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Alves I, Giemza J, Blum MGB, Bernhardsson C, Chatel S, Karakachoff M, Saint Pierre A, Herzig AF, Olaso R, Monteil M, Gallien V, Cabot E, Svensson E, Bacq D, Baron E, Berthelier C, Besse C, Blanché H, Bocher O, Boland A, Bonnaud S, Charpentier E, Dandine-Roulland C, Férec C, Fruchet C, Lecointe S, Le Floch E, Ludwig TE, Marenne G, Meyer V, Quellery E, Racimo F, Rouault K, Sandron F, Schott JJ, Velo-Suarez L, Violleau J, Willerslev E, Coativy Y, Jézéquel M, Le Bris D, Nicolas C, Pailler Y, Goldberg M, Zins M, Le Marec H, Jakobsson M, Darlu P, Génin E, Deleuze JF, Redon R, Dina C. Human genetic structure in Northwest France provides new insights into West European historical demography. Nat Commun 2024; 15:6710. [PMID: 39112481 PMCID: PMC11306750 DOI: 10.1038/s41467-024-51087-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 07/29/2024] [Indexed: 08/10/2024] Open
Abstract
The demographical history of France remains largely understudied despite its central role toward understanding modern population structure across Western Europe. Here, by exploring publicly available Europe-wide genotype datasets together with the genomes of 3234 present-day and six newly sequenced medieval individuals from Northern France, we found extensive fine-scale population structure across Brittany and the downstream Loire basin and increased population differentiation between the northern and southern sides of the river Loire, associated with higher proportions of steppe vs. Neolithic-related ancestry. We also found increased allele sharing between individuals from Western Brittany and those associated with the Bell Beaker complex. Our results emphasise the need for investigating local populations to better understand the distribution of rare (putatively deleterious) variants across space and the importance of common genetic legacy in understanding the sharing of disease-related alleles between Brittany and people from western Britain and Ireland.
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Affiliation(s)
- Isabel Alves
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
- Université de Strasbourg, CNRS, GMGM, Strasbourg, France
| | - Joanna Giemza
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Michael G B Blum
- TIMC-IMAG, UMR 5525 CNRS, Univ. Grenoble Alpes, Grenoble, France
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, Uppsala University, Uppsala, Sweden
| | - Stéphanie Chatel
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Matilde Karakachoff
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
- Nantes Université, CHU Nantes, Pôle Hospitalo-Universitaire 11: Santé Publique, Clinique des données, INSERMCIC 1413, Nantes, France
| | | | | | - Robert Olaso
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
- Labex GenMed, Evry, France
| | - Martial Monteil
- Nantes Université, CNRS, Ministère de la Culture, CReAAH, LARA, Nantes, France
| | - Véronique Gallien
- INRAP - Institut national de recherches archéologiques préventives, Paris, France
- CEPAM UMR7264 - Culture et Environnements, Préhistoire, Antiquité, Moyen-Age, Nice, France
| | - Elodie Cabot
- INRAP - Institut national de recherches archéologiques préventives, Paris, France
- Anthropologie Bio-Culturelle, Droit, Ethique et Santé, Faculté de Médecine Site Nord, Marseille, France
| | - Emma Svensson
- Department of Organismal Biology, Human Evolution, Uppsala University, Uppsala, Sweden
| | - Delphine Bacq
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
- Labex GenMed, Evry, France
| | - Estelle Baron
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Charlotte Berthelier
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Céline Besse
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
- Labex GenMed, Evry, France
| | | | - Ozvan Bocher
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
| | - Anne Boland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
- Labex GenMed, Evry, France
| | - Stéphanie Bonnaud
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Eric Charpentier
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Claire Dandine-Roulland
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
- Labex GenMed, Evry, France
| | - Claude Férec
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHRU Brest, Brest, France
| | - Christine Fruchet
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Simon Lecointe
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Edith Le Floch
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
- Labex GenMed, Evry, France
| | - Thomas E Ludwig
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHRU Brest, Brest, France
| | | | - Vincent Meyer
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
| | - Elisabeth Quellery
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Fernando Racimo
- Section for Molecular Ecology and Evolution, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karen Rouault
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHRU Brest, Brest, France
| | - Florian Sandron
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
- Labex GenMed, Evry, France
| | - Jean-Jacques Schott
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | | | - Jade Violleau
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Eske Willerslev
- Lundbeck GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Yves Coativy
- Centre de Recherche Bretonne et Celtique, UR 4451, Université de Bretagne Occidentale, Brest, France
| | - Mael Jézéquel
- Centre de Recherche Bretonne et Celtique, UR 4451, Université de Bretagne Occidentale, Brest, France
| | - Daniel Le Bris
- Centre de Recherche Bretonne et Celtique, UR 4451, Université de Bretagne Occidentale, Brest, France
| | - Clément Nicolas
- CNRS UMR 8215 Trajectoires, Université Paris 1 Panthéon-Sorbonne, Centre Malher, 9 rue Malher, Paris, France
| | - Yvan Pailler
- CPJ ArMeRIE UBO, UMR 6554 LETG, CNRS, Université de Brest, Université de Nantes, Université de Rennes 2, Institut Universitaire Européen de la Mer, Plouzané, France
| | - Marcel Goldberg
- Université Paris Cité, "Population-based Cohorts Unit", INSERM, Paris Saclay University, UVSQ, Paris, France
| | - Marie Zins
- Université Paris Cité, "Population-based Cohorts Unit", INSERM, Paris Saclay University, UVSQ, Paris, France
| | - Hervé Le Marec
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Uppsala University, Uppsala, Sweden
| | - Pierre Darlu
- UMR 7206 Eco-anthropologie, Musée de l'Homme, MNHN, CNRS, Université de Paris Cité, Paris, France
| | - Emmanuelle Génin
- Univ Brest, Inserm, EFS, UMR 1078, GGB, Brest, France
- CHRU Brest, Brest, France
| | - Jean-François Deleuze
- Université Paris-Saclay, CEA, Centre National de Recherche en Génomique Humaine (CNRGH), Evry, France
- Labex GenMed, Evry, France
- Fondation Jean Dausset, CEPH, Paris, France
| | - Richard Redon
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France.
| | - Christian Dina
- Nantes Université, CHU Nantes, CNRS, INSERM, l'institut du thorax, Nantes, France.
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Gyuris B, Vyazov L, Türk A, Flegontov P, Szeifert B, Langó P, Mende BG, Csáky V, Chizhevskiy AA, Gazimzyanov IR, Khokhlov AA, Kolonskikh AG, Matveeva NP, Ruslanova RR, Rykun MP, Sitdikov A, Volkova EV, Botalov SG, Bugrov DG, Grudochko IV, Komar O, Krasnoperov AA, Poshekhonova OE, Chikunova I, Sungatov F, Stashenkov DA, Zubov S, Zelenkov AS, Ringbauer H, Cheronet O, Pinhasi R, Akbari A, Rohland N, Mallick S, Reich D, Szécsényi-Nagy A. Long shared haplotypes identify the Southern Urals as a primary source for the 10th century Hungarians. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.21.599526. [PMID: 39091721 PMCID: PMC11291037 DOI: 10.1101/2024.07.21.599526] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
During the Hungarian Conquest in the 10th century CE, the early medieval Magyars, a group of mounted warriors from Eastern Europe, settled in the Carpathian Basin. They likely introduced the Hungarian language to this new settlement area, during an event documented by both written sources and archaeological evidence. Previous archaeogenetic research identified the newcomers as migrants from the Eurasian steppe. However, genome-wide ancient DNA from putative source populations has not been available to test alternative theories of their precise source. We generated genome-wide ancient DNA data for 131 individuals from candidate archaeological contexts in the Circum-Uralic region in present-day Russia. Our results tightly link the Magyars to people of the Early Medieval Karayakupovo archaeological horizon on both the European and Asian sides of the southern Urals. Our analyes show that ancestors of the people of the Karayakupovo archaeological horizon were established in the Southern Urals by the Iron Age and that their descendants persisted locally in the Volga-Kama region until at least the 14th century.
