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Özkan M, Gürün K, Yüncü E, Vural KB, Atağ G, Akbaba A, Fidan FR, Sağlıcan E, Altınışık EN, Koptekin D, Pawłowska K, Hodder I, Adcock SE, Arbuckle BS, Steadman SR, McMahon G, Erdal YS, Bilgin CC, Togan İ, Geigl EM, Götherström A, Grange T, Özer F, Somel M. The first complete genome of the extinct European wild ass (Equus hemionus hydruntinus). Mol Ecol 2024; 33:e17440. [PMID: 38946459 DOI: 10.1111/mec.17440] [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: 07/11/2023] [Revised: 05/17/2024] [Accepted: 06/14/2024] [Indexed: 07/02/2024]
Abstract
We present palaeogenomes of three morphologically unidentified Anatolian equids dating to the first millennium BCE, sequenced to a coverage of 0.6-6.4×. Mitochondrial DNA haplotypes of the Anatolian individuals clustered with those of Equus hydruntinus (or Equus hemionus hydruntinus), the extinct European wild ass, secular name 'hydruntine'. Further, the Anatolian wild ass whole genome profiles fell outside the genomic diversity of other extant and past Asiatic wild ass (E. hemionus) lineages. These observations suggest that the three Anatolian wild asses represent hydruntines, making them the latest recorded survivors of this lineage, about a millennium later than the latest observations in the zooarchaeological record. Our mitogenomic and genomic analyses indicate that E. h. hydruntinus was a clade belonging to ancient and present-day E. hemionus lineages that radiated possibly between 0.6 and 0.8 Mya. We also find evidence consistent with recent gene flow between hydruntines and Middle Eastern wild asses. Analyses of genome-wide heterozygosity and runs of homozygosity suggest that the Anatolian wild ass population may have lost genetic diversity by the mid-first millennium BCE, a possible sign of its eventual demise.
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Affiliation(s)
- Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ali Akbaba
- Department of Anthropology, Ankara University, Ankara, Turkey
- Alparslan University, Muş, Turkey
| | - Fatma Rabia Fidan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Cancer Dynamics Laboratory, The Francis Crick Institute, London, UK
| | - Ekin Sağlıcan
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Ezgi N Altınışık
- Department of Anthropology, Human_G Laboratory, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Kamilla Pawłowska
- Department of Palaeoenvironmental Research, Adam Mickiewicz University, Poznań, Poland
| | - Ian Hodder
- Department of Anthropology, Stanford University, Stanford, California, USA
| | - Sarah E Adcock
- Institute for the Study of the Ancient World, New York University, New York, New York, USA
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Sharon R Steadman
- Department of Sociology/Anthropology, SUNY Cortland, Cortland, New York, USA
| | - Gregory McMahon
- Classics, Humanities and Italian Studies Department, University of New Hampshire, Durham, New Hampshire, USA
| | - Yılmaz Selim Erdal
- Department of Anthropology, Human_G Laboratory, Hacettepe University, Ankara, Turkey
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Eva-Maria Geigl
- Institut Jacques Monod, CNRS, Université de Paris, Paris, France
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Thierry Grange
- Institut Jacques Monod, CNRS, Université de Paris, Paris, France
| | - Füsun Özer
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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2
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Aktürk Ş, Mapelli I, Güler MN, Gürün K, Katırcıoğlu B, Vural KB, Sağlıcan E, Çetin M, Yaka R, Sürer E, Atağ G, Çokoğlu SS, Sevkar A, Altınışık NE, Koptekin D, Somel M. Benchmarking kinship estimation tools for ancient genomes using pedigree simulations. Mol Ecol Resour 2024; 24:e13960. [PMID: 38676702 DOI: 10.1111/1755-0998.13960] [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: 11/25/2023] [Revised: 03/19/2024] [Accepted: 03/28/2024] [Indexed: 04/29/2024]
Abstract
There is growing interest in uncovering genetic kinship patterns in past societies using low-coverage palaeogenomes. Here, we benchmark four tools for kinship estimation with such data: lcMLkin, NgsRelate, KIN, and READ, which differ in their input, IBD estimation methods, and statistical approaches. We used pedigree and ancient genome sequence simulations to evaluate these tools when only a limited number (1 to 50 K, with minor allele frequency ≥0.01) of shared SNPs are available. The performance of all four tools was comparable using ≥20 K SNPs. We found that first-degree related pairs can be accurately classified even with 1 K SNPs, with 85% F1 scores using READ and 96% using NgsRelate or lcMLkin. Distinguishing third-degree relatives from unrelated pairs or second-degree relatives was also possible with high accuracy (F1 > 90%) with 5 K SNPs using NgsRelate and lcMLkin, while READ and KIN showed lower success (69 and 79% respectively). Meanwhile, noise in population allele frequencies and inbreeding (first-cousin mating) led to deviations in kinship coefficients, with different sensitivities across tools. We conclude that using multiple tools in parallel might be an effective approach to achieve robust estimates on ultra-low-coverage genomes.
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Affiliation(s)
- Şevval Aktürk
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Merve N Güler
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Büşra Katırcıoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Çetin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sevim Seda Çokoğlu
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Arda Sevkar
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
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3
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Bagnasco G, Marzullo M, Cattaneo C, Biehler-Gomez L, Mazzarelli D, Ricciardi V, Müller W, Coppa A, McLaughlin R, Motta L, Prato O, Schmidt F, Gaveriaux F, Marras GB, Millet MA, Madgwick R, Ballantyne R, Makarewicz CA, Trentacoste A, Reimer P, Mattiangeli V, Bradley DG, Malone C, Esposito C, Breslin EM, Stoddart S. Bioarchaeology aids the cultural understanding of six characters in search of their agency (Tarquinia, ninth-seventh century BC, central Italy). Sci Rep 2024; 14:11895. [PMID: 38806487 PMCID: PMC11133411 DOI: 10.1038/s41598-024-61052-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 04/30/2024] [Indexed: 05/30/2024] Open
Abstract
Etruria contained one of the great early urban civilisations in the Italian peninsula during the first millennium BC, much studied from a cultural, humanities-based, perspective, but relatively little with scientific data, and rarely in combination. We have addressed the unusual location of twenty inhumations found in the sacred heart of the Etruscan city of Tarquinia, focusing on six of these as illustrative, contrasting with the typical contemporary cremations found in cemeteries on the edge of the city. The cultural evidence suggests that the six skeletons were also distinctive in their ritualization and memorialisation. Focusing on the six, as a representative sample, the scientific evidence of osteoarchaeology, isotopic compositions, and ancient DNA has established that these appear to show mobility, diversity and violence through an integrated bioarchaeological approach. The combination of multiple lines of evidence makes major strides towards a deeper understanding of the role of these extraordinary individuals in the life of the early city of Etruria.
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Affiliation(s)
- G Bagnasco
- Dipartimento di Beni Culturali e Ambientali, CRC "Progetto Tarquinia", Università degli Studi di Milano, Milan, Italy.
| | - M Marzullo
- Dipartimento di Beni Culturali e Ambientali, CRC "Progetto Tarquinia", Università degli Studi di Milano, Milan, Italy
| | - C Cattaneo
- LABANOF (Laboratorio di Antropologia e Odontologia Forense), Università degli Studi di Milano, Milan, Italy
| | - L Biehler-Gomez
- LABANOF (Laboratorio di Antropologia e Odontologia Forense), Università degli Studi di Milano, Milan, Italy
| | - D Mazzarelli
- LABANOF (Laboratorio di Antropologia e Odontologia Forense), Università degli Studi di Milano, Milan, Italy
| | - V Ricciardi
- LABANOF (Laboratorio di Antropologia e Odontologia Forense), Università degli Studi di Milano, Milan, Italy
| | - W Müller
- Institute of Geosciences, Goethe University, Frankfurt, Frankfurt am Main, Germany
- Frankfurt Isotope and Element Research Center (FIERCE), Goethe University, Frankfurt, Frankfurt am Main, Germany
| | - A Coppa
- Dipartimento di Storia Antropologia Religioni Arte Spettacolo, Sapienza Università di Roma, Rome, Italy
| | - R McLaughlin
- Hamilton Institute, Maynooth University, Maynooth, Ireland
| | - L Motta
- Department of Classical Studies and Program in the Environment, University of Michigan, Ann Arbor, USA
| | - O Prato
- Institute of Archaeology, UCL University College London, London, UK
| | | | - F Gaveriaux
- Kelsey Museum of Archaeology, University of Michigan, Ann Arbor, USA
| | | | - M A Millet
- School of Earth and Environmental Sciences, Cardiff University, Cardiff, CF10 3AT, UK
| | - R Madgwick
- Cardiff School of History, Archaeology and Religion, Cardiff University, Cardiff, UK
| | - R Ballantyne
- School of Archaeology, University of Oxford, Oxford, UK
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | - C A Makarewicz
- Institut für Ur- und Frühgeschichte, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - A Trentacoste
- Institut für Ur- und Frühgeschichte, Christian-Albrechts-Universität zu Kiel, Kiel, Germany
| | - P Reimer
- School of Natural and Built Environment, Queen's University Belfast, Belfast, BT7 1NN, UK
| | - V Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin2, Ireland
| | - D G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin2, Ireland
| | - C Malone
- School of Natural and Built Environment, Queen's University Belfast, Belfast, BT7 1NN, UK
| | - C Esposito
- Dipartimento di Beni Culturali, Alma Mater Studiorum, Università di Bologna, Ravenna, Italy
| | - E M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin2, Ireland
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4
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Heraclides A, Aristodemou A, Georgiou AN, Antoniou M, Ilgner E, Davranoglou LR. Palaeogenomic insights into the origins of early settlers on the island of Cyprus. Sci Rep 2024; 14:9632. [PMID: 38671010 PMCID: PMC11053055 DOI: 10.1038/s41598-024-60161-z] [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: 06/09/2023] [Accepted: 04/19/2024] [Indexed: 04/28/2024] Open
Abstract
Archaeological evidence supports sporadic seafaring visits to the Eastern Mediterranean island of Cyprus by Epipaleolithic hunter-gatherers over 12,000 years ago, followed by permanent settlements during the early Neolithic. The geographical origins of these early seafarers have so far remained elusive. By systematically analysing all available genomes from the late Pleistocene to early Holocene Near East (c. 14,000-7000 cal BCE), we provide a comprehensive overview of the genetic landscape of the early Neolithic Fertile Crescent and Anatolia and infer the likely origins of three recently published genomes from Kissonerga-Mylouthkia (Cypriot Late Pre-Pottery Neolithic B, c. 7600-6800 cal BCE). These appear to derive roughly 80% of their ancestry from Aceramic Neolithic Central Anatolians residing in or near the Konya plain, and the remainder from a genetically basal Levantine population. Based on genome-wide weighted ancestry covariance analysis, we infer that this admixture event took place roughly between 14,000 and 10,000 BCE, coinciding with the transition from the Cypriot late Epipaleolithic to the Pre-Pottery Neolithic A (PPNA). Additionally, we identify strong genetic affinities between the examined Cypro-LPPNB individuals and later northwestern Anatolians and the earliest European Neolithic farmers. Our results inform archaeological evidence on prehistoric demographic processes in the Eastern Mediterranean, providing important insights into early seafaring, maritime connections, and insular settlement.
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Affiliation(s)
- Alexandros Heraclides
- School of Sciences, European University Cyprus, 6 Diogenis Str., 2404 Engomi, P.O. Box: 22006, 1516, Nicosia, Cyprus.
| | - Aris Aristodemou
- Department of Infectious Disease, Faculty of Medicine, Imperial College London, London, UK
| | - Andrea N Georgiou
- School of Sciences, European University Cyprus, 6 Diogenis Str., 2404 Engomi, P.O. Box: 22006, 1516, Nicosia, Cyprus
| | - Marios Antoniou
- Department of Electrical and Computer Engineering, University of Thessaly, Volos, Greece
| | - Elisabeth Ilgner
- School of Archaeology/Merton College, University of Oxford, Oxford, UK
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5
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Gill H, Lee J, Jeong C. Reconstructing the Genetic Relationship between Ancient and Present-Day Siberian Populations. Genome Biol Evol 2024; 16:evae063. [PMID: 38526010 PMCID: PMC10999361 DOI: 10.1093/gbe/evae063] [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: 11/30/2023] [Revised: 02/22/2024] [Accepted: 03/21/2024] [Indexed: 03/26/2024] Open
Abstract
Human populations across a vast area in northern Eurasia, from Fennoscandia to Chukotka, share a distinct genetic component often referred to as the Siberian ancestry. Most enriched in present-day Samoyedic-speaking populations such as Nganasans, its origins and history still remain elusive despite the growing list of ancient and present-day genomes from Siberia. Here, we reanalyze published ancient and present-day Siberian genomes focusing on the Baikal and Yakutia, resolving key questions regarding their genetic history. First, we show a long-term presence of a unique genetic profile in southern Siberia, up to 6,000 yr ago, which distinctly shares a deep ancestral connection with Native Americans. Second, we provide plausible historical models tracing genetic changes in West Baikal and Yakutia in fine resolution. Third, the Middle Neolithic individual from Yakutia, belonging to the Belkachi culture, serves as the best source so far available for the spread of the Siberian ancestry into Fennoscandia and Greenland. These findings shed light on the genetic legacy of the Siberian ancestry and provide insights into the complex interplay between different populations in northern Eurasia throughout history.
