1
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Gretzinger J, Schmitt F, Mötsch A, Carlhoff S, Lamnidis TC, Huang Y, Ringbauer H, Knipper C, Francken M, Mandt F, Hansen L, Freund C, Posth C, Rathmann H, Harvati K, Wieland G, Granehäll L, Maixner F, Zink A, Schier W, Krausse D, Krause J, Schiffels S. Evidence for dynastic succession among early Celtic elites in Central Europe. Nat Hum Behav 2024; 8:1467-1480. [PMID: 38831077 PMCID: PMC11343710 DOI: 10.1038/s41562-024-01888-7] [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: 04/15/2024] [Indexed: 06/05/2024]
Abstract
The early Iron Age (800 to 450 BCE) in France, Germany and Switzerland, known as the 'West-Hallstattkreis', stands out as featuring the earliest evidence for supra-regional organization north of the Alps. Often referred to as 'early Celtic', suggesting tentative connections to later cultural phenomena, its societal and population structure remain enigmatic. Here we present genomic and isotope data from 31 individuals from this context in southern Germany, dating between 616 and 200 BCE. We identify multiple biologically related groups spanning three elite burials as far as 100 km apart, supported by trans-regional individual mobility inferred from isotope data. These include a close biological relationship between two of the richest burial mounds of the Hallstatt culture. Bayesian modelling points to an avuncular relationship between the two individuals, which may suggest a practice of matrilineal dynastic succession in early Celtic elites. We show that their ancestry is shared on a broad geographic scale from Iberia throughout Central-Eastern Europe, undergoing a decline after the late Iron Age (450 BCE to ~50 CE).
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Felicitas Schmitt
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Angela Mötsch
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Selina Carlhoff
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Yilei Huang
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Harald Ringbauer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Corina Knipper
- Curt Engelhorn Zentrum Archäometrie gGmbH, Mannheim, Germany
| | - Michael Francken
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Franziska Mandt
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Leif Hansen
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Cäcilia Freund
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cosimo Posth
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Hannes Rathmann
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Katerina Harvati
- Institute for Archaeological Sciences, Department of Geosciences, Eberhard Karls University of Tübingen, Tübingen, Germany
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Eberhard Karls University of Tübingen, Tübingen, Germany
- DFG Center for Advanced Studies in the Humanities 'Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past', Eberhard Karls University of Tübingen, Tübingen, Germany
| | - Günther Wieland
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany
| | - Lena Granehäll
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Bolzano, Italy
| | - Wolfram Schier
- Institut für Prähistorische Archäologie, Freie Universität Berlin, Berlin, Germany
| | - Dirk Krausse
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart, Esslingen, Germany.
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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2
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Sasso S, Saag L, Spros R, Beneker O, Molinaro L, Biagini SA, Lehouck A, Van De Vijver K, Hui R, D’Atanasio E, Kushniarevich A, Kabral H, Metspalu E, Guellil M, Ali MQA, Geypen J, Hoebreckx M, Berk B, De Winter N, Driesen P, Pijpelink A, Van Damme P, Scheib CL, Deschepper E, Deckers P, Snoeck C, Dewilde M, Ervynck A, Tambets K, Larmuseau MHD, Kivisild T. Capturing the fusion of two ancestries and kinship structures in Merovingian Flanders. Proc Natl Acad Sci U S A 2024; 121:e2406734121. [PMID: 38913897 PMCID: PMC11228521 DOI: 10.1073/pnas.2406734121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/17/2024] [Indexed: 06/26/2024] Open
Abstract
The Merovingian period (5th to 8th cc AD) was a time of demographic, socioeconomic, cultural, and political realignment in Western Europe. Here, we report the whole-genome shotgun sequence data of 30 human skeletal remains from a coastal Late Merovingian site of Koksijde (675 to 750 AD), alongside 18 remains from two Early to Late Medieval sites in present-day Flanders, Belgium. We find two distinct ancestries, one shared with Early Medieval England and the Netherlands, while the other, minor component, reflecting likely continental Gaulish ancestry. Kinship analyses identified no large pedigrees characteristic to elite burials revealing instead a high modularity of distant relationships among individuals of the main ancestry group. In contrast, individuals with >90% Gaulish ancestry had no kinship links among sampled individuals. Evidence for population structure and major differences in the extent of Gaulish ancestry in the main group, including in a mother-daughter pair, suggests ongoing admixture in the community at the time of their burial. The isotopic and genetic evidence combined supports a model by which the burials, representing an established coastal nonelite community, had incorporated migrants from inland populations. The main group of burials at Koksijde shows an abundance of >5 cM long shared allelic intervals with the High Medieval site nearby, implying long-term continuity and suggesting that similarly to Britain, the Early Medieval ancestry shifts left a significant and long-lasting impact on the genetic makeup of the Flemish population. We find substantial allele frequency differences between the two ancestry groups in pigmentation and diet-associated variants, including those linked with lactase persistence, likely reflecting ancestry change rather than local adaptation.
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Affiliation(s)
- Stefania Sasso
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Rachèl Spros
- Research Unit: Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, 1050Brussels, Belgium
- Research Unit: Social History of Capitalism, Vrije Universiteit Brussel, 1050Brussels, Belgium
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
| | | | - Simone A. Biagini
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
- Institut de Biologia Evolutiva, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003Barcelona, Spain
| | | | | | - Ruoyun Hui
- Alan Turing Institute, NW1 2DBLondon, United Kingdom
| | - Eugenia D’Atanasio
- Institute of Molecular Biology and Pathology, Italian National Research Council, Rome, Italy
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Helja Kabral
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | - Meriam Guellil
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Evolutionary Anthropology, University of Vienna, 1030Vienna, Austria
| | | | | | | | - Birgit Berk
- Birgit Berk Fysische Anthropologie, 6231ECMeerssen, Netherlands
| | | | | | - April Pijpelink
- Crematie en Inhumatie Analyse (CRINA) Fysische Antropologie, 5237JG 's-Hertogenbosch, Netherlands
| | - Philip Van Damme
- Department of Neurology, KU Leuven and Center for Brain & Disease Research Vlaamse Instituut voor Biotechnologie, 3000Leuven, Belgium
- Department of Neurosciences, KU Leuven and Center for Brain & Disease Research VIB, 3000Leuven, Belgium
| | - Christiana L. Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Zoology, University of Cambridge, CB2 3EJCambridge, United Kingdom
- Department of Archaeology, University of Cambridge, CB2 3DZCambridge, United Kingdom
- St John’s College, University of Cambridge, CB2 1TPCambridge, United Kingdom
| | - Ewoud Deschepper
- Historical Archaeology Research Group, Department of Archaeology, Ghent University, 9000Ghent, Belgium
| | | | - Christophe Snoeck
- Research Unit: Archaeology, Environmental Changes and Geo-Chemistry (AMGC), Vrije Universiteit Brussel, 1050Brussels, Belgium
| | | | | | - Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
| | | | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu51010, Estonia
- Department of Human Genetics, KU Leuven, 3000Leuven, Belgium
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3
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Jackson I, Woodman P, Dowd M, Fibiger L, Cassidy LM. Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts. Mol Biol Evol 2024; 41:msae017. [PMID: 38533900 DOI: 10.1093/molbev/msae017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 01/19/2024] [Accepted: 01/26/2024] [Indexed: 03/28/2024] Open
Abstract
Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.
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Affiliation(s)
- Iseult Jackson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- The SFI Centre for Research Training in Genomics Data Science, University of Galway, Galway, Ireland
| | - Peter Woodman
- Department of Archaeology, University College Cork, Cork, Ireland
| | - Marion Dowd
- Faculty of Science, Atlantic Technological University, Sligo, Ireland
| | - Linda Fibiger
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
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4
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Poyraz L, Colbran LL, Mathieson I. Predicting Functional Consequences of Recent Natural Selection in Britain. Mol Biol Evol 2024; 41:msae053. [PMID: 38466119 PMCID: PMC10962637 DOI: 10.1093/molbev/msae053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Revised: 02/02/2024] [Accepted: 03/01/2024] [Indexed: 03/12/2024] Open
Abstract
Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are noncoding, so we expect that a large proportion of the phenotypic effects of selection will also act through noncoding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation [JTI]) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4,500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (false discovery rate [FDR] < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-single nucleotide polymorphism (SNP) selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally, we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.
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Affiliation(s)
- Lin Poyraz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Laura L Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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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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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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7
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Hui R, Scheib CL, D’Atanasio E, Inskip SA, Cessford C, Biagini SA, Wohns AW, Ali MQ, Griffith SJ, Solnik A, Niinemäe H, Ge XJ, Rose AK, Beneker O, O’Connell TC, Robb JE, Kivisild T. Genetic history of Cambridgeshire before and after the Black Death. SCIENCE ADVANCES 2024; 10:eadi5903. [PMID: 38232165 PMCID: PMC10793959 DOI: 10.1126/sciadv.adi5903] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 12/14/2023] [Indexed: 01/19/2024]
Abstract
The extent of the devastation of the Black Death pandemic (1346-1353) on European populations is known from documentary sources and its bacterial source illuminated by studies of ancient pathogen DNA. What has remained less understood is the effect of the pandemic on human mobility and genetic diversity at the local scale. Here, we report 275 ancient genomes, including 109 with coverage >0.1×, from later medieval and postmedieval Cambridgeshire of individuals buried before and after the Black Death. Consistent with the function of the institutions, we found a lack of close relatives among the friars and the inmates of the hospital in contrast to their abundance in general urban and rural parish communities. While we detect long-term shifts in local genetic ancestry in Cambridgeshire, we find no evidence of major changes in genetic ancestry nor higher differentiation of immune loci between cohorts living before and after the Black Death.
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Affiliation(s)
- Ruoyun Hui
- Alan Turing Institute, London, UK
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - Christiana L. Scheib
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- St John’s College, University of Cambridge, Cambridge, UK
| | | | - Sarah A. Inskip
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- School of Archaeology and Ancient History, University of Leicester, Leicester, UK
| | - Craig Cessford
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Cambridge Archaeological Unit, Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Anthony W. Wohns
- School of Medicine, Stanford University, Stanford, CA, USA
- Department of Genetics and Biology, Stanford University, Stanford, CA, USA
| | | | - Samuel J. Griffith
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Helja Niinemäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Xiangyu Jack Ge
- Wellcome Genome Campus, Wellcome Sanger Institute, Hinxton, UK
| | - Alice K. Rose
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Department of Archaeology, University of Durham, Durham, UK
| | - Owyn Beneker
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Tamsin C. O’Connell
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
| | - John E. Robb
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Toomas Kivisild
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
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8
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Silva M, Booth T, Moore J, Anastasiadou K, Walker D, Gilardet A, Barrington C, Kelly M, Williams M, Henderson M, Smith A, Bowsher D, Montgomery J, Skoglund P. An individual with Sarmatian-related ancestry in Roman Britain. Curr Biol 2024; 34:204-212.e6. [PMID: 38118448 DOI: 10.1016/j.cub.2023.11.049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/10/2023] [Accepted: 11/21/2023] [Indexed: 12/22/2023]
Abstract
In the second century CE the Roman Empire had increasing contact with Sarmatians, nomadic Iranian speakers occupying an area stretching from the Pontic-Caspian steppe to the Carpathian mountains, both in the Caucasus and in the Danubian borders of the empire.1,2,3 In 175 CE, following their defeat in the Marcomannic Wars, emperor Marcus Aurelius drafted Sarmatian cavalry into Roman legions and deployed 5,500 Sarmatian soldiers to Britain, as recorded by contemporary historian Cassius Dio.4,5 Little is known about where the Sarmatian cavalry were stationed, and no individuals connected with this historically attested event have been identified to date, leaving its impact on Britain largely unknown. Here we document Caucasus- and Sarmatian-related ancestry in the whole genome of a Roman-period individual (126-228 calibrated [cal.] CE)-an outlier without traceable ancestry related to local populations in Britain-recovered from a farmstead site in present-day Cambridgeshire, UK. Stable isotopes support a life history of mobility during childhood. Although several scenarios are possible, the historical deployment of Sarmatians to Britain provides a parsimonious explanation for this individual's extraordinary life history. Regardless of the factors behind his migrations, these results highlight how long-range mobility facilitated by the Roman Empire impacted provincial locations outside of urban centers.
