendale, MI, 49401, USA
| | - Sarah H Ledogar
- Department of Archaeology, Classics, and History, University of New England, Armidale, NSW, 2351, Australia
| | - Mykhailo Sokhatsky
- Borschiv Regional Museum of Local Lore, Borschiv, Ternopil Oblast, Ukraine
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
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17
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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: 7] [Impact Index Per Article: 3.5] [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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18
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Balanovska EV, Gorin IO, Ponomarev GY, Pylev VY, Petrushenko VS, Markina NV, Mamaeva AD, Larin AK, Agdzhoyan AT. Footprints of interaction among Finniс-speaking, Slavic, and Turkic-speaking populations in modern gene pool and their reflection in pharmacogenetics. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2022. [DOI: 10.24075/brsmu.2022.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Genetic contribution of pre-Slavic populations to gene pools of modern Russia is increasingly relevant, along with genetic footprints of the Golden Horde invasion. The novel genome-wide approaches enable advanced solutions in this field. The study aimed at searching for the footprints of genetic interaction among Finnicspeaking, Slavic and Turkic-speaking populations of Central Russia and Volga Region and their reflection in pharmacogenetic landscape. Modeling ancestral components by ADMIXTURE software and their mapping involved genome-wide genotyping data for 248 individual genomes representing 47 populations of 9 ethnic groups. Of specific ancestral components identified in each of the Finnic-speaking peoples, only Mordovian ancestral components are common for all populations within the studied geographic area, regardless of their linguistic affiliation. Gene pools of Russian populations include 80% of intrinsic component, 19% contribution from Finnic-speaking peoples, and 1% of Central Asian influence. The Tatar gene pool combines all identified ancestral components, including 81% contribution from Finnic-speaking peoples and only 12% of Central Asian influence, which prevents using it as a reference for the assessment of Golden Horde footprints in Russian gene pools. A map of genetic distances from Ryazan Russians based on a panel of 42 pharmacogenetic markers reveals a landscape strikingly independent from the selectively neutral ancestral genomic patterns. For instance, populations of Mordovia, Kaluga, Smolensk, and Kostroma regions are the closest to Ryazan Russians in pharmacogenetic status, whereas populations of Ryazan and Nizhny Novgorod regions have strikingly divergent pharmacogenetic status despite the similarity of the selectively neutral ancestral genomic patterns. These findings confirm the relevance of targeted pharmacogenetic characterization for gene pools of Russia.
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Affiliation(s)
- EV Balanovska
- Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - IO Gorin
- Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - GYu Ponomarev
- Vavilov Institute of General Genetics, Moscow, Russia
| | - VYu Pylev
- Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - VS Petrushenko
- Bochkov Research Centre of Medical Genetics, Moscow, Russia
| | - NV Markina
- Vavilov Institute of General Genetics, Moscow, Russia
| | - AD Mamaeva
- Vavilov Institute of General Genetics, Moscow, Russia
| | - AK Larin
- Federal Research and Clinical Center of Physical-Chemical Medicine, Moscow, Russia
| | - AT Agdzhoyan
- Vavilov Institute of General Genetics, Moscow, Russia
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19
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Marciniak S, Bergey CM, Silva AM, Hałuszko A, Furmanek M, Veselka B, Velemínský P, Vercellotti G, Wahl J, Zariņa G, Longhi C, Kolář J, Garrido-Pena R, Flores-Fernández R, Herrero-Corral AM, Simalcsik A, Müller W, Sheridan A, Miliauskienė Ž, Jankauskas R, Moiseyev V, Köhler K, Király Á, Gamarra B, Cheronet O, Szeverényi V, Kiss V, Szeniczey T, Kiss K, Zoffmann ZK, Koós J, Hellebrandt M, Maier RM, Domboróczki L, Virag C, Novak M, Reich D, Hajdu T, von Cramon-Taubadel N, Pinhasi R, Perry GH. An integrative skeletal and paleogenomic analysis of stature variation suggests relatively reduced health for early European farmers. Proc Natl Acad Sci U S A 2022; 119:e2106743119. [PMID: 35389750 PMCID: PMC9169634 DOI: 10.1073/pnas.2106743119] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Accepted: 02/24/2022] [Indexed: 12/02/2022] Open
Abstract
Human culture, biology, and health were shaped dramatically by the onset of agriculture ∼12,000 y B.P. This shift is hypothesized to have resulted in increased individual fitness and population growth as evidenced by archaeological and population genomic data alongside a decline in physiological health as inferred from skeletal remains. Here, we consider osteological and ancient DNA data from the same prehistoric individuals to study human stature variation as a proxy for health across a transition to agriculture. Specifically, we compared “predicted” genetic contributions to height from paleogenomic data and “achieved” adult osteological height estimated from long bone measurements for 167 individuals across Europe spanning the Upper Paleolithic to Iron Age (∼38,000 to 2,400 B.P.). We found that individuals from the Neolithic were shorter than expected (given their individual polygenic height scores) by an average of −3.82 cm relative to individuals from the Upper Paleolithic and Mesolithic (P = 0.040) and −2.21 cm shorter relative to post-Neolithic individuals (P = 0.068), with osteological vs. expected stature steadily increasing across the Copper (+1.95 cm relative to the Neolithic), Bronze (+2.70 cm), and Iron (+3.27 cm) Ages. These results were attenuated when we additionally accounted for genome-wide genetic ancestry variation: for example, with Neolithic individuals −2.82 cm shorter than expected on average relative to pre-Neolithic individuals (P = 0.120). We also incorporated observations of paleopathological indicators of nonspecific stress that can persist from childhood to adulthood in skeletal remains into our model. Overall, our work highlights the potential of integrating disparate datasets to explore proxies of health in prehistory.