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Affiliation(s)
- Haechan Gill
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Juhyeon Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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6
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Sirak K, Jansen Van Rensburg J, Brielle E, Chen B, Lazaridis I, Ringbauer H, Mah M, Mallick S, Micco A, Rohland N, Callan K, Curtis E, Kearns A, Lawson AM, Workman JN, Zalzala F, Ahmed Al-Orqbi AS, Ahmed Salem EM, Salem Hasan AM, Britton DC, Reich D. Medieval DNA from Soqotra points to Eurasian origins of an isolated population at the crossroads of Africa and Arabia. Nat Ecol Evol 2024; 8:817-829. [PMID: 38332026 PMCID: PMC11009077 DOI: 10.1038/s41559-024-02322-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/11/2023] [Indexed: 02/10/2024]
Abstract
Soqotra, an island situated at the mouth of the Gulf of Aden in the northwest Indian Ocean between Africa and Arabia, is home to ~60,000 people subsisting through fishing and semi-nomadic pastoralism who speak a Modern South Arabian language. Most of what is known about Soqotri history derives from writings of foreign travellers who provided little detail about local people, and the geographic origins and genetic affinities of early Soqotri people has not yet been investigated directly. Here we report genome-wide data from 39 individuals who lived between ~650 and 1750 CE at six locations across the island and document strong genetic connections between Soqotra and the similarly isolated Hadramawt region of coastal South Arabia that likely reflects a source for the peopling of Soqotra. Medieval Soqotri can be modelled as deriving ~86% of their ancestry from a population such as that found in the Hadramawt today, with the remaining ~14% best proxied by an Iranian-related source with up to 2% ancestry from the Indian sub-continent, possibly reflecting genetic exchanges that occurred along with archaeologically documented trade from these regions. In contrast to all other genotyped populations of the Arabian Peninsula, genome-level analysis of the medieval Soqotri is consistent with no sub-Saharan African admixture dating to the Holocene. The deep ancestry of people from medieval Soqotra and the Hadramawt is also unique in deriving less from early Holocene Levantine farmers and more from groups such as Late Pleistocene hunter-gatherers from the Levant (Natufians) than other mainland Arabians. This attests to migrations by early farmers having less impact in southernmost Arabia and Soqotra and provides compelling evidence that there has not been complete population replacement between the Pleistocene and Holocene throughout the Arabian Peninsula. Medieval Soqotra harboured a small population that showed qualitatively different marriage practices from modern Soqotri, with first-cousin unions occurring significantly less frequently than today.
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Affiliation(s)
- Kendra Sirak
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | | | - Esther Brielle
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Bowen Chen
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Iosif Lazaridis
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Harald Ringbauer
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthew Mah
- 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 Harvard and MIT, Cambridge, MA, USA
| | - Swapan Mallick
- 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 Harvard and MIT, Cambridge, MA, USA
| | - Adam Micco
- 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
| | - Kimberly Callan
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Elizabeth Curtis
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Aisling Kearns
- 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
| | - J Noah Workman
- 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
| | | | | | | | | | - 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 Harvard and MIT, Cambridge, MA, USA
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7
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Vallini L, Zampieri C, Shoaee MJ, Bortolini E, Marciani G, Aneli S, Pievani T, Benazzi S, Barausse A, Mezzavilla M, Petraglia MD, Pagani L. The Persian plateau served as hub for Homo sapiens after the main out of Africa dispersal. Nat Commun 2024; 15:1882. [PMID: 38528002 DOI: 10.1038/s41467-024-46161-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Accepted: 02/16/2024] [Indexed: 03/27/2024] Open
Abstract
A combination of evidence, based on genetic, fossil and archaeological findings, indicates that Homo sapiens spread out of Africa between ~70-60 thousand years ago (kya). However, it appears that once outside of Africa, human populations did not expand across all of Eurasia until ~45 kya. The geographic whereabouts of these early settlers in the timeframe between ~70-60 to 45 kya has been difficult to reconcile. Here we combine genetic evidence and palaeoecological models to infer the geographic location that acted as the Hub for our species during the early phases of colonisation of Eurasia. Leveraging on available genomic evidence we show that populations from the Persian Plateau carry an ancestry component that closely matches the population that settled the Hub outside Africa. With the paleoclimatic data available to date, we built ecological models showing that the Persian Plateau was suitable for human occupation and that it could sustain a larger population compared to other West Asian regions, strengthening this claim.
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Affiliation(s)
| | - Carlo Zampieri
- Department of Biology, University of Padova, Padova, Italy
| | - Mohamed Javad Shoaee
- Department of Archaeology, Max Planck Institute for Geoanthropology, Jena, Germany
| | - Eugenio Bortolini
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
| | - Giulia Marciani
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
- Research Unit Prehistory and Anthropology, Department of Physical Sciences, Earth and Environment, University of Siena, Siena, Italy
| | - Serena Aneli
- Department of Public Health Sciences and Pediatrics, University of Turin, Turin, Italy
| | - Telmo Pievani
- Department of Biology, University of Padova, Padova, Italy
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Bologna, Italy
| | - Alberto Barausse
- Department of Biology, University of Padova, Padova, Italy
- Department of Industrial Engineering, University of Padova, Padova, Italy
| | | | - Michael D Petraglia
- Human Origins Program, Smithsonian Institution, Washington, DC, 20560, USA
- School of Social Science, The University of Queensland, Brisbane, QLD, Australia
- Australian Research Centre for Human Evolution, Griffith University, Brisbane, QLD, Australia
| | - Luca Pagani
- Department of Biology, University of Padova, Padova, Italy.
- Institute of Genomics, University of Tartu, Tartu, Estonia.
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8
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Martiniano R, Haber M, Almarri MA, Mattiangeli V, Kuijpers MCM, Chamel B, Breslin EM, Littleton J, Almahari S, Aloraifi F, Bradley DG, Lombard P, Durbin R. Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. CELL GENOMICS 2024; 4:100507. [PMID: 38417441 PMCID: PMC10943591 DOI: 10.1016/j.xgen.2024.100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Revised: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/01/2024]
Abstract
The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.
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Affiliation(s)
- Rui Martiniano
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK.
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham Dubai, Dubai, United Arab Emirates
| | - Mohamed A Almarri
- Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Berenice Chamel
- Institut Français du Proche-Orient (MEAE/CNRS), Beirut, Lebanon
| | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Judith Littleton
- School of Social Sciences, University of Auckland, Auckland, New Zealand
| | - Salman Almahari
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain
| | - Fatima Aloraifi
- Mersey and West Lancashire Teaching Hospitals NHS Trust, Whiston Hospital, Warrington Road, Prescot, L35 5DR Liverpool, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierre Lombard
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain; Archéorient UMR 5133, CNRS, Université Lyon 2, Maison de l'Orient et de la Méditerranée - Jean Pouilloux, Lyon, France
| | - Richard Durbin
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK.
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9
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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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10
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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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11
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Irving-Pease EK, Refoyo-Martínez A, Barrie W, Ingason A, Pearson A, Fischer A, Sjögren KG, Halgren AS, Macleod R, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn AH, Speidel L, Stern AJ, Scorrano G, Ramsøe A, Schork AJ, Rosengren A, Zhao L, Kristiansen K, Iversen AKN, Fugger L, Sudmant PH, Lawson DJ, Durbin R, Korneliussen T, Werge T, Allentoft ME, Sikora M, Nielsen R, Racimo F, Willerslev E. The selection landscape and genetic legacy of ancient Eurasians. Nature 2024; 625:312-320. [PMID: 38200293 PMCID: PMC10781624 DOI: 10.1038/s41586-023-06705-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Accepted: 10/03/2023] [Indexed: 01/12/2024]
Abstract
The Holocene (beginning around 12,000 years ago) encompassed some of the most significant changes in human evolution, with far-reaching consequences for the dietary, physical and mental health of present-day populations. Using a dataset of more than 1,600 imputed ancient genomes1, we modelled the selection landscape during the transition from hunting and gathering, to farming and pastoralism across West Eurasia. We identify key selection signals related to metabolism, including that selection at the FADS cluster began earlier than previously reported and that selection near the LCT locus predates the emergence of the lactase persistence allele by thousands of years. We also find strong selection in the HLA region, possibly due to increased exposure to pathogens during the Bronze Age. Using ancient individuals to infer local ancestry tracts in over 400,000 samples from the UK Biobank, we identify widespread differences in the distribution of Mesolithic, Neolithic and Bronze Age ancestries across Eurasia. By calculating ancestry-specific polygenic risk scores, we show that height differences between Northern and Southern Europe are associated with differential Steppe ancestry, rather than selection, and that risk alleles for mood-related phenotypes are enriched for Neolithic farmer ancestry, whereas risk alleles for diabetes and Alzheimer's disease are enriched for Western hunter-gatherer ancestry. Our results indicate that ancient selection and migration were large contributors to the distribution of phenotypic diversity in present-day Europeans.
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Affiliation(s)
- Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Zoology, University of Cambridge, Cambridge, UK
| | - Anders Fischer
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Alma S Halgren
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | - Ruairidh Macleod
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- UCL Genetics Institute, University College London, London, UK
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie, Muséum national d'Histoire naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew H Vaughn
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Leo Speidel
- UCL Genetics Institute, University College London, London, UK
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
| | - Aaron J Stern
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Abigail Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew J Schork
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Lei Zhao
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Astrid K N Iversen
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Lars Fugger
- Oxford Centre for Neuroinflammation, Nuffield Department of Clinical Neurosciences, John Radcliffe Hospital, University of Oxford, Oxford, UK
- Department of Clinical Medicine, Aarhus University Hospital, Aarhus, Denmark
- MRC Human Immunology Unit, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Cambridge, UK
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Science, Curtin University, Perth, Western Australia, Australia
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Departments of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
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12
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Mattila TM, Svensson EM, Juras A, Günther T, Kashuba N, Ala-Hulkko T, Chyleński M, McKenna J, Pospieszny Ł, Constantinescu M, Rotea M, Palincaș N, Wilk S, Czerniak L, Kruk J, Łapo J, Makarowicz P, Potekhina I, Soficaru A, Szmyt M, Szostek K, Götherström A, Storå J, Netea MG, Nikitin AG, Persson P, Malmström H, Jakobsson M. Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe. Commun Biol 2023; 6:793. [PMID: 37558731 PMCID: PMC10412644 DOI: 10.1038/s42003-023-05131-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.
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Affiliation(s)
- Tiina M Mattila
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden.
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Natalija Kashuba
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Department of Archaeology and Ancient History, Uppsala University, 75126, Uppsala, Sweden
| | - Terhi Ala-Hulkko
- Geography Research Unit, University of Oulu, 90014, Oulu, Finland
- Kerttu Saalasti Institute, University of Oulu, 90014, Oulu, Finland
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
- Institute of Archaeology, University of Gdańsk, 80-851, Gdańsk, Poland
| | - Mihai Constantinescu
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, 050711, Bucharest, Romania
- Faculty of History, University of Bucharest, 030167, Bucharest, Romania
| | - Mihai Rotea
- National History Museum of Transylvania, Cluj-Napoca, Romania
| | - Nona Palincaș
- Vasile Pârvan Institute of Archaeology, Bucharest, Romania
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, 31-007, Kraków, Poland
- Karkonosze Museum, 58-500, Jelenia Góra, Poland
| | - Lech Czerniak
- Institute of Archaeology, University of Gdańsk, 80-851, Gdańsk, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, 31-016, Kraków, Poland
| | - Jerzy Łapo
- Museum of Folk Culture, 11-600, Węgorzewo, Poland
| | - Przemysław Makarowicz
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210, Kyiv, Ukraine
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, 3008, Bern, Switzerland
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, 050711, Bucharest, Romania
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
- Archaeological Museum, 61-781, Poznań, Poland
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, 01-938, Warszawa, Poland
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University and the Swedish Museum of Natural History, 106 91, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91, Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 106 91, Stockholm, Sweden
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - Alexey G Nikitin
- Grand Valley State University, Department of Biology, Allendale, MI, 49401, USA
| | - Per Persson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Museum of Cultural History, University of Oslo, 0130, Oslo, Norway
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden.
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa.
- SciLifeLab, Uppsala University, 75105, Uppsala, Sweden.
