1
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Larsson MNA, Morell Miranda P, Pan L, Başak Vural K, Kaptan D, Rodrigues Soares AE, Kivikero H, Kantanen J, Somel M, Özer F, Johansson AM, Storå J, Günther T. Ancient Sheep Genomes Reveal Four Millennia of North European Short-Tailed Sheep in the Baltic Sea Region. Genome Biol Evol 2024; 16:evae114. [PMID: 38795367 PMCID: PMC11162877 DOI: 10.1093/gbe/evae114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 04/24/2024] [Accepted: 05/21/2024] [Indexed: 05/27/2024] Open
Abstract
Sheep are among the earliest domesticated livestock species, with a wide variety of breeds present today. However, it remains unclear how far back this diversity goes, with formal documentation only dating back a few centuries. North European short-tailed (NEST) breeds are often assumed to be among the oldest domestic sheep populations, even thought to represent relicts of the earliest sheep expansions during the Neolithic period reaching Scandinavia <6,000 years ago. This study sequenced the genomes (up to 11.6X) of five sheep remains from the Baltic islands of Gotland and Åland, dating from the Late Neolithic (∼4,100 cal BP) to historical times (∼1,600 CE). Our findings indicate that these ancient sheep largely possessed the genetic characteristics of modern NEST breeds, suggesting a substantial degree of long-term continuity of this sheep type in the Baltic Sea region. Despite the wide temporal spread, population genetic analyses show high levels of affinity between the ancient genomes and they also exhibit relatively high genetic diversity when compared to modern NEST breeds, implying a loss of diversity in most breeds during the last centuries associated with breed formation and recent bottlenecks. Our results shed light on the development of breeds in Northern Europe specifically as well as the development of genetic diversity in sheep breeds, and their expansion from the domestication center in general.
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Affiliation(s)
- Martin N A Larsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Pedro Morell Miranda
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Li Pan
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | | | - Hanna Kivikero
- Department of Culture, University of Helsinki, Helsinki, Finland
| | - Juha Kantanen
- Natural Resources Institute Finland, Jokioinen, Finland
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Anna M Johansson
- Department of Animal Biosciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
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2
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Bergfeldt N, Kırdök E, Oskolkov N, Mirabello C, Unneberg P, Malmström H, Fraser M, Sanchez-Quinto F, Jorgensen R, Skar B, Lidén K, Jakobsson M, Storå J, Götherström A. Identification of microbial pathogens in Neolithic Scandinavian humans. Sci Rep 2024; 14:5630. [PMID: 38453993 PMCID: PMC10920878 DOI: 10.1038/s41598-024-56096-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.
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Affiliation(s)
- Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Nikolay Oskolkov
- Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden
| | - Claudio Mirabello
- Science for Life Laboratory, Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Magdalena Fraser
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | | | - Roger Jorgensen
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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3
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Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. Proc Natl Acad Sci U S A 2024; 121:e2312377121. [PMID: 38363870 PMCID: PMC10907250 DOI: 10.1073/pnas.2312377121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/09/2024] [Indexed: 02/18/2024] Open
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
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Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
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4
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Fischer A, Sjögren KG, Jensen TZT, Jørkov ML, Lysdahl P, Vimala T, Refoyo-Martínez A, Scorrano G, Price TD, Gröcke DR, Gotfredsen AB, Sørensen L, Alexandersen V, Wåhlin S, Stenderup J, Bennike O, Ingason A, Iversen R, Sikora M, Racimo F, Willerslev E, Allentoft ME, Kristiansen K. Vittrup Man-The life-history of a genetic foreigner in Neolithic Denmark. PLoS One 2024; 19:e0297032. [PMID: 38354111 PMCID: PMC10866469 DOI: 10.1371/journal.pone.0297032] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 12/26/2023] [Indexed: 02/16/2024] Open
Abstract
The lethally maltreated body of Vittrup Man was deposited in a Danish bog, probably as part of a ritualised sacrifice. It happened between c. 3300 and 3100 cal years BC, i.e., during the period of the local farming-based Funnel Beaker Culture. In terms of skull morphological features, he differs from the majority of the contemporaneous farmers found in Denmark, and associates with hunter-gatherers, who inhabited Scandinavia during the previous millennia. His skeletal remains were selected for transdisciplinary analysis to reveal his life-history in terms of a population historical perspective. We report the combined results of an integrated set of genetic, isotopic, physical anthropological and archaeological analytical approaches. Strontium signature suggests a foreign birthplace that could be in Norway or Sweden. In addition, enamel oxygen isotope values indicate that as a child he lived in a colder climate, i.e., to the north of the regions inhabited by farmers. Genomic data in fact demonstrates that he is closely related to Mesolithic humans known from Norway and Sweden. Moreover, dietary stable isotope analyses on enamel and bone collagen demonstrate a fisher-hunter way of life in his childhood and a diet typical of farmers later on. Such a variable life-history is also reflected by proteomic analysis of hardened organic deposits on his teeth, indicating the consumption of forager food (seal, whale and marine fish) as well as farmer food (sheep/goat). From a dietary isotopic transect of one of his teeth it is shown that his transfer between societies of foragers and farmers took place near to the end of his teenage years.