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Affiliation(s)
- Stephanie Marciniak
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
| | - Christina M. Bergey
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ 08854
| | - Ana Maria Silva
- Research Centre for Anthropology and Health (Centro de Investigação em Antropologia e Saúde - CIAS), Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
- Archeology Center of the University of Lisbon (UNIARQ), University of Lisbon, Lisbon 1600-214, Portugal
| | - Agata Hałuszko
- Institute of Archaeology, University of Wrocław, Wrocław 50-139, Poland
- Archeolodzy.org Foundation, Wrocław 50-316, Poland
| | - Mirosław Furmanek
- Institute of Archaeology, University of Wrocław, Wrocław 50-139, Poland
| | - Barbara Veselka
- Department of Chemistry, Analytical Environmental and Geo-Chemistry Research Unit, Vrije Univeristeit Brussels, Brussels 1050, Belgium
- Department of Art Studies and Archaeology, Maritime Cultures Research Institute, Vrije Univeristeit Brussels, Brussels 1050, Belgium
| | - Petr Velemínský
- Department of Anthropology, National Museum, Prague 115-79, Czech Republic
| | - Giuseppe Vercellotti
- Department of Anthropology, Ohio State University, Columbus, OH 43210
- Institute for Research and Learning in Archaeology and Bioarchaeology, Columbus, OH 43215
| | - Joachim Wahl
- Institute for Scientific Archaeology, Working Group Palaeoanthropology, University of Tübingen, Tübingen 72074, Germany
| | - Gunita Zariņa
- Institute of Latvian History, University of Latvia, Riga 1050, Latvia
| | - Cristina Longhi
- Soprintendenza Archeologia, Belle Arti e Paesaggio, Rome 00186, Italy
| | - Jan Kolář
- Department of Vegetation Ecology, Institute of Botany of the Czech Academy of Sciences, Průhonice 252-43, Czech Republic
- Institute of Archaeology and Museology, Masaryk University, Brno 602-00, Czech Republic
| | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | | | | | - Angela Simalcsik
- Olga Necrasov Center for Anthropological Research, Romanian Academy - Iasi Branch, Iasi 700481, Romania
- Orheiul Vechi Cultural-Natural Reserve, Orhei 3506, Republic of Moldova
| | - Werner Müller
- Laboratoire d'archéozoologie, Université de Neuchâtel, Neuchâtel 2000, Switzerland
| | - Alison Sheridan
- Department of Scottish History & Archaeology, National Museums Scotland, Edinburgh EH1 1JF, Scotland
| | - Žydrūnė Miliauskienė
- Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius 01513, Lithuania
| | - Rimantas Jankauskas
- Department of Anatomy, Histology and Anthropology, Vilnius University, Vilnius 01513, Lithuania
| | - Vyacheslav Moiseyev
- Department of Physical Anthropology, Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia
| | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary
| | - Ágnes Király
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, Tarragona 43007, Spain
- Departament d’Història i Història de l’Art, Universitat Rovira i Virgili, Tarragona 43003, Spain
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna 1030, Austria
| | - Vajk Szeverényi
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary
- Department of Archaeology, Déri Múzeum, Debrecen 4026, Hungary
| | - Viktória Kiss
- Institute of Archaeology, Research Centre for the Humanities, Eötvös Loránd Research Network, Budapest 1097, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary
| | - Krisztián Kiss
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary
- Department of Anthropology, Hungarian Natural History Museum, Budapest 1083, Hungary
| | | | - Judit Koós
- Department of Archaeology, Herman Ottó Museum, Miskolc 3530, Hungary
| | | | - Robert M. Maier
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - László Domboróczki
- Department of Archaeology, István Dobó Castle Museum, Eger 3300, Hungary
| | - Cristian Virag
- Department of Archaeology, Satu Mare County Museum, Satu Mare 440031, Romania
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb 10000, Croatia
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138
- The Max Planck–Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Boston, MA 02115
- Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA 02142
- HHMI, Harvard Medical School, Cambridge, MA 02138
| | - Tamás Hajdu
- Department of Biological Anthropology, Eötvös Loránd University, Budapest 1053, Hungary
| | - Noreen von Cramon-Taubadel
- Buffalo Human Evolutionary Morphology Lab, Department of Anthropology, University at Buffalo, Buffalo, NY 14261-0026
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna 1030, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Vienna 1030, Austria
| | - George H. Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802
- Department of Biology, Pennsylvania State University, University Park, PA 16802
- Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA 16802
- Deutsche Forschungsgemeinschaft (DFG) Center for Advanced Studies, University of Tübingen, Tübingen 72074, Germany
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20
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Wohns AW, Wong Y, Jeffery B, Akbari A, Mallick S, Pinhasi R, Patterson N, Reich D, Kelleher J, McVean G. A unified genealogy of modern and ancient genomes. Science 2022; 375:eabi8264. [PMID: 35201891 PMCID: PMC10027547 DOI: 10.1126/science.abi8264] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
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Affiliation(s)
- Anthony Wilder Wohns
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ali Akbari
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Swapan Mallick
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; 1090 Vienna, Austria
| | - Nick Patterson
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - David Reich
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
- Corresponding author.
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21
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Guellil M, Keller M, Dittmar JM, Inskip SA, Cessford C, Solnik A, Kivisild T, Metspalu M, Robb JE, Scheib CL. An invasive Haemophilus influenzae serotype b infection in an Anglo-Saxon plague victim. Genome Biol 2022; 23:22. [PMID: 35109894 PMCID: PMC8812261 DOI: 10.1186/s13059-021-02580-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 12/13/2021] [Indexed: 12/16/2022] Open
Abstract
Background The human pathogen Haemophilus influenzae was the main cause of bacterial meningitis in children and a major cause of worldwide infant mortality before the introduction of a vaccine in the 1980s. Although the occurrence of serotype b (Hib), the most virulent type of H. influenzae, has since decreased, reports of infections with other serotypes and non-typeable strains are on the rise. While non-typeable strains have been studied in-depth, very little is known of the pathogen’s evolutionary history, and no genomes dating prior to 1940 were available. Results We describe a Hib genome isolated from a 6-year-old Anglo-Saxon plague victim, from approximately 540 to 550 CE, Edix Hill, England, showing signs of invasive infection on its skeleton. We find that the genome clusters in phylogenetic division II with Hib strain NCTC8468, which also caused invasive disease. While the virulence profile of our genome was distinct, its genomic similarity to NCTC8468 points to mostly clonal evolution of the clade since the 6th century. We also reconstruct a partial Yersinia pestis genome, which is likely identical to a published first plague pandemic genome of Edix Hill. Conclusions Our study presents the earliest genomic evidence for H. influenzae, points to the potential presence of larger genomic diversity in the phylogenetic division II serotype b clade in the past, and allows the first insights into the evolutionary history of this major human pathogen. The identification of both plague and Hib opens questions on the effect of plague in immunocompromised individuals already affected by infectious diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s13059-021-02580-z.
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Affiliation(s)
- Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia.
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia.
| | - Jenna M Dittmar
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK.,Department of Archaeology, University of Aberdeen, St. Mary's, Elphinstone Road, Aberdeen, Scotland, AB24 3UF, UK
| | - Sarah A Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK.,School of Archaeology and Ancient History, University of Leicester, University Road, Leicester, LE1 7RH, UK
| | - Craig Cessford
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge, CB2 3ER, UK.,Cambridge Archaeological Unit, University of Cambridge, 34 A&B Storey's Way, Cambridge, CB3 0DT, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia.,Department of Human Genetics, KU Leuven, Herestraat 49, B-3000, Leuven, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia
| | - John E Robb
- Department of Archaeology, University of Cambridge, Downing Street, Cambridge, CB2 3DZ, UK
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, 51010, Tartu, Estonia. .,St John's College, University of Cambridge, St John's Street, Cambridge, CB2 1TP, UK.