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13
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Lee J, Miller BK, Bayarsaikhan J, Johannesson E, Ventresca Miller A, Warinner C, Jeong C. Genetic population structure of the Xiongnu Empire at imperial and local scales. SCIENCE ADVANCES 2023; 9:eadf3904. [PMID: 37058560 PMCID: PMC10104459 DOI: 10.1126/sciadv.adf3904] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 03/16/2023] [Indexed: 06/19/2023]
Abstract
The Xiongnu established the first nomadic imperial power, controlling the Eastern Eurasian steppe from ca. 200 BCE to 100 CE. Recent archaeogenetic studies identified extreme levels of genetic diversity across the empire, corroborating historical records of the Xiongnu Empire being multiethnic. However, it has remained unknown how this diversity was structured at the local community level or by sociopolitical status. To address this, we investigated aristocratic and local elite cemeteries at the western frontier of the empire. Analyzing genome-wide data from 18 individuals, we show that genetic diversity within these communities was comparable to the empire as a whole, and that high diversity was also observed within extended families. Genetic heterogeneity was highest among the lowest-status individuals, implying diverse origins, while higher-status individuals harbored less genetic diversity, suggesting that elite status and power was concentrated within specific subsets of the broader Xiongnu population.
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Affiliation(s)
- Juhyeon Lee
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
| | - Bryan K. Miller
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
- History of Art, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jamsranjav Bayarsaikhan
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- National Museum of Mongolia, Ulaanbaatar, Mongolia
| | | | - Alicia Ventresca Miller
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
- Museum of Anthropological Archaeology, University of Michigan, Ann Arbor, MI 48109, USA
- Department of Anthropology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Christina Warinner
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
- Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Choongwon Jeong
- School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea
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14
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Davy T, Ju D, Mathieson I, Skoglund P. Hunter-gatherer admixture facilitated natural selection in Neolithic European farmers. Curr Biol 2023; 33:1365-1371.e3. [PMID: 36963383 PMCID: PMC10153476 DOI: 10.1016/j.cub.2023.02.049] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/17/2022] [Accepted: 02/15/2023] [Indexed: 03/26/2023]
Abstract
Ancient DNA has revealed multiple episodes of admixture in human prehistory during geographic expansions associated with cultural innovations. One important example is the expansion of Neolithic agricultural groups out of the Near East into Europe and their consequent admixture with Mesolithic hunter-gatherers.1,2,3,4 Ancient genomes from this period provide an opportunity to study the role of admixture in providing new genetic variation for selection to act upon, and also to identify genomic regions that resisted hunter-gatherer introgression and may thus have contributed to agricultural adaptations. We used genome-wide DNA from 677 individuals spanning Mesolithic and Neolithic Europe to infer ancestry deviations in the genomes of admixed individuals and to test for natural selection after admixture by testing for deviations from a genome-wide null distribution. We find that the region around the pigmentation-associated gene SLC24A5 shows the greatest overrepresentation of Neolithic local ancestry in the genome (|Z| = 3.46). In contrast, we find the greatest overrepresentation of Mesolithic ancestry across the major histocompatibility complex (MHC; |Z| = 4.21), a major immunity locus, which also shows allele frequency deviations indicative of selection following admixture (p = 1 × 10-56). This could reflect negative frequency-dependent selection on MHC alleles common in Neolithic populations or that Mesolithic alleles were positively selected for and facilitated adaptation in Neolithic populations to pathogens or other environmental factors. Our study extends previous results that highlight immune function and pigmentation as targets of adaptation in more recent populations to selection processes in the Stone Age.
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Affiliation(s)
- Tom Davy
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
| | - Dan Ju
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Iain Mathieson
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, 415 Curie Blvd, Philadelphia, PA 19104, USA
| | - Pontus Skoglund
- Ancient Genomics Laboratory, Francis Crick Institute, 1 Midland Road, NW1 1AT London, UK.
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15
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Mobility and kinship in the world's first village societies. Proc Natl Acad Sci U S A 2023; 120:e2209480119. [PMID: 36649403 PMCID: PMC9942817 DOI: 10.1073/pnas.2209480119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Around 10,000 y ago in southwest Asia, the cessation of a mobile lifestyle and the emergence of the first village communities during the Neolithic marked a fundamental change in human history. The first communities were small (tens to hundreds of individuals) but remained semisedentary. So-called megasites appeared soon after, occupied by thousands of more sedentary inhabitants. Accompanying this shift, the material culture and ancient ecological data indicate profound changes in economic and social behavior. A shift from residential to logistical mobility and increasing population size are clear and can be explained by either changes in fertility and/or aggregation of local groups. However, as sedentism increased, small early communities likely risked inbreeding without maintaining or establishing exogamous relationships typical of hunter-gatherers. Megasites, where large populations would have made endogamy sustainable, could have avoided this risk. To examine the role of kinship practices in the rise of megasites, we measured strontium and oxygen isotopes in tooth enamel from 99 individuals buried at Pınarbaşı, Boncuklu, and Çatalhöyük (Turkey) over 7,000 y. These sites are geographically proximate and, critically, span both early sedentary behaviors (Pınarbaşı and Boncuklu) and the rise of a local megasite (Çatalhöyük). Our data are consistent with the presence of only local individuals at Pınarbaşı and Boncuklu, whereas at Çatalhöyük, several nonlocals are present. The Çatalhöyük data stand in contrast to other megasites where bioarchaeological evidence has pointed to strict endogamy. These different kinship behaviors suggest that megasites may have arisen by employing unique, community-specific kinship practices.
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16
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Isotopic and DNA analyses reveal multiscale PPNB mobility and migration across Southeastern Anatolia and the Southern Levant. Proc Natl Acad Sci U S A 2023; 120:e2210611120. [PMID: 36649412 PMCID: PMC9942848 DOI: 10.1073/pnas.2210611120] [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: 01/19/2023] Open
Abstract
Growing reliance on animal and plant domestication in the Near East and beyond during the Pre-Pottery Neolithic B (PPNB) (the ninth to eighth millennium BC) has often been associated with a "revolutionary" social transformation from mobility toward more sedentary lifestyles. We are able to yield nuanced insights into the process of the Neolithization in the Near East based on a bioarchaeological approach integrating isotopic and archaeogenetic analyses on the bone remains recovered from Nevalı Çori, a site occupied from the early PPNB in Turkey where some of the earliest evidence of animal and plant domestication emerged, and from Ba'ja, a typical late PPNB site in Jordan. In addition, we present the archaeological sequence of Nevalı Çori together with newly generated radiocarbon dates. Our results are based on strontium (87Sr/86Sr), carbon, and oxygen (δ18O and δ13Ccarb) isotopic analyses conducted on 28 human and 29 animal individuals from the site of Nevalı Çori. 87Sr/86Sr results indicate mobility and connection with the contemporaneous surrounding sites during the earlier PPNB prior to an apparent decline in this mobility at a time of growing reliance on domesticates. Genome-wide data from six human individuals from Nevalı Çori and Ba'ja demonstrate a diverse gene pool at Nevalı Çori that supports connectedness within the Fertile Crescent during the earlier phases of Neolithization and evidence of consanguineous union in the PPNB Ba'ja and the Iron Age Nevalı Çori.
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17
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Koptekin D, Yüncü E, Rodríguez-Varela R, Altınışık NE, Psonis N, Kashuba N, Yorulmaz S, George R, Kazancı DD, Kaptan D, Gürün K, Vural KB, Gemici HC, Vassou D, Daskalaki E, Karamurat C, Lagerholm VK, Erdal ÖD, Kırdök E, Marangoni A, Schachner A, Üstündağ H, Shengelia R, Bitadze L, Elashvili M, Stravopodi E, Özbaşaran M, Duru G, Nafplioti A, Rose CB, Gencer T, Darbyshire G, Gavashelishvili A, Pitskhelauri K, Çevik Ö, Vuruşkan O, Kyparissi-Apostolika N, Büyükkarakaya AM, Oğuzhanoğlu U, Günel S, Tabakaki E, Aliev A, Ibrahimov A, Shadlinski V, Sampson A, Kılınç GM, Atakuman Ç, Stamatakis A, Poulakakis N, Erdal YS, Pavlidis P, Storå J, Özer F, Götherström A, Somel M. Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean. Curr Biol 2023; 33:41-57.e15. [PMID: 36493775 PMCID: PMC9839366 DOI: 10.1016/j.cub.2022.11.034] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/13/2022] [Accepted: 11/15/2022] [Indexed: 12/13/2022]
Abstract
We present a spatiotemporal picture of human genetic diversity in Anatolia, Iran, Levant, South Caucasus, and the Aegean, a broad region that experienced the earliest Neolithic transition and the emergence of complex hierarchical societies. Combining 35 new ancient shotgun genomes with 382 ancient and 23 present-day published genomes, we found that genetic diversity within each region steadily increased through the Holocene. We further observed that the inferred sources of gene flow shifted in time. In the first half of the Holocene, Southwest Asian and the East Mediterranean populations homogenized among themselves. Starting with the Bronze Age, however, regional populations diverged from each other, most likely driven by gene flow from external sources, which we term "the expanding mobility model." Interestingly, this increase in inter-regional divergence can be captured by outgroup-f3-based genetic distances, but not by the commonly used FST statistic, due to the sensitivity of FST, but not outgroup-f3, to within-population diversity. Finally, we report a temporal trend of increasing male bias in admixture events through the Holocene.
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Affiliation(s)
- Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey,Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey,Corresponding author
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, Stockholm, Sweden,Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - N. Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe 06800, Ankara, Turkey
| | - Nikolaos Psonis
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology – Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece
| | - Natalia Kashuba
- Department of Archaeology and Ancient History, Archaeology, Uppsala University, Uppsala, Sweden
| | - Sevgi Yorulmaz
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Robert George
- Centre for Palaeogenetics, Stockholm, Sweden,School of Medicine, University of Notre Dame, Sydney, Australia
| | - Duygu Deniz Kazancı
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey,Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe 06800, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Hasan Can Gemici
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Despoina Vassou
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology – Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece
| | - Evangelia Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Cansu Karamurat
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Vendela K. Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden,Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ömür Dilek Erdal
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Emrah Kırdök
- Department of Biotechnology, Mersin University, 33343 Yenişehir, Mersin, Turkey
| | | | - Andreas Schachner
- Deutsches Archäologisches Institut, Inönü Cad. 10, Gümüşsuyu, 34437 İstanbul, Turkey
| | - Handan Üstündağ
- Department of Archaeology, Anadolu University, 26470 Eskişehir, Turkey
| | - Ramaz Shengelia
- Department of the History of Medicine and Bioethics, Tbilisi State Medical University, Tbilisi 0162, Georgia
| | - Liana Bitadze
- Institute of History and Ethnology, Tbilisi State University, Tbilisi, Georgia
| | - Mikheil Elashvili
- Cultural Heritage and Environment Research Center, School of Natural Sciences and Medicine, Ilia State University, Tbilisi, Georgia
| | - Eleni Stravopodi
- Ephorate of Palaeoanthropology and Speleology, Ministry of Culture and Sports, 11636 Athens, Greece
| | | | - Güneş Duru
- Mimar Sinan Fine Arts University, 34134 Istanbul, Turkey
| | - Argyro Nafplioti
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology – Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece
| | - C. Brian Rose
- Department of Classical Studies, University of Pennsylvania, Philadelphia, PA, USA
| | - Tuğba Gencer
- Department of History of Medicine and Ethics, Cerrahpasa Faculty of Medicine, Istanbul University, Istanbul, Turkey
| | | | - Alexander Gavashelishvili
- Center of Biodiversity Studies, Institute of Ecology, Ilia State University, Cholokashvili Str. 5, Tbilisi 0162, Georgia
| | | | - Özlem Çevik
- Department of Archaeology, Trakya University, Edirne, Turkey
| | - Osman Vuruşkan
- Department of Archaeology, Trakya University, Edirne, Turkey
| | | | - Ali Metin Büyükkarakaya
- Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey,Human Behavioral Ecology and Archaeometry Laboratory (IDEA Lab), Hacettepe University, Ankara, Turkey
| | - Umay Oğuzhanoğlu
- Department of Archaeology, Pamukkale University, Denizli, Turkey
| | - Sevinç Günel
- Department of Archaeology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Eugenia Tabakaki
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology – Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece
| | - Akper Aliev
- Azerbaijan DNA Project, Family Tree DNA, Houston, TX, USA
| | | | | | - Adamantios Sampson
- Department of Mediterranean Studies, University of Aegean, Dimokratias st., 85100 Rhodes, Greece
| | - Gülşah Merve Kılınç
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Çiğdem Atakuman
- Institute of Social Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Alexandros Stamatakis
- Computational Molecular Evolution Group, Heidelberg Institute for Theoretical Studies, 69118 Heidelberg, Germany,Institute for Theoretical Informatics, Karlsruhe Institute of Technology, 76131 Karlsruhe, Germany
| | - Nikos Poulakakis
- Ancient DNA Lab, Institute of Molecular Biology and Biotechnology (IMBB), Foundation for Research and Technology – Hellas (FORTH), N. Plastira 100, Vassilika Vouton, GR-70013 Irakleio, Greece,Natural History Museum of Crete, School of Sciences and Engineering, University of Crete, Knossos Avenue, 71409 Irakleio, Greece,Department of Biology, School of Sciences and Engineering, University of Crete, Vassilika Vouton, 70013 Irakleio, Greece
| | - Yılmaz Selim Erdal
- Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe 06800, Ankara, Turkey,Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Pavlos Pavlidis
- Institute of Computer Science, Foundation for Research and Technology-Hellas (FORTH), 70013 Heraklion, Greece
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Füsun Özer
- Human-G Laboratory, Department of Anthropology, Hacettepe University, Beytepe 06800, Ankara, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden,Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden,Corresponding author
| | - Mehmet Somel
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey,Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey,Corresponding author
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18
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Söylev A, Çokoglu SS, Koptekin D, Alkan C, Somel M. CONGA: Copy number variation genotyping in ancient genomes and low-coverage sequencing data. PLoS Comput Biol 2022; 18:e1010788. [PMID: 36516232 PMCID: PMC9873172 DOI: 10.1371/journal.pcbi.1010788] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2022] [Revised: 01/24/2023] [Accepted: 12/03/2022] [Indexed: 12/15/2022] Open
Abstract
To date, ancient genome analyses have been largely confined to the study of single nucleotide polymorphisms (SNPs). Copy number variants (CNVs) are a major contributor of disease and of evolutionary adaptation, but identifying CNVs in ancient shotgun-sequenced genomes is hampered by typical low genome coverage (<1×) and short fragments (<80 bps), precluding standard CNV detection software to be effectively applied to ancient genomes. Here we present CONGA, tailored for genotyping CNVs at low coverage. Simulations and down-sampling experiments suggest that CONGA can genotype deletions >1 kbps with F-scores >0.75 at ≥1×, and distinguish between heterozygous and homozygous states. We used CONGA to genotype 10,002 outgroup-ascertained deletions across a heterogenous set of 71 ancient human genomes spanning the last 50,000 years, produced using variable experimental protocols. A fraction of these (21/71) display divergent deletion profiles unrelated to their population origin, but attributable to technical factors such as coverage and read length. The majority of the sample (50/71), despite originating from nine different laboratories and having coverages ranging from 0.44×-26× (median 4×) and average read lengths 52-121 bps (median 69), exhibit coherent deletion frequencies. Across these 50 genomes, inter-individual genetic diversity measured using SNPs and CONGA-genotyped deletions are highly correlated. CONGA-genotyped deletions also display purifying selection signatures, as expected. CONGA thus paves the way for systematic CNV analyses in ancient genomes, despite the technical challenges posed by low and variable genome coverage.