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Affiliation(s)
- Anders Fischer
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | | | - Marie Louise Jørkov
- Laboratory of Biological Anthropology, University of Copenhagen, Copenhagen, Denmark
| | - Per Lysdahl
- Vendsyssel Historical Museum, Hjørring, Denmark
| | - Tharsika Vimala
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | | | | | - T. Douglas Price
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, Wisconsin, United States of America
| | - Darren R. Gröcke
- Department of Earth Sciences, Durham University, Durham, England, United Kingdom
| | | | | | - Verner Alexandersen
- Laboratory of Biological Anthropology, University of Copenhagen, Copenhagen, Denmark
| | | | - Jesper Stenderup
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | - Ole Bennike
- Geological Survey of Denmark and Greenland, Copenhagen, Denmark
| | - Andrés Ingason
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Copenhagen, Denmark
| | - Rune Iversen
- The Saxo Institute—Section of Archaeology, University of Copenhagen, Copenhagen S, Denmark
| | - Martin Sikora
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | - Fernando Racimo
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
| | - Eske Willerslev
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
- Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Morten E. Allentoft
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Australia
| | - Kristian Kristiansen
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Globe Institute, University of Copenhagen, Copenhagen K, Denmark
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5
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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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6
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Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.11.548607. [PMID: 37503227 PMCID: PMC10370008 DOI: 10.1101/2023.07.11.548607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
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Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
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7
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Allentoft ME, Sikora M, Fischer A, Sjögren KG, Ingason A, Macleod R, Rosengren A, Schulz Paulsson B, Jørkov MLS, Novosolov M, Stenderup J, Price TD, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Sørensen L, Nielsen PO, Rasmussen P, Jensen TZT, Refoyo-Martínez A, Irving-Pease EK, Barrie W, Pearson A, Sousa da Mota B, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn A, Vinner L, Renaud G, Stern A, Johannsen NN, Ramsøe AD, Schork AJ, Ruter A, Gotfredsen AB, Henning Nielsen B, Brinch Petersen E, Kannegaard E, Hansen J, Buck Pedersen K, Pedersen L, Klassen L, Meldgaard M, Johansen M, Uldum OC, Lotz P, Lysdahl P, Bangsgaard P, Petersen PV, Maring R, Iversen R, Wåhlin S, Anker Sørensen S, Andersen SH, Jørgensen T, Lynnerup N, Lawson DJ, Rasmussen S, Korneliussen TS, Kjær KH, Durbin R, Nielsen R, Delaneau O, Werge T, Kristiansen K, Willerslev E. 100 ancient genomes show repeated population turnovers in Neolithic Denmark. Nature 2024; 625:329-337. [PMID: 38200294 PMCID: PMC10781617 DOI: 10.1038/s41586-023-06862-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024]
Abstract
Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
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Affiliation(s)
- Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia.
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Anders Fischer
- Cluster of Excellence ROOTS, Kiel University, Kiel, Germany
- Sealand Archaeology, Kalundborg, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, Gothenburg University, Göteborg, Sweden
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ruairidh Macleod
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Maria Novosolov
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | | | | | | | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alice Pearson
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), Dpt ABBA, Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Vaughn
- Center for Computational Biology, University of California, Berkeley, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aaron Stern
- Center for Computational Biology, University of California, Berkeley, USA
| | | | - Abigail Daisy Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Joseph Schork
- Laboratory of Biological Anthropology, University of Copenhagen, Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anthony Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anne Birgitte Gotfredsen
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | | | - Morten Meldgaard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Health and Nature, University of Greenland, Nuuk, Greenland
| | | | | | - Per Lotz
- Museum Nordsjælland, Hillerød, Denmark
- Museum Vestsjælland, Holbæk, Denmark
| | - Per Lysdahl
- Vendsyssel Historiske Museum, Hjørring, Denmark
| | - Pernille Bangsgaard
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rikke Maring
- Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark
- Museum Østjylland, Randers, Denmark
| | - Rune Iversen
- The Saxo Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Niels Lynnerup
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Simon Rasmussen
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | | | - Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, Gothenburg University, Göteborg, Sweden
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
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8
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Chyleński M, Makarowicz P, Juras A, Krzewińska M, Pospieszny Ł, Ehler E, Breszka A, Górski J, Taras H, Szczepanek A, Polańska M, Włodarczak P, Lasota-Kuś A, Wójcik I, Romaniszyn J, Szmyt M, Kośko A, Ignaczak M, Sadowski S, Matoga A, Grossman A, Ilchyshyn V, Yahodinska MO, Romańska A, Tunia K, Przybyła M, Grygiel R, Szostek K, Dabert M, Götherström A, Jakobsson M, Malmström H. Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age. Nat Commun 2023; 14:4395. [PMID: 37528090 PMCID: PMC10393988 DOI: 10.1038/s41467-023-40072-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/07/2023] [Indexed: 08/03/2023] Open
Abstract
The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.