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22
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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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23
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Balanovska EV, Gorin IO, Koshel SM, Balanovsky OP. Gene Geographic Atlas of DNA Markers Controlling Human Eye and Hair Color. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421120036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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24
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Phylogenetic history of patrilineages rare in northern and eastern Europe from large-scale re-sequencing of human Y-chromosomes. Eur J Hum Genet 2021; 29:1510-1519. [PMID: 33958743 PMCID: PMC8484622 DOI: 10.1038/s41431-021-00897-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/13/2021] [Indexed: 02/07/2023] Open
Abstract
The most frequent Y-chromosomal (chrY) haplogroups in northern and eastern Europe (NEE) are well-known and thoroughly characterised. Yet a considerable number of men in every population carry rare paternal lineages with estimated frequencies around 5%. So far, limited sample-sizes and insufficient resolution of genotyping have obstructed a truly comprehensive look into the variety of rare paternal lineages segregating within populations and potential signals of population history that such lineages might convey. Here we harness the power of massive re-sequencing of human Y chromosomes to identify previously unknown population-specific clusters among rare paternal lineages in NEE. We construct dated phylogenies for haplogroups E2-M215, J2-M172, G-M201 and Q-M242 on the basis of 421 (of them 282 novel) high-coverage chrY sequences collected from large-scale databases focusing on populations of NEE. Within these otherwise rare haplogroups we disclose lineages that began to radiate ~1-3 thousand years ago in Estonia and Sweden and reveal male phylogenetic patterns testifying of comparatively recent local demographic expansions. Conversely, haplogroup Q lineages bear evidence of ancient Siberian influence lingering in the modern paternal gene pool of northern Europe. We assess the possible direction of influx of ancestral carriers for some of these male lineages. In addition, we demonstrate the congruency of paternal haplogroup composition of our dataset with two independent population-based cohorts from Estonia and Sweden.
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25
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Caramelli D, Posth C, Rickards O. Reconstruction of the human peopling of Europe: a genetic insight. Ann Hum Biol 2021; 48:175-178. [PMID: 34459346 DOI: 10.1080/03014460.2021.1955472] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- David Caramelli
- Department of Biology, University of Florence, Florence, Italy
| | - Cosimo Posth
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Olga Rickards
- Department of Biology, Centre of Molecular Anthropology for Ancient DNA Studies, University of Rome "Tor Vergata", Rome, Italy
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26
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Feldman M, Gnecchi-Ruscone GA, Lamnidis TC, Posth C. Where Asia meets Europe - recent insights from ancient human genomics. Ann Hum Biol 2021; 48:191-202. [PMID: 34459345 DOI: 10.1080/03014460.2021.1949039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
CONTEXT The peopling of Europe by modern humans is a widely debated topic in the field of modern and ancient genomics. While several recent syntheses have focussed on this topic, little has been discussed about the genetic history of populations in the continent's surrounding regions. OBJECTIVE We explore genetic transformations in three key areas that played an essential role in the formation of the European genetic landscape through time, focussing on the periods spanning from the Epipalaeolithic/Mesolithic and up until the Iron Age. METHODS We review published ancient genomic studies and integrate the associated data to provide a quantification and visualisation of major trends in the population histories of the Near East, the western Eurasian Steppe and North East Europe. RESULTS We describe cross-regional as well as localised prehistoric demographic shifts and discuss potential research directions while highlighting geo-temporal gaps in the data. CONCLUSION In recent years, archaeogenetic studies have contributed to the understanding of human genetic diversity through time in regions located at the doorstep of Europe. Further studies focussing on these areas will allow for a better characterisation of genetic shifts and regionally-specific patterns of admixture across western Eurasia.
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Affiliation(s)
- Michal Feldman
- Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Guido A Gnecchi-Ruscone
- Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Thiseas C Lamnidis
- Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Cosimo Posth
- Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany
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27
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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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28
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Scorrano G, Yediay FE, Pinotti T, Feizabadifarahani M, Kristiansen K. The genetic and cultural impact of the Steppe migration into Europe. Ann Hum Biol 2021; 48:223-233. [PMID: 34459341 DOI: 10.1080/03014460.2021.1942984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND During the early 3rd millennium BCE migration from Pontic Steppe, mainly related to Yamnaya culture, has affected European populations both culturally and genetically, however, it has long been debated to what extent this migration was male-driven, and how this replacement process took place which eliminated partially/largely Neolithic male lines over time. AIM This paper aims to evaluate the influence of the Steppe migration on European Bronze Age populations by calculating both male and female genetic contributions of the Steppe-related ancestry to the European Bronze Age populations. With this approach, we will be able to clarify the hypotheses on whether it was male-biased migration or not. SUBJECTS AND METHODS To evaluate the genetic impact and the proportion of the Steppe-related ancestry to the European Bronze Age populations, we performed PCA and qpAdm analyses by using published genome-wide data. In addition, we quantified male and female genetic contribution into Europe by using the analysis of uniparental markers and the X-chromosome. RESULTS The Steppe migration had a considerable impact on the genetic makeup of the Bronze Age European populations. The data suggest that the Steppe-related ancestry arriving into Central Europe was male-driven, dominantly in the Corded Ware culture populations and lesser in the Bell Beaker populations. In fact, there is no evidence that this migration had a significant input on the mitochondrial genetic pool of all European Bronze Age populations. CONCLUSIONS Our analyses suggest that the Steppe-related ancestry had genetic impact on mainly Central-Eastern Europe. Moreover, this migration was male-driven for most of the Central European populations belonging to the Corded Ware groups, and to a lesser extent for the Bell Beaker groups.
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Affiliation(s)
- Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fulya Eylem Yediay
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomaz Pinotti
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Laboratório de Biodiversidade e Evolução Molecular (LBEM), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
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29
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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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30
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Maisano Delser P, Jones ER, Hovhannisyan A, Cassidy L, Pinhasi R, Manica A. A curated dataset of modern and ancient high-coverage shotgun human genomes. Sci Data 2021; 8:202. [PMID: 34349118 PMCID: PMC8338957 DOI: 10.1038/s41597-021-00980-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2020] [Accepted: 06/10/2021] [Indexed: 11/09/2022] Open
Abstract
Over the last few years, genome-wide data for a large number of ancient human samples have been collected. Whilst datasets of captured SNPs have been collated, high coverage shotgun genomes (which are relatively few but allow certain types of analyses not possible with ascertained captured SNPs) have to be reprocessed by individual groups from raw reads. This task is computationally intensive. Here, we release a dataset including 35 whole-genome sequenced samples, previously published and distributed worldwide, together with the genetic pipeline used to process them. The dataset contains 72,041,355 sites called across 19 ancient and 16 modern individuals and includes sequence data from four previously published ancient samples which we sequenced to higher coverage (10-18x). Such a resource will allow researchers to analyse their new samples with the same genetic pipeline and directly compare them to the reference dataset without re-processing published samples. Moreover, this dataset can be easily expanded to increase the sample distribution both across time and space.