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Affiliation(s)
- Arda Söylev
- Department of Computer Engineering, Konya Food and Agriculture University, Konya, Turkey
- Institute for Medical Biometry and Bioinformatics, Medical Faculty, Heinrich Heine University, Düsseldorf, Germany
- * E-mail: (AS); (MS)
| | | | - Dilek Koptekin
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - Can Alkan
- Department of Computer Engineering, Bilkent University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biology, Middle East Technical University, Ankara, Turkey
- * E-mail: (AS); (MS)
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19
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Altınışık NE, Kazancı DD, Aydoğan A, Gemici HC, Erdal ÖD, Sarıaltun S, Vural KB, Koptekin D, Gürün K, Sağlıcan E, Fernandes D, Çakan G, Koruyucu MM, Lagerholm VK, Karamurat C, Özkan M, Kılınç GM, Sevkar A, Sürer E, Götherström A, Atakuman Ç, Erdal YS, Özer F, Erim Özdoğan A, Somel M. A genomic snapshot of demographic and cultural dynamism in Upper Mesopotamia during the Neolithic Transition. SCIENCE ADVANCES 2022; 8:eabo3609. [PMID: 36332018 PMCID: PMC9635823 DOI: 10.1126/sciadv.abo3609] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 09/16/2022] [Indexed: 06/16/2023]
Abstract
Upper Mesopotamia played a key role in the Neolithic Transition in Southwest Asia through marked innovations in symbolism, technology, and diet. We present 13 ancient genomes (c. 8500 to 7500 cal BCE) from Pre-Pottery Neolithic Çayönü in the Tigris basin together with bioarchaeological and material culture data. Our findings reveal that Çayönü was a genetically diverse population, carrying mixed ancestry from western and eastern Fertile Crescent, and that the community received immigrants. Our results further suggest that the community was organized along biological family lines. We document bodily interventions such as head shaping and cauterization among the individuals examined, reflecting Çayönü's cultural ingenuity. Last, we identify Upper Mesopotamia as the likely source of eastern gene flow into Neolithic Anatolia, in line with material culture evidence. We hypothesize that Upper Mesopotamia's cultural dynamism during the Neolithic Transition was the product not only of its fertile lands but also of its interregional demographic connections.
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Affiliation(s)
- N. Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Duygu Deniz Kazancı
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ayça Aydoğan
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Hasan Can Gemici
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Ömür Dilek Erdal
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Savaş Sarıaltun
- Department of Museology and Cultural Heritage Management, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Dilek Koptekin
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Daniel Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Gökhan Çakan
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Meliha Melis Koruyucu
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Cansu Karamurat
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Sıhhiye, Ankara, Turkey
| | - Arda Sevkar
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Yılmaz Selim Erdal
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
- Husbio-L Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Füsun Özer
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Beytepe, Ankara, Turkey
| | - Aslı Erim Özdoğan
- Department of Archaeology, Çanakkale Onsekiz Mart University, Çanakkale 17100, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
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Lazaridis I, Alpaslan-Roodenberg S, Acar A, Açıkkol A, Agelarakis A, Aghikyan L, Akyüz U, Andreeva D, Andrijasevic 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, Carlson KSD, Eccles LR, Elenski N, Engin A, Erdoğan N, ErirPazarcı 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 D, 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, Milasinovic 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, SönmezSözer 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. Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia. Science 2022; 377:982-987. [PMID: 36007054 PMCID: PMC9983685 DOI: 10.1126/science.abq0762] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
We present the first ancient DNA data from the Pre-Pottery Neolithic of Mesopotamia (Southeastern Turkey and Northern Iraq), Cyprus, and the Northwestern Zagros, along with the first data from Neolithic Armenia. We show that these and neighboring populations were formed through admixture of pre-Neolithic sources related to Anatolian, Caucasus, and Levantine hunter-gatherers, forming a Neolithic continuum of ancestry mirroring the geography of West Asia. By analyzing Pre-Pottery and Pottery Neolithic populations of Anatolia, we show that the former were derived from admixture between Mesopotamian-related and local Epipaleolithic-related sources, but the latter experienced additional Levantine-related gene flow, thus documenting at least two pulses of migration from the Fertile Crescent heartland to the early farmers of Anatolia.
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Affiliation(s)
- Iosif Lazaridis
- Department for Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Corresponding authors. Iosif Lazaridis (), Songül Alpaslan-Roodenberg (), Ron Pinhasi (), David Reich ()
| | - Songül Alpaslan-Roodenberg
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA,Department of Evolutionary Anthropology, University of Vienna, 1090 Vienna, Austria,Corresponding authors. Iosif Lazaridis (), Songül Alpaslan-Roodenberg (), Ron Pinhasi (), David Reich ()
| | - Ayşe Acar
- Mardin Artuklu University, Faculty of Letters, Department of Anthropology, Artuklu, 47510, Mardin, Turkey
| | - Ayşen Açıkkol
- Sivas Cumhuriyet University, Faculty of Letters, Department of Anthropology, 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
- Burdur Mehmet Akif University, Faculty of Arts and Science, Department of Anthropology, 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, Tirana 1010, 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
- Van Yüzüncü Yıl University, Faculty of Humanities, Department of Archaeology, 65090 Tuşba, Van, Turkey
| | - Ahmet Bilir
- Düzce University, Faculty of Science and Letters, Department of Archaeology, 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 Kotor, Montenegro
| | | | - Katharina Buttinger
- Department of Evolutionary Anthropology, University of Vienna, 1090 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, 1090 Vienna, Austria
| | - Stefan Chohadzhiev
- University of Veliko Tarnovo “St. St. Cyril and 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
- University of Cincinnati, Department of Classics, Cincinnati, OH 45221, USA
| | | | - Valentin Dergachev
- Center of Archaeology, Institute of Cultural Heritage, Academy of Science of Moldova, 2001 Chișinău, Moldova
| | - Zafer Derin
- Ege University, Faculty of Letters, Department of Archaeology, 35100 Bornova-Izmir, Turkey
| | - Sylvia Deskaj
- University of Michigan, Museum of Anthropological Archaeology, 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
- Gaziantep University, Faculty of Science and Letters, Department of Archaeology, 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, 1090 Vienna, Austria,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, 1090 Vienna, Austria
| | - Alin Frînculeasa
- Prahova County Museum of History and Archaeology, 100042 Ploiești, Romania
| | - Michael L. Galaty
- University of Michigan, Museum of Anthropological Archaeology, Ann Arbor, MI 48109, USA
| | - Beatriz Gamarra
- Institut Català de Paleoecologia Humana i Evolució Social, 43007 Tarragona, Spain,Universitat Rovira i Virgili, Departament d’Història i Història de l’Art, 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
- Çukurova University, Faculty of Science and Letters, Department of Archaeology, 01330 BalçalıSarıçam-Adana, Turkey
| | - Timur Gültekin
- Ankara University, Faculty of Humanities, Department of Anthropology, 06100 Sıhhiye, Ankara, Turkey
| | - Serkan Gündüz
- Uludağ University, Faculty of Science and Letters, Department of Archaeology, 16059 Görükle, Bursa, Turkey
| | - Tamás Hajdu
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary,Department of Anthropology, Hungarian Natural History Museum, 1117 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
| | | | - 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
- Atatürk University, Faculty of Letters, Department of Archaeology, 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, 1090 Vienna, Austria
| | - Douglas 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, Budapest, Hungary,Department of Anthropology, Hungarian Natural History Museum, 1117 Budapest, Hungary
| | - Sinan Kılıç
- Van Yüzüncü Yıl University, Faculty of Humanities, Department of Archaeology, 65090 Tuşba, Van, Turkey
| | - Paul Klostermann
- Natural History Museum Vienna, Department of Anthropology, 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, UC 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 & Arts, St. Peter-Bezirk 10, A-5020 Salzburg, Austria
| | - Kirsi O. Lorentz
- The Cyprus Institute, Science and Technology in Archaeology and Culture Research Center, 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, 1090 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 for 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 for Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA,Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - 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, 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, 1090 Vienna, Austria
| | - Nurettin Öztürk
- Atatürk University, Faculty of Letters, Department of Archaeology, 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 for 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
- 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
- University of Wisconsin-Madison, Laboratory for Archaeological Chemistry, 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 Palaeontology and Geology, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Kamal Raeuf Aziz
- Sulaimaniyah Directorate of Antiquities and Heritage, Sulaimaniyah, 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
- Bulgarian Academy of Science, Institute of Experimental Morphology, Pathology and Archeology with Museum, 1113 Sofia, Bulgaria
| | - Mustafa Şahin
- Uludağ University, Faculty of Science and Letters, Department of Archaeology, 16059 Görükle, Bursa, Turkey
| | - Ayşegül Şarbak
- Hitit University, Faculty of Science and Letters, Department of Antrophology, 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, 1090 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
- Ankara University, Faculty of Language and History - Geography, Department of Anthropology, 06100 Sıhhiye, Ankara, Turkey
| | - Michel Shamoon-Pour
- Binghamton University, 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 Laboratorary 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
- Fr. I. Rainer” Institute of Anthropology, 050711 Bucharest, Romania
| | - Bilal Söğüt
- Pamukkale University, Faculty of Science and Arts, Department of Archaeology, 20070 Denizli, Turkey
| | | | - Çilem SönmezSözer
- Ankara University, Faculty of Language and History - Geography, Department of Anthropology, 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
- University of Cincinnati, Department of Classics, Cincinnati, OH 45221, USA
| | - Fadime Suata-Alpaslan
- Istanbul University, Faculty of Letters, Department of Anthropology, 34134 Istanbul, Turkey
| | - Alexander Suvorov
- Department of Cultures, University of Helsinki, 00100 Helsinki, Finland
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, 1097 Budapest, Hungary
| | - Tamás Szeniczey
- Department of Biological Anthropology, Institute of Biology, Eötvös Loránd University, Budapest, Hungary,Department of Anthropology, Hungarian Natural History Museum, 1117 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,University of Avignon, Avignon, France
| | | | - Sevi Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Atila Türker
- Ondokuz Mayıs University, Faculty of Science and Letters, Department of Archaeology, 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, 1090 Vienna, Austria
| | - Sam Walsh
- Department of Archaeology, University of Reading, Reading, RG6 6AB, 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-Social Sciences, Bryn Athyn College, Bryn Athyn, PA 19009, USA,University of Pennsylvania, Penn Museum, PA 19104, USA
| | - Evgenii Yarovoy
- Moscow Region State University, Moscow Region, 141014 Mytishi, Russia
| | - Alper Yener Yavuz
- Burdur Mehmet Akif Ersoy University, Istiklal Campus, Department of Anthropology, 15100 Burdur, Turkey
| | - Hakan Yılmaz
- Van Yüzüncü Yıl University, Faculty of Humanities, Department of Archaeology, 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, 1090 Vienna, Austria
| | - Zhao Zhang
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Rafet Çavuşoğlu
- Van Yüzüncü Yıl University, Faculty of Humanities, Department of Archaeology, 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, 1090 Vienna, Austria,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.,Corresponding authors. Iosif Lazaridis (), Songül Alpaslan-Roodenberg (), Ron Pinhasi (), David Reich ()
| | - David Reich
- Department for 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,Corresponding authors. Iosif Lazaridis (), Songül Alpaslan-Roodenberg (), Ron Pinhasi (), David Reich ()
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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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Silva NM, Kreutzer S, Souleles A, Triantaphyllou S, Kotsakis K, Urem-Kotsou D, Halstead P, Efstratiou N, Kotsos S, Karamitrou-Mentessidi G, Adaktylou F, Chondroyianni-Metoki A, Pappa M, Ziota C, Sampson A, Papathanasiou A, Vitelli K, Cullen T, Kyparissi-Apostolika N, Lanz AZ, Peters J, Rio J, Wegmann D, Burger J, Currat M, Papageorgopoulou C. Ancient mitochondrial diversity reveals population homogeneity in Neolithic Greece and identifies population dynamics along the Danubian expansion axis. Sci Rep 2022; 12:13474. [PMID: 35931723 PMCID: PMC9356035 DOI: 10.1038/s41598-022-16745-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Accepted: 07/14/2022] [Indexed: 11/09/2022] Open
Abstract
The aim of the study is to investigate mitochondrial diversity in Neolithic Greece and its relation to hunter-gatherers and farmers who populated the Danubian Neolithic expansion axis. We sequenced 42 mitochondrial palaeogenomes from Greece and analysed them together with European set of 328 mtDNA sequences dating from the Early to the Final Neolithic and 319 modern sequences. To test for population continuity through time in Greece, we use an original structured population continuity test that simulates DNA from different periods by explicitly considering the spatial and temporal dynamics of populations. We explore specific scenarios of the mode and tempo of the European Neolithic expansion along the Danubian axis applying spatially explicit simulations coupled with Approximate Bayesian Computation. We observe a striking genetic homogeneity for the maternal line throughout the Neolithic in Greece whereas population continuity is rejected between the Neolithic and present-day Greeks. Along the Danubian expansion axis, our best-fitting scenario supports a substantial decrease in mobility and an increasing local hunter-gatherer contribution to the gene-pool of farmers following the initial rapid Neolithic expansion. Οur original simulation approach models key demographic parameters rather than inferring them from fragmentary data leading to a better understanding of this important process in European prehistory.