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Affiliation(s)
- Balázs Gyuris
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
- Doctoral School of Biology, ELTE Eötvös Loránd University; Budapest, Hungary
| | - Leonid Vyazov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava; Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
| | - Attila Türk
- Department of Archaeology, Faculty of Humanities and Social Sciences, Pázmány Péter Catholic University; Budapest, Hungary
- Hungarian Prehistory Research group, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava; Ostrava, Czechia
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
| | - Bea Szeifert
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Péter Langó
- Institute of Archaeology, HUN-REN Research Centre for the Humanities, Hungarian Research Network (HUN-REN); Budapest, Hungary
- Department of Archaeology, Faculty of Humanities and Social Sciences, Pázmány Péter Catholic University; Budapest, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Veronika Csáky
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
| | - Andrey A Chizhevskiy
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
| | | | | | - Aleksandr G Kolonskikh
- R.G. Kuzeev Institute of Ethnological Studies, Ufa Federal Research Scientific Center of Russian Academy of Sciences; Ufa, Republic of Bashkortostan, Russia
| | | | - Rida R Ruslanova
- National Museum of the Republic of Bashkortostan; Ufa, Republic of Bashkortostan, Russia
| | | | - Ayrat Sitdikov
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
- Department of Archaeology, Kazan Federal University, Kazan, Republic of Tatarstan, Russia
| | - Elizaveta V Volkova
- Institute of Archaeology of the Academy of Sciences of the Republic of Tatarstan; Kazan, Republic of Tatarstan, Russia
| | - Sergei G Botalov
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences; Chelyabinsk, Russia
| | - Dmitriy G Bugrov
- National Museum of Tatarstan Republic; Kazan, Republic of Tatarstan, Russia
| | - Ivan V Grudochko
- South Ural Branch of the Institute of History and Archeology, Ural Branch of the Russian Academy of Sciences; Chelyabinsk, Russia
| | - Oleksii Komar
- Institute of Archaeology, National Academy of Sciences of Ukraine; Kyiv, Ukraine
| | - Alexander A Krasnoperov
- Udmurt Institute of History, Language and Literature, Udmurt Federal Research Center, Ural Branch of the Russian Academy of Sciences; Izhevsk, Udmurt Republic, Russia
| | - Olga E Poshekhonova
- Institute of the Problems of Northern Development, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences; Tyumen, Russia
| | - Irina Chikunova
- Institute of the Problems of Northern Development, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences; Tyumen, Russia
| | - Flarit Sungatov
- Institute of History, Language and Literature, Ufa Federal Research Scientific Center of Russian Academy of Sciences; Ufa, Republic of Bashkortostan, Russia
| | - Dmitrii A Stashenkov
- Samara Regional Museum of History and Local Lore named after P. V. Alabin; Samara, Russia
| | - Sergei Zubov
- Research Laboratory of Archeology, Samara National Research University; Samara, Russia
| | | | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology; Leipzig, Germany
| | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna; Vienna, Austria
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; Vienna, Austria
| | - Ali Akbari
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02138, USA
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02138, USA
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02138, USA
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities; Budapest, Hungary
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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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Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. Proc Natl Acad Sci U S A 2024; 121:e2312377121. [PMID: 38363870 PMCID: PMC10907250 DOI: 10.1073/pnas.2312377121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 01/09/2024] [Indexed: 02/18/2024] Open
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 y, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
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Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA95616
- Department of Evolution and Ecology, University of California, Davis, CA95616
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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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Simon A, Coop G. The contribution of gene flow, selection, and genetic drift to five thousand years of human allele frequency change. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.07.11.548607. [PMID: 37503227 PMCID: PMC10370008 DOI: 10.1101/2023.07.11.548607] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
Abstract
Genomic time series from experimental evolution studies and ancient DNA datasets offer us a chance to directly observe the interplay of various evolutionary forces. We show how the genome-wide variance in allele frequency change between two time points can be decomposed into the contributions of gene flow, genetic drift, and linked selection. In closed populations, the contribution of linked selection is identifiable because it creates covariances between time intervals, and genetic drift does not. However, repeated gene flow between populations can also produce directionality in allele frequency change, creating covariances. We show how to accurately separate the fraction of variance in allele frequency change due to admixture and linked selection in a population receiving gene flow. We use two human ancient DNA datasets, spanning around 5,000 years, as time transects to quantify the contributions to the genome-wide variance in allele frequency change. We find that a large fraction of genome-wide change is due to gene flow. In both cases, after correcting for known major gene flow events, we do not observe a signal of genome-wide linked selection. Thus despite the known role of selection in shaping long-term polymorphism levels, and an increasing number of examples of strong selection on single loci and polygenic scores from ancient DNA, it appears to be gene flow and drift, and not selection, that are the main determinants of recent genome-wide allele frequency change. Our approach should be applicable to the growing number of contemporary and ancient temporal population genomics datasets.
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Affiliation(s)
- Alexis Simon
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
| | - Graham Coop
- Center for Population Biology, University of California, Davis, CA 95616
- Department of Evolution and Ecology, University of California, Davis, CA 95616
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9
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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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10
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Olalde I, Carrión P, Mikić I, Rohland N, Mallick S, Lazaridis I, Mah M, Korać M, Golubović S, Petković S, Miladinović-Radmilović N, Vulović D, Alihodžić T, Ash A, Baeta M, Bartík J, Bedić Ž, Bilić M, Bonsall C, Bunčić M, Bužanić D, Carić M, Čataj L, Cvetko M, Drnić I, Dugonjić A, Đukić A, Đukić K, Farkaš Z, Jelínek P, Jovanovic M, Kaić I, Kalafatić H, Krmpotić M, Krznar S, Leleković T, M de Pancorbo M, Matijević V, Milošević Zakić B, Osterholtz AJ, Paige JM, Tresić Pavičić D, Premužić Z, Rajić Šikanjić P, Rapan Papeša A, Paraman L, Sanader M, Radovanović I, Roksandic M, Šefčáková A, Stefanović S, Teschler-Nicola M, Tončinić D, Zagorc B, Callan K, Candilio F, Cheronet O, Fernandes D, Kearns A, Lawson AM, Mandl K, Wagner A, Zalzala F, Zettl A, Tomanović Ž, Keckarević D, Novak M, Harper K, McCormick M, Pinhasi R, Grbić M, Lalueza-Fox C, Reich D. A genetic history of the Balkans from Roman frontier to Slavic migrations. Cell 2023; 186:5472-5485.e9. [PMID: 38065079 PMCID: PMC10752003 DOI: 10.1016/j.cell.2023.10.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Revised: 08/22/2023] [Accepted: 10/18/2023] [Indexed: 12/18/2023]
Abstract
The rise and fall of the Roman Empire was a socio-political process with enormous ramifications for human history. The Middle Danube was a crucial frontier and a crossroads for population and cultural movement. Here, we present genome-wide data from 136 Balkan individuals dated to the 1st millennium CE. Despite extensive militarization and cultural influence, we find little ancestry contribution from peoples of Italic descent. However, we trace a large-scale influx of people of Anatolian ancestry during the Imperial period. Between ∼250 and 550 CE, we detect migrants with ancestry from Central/Northern Europe and the Steppe, confirming that "barbarian" migrations were propelled by ethnically diverse confederations. Following the end of Roman control, we detect the large-scale arrival of individuals who were genetically similar to modern Eastern European Slavic-speaking populations, who contributed 30%-60% of the ancestry of Balkan people, representing one of the largest permanent demographic changes anywhere in Europe during the Migration Period.