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Affiliation(s)
- Pierpaolo Maisano Delser
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland.
| | - Eppie R Jones
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK
- Genomics Medicine Ireland, Dublin, Ireland
| | - Anahit Hovhannisyan
- Institute of Molecular Biology, National Academy of Sciences, 7 Hasratyan Street, 0014, Yerevan, Armenia
| | - Lara Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, 2, Ireland
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ, UK.
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31
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Juras A, Ehler E, Chyleński M, Pospieszny Ł, Spinek AE, Malmström H, Krzewińska M, Szostek K, Pasterkiewicz W, Florek M, Wilk S, Mnich B, Kruk J, Szmyt M, Kozieł S, Götherström A, Jakobsson M, Dabert M. Maternal genetic origin of the late and final Neolithic human populations from present-day Poland. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:223-236. [PMID: 34308549 DOI: 10.1002/ajpa.24372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK.,Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
| | - Anna Elżbieta Spinek
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, Warszawa, Poland
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Kraków, Poland.,The Karkonosze Museum in Jelenia Góra, Jelenia Góra, Poland
| | - Barbara Mnich
- Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University in Kraków, Kraków, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Kraków, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland.,Archaeological Museum, Poznań, Poland
| | - Sławomir Kozieł
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
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32
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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: 7] [Impact Index Per Article: 2.3] [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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Svensson E, Günther T, Hoischen A, Hervella M, Munters AR, Ioana M, Ridiche F, Edlund H, van Deuren RC, Soficaru A, de-la-Rua C, Netea MG, Jakobsson M. Genome of Peştera Muierii skull shows high diversity and low mutational load in pre-glacial Europe. Curr Biol 2021; 31:2973-2983.e9. [PMID: 34010592 DOI: 10.1016/j.cub.2021.04.045] [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: 12/03/2020] [Revised: 04/09/2021] [Accepted: 04/19/2021] [Indexed: 11/24/2022]
Abstract
Few complete human genomes from the European Early Upper Palaeolithic (EUP) have been sequenced. Using novel sampling and DNA extraction approaches, we sequenced the genome of a woman from "Peştera Muierii," Romania who lived ∼34,000 years ago to 13.5× coverage. The genome shows similarities to modern-day Europeans, but she is not a direct ancestor. Although her cranium exhibits both modern human and Neanderthal features, the genome shows similar levels of Neanderthal admixture (∼3.1%) to most EUP humans but only half compared to the ∼40,000-year-old Peştera Oase 1. All EUP European hunter-gatherers display high genetic diversity, demonstrating that the severe loss of diversity occurred during and after the Last Glacial Maximum (LGM) rather than just during the out-of-Africa migration. The prevalence of genetic diseases is expected to increase with low diversity; however, pathogenic variant load was relatively constant from EUP to modern times, despite post-LGM hunter-gatherers having the lowest diversity ever observed among Europeans.
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Affiliation(s)
- Emma Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
| | - Alexander Hoischen
- Department of Human Genetics, Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Mihai Ioana
- Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | | | - Hanna Edlund
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Rosanne C van Deuren
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands
| | - Andrei Soficaru
- "Francisc J. Rainer" Institute of Anthropology, Romanian Academy, 050474 Bucharest, Romania
| | - Concepción de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B° Sarriena s/n 48940 Leioa, Bizkaia, Spain
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, 6526 Nijmegen, the Netherlands; Laboratory of Human Genetics, University of Medicine and Pharmacy, Craiova, Romania
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 752 36 Uppsala, Sweden.
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34
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Saupe T, Montinaro F, Scaggion C, Carrara N, Kivisild T, D'Atanasio E, Hui R, Solnik A, Lebrasseur O, Larson G, Alessandri L, Arienzo I, De Angelis F, Rolfo MF, Skeates R, Silvestri L, Beckett J, Talamo S, Dolfini A, Miari M, Metspalu M, Benazzi S, Capelli C, Pagani L, Scheib CL. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula. Curr Biol 2021; 31:2576-2591.e12. [PMID: 33974848 DOI: 10.1016/j.cub.2021.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/28/2020] [Accepted: 04/09/2021] [Indexed: 12/30/2022]
Abstract
Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.
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Affiliation(s)
- Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia.
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Cinzia Scaggion
- Department of Geosciences, University of Padova, Via Gradenigo 6, Padova 35131, Italy
| | - Nicola Carrara
- Museum of Anthropology, University of Padova, Palazzo Cavalli, via Giotto 1, Padova 35121, 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 3000, Belgium
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ophélie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK; Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Greger Larson
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Luca Alessandri
- Groningen Institute of Archaeology, University of Groningen, Poststraat 6, Groningen 9712, the Netherlands
| | - Ilenia Arienzo
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata," Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Letizia Silvestri
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | | | - Sahra Talamo
- Department of Chemistry "Giacomo Ciamician," University of Bologna, Via Selmi 2, Bologna 40126, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Andrea Dolfini
- School of History, Classics and Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Monica Miari
- Superintendency of Archeology, Fine Arts and Landscape for the metropolitan city of Bologna and the provinces of Modena, Reggio Emilia and Ferrara, Comune di Bologna, Sede Via Belle Arti n. 52, Bologna 40126, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1, Ravenna 40126, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi, 58/B, Padova 35122, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; St. John's College, University of Cambridge, St. John's Street, Cambridge CB2 1TP, UK.
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35
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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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36
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Abstract
Cultural diversity is disappearing quickly. Whilst a phylogenetic approach makes explicit the continuous extinction of cultures, and the generation of new ones, cultural evolutionary changes such as the rise of agriculture or more recently colonisation can cause periods of mass cultural extinction. At the current rate, 90% of languages will become extinct or moribund by the end of this century. Unlike biological extinction, cultural extinction does not necessarily involve genetic extinction or even deaths, but results from the disintegration of a social entity and discontinuation of culture-specific behaviours. Here we propose an analytical framework to examine the phenomenon of cultural extinction. When examined over millennia, extinctions of cultural traits or institutions can be studied in a phylogenetic comparative framework that incorporates archaeological data on ancestral states. Over decades or centuries, cultural extinction can be studied in a behavioural ecology framework to investigate how the fitness consequences of cultural behaviours and population dynamics shift individual behaviours away from the traditional norms. Frequency-dependent costs and benefits are key to understanding both the origin and the loss of cultural diversity. We review recent evolutionary studies that have informed cultural extinction processes and discuss avenues of future studies.