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Affiliation(s)
- Nuno M Silva
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University of Mainz, 55099, Mainz, Germany.,Functional Genomics Center Zurich/GEML, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece
| | - Sevasti Triantaphyllou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Kostas Kotsakis
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece
| | - Paul Halstead
- Emeritus, Department of Archaeology, University of Sheffield, Sheffield, S1 3NJ, UK
| | - Nikos Efstratiou
- Faculty of Philosophy, School of History and Archaeology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Stavros Kotsos
- Ephorate of Antiquities of Thessaloniki City, Hellenic Ministry of Culture and Sports, 54003, Thessaloniki, Greece
| | | | - Fotini Adaktylou
- Ephorate of Antiquities of Chalcidice and Mount Athos, Hellenic Ministry of Culture and Sports, 63100, Poligiros Chalcidice, Greece
| | | | - Maria Pappa
- Ephorate of Antiquities of Thessaloniki Region, Hellenic Ministry of Culture and Sports, 54646, Thessaloniki, Greece
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100, Florina, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of Aegean, 85132, Rhodes, Greece
| | - Anastasia Papathanasiou
- Ephorate of Paleoanthropology and Speleology, Hellenic Ministry of Culture and Sports, 11636, Athens, Greece
| | - Karen Vitelli
- Prof. Emerita, Department of Anthropology, Franchthi Cave Project, Indiana University Bloomington, Bloomington, USA
| | - Tracey Cullen
- American School of Classical Studies at Athens, Princeton, NJ, USA
| | - Nina Kyparissi-Apostolika
- Ephor Emerita of the Ephorate of Paleoanthropology and Speleology, Hellenic Ministry of Culture and Sports, 11636, Athens, Greece
| | - Andrea Zeeb Lanz
- General Direction for Cultural Heritage of Rhineland-Palatinate, Speyer, Germany
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, Munich, Germany.,SNSB, State Collection of Palaeoanatomy Munich, Munich, Germany
| | - Jérémy Rio
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University of Mainz, 55099, Mainz, Germany.,Functional Genomics Center Zurich/GEML, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Mathias Currat
- Department of Genetics & Evolution, University of Geneva, Geneva, Switzerland. .,Institute of Genetics and Genomics in Geneva (IGE3), University of Geneva, Geneva, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History & Ethnology, Democritus University of Thrace, 69100, Komotini, Greece.
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23
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Ariano B, Mattiangeli V, Breslin EM, Parkinson EW, McLaughlin TR, Thompson JE, Power RK, Stock JT, Mercieca-Spiteri B, Stoddart S, Malone C, Gopalakrishnan S, Cassidy LM, Bradley DG. Ancient Maltese genomes and the genetic geography of Neolithic Europe. Curr Biol 2022; 32:2668-2680.e6. [PMID: 35588742 PMCID: PMC9245899 DOI: 10.1016/j.cub.2022.04.069] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/07/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans.
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Affiliation(s)
- Bruno Ariano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eóin W Parkinson
- Department of Classics and Archaeology, University of Malta, Msida 2080, Malta
| | - T Rowan McLaughlin
- Department of Scientific Research, The British Museum, Great Russell Street, London WC1B 3DG, UK
| | - Jess E Thompson
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ronika K Power
- Department of History and Archaeology, Macquarie University, 25B Wally's Walk, Sydney, NSW, Australia
| | - Jay T Stock
- Department of Anthropology, Western University, 1151 Richmond St, London, ON N6G 2V4, Canada
| | | | - Simon Stoddart
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Caroline Malone
- School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, UK
| | - Shyam Gopalakrishnan
- GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark.
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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24
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Assessing temporal and geographic contacts across the Adriatic Sea through the analysis of genome-wide data from Southern Italy. Genomics 2022; 114:110405. [PMID: 35709925 DOI: 10.1016/j.ygeno.2022.110405] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 06/01/2022] [Accepted: 06/09/2022] [Indexed: 11/22/2022]
Abstract
Southern Italy was characterised by a complex prehistory that started with different Palaeolithic cultures, later followed by the Neolithization and the demic dispersal from the Pontic-Caspian Steppe during the Bronze Age. Archaeological and historical evidences point to a link between Southern Italians and the Balkans still present in modern times. To shed light on these dynamics, we analysed around 700 South Mediterranean genomes combined with informative ancient DNAs. Our findings revealed high affinities of South-Eastern Italians with modern Eastern Peloponnesians, and a closer affinity of ancient Greek genomes with those from specific regions of South Italy than modern Greek genomes. The higher similarity could be associated with a Bronze Age component ultimately originating from the Caucasus with high Iranian and Anatolian Neolithic ancestries. Furthermore, extremely differentiated allele frequencies among Northern and Southern Italy revealed putatively adapted SNPs in genes involved in alcohol metabolism, nevi features and immunological traits.
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25
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Srigyan M, Bolívar H, Ureña I, Santana J, Petersen A, Iriarte E, Kırdök E, Bergfeldt N, Mora A, Jakobsson M, Abdo K, Braemer F, Smith C, Ibañez JJ, Götherström A, Günther T, Valdiosera C. Bioarchaeological evidence of one of the earliest Islamic burials in the Levant. Commun Biol 2022; 5:554. [PMID: 35672445 PMCID: PMC9174286 DOI: 10.1038/s42003-022-03508-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 05/20/2022] [Indexed: 11/27/2022] Open
Abstract
The Middle East plays a central role in human history harbouring a vast diversity of ethnic, cultural and religious groups. However, much remains to be understood about past and present genomic diversity in this region. Here we present a multidisciplinary bioarchaeological analysis of two individuals dated to the late 7th and early 8th centuries, the Umayyad Era, from Tell Qarassa, an open-air site in modern-day Syria. Radiocarbon dates and burial type are consistent with one of the earliest Islamic Arab burials in the Levant. Interestingly, we found genomic similarity to a genotyped group of modern-day Bedouins and Saudi rather than to most neighbouring Levantine groups. This study represents the genomic analysis of a secondary use site with characteristics consistent with an early Islamic burial in the Levant. We discuss our findings and possible historic scenarios in the light of forces such as genetic drift and their possible interaction with religious and cultural processes (including diet and subsistence practices). Ancient genomic and archaeological data combine to identify a surprisingly early Islamic burial in modern day Syria.
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Affiliation(s)
- Megha Srigyan
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Department of Ecology and Evolutionary Biology, University of California Santa Cruz, Santa Cruz, CA, 95064, USA
| | - Héctor Bolívar
- Centre for Palaeogenetics, 10691, Stockholm, Sweden.,Instituto del Patrimonio Cultural de España, 28040, Madrid, Spain
| | - Irene Ureña
- Centre for Palaeogenetics, 10691, Stockholm, Sweden
| | - Jonathan Santana
- Department of Historical Sciences, Universidad de Las Palmas de Gran Canaria, Las Palmas de G.C., E35001, Spain
| | | | - Eneko Iriarte
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain
| | - Emrah Kırdök
- Department of Biotechnology, Mersin University, 33343, Mersin, Turkey
| | | | - Alice Mora
- Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Khaled Abdo
- General Directorate of Antiquities and Museums, Damascus, Syrian Arab Republic
| | - Frank Braemer
- Université Côte d'Azur, CNRS, Culture et Environment, Préhistoire Antiquité Moyen Age, Nice, France
| | - Colin Smith
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain.,Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Juan José Ibañez
- Archaeology of Social Dynamics, Milà i Fontanals Institution, Spanish National Research Council (CSIC), Barcelona, Spain
| | | | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.
| | - Cristina Valdiosera
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001, Burgos, Spain. .,Dept. Archaeology and History, La Trobe University, Melbourne, VIC, 3086, Australia.
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26
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Chintalapati M, Patterson N, Moorjani P. The spatiotemporal patterns of major human admixture events during the European Holocene. eLife 2022; 11:77625. [PMID: 35635751 PMCID: PMC9293011 DOI: 10.7554/elife.77625] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.
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Affiliation(s)
- Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nick Patterson
- Program in Medical and Population Genetics, Broad Institute, Cambridge, United States
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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27
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Bioarchaeological and palaeogenomic portrait of two Pompeians that died during the eruption of Vesuvius in 79 AD. Sci Rep 2022; 12:6468. [PMID: 35618734 PMCID: PMC9135728 DOI: 10.1038/s41598-022-10899-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/08/2022] [Indexed: 12/12/2022] Open
Abstract
The archaeological site of Pompeii is one of the 54 UNESCO World Heritage sites in Italy, thanks to its uniqueness: the town was completely destroyed and buried by a Vesuvius’ eruption in 79 AD. In this work, we present a multidisciplinary approach with bioarchaeological and palaeogenomic analyses of two Pompeian human remains from the Casa del Fabbro. We have been able to characterize the genetic profile of the first Pompeian’ genome, which has strong affinities with the surrounding central Italian population from the Roman Imperial Age. Our findings suggest that, despite the extensive connection between Rome and other Mediterranean populations, a noticeable degree of genetic homogeneity exists in the Italian peninsula at that time. Moreover, palaeopathological analyses identified the presence of spinal tuberculosis and we further investigated the presence of ancient DNA from Mycobacterium tuberculosis. In conclusion, our study demonstrates the power of a combined approach to investigate ancient humans and confirms the possibility to retrieve ancient DNA from Pompeii human remains. Our initial findings provide a foundation to promote an intensive and extensive paleogenetic analysis in order to reconstruct the genetic history of population from Pompeii, a unique archaeological site.