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Affiliation(s)
- Iñigo Olalde
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain; Ikerbasque-Basque Foundation of Science, Bilbao, Spain; Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.
| | - Pablo Carrión
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | | | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Mah
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | | | | | | | | | | | | | - Abigail Ash
- Department of Archaeology, Durham University, Durham, UK
| | - Miriam Baeta
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Juraj Bartík
- Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic
| | - Željka Bedić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | | | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, UK
| | - Maja Bunčić
- Archaeological Museum in Zagreb, Zagreb, Croatia
| | - Domagoj Bužanić
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Mario Carić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Lea Čataj
- Division for Archaeological Heritage, Croatian Conservation Institute, Zagreb, Croatia
| | - Mirna Cvetko
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Ivan Drnić
- Archaeological Museum in Zagreb, Zagreb, Croatia
| | | | - Ana Đukić
- Archaeological Museum in Zagreb, Zagreb, Croatia
| | - Ksenija Đukić
- Center of Bone Biology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Zdeněk Farkaš
- Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic
| | - Pavol Jelínek
- Slovak National Museum-Archaeological Museum, Bratislava, Slovak Republic
| | | | - Iva Kaić
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Marijana Krmpotić
- Department for Archaeology, Croatian Conservation Institute, Zagreb, Croatia
| | | | - Tino Leleković
- Archaeology Division, Croatian Academy of Sciences and Arts, Zagreb, Croatia
| | - Marian M de Pancorbo
- BIOMICs Research Group, Department of Zoology and Animal Cell Biology, University of the Basque Country UPV/EHU, Vitoria-Gasteiz, Spain
| | - Vinka Matijević
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Anna J Osterholtz
- Department of Anthropology and Middle Eastern Cultures, Mississippi State University, Starkville, MS, USA
| | - Julianne M Paige
- Department of Anthropology, University of Nevada, Las Vegas, NV, USA
| | | | | | - Petra Rajić Šikanjić
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | | | | | - Mirjana Sanader
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | | | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada
| | - Alena Šefčáková
- Department of Anthropology, Slovak National Museum-Natural History Museum, Bratislava, Slovak Republic
| | - Sofia Stefanović
- Laboratory for Bioarchaeology, Faculty of Philosophy, University of Belgrade, Belgrade, Serbia
| | - Maria Teschler-Nicola
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Department of Anthropology, Natural History Museum Vienna, Vienna, Austria
| | - Domagoj Tončinić
- Faculty of Humanities and Social Sciences, University of Zagreb, Zagreb, Croatia
| | - Brina Zagorc
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Kim Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | | | - Olivia Cheronet
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Research Centre for Anthropology and Health (CIAS), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Aisling Kearns
- Department of Genetics, 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
| | - Kirsten Mandl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Anna Wagner
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Fatma Zalzala
- Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Anna Zettl
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
| | - Željko Tomanović
- Faculty of Biology, University of Belgrade, Belgrade, Serbia; Serbian Academy of Sciences and Arts, Belgrade, Serbia
| | | | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
| | - Kyle Harper
- Department of Classics and Letters, University of Oklahoma, Norman, OK, USA; Santa Fe Institute, Santa Fe, NM, USA
| | - Michael McCormick
- Department of History, Harvard University, Cambridge, MA, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Harvard University, Cambridge, MA, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria; Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
| | - Miodrag Grbić
- Faculty of Biology, University of Belgrade, Belgrade, Serbia; Department of Biology, University of Western Ontario, London, ON, Canada; Department of Agriculture and Food, Universidad de La Rioja, Logroño, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain; Museu de Ciències Naturals de Barcelona, Barcelona, Spain.
| | - David Reich
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA; Department of Genetics, Harvard Medical School, Boston, MA, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA; Broad Institute of MIT and Harvard, Cambridge, MA, USA.
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11
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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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12
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Tretmanis JM, Jay F, Avila-Árcos MC, Huerta-Sanchez E. Simulation-based Benchmarking of Ancient Haplotype Inference for Detecting Population Structure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.28.560049. [PMID: 37808674 PMCID: PMC10557694 DOI: 10.1101/2023.09.28.560049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
Paleogenomic data has informed us about the movements, growth, and relationships of ancient populations. It has also given us context for medically relevant adaptations that appear in present-day humans due to introgression from other hominids, and it continues to help us characterize the evolutionary history of humans. However, ancient DNA (aDNA) presents several practical challenges as various factors such as deamination, high fragmentation, environmental contamination of aDNA, and low amounts of recoverable endogenous DNA, make aDNA recovery and analysis more difficult than modern DNA. Most studies with aDNA leverage only SNP data, and only a few studies have made inferences on human demographic history based on haplotype data, possibly because haplotype estimation (or phasing) has not yet been systematically evaluated in the context of aDNA. Here, we evaluate how the unique challenges of aDNA can impact phasing quality. We also develop a software tool that simulates aDNA taking into account the features of aDNA as well as the evolutionary history of the population. We measured phasing error as a function of aDNA quality and demographic history, and found that low phasing error is achievable even for very ancient individuals (~ 400 generations in the past) as long as contamination and read depth are adequate. Our results show that population splits or bottleneck events occurring between the reference and phased populations affect phasing quality, with bottlenecks resulting in the highest average error rates. Finally, we found that using estimated haplotypes, even if not completely accurate, is superior to using the simulated genotype data when reconstructing changes in population structure after population splits between present-day and ancient populations.
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Affiliation(s)
| | - Flora Jay
- Interdisciplinary Laboratory of Numerical Sciences, Université Paris-Saclay
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13
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Serrano JG, Ordóñez AC, Santana J, Sánchez-Cañadillas E, Arnay M, Rodríguez-Rodríguez A, Morales J, Velasco-Vázquez J, Alberto-Barroso V, Delgado-Darias T, de Mercadal MCC, Hernández JC, Moreno-Benítez MA, Pais J, Ringbauer H, Sikora M, McColl H, Pino-Yanes M, Ferrer MH, Bustamante CD, Fregel R. The genomic history of the indigenous people of the Canary Islands. Nat Commun 2023; 14:4641. [PMID: 37582830 PMCID: PMC10427657 DOI: 10.1038/s41467-023-40198-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 07/17/2023] [Indexed: 08/17/2023] Open
Abstract
The indigenous population of the Canary Islands, which colonized the archipelago around the 3rd century CE, provides both a window into the past of North Africa and a unique model to explore the effects of insularity. We generate genome-wide data from 40 individuals from the seven islands, dated between the 3rd-16rd centuries CE. Along with components already present in Moroccan Neolithic populations, the Canarian natives show signatures related to Bronze Age expansions in Eurasia and trans-Saharan migrations. The lack of gene flow between islands and constant or decreasing effective population sizes suggest that populations were isolated. While some island populations maintained relatively high genetic diversity, with the only detected bottleneck coinciding with the colonization time, other islands with fewer natural resources show the effects of insularity and isolation. Finally, consistent genetic differentiation between eastern and western islands points to a more complex colonization process than previously thought.
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Affiliation(s)
- Javier G Serrano
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Alejandra C Ordóñez
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Jonathan Santana
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Elías Sánchez-Cañadillas
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Matilde Arnay
- Bioanthropology: Paleopathology, Diet and Nutrition in Ancient Populations Group, Department of Prehistory, Anthropology and Ancient History, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | - Amelia Rodríguez-Rodríguez
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Jacob Morales
- Tarha Group, Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | - Javier Velasco-Vázquez
- Servicio de Patrimonio Histórico, Cabildo de Gran Canaria, Las Palmas de Gran Canaria, Las Palmas, Spain
| | | | | | | | - Juan Carlos Hernández
- Museo Arqueológico de La Gomera, San Sebastián de La Gomera, Santa Cruz de Tenerife, Spain
| | | | - Jorge Pais
- Museo Arqueológico Benahoarita, Los Llanos de Aridane, Santa Cruz de Tenerife, Spain
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Maria Pino-Yanes
- Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
- CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Mariano Hernández Ferrer
- Molecular Genetics and Biodiversity Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain
| | | | - Rosa Fregel
- Evolution, Paleogenomics and Population Genetics Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, San Cristóbal de La Laguna, Santa Cruz de Tenerife, Spain.