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Affiliation(s)
- Marina Silva
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
| | - Thomas Booth
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Joanna Moore
- Department of Archaeology, Durham University, Lower Mountjoy, South Rd, DH1 3LE, Durham, United Kingdom
| | - Kyriaki Anastasiadou
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Don Walker
- Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK
| | - Alexandre Gilardet
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Christopher Barrington
- Bioinformatics and Biostatistics, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Monica Kelly
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Mia Williams
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK
| | - Michael Henderson
- Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK
| | - Alex Smith
- Headland Archaeology, 13 Jane Street, Edinburgh EH6 5HE, UK
| | - David Bowsher
- Museum of London Archaeology (MOLA), Mortimer Wheeler House, 46 Eagle Wharf Road, London N1 7ED, UK
| | - Janet Montgomery
- Department of Archaeology, Durham University, Lower Mountjoy, South Rd, DH1 3LE, Durham, United Kingdom.
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, 1 Midland Road, London NW1 1AT, UK.
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9
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Poyraz L, Colbran LL, Mathieson I. Predicting functional consequences of recent natural selection in Britain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.16.562549. [PMID: 37904954 PMCID: PMC10614889 DOI: 10.1101/2023.10.16.562549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Ancient DNA can directly reveal the contribution of natural selection to human genomic variation. However, while the analysis of ancient DNA has been successful at identifying genomic signals of selection, inferring the phenotypic consequences of that selection has been more difficult. Most trait-associated variants are non-coding, so we expect that a large proportion of the phenotypic effects of selection will also act through non-coding variation. Since we cannot measure gene expression directly in ancient individuals, we used an approach (Joint-Tissue Imputation; JTI) developed to predict gene expression from genotype data. We tested for changes in the predicted expression of 17,384 protein coding genes over a time transect of 4500 years using 91 present-day and 616 ancient individuals from Britain. We identified 28 genes at seven genomic loci with significant (FDR < 0.05) changes in predicted expression levels in this time period. We compared the results from our transcriptome-wide scan to a genome-wide scan based on estimating per-SNP selection coefficients from time series data. At five previously identified loci, our approach allowed us to highlight small numbers of genes with evidence for significant shifts in expression from peaks that in some cases span tens of genes. At two novel loci (SLC44A5 and NUP85), we identify selection on gene expression not captured by scans based on genomic signatures of selection. Finally we show how classical selection statistics (iHS and SDS) can be combined with JTI models to incorporate functional information into scans that use present-day data alone. These results demonstrate the potential of this type of information to explore both the causes and consequences of natural selection.
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Affiliation(s)
- Lin Poyraz
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Department of Computational Biology, Cornell University, Ithaca, NY, USA
| | - Laura L. Colbran
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
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10
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Vyas DN, Koncz I, Modi A, Mende BG, Tian Y, Francalacci P, Lari M, Vai S, Straub P, Gallina Z, Szeniczey T, Hajdu T, Pejrani Baricco L, Giostra C, Radzevičiūtė R, Hofmanová Z, Évinger S, Bernert Z, Pohl W, Caramelli D, Vida T, Geary PJ, Veeramah KR. Fine-scale sampling uncovers the complexity of migrations in 5th-6th century Pannonia. Curr Biol 2023; 33:3951-3961.e11. [PMID: 37633281 DOI: 10.1016/j.cub.2023.07.063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/20/2023] [Accepted: 07/31/2023] [Indexed: 08/28/2023]
Abstract
As the collapse of the Western Roman Empire accelerated during the 4th and 5th centuries, arriving "barbarian" groups began to establish new communities in the border provinces of the declining (and eventually former) empire. This was a time of significant cultural and political change throughout not only these border regions but Europe as a whole.1,2 To better understand post-Roman community formation in one of these key frontier zones after the collapse of the Hunnic movement, we generated new paleogenomic data for a set of 38 burials from a time series of three 5th century cemeteries3,4,5 at Lake Balaton, Hungary. We utilized a comprehensive sampling approach to characterize these cemeteries along with data from 38 additional burials from a previously published mid-6th century site6 and analyzed them alongside data from over 550 penecontemporaneous individuals.7,8,9,10,11,12,13,14,15,16,17,18,19 The range of genetic diversity in all four of these local burial communities is extensive and wider ranging than penecontemporaneous Europeans sequenced to date. Despite many commonalities in burial customs and demography, we find that there were substantial differences in genetic ancestry between the sites. We detect evidence of northern European gene flow into the Lake Balaton region. Additionally, we observe a statistically significant association between dress artifacts and genetic ancestry among 5th century genetically female burials. Our analysis shows that the formation of early Medieval communities was a multifarious process even at a local level, consisting of genetically heterogeneous groups.
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Affiliation(s)
- Deven N Vyas
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
| | - István Koncz
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Múzeum krt. 4/B, 1088 Budapest, Hungary
| | - Alessandra Modi
- Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, Research Centre for the Humanities, Tóth Kálmán utca 4, 1097 Budapest, Hungary
| | - Yijie Tian
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA
| | - Paolo Francalacci
- Dipartimento di Scienze della Vita e dell'Ambiente, Università di Cagliari, Via T. Fiorelli 1, 09126 Cagliari, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Firenze, Italy
| | - Stefania Vai
- Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Firenze, Italy
| | | | | | - Tamás Szeniczey
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary
| | - Tamás Hajdu
- Department of Biological Anthropology, ELTE - Eötvös Loránd University, Pázmány Péter sétány 1/c, 1117 Budapest, Hungary
| | - Luisella Pejrani Baricco
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la Città Metropolitana di Torino, piazza San Giovanni 2, 10122 Torino, Italy
| | - Caterina Giostra
- Dipartimento di Storia, Archeologia e Storia dell'Arte, Università Cattolica del Sacro Cuore, Largo A. Gemelli, 1, 20123 Milano, Italy
| | - Rita Radzevičiūtė
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Zuzana Hofmanová
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany; Department of Archaeology and Museology, Faculty of Arts, Masaryk University, Arna Nováka 1/1, Brno 60200, Czech Republic
| | - Sándor Évinger
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Zsolt Bernert
- Department of Anthropology, Hungarian Natural History Museum, Ludovika tér 2-6, 1083 Budapest, Hungary
| | - Walter Pohl
- Institute for Medieval Research, Austrian Academy of Sciences, Dr-Ignaz-Seipel-Platz 2, 1020 Vienna, Austria; Institute for Austrian Historical Research, University of Vienna, Universitätsring 1, 1010 Vienna, Austria
| | - David Caramelli
- Dipartimento di Biologia, Università degli Studi di Firenze, Via del Proconsolo 12, 50122 Firenze, Italy.
| | - Tivadar Vida
- Institute of Archaeological Sciences, ELTE - Eötvös Loránd University, Múzeum krt. 4/B, 1088 Budapest, Hungary.
| | - Patrick J Geary
- School of Historical Studies, Institute for Advanced Study, 1 Einstein Drive, Princeton, NJ 08540, USA.
| | - Krishna R Veeramah
- Department of Ecology and Evolution, Stony Brook University, 650 Life Sciences Building, Stony Brook, NY 11794, USA.
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11
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Depaermentier ML, Krause-Kyora B, Hajdas I, Kempf M, Kuhn T, Spichtig N, Schwarz PA, Gerling C. Bioarchaeological analyses reveal long-lasting continuity at the periphery of the Late Antique Roman Empire. iScience 2023; 26:107034. [PMID: 37360687 PMCID: PMC10285633 DOI: 10.1016/j.isci.2023.107034] [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: 12/14/2022] [Revised: 03/23/2023] [Accepted: 05/31/2023] [Indexed: 06/28/2023] Open
Abstract
The Basel-Waisenhaus burial community (Switzerland) has been traditionally interpreted as immigrated Alamans because of the location and dating of the burial ground - despite the typical late Roman funeral practices. To evaluate this hypothesis, multi-isotope and aDNA analyses were conducted on the eleven individuals buried there. The results show that the burial ground was occupied around AD 400 by people belonging largely to one family, whereas isotope and genetic records most probably point toward a regionally organized and indigenous, instead of an immigrated, community. This strengthens the recently advanced assumption that the withdrawal of the Upper Germanic-Rhaetian limes after the "Crisis of the Third Century AD" was not necessarily related to a replacement of the local population by immigrated Alamannic peoples, suggesting a long-lasting continuity of occupation at the Roman periphery at the Upper and High Rhine region.
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Affiliation(s)
- Margaux L.C. Depaermentier
- Department of Ancient Civilizations, Prehistoric and Early Historic and Provincial Roman Archaeology, Vindonissa Professorship, University of Basel, Petersgraben 51, 4051 Basel, Switzerland
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Straße 12, 24105 Kiel, Germany
| | - Irka Hajdas
- Laboratory of Ion Beam Physics, ETH Zurich, Otto-Stern-Weg 5 HPK H31, 8093 Zurich, Switzerland
| | - Michael Kempf
- Department of Geography, Physical Geography, Landscape Ecology and Geoinformation, Kiel University, Ludewig-Meyn-Str. 8, 24098 Kiel, Germany
| | - Thomas Kuhn
- Aquatic and Isotope Biogeochemistry, Department of Environmental Sciences, University of Basel, Bernoullistrasse 30, 4056 Basel, Switzerland
| | - Norbert Spichtig
- Archäologische Bodenforschung Basel-Stadt, Petersgraben 11, 4001 Basel, Switzerland
| | - Peter-Andrew Schwarz
- Department of Ancient Civilizations, Prehistoric and Early Historic and Provincial Roman Archaeology, Vindonissa Professorship, University of Basel, Petersgraben 51, 4051 Basel, Switzerland
| | - Claudia Gerling
- Department of Ancient Civilizations, Prehistoric and Early Historic and Provincial Roman Archaeology, Vindonissa Professorship, University of Basel, Petersgraben 51, 4051 Basel, Switzerland
- Integrative Prehistory and Archaeological Science, Department of Environmental Sciences, University of Basel, Spalenring 145, 4055 Basel, Switzerland
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12
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Jackson A, Lin SJ, Jones EA, Chandler KE, Orr D, Moss C, Haider Z, Ryan G, Holden S, Harrison M, Burrows N, Jones WD, Loveless M, Petree C, Stewart H, Low K, Donnelly D, Lovell S, Drosou K, Varshney GK, Banka S. Clinical, genetic, epidemiologic, evolutionary, and functional delineation of TSPEAR-related autosomal recessive ectodermal dysplasia 14. HGG ADVANCES 2023; 4:100186. [PMID: 37009414 PMCID: PMC10064225 DOI: 10.1016/j.xhgg.2023.100186] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 02/27/2023] [Indexed: 06/11/2023] Open
Abstract
TSPEAR variants cause autosomal recessive ectodermal dysplasia (ARED) 14. The function of TSPEAR is unknown. The clinical features, the mutation spectrum, and the underlying mechanisms of ARED14 are poorly understood. Combining data from new and previously published individuals established that ARED14 is primarily characterized by dental anomalies such as conical tooth cusps and hypodontia, like those seen in individuals with WNT10A-related odontoonychodermal dysplasia. AlphaFold-predicted structure-based analysis showed that most of the pathogenic TSPEAR missense variants likely destabilize the β-propeller of the protein. Analysis of 100000 Genomes Project (100KGP) data revealed multiple founder TSPEAR variants across different populations. Mutational and recombination clock analyses demonstrated that non-Finnish European founder variants likely originated around the end of the last ice age, a period of major climatic transition. Analysis of gnomAD data showed that the non-Finnish European population TSPEAR gene-carrier rate is ∼1/140, making it one of the commonest AREDs. Phylogenetic and AlphaFold structural analyses showed that TSPEAR is an ortholog of drosophila Closca, an extracellular matrix-dependent signaling regulator. We, therefore, hypothesized that TSPEAR could have a role in enamel knot, a structure that coordinates patterning of developing tooth cusps. Analysis of mouse single-cell RNA sequencing (scRNA-seq) data revealed highly restricted expression of Tspear in clusters representing enamel knots. A tspeara -/-;tspearb -/- double-knockout zebrafish model recapitulated the clinical features of ARED14 and fin regeneration abnormalities of wnt10a knockout fish, thus suggesting interaction between tspear and wnt10a. In summary, we provide insights into the role of TSPEAR in ectodermal development and the evolutionary history, epidemiology, mechanisms, and consequences of its loss of function variants.