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28
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The genomic origins of the world's first farmers. Cell 2022; 185:1842-1859.e18. [PMID: 35561686 PMCID: PMC9166250 DOI: 10.1016/j.cell.2022.04.008] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 03/04/2022] [Accepted: 04/06/2022] [Indexed: 11/24/2022]
Abstract
The precise genetic origins of the first Neolithic farming populations in Europe and Southwest Asia, as well as the processes and the timing of their differentiation, remain largely unknown. Demogenomic modeling of high-quality ancient genomes reveals that the early farmers of Anatolia and Europe emerged from a multiphase mixing of a Southwest Asian population with a strongly bottlenecked western hunter-gatherer population after the last glacial maximum. Moreover, the ancestors of the first farmers of Europe and Anatolia went through a period of extreme genetic drift during their westward range expansion, contributing highly to their genetic distinctiveness. This modeling elucidates the demographic processes at the root of the Neolithic transition and leads to a spatial interpretation of the population history of Southwest Asia and Europe during the late Pleistocene and early Holocene.
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29
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Gelabert P, Schmidt RW, Fernandes DM, Karsten JK, Harper TK, Madden GD, Ledogar SH, Sokhatsky M, Oota H, Kennett DJ, Pinhasi R. Genomes from Verteba cave suggest diversity within the Trypillians in Ukraine. Sci Rep 2022; 12:7242. [PMID: 35508651 PMCID: PMC9068698 DOI: 10.1038/s41598-022-11117-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 04/15/2022] [Indexed: 11/24/2022] Open
Abstract
The transition to agriculture occurred relatively late in Eastern Europe, leading researchers to debate whether it was a gradual, interactive process or a colonisation event. In the forest and forest-steppe regions of Ukraine, farming appeared during the fifth millennium BCE, associated with the Cucuteni-Trypillia cultural complex (CTCC, ~ 5000–3000 BCE). Across Europe, the Neolithisation process was highly variable across space and over time. Here, we investigate the population dynamics of early agriculturalists from the eastern forest-steppe region based on the analyses of 20 ancient genomes from the site of Verteba Cave (3935–825 cal BCE). Results reveal that the CTCC individuals’ ancestry is related to both western hunter-gatherers and Near Eastern farmers, has no local ancestry associated with Ukrainian Neolithic hunter-gatherers and has steppe ancestry. An Early Bronze Age individual has an ancestry profile related to the Yamnaya expansions but with 20% of ancestry related to the other Trypillian individuals, which suggests admixture between the Trypillians and the incoming populations carrying steppe-related ancestry. A Late Bronze Age individual dated to 980–825 cal BCE has a genetic profile indicating affinity to Beaker-related populations, detected close to 1000 years after the end of the Bell Beaker phenomenon during the third millennium BCE.
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Affiliation(s)
- Pere Gelabert
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
| | - Ryan W Schmidt
- University of Porto, CIBIO-InBIO, Rua Padre Armando Quintas, nº 7, 4485-661, Vairão, Portugal. .,School of Archaeology & Earth Institute, University College, Dublin, Belfield, Dublin 4, Ireland.
| | - Daniel M Fernandes
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria.,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Jordan K Karsten
- Department of Anthropology, Global Religions, and Cultures, University of Wisconsin-Oshkosh, 800 Algoma Blvd, Oshkosh, WI, 54901, USA
| | - Thomas K Harper
- Institute for European and Mediterranean Archaeology, State University of New York at Buffalo, Buffalo, NY, 14260, USA
| | - Gwyn D Madden
- Department of Anthropology, Grand Valley State University, 1 Campus Dr., Allendale, MI, 49401, USA
| | - Sarah H Ledogar
- Department of Archaeology, Classics, and History, University of New England, Armidale, NSW, 2351, Australia
| | - Mykhailo Sokhatsky
- Borschiv Regional Museum of Local Lore, Borschiv, Ternopil Oblast, Ukraine
| | - Hiroki Oota
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Douglas J Kennett
- Department of Anthropology, University of California, Santa Barbara, CA, 93106, USA
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, Vienna, Austria. .,Human Evolution and Archaeological Sciences, University of Vienna, Vienna, Austria.
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30
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Genomic and dietary discontinuities during the Mesolithic and Neolithic in Sicily. iScience 2022; 25:104244. [PMID: 35494246 PMCID: PMC9051636 DOI: 10.1016/j.isci.2022.104244] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 03/21/2022] [Accepted: 04/07/2022] [Indexed: 11/23/2022] Open
Abstract
Sicily is a key region for understanding the agricultural transition in the Mediterranean because of its central position. Here, we present genomic and stable isotopic data for 19 prehistoric Sicilians covering the Mesolithic to Bronze Age periods (10,700–4,100 yBP). We find that Early Mesolithic hunter-gatherers (HGs) from Sicily are a highly drifted lineage of the Early Holocene western European HGs, whereas Late Mesolithic HGs carry ∼20% ancestry related to northern and (south) eastern European HGs, indicating substantial gene flow. Early Neolithic farmers are genetically most similar to farmers from the Balkans and Greece, with only ∼7% of ancestry from local Mesolithic HGs. The genetic discontinuities during the Mesolithic and Early Neolithic match the changes in material culture and diet. Three outlying individuals dated to ∼8,000 yBP; however, suggest that hunter-gatherers interacted with incoming farmers at Grotta dell’Uzzo, resulting in a mixed economy and diet for a brief interlude at the Mesolithic-Neolithic transition. Genetic transition between Early Mesolithic and Late Mesolithic hunter-gatherers A near-complete genetic turnover during the Mesolithic-Neolithic transition Exchange of subsistence practices between hunter-gatherers and early farmers
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31
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Schotsmans EMJ, Busacca G, Lin SC, Vasić M, Lingle AM, Veropoulidou R, Mazzucato C, Tibbetts B, Haddow SD, Somel M, Toksoy-Köksal F, Knüsel CJ, Milella M. New insights on commemoration of the dead through mortuary and architectural use of pigments at Neolithic Çatalhöyük, Turkey. Sci Rep 2022; 12:4055. [PMID: 35260577 PMCID: PMC8904496 DOI: 10.1038/s41598-022-07284-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 02/10/2022] [Indexed: 11/25/2022] Open
Abstract
The cultural use of pigments in human societies is associated with ritual activities and the creation of social memory. Neolithic Çatalhöyük (Turkey, 7100–5950 cal BC) provides a unique case study for the exploration of links between pigments in burials, demographic data and colourants in contemporary architectural contexts. This study presents the first combined analysis of funerary and architectural evidence of pigment use in Neolithic Anatolia and discusses the possible social processes underlying the observed statistical patterns. Results reveal that pigments were either applied directly to the deceased or included in the grave as a burial association. The most commonly used pigment was red ochre. Cinnabar was mainly applied to males and blue/green pigment was associated with females. A correlation was found between the number of buried individuals and the number of painted layers in the buildings. Mortuary practices seem to have followed specific selection processes independent of sex and age-at-death of the deceased. This study offers new insights about the social factors involved in pigment use in this community, and contributes to the interpretation of funerary practices in Neolithic Anatolia. Specifically, it suggests that visual expression, ritual performance and symbolic associations were elements of shared long-term socio-cultural practices.
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Affiliation(s)
- E M J Schotsmans
- Laboratoire d'Anthropologie des Populations Passées et Présentes (PACEA), UMR 5199, Université de Bordeaux, Pessac, France. .,Centre for Archaeological Science, University of Wollongong, Wollongong, Australia.
| | | | - S C Lin
- Centre for Archaeological Science, University of Wollongong, Wollongong, Australia.,ARC Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, Australia
| | | | - A M Lingle
- School of History, Archaeology, and Religion, Cardiff University, Cardiff, UK
| | - R Veropoulidou
- Museum of Byzantine Culture, Hellenic Ministry of Culture and Sports, Thessaloníki, Greece
| | - C Mazzucato
- Department of Anthropology, Stanford University, Stanford, USA
| | - B Tibbetts
- Department of Archaeology, University of Exeter, Exeter, UK
| | - S D Haddow
- Department of Cross-Cultural and Regional Studies, University of Copenhagen, Copenhagen, Denmark
| | - M Somel
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - F Toksoy-Köksal
- Department of Geological Engineering, Middle East Technical University (METU), Ankara, Turkey
| | - C J Knüsel
- Laboratoire d'Anthropologie des Populations Passées et Présentes (PACEA), UMR 5199, Université de Bordeaux, Pessac, France
| | - M Milella
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
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32
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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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33
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Aneli S, Saupe T, Montinaro F, Solnik A, Molinaro L, Scaggion C, Carrara N, Raveane A, Kivisild T, Metspalu M, Scheib CL, Pagani L. The genetic origin of Daunians and the Pan-Mediterranean southern Italian Iron Age context. Mol Biol Evol 2022; 39:6509524. [PMID: 35038748 PMCID: PMC8826970 DOI: 10.1093/molbev/msac014] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The geographical location and shape of Apulia, a narrow land stretching out in the sea at the South of Italy, made this region a Mediterranean crossroads connecting Western Europe and the Balkans. Such movements culminated at the beginning of the Iron Age with the Iapygian civilization which consisted of three cultures: Peucetians, Messapians, and Daunians. Among them, the Daunians left a peculiar cultural heritage, with one-of-a-kind stelae and pottery, but, despite the extensive archaeological literature, their origin has been lost to time. In order to shed light on this and to provide a genetic picture of Iron Age Southern Italy, we collected and sequenced human remains from three archaeological sites geographically located in Northern Apulia (the area historically inhabited by Daunians) and radiocarbon dated between 1157 and 275 calBCE. We find that Iron Age Apulian samples are still distant from the genetic variability of modern-day Apulians, they show a degree of genetic heterogeneity comparable with the cosmopolitan Republican and Imperial Roman civilization, even though a few kilometers and centuries separate them, and they are well inserted into the Iron Age Pan-Mediterranean genetic landscape. Our study provides for the first time a window on the genetic make-up of pre-Roman Apulia, whose increasing connectivity within the Mediterranean landscape, would have contributed to laying the foundation for modern genetic variability. In this light, the genetic profile of Daunians may be compatible with an at least partial autochthonous origin, with plausible contributions from the Balkan peninsula.
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Affiliation(s)
- Serena Aneli
- Department of Biology, University of Padua, Via Ugo Bassi, 58b, Padova 35121, Italy
| | - Tina Saupe
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Anu Solnik
- Core Facility,Institute of Genomics,University of Tartu, Riia 23B, Tartu, 51010 Estonia
| | - Ludovica Molinaro
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Cinzia Scaggion
- Department of Geosciences, University of Padua, Via Giovanni Gradenigo, 6, Padova 35131, Italy
| | - Nicola Carrara
- Anthropology Museum,University of Padova,Via Giotto, 1, Padova 35121, Italy
| | - Alessandro Raveane
- Laboratory of Hematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Toomas Kivisild
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia.,Department of Human Genetics, KU Leuven, Leuven, Herestraat 49, B-3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Christiana L Scheib
- Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia.,St John's College, Cambridge, CB2 1TP, United Kingdom
| | - Luca Pagani
- Department of Biology, University of Padua, Via Ugo Bassi, 58b, Padova 35121, Italy.,Estonian Biocentre,Institute of Genomics,University of Tartu, Riia 23B, Tartu 51010, Estonia
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34
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Yurtman E, Özer O, Yüncü E, Dağtaş ND, Koptekin D, Çakan YG, Özkan M, Akbaba A, Kaptan D, Atağ G, Vural KB, Gündem CY, Martin L, Kılınç GM, Ghalichi A, Açan SC, Yaka R, Sağlıcan E, Lagerholm VK, Krzewińska M, Günther T, Morell Miranda P, Pişkin E, Şevketoğlu M, Bilgin CC, Atakuman Ç, Erdal YS, Sürer E, Altınışık NE, Lenstra JA, Yorulmaz S, Abazari MF, Hoseinzadeh J, Baird D, Bıçakçı E, Çevik Ö, Gerritsen F, Özbal R, Götherström A, Somel M, Togan İ, Özer F. Archaeogenetic analysis of Neolithic sheep from Anatolia suggests a complex demographic history since domestication. Commun Biol 2021; 4:1279. [PMID: 34773064 PMCID: PMC8589978 DOI: 10.1038/s42003-021-02794-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 10/15/2021] [Indexed: 12/26/2022] Open
Abstract
Sheep were among the first domesticated animals, but their demographic history is little understood. Here we analyzed nuclear polymorphism and mitochondrial data (mtDNA) from ancient central and west Anatolian sheep dating from Epipaleolithic to late Neolithic, comparatively with modern-day breeds and central Asian Neolithic/Bronze Age sheep (OBI). Analyzing ancient nuclear data, we found that Anatolian Neolithic sheep (ANS) are genetically closest to present-day European breeds relative to Asian breeds, a conclusion supported by mtDNA haplogroup frequencies. In contrast, OBI showed higher genetic affinity to present-day Asian breeds. These results suggest that the east-west genetic structure observed in present-day breeds had already emerged by 6000 BCE, hinting at multiple sheep domestication episodes or early wild introgression in southwest Asia. Furthermore, we found that ANS are genetically distinct from all modern breeds. Our results suggest that European and Anatolian domestic sheep gene pools have been strongly remolded since the Neolithic.