- Department of Genetics, Stanford University, Stanford, CA, USA.
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14
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Lalueza-Fox C. Across the North Sea and beyond. Trends Genet 2023; 39:240-241. [PMID: 36822963 DOI: 10.1016/j.tig.2023.01.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 01/23/2023] [Indexed: 02/23/2023]
Abstract
Increasing numbers of ancient genomes from the Viking period retrieved across the North Sea regions are revealing a complex layer of genetic ancestries and a past cosmopolitanism that was triggered by different mobility patterns.
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Affiliation(s)
- Carles Lalueza-Fox
- Natural Sciences Museum of Barcelona, Barcelona, Spain; Institute of Evolutionary Biology, Barcelona, Spain.
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15
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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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16
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Estimating human mobility in Holocene Western Eurasia with large-scale ancient genomic data. Proc Natl Acad Sci U S A 2023; 120:e2218375120. [PMID: 36821583 PMCID: PMC9992830 DOI: 10.1073/pnas.2218375120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
The recent increase in openly available ancient human DNA samples allows for large-scale meta-analysis applications. Trans-generational past human mobility is one of the key aspects that ancient genomics can contribute to since changes in genetic ancestry-unlike cultural changes seen in the archaeological record-necessarily reflect movements of people. Here, we present an algorithm for spatiotemporal mapping of genetic profiles, which allow for direct estimates of past human mobility from large ancient genomic datasets. The key idea of the method is to derive a spatial probability surface of genetic similarity for each individual in its respective past. This is achieved by first creating an interpolated ancestry field through space and time based on multivariate statistics and Gaussian process regression and then using this field to map the ancient individuals into space according to their genetic profile. We apply this algorithm to a dataset of 3138 aDNA samples with genome-wide data from Western Eurasia in the last 10,000 y. Finally, we condense this sample-wise record with a simple summary statistic into a diachronic measure of mobility for subregions in Western, Central, and Southern Europe. For regions and periods with sufficient data coverage, our similarity surfaces and mobility estimates show general concordance with previous results and provide a meta-perspective of genetic changes and human mobility.
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17
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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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18
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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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19
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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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20
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Wohns AW, Wong Y, Jeffery B, Akbari A, Mallick S, Pinhasi R, Patterson N, Reich D, Kelleher J, McVean G. A unified genealogy of modern and ancient genomes. Science 2022; 375:eabi8264. [PMID: 35201891 PMCID: PMC10027547 DOI: 10.1126/science.abi8264] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The sequencing of modern and ancient genomes from around the world has revolutionized our understanding of human history and evolution. However, the problem of how best to characterize ancestral relationships from the totality of human genomic variation remains unsolved. Here, we address this challenge with nonparametric methods that enable us to infer a unified genealogy of modern and ancient humans. This compact representation of multiple datasets explores the challenges of missing and erroneous data and uses ancient samples to constrain and date relationships. We demonstrate the power of the method to recover relationships between individuals and populations as well as to identify descendants of ancient samples. Finally, we introduce a simple nonparametric estimator of the geographical location of ancestors that recapitulates key events in human history.
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Affiliation(s)
- Anthony Wilder Wohns
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Yan Wong
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ben Jeffery
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Ali Akbari
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Swapan Mallick
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna; 1090 Vienna, Austria
| | - Nick Patterson
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - David Reich
- Broad Institute of MIT and Harvard; Cambridge, MA 02142, USA
- Department of Human Evolutionary Biology, Harvard University; Cambridge, MA 02138, USA
- Howard Hughes Medical Institute; Boston, MA 02115, USA
- Department of Genetics, Harvard Medical School; Boston, MA 02115, USA
| | - Jerome Kelleher
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
| | - Gil McVean
- Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford; Oxford OX3 7LF, UK
- Corresponding author.
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21
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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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22
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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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23
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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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24
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Britton K, Crowley BE, Bataille CP, Miller JH, Wooller MJ. Silver Linings at the Dawn of a “Golden Age”. Front Ecol Evol 2021. [DOI: 10.3389/fevo.2021.748938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Nearly four decades after the first applications of strontium isotope analyses in archaeology and paleoecology research, it could be said that we are entering a “Golden Age”. Here, we reflect on major past developments and current strengths in strontium isotope research, as well as speculate on future directions. We review (1) the currently limited number of (but much needed) controlled feeding experiments, (2) recent advances in isoscape mapping and spatial assignment, and (3) the strength of multi-proxy approaches (including both the integration of strontium isotopes with other isotope systems and complementary techniques such as ancient DNA analyses). We also explore the integration of strontium isotope research with other types of paleoecological or archaeology data, as well as with evidence and interpretative frameworks from other fields (such as conservation ecology, conservation paleobiology or history). This blending is critical as we seek to advance the field beyond simply distinguishing local or relatively sedentary individuals from those that were non-local or highly mobile. We finish with a call for future research centered on balancing methodological developments and novel applications with critical self-reflection, deeper theoretical considerations and cross-disciplinarity.
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25
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De Angelis F, Veltre V, Romboni M, Di Corcia T, Scano G, Martínez-Labarga C, Catalano P, Rickards O. Ancient genomes from a rural site in Imperial Rome (1 st-3 rd cent. CE): a genetic junction in the Roman Empire. Ann Hum Biol 2021; 48:234-246. [PMID: 34459338 DOI: 10.1080/03014460.2021.1944313] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
BACKGROUND Rome became the prosperous Capital of the Roman Empire through the political and military conquests of neighbouring areas. People were able to move Romeward modifying the Rome area's demographic structure. However, the genomic evidence for the population of one of the broadest Empires in antiquity has been sparse until recently. AIM The genomic analysis of people buried in Quarto Cappello del Prete (QCP) necropolis was carried out to help elucidate the genomic structure of Imperial Rome inhabitants. SUBJECTS AND METHODS We recruited twenty-five individuals from QCP for ancient DNA analysis through whole-genome sequencing. Multiple investigations were carried out to unveil the genetic components featuring in the studied samples and the community's putative demographic structure. RESULTS We generated reliable whole-genome data for 7 samples surviving quality controls. The distribution of Imperial Romans from QCP partly overlaps with present-day Southern Mediterranean and Southern-Near Eastern populations. CONCLUSION The genomic legacy with the south-eastern shores of the Mediterranean Sea and the Central and Western Northern-African coast funerary influence pave the way for considering people buried in QCP as resembling a Punic-derived human group.