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Affiliation(s)
- Adam Jackson
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Sheng-Jia Lin
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Elizabeth A. Jones
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Kate E. Chandler
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - David Orr
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
| | - Celia Moss
- Department of Dermatology, Birmingham Children’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Zahra Haider
- Department of Dermatology, Birmingham Children’s Hospital, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Gavin Ryan
- West Midlands Regional Genetics Laboratory, Birmingham Women’s and Children’s NHS Foundation Trust, Birmingham, UK
| | - Simon Holden
- Clinical Genetics, Addenbrooke’s Hospital, Cambridge, UK
| | - Mike Harrison
- Department of Pediatric Dentistry, Guy’s and St Thomas' Dental Institute, London, UK
| | - Nigel Burrows
- Department of Dermatology, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Wendy D. Jones
- North East Thames Regional Genetics Service, Great Ormond Street Hospital for Children, Great Ormond Street NHS Foundation Trust, London, UK
| | - Mary Loveless
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Cassidy Petree
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Helen Stewart
- Oxford Centre for Genomic Medicine, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Karen Low
- Department of Clinical Genetics, St Michael’s Hospital, Bristol, UK
| | - Deirdre Donnelly
- Department of Genetic Medicine, Belfast HSC Trust, Lisburn Road, Belfast, UK
| | - Simon Lovell
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
| | - Konstantina Drosou
- Department of Earth and Environmental Sciences, Manchester Institute of Biotechnology, University of Manchester, Manchester, UK
- Division of Cell Matrix Biology and Regenerative Medicine, Faculty of Biology, Medicine and Health, University of Manchester, 99 Oxford Road, Manchester, UK
| | - Gaurav K. Varshney
- Genes and Human Disease Research Program, Oklahoma Medical Research Foundation, Oklahoma City, OK, USA
| | - Siddharth Banka
- Division of Evolution, Infection and Genomics, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester, UK
- Manchester Centre for Genomic Medicine, St Mary’s Hospital, Manchester University NHS Foundation Trust, Health Innovation Manchester, Manchester, UK
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13
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Barton AR, Santander CG, Skoglund P, Moltke I, Reich D, Mathieson I. Insufficient evidence for natural selection associated with the Black Death. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.14.532615. [PMID: 36993413 PMCID: PMC10055098 DOI: 10.1101/2023.03.14.532615] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Klunk et al. analyzed ancient DNA data from individuals in London and Denmark before, during and after the Black Death [1], and argued that allele frequency changes at immune genes were too large to be produced by random genetic drift and thus must reflect natural selection. They also identified four specific variants that they claimed show evidence of selection including at ERAP2, for which they estimate a selection coefficient of 0.39-several times larger than any selection coefficient on a common human variant reported to date. Here we show that these claims are unsupported for four reasons. First, the signal of enrichment of large allele frequency changes in immune genes comparing people in London before and after the Black Death disappears after an appropriate randomization test is carried out: the P value increases by ten orders of magnitude and is no longer significant. Second, a technical error in the estimation of allele frequencies means that none of the four originally reported loci actually pass the filtering thresholds. Third, the filtering thresholds do not adequately correct for multiple testing. Finally, in the case of the ERAP2 variant rs2549794, which Klunk et al. show experimentally may be associated with a host interaction with Y. pestis, we find no evidence of significant frequency change either in the data that Klunk et al. report, or in published data spanning 2,000 years. While it remains plausible that immune genes were subject to natural selection during the Black Death, the magnitude of this selection and which specific genes may have been affected remains unknown.
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Affiliation(s)
- Alison R. Barton
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Cindy G. Santander
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - Pontus Skoglund
- Ancient Genomics Laboratory, The Francis Crick Institute, London NW1 1AT, UK
| | - Ida Moltke
- Department of Biology, University of Copenhagen, Copenhagen, DK-2200, Denmark
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia PA 19104, USA
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14
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Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, Kilinc GM, Kjellström A, Papmehl-Dufay L, Alfsdotter C, Berglund B, Alrawi L, Kashuba N, Sobrado V, Lagerholm VK, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Munters AR, Bernhardsson C, Skar B, Christophersen A, Turner-Walker G, Gopalakrishnan S, Daskalaki E, Omrak A, Pérez-Ramallo P, Skoglund P, Girdland-Flink L, Gunnarsson F, Hedenstierna-Jonson C, Gilbert MTP, Lidén K, Jakobsson M, Einarsson L, Victor H, Krzewińska M, Zachrisson T, Storå J, Stefánsson K, Helgason A, Götherström A. The genetic history of Scandinavia from the Roman Iron Age to the present. Cell 2023; 186:32-46.e19. [PMID: 36608656 DOI: 10.1016/j.cell.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023]
Abstract
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland
| | - Gulsah Merve Kilinc
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Clara Alfsdotter
- Department of Archaeology, Bohusläns Museum, Museigatan 1, 451 19 Udevalla, Sweden
| | - Birgitta Berglund
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Loey Alrawi
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Ancient History, Archaeology, Uppsala University, 752 38 Uppsala, Sweden; Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Verónica Sobrado
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, 166 0450 Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Axel Christophersen
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Gordon Turner-Walker
- Department of Archaeology and Anthropology National Museum of Natural Science, 404023 Taichung City, Taiwan
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eva Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany; Department of Medical and Surgical Specialities, Faculty of Medicine and Nursing, University of the Basque Country (EHU), Donostia-San Sebastián 20014, Spain
| | | | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, AB24 3FX Aberdeen, UK; School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Fredrik Gunnarsson
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Lars Einarsson
- Kronan, Marine Archaeological Department, Kalmar County Museum, Box 104, Kalmar S-39121, Sweden
| | - Helena Victor
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland.
| | - Anders Götherström
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
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15
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Gretzinger J, Sayer D, Justeau P, Altena E, Pala M, Dulias K, Edwards CJ, Jodoin S, Lacher L, Sabin S, Vågene ÅJ, Haak W, Ebenesersdóttir SS, Moore KHS, Radzeviciute R, Schmidt K, Brace S, Bager MA, Patterson N, Papac L, Broomandkhoshbacht N, Callan K, Harney É, Iliev L, Lawson AM, Michel M, Stewardson K, Zalzala F, Rohland N, Kappelhoff-Beckmann S, Both F, Winger D, Neumann D, Saalow L, Krabath S, Beckett S, Van Twest M, Faulkner N, Read C, Barton T, Caruth J, Hines J, Krause-Kyora B, Warnke U, Schuenemann VJ, Barnes I, Dahlström H, Clausen JJ, Richardson A, Popescu E, Dodwell N, Ladd S, Phillips T, Mortimer R, Sayer F, Swales D, Stewart A, Powlesland D, Kenyon R, Ladle L, Peek C, Grefen-Peters S, Ponce P, Daniels R, Spall C, Woolcock J, Jones AM, Roberts AV, Symmons R, Rawden AC, Cooper A, Bos KI, Booth T, Schroeder H, Thomas MG, Helgason A, Richards MB, Reich D, Krause J, Schiffels S. The Anglo-Saxon migration and the formation of the early English gene pool. Nature 2022; 610:112-119. [PMID: 36131019 PMCID: PMC9534755 DOI: 10.1038/s41586-022-05247-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 08/17/2022] [Indexed: 11/09/2022]
Abstract
The history of the British Isles and Ireland is characterized by multiple periods of major cultural change, including the influential transformation after the end of Roman rule, which precipitated shifts in language, settlement patterns and material culture1. The extent to which migration from continental Europe mediated these transitions is a matter of long-standing debate2-4. Here we study genome-wide ancient DNA from 460 medieval northwestern Europeans-including 278 individuals from England-alongside archaeological data, to infer contemporary population dynamics. We identify a substantial increase of continental northern European ancestry in early medieval England, which is closely related to the early medieval and present-day inhabitants of Germany and Denmark, implying large-scale substantial migration across the North Sea into Britain during the Early Middle Ages. As a result, the individuals who we analysed from eastern England derived up to 76% of their ancestry from the continental North Sea zone, albeit with substantial regional variation and heterogeneity within sites. We show that women with immigrant ancestry were more often furnished with grave goods than women with local ancestry, whereas men with weapons were as likely not to be of immigrant ancestry. A comparison with present-day Britain indicates that subsequent demographic events reduced the fraction of continental northern European ancestry while introducing further ancestry components into the English gene pool, including substantial southwestern European ancestry most closely related to that seen in Iron Age France5,6.