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Affiliation(s)
- Erinç Yurtman
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Onur Özer
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Emmy Noether Group Evolutionary Immunogenomics, Max Planck Institute for Evolutionary Biology, Plön, Germany
| | - Eren Yüncü
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Nihan Dilşad Dağtaş
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University, Ankara, Turkey
| | | | - Mustafa Özkan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ali Akbaba
- Department of Anthropology, Ankara University, Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Gözde Atağ
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | | | - Louise Martin
- Institute of Archaeology, University College London, London, UK
| | - Gülşah Merve Kılınç
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, Ankara, Turkey
| | - Ayshin Ghalichi
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
- Department of Archaeogenetics, Max-Planck Institute for the Science of Human History, Jena, Germany
| | - Sinan Can Açan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Stockholm, Sweden
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Stockholm, Sweden
| | - Torsten Günther
- Department of Organismal Biology, Human Evolution Research Program, Uppsala University, Uppsala, Sweden
| | - Pedro Morell Miranda
- Department of Organismal Biology, Human Evolution Research Program, Uppsala University, Uppsala, Sweden
| | - Evangelia Pişkin
- Department of Settlement Archaeology, Middle East Technical University, Ankara, Turkey
| | - Müge Şevketoğlu
- Centre for Archaeology, Cultural Heritage and Conservation, Cyprus International University, Nicosia, Cyprus
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, Ankara, Turkey
| | - Yılmaz Selim Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey
- Molecular Anthropology Group (Human_G), Hacettepe University, Ankara, Turkey
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey
- Molecular Anthropology Group (Human_G), Hacettepe University, Ankara, Turkey
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, Netherlands
| | - Sevgi Yorulmaz
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mohammad Foad Abazari
- Research Center for Clinical Virology, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Douglas Baird
- Department of Archaeology, Classics, and Egyptology, University of Liverpool, Liverpool, UK
| | - Erhan Bıçakçı
- Department of Prehistory, Istanbul University, Laleli, Istanbul, Turkey
| | - Özlem Çevik
- Department of Archaeology, Trakya University, Edirne, Turkey
| | | | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, Istanbul, Turkey
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, University of Stockholm, Stockholm, Sweden
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey.
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey.
- Molecular Anthropology Group (Human_G), Hacettepe University, Ankara, Turkey.
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35
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Ceballos FC, Gürün K, Altınışık NE, Gemici HC, Karamurat C, Koptekin D, Vural KB, Mapelli I, Sağlıcan E, Sürer E, Erdal YS, Götherström A, Özer F, Atakuman Ç, Somel M. Human inbreeding has decreased in time through the Holocene. Curr Biol 2021; 31:3925-3934.e8. [PMID: 34216555 DOI: 10.1016/j.cub.2021.06.027] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 04/19/2021] [Accepted: 06/10/2021] [Indexed: 10/21/2022]
Abstract
The history of human inbreeding is controversial.1 In particular, how the development of sedentary and/or agricultural societies may have influenced overall inbreeding levels, relative to those of hunter-gatherer communities, is unclear.2-5 Here, we present an approach for reliable estimation of runs of homozygosity (ROHs) in genomes with ≥3× mean sequence coverage across >1 million SNPs and apply this to 411 ancient Eurasian genomes from the last 15,000 years.5-34 We show that the frequency of inbreeding, as measured by ROHs, has decreased over time. The strongest effect is associated with the Neolithic transition, but the trend has since continued, indicating a population size effect on inbreeding prevalence. We further show that most inbreeding in our historical sample can be attributed to small population size instead of consanguinity. Cases of high consanguinity were rare and only observed among members of farming societies in our sample. Despite the lack of evidence for common consanguinity in our ancient sample, consanguineous traditions are today prevalent in various modern-day Eurasian societies,1,35-37 suggesting that such practices may have become widespread within the last few millennia.
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Affiliation(s)
- Francisco C Ceballos
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Kanat Gürün
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - N Ezgi Altınışık
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Ankara, Turkey
| | - Hasan Can Gemici
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Cansu Karamurat
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Dilek Koptekin
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University, 06800 Ankara, Turkey
| | - Yılmaz Selim Erdal
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Ankara, Turkey
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Centre for Palaeogenetics, Svante Arrhenius väg 20C, 106 91 Stockholm, Sweden
| | - Füsun Özer
- Human-G Laboratory, Department of Anthropology, Hacettepe University, 06800 Ankara, Turkey
| | - Çiğdem Atakuman
- Department of Settlement Archaeology, Middle East Technical University, 06800 Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, 06800 Ankara, Turkey.
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36
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The genetic structure of the Turkish population reveals high levels of variation and admixture. Proc Natl Acad Sci U S A 2021; 118:2026076118. [PMID: 34426522 DOI: 10.1073/pnas.2026076118] [Citation(s) in RCA: 40] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The construction of population-based variomes has contributed substantially to our understanding of the genetic basis of human inherited disease. Here, we investigated the genetic structure of Turkey from 3,362 unrelated subjects whose whole exomes (n = 2,589) or whole genomes (n = 773) were sequenced to generate a Turkish (TR) Variome that should serve to facilitate disease gene discovery in Turkey. Consistent with the history of present-day Turkey as a crossroads between Europe and Asia, we found extensive admixture between Balkan, Caucasus, Middle Eastern, and European populations with a closer genetic relationship of the TR population to Europeans than hitherto appreciated. We determined that 50% of TR individuals had high inbreeding coefficients (≥0.0156) with runs of homozygosity longer than 4 Mb being found exclusively in the TR population when compared to 1000 Genomes Project populations. We also found that 28% of exome and 49% of genome variants in the very rare range (allele frequency < 0.005) are unique to the modern TR population. We annotated these variants based on their functional consequences to establish a TR Variome containing alleles of potential medical relevance, a repository of homozygous loss-of-function variants and a TR reference panel for genotype imputation using high-quality haplotypes, to facilitate genome-wide association studies. In addition to providing information on the genetic structure of the modern TR population, these data provide an invaluable resource for future studies to identify variants that are associated with specific phenotypes as well as establishing the phenotypic consequences of mutations in specific genes.
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37
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Feldman M, Gnecchi-Ruscone GA, Lamnidis TC, Posth C. Where Asia meets Europe - recent insights from ancient human genomics. Ann Hum Biol 2021; 48:191-202. [PMID: 34459345 DOI: 10.1080/03014460.2021.1949039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
CONTEXT The peopling of Europe by modern humans is a widely debated topic in the field of modern and ancient genomics. While several recent syntheses have focussed on this topic, little has been discussed about the genetic history of populations in the continent's surrounding regions. OBJECTIVE We explore genetic transformations in three key areas that played an essential role in the formation of the European genetic landscape through time, focussing on the periods spanning from the Epipalaeolithic/Mesolithic and up until the Iron Age. METHODS We review published ancient genomic studies and integrate the associated data to provide a quantification and visualisation of major trends in the population histories of the Near East, the western Eurasian Steppe and North East Europe. RESULTS We describe cross-regional as well as localised prehistoric demographic shifts and discuss potential research directions while highlighting geo-temporal gaps in the data. CONCLUSION In recent years, archaeogenetic studies have contributed to the understanding of human genetic diversity through time in regions located at the doorstep of Europe. Further studies focussing on these areas will allow for a better characterisation of genetic shifts and regionally-specific patterns of admixture across western Eurasia.
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Affiliation(s)
- Michal Feldman
- Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Guido A Gnecchi-Ruscone
- Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Thiseas C Lamnidis
- Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Cosimo Posth
- Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, Tübingen, Germany.,Department of Archaeogentics, Max Planck Institute for the Science of Human History, Jena, Germany
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38
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Serrano JG, Ordóñez AC, Fregel R. Paleogenomics of the prehistory of Europe: human migrations, domestication and disease. Ann Hum Biol 2021; 48:179-190. [PMID: 34459342 DOI: 10.1080/03014460.2021.1942205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.
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Affiliation(s)
- Javier G Serrano
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
| | - Alejandra C Ordóñez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain.,Departamento Geografía e Historia, Facultad de Humanidades, Universidad de La Laguna, La Laguna, Spain
| | - Rosa Fregel
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
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39
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Scorrano G, Yediay FE, Pinotti T, Feizabadifarahani M, Kristiansen K. The genetic and cultural impact of the Steppe migration into Europe. Ann Hum Biol 2021; 48:223-233. [PMID: 34459341 DOI: 10.1080/03014460.2021.1942984] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
BACKGROUND During the early 3rd millennium BCE migration from Pontic Steppe, mainly related to Yamnaya culture, has affected European populations both culturally and genetically, however, it has long been debated to what extent this migration was male-driven, and how this replacement process took place which eliminated partially/largely Neolithic male lines over time. AIM This paper aims to evaluate the influence of the Steppe migration on European Bronze Age populations by calculating both male and female genetic contributions of the Steppe-related ancestry to the European Bronze Age populations. With this approach, we will be able to clarify the hypotheses on whether it was male-biased migration or not. SUBJECTS AND METHODS To evaluate the genetic impact and the proportion of the Steppe-related ancestry to the European Bronze Age populations, we performed PCA and qpAdm analyses by using published genome-wide data. In addition, we quantified male and female genetic contribution into Europe by using the analysis of uniparental markers and the X-chromosome. RESULTS The Steppe migration had a considerable impact on the genetic makeup of the Bronze Age European populations. The data suggest that the Steppe-related ancestry arriving into Central Europe was male-driven, dominantly in the Corded Ware culture populations and lesser in the Bell Beaker populations. In fact, there is no evidence that this migration had a significant input on the mitochondrial genetic pool of all European Bronze Age populations. CONCLUSIONS Our analyses suggest that the Steppe-related ancestry had genetic impact on mainly Central-Eastern Europe. Moreover, this migration was male-driven for most of the Central European populations belonging to the Corded Ware groups, and to a lesser extent for the Bell Beaker groups.
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Affiliation(s)
- Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fulya Eylem Yediay
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thomaz Pinotti
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Laboratório de Biodiversidade e Evolução Molecular (LBEM), Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
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40
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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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41
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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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42
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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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43
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Ingman T, Eisenmann S, Skourtanioti E, Akar M, Ilgner J, Gnecchi Ruscone GA, le Roux P, Shafiq R, Neumann GU, Keller M, Freund C, Marzo S, Lucas M, Krause J, Roberts P, Yener KA, Stockhammer PW. Human mobility at Tell Atchana (Alalakh), Hatay, Turkey during the 2nd millennium BC: Integration of isotopic and genomic evidence. PLoS One 2021; 16:e0241883. [PMID: 34191795 PMCID: PMC8244877 DOI: 10.1371/journal.pone.0241883] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Accepted: 05/28/2021] [Indexed: 11/21/2022] Open
Abstract
The Middle and Late Bronze Age, a period roughly spanning the 2nd millennium BC (ca. 2000–1200 BC) in the Near East, is frequently referred to as the first ‘international age’, characterized by intense and far-reaching contacts between different entities from the eastern Mediterranean to the Near East and beyond. In a large-scale tandem study of stable isotopes and ancient DNA of individuals excavated at Tell Atchana (Alalakh, located in Hatay, Turkey), we explored the role of mobility at the capital of a regional kingdom, named Mukish during the Late Bronze Age, which spanned the Amuq Valley and some areas beyond. We generated strontium and oxygen isotope data from dental enamel for 53 individuals and 77 individuals, respectively, and added ancient DNA data of 10 newly sequenced individuals to a dataset of 27 individuals published in 2020. Additionally, we improved the DNA coverage of one individual from this 2020 dataset. The DNA data revealed a very homogeneous gene pool. This picture of an overwhelmingly local ancestry was consistent with the evidence of local upbringing in most of the individuals indicated by the isotopic data, where only five were found to be non-local. High levels of contact, trade, and exchange of ideas and goods in the Middle and Late Bronze Ages, therefore, seem not to have translated into high levels of individual mobility detectable at Tell Atchana.