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Affiliation(s)
- Hanzhi Zhang
- Department of Anthropology, University College London, LondonWC1H 0BW, UK
| | - Ruth Mace
- Department of Anthropology, University College London, LondonWC1H 0BW, UK
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Capodiferro MR, Aram B, Raveane A, Rambaldi Migliore N, Colombo G, Ongaro L, Rivera J, Mendizábal T, Hernández-Mora I, Tribaldos M, Perego UA, Li H, Scheib CL, Modi A, Gòmez-Carballa A, Grugni V, Lombardo G, Hellenthal G, Pascale JM, Bertolini F, Grieco GS, Cereda C, Lari M, Caramelli D, Pagani L, Metspalu M, Friedrich R, Knipper C, Olivieri A, Salas A, Cooke R, Montinaro F, Motta J, Torroni A, Martín JG, Semino O, Malhi RS, Achilli A. Archaeogenomic distinctiveness of the Isthmo-Colombian area. Cell 2021; 184:1706-1723.e24. [PMID: 33761327 PMCID: PMC8024902 DOI: 10.1016/j.cell.2021.02.040] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/20/2020] [Accepted: 02/18/2021] [Indexed: 01/09/2023]
Abstract
The recently enriched genomic history of Indigenous groups in the Americas is still meager concerning continental Central America. Here, we report ten pre-Hispanic (plus two early colonial) genomes and 84 genome-wide profiles from seven groups presently living in Panama. Our analyses reveal that pre-Hispanic demographic events contributed to the extensive genetic structure currently seen in the area, which is also characterized by a distinctive Isthmo-Colombian Indigenous component. This component drives these populations on a specific variability axis and derives from the local admixture of different ancestries of northern North American origin(s). Two of these ancestries were differentially associated to Pleistocene Indigenous groups that also moved into South America, leaving heterogenous genetic footprints. An additional Pleistocene ancestry was brought by a still unsampled population of the Isthmus (UPopI) that remained restricted to the Isthmian area, expanded locally during the early Holocene, and left genomic traces up to the present day.
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Affiliation(s)
| | - Bethany Aram
- Department of Geography, History and Philosophy, the Pablo de Olavide University of Seville, Seville 41013, Spain
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy; Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | - Nicola Rambaldi Migliore
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Giulia Colombo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Linda Ongaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Javier Rivera
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Tomás Mendizábal
- Patronato Panamá Viejo, Panama City 0823-05096, Panama; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Iosvany Hernández-Mora
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia
| | - Maribel Tribaldos
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Ugo Alessandro Perego
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Hongjie Li
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Alessandra Modi
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Alberto Gòmez-Carballa
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Viola Grugni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Gianluca Lombardo
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Garrett Hellenthal
- UCL Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Juan Miguel Pascale
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Francesco Bertolini
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan 20141, Italy
| | | | - Cristina Cereda
- Genomic and Post-Genomic Center, National Neurological Institute C. Mondino, Pavia 27100, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence 50122, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence 50122, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology, University of Padua, Padua 35121, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Ronny Friedrich
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Corina Knipper
- Curt Engelhorn Center Archaeometry (CEZA), Mannheim 68159, Germany
| | - Anna Olivieri
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Antonio Salas
- Unidade de Xenética, Instituto de Ciencias Forenses (INCIFOR), Facultade de Medicina, Universidade de Santiago de Compostela, 15782 Galicia, Spain; GenPoB Research Group, Instituto de Investigación Sanitarias (IDIS), Hospital Clínico Universitario de Santiago de Compostela (SERGAS), 15706 Galicia, Spain
| | - Richard Cooke
- Smithsonian Tropical Research Institute, Panama City 0843-03092, Panama; Sistema Nacional de Investigadores, Secretaría Nacional de Ciencia y Tecnología, Ciudad del Saber, Clayton 0816-02852, Panama
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Bari 70125, Italy
| | - Jorge Motta
- Gorgas Memorial Institute for Health Studies, Panama City 0816-02593, Panama
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Juan Guillermo Martín
- Department of History and Social Sciences, Universidad del Norte, Barranquilla 080001, Colombia; Coiba Scientific Station (COIBA AIP), City of Knowledge, Clayton 0843-03081, Panama
| | - Ornella Semino
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy
| | - Ripan Singh Malhi
- Department of Anthropology, Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
| | - Alessandro Achilli
- Department of Biology and Biotechnology "L. Spallanzani," University of Pavia, Pavia 27100, Italy.
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Immel A, Pierini F, Rinne C, Meadows J, Barquera R, Szolek A, Susat J, Böhme L, Dose J, Bonczarowska J, Drummer C, Fuchs K, Ellinghaus D, Kässens JC, Furholt M, Kohlbacher O, Schade-Lindig S, Franke A, Schreiber S, Krause J, Müller J, Lenz TL, Nebel A, Krause-Kyora B. Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry. Commun Biol 2021; 4:113. [PMID: 33495542 PMCID: PMC7835224 DOI: 10.1038/s42003-020-01627-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2020] [Accepted: 12/20/2020] [Indexed: 02/08/2023] Open
Abstract
The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections. Alexander Immel et al. performed genome-wide analyses of 42 individuals from a collective burial in Niedertiefenbach, Germany from the Wartberg Culture. The authors find that this population had a large hunter-gatherer ancestry component and a distinct HLA pool, which indicates immune defenses against viral pathogens.
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Affiliation(s)
- Alexander Immel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Federica Pierini
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306, Plön, Germany
| | - Christoph Rinne
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - John Meadows
- Leibniz Laboratory for AMS Dating and Isotope Research, Kiel University, Max-Eyth-Strasse 11-13, 24118, Kiel, Germany.,Centre for Baltic and Scandinavian Archaeology (ZBSA), Schloss Gottorf, 24837, Schleswig, Germany
| | - Rodrigo Barquera
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, 07745, Jena, Germany
| | - András Szolek
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany
| | - Julian Susat
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Lisa Böhme
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Janina Dose
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Joanna Bonczarowska
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Clara Drummer
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - Katharina Fuchs
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - David Ellinghaus
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Jan Christian Kässens
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Martin Furholt
- Department of Archaeology, Conservation and History, University of Oslo, Blindernveien 11, 0371, Oslo, Norway
| | - Oliver Kohlbacher
- Applied Bioinformatics, Department for Computer Science, University of Tübingen, Sand 14, 72076, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076, Tübingen, Germany.,Institute for Translational Bioinformatics, University Hospital Tübingen, Hoppe-Seyler-Strasse 9, 72076, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany
| | - Sabine Schade-Lindig
- Landesamt für Denkmalpflege Hessen, hessenARCHÄOLOGIE, Schloss Biebrich, 65203, Wiesbaden, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany.,Department of General Internal Medicine, University Hospital Schleswig-Holstein, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Khalaische Strasse 10, 07745, Jena, Germany
| | - Johannes Müller
- Institute of Pre- and Protohistoric Archaeology, Kiel University, Johanna-Mestorf-Strasse 2-6, 24118, Kiel, Germany
| | - Tobias L Lenz
- Research Group for Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, 24306, Plön, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Strasse 12, 24105, Kiel, Germany.