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Affiliation(s)
- Joscha Gretzinger
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | | | - Maria Pala
- University of Huddersfield, Huddersfield, UK
| | - Katharina Dulias
- University of Huddersfield, Huddersfield, UK
- Institute of Geosystems and Bioindication, Technische Universität Braunschweig, Braunschweig, Germany
| | - Ceiridwen J Edwards
- University of Huddersfield, Huddersfield, UK
- University of Oxford, Oxford, UK
| | | | - Laura Lacher
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Susanna Sabin
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ, USA
| | - Åshild J Vågene
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Wolfgang Haak
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - Rita Radzeviciute
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Martina Abenhus Bager
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Luka Papac
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Éadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | | | - Frank Both
- Landesmuseum Natur und Mensch, Oldenburg, Germany
| | | | | | - Lars Saalow
- Landesamt für Kultur und Denkmalpflege Mecklenburg-Vorpommern, Schwerin, Germany
| | - Stefan Krabath
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
- Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, Cranfield, UK
- Melbourne Dental School, University of Melbourne, Melbourne, Victoria, Australia
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Neil Faulkner
- Sedgeford Historical and Archaeological Research Project, Sedgeford, UK
| | - Chris Read
- The Atlantic Technological University, Sligo, Ireland
| | | | | | | | | | | | - Verena J Schuenemann
- University of Zurich, Zurich, Switzerland
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | | | - Andrew Richardson
- Canterbury Archaeological Trust, Canterbury, UK
- Isle Heritage CIC, Sandgate, UK
| | | | | | | | | | - Richard Mortimer
- Oxford Archaeology East, Cambridge, UK
- Cotswold Archaeology, Needham Market, UK
| | - Faye Sayer
- University of Birmingham, Birmingham, UK
| | - Diana Swales
- Centre for Anatomy and Human Identification (CAHID), University of Dundee, Dundee, UK
| | | | | | - Robert Kenyon
- East Dorset Antiquarian Society (EDAS), West Bexington, UK
| | - Lilian Ladle
- Department of Archaeology and Anthropology, Bournemouth University, Poole, UK
| | - Christina Peek
- Institute for Historical Coastal Research (NIhK), Wilhelmshaven, Germany
| | | | | | | | | | | | | | | | | | - Anooshka C Rawden
- Fishbourne Roman Palace, Fishbourne, UK
- South Downs Centre, Midhurst, UK
| | - Alan Cooper
- BlueSkyGenetics, Adelaide, South Australia, Australia
| | - Kirsten I Bos
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Hannes Schroeder
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Agnar Helgason
- deCODE Genetics/AMGEN Inc., Reykjavík, Iceland
- Department of Anthropology, School of Social Sciences, University of Iceland, Reykjavík, Iceland
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Johannes Krause
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stephan Schiffels
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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16
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Ancient DNA reveals details about early medieval migration into England. Nature 2022:10.1038/d41586-022-02269-8. [PMID: 36131059 DOI: 10.1038/d41586-022-02269-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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17
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Lazaridis I, Alpaslan-Roodenberg S, Acar A, Açıkkol A, Agelarakis A, Aghikyan L, Akyüz U, Andreeva D, Andrijašević G, Antonović D, Armit I, Atmaca A, Avetisyan P, Aytek Aİ, Bacvarov K, Badalyan R, Bakardzhiev S, Balen J, Bejko L, Bernardos R, Bertsatos A, Biber H, Bilir A, Bodružić M, Bonogofsky M, Bonsall C, Borić D, Borovinić N, Bravo Morante G, Buttinger K, Callan K, Candilio F, Carić M, Cheronet O, Chohadzhiev S, Chovalopoulou ME, Chryssoulaki S, Ciobanu I, Čondić N, Constantinescu M, Cristiani E, Culleton BJ, Curtis E, Davis J, Demcenco TI, Dergachev V, Derin Z, Deskaj S, Devejyan S, Djordjević V, Duffett Carlson KS, Eccles LR, Elenski N, Engin A, Erdoğan N, Erir-Pazarcı S, Fernandes DM, Ferry M, Freilich S, Frînculeasa A, Galaty ML, Gamarra B, Gasparyan B, Gaydarska B, Genç E, Gültekin T, Gündüz S, Hajdu T, Heyd V, Hobosyan S, Hovhannisyan N, Iliev I, Iliev L, Iliev S, İvgin İ, Janković I, Jovanova L, Karkanas P, Kavaz-Kındığılı B, Kaya EH, Keating D, Kennett DJ, Deniz Kesici S, Khudaverdyan A, Kiss K, Kılıç S, Klostermann P, Kostak Boca Negra Valdes S, Kovačević S, Krenz-Niedbała M, Krznarić Škrivanko M, Kurti R, Kuzman P, Lawson AM, Lazar C, Leshtakov K, Levy TE, Liritzis I, Lorentz KO, Łukasik S, Mah M, Mallick S, Mandl K, Martirosyan-Olshansky K, Matthews R, Matthews W, McSweeney K, Melikyan V, Micco A, Michel M, Milašinović L, Mittnik A, Monge JM, Nekhrizov G, Nicholls R, Nikitin AG, Nikolov V, Novak M, Olalde I, Oppenheimer J, Osterholtz A, Özdemir C, Özdoğan KT, Öztürk N, Papadimitriou N, Papakonstantinou N, Papathanasiou A, Paraman L, Paskary EG, Patterson N, Petrakiev I, Petrosyan L, Petrova V, Philippa-Touchais A, Piliposyan A, Pocuca Kuzman N, Potrebica H, Preda-Bălănică B, Premužić Z, Price TD, Qiu L, Radović S, Raeuf Aziz K, Rajić Šikanjić P, Rasheed Raheem K, Razumov S, Richardson A, Roodenberg J, Ruka R, Russeva V, Şahin M, Şarbak A, Savaş E, Schattke C, Schepartz L, Selçuk T, Sevim-Erol A, Shamoon-Pour M, Shephard HM, Sideris A, Simalcsik A, Simonyan H, Sinika V, Sirak K, Sirbu G, Šlaus M, Soficaru A, Söğüt B, Sołtysiak A, Sönmez-Sözer Ç, Stathi M, Steskal M, Stewardson K, Stocker S, Suata-Alpaslan F, Suvorov A, Szécsényi-Nagy A, Szeniczey T, Telnov N, Temov S, Todorova N, Tota U, Touchais G, Triantaphyllou S, Türker A, Ugarković M, Valchev T, Veljanovska F, Videvski Z, Virag C, Wagner A, Walsh S, Włodarczak P, Workman JN, Yardumian A, Yarovoy E, Yavuz AY, Yılmaz H, Zalzala F, Zettl A, Zhang Z, Çavuşoğlu R, Rohland N, Pinhasi R, Reich D. The genetic history of the Southern Arc: A bridge between West Asia and Europe. Science 2022; 377:eabm4247. [PMID: 36007055 PMCID: PMC10064553 DOI: 10.1126/science.abm4247] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
By sequencing 727 ancient individuals from the Southern Arc (Anatolia and its neighbors in Southeastern Europe and West Asia) over 10,000 years, we contextualize its Chalcolithic period and Bronze Age (about 5000 to 1000 BCE), when extensive gene flow entangled it with the Eurasian steppe. Two streams of migration transmitted Caucasus and Anatolian/Levantine ancestry northward, and the Yamnaya pastoralists, formed on the steppe, then spread southward into the Balkans and across the Caucasus into Armenia, where they left numerous patrilineal descendants. Anatolia was transformed by intra-West Asian gene flow, with negligible impact of the later Yamnaya migrations. This contrasts with all other regions where Indo-European languages were spoken, suggesting that the homeland of the Indo-Anatolian language family was in West Asia, with only secondary dispersals of non-Anatolian Indo-Europeans from the steppe.
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Affiliation(s)
- Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Songül Alpaslan-Roodenberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Ayşe Acar
- Department of Anthropology, Faculty of Letters, Mardin Artuklu University, 47510 Artuklu, Mardin, Turkey
| | - Ayşen Açıkkol
- Department of Anthropology, Faculty of Letters, Sivas Cumhuriyet University, 58140 Sivas, Turkey
| | | | - Levon Aghikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Uğur Akyüz
- Samsun Museum of Archeology and Ethnography, Kale Mahallesi, Merkez, İlkadım, 55030 Samsun, Turkey
| | | | | | | | - Ian Armit
- Department of Archaeology, University of York, York YO1 7EP, UK
| | - Alper Atmaca
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Pavel Avetisyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Ahmet İhsan Aytek
- Department of Anthropology, Faculty of Arts and Science, Burdur Mehmet Akif University, 15100 Burdur, Turkey
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Ruben Badalyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Lorenc Bejko
- Department of Archaeology and Heritage Studies, University of Tirana, 1010 Tirana, Albania
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Andreas Bertsatos
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Hanifi Biber
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Ahmet Bilir
- Department of Archaeology, Faculty of Science and Letters, Düzce University, 81620 Düzce, Turkey
| | | | | | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, NY 10027, USA
| | - Nikola Borovinić
- Center for Conservation and Archaeology of Montenegro, 81250 Cetinje, Montenegro
| | | | - Katharina Buttinger
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Stefan Chohadzhiev
- Department of Archaeology, University of Veliko Tarnovo "St. Cyril and St. Methodius," 5003 Veliko Tarnovo, Bulgaria
| | - Maria-Eleni Chovalopoulou
- Department of Animal and Human Physiology, Faculty of Biology, School of Sciences, National and Kapodistrian University of Athens, 10679 Athens, Greece
| | - Stella Chryssoulaki
- Hellenic Ministry of Culture and Sports, Ephorate of Antiquities of Piraeus and the Islands, 10682 Piraeus, Greece
| | - Ion Ciobanu
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,National Archaeological Agency, 2012 Chișinău, Moldova
| | | | | | - Emanuela Cristiani
- Department of Oral and Maxillo-Facial Sciences, Sapienza University of Rome, 00161 Rome, Italy
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jack Davis
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | | | - Valentin Dergachev
- Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, 2001 Chișinău, Moldova
| | - Zafer Derin
- Department of Archaeology, Faculty of Letters, Ege University, 35100 Bornova-Izmir, Turkey
| | - Sylvia Deskaj
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Seda Devejyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | | | - Laurie R Eccles
- Human Paleoecology and Isotope Geochemistry Lab, Department of Anthropology, The Pennsylvania State University, University Park, PA 16802, USA
| | - Nedko Elenski
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Atilla Engin
- Department of Archaeology, Faculty of Science and Letters, Gaziantep University, 27310 Gaziantep, Turkey
| | - Nihat Erdoğan
- Mardin Archaeological Museum, Şar, Cumhuriyet Meydanı üstü, 47100 Artuklu, Mardin, Turkey
| | | | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, 100042 Ploiești, Romania
| | - Michael L Galaty
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, 43007 Tarragona, Spain.,Departament d'Història i Història de l'Art, Universitat Rovira i Virgili, 43002 Tarragona, Spain.,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Boris Gasparyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | | | - Elif Genç
- Department of Archaeology, Faculty of Science and Letters, Çukurova University, 01330 Balçalı-Sarıçam-Adana, Turkey
| | - Timur Gültekin
- Department of Anthropology, Faculty of Humanities, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Serkan Gündüz
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Volker Heyd
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Suren Hobosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Nelli Hovhannisyan
- Department of Ecology and Nature Protection, Yerevan State University, 0025 Yerevan, Armenia
| | - Iliya Iliev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | - Lora Iliev
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - İlkay İvgin
- Ministry of Culture and Tourism, İsmet İnönü Bulvarı, 06100 Emek, Ankara, Turkey
| | - Ivor Janković
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Lence Jovanova
- Museum of the City of Skopje, 1000 Skopje, North Macedonia
| | - Panagiotis Karkanas
- Malcolm H. Wiener Laboratory, American School of Classical Studies at Athens, 10676 Athens, Greece
| | - Berna Kavaz-Kındığılı
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | - Esra Hilal Kaya
- Muğla Archaeological Museum and Yatağan Thermal Power Generation Company, Rescue Excavations, 48000 Muğla, Turkey
| | - Denise Keating
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Douglas J Kennett
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA.,Department of Anthropology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Seda Deniz Kesici
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | | | - Krisztián Kiss
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary.,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Sinan Kılıç