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Affiliation(s)
- Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Virginia Veltre
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy.,PhD Program in Evolutionary Biology and Ecology, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Marco Romboni
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Tullia Di Corcia
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Giuseppina Scano
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Cristina Martínez-Labarga
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Paola Catalano
- Former Soprintendenza Speciale Archeologia, Belle Arti e Paesaggio di Roma. Piazza dei Cinquecento, Rome, Italy
| | - Olga Rickards
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome Tor Vergata, Rome, Italy
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26
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Speidel L, Cassidy L, Davies RW, Hellenthal G, Skoglund P, Myers SR. Inferring Population Histories for Ancient Genomes Using Genome-Wide Genealogies. Mol Biol Evol 2021; 38:3497-3511. [PMID: 34129037 PMCID: PMC8383901 DOI: 10.1093/molbev/msab174] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Ancient genomes anchor genealogies in directly observed historical genetic variation and contextualize ancestral lineages with archaeological insights into their geography and cultural associations. However, the majority of ancient genomes are of lower coverage and cannot be directly built into genealogies. Here, we present a fast and scalable method, Colate, the first approach for inferring ancestral relationships through time between low-coverage genomes without requiring phasing or imputation. Our approach leverages sharing patterns of mutations dated using a genealogy to infer coalescence rates. For deeply sequenced ancient genomes, we additionally introduce an extension of the Relate algorithm for joint inference of genealogies incorporating such genomes. Application to 278 present-day and 430 ancient DNA samples of >0.5x mean coverage allows us to identify dynamic population structure and directional gene flow between early farmer and European hunter-gatherer groups. We further show that the previously reported, but still unexplained, increase in the TCC/TTC mutation rate, which is strongest in West Eurasia today, was already present at similar strength and widespread in the Late Glacial Period ~10k-15k years ago, but is not observed in samples >30k years old. It is strongest in Neolithic farmers, and highly correlated with recent coalescence rates between other genomes and a 10,000-year-old Anatolian hunter-gatherer. This suggests gene-flow among ancient peoples postdating the last glacial maximum as widespread and localizes the driver of this mutational signal in both time and geography in that region. Our approach should be widely applicable in future for addressing other evolutionary questions, and in other species.
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Affiliation(s)
- Leo Speidel
- Francis Crick Institute, London, United Kingdom
- Genetics Institute, University College London, London, United Kingdom
| | - Lara Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Republic of Ireland
| | - Robert W Davies
- Department of Statistics, University of Oxford, Oxford, United Kingdom
| | | | | | - Simon R Myers
- Department of Statistics, University of Oxford, Oxford, United Kingdom
- Wellcome Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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27
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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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28
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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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29
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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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30
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Niemann J, Gopalakrishnan S, Yamaguchi N, Ramos-Madrigal J, Wales N, Gilbert MTP, Sinding MHS. Extended survival of Pleistocene Siberian wolves into the early 20th century on the island of Honshū. iScience 2021; 24:101904. [PMID: 33364590 PMCID: PMC7753132 DOI: 10.1016/j.isci.2020.101904] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Revised: 10/30/2020] [Accepted: 12/03/2020] [Indexed: 01/19/2023] Open
Abstract
The Japanese or Honshū wolf was one the most distinct gray wolf subspecies due to its small stature and endemicity to the islands of Honshū, Shikoku, and Kyūshū. Long revered as a guardian of farmers and travellers, it was persecuted from the 17th century following a rabies epidemic, which led to its extinction in the early 20th century. To better understand its evolutionary history, we sequenced the nuclear genome of a 19th century Honshū wolf specimen to an average depth of coverage of 3.7✕. We find Honshū wolves were closely related to a lineage of Siberian wolves that were previously believed to have gone extinct in the Late Pleistocene, thereby extending the survival of this ancient lineage until the early 20th century. We also detected significant gene flow between Japanese dogs and the Honshū wolf, corroborating previous reports on Honshū wolf dog interbreeding. Generated 3.7✕ nuclear genome of the extinct Honshu wolf The Honshū wolf belonged to the lineage of Siberian Pleistocene wolves There was gene flow between Honshū wolves and Japanese dogs
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Affiliation(s)
- Jonas Niemann
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- BioArch, Department of Archaeology, University of York, York, UK
- Corresponding author
| | - Shyam Gopalakrishnan
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nobuyuki Yamaguchi
- Institute of Tropical Biodiversity and Sustainable Development, University Malaysia Terengganu, Kuala Nerus, Terengganu 21030, Malaysia
| | - Jazmín Ramos-Madrigal
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Nathan Wales
- BioArch, Department of Archaeology, University of York, York, UK
| | - M. Thomas P. Gilbert
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- University Museum, NTNU, Trondheim, Norway
| | - Mikkel-Holger S. Sinding
- Section for Evolutionary Genomics, the GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
- Greenland Institute of Natural Resources, Nuuk, Greenland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Corresponding author
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31
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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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32
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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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33
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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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34
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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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35
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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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36
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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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37
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38
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Abstract
Measurements of prehistoric human skeletal remains provide a record of changes in height and other anthropometric traits over time. Often, these changes are interpreted in terms of plastic developmental response to shifts in diet, climate, or other environmental factors. These changes can also be genetic in origin, but, until recently, it has been impossible to separate the effects of genetics and environment. Here, we use ancient DNA to directly estimate genetic changes in phenotypes and to identify changes driven not by genetics, but by environment. We show that changes over the past 35,000 y are largely predicted by genetics but also identify specific shifts that are more likely to be environmentally driven. The relative contributions of genetics and environment to temporal and geographic variation in human height remain largely unknown. Ancient DNA has identified changes in genetic ancestry over time, but it is not clear whether those changes in ancestry are associated with changes in height. Here, we directly test whether changes over the past 38,000 y in European height predicted using DNA from 1,071 ancient individuals are consistent with changes observed in 1,159 skeletal remains from comparable populations. We show that the observed decrease in height between the Early Upper Paleolithic and the Mesolithic is qualitatively predicted by genetics. Similarly, both skeletal and genetic height remained constant between the Mesolithic and Neolithic and increased between the Neolithic and Bronze Age. Sitting height changes much less than standing height—consistent with genetic predictions—although genetics predicts a small post-Neolithic increase that is not observed in skeletal remains. Geographic variation in stature is also qualitatively consistent with genetic predictions, particularly with respect to latitude. Finally, we hypothesize that an observed decrease in genetic heel bone mineral density in the Neolithic reflects adaptation to the decreased mobility indicated by decreased femoral bending strength. This study provides a model for interpreting phenotypic changes predicted from ancient DNA and demonstrates how they can be combined with phenotypic measurements to understand the relative contribution of genetic and developmentally plastic responses to environmental change.
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39
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Harney É, Nayak A, Patterson N, Joglekar P, Mushrif-Tripathy V, Mallick S, Rohland N, Sedig J, Adamski N, Bernardos R, Broomandkhoshbacht N, Culleton BJ, Ferry M, Harper TK, Michel M, Oppenheimer J, Stewardson K, Zhang Z, Harashawaradhana, Bartwal MS, Kumar S, Diyundi SC, Roberts P, Boivin N, Kennett DJ, Thangaraj K, Reich D, Rai N. Ancient DNA from the skeletons of Roopkund Lake reveals Mediterranean migrants in India. Nat Commun 2019; 10:3670. [PMID: 31431628 PMCID: PMC6702210 DOI: 10.1038/s41467-019-11357-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 06/26/2019] [Indexed: 11/24/2022] Open
Abstract
Situated at over 5,000 meters above sea level in the Himalayan Mountains, Roopkund Lake is home to the scattered skeletal remains of several hundred individuals of unknown origin. We report genome-wide ancient DNA for 38 skeletons from Roopkund Lake, and find that they cluster into three distinct groups. A group of 23 individuals have ancestry that falls within the range of variation of present-day South Asians. A further 14 have ancestry typical of the eastern Mediterranean. We also identify one individual with Southeast Asian-related ancestry. Radiocarbon dating indicates that these remains were not deposited simultaneously. Instead, all of the individuals with South Asian-related ancestry date to ~800 CE (but with evidence of being deposited in more than one event), while all other individuals date to ~1800 CE. These differences are also reflected in stable isotope measurements, which reveal a distinct dietary profile for the two main groups. Remains of several hundred humans are scattered around Roopkund Lake, situated over 5,000 meters above sea level in the Himalayan Mountains. Here the authors analyze genome-wide data from 38 skeletons and find 3 clusters with different ancestries and dates, showing the people were desposited in multiple catastrophic events.