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Saag L, Vasilyev SV, Varul L, Kosorukova NV, Gerasimov DV, Oshibkina SV, Griffith SJ, Solnik A, Saag L, D'Atanasio E, Metspalu E, Reidla M, Rootsi S, Kivisild T, Scheib CL, Tambets K, Kriiska A, Metspalu M. Genetic ancestry changes in Stone to Bronze Age transition in the East European plain. SCIENCE ADVANCES 2021; 7:7/4/eabd6535. [PMID: 33523926 PMCID: PMC7817100 DOI: 10.1126/sciadv.abd6535] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 12/01/2020] [Indexed: 05/11/2023]
Abstract
The transition from Stone to Bronze Age in Central and Western Europe was a period of major population movements originating from the Ponto-Caspian Steppe. Here, we report new genome-wide sequence data from 30 individuals north of this area, from the understudied western part of present-day Russia, including 3 Stone Age hunter-gatherers (10,800 to 4250 cal BCE) and 26 Bronze Age farmers from the Corded Ware complex Fatyanovo Culture (2900 to 2050 cal BCE). We show that Eastern hunter-gatherer ancestry was present in northwestern Russia already from around 10,000 BCE. Furthermore, we see a change in ancestry with the arrival of farming-Fatyanovo Culture individuals were genetically similar to other Corded Ware cultures, carrying a mixture of Steppe and European early farmer ancestry. Thus, they likely originate from a fast migration toward the northeast from somewhere near modern-day Ukraine-the closest area where these ancestries coexisted from around 3000 BCE.
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Affiliation(s)
- Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
| | - Sergey V Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow 119991, Russia
| | - Liivi Varul
- Archaeological Research Collection, School of Humanities, Tallinn University, Tallinn 10130, Estonia
| | - Natalia V Kosorukova
- Cherepovets State University and Cherepovets Museum Association, Cherepovets 162600, Russia
| | - Dmitri V Gerasimov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg 199034, Russia
| | | | - Samuel J Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Anu Solnik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Lauri Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, National Research Council, Rome 00185, Italy
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Department of Human Genetics, KU Leuven, Leuven 3000, Belgium
| | - Christiana Lyn Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- St. John's College, University of Cambridge, Cambridge CB2 1TP, UK
| | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Aivar Kriiska
- Department of Archaeology, Institute of History and Archaeology, University of Tartu, Tartu 51014, Estonia.
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu 51010, Estonia.
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40
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Santos P, Gonzàlez-Fortes G, Trucchi E, Ceolin A, Cordoni G, Guardiano C, Longobardi G, Barbujani G. More Rule than Exception: Parallel Evidence of Ancient Migrations in Grammars and Genomes of Finno-Ugric Speakers. Genes (Basel) 2020; 11:E1491. [PMID: 33322364 PMCID: PMC7763979 DOI: 10.3390/genes11121491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/25/2020] [Accepted: 12/09/2020] [Indexed: 11/27/2022] Open
Abstract
To reconstruct aspects of human demographic history, linguistics and genetics complement each other, reciprocally suggesting testable hypotheses on population relationships and interactions. Relying on a linguistic comparative method based on syntactic data, here we focus on the non-straightforward relation of genes and languages among Finno-Ugric (FU) speakers, in comparison to their Indo-European (IE) and Altaic (AL) neighbors. Syntactic analysis, in agreement with the indications of more traditional linguistic levels, supports at least three distinct clusters, corresponding to these three Eurasian families; yet, the outliers of the FU group show linguistic convergence with their geographical neighbors. By analyzing genome-wide data in both ancient and contemporary populations, we uncovered remarkably matching patterns, with north-western FU speakers linguistically and genetically closer in parallel degrees to their IE-speaking neighbors, and eastern FU speakers to AL speakers. Therefore, our analysis indicates that plausible cross-family linguistic interference effects were accompanied, and possibly caused, by recognizable demographic processes. In particular, based on the comparison of modern and ancient genomes, our study identified the Pontic-Caspian steppes as the possible origin of the demographic processes that led to the expansion of FU languages into Europe.
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Affiliation(s)
- Patrícia Santos
- CNRS, UMR 5199—PACEA, Université de Bordeaux, Bâtiment B8, Allée Geoffroy Saint Hilaire, 33615 Pessac, France;
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy;
| | - Gloria Gonzàlez-Fortes
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy;
| | - Emiliano Trucchi
- Department of Life and Environmental Sciences, Marche Polytechnic University, 60131 Ancona, Italy;
| | - Andrea Ceolin
- Dipartimento di Comunicazione ed Economia, Università di Modena e Reggio Emilia, 42121 Reggio Emilia, Italy; (A.C.); (C.G.)
| | - Guido Cordoni
- School of Veterinary Medicine, University of Surrey, Guildford GU2 7AL, UK;
| | - Cristina Guardiano
- Dipartimento di Comunicazione ed Economia, Università di Modena e Reggio Emilia, 42121 Reggio Emilia, Italy; (A.C.); (C.G.)
| | - Giuseppe Longobardi
- Department of Language and Linguistic Science, University of York, York YO10 5DD, UK;
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121 Ferrara, Italy;
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41
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Low Prevalence of Lactase Persistence in Bronze Age Europe Indicates Ongoing Strong Selection over the Last 3,000 Years. Curr Biol 2020; 30:4307-4315.e13. [DOI: 10.1016/j.cub.2020.08.033] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 07/07/2020] [Accepted: 08/07/2020] [Indexed: 11/20/2022]
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Abstract
The study of ancient genomes has burgeoned at an incredible rate in the last decade. The result is a shift in archaeological narratives, bringing with it a fierce debate on the place of genetics in anthropological research. Archaeogenomics has challenged and scrutinized fundamental themes of anthropological research, including human origins, movement of ancient and modern populations, the role of social organization in shaping material culture, and the relationship between culture, language, and ancestry. Moreover, the discussion has inevitably invoked new debates on indigenous rights, ownership of ancient materials, inclusion in the scientific process, and even the meaning of what it is to be a human. We argue that the broad and seemingly daunting ethical, methodological, and theoretical challenges posed by archaeogenomics, in fact, represent the very cutting edge of social science research. Here, we provide a general review of the field by introducing the contemporary discussion points and summarizing methodological and ethical concerns, while highlighting the exciting possibilities of ancient genome studies in archaeology from an anthropological perspective.