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Paul Klostermann
- Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | | | | | | | | | - Rovena Kurti
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Pasko Kuzman
- National Museum in Ohrid, 6000 Ohrid, North Macedonia
| | - Ann Marie Lawson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Catalin Lazar
- ArchaeoSciences Division, Research Institute of the University of Bucharest, University of Bucharest, 050663 Bucharest, Romania
| | - Krassimir Leshtakov
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Thomas E Levy
- Department of Anthropology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Ioannis Liritzis
- Key Research Institute of Yellow River Civilization and Sustainable Development and the Collaborative Innovation Center on Yellow River Civilization of Henan Province, Laboratory of Yellow River Cultural Heritage, Henan University, 475001 Kaifeng, China.,European Academy of Sciences and Arts, 5020 Salzburg, Austria
| | - Kirsi O Lorentz
- Science and Technology in Archaeology and Culture Research Center, The Cyprus Institute, 2121 Aglantzia, Nicosia, Cyprus
| | - Sylwia Łukasik
- Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614 Poznań, Poland
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | | | - Roger Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Wendy Matthews
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Kathleen McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Varduhi Melikyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Adam Micco
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Megan Michel
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | | | - Alissa Mittnik
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet M Monge
- University of Pennsylvania Museum of Archaeology and Anthropology, Philadelphia, PA 19104, USA
| | - Georgi Nekhrizov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Rebecca Nicholls
- School of Archaeological and Forensic Sciences, Faculty of Life Sciences, University of Bradford, Bradford BD7 1DP, UK
| | - Alexey G Nikitin
- Department of Biology, Grand Valley State University, Allendale, MI 49401, USA
| | - Vassil Nikolov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 1000 Sofia, Bulgaria
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,BIOMICs Research Group, University of the Basque Country UPV/EHU, 01006 Vitoria-Gasteiz, Spain
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Osterholtz
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Mississippi State, MS 39762, USA
| | - Celal Özdemir
- Amasya Archaeology Museum, Mustafa Kemal Paşa Caddesi, 05000 Amasya, Turkey
| | - Kadir Toykan Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Nurettin Öztürk
- Department of Archaeology, Faculty of Letters, Atatürk University, 25100 Erzurum, Turkey
| | | | - Niki Papakonstantinou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoantropology and Speleology, Greek Ministry of Culture, 11636 Athens, Greece
| | | | | | - Nick Patterson
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Ilian Petrakiev
- Regional Museum of History - Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Levon Petrosyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
| | - Vanya Petrova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | | | - Ashot Piliposyan
- Department of Armenian History, Armenian State Pedagogical University After Khachatur Abovyan, 0010 Yerevan, Armenia
| | | | - Hrvoje Potrebica
- Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | | | | | - T Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin-Madison, Madison, WI 53706, USA
| | - Lijun Qiu
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Siniša Radović
- Institute for Quaternary Paleontology and Geology, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Kamal Raeuf Aziz
- Sulaymaniyah Directorate of Antiquities and Heritage, 46010 Sulaymaniyah, Iraq
| | - Petra Rajić Šikanjić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000 Zagreb, Croatia
| | | | - Sergei Razumov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Amy Richardson
- Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Jacob Roodenberg
- The Netherlands Institute for the Near East, 2311 Leiden, Netherlands
| | - Rudenc Ruka
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania
| | - Victoria Russeva
- Institute of Experimental Morphology, Pathology and Archeology with Museum, Bulgarian Academy of Science, 1113 Sofia, Bulgaria
| | - Mustafa Şahin
- Department of Archaeology, Faculty of Science and Letters, Bursa Uludağ University, 16059 Görükle, Bursa, Turkey
| | - Ayşegül Şarbak
- Department of Anthropology, Faculty of Science and Letters, Hitit University, 19040 Çorum, Turkey
| | - Emre Savaş
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Constanze Schattke
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Lynne Schepartz
- School of Anatomical Sciences, The University of the Witwatersrand, 2193 Johannesburg, South Africa
| | - Tayfun Selçuk
- Bodrum Museum of Underwater Archeology, Çarşı Neighbourhood, 48400 Bodrum, Muğla, Turkey
| | - Ayla Sevim-Erol
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Michel Shamoon-Pour
- Department of Anthropology, Binghamton University, Binghamton, NY 13902, USA
| | | | - Athanasios Sideris
- Institute of Classical Archaeology, Charles University, 11636 Prague, Czechia
| | - Angela Simalcsik
- "Orheiul Vechi" Cultural-Natural Reserve, Institute of Bioarchaeological and Ethnocultural Research, 3552 Butuceni, Moldova.,"Olga Necrasov" Centre of Anthropological Research, Romanian Academy Iași Branch, 2012 Iaşi Romania
| | - Hakob Simonyan
- Scientific Research Center of the Historical and Cultural Heritage, 0010 Yerevan, Armenia
| | - Vitalij Sinika
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Kendra Sirak
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ghenadie Sirbu
- Thracology Scientific Research Laboratory of the State University of Moldova, Department of Academic Management, Academy of Science of Moldova, 2009 Chișinău, Moldova
| | - Mario Šlaus
- Anthropological Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, 050711 Bucharest, Romania
| | - Bilal Söğüt
- Department of Archaeology, Faculty of Science and Arts, Pamukkale University, 20070 Denizli, Turkey
| | | | - Çilem Sönmez-Sözer
- Department of Anthropology, Faculty of Language and History - Geography, Ankara University, 06100 Sıhhiye, Ankara, Turkey
| | - Maria Stathi
- Ephorate of Antiquities of East Attica, Ministry of Culture and Sports, 10682 Athens, Greece
| | - Martin Steskal
- Austrian Archaeological Institute at the Austrian Academy of Sciences, 1190 Vienna, Austria
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Sharon Stocker
- Department of Classics, University of Cincinnati, Cincinnati, OH 45221, USA
| | - Fadime Suata-Alpaslan
- Department of Anthropology, Faculty of Letters, Istanbul University, 34134 Istanbul, Turkey
| | - Alexander Suvorov
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, Research Centre for the Humanities, Eötvös Loránd Research Network, 1097 Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, 1053 Budapest, Hungary
| | - Nikolai Telnov
- Pridnestrovian University named after Taras Shevchenko, 3300 Tiraspol, Moldova
| | - Strahil Temov
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | - Nadezhda Todorova
- Department of Archaeology, St. Kliment Ohridski University of Sofia, 1504 Sofia, Bulgaria
| | - Ulsi Tota
- Prehistory Department, Albanian Institute of Archaeology, Academy of Albanian Studies, 1000 Tirana, Albania.,Culture and Patrimony Department, University of Avignon, F-84029 Avignon, France
| | - Gilles Touchais
- Department of the History of Art and Archaeology, Université Paris 1 Panthéon-Sorbonne, 75006 Paris, France
| | - Sevi Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Atila Türker
- Department of Archaeology, Faculty of Science and Letters, Ondokuz Mayıs University, 55139 Atakum-Samsun, Turkey
| | | | - Todor Valchev
- Yambol Regional Historical Museum, 8600 Yambol, Bulgaria
| | | | - Zlatko Videvski
- Archaeology Museum of North Macedonia, 1000 Skopje, North Macedonia
| | | | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Sam Walsh
- School of Natural Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, 31-016 Kraków, Poland
| | - J Noah Workman
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Bryn Athyn, PA 19009, USA.,Penn Museum, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Evgenii Yarovoy
- History of the Ancient World and Middle Ages Department, Moscow Region State University, Moscow Region, 141014 Mytishi, Russia
| | - Alper Yener Yavuz
- Department of Anthropology, Burdur Mehmet Akif Ersoy University, Istiklal Campus, 15100 Burdur, Turkey
| | - Hakan Yılmaz
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rafet Çavuşoğlu
- Department of Archaeology, Faculty of Humanities, Van Yüzüncü Yıl University, 65090 Tuşba, Van, Turkey
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, 1030 Vienna, Austria
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
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18
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Huang X, Xia ZY, Bin X, He G, Guo J, Adnan A, Yin L, Huang Y, Zhao J, Yang Y, Ma F, Li Y, Hu R, Yang T, Wei LH, Wang CC. Genomic Insights Into the Demographic History of the Southern Chinese. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.853391] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Southern China is the birthplace of rice-cultivating agriculture and different language families and has also witnessed various human migrations that facilitated cultural diffusions. The fine-scale demographic history in situ that forms present-day local populations, however, remains unclear. To comprehensively cover the genetic diversity in East and Southeast Asia, we generated genome-wide SNP data from 211 present-day Southern Chinese and co-analyzed them with ∼1,200 ancient and modern genomes. In Southern China, language classification is significantly associated with genetic variation but with a different extent of predictability, and there is strong evidence for recent shared genetic history particularly in Hmong–Mien and Austronesian speakers. A geography-related genetic sub-structure that represents the major genetic variation in Southern East Asians is established pre-Holocene and its extremes are represented by Neolithic Fujianese and First Farmers in Mainland Southeast Asia. This sub-structure is largely reduced by admixture in ancient Southern Chinese since > ∼2,000 BP, which forms a “Southern Chinese Cluster” with a high level of genetic homogeneity. Further admixture characterizes the demographic history of the majority of Hmong–Mien speakers and some Kra-Dai speakers in Southwest China happened ∼1,500–1,000 BP, coeval to the reigns of local chiefdoms. In Yellow River Basin, we identify a connection of local populations to genetic sub-structure in Southern China with geographical correspondence appearing > ∼9,000 BP, while the gene flow likely closely related to “Southern Chinese Cluster” since the Longshan period (∼5,000–4,000 BP) forms ancestry profile of Han Chinese Cline.
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19
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Laidre KL, Supple MA, Born EW, Regehr EV, Wiig Ø, Ugarte F, Aars J, Dietz R, Sonne C, Hegelund P, Isaksen C, Akse GB, Cohen B, Stern HL, Moon T, Vollmers C, Corbett-Detig R, Paetkau D, Shapiro B. Glacial ice supports a distinct and undocumented polar bear subpopulation persisting in late 21st-century sea-ice conditions. Science 2022; 376:1333-1338. [PMID: 35709290 DOI: 10.1126/science.abk2793] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Polar bears are susceptible to climate warming because of their dependence on sea ice, which is declining rapidly. We present the first evidence for a genetically distinct and functionally isolated group of polar bears in Southeast Greenland. These bears occupy sea-ice conditions resembling those projected for the High Arctic in the late 21st century, with an annual ice-free period that is >100 days longer than the estimated fasting threshold for the species. Whereas polar bears in most of the Arctic depend on annual sea ice to catch seals, Southeast Greenland bears have a year-round hunting platform in the form of freshwater glacial mélange. This suggests that marine-terminating glaciers, although of limited availability, may serve as previously unrecognized climate refugia. Conservation of Southeast Greenland polar bears, which meet criteria for recognition as the world's 20th polar bear subpopulation, is necessary to preserve the genetic diversity and evolutionary potential of the species.