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Affiliation(s)
- Éadaoin Harney
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA.,The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Ayushi Nayak
- Department of Archaeology, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142 USA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | | | | | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, MA, 02142 USA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Jakob Sedig
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Nicole Adamski
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Rebecca Bernardos
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Brendan J Culleton
- Institutes of Energy and the Environment, The Pennsylvania State University, University Park, PA, 16802, USA.,Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Thomas K Harper
- Department of Anthropology, The Pennsylvania State University, University Park, PA, 16802, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA.,The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, D-07745, Jena, Germany
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Harashawaradhana
- Anthropological Survey of India, North West Regional Centre, Dehradun, 248195, India
| | | | - Sachin Kumar
- CSIR Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.,Birbal Sahni Institute of Palaeosciences, Lucknow, Uttar Pradesh, 226007, India
| | | | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
| | - Kumarasamy Thangaraj
- CSIR Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India
| | - David Reich
- The Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA, 02138, USA. .,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA. .,Broad Institute of Harvard and MIT, Cambridge, MA, 02142 USA, USA. .,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA.
| | - Niraj Rai
- CSIR Centre for Cellular and Molecular Biology, Hyderabad, Telangana, 500007, India.,Birbal Sahni Institute of Palaeosciences, Lucknow, Uttar Pradesh, 226007, India
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40
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Ralf A, Montiel González D, Zhong K, Kayser M. Yleaf: Software for Human Y-Chromosomal Haplogroup Inference from Next-Generation Sequencing Data. Mol Biol Evol 2019. [PMID: 29518227 DOI: 10.1093/molbev/msy032] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Next-generation sequencing (NGS) technologies offer immense possibilities given the large genomic data they simultaneously deliver. The human Y-chromosome serves as good example how NGS benefits various applications in evolution, anthropology, genealogy, and forensics. Prior to NGS, the Y-chromosome phylogenetic tree consisted of a few hundred branches, based on NGS data, it now contains many thousands. The complexity of both, Y tree and NGS data provide challenges for haplogroup assignment. For effective analysis and interpretation of Y-chromosome NGS data, we present Yleaf, a publically available, automated, user-friendly software for high-resolution Y-chromosome haplogroup inference independently of library and sequencing methods.
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Affiliation(s)
- Arwin Ralf
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Kaiyin Zhong
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Centre Rotterdam, Rotterdam, The Netherlands
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41
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The Genetic Variability of APOE in Different Human Populations and Its Implications for Longevity. Genes (Basel) 2019; 10:genes10030222. [PMID: 30884759 PMCID: PMC6471373 DOI: 10.3390/genes10030222] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2019] [Revised: 03/01/2019] [Accepted: 03/12/2019] [Indexed: 12/11/2022] Open
Abstract
Human longevity is a complex phenotype resulting from the combinations of context-dependent gene-environment interactions that require analysis as a dynamic process in a cohesive ecological and evolutionary framework. Genome-wide association (GWAS) and whole-genome sequencing (WGS) studies on centenarians pointed toward the inclusion of the apolipoprotein E (APOE) polymorphisms ε2 and ε4, as implicated in the attainment of extreme longevity, which refers to their effect in age-related Alzheimer's disease (AD) and cardiovascular disease (CVD). In this case, the available literature on APOE and its involvement in longevity is described according to an anthropological and population genetics perspective. This aims to highlight the evolutionary history of this gene, how its participation in several biological pathways relates to human longevity, and which evolutionary dynamics may have shaped the distribution of APOE haplotypes across the globe. Its potential adaptive role will be described along with implications for the study of longevity in different human groups. This review also presents an updated overview of the worldwide distribution of APOE alleles based on modern day data from public databases and ancient DNA samples retrieved from literature in the attempt to understand the spatial and temporal frame in which present-day patterns of APOE variation evolved.
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42
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Vai S, Brunelli A, Modi A, Tassi F, Vergata C, Pilli E, Lari M, Susca RR, Giostra C, Baricco LP, Bedini E, Koncz I, Vida T, Mende BG, Winger D, Loskotová Z, Veeramah K, Geary P, Barbujani G, Caramelli D, Ghirotto S. A genetic perspective on Longobard-Era migrations. Eur J Hum Genet 2019; 27:647-656. [PMID: 30651584 DOI: 10.1038/s41431-018-0319-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2018] [Revised: 11/15/2018] [Accepted: 12/04/2018] [Indexed: 11/09/2022] Open
Abstract
From the first century AD, Europe has been interested by population movements, commonly known as Barbarian migrations. Among these processes, the one involving the Longobard culture interested a vast region, but its dynamics and demographic impact remains largely unknown. Here we report 87 new complete mitochondrial sequences coming from nine early-medieval cemeteries located along the area interested by the Longobard migration (Czech Republic, Hungary and Italy). From the same areas, we sampled necropoleis characterized by cultural markers associated with the Longobard culture (LC) and coeval burials where no such markers were found, or with a chronology slightly preceding the presumed arrival of the Longobards in that region (NLC). Population genetics analysis and demographic modeling highlighted a similarity between LC individuals, as reflected by the sharing of quite rare haplogroups and by the degree of genetic resemblance between Hungarian and Italian LC necropoleis estimated via a Bayesian approach, ABC. The demographic model receiving the strongest statistical support also postulates a contact between LC and NLC communities, thus indicating a complex dynamics of admixture in medieval Europe.
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Affiliation(s)
- Stefania Vai
- Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy
| | - Andrea Brunelli
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121, Ferrara, Italy.,Fondazione Edmund Mach, 38010, San Michele all'Adige, Italy
| | - Alessandra Modi
- Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy
| | - Francesca Tassi
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121, Ferrara, Italy
| | - Chiara Vergata
- Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy
| | - Elena Pilli
- Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy
| | - Roberta Rosa Susca
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121, Ferrara, Italy
| | - Caterina Giostra
- Dipartimento di Storia, Archeologia e Storia dell'arte, Università Cattolica del Sacro Cuore, 20123, Milano, Italy
| | | | - Elena Bedini
- Dipartimento di Storia, Archeologia e Storia dell'arte, Università Cattolica del Sacro Cuore, 20123, Milano, Italy
| | - István Koncz
- Institute of Archaeological Sciences, Eötvös Loránd University, Múzeum körút 4/B, Budapest, 1088, Hungary
| | - Tivadar Vida
- Institute of Archaeological Sciences, Eötvös Loránd University, Múzeum körút 4/B, Budapest, 1088, Hungary.,Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Balázs Gusztáv Mende
- Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Daniel Winger
- Heinrich Schliemann Institut für Altertumswissenschaften Universität Rostock, Rostock, 18055, Germany
| | - Zuzana Loskotová
- Institute of Archaeology of the Czech Academy of Sciences, Brno, Czechia
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, 11790, USA
| | - Patrick Geary
- School of Historical Studies, Institute for Advanced Study, Princeton, NJ, 08540, USA
| | - Guido Barbujani
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121, Ferrara, Italy
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, 50122, Florence, Italy.
| | - Silvia Ghirotto
- Dipartimento di Scienze della Vita e Biotecnologie, Università di Ferrara, 44121, Ferrara, Italy.