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Affiliation(s)
- Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, State University of New York, Buffalo, New York 14221, USA
| | - Michael Frachetti
- Department of Anthropology, Washington University in St. Louis, St. Louis, Missouri 63130, USA
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43
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Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Buś MM, de Barros Damgaard P, Martiniano R, Renaud G, Bhérer C, Moreno-Mayar JV, Fotakis AK, Allen M, Allmäe R, Molak M, Cappellini E, Scorrano G, McColl H, Buzhilova A, Fox A, Albrechtsen A, Schütz B, Skar B, Arcini C, Falys C, Jonson CH, Błaszczyk D, Pezhemsky D, Turner-Walker G, Gestsdóttir H, Lundstrøm I, Gustin I, Mainland I, Potekhina I, Muntoni IM, Cheng J, Stenderup J, Ma J, Gibson J, Peets J, Gustafsson J, Iversen KH, Simpson L, Strand L, Loe L, Sikora M, Florek M, Vretemark M, Redknap M, Bajka M, Pushkina T, Søvsø M, Grigoreva N, Christensen T, Kastholm O, Uldum O, Favia P, Holck P, Sten S, Arge SV, Ellingvåg S, Moiseyev V, Bogdanowicz W, Magnusson Y, Orlando L, Pentz P, Jessen MD, Pedersen A, Collard M, Bradley DG, Jørkov ML, Arneborg J, Lynnerup N, Price N, Gilbert MTP, Allentoft ME, Bill J, Sindbæk SM, Hedeager L, Kristiansen K, Nielsen R, Werge T, Willerslev E. Population genomics of the Viking world. Nature 2020. [PMID: 32939067 DOI: 10.1038/s41586-020–2688-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
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Affiliation(s)
- Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.,Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,School of Statistical Sciences, University of Bristol, Bristol, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Mikkel W Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,HSE University, Russian Federation National Research University Higher School of Economics, Moscow, Russia
| | - Helene Wilhelmson
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden.,Sydsvensk Arkeologi AB, Kristianstad, Sweden
| | - Magdalena M Buś
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Claude Bhérer
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Scorrano
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Allison Fox
- Manx National Heritage, Douglas, Isle of Man
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Birgitte Skar
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Caroline Arcini
- The Archaeologists, National Historical Museums, Stockholm, Sweden
| | - Ceri Falys
- Thames Valley Archaeological Services (TVAS), Reading, UK
| | | | | | - Denis Pezhemsky
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Gordon Turner-Walker
- Department of Cultural Heritage Conservation, National Yunlin University of Science and Technology, Douliou, Taiwan
| | | | - Inge Lundstrøm
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ingrid Gustin
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology of National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Italo M Muntoni
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le Province di Barletta, Andria, Trani e Foggia, Foggia, Italy
| | - Jade Cheng
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jilong Ma
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Julie Gibson
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jüri Peets
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | | | - Katrine H Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | | | - Lisa Strand
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, UK
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Sklodowska University in Lublin, Lublin, Poland
| | | | - Mark Redknap
- Department of History and Archaeology, Amgueddfa Cymru-National Museum Wales, Cardiff, UK
| | - Monika Bajka
- Trzy Epoki Archaeological Service, Klimontów, Poland
| | | | | | - Natalia Grigoreva
- Department of Slavic-Finnish Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | | | - Ole Kastholm
- Department of Research and Heritage, Roskilde Museum, Roskilde, Denmark
| | | | - Pasquale Favia
- Department of Humanities, University of Foggia, Foggia, Italy
| | - Per Holck
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sabine Sten
- Department of Archaeology and Ancient History, Uppsala University Campus Gotland, Visby, Sweden
| | - Símun V Arge
- Tjóðsavnið - Faroe Islands National Museum, Tórshavn, Faroe Islands
| | - Sturla Ellingvåg
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vayacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St Petersburg, Russia
| | | | | | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Peter Pentz
- National Museum of Denmark, Copenhagen, Denmark
| | | | | | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marie Louise Jørkov
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jette Arneborg
- National Museum of Denmark, Copenhagen, Denmark.,School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Niels Lynnerup
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Neil Price
- Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Natural History, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - 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
| | - Jan Bill
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Søren M Sindbæk
- Centre for Urban Network Evolutions (UrbNet), School of Culture and Society, Aarhus University, Højbjerg, Denmark
| | - Lotte Hedeager
- Institute of Archaeology, Conservation and History, Oslo, Norway
| | | | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. .,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. .,The Wellcome Trust Sanger Institute, Cambridge, UK.
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44
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Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Buś MM, de Barros Damgaard P, Martiniano R, Renaud G, Bhérer C, Moreno-Mayar JV, Fotakis AK, Allen M, Allmäe R, Molak M, Cappellini E, Scorrano G, McColl H, Buzhilova A, Fox A, Albrechtsen A, Schütz B, Skar B, Arcini C, Falys C, Jonson CH, Błaszczyk D, Pezhemsky D, Turner-Walker G, Gestsdóttir H, Lundstrøm I, Gustin I, Mainland I, Potekhina I, Muntoni IM, Cheng J, Stenderup J, Ma J, Gibson J, Peets J, Gustafsson J, Iversen KH, Simpson L, Strand L, Loe L, Sikora M, Florek M, Vretemark M, Redknap M, Bajka M, Pushkina T, Søvsø M, Grigoreva N, Christensen T, Kastholm O, Uldum O, Favia P, Holck P, Sten S, Arge SV, Ellingvåg S, Moiseyev V, Bogdanowicz W, Magnusson Y, Orlando L, Pentz P, Jessen MD, Pedersen A, Collard M, Bradley DG, Jørkov ML, Arneborg J, Lynnerup N, Price N, Gilbert MTP, Allentoft ME, Bill J, Sindbæk SM, Hedeager L, Kristiansen K, Nielsen R, Werge T, Willerslev E. Population genomics of the Viking world. Nature 2020; 585:390-396. [PMID: 32939067 DOI: 10.1038/s41586-020-2688-8] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
Abstract
The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
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Affiliation(s)
- Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.,Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,School of Statistical Sciences, University of Bristol, Bristol, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Mikkel W Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,HSE University, Russian Federation National Research University Higher School of Economics, Moscow, Russia
| | - Helene Wilhelmson
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden.,Sydsvensk Arkeologi AB, Kristianstad, Sweden
| | - Magdalena M Buś
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Claude Bhérer
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Scorrano
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Allison Fox
- Manx National Heritage, Douglas, Isle of Man
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Birgitte Skar
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Caroline Arcini
- The Archaeologists, National Historical Museums, Stockholm, Sweden
| | - Ceri Falys
- Thames Valley Archaeological Services (TVAS), Reading, UK
| | | | | | - Denis Pezhemsky
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Gordon Turner-Walker
- Department of Cultural Heritage Conservation, National Yunlin University of Science and Technology, Douliou, Taiwan
| | | | - Inge Lundstrøm
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ingrid Gustin
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology of National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Italo M Muntoni
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le Province di Barletta, Andria, Trani e Foggia, Foggia, Italy
| | - Jade Cheng
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jilong Ma
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Julie Gibson
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jüri Peets
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | | | - Katrine H Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | | | - Lisa Strand
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, UK
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Sklodowska University in Lublin, Lublin, Poland
| | | | - Mark Redknap
- Department of History and Archaeology, Amgueddfa Cymru-National Museum Wales, Cardiff, UK
| | - Monika Bajka
- Trzy Epoki Archaeological Service, Klimontów, Poland
| | | | | | - Natalia Grigoreva
- Department of Slavic-Finnish Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | | | - Ole Kastholm
- Department of Research and Heritage, Roskilde Museum, Roskilde, Denmark
| | | | - Pasquale Favia
- Department of Humanities, University of Foggia, Foggia, Italy
| | - Per Holck
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sabine Sten
- Department of Archaeology and Ancient History, Uppsala University Campus Gotland, Visby, Sweden
| | - Símun V Arge
- Tjóðsavnið - Faroe Islands National Museum, Tórshavn, Faroe Islands
| | - Sturla Ellingvåg
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vayacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St Petersburg, Russia
| | | | | | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Peter Pentz
- National Museum of Denmark, Copenhagen, Denmark
| | | | | | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marie Louise Jørkov
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jette Arneborg
- National Museum of Denmark, Copenhagen, Denmark.,School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Niels Lynnerup
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Neil Price
- Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Natural History, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - 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
| | - Jan Bill
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Søren M Sindbæk
- Centre for Urban Network Evolutions (UrbNet), School of Culture and Society, Aarhus University, Højbjerg, Denmark
| | - Lotte Hedeager
- Institute of Archaeology, Conservation and History, Oslo, Norway
| | | | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. .,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. .,The Wellcome Trust Sanger Institute, Cambridge, UK.