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Affiliation(s)
- Kristin L Laidre
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA.,Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | - Megan A Supple
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Erik W Born
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | - Eric V Regehr
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA
| | - Øystein Wiig
- Natural History Museum, University of Oslo, Blindern, NO-0318 Oslo, Norway
| | - Fernando Ugarte
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | - Jon Aars
- Norwegian Polar Institute, Fram Centre, NO-9296 Tromsø, Norway
| | - Rune Dietz
- Department of Ecoscience and Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
| | - Christian Sonne
- Department of Ecoscience and Arctic Research Centre, Aarhus University, DK-4000 Roskilde, Denmark
| | - Peter Hegelund
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | - Carl Isaksen
- Greenland Institute of Natural Resources, 3900 Nuuk, Greenland
| | | | - Benjamin Cohen
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA
| | - Harry L Stern
- Polar Science Center, Applied Physics Laboratory, University of Washington, Seattle, WA 98105, USA
| | - Twila Moon
- National Snow and Ice Data Center, Cooperative Institute for Research In Environmental Sciences (CIRES), University of Colorado, Boulder, CO 80309, USA
| | - Christopher Vollmers
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - Russ Corbett-Detig
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
| | - David Paetkau
- Wildlife Genetics International, Nelson, BC V1L 5P9, Canada
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, Santa Cruz, CA 95064, USA
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20
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Gelabert P, Blazyte A, Chang Y, Fernandes DM, Jeon S, Hong JG, Yoon J, Ko Y, Oberreiter V, Cheronet O, Özdoğan KT, Sawyer S, Yang S, Greytak EM, Choi H, Kim J, Kim JI, Jeong C, Bae K, Bhak J, Pinhasi R. Northeastern Asian and Jomon-related genetic structure in the Three Kingdoms period of Gimhae, Korea. Curr Biol 2022; 32:3232-3244.e6. [PMID: 35732180 DOI: 10.1016/j.cub.2022.06.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2021] [Revised: 04/05/2022] [Accepted: 06/01/2022] [Indexed: 11/19/2022]
Abstract
The genetic history of prehistoric and protohistoric Korean populations is not well understood because only a small number of ancient genomes are available. Here, we report the first paleogenomic data from the Korean Three Kingdoms period, a crucial point in the cultural and historic formation of Korea. These data comprise eight shotgun-sequenced genomes from ancient Korea (0.7×-6.1× coverage). They were derived from two archeological sites in Gimhae: the Yuha-ri shell mound and the Daesung-dong tumuli, the latter being the most important funerary complex of the Gaya confederacy. All individuals are from between the 4th and 5th century CE and are best modeled as an admixture between a northern China Bronze Age genetic source and a source of Jomon-related ancestry that shares similarities with the present-day genomes from Japan. The observed substructure and proportion of Jomon-related ancestry suggest the presence of two genetic groups within the population and diversity among the Gaya population. We could not correlate the genomic differences between these two groups with either social status or sex. All the ancient individuals' genomic profiles, including phenotypically relevant SNPs associated with hair and eye color, facial morphology, and myopia, imply strong genetic and phenotypic continuity with modern Koreans for the last 1,700 years.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
| | - Asta Blazyte
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Yongjoon Chang
- Daegu National Museum, 321 Cheongho-ro, Suseong-gu, Daegu 42111, Republic of Korea
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Sungwon Jeon
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Clinomics Inc., UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Jin Geun Hong
- Jeonju National Museum, 249 Ssukgogae-ro, Wansan-gu, Jeonju-si, Jeollabuk-do 55070, Republic of Korea
| | - Jiyeon Yoon
- Gongju National Museum, 34 Gwangwangdanji-gil, Gongju-si, Chungcheongnam-do 32535, Republic of Korea
| | - Youngmin Ko
- National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria
| | - Songhyok Yang
- National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea
| | | | - Hansol Choi
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea
| | - Jungeun Kim
- Personal Genomics Institute (PGI), Genome Research Foundation (GRF), Cheongju 28160, Republic of Korea
| | - Jong-Il Kim
- Department of Archaeology and Art History, Seoul National University, 1 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Choongwon Jeong
- Seoul National University, School of Biological Sciences, 599 Gwanak-ro, Gwanak-gu, Seoul 08826, Republic of Korea
| | - Kidong Bae
- National Museum of Korea, 137 Seobinggo-ro, Yongsan-gu, Seoul 04383, Republic of Korea.
| | - Jong Bhak
- Korean Genomics Center (KOGIC), Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Department of Biomedical Engineering, College of Information and Biotechnology, Ulsan National Institute of Science and Technology (UNIST), UNIST-gil 50, Ulsan 44919, Republic of Korea; Clinomics Inc., UNIST-gil 50, Ulsan 44919, Republic of Korea.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
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21
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Population dynamics and genetic connectivity in recent chimpanzee history. CELL GENOMICS 2022; 2:None. [PMID: 35711737 PMCID: PMC9188271 DOI: 10.1016/j.xgen.2022.100133] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 12/29/2021] [Accepted: 04/15/2022] [Indexed: 11/22/2022]
Abstract
Knowledge on the population history of endangered species is critical for conservation, but whole-genome data on chimpanzees (Pan troglodytes) is geographically sparse. Here, we produced the first non-invasive geolocalized catalog of genomic diversity by capturing chromosome 21 from 828 non-invasive samples collected at 48 sampling sites across Africa. The four recognized subspecies show clear genetic differentiation correlating with known barriers, while previously undescribed genetic exchange suggests that these have been permeable on a local scale. We obtained a detailed reconstruction of population stratification and fine-scale patterns of isolation, migration, and connectivity, including a comprehensive picture of admixture with bonobos (Pan paniscus). Unlike humans, chimpanzees did not experience extended episodes of long-distance migrations, which might have limited cultural transmission. Finally, based on local rare variation, we implement a fine-grained geolocalization approach demonstrating improved precision in determining the origin of confiscated chimpanzees.
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22
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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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23
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Fischer CE, Pemonge MH, Ducoussau I, Arzelier A, Rivollat M, Santos F, Barrand Emam H, Bertaud A, Beylier A, Ciesielski E, Dedet B, Desenne S, Duday H, Chenal F, Gailledrat E, Goepfert S, Gorgé O, Gorgues A, Kuhnle G, Lambach F, Lefort A, Mauduit A, Maziere F, Oudry S, Paresys C, Pinard E, Plouin S, Richard I, Roth-Zehner M, Roure R, Thevenet C, Thomas Y, Rottier S, Deguilloux MF, Pruvost M. Origin and mobility of Iron Age Gaulish groups in present-day France revealed through archaeogenomics. iScience 2022; 25:104094. [PMID: 35402880 PMCID: PMC8983337 DOI: 10.1016/j.isci.2022.104094] [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: 12/14/2021] [Revised: 02/17/2022] [Accepted: 03/13/2022] [Indexed: 11/17/2022] Open
Abstract
The Iron Age period occupies an important place in French history because the Gauls are regularly presented as the direct ancestors of the extant French population. We documented here the genomic diversity of Iron Age communities originating from six French regions. The 49 acquired genomes permitted us to highlight an absence of discontinuity between Bronze Age and Iron Age groups in France, lending support to a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. Genomic analyses revealed strong genetic homogeneity among the regional groups associated with distinct archaeological cultures. This genomic homogenization appears to be linked to individuals' mobility between regions and gene flow with neighbouring groups from England and Spain. Thus, the results globally support a common genomic legacy for the Iron Age population of modern-day France that could be linked to recurrent gene flow between culturally differentiated communities.
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Affiliation(s)
- Claire-Elise Fischer
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
- Corresponding author
| | | | - Isaure Ducoussau
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Ana Arzelier
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Maïté Rivollat
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
- Department of Archaeogenetics, Max Planck Institue for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Frederic Santos
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Hélène Barrand Emam
- ANTEA-Archéologie, Habsheim, France
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
| | - Alexandre Bertaud
- UMR-5607 Ausonius, Université Bordeaux Montaigne, Maison de l’Archéologie, 8 Esplanade des Antilles, 33600 Pessac, France
| | - Alexandre Beylier
- Service Archéologie Sète Agglopôle Mediterranée, 34110 Frontignan, France
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Elsa Ciesielski
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Bernard Dedet
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Sophie Desenne
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 8215 Trajectoires, CNRS, Université Paris 1 Pantheon Sorbonne, 92023 Nanterre, France
| | - Henri Duday
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Fanny Chenal
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
| | - Eric Gailledrat
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Sébastien Goepfert
- ANTEA-Archéologie, Habsheim, France
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
| | - Olivier Gorgé
- Institut de Recherche Biomédicale des Armées, Place Général Valérie André, 91220 Brétigny-sur-Orge, France
| | - Alexis Gorgues
- UMR-5607 Ausonius, Université Bordeaux Montaigne, Maison de l’Archéologie, 8 Esplanade des Antilles, 33600 Pessac, France
| | - Gertrud Kuhnle
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart Referat 84.2, Operative Archäologie Dienstsitz Freiburg Günterstalstraße 67, 79100 Freiburg im Breisgau, Germany
| | - François Lambach
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Anthony Lefort
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
| | | | - Florent Maziere
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
| | - Sophie Oudry
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR-7268 ADES, CNRS, Université Aix-Marseille, EFS, 13015 Marseille, France
| | - Cécile Paresys
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 7264 CEPAM, CNRS Université Nice Sophia Antipolis, 06357 Nice Cedex 4, France
| | - Estelle Pinard
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 8215 Trajectoires, CNRS, Université Paris 1 Pantheon Sorbonne, 92023 Nanterre, France
| | - Suzanne Plouin
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
| | - Isabelle Richard
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 7264 CEPAM, CNRS Université Nice Sophia Antipolis, 06357 Nice Cedex 4, France
| | - Muriel Roth-Zehner
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
- Archéologie Alsace, 11 Rue Champollion, 67600 Sélestat, France
| | - Réjane Roure
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Corinne Thevenet
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 8215 Trajectoires, CNRS, Université Paris 1 Pantheon Sorbonne, 92023 Nanterre, France
| | - Yohann Thomas
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
| | - Stéphane Rottier
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | | | - Mélanie Pruvost
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
- Corresponding author
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24
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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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25
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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:msac014. [PMID: 35038748 PMCID: PMC8826970 DOI: 10.1093/molbev/msac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [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, Padova, Italy
| | - Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Biology-Genetics, University of Bari, Bari, Italy
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Ludovica Molinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cinzia Scaggion
- Department of Geosciences, University of Padua, Padova, Italy
| | - Nicola Carrara
- Anthropology Museum, University of Padova, Padova, Italy
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Mait Metspalu
- 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, Cambridge, United Kingdom
| | - Luca Pagani
- Department of Biology, University of Padua, Padova, Italy
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
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26
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Mathieson I, Terhorst J. Direct detection of natural selection in Bronze Age Britain. Genome Res 2022; 32:2057-2067. [PMID: 36316157 PMCID: PMC9808619 DOI: 10.1101/gr.276862.122] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/29/2022] [Indexed: 11/04/2022]
Abstract
We developed a novel method for efficiently estimating time-varying selection coefficients from genome-wide ancient DNA data. In simulations, our method accurately recovers selective trajectories and is robust to misspecification of population size. We applied it to a large data set of ancient and present-day human genomes from Britain and identified seven loci with genome-wide significant evidence of selection in the past 4500 yr. Almost all of them can be related to increased vitamin D or calcium levels, suggesting strong selective pressure on these or related phenotypes. However, the strength of selection on individual loci varied substantially over time, suggesting that cultural or environmental factors moderated the genetic response. Of 28 complex anthropometric and metabolic traits, skin pigmentation was the only one with significant evidence of polygenic selection, further underscoring the importance of phenotypes related to vitamin D. Our approach illustrates the power of ancient DNA to characterize selection in human populations and illuminates the recent evolutionary history of Britain.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Jonathan Terhorst
- Department of Statistics, University of Michigan, Ann Arbor, Michigan 48109, USA
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27
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Large-scale migration into Britain during the Middle to Late Bronze Age. Nature 2021; 601:588-594. [PMID: 34937049 DOI: 10.1038/s41586-021-04287-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 11/29/2021] [Indexed: 11/08/2022]
Abstract
Present-day people from England and Wales harbour more ancestry derived from Early European Farmers (EEF) than people of the Early Bronze Age1. To understand this, we generated genome-wide data from 793 individuals, increasing data from the Middle to Late Bronze and Iron Age in Britain by 12-fold, and Western and Central Europe by 3.5-fold. Between 1000 and 875 BC, EEF ancestry increased in southern Britain (England and Wales) but not northern Britain (Scotland) due to incorporation of migrants who arrived at this time and over previous centuries, and who were genetically most similar to ancient individuals from France. These migrants contributed about half the ancestry of Iron Age people of England and Wales, thereby creating a plausible vector for the spread of early Celtic languages into Britain. These patterns are part of a broader trend of EEF ancestry becoming more similar across central and western Europe in the Middle to Late Bronze Age, coincident with archaeological evidence of intensified cultural exchange2-6. There was comparatively less gene flow from continental Europe during the Iron Age, and Britain's independent genetic trajectory is also reflected in the rise of the allele conferring lactase persistence to ~50% by this time compared to ~7% in central Europe where it rose rapidly in frequency only a millennium later. This suggests that dairy products were used in qualitatively different ways in Britain and in central Europe over this period.