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Fischer CE, Lefort A, Pemonge MH, Couture-Veschambre C, Rottier S, Deguilloux MF. The multiple maternal legacy of the Late Iron Age group of Urville-Nacqueville (France, Normandy) documents a long-standing genetic contact zone in northwestern France. PLoS One 2018; 13:e0207459. [PMID: 30521562 PMCID: PMC6283558 DOI: 10.1371/journal.pone.0207459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 10/31/2018] [Indexed: 11/18/2022] Open
Abstract
The compilation of archaeological and genetic data for ancient European human groups has provided persuasive evidence for a complex series of migrations, population replacements and admixture until the Bronze Age. If the Bronze-to-Iron Age transition has been well documented archaeologically, ancient DNA (aDNA) remains rare for the latter period and does not precisely reflect the genetic diversity of European Celtic groups. In order to document the evolution of European communities, we analysed 45 individuals from the Late Iron Age (La Tène) Urville-Nacqueville necropolis in northwestern France, a region recognized as a major cultural contact zone between groups from both sides of the Channel. The characterization of 37 HVS-I mitochondrial sequences and 40 haplogroups provided the largest maternal gene pool yet recovered for the European Iron Age. First, descriptive analyses allowed us to demonstrate the presence of substantial amounts of steppe-related mitochondrial ancestry in the community, which is consistent with the expansion of Bell Beaker groups bearing an important steppe legacy in northwestern Europe at approximately 2500 BC. Second, maternal genetic affinities highlighted with Bronze Age groups from Great Britain and the Iberian Peninsula regions tends to support the idea that the continuous cultural exchanges documented archaeologically across the Channel and along the Atlantic coast (during and after the Bronze Age period) were accompanied by significant gene flow. Lastly, our results suggest a maternal genetic continuity between Bronze Age and Iron Age groups that would argue in favour of a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. The palaeogenetic data gathered for the Urville-Nacqueville group constitute an important step in the biological characterization of European Iron age groups. Clearly, more numerous and diachronic aDNA data are needed to fully understand the complex relationship between the cultural and biological evolution of groups from the period.
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Affiliation(s)
- Claire-Elise Fischer
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
- * E-mail:
| | - Anthony Lefort
- Inrap Grand-Ouest, Boulevard de l’Europe, Bourguébus, France
| | - Marie-Hélène Pemonge
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
| | - Christine Couture-Veschambre
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
| | - Stéphane Rottier
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
| | - Marie-France Deguilloux
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
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44
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Abstract
Variation at the FADS1/FADS2 gene cluster is functionally associated with differences in lipid metabolism and is often hypothesized to reflect adaptation to an agricultural diet. Here, we test the evidence for this relationship using both modern and ancient DNA data. We show that almost all the inhabitants of Europe carried the ancestral allele until the derived allele was introduced ∼8,500 years ago by Early Neolithic farming populations. However, we also show that it was not under strong selection in these populations. We find that this allele, and other proposed agricultural adaptations at LCT/MCM6 and SLC22A4, were not strongly selected until much later, perhaps as late as the Bronze Age. Similarly, increased copy number variation at the salivary amylase gene AMY1 is not linked to the development of agriculture although, in this case, the putative adaptation precedes the agricultural transition. Our analysis shows that selection at the FADS locus was not tightly linked to the initial introduction of agriculture and the Neolithic transition. Further, it suggests that the strongest signals of recent human adaptation in Europe did not coincide with the Neolithic transition but with more recent changes in environment, diet, or efficiency of selection due to increases in effective population size.
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Affiliation(s)
- Sara Mathieson
- Department of Computer Science, Swarthmore College, Swarthmore, PA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
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45
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de Filippo C, Meyer M, Prüfer K. Quantifying and reducing spurious alignments for the analysis of ultra-short ancient DNA sequences. BMC Biol 2018; 16:121. [PMID: 30359256 PMCID: PMC6202837 DOI: 10.1186/s12915-018-0581-9] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 09/27/2018] [Indexed: 04/25/2023] Open
Abstract
BACKGROUND The study of ancient DNA is hampered by degradation, resulting in short DNA fragments. Advances in laboratory methods have made it possible to retrieve short DNA fragments, thereby improving access to DNA preserved in highly degraded, ancient material. However, such material contains large amounts of microbial contamination in addition to DNA fragments from the ancient organism. The resulting mixture of sequences constitutes a challenge for computational analysis, since microbial sequences are hard to distinguish from the ancient sequences of interest, especially when they are short. RESULTS Here, we develop a method to quantify spurious alignments based on the presence or absence of rare variants. We find that spurious alignments are enriched for mismatches and insertion/deletion differences and lack substitution patterns typical of ancient DNA. The impact of spurious alignments can be reduced by filtering on these features and by imposing a sample-specific minimum length cutoff. We apply this approach to sequences from four ~ 430,000-year-old Sima de los Huesos hominin remains, which contain particularly short DNA fragments, and increase the amount of usable sequence data by 17-150%. This allows us to place a third specimen from the site on the Neandertal lineage. CONCLUSIONS Our method maximizes the sequence data amenable to genetic analysis from highly degraded ancient material and avoids pitfalls that are associated with the analysis of ultra-short DNA sequences.
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Affiliation(s)
- Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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46
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O’Sullivan N, Posth C, Coia V, Schuenemann VJ, Price TD, Wahl J, Pinhasi R, Zink A, Krause J, Maixner F. Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard. SCIENCE ADVANCES 2018; 4:eaao1262. [PMID: 30191172 PMCID: PMC6124919 DOI: 10.1126/sciadv.aao1262] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 05/31/2018] [Indexed: 05/25/2023]
Abstract
From historical and archeological records, it is posited that the European medieval household was a combination of close relatives and recruits. However, this kinship structure has not yet been directly tested at a genomic level on medieval burials. The early 7th century CE burial at Niederstotzingen, discovered in 1962, is the most complete and richest example of Alemannic funerary practice in Germany. Excavations found 13 individuals who were buried with an array of inscribed bridle gear, jewelry, armor, and swords. These artifacts support the view that the individuals had contact with France, northern Italy, and Byzantium. This study analyzed genome-wide sequences recovered from the remains, in tandem with analysis of the archeological context, to reconstruct kinship and the extent of outside contact. Eleven individuals had sufficient DNA preservation to genetically sex them as male and identify nine unique mitochondrial haplotypes and two distinct Y chromosome lineages. Genome-wide analyses were performed on eight individuals to estimate genetic affiliation to modern west Eurasians and genetic kinship at the burial. Five individuals were direct relatives. Three other individuals were not detectably related; two of these showed genomic affinity to southern Europeans. The genetic makeup of the individuals shares no observable pattern with their orientation in the burial or the cultural association of their grave goods, with the five related individuals buried with grave goods associated with three diverse cultural origins. These findings support the idea that not only were kinship and fellowship held in equal regard: Diverse cultural appropriation was practiced among closely related individuals as well.
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Affiliation(s)
- Niall O’Sullivan
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Valentina Coia
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Verena J. Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
- Senckenberg Center for Human Evolution and Paleoecology, Palaeoanthropology, University of Tübingen, 72070 Tübingen, Germany
| | - T. Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin, 1180 Observatory Drive, Madison, WI 53706, USA
| | - Joachim Wahl
- State Office for Cultural Heritage Management Baden-Württemberg, Osteology, D-78467 Konstanz, Germany
- Institute for Archaeological Sciences, Palaeoanthropology, University of Tübingen, 72070 Tübingen, Germany
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
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47
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Abstract
The first decade of ancient genomics has revolutionized the study of human prehistory and evolution. We review new insights based on prehistoric modern human genomes, including greatly increased resolution of the timing and structure of the out-of-Africa expansion, the diversification of present-day non-African populations, and the earliest expansions of those populations into Eurasia and America. Prehistoric genomes now document population transformations on every inhabited continent—in particular the effect of agricultural expansions in Africa, Europe, and Oceania—and record a history of natural selection that shapes present-day phenotypic diversity. Despite these advances, much remains unknown, in particular about the genomic histories of Asia (the most populous continent) and Africa (the continent that contains the most genetic diversity). Ancient genomes from these and other regions, integrated with a growing understanding of the genomic basis of human phenotypic diversity, will be in focus during the next decade of research in the field.