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45
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Lodewijk GA, Fernandes DP, Vretzakis I, Savage JE, Jacobs FMJ. Evolution of Human Brain Size-Associated NOTCH2NL Genes Proceeds toward Reduced Protein Levels. Mol Biol Evol 2020; 37:2531-2548. [PMID: 32330268 PMCID: PMC7475042 DOI: 10.1093/molbev/msaa104] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ever since the availability of genomes from Neanderthals, Denisovans, and ancient humans, the field of evolutionary genomics has been searching for protein-coding variants that may hold clues to how our species evolved over the last ∼600,000 years. In this study, we identify such variants in the human-specific NOTCH2NL gene family, which were recently identified as possible contributors to the evolutionary expansion of the human brain. We find evidence for the existence of unique protein-coding NOTCH2NL variants in Neanderthals and Denisovans which could affect their ability to activate Notch signaling. Furthermore, in the Neanderthal and Denisovan genomes, we find unusual NOTCH2NL configurations, not found in any of the modern human genomes analyzed. Finally, genetic analysis of archaic and modern humans reveals ongoing adaptive evolution of modern human NOTCH2NL genes, identifying three structural variants acting complementary to drive our genome to produce a lower dosage of NOTCH2NL protein. Because copy-number variations of the 1q21.1 locus, encompassing NOTCH2NL genes, are associated with severe neurological disorders, this seemingly contradicting drive toward low levels of NOTCH2NL protein indicates that the optimal dosage of NOTCH2NL may have not yet been settled in the human population.
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Affiliation(s)
- Gerrald A Lodewijk
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Diana P Fernandes
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Iraklis Vretzakis
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeanne E Savage
- Department of Complex Trait Genetics, Center for Neurogenomics and Cognitive Research, VU University, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics
| | - Frank M J Jacobs
- Swammerdam Institute for Life Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Amsterdam Neuroscience, Complex Trait Genetics
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46
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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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Coutinho A, Günther T, Munters AR, Svensson EM, Götherström A, Storå J, Malmström H, Jakobsson M. The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:638-649. [PMID: 32497286 DOI: 10.1002/ajpa.24079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/26/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences. METHODS We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools. RESULTS The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style. CONCLUSION We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.
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Affiliation(s)
- Alexandra Coutinho
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa
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Juras A, Makarowicz P, Chyleński M, Ehler E, Malmström H, Krzewińska M, Pospieszny Ł, Górski J, Taras H, Szczepanek A, Polańska M, Włodarczak P, Szyca A, Lasota-Kuś A, Wójcik I, Jakobsson M, Dabert M. Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:176-188. [PMID: 32297323 DOI: 10.1002/ajpa.24057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 03/13/2020] [Accepted: 03/21/2020] [Indexed: 12/31/2022]
Abstract
OBJECTIVE In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes. MATERIALS AND METHODS We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyżow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS 14 C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples. RESULTS Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyżów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study. DISCUSSION Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyżów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | | | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | - Edvard Ehler
- Department of Biology and Environmental Studies, Charles University, Faculty of Education, Praha 1, Czech Republic
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, UPpSala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Łukasz Pospieszny
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
| | - Jacek Górski
- Department of History and Cultural Heritage, University of Pope Jan Paweł II, Kraków, Poland
- Archaeological Museum in Cracow, Kraków, Poland
| | - Halina Taras
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | - Marta Polańska
- Department of Material and Spiritual Culture, Lublin Museum, Lublin, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | - Agnieszka Szyca
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Poland
| | - Anna Lasota-Kuś
- Institute of Archaeology and Ethnology, Polish Academy of Science, Kraków, Poland
| | | | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology and SciLifeLab, Uppsala University, UPpSala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Poznań, Poland
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50
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The spread of steppe and Iranian-related ancestry in the islands of the western Mediterranean. Nat Ecol Evol 2020; 4:334-345. [PMID: 32094539 PMCID: PMC7080320 DOI: 10.1038/s41559-020-1102-0] [Citation(s) in RCA: 64] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 01/08/2020] [Indexed: 11/08/2022]
Abstract
Steppe-pastoralist-related ancestry reached Central Europe by at least 2500 BC, whereas Iranian farmer-related ancestry was present in Aegean Europe by at least 1900 BC. However, the spread of these ancestries into the western Mediterranean, where they have contributed to many populations that live today, remains poorly understood. Here, we generated genome-wide ancient-DNA data from the Balearic Islands, Sicily and Sardinia, increasing the number of individuals with reported data from 5 to 66. The oldest individual from the Balearic Islands (~2400 BC) carried ancestry from steppe pastoralists that probably derived from west-to-east migration from Iberia, although two later Balearic individuals had less ancestry from steppe pastoralists. In Sicily, steppe pastoralist ancestry arrived by ~2200 BC, in part from Iberia; Iranian-related ancestry arrived by the mid-second millennium BC, contemporary to its previously documented spread to the Aegean; and there was large-scale population replacement after the Bronze Age. In Sardinia, nearly all ancestry derived from the island's early farmers until the first millennium BC, with the exception of an outlier from the third millennium BC, who had primarily North African ancestry and who-along with an approximately contemporary Iberian-documents widespread Africa-to-Europe gene flow in the Chalcolithic. Major immigration into Sardinia began in the first millennium BC and, at present, no more than 56-62% of Sardinian ancestry is from its first farmers. This value is lower than previous estimates, highlighting that Sardinia, similar to every other region in Europe, has been a stage for major movement and mixtures of people.
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