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28
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Shirsekar G, Devos J, Latorre SM, Blaha A, Queiroz Dias M, González Hernando A, Lundberg DS, Burbano HA, Fenster CB, Weigel D. Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia. Mol Biol Evol 2021; 38:5328-5344. [PMID: 34499163 PMCID: PMC8662644 DOI: 10.1093/molbev/msab268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.
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Affiliation(s)
- Gautam Shirsekar
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jane Devos
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Andreas Blaha
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | - Derek S Lundberg
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hernán A Burbano
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Charles B Fenster
- Oak Lake Field Station, Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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29
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Stewart A. Bridging the gap: Using biological data from teeth to comment on social identity of archeological populations from early Anglo-Saxon, England. Ann Anat 2021; 240:151876. [PMID: 34890784 DOI: 10.1016/j.aanat.2021.151876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Revised: 11/08/2021] [Accepted: 11/24/2021] [Indexed: 11/30/2022]
Abstract
Human teeth are storytellers, in that, through analysis of their size and shape osteoarchaeologists are able to 'talk' to the dead and translate biological data into social meaning. This concept has been explored in parts of the world through investigations of biological similarity and kinship, but few have focused in depth on early medieval populations who emphasized the importance of family and kinship. This paper presents the results from four early Anglo-Saxon cemeteries which highlight the utility of dental metrics in identifying biological similarity within the skeletal assemblages. 5988 mesiodistal and buccolingual measurements were recorded from the identifiable permanent dentition of adult individuals from early Anglo-Saxon cemeteries in the UK counties of Cambridgeshire and Kent. Results from statistical hierarchical cluster analysis of dental metric data revealed that it was possible to identify individuals within the cemetery sites that were more similar to one another according to their dental metrics. This similarity was not attributed statistically to biological sex or shared familial environment, as similarity between individuals could be found between males and females and few significant differences were found across the sites sampled. It was found that tooth metrics provided a meaningful biological dataset from which current theories regarding the identity of Anglo-Saxon individuals and families could be refined and improved. These types of data are useful as building blocks which help to bridge the gap between social constructs and human skeletal remains in order to substantiate interpretations about past populations in more significant ways. This work supports the need for multidisciplinary approaches to bioarchaeological investigations of past people while highlighting the utility of human dentition to enhance such areas of study.
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30
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Cox SL, Moots HM, Stock JT, Shbat A, Bitarello BD, Nicklisch N, Alt KW, Haak W, Rosenstock E, Ruff CB, Mathieson I. Predicting skeletal stature using ancient
DNA. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2021. [PMCID: PMC9298243 DOI: 10.1002/ajpa.24426] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Samantha L. Cox
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
- Physical Anthropology Section, Penn Museum University of Pennsylvania Philadelphia Pennsylvania USA
| | - Hannah M. Moots
- Department of Anthropology Stanford University Stanford California USA
| | - Jay T. Stock
- Department of Anthropology Western University London Ontario Canada
- Department of Archaeology Max Planck Institute for the Science of Human History Jena Germany
| | - Andrej Shbat
- Institute of Anatomy, First Faculty of Medicine Charles University Prague Czech Republic
| | - Bárbara D. Bitarello
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History Danube Private University Krems Austria
| | - Kurt W. Alt
- Center of Natural and Cultural Human History Danube Private University Krems Austria
| | - Wolfgang Haak
- Department of Archaeogenetics Max Planck Institute for the Science of Human History Jena Germany
| | - Eva Rosenstock
- Bonn Center for ArchaeoSciences Institut für Archäologie und Kulturanthropologie, Universität Bonn Bonn Germany
| | - Christopher B. Ruff
- Center for Functional Anatomy and Evolution Johns Hopkins University School of Medicine Baltimore Maryland USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine University of Pennsylvania Philadelphia Pennsylvania USA
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31
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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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32
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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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33
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Freilich S, Ringbauer H, Los D, Novak M, Pavičić DT, Schiffels S, Pinhasi R. Reconstructing genetic histories and social organisation in Neolithic and Bronze Age Croatia. Sci Rep 2021; 11:16729. [PMID: 34408163 PMCID: PMC8373892 DOI: 10.1038/s41598-021-94932-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 07/13/2021] [Indexed: 02/07/2023] Open
Abstract
Ancient DNA studies have revealed how human migrations from the Neolithic to the Bronze Age transformed the social and genetic structure of European societies. Present-day Croatia lies at the heart of ancient migration routes through Europe, yet our knowledge about social and genetic processes here remains sparse. To shed light on these questions, we report new whole-genome data for 28 individuals dated to between ~ 4700 BCE-400 CE from two sites in present-day eastern Croatia. In the Middle Neolithic we evidence first cousin mating practices and strong genetic continuity from the Early Neolithic. In the Middle Bronze Age community that we studied, we find multiple closely related males suggesting a patrilocal social organisation. We also find in that community an unexpected genetic ancestry profile distinct from individuals found at contemporaneous sites in the region, due to the addition of hunter-gatherer-related ancestry. These findings support archaeological evidence for contacts with communities further north in the Carpathian Basin. Finally, an individual dated to Roman times exhibits an ancestry profile that is broadly present in the region today, adding an important data point to the substantial shift in ancestry that occurred in the region between the Bronze Age and today.
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Affiliation(s)
- Suzanne Freilich
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria.
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
| | | | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, 10000, Zagreb, Croatia
| | | | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1090, Vienna, Austria.
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34
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Gelabert P, Sawyer S, Bergström A, Margaryan A, Collin TC, Meshveliani T, Belfer-Cohen A, Lordkipanidze D, Jakeli N, Matskevich Z, Bar-Oz G, Fernandes DM, Cheronet O, Özdoğan KT, Oberreiter V, Feeney RNM, Stahlschmidt MC, Skoglund P, Pinhasi R. Genome-scale sequencing and analysis of human, wolf, and bison DNA from 25,000-year-old sediment. Curr Biol 2021; 31:3564-3574.e9. [PMID: 34256019 PMCID: PMC8409484 DOI: 10.1016/j.cub.2021.06.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 04/23/2021] [Accepted: 06/09/2021] [Indexed: 01/07/2023]
Abstract
Cave sediments have been shown to preserve ancient DNA but so far have not yielded the genome-scale information of skeletal remains. We retrieved and analyzed human and mammalian nuclear and mitochondrial environmental "shotgun" genomes from a single 25,000-year-old Upper Paleolithic sediment sample from Satsurblia cave, western Georgia:first, a human environmental genome with substantial basal Eurasian ancestry, which was an ancestral component of the majority of post-Ice Age people in the Near East, North Africa, and parts of Europe; second, a wolf environmental genome that is basal to extant Eurasian wolves and dogs and represents a previously unknown, likely extinct, Caucasian lineage; and third, a European bison environmental genome that is basal to present-day populations, suggesting that population structure has been substantially reshaped since the Last Glacial Maximum. Our results provide new insights into the Late Pleistocene genetic histories of these three species and demonstrate that direct shotgun sequencing of sediment DNA, without target enrichment methods, can yield genome-wide data informative of ancestry and phylogenetic relationships.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
| | - Susanna Sawyer
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anders Bergström
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ashot Margaryan
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Thomas C Collin
- School of Medicine, University College Dublin, Dublin, Ireland
| | - Tengiz Meshveliani
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Anna Belfer-Cohen
- Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - David Lordkipanidze
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | - Nino Jakeli
- Georgian National Museum, Institute of Paleoanthropology and Paleobiology, Tbilisi, Georgia
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kadir T Özdoğan
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Victoria Oberreiter
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | | | - Mareike C Stahlschmidt
- Department of Human Evolution, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, London, UK.
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.
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35
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Plomp KA, Dobney K, Collard M. A 3D basicranial shape-based assessment of local and continental northwest European ancestry among 5th to 9th century CE Anglo-Saxons. PLoS One 2021; 16:e0252477. [PMID: 34161340 PMCID: PMC8221467 DOI: 10.1371/journal.pone.0252477] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Accepted: 05/14/2021] [Indexed: 12/05/2022] Open
Abstract
The settlement of Great Britain by Germanic-speaking people from continental northwest Europe in the Early Medieval period (early 5th to mid 11th centuries CE) has long been recognised as an important event, but uncertainty remains about the number of settlers and the nature of their relationship with the preexisting inhabitants of the island. In the study reported here, we sought to shed light on these issues by using 3D shape analysis techniques to compare the cranial bases of Anglo-Saxon skeletons to those of skeletons from Great Britain that pre-date the Early Medieval period and skeletons from Denmark that date to the Iron Age. Analyses that focused on Early Anglo-Saxon skeletons indicated that between two-thirds and three-quarters of Anglo-Saxon individuals were of continental northwest Europe ancestry, while between a quarter and one-third were of local ancestry. In contrast, analyses that focused on Middle Anglo-Saxon skeletons suggested that 50–70% were of local ancestry, while 30–50% were of continental northwest Europe ancestry. Our study suggests, therefore, that ancestry in Early Medieval Britain was similar to what it is today—mixed and mutable.
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Affiliation(s)
- Kimberly A. Plomp
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Archaeology, Classics, Egyptology, University of Liverpool, Liverpool, United Kingdom
- * E-mail: (KAP); (MC)
| | - Keith Dobney
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Archaeology, Classics, Egyptology, University of Liverpool, Liverpool, United Kingdom
- School of Historical and Philosophical Inquiry, University of Sydney, Sydney, NSW, Australia
| | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail: (KAP); (MC)
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36
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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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37
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Plomp KA, Gestsdóttir H, Dobney K, Price N, Collard M. The composition of the founding population of Iceland: A new perspective from 3D analyses of basicranial shape. PLoS One 2021; 16:e0246059. [PMID: 33556115 PMCID: PMC7870008 DOI: 10.1371/journal.pone.0246059] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 01/12/2021] [Indexed: 11/18/2022] Open
Abstract
The settlement of Iceland in the Viking Age has been the focus of much research, but the composition of the founding population remains the subject of debate. Some lines of evidence suggest that almost all the founding population were Scandinavian, while others indicate a mix of Scandinavians and people of Scottish and Irish ancestry. To explore this issue further, we used three-dimensional techniques to compare the basicrania of skeletons from archaeological sites in Iceland, Scandinavia, and the British Isles. Our analyses yielded two main results. One was that the founding population likely consisted of roughly equal numbers of Scandinavians and people from the British Isles. The other was that the immigrants who originated from the British Isles included individuals of southern British ancestry as well as individuals of Scottish and Irish ancestry. The first of these findings is consistent with the results of recent analyses of modern and ancient DNA, while the second is novel. Our study, therefore, strengthens the idea that the founding population was a mix of Scandinavians and people from the British Isles, but also raises a new possibility regarding the regions from which the settlers originated.