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Affiliation(s)
- Maciej Chyleński
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Przemysław Makarowicz
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Anna Juras
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland.
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91, Stockholm, Sweden
- Centre for Palaeogentics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Łukasz Pospieszny
- Institute of Archaeology, University of Gdańsk, ul. Bielańska 5, 80-851, Gdańsk, Poland
- Department of Anthropology and Archaeology, University of Bristol, 43 Woodland Road, Bristol, BS8 1UU, UK
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Prague, Czech Republic
| | - Agnieszka Breszka
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Jacek Górski
- Department of History and Cultural Heritage, University of Pope Jan Paweł II, Kanonicza 9, 31-002, Cracow, Poland
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Halina Taras
- Institute of Archaeology, Maria Curie-Skłodowska University, M.C.-Skłodowska sq. 4, 20-031, Lublin, Poland
| | - Anita Szczepanek
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Marta Polańska
- Department of Material and Spiritual Culture, Lublin Museum, Zamkowa 9, 20-117, Lublin, Poland
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Anna Lasota-Kuś
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Irena Wójcik
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Jan Romaniszyn
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
- Archaeological Museum in Poznań, Wodna 27, 61-781, Poznań, Poland
| | - Aleksander Kośko
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Marcin Ignaczak
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 7, 61- 614, Poznań, Poland
| | - Sylwester Sadowski
- Institute of Archaeology, Maria Curie-Skłodowska University, M.C.-Skłodowska sq. 4, 20-031, Lublin, Poland
| | - Andrzej Matoga
- Archaeological Museum in Cracow, Senacka 3, 31-002, Cracow, Poland
| | - Anna Grossman
- Muzeum Archeologiczne w Biskupinie, Biskupin 17, 88-410, Gąsawa, Poland
| | - Vasyl Ilchyshyn
- Zaliztsi Museum of Local Lore, Schevchenka 51, Zalizhtsi, 47243, Ternopil reg, Ukraine
| | - Maryna O Yahodinska
- Ternopil Regional Center for Protection and Research of Cultural Heritage Sites, Kyyivs'ka 3а, 46016, Ternopil, Ukraine
| | - Adriana Romańska
- Wojewódzki Urząd Ochrony Zabytków, Gołębia 2, 61-840, Poznań, Poland
| | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Science, Sławkowska 17, 31-016, Cracow, Poland
| | - Marcin Przybyła
- Archaeological company "Dolmen Marcin Przybyła, Michał Podsiadło s.c.", Serkowskiego Sq. 8/3, 30-512, Cracow, Poland
| | - Ryszard Grygiel
- Museum of Archaeology and Ethnography in Łódź, Plac Wolności 14, 91-415, Łódź, Poland
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszynski University in Warsaw, Wóycickiego 1/3, 01-938, Warsaw, Poland
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Uniwersytetu Poznańskiego 6, 61-614, Poznań, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Lilla Frescativägen 7, SE-106 91, Stockholm, Sweden
- Centre for Palaeogentics, Svante Arrhenius väg 20C, SE-106 91, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
- SciLifeLab, Stockholm and Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden.
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa.
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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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Genomic Steppe ancestry in skeletons from the Neolithic Single Grave Culture in Denmark. PLoS One 2021; 16:e0244872. [PMID: 33444387 PMCID: PMC7808695 DOI: 10.1371/journal.pone.0244872] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/17/2020] [Indexed: 11/19/2022] Open
Abstract
The Gjerrild burial provides the largest and best-preserved assemblage of human skeletal material presently known from the Single Grave Culture (SGC) in Denmark. For generations it has been debated among archaeologists if the appearance of this archaeological complex represents a continuation of the previous Neolithic communities, or was facilitated by incoming migrants. We sampled and analysed five skeletons from the Gjerrild cist, buried over a period of c. 300 years, 2600/2500–2200 cal BCE. Despite poor DNA preservation, we managed to sequence the genome (>1X) of one individual and the partial genomes (0.007X and 0.02X) of another two individuals. Our genetic data document a female (Gjerrild 1) and two males (Gjerrild 5 + 8), harbouring typical Neolithic K2a and HV0 mtDNA haplogroups, but also a rare basal variant of the R1b1 Y-chromosomal haplogroup. Genome-wide analyses demonstrate that these people had a significant Yamnaya-derived (i.e. steppe) ancestry component and a close genetic resemblance to the Corded Ware (and related) groups that were present in large parts of Northern and Central Europe at the time. Assuming that the Gjerrild skeletons are genetically representative of the population of the SGC in broader terms, the transition from the local Neolithic Funnel Beaker Culture (TRB) to SGC is not characterized by demographic continuity. Rather, the emergence of SGC in Denmark was part of the Late Neolithic and Early Bronze Age population expansion that swept across the European continent in the 3rd millennium BCE, resulting in various degrees of genetic replacement and admixture processes with previous Neolithic populations.
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