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Affiliation(s)
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19103, USA
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48
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Krzewińska M, Kjellström A, Günther T, Hedenstierna-Jonson C, Zachrisson T, Omrak A, Yaka R, Kılınç GM, Somel M, Sobrado V, Evans J, Knipper C, Jakobsson M, Storå J, Götherström A. Genomic and Strontium Isotope Variation Reveal Immigration Patterns in a Viking Age Town. Curr Biol 2018; 28:2730-2738.e10. [PMID: 30146150 DOI: 10.1016/j.cub.2018.06.053] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/13/2018] [Accepted: 06/21/2018] [Indexed: 02/03/2023]
Abstract
The impact of human mobility on the northern European urban populations during the Viking and Early Middle Ages and its repercussions in Scandinavia itself are still largely unexplored. Our study of the demographics in the final phase of the Viking era is the first comprehensive multidisciplinary investigation that includes genetics, isotopes, archaeology, and osteology on a larger scale. This early Christian dataset is particularly important as the earlier common pagan burial tradition during the Iron Age was cremation, hindering large-scale DNA analyses. We present genome-wide sequence data from 23 individuals from the 10th to 12th century Swedish town of Sigtuna. The data revealed high genetic diversity among the early urban residents. The observed variation exceeds the genetic diversity in distinct modern-day and Iron Age groups of central and northern Europe. Strontium isotope data suggest mixed local and non-local origin of the townspeople. Our results uncover the social system underlying the urbanization process of the Viking World of which mobility was an intricate part and was comparable between males and females. The inhabitants of Sigtuna were heterogeneous in their genetic affinities, probably reflecting both close and distant connections through an established network, confirming that early urbanization processes in northern Europe were driven by migration.
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Affiliation(s)
- Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden.
| | - Anna Kjellström
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden.
| | - Torsten Günther
- Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18C, 752 36 Uppsala, Sweden
| | - Charlotte Hedenstierna-Jonson
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Torun Zachrisson
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Ayça Omrak
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, 06800 Tandogan, Ankara, Turkey
| | - Gülşah Merve Kılınç
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Tandogan, Ankara, Turkey
| | - Veronica Sobrado
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Jane Evans
- NERC Isotope Geosciences Laboratory British Geological Survey, Keyworth, Nottingham NG12 5GG, UK
| | - Corina Knipper
- Curt-Engelhorn-Zentrum Archäometrie, D6, 3, 68159 Mannheim, Germany
| | - Mattias Jakobsson
- Department of Organismal Biology, Evolutionary Biology Centre, Norbyvägen 18C, 752 36 Uppsala, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Lilla Frescativägen 7, 106 91 Stockholm, Sweden; Science for Life Laboratory, Tomtebodavägen 23A, 17165 Solna, Sweden.
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49
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Ebenesersdóttir SS, Sandoval-Velasco M, Gunnarsdóttir ED, Jagadeesan A, Guðmundsdóttir VB, Thordardóttir EL, Einarsdóttir MS, Moore KHS, Sigurðsson Á, Magnúsdóttir DN, Jónsson H, Snorradóttir S, Hovig E, Møller P, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Cavalleri GL, Gilbert E, Lalueza-Fox C, Walser JW, Kristjánsdóttir S, Gopalakrishnan S, Árnadóttir L, Magnússon ÓÞ, Gilbert MTP, Stefánsson K, Helgason A. Ancient genomes from Iceland reveal the making of a human population. Science 2018; 360:1028-1032. [PMID: 29853688 DOI: 10.1126/science.aar2625] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 04/25/2018] [Indexed: 12/14/2022]
Abstract
Opportunities to directly study the founding of a human population and its subsequent evolutionary history are rare. Using genome sequence data from 27 ancient Icelanders, we demonstrate that they are a combination of Norse, Gaelic, and admixed individuals. We further show that these ancient Icelanders are markedly more similar to their source populations in Scandinavia and the British-Irish Isles than to contemporary Icelanders, who have been shaped by 1100 years of extensive genetic drift. Finally, we report evidence of unequal contributions from the ancient founders to the contemporary Icelandic gene pool. These results provide detailed insights into the making of a human population that has proven extraordinarily useful for the discovery of genotype-phenotype associations.
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Affiliation(s)
- S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland. .,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Marcela Sandoval-Velasco
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | - Ellen D Gunnarsdóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Anuradha Jagadeesan
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Valdís B Guðmundsdóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Elísabet L Thordardóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | - Margrét S Einarsdóttir
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
| | | | | | | | | | | | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Institute for Cancer Genetics and Informatics, Oslo University Hospital, Oslo, Norway.,Department of Informatics, University of Oslo, Oslo, Norway
| | - Pål Møller
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Human Medicine, Universität Witten/Herdecke, Witten, Germany.,Research Group Inherited Cancer, Department of Medical Genetics, Oslo University Hospital, Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark.,Danish Headache Center, Department of Neurology, Copenhagen University hospital, DK-2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark
| | - Gianpiero L Cavalleri
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, Ireland
| | - Edmund Gilbert
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St. Stephen's Green, Dublin, Ireland
| | | | - Joe W Walser
- National Museum of Iceland, Reykjavik, Iceland.,Department of Archaeology, University of Iceland, Reykjavik, Iceland
| | - Steinunn Kristjánsdóttir
- National Museum of Iceland, Reykjavik, Iceland.,Department of Archaeology, University of Iceland, Reykjavik, Iceland
| | - Shyam Gopalakrishnan
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark
| | | | | | - M Thomas P Gilbert
- Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade 5-7, 1350 Copenhagen K, Denmark.,Norwegian University of Science and Techonology, University Museum, 7491 Trondheim, Norway
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland. .,Faculity of Medicine, University of Iceland, Reykjavik, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., Reykjavik Iceland. .,Department of Anthropology, University of Iceland, Reykjavik, Iceland
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50
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De Angelis F, Scorrano G, Martínez-Labarga C, Scano G, Macciardi F, Rickards O. Mitochondrial variability in the Mediterranean area: a complex stage for human migrations. Ann Hum Biol 2018; 45:5-19. [PMID: 29382277 DOI: 10.1080/03014460.2017.1416172] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
CONTEXT The Mediterranean area has always played a significant role in human dispersal due to the large number of migratory events contributing to shape the cultural features and the genetic pool of its populations. OBJECTIVE This paper aims to review and diachronically describe the mitogenome variability in the Mediterranean population and the main demic diffusions that occurred in this area over time. METHODS Frequency distributions of the leading mitochondrial haplogroups have been geographically and chronologically evaluated. The variability of U5b and K lineages has been focussed to broaden the knowledge of their genetic histories. RESULTS The mitochondrial genetic makeup of Palaeolithic hunter-gatherers is poorly defined within the extant Mediterranean populations, since only a few traces of their genetic contribution are still detectable. The Neolithic lineages are more represented, suggesting that the Neolithic revolution had a marked effect on the peopling of the Mediterranean area. The largest effect, however, was provided by historical migrations. CONCLUSION Although the mitogenome variability has been widely used to try and clarify the evolution of the Mediterranean genetic makeup throughout almost 50 000 years, it is necessary to collect whole genome data on both extinct and extant populations from this area to fully reconstruct and interpret the impact of multiple migratory waves and their cultural and genetic consequences on the structure of the Mediterranean populations.
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Affiliation(s)
- Flavio De Angelis
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Gabriele Scorrano
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Cristina Martínez-Labarga
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Giuseppina Scano
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
| | - Fabio Macciardi
- b Laboratory of Molecular Psychiatry, Department of Psychiatry and Human Behavior , University of California , Irvine , CA , USA
| | - Olga Rickards
- a Centre of Molecular Anthropology for Ancient DNA Studies , University of Rome "Tor Vergata" , Rome , Italy
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