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Affiliation(s)
- Kimberly A. Plomp
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Archaeology, Classics, and Egyptology, University of Liverpool, Liverpool, United Kingdom
| | | | - Keith Dobney
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- Department of Archaeology, Classics, and Egyptology, University of Liverpool, Liverpool, United Kingdom
- School of Historical and Philosophical Inquiry, University of Sydney, Sydney, NSW, Australia
- Department of Archaeology, University of Aberdeen, Aberdeen, United Kingdom
| | - Neil Price
- Department of Archaeology, University of Aberdeen, Aberdeen, United Kingdom
- Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
| | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Columbia, Canada
- * E-mail:
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38
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Feuerborn TR, Palkopoulou E, van der Valk T, von Seth J, Munters AR, Pečnerová P, Dehasque M, Ureña I, Ersmark E, Lagerholm VK, Krzewińska M, Rodríguez-Varela R, Götherström A, Dalén L, Díez-Del-Molino D. Competitive mapping allows for the identification and exclusion of human DNA contamination in ancient faunal genomic datasets. BMC Genomics 2020; 21:844. [PMID: 33256612 PMCID: PMC7708127 DOI: 10.1186/s12864-020-07229-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Accepted: 11/16/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND After over a decade of developments in field collection, laboratory methods and advances in high-throughput sequencing, contamination remains a key issue in ancient DNA research. Currently, human and microbial contaminant DNA still impose challenges on cost-effective sequencing and accurate interpretation of ancient DNA data. RESULTS Here we investigate whether human contaminating DNA can be found in ancient faunal sequencing datasets. We identify variable levels of human contamination, which persists even after the sequence reads have been mapped to the faunal reference genomes. This contamination has the potential to affect a range of downstream analyses. CONCLUSIONS We propose a fast and simple method, based on competitive mapping, which allows identifying and removing human contamination from ancient faunal DNA datasets with limited losses of true ancient data. This method could represent an important tool for the ancient DNA field.
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Affiliation(s)
- Tatiana R Feuerborn
- Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Centre for Palaeogenetics, Stockholm, Sweden.
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
| | - Tom van der Valk
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Johanna von Seth
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, Uppsala University, Uppsala, Sweden
| | | | - Marianne Dehasque
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - Irene Ureña
- Department of Animal Breeding, INIA, Madrid, Spain
| | - Erik Ersmark
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Ricardo Rodríguez-Varela
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Zoology, Stockholm University, Stockholm, Sweden
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
- Centre for Palaeogenetics, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
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39
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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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40
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Martiniano R, Garrison E, Jones ER, Manica A, Durbin R. Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graph. Genome Biol 2020; 21:250. [PMID: 32943086 PMCID: PMC7499850 DOI: 10.1186/s13059-020-02160-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Accepted: 08/27/2020] [Indexed: 01/11/2023] Open
Abstract
BACKGROUND During the last decade, the analysis of ancient DNA (aDNA) sequence has become a powerful tool for the study of past human populations. However, the degraded nature of aDNA means that aDNA molecules are short and frequently mutated by post-mortem chemical modifications. These features decrease read mapping accuracy and increase reference bias, in which reads containing non-reference alleles are less likely to be mapped than those containing reference alleles. Alternative approaches have been developed to replace the linear reference with a variation graph which includes known alternative variants at each genetic locus. Here, we evaluate the use of variation graph software vg to avoid reference bias for aDNA and compare with existing methods. RESULTS We use vg to align simulated and real aDNA samples to a variation graph containing 1000 Genome Project variants and compare with the same data aligned with bwa to the human linear reference genome. Using vg leads to a balanced allelic representation at polymorphic sites, effectively removing reference bias, and more sensitive variant detection in comparison with bwa, especially for insertions and deletions (indels). Alternative approaches that use relaxed bwa parameter settings or filter bwa alignments can also reduce bias but can have lower sensitivity than vg, particularly for indels. CONCLUSIONS Our findings demonstrate that aligning aDNA sequences to variation graphs effectively mitigates the impact of reference bias when analyzing aDNA, while retaining mapping sensitivity and allowing detection of variation, in particular indel variation, that was previously missed.
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Affiliation(s)
- Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, CB3 0DH UK
| | - Erik Garrison
- Wellcome Sanger Institute, Cambridge, CB10 1SA UK
- Genomics Institute, University of California, Santa Cruz, CA 95064 USA
| | - Eppie R. Jones
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ UK
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge, CB2 3EJ UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, CB3 0DH UK
- Wellcome Sanger Institute, Cambridge, CB10 1SA UK
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41
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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: 76] [Impact Index Per Article: 19.0] [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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42
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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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43
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Barquera R, Krause J. An ancient view on host pathogen interaction across time and space. Curr Opin Immunol 2020; 65:65-69. [PMID: 32603999 DOI: 10.1016/j.coi.2020.05.004] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 05/18/2020] [Indexed: 11/30/2022]
Abstract
The ancient DNA revolution provided diverse fields with an unprecedented opportunity to look back into the past and shed light on research aspects that were until now subject to speculation and inference from modern data. In particular enrichment methods that allow the targeted retrieval of millions of SNP positions from ancient human genomes, or even complete bacterial and viral genomes have the potential to revolutionize our understanding of host pathogen interactions. Ancient DNA combined with new bioinformatic tools now even allows actual allele calling for immunogenetic systems such as Human Leukocyte Antigen (HLA) across time and space. The coming years will provide us with frequency data of human immunity genes, such as HLA, as well as genome wide data of ancient pathogens from many time periods of human history, and will therefore provide us with a dynamic view on historical human adaptation to pathogen exposure on a population wide scale.
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Affiliation(s)
- Rodrigo Barquera
- Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745, Jena, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History (MPI-SHH), Kahlaische Str. 10, 07745, Jena, Germany.
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44
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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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45
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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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46
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de Boer E, Yang MA, Kawagoe A, Barnes GL. Japan considered from the hypothesis of farmer/language spread. EVOLUTIONARY HUMAN SCIENCES 2020; 2:e13. [PMID: 37588377 PMCID: PMC10427481 DOI: 10.1017/ehs.2020.7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Formally, the Farming/Language Dispersal hypothesis as applied to Japan relates to the introduction of agriculture and spread of the Japanese language (between ca. 500 BC-AD 800). We review current data from genetics, archaeology, and linguistics in relation to this hypothesis. However, evidence bases for these disciplines are drawn from different periods. Genetic data have primarily been sampled from present-day Japanese and prehistoric Jōmon peoples (14,000-300 BC), preceding the introduction of rice agriculture. The best archaeological evidence for agriculture comes from western Japan during the Yayoi period (ca. 900 BC-AD 250), but little is known about northeastern Japan, which is a focal point here. And despite considerable hypothesizing about prehistoric language, the spread of historic languages/ dialects through the islands is more accessible but difficult to relate to prehistory. Though the lack of Yayoi skeletal material available for DNA analysis greatly inhibits direct study of how the pre-agricultural Jōmon peoples interacted with rice agriculturalists, our review of Jōmon genetics sets the stage for further research into their relationships. Modern linguistic research plays an unexpected role in bringing Izumo (Shimane Prefecture) and the Japan Sea coast into consideration in the populating of northeastern Honshu by agriculturalists beyond the Kantō region.
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Affiliation(s)
- Elisabeth de Boer
- Faculty of East Asian Studies, Ruhr-Universität Bochum, Bochum, Germany
| | - Melinda A. Yang
- Department of Biology, University of Richmond, Richmond, Virginia, USA
| | - Aileen Kawagoe
- Department of Social Studies, New International School of Japan, Tokyo, Japan
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47
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Mapping co-ancestry connections between the genome of a Medieval individual and modern Europeans. Sci Rep 2020; 10:6843. [PMID: 32321996 PMCID: PMC7176696 DOI: 10.1038/s41598-020-64007-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 04/06/2020] [Indexed: 11/08/2022] Open
Abstract
Historical genetic links among similar populations can be difficult to establish. Identity by descent (IBD) analyses find genomic blocks that represent direct genealogical relationships among individuals. However, this method has rarely been applied to ancient genomes because IBD stretches are progressively fragmented by recombination and thus not recognizable after few tens of generations. To explore such genealogical relationships, we estimated long IBD blocks among modern Europeans, generating networks to uncover the genetic structures. We found that Basques, Sardinians, Icelanders and Orcadians form, each of them, highly intraconnected sub-clusters in a European network, indicating dense genealogical links within small, isolated populations. We also exposed individual genealogical links -such as the connection between one Basque and one Icelandic individual- that cannot be uncovered with other, widely used population genetics methods such as PCA or ADMIXTURE. Moreover, using ancient DNA technology we sequenced a Late Medieval individual (Barcelona, Spain) to high genomic coverage and identified IBD blocks shared between her and modern Europeans. The Medieval IBD blocks are statistically overrepresented only in modern Spaniards, which is the geographically closest population. This approach can be used to produce a fine-scale reflection of shared ancestry across different populations of the world, offering a direct genetic link from the past to the present.
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Wang K, Mathieson I, O’Connell J, Schiffels S. Tracking human population structure through time from whole genome sequences. PLoS Genet 2020; 16:e1008552. [PMID: 32150539 PMCID: PMC7082067 DOI: 10.1371/journal.pgen.1008552] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 03/19/2020] [Accepted: 12/04/2019] [Indexed: 11/18/2022] Open
Abstract
The genetic diversity of humans, like many species, has been shaped by a complex pattern of population separations followed by isolation and subsequent admixture. This pattern, reaching at least as far back as the appearance of our species in the paleontological record, has left its traces in our genomes. Reconstructing a population's history from these traces is a challenging problem. Here we present a novel approach based on the Multiple Sequentially Markovian Coalescent (MSMC) to analyze the separation history between populations. Our approach, called MSMC-IM, uses an improved implementation of the MSMC (MSMC2) to estimate coalescence rates within and across pairs of populations, and then fits a continuous Isolation-Migration model to these rates to obtain a time-dependent estimate of gene flow. We show, using simulations, that our method can identify complex demographic scenarios involving post-split admixture or archaic introgression. We apply MSMC-IM to whole genome sequences from 15 worldwide populations, tracking the process of human genetic diversification. We detect traces of extremely deep ancestry between some African populations, with around 1% of ancestry dating to divergences older than a million years ago.
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Affiliation(s)
- Ke Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
| | - Jared O’Connell
- 23andMe Inc., Mountain View, California, United States of America
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
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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: 65] [Impact Index Per Article: 16.3] [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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Albers PK, McVean G. Dating genomic variants and shared ancestry in population-scale sequencing data. PLoS Biol 2020; 18:e3000586. [PMID: 31951611 PMCID: PMC6992231 DOI: 10.1371/journal.pbio.3000586] [Citation(s) in RCA: 93] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Revised: 01/30/2020] [Accepted: 01/02/2020] [Indexed: 12/31/2022] Open
Abstract
The origin and fate of new mutations within species is the fundamental process underlying evolution. However, while much attention has been focused on characterizing the presence, frequency, and phenotypic impact of genetic variation, the evolutionary histories of most variants are largely unexplored. We have developed a nonparametric approach for estimating the date of origin of genetic variants in large-scale sequencing data sets. The accuracy and robustness of the approach is demonstrated through simulation. Using data from two publicly available human genomic diversity resources, we estimated the age of more than 45 million single-nucleotide polymorphisms (SNPs) in the human genome and release the Atlas of Variant Age as a public online database. We characterize the relationship between variant age and frequency in different geographical regions and demonstrate the value of age information in interpreting variants of functional and selective importance. Finally, we use allele age estimates to power a rapid approach for inferring the ancestry shared between individual genomes and to quantify genealogical relationships at different points in the past, as well as to describe and explore the evolutionary history of modern human populations.
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Affiliation(s)
- Patrick K. Albers
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
- * E-mail:
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, United Kingdom
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