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Affiliation(s)
- Tara Ingman
- Koç University Research Center for Anatolian Civilizations (ANAMED), Koc University, Istanbul, Turkey
- * E-mail: (TI); (SE); (KAY); (PWS)
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- * E-mail: (TI); (SE); (KAY); (PWS)
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Murat Akar
- Department of Archaeology, Mustafa Kemal University, Alahan-Antakya, Hatay, Turkey
| | - Jana Ilgner
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | | | - Petrus le Roux
- Department of Geological Sciences, University of Cape Town, Rondebosch, South Africa
| | - Rula Shafiq
- Anthropology Department, Yeditepe University, Istanbul, Turkey
| | - Gunnar U. Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Marcel Keller
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Cäcilia Freund
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sara Marzo
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Mary Lucas
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Patrick Roberts
- Department of Archaeology, Max Planck Institute for the Science of Human History, Jena, Germany
| | - K. Aslıhan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, United States of America
- * E-mail: (TI); (SE); (KAY); (PWS)
| | - Philipp W. Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich, Germany
- * E-mail: (TI); (SE); (KAY); (PWS)
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44
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Clemente F, Unterländer M, Dolgova O, Amorim CEG, Coroado-Santos F, Neuenschwander S, Ganiatsou E, Cruz Dávalos DI, Anchieri L, Michaud F, Winkelbach L, Blöcher J, Arizmendi Cárdenas YO, Sousa da Mota B, Kalliga E, Souleles A, Kontopoulos I, Karamitrou-Mentessidi G, Philaniotou O, Sampson A, Theodorou D, Tsipopoulou M, Akamatis I, Halstead P, Kotsakis K, Urem-Kotsou D, Panagiotopoulos D, Ziota C, Triantaphyllou S, Delaneau O, Jensen JD, Moreno-Mayar JV, Burger J, Sousa VC, Lao O, Malaspinas AS, Papageorgopoulou C. The genomic history of the Aegean palatial civilizations. Cell 2021; 184:2565-2586.e21. [PMID: 33930288 PMCID: PMC8127963 DOI: 10.1016/j.cell.2021.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022]
Abstract
The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.
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Affiliation(s)
- Florian Clemente
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Martina Unterländer
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece; Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Olga Dolgova
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carlos Eduardo G Amorim
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Francisco Coroado-Santos
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Elissavet Ganiatsou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diana I Cruz Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lucas Anchieri
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Frédéric Michaud
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Yami Ommar Arizmendi Cárdenas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Eleni Kalliga
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Ioannis Kontopoulos
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Olga Philaniotou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece
| | - Dimitra Theodorou
- Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture and Sports, 50004 Kozani, Greece
| | - Metaxia Tsipopoulou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Ioannis Akamatis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paul Halstead
- Department of Archaeology, University of Sheffield, Minalloy House, 10-16 Regent St., Sheffield S1 3NJ, UK
| | - Kostas Kotsakis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diamantis Panagiotopoulos
- Institute of Classical Archaeology, University of Heidelberg, Marstallhof 4, 69117 Heidelberg, Germany
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100 Florina, Greece
| | - Sevasti Triantaphyllou
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - J Víctor Moreno-Mayar
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark; National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Vitor C Sousa
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece.
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45
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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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46
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Yaka R, Mapelli I, Kaptan D, Doğu A, Chyleński M, Erdal ÖD, Koptekin D, Vural KB, Bayliss A, Mazzucato C, Fer E, Çokoğlu SS, Lagerholm VK, Krzewińska M, Karamurat C, Gemici HC, Sevkar A, Dağtaş ND, Kılınç GM, Adams D, Munters AR, Sağlıcan E, Milella M, Schotsmans EMJ, Yurtman E, Çetin M, Yorulmaz S, Altınışık NE, Ghalichi A, Juras A, Bilgin CC, Günther T, Storå J, Jakobsson M, de Kleijn M, Mustafaoğlu G, Fairbairn A, Pearson J, Togan İ, Kayacan N, Marciniak A, Larsen CS, Hodder I, Atakuman Ç, Pilloud M, Sürer E, Gerritsen F, Özbal R, Baird D, Erdal YS, Duru G, Özbaşaran M, Haddow SD, Knüsel CJ, Götherström A, Özer F, Somel M. Variable kinship patterns in Neolithic Anatolia revealed by ancient genomes. Curr Biol 2021; 31:2455-2468.e18. [PMID: 33857427 PMCID: PMC8210650 DOI: 10.1016/j.cub.2021.03.050] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2020] [Revised: 01/08/2021] [Accepted: 03/15/2021] [Indexed: 12/21/2022]
Abstract
The social organization of the first fully sedentary societies that emerged during the Neolithic period in Southwest Asia remains enigmatic,1 mainly because material culture studies provide limited insight into this issue. However, because Neolithic Anatolian communities often buried their dead beneath domestic buildings,2 household composition and social structure can be studied through these human remains. Here, we describe genetic relatedness among co-burials associated with domestic buildings in Neolithic Anatolia using 59 ancient genomes, including 22 new genomes from Aşıklı Höyük and Çatalhöyük. We infer pedigree relationships by simultaneously analyzing multiple types of information, including autosomal and X chromosome kinship coefficients, maternal markers, and radiocarbon dating. In two early Neolithic villages dating to the 9th and 8th millennia BCE, Aşıklı Höyük and Boncuklu, we discover that siblings and parent-offspring pairings were frequent within domestic structures, which provides the first direct indication of close genetic relationships among co-burials. In contrast, in the 7th millennium BCE sites of Çatalhöyük and Barcın, where we study subadults interred within and around houses, we find close genetic relatives to be rare. Hence, genetic relatedness may not have played a major role in the choice of burial location at these latter two sites, at least for subadults. This supports the hypothesis that in Çatalhöyük,3, 4, 5 and possibly in some other Neolithic communities, domestic structures may have served as burial location for social units incorporating biologically unrelated individuals. Our results underscore the diversity of kin structures in Neolithic communities during this important phase of sociocultural development. Genetic kinship estimated from co-buried individuals’ genomes in Neolithic Anatolia Close relatives are common among co-burials in Aşıklı and Boncuklu Many unrelated infants found buried in the same building in Çatalhöyük and Barcın Neolithic societies in Southwest Asia may have held diverse concepts of kinship
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Affiliation(s)
- Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey.
| | - Igor Mapelli
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Damla Kaptan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Ayça Doğu
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Maciej Chyleński
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - Ömür Dilek Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Dilek Koptekin
- Department of Health Informatics, Middle East Technical University (METU), Historic England, London, UK
| | - Kıvılcım Başak Vural
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Alex Bayliss
- Scientific Dating, Historic England, London, UK; Biological & Environmental Sciences, University of Stirling, Stirling, UK
| | - Camilla Mazzucato
- Department of Anthropology, Stanford University, Stanford, CA, 94303 USA
| | - Evrim Fer
- Department of Genetics, University of Arizona, 85719, Tucson, AZ, USA
| | - Sevim Seda Çokoğlu
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Vendela Kempe Lagerholm
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Centre for Palaeogenetics, Stockholm, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, Stockholm, Sweden; Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Cansu Karamurat
- Graduate School of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Hasan Can Gemici
- Graduate School of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Arda Sevkar
- Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Nihan Dilşad Dağtaş
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Gülşah Merve Kılınç
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey; Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100, Ankara, Turkey
| | - Donovan Adams
- Department of Anthropology, University of Central Florida, Uppsala University, 751 05 Uppsala, Sweden
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden; SciLife Lab, Uppsala University, 751 05 Uppsala, Sweden
| | - Ekin Sağlıcan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Marco Milella
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, CH-3007 Bern, Switzerland
| | - Eline M J Schotsmans
- Centre for Archaeological Science, University of Wollongong, Wollongong, Australia; UMR 5199, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux, Pessac, France
| | - Erinç Yurtman
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Mehmet Çetin
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Sevgi Yorulmaz
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - N Ezgi Altınışık
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Ayshin Ghalichi
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey; Department of Archaeogenetics, Max-Planck Institute for the Science of Human History, Kahlaische Strasse 10, D-07745, Jena, Germany
| | - Anna Juras
- Institute of Human Biology and Evolution, Faculty of Biology, Adam Mickiewicz University, Poznań, Poland
| | - C Can Bilgin
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 751 05 Uppsala, Sweden
| | - Maurice de Kleijn
- Spatial Information Laboratory (SPINlab) at the Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Gökhan Mustafaoğlu
- Department of Archaeology, Faculty of Letters, Ankara Hacı Bayram Veli University, Abant 1 Cad. No:10/2D, Yenimahalle, Ankara
| | - Andrew Fairbairn
- School of Social Science, The University of Queensland, Michie Building, St Lucia, Brisbane, QLD, Australia
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 8-14 Abercromby Square, Liverpool, L69 7WZ, UK
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Nurcan Kayacan
- Department of Prehistory, Faculty of Letters, Istanbul University, Ordu Cad. No: 6, 34459, Laleli, Istanbul
| | | | | | - Ian Hodder
- Department of Anthropology, Stanford University, Stanford, CA, 94303 USA
| | - Çiğdem Atakuman
- Institute of Social Sciences, Middle East Technical University (METU), Ankara, Turkey
| | - Marin Pilloud
- Department of Anthropology, University of Nevada, Reno
| | - Elif Sürer
- Department of Modeling and Simulation, Graduate School of Informatics, Middle East Technical University (METU), Ankara, Turkey
| | | | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, 34450 Istanbul, Turkey
| | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 8-14 Abercromby Square, Liverpool, L69 7WZ, UK
| | - Yılmaz Selim Erdal
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey
| | - Güneş Duru
- Mimar Sinan Fine Arts University, Istanbul 34134, Turkey
| | | | - Scott D Haddow
- Department of Cross-Cultural and Regional Studies, University of Copenhagen, Copenhagen, Denmark
| | - Christopher J Knüsel
- UMR 5199, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA), Université de Bordeaux, Pessac, France
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden; Centre for Palaeogenetics, Stockholm, Sweden.
| | - Füsun Özer
- Department of Anthropology, Hacettepe University, Ankara, Turkey; Human G Lab, Department of Anthropology, Hacettepe University, Ankara, Turkey.
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University (METU), Ankara, Turkey.
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Heterogeneous Hunter-Gatherer and Steppe-Related Ancestries in Late Neolithic and Bell Beaker Genomes from Present-Day France. Curr Biol 2021; 31:1072-1083.e10. [PMID: 33434506 DOI: 10.1016/j.cub.2020.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 12/17/2022]
Abstract
The transition from the Late Neolithic to the Bronze Age has witnessed important population and societal changes in western Europe.1 These include massive genomic contributions of pastoralist herders originating from the Pontic-Caspian steppes2,3 into local populations, resulting from complex interactions between collapsing hunter-gatherers and expanding farmers of Anatolian ancestry.4-8 This transition is documented through extensive ancient genomic data from present-day Britain,9,10 Ireland,11,12 Iberia,13 Mediterranean islands,14,15 and Germany.8 It remains, however, largely overlooked in France, where most focus has been on the Middle Neolithic (n = 63),8,9,16 with the exception of one Late Neolithic genome sequenced at 0.05× coverage.16 This leaves the key transitional period covering ∼3,400-2,700 cal. years (calibrated years) BCE genetically unsampled and thus the exact time frame of hunter-gatherer persistence and arrival of steppe migrations unknown. To remediate this, we sequenced 24 ancient human genomes from France spanning ∼3,400-1,600 cal. years BCE. This reveals Late Neolithic populations that are genetically diverse and include individuals with dark skin, hair, and eyes. We detect heterogeneous hunter-gatherer ancestries within Late Neolithic communities, reaching up to ∼63.3% in some individuals, and variable genetic contributions of steppe herders in Bell Beaker populations. We provide an estimate as late as ∼3,800 years BCE for the admixture between Neolithic and Mesolithic populations and as early as ∼2,650 years BCE for the arrival of steppe-related ancestry. The genomic heterogeneity characterized underlines the complex history of human interactions even at the local scale.
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Böck J, Krogsaeter E, Passon M, Chao YK, Sharma S, Grallert H, Peters A, Grimm C. Human genome diversity data reveal that L564P is the predominant TPC2 variant and a prerequisite for the blond hair associated M484L gain-of-function effect. PLoS Genet 2021; 17:e1009236. [PMID: 33465068 PMCID: PMC7845996 DOI: 10.1371/journal.pgen.1009236] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Revised: 01/29/2021] [Accepted: 10/29/2020] [Indexed: 12/29/2022] Open
Abstract
The endo-lysosomal two-pore channel (TPC2) has been established as an intracellular cation channel of significant physiological and pathophysiological relevance in recent years. For example, TPC2-/- mice show defects in cholesterol degradation, leading to hypercholesterinemia; TPC2 absence also results in mature-onset obesity, and a role in glucagon secretion and diabetes has been proposed. Infections with bacterial toxins or viruses e.g., cholera toxin or Ebola virus result in reduced infectivity rates in the absence of TPC2 or after pharmacological blockage, and TPC2-/- cancer cells lose their ability to migrate and metastasize efficiently. Finally, melanin production is affected by changes in hTPC2 activity, resulting in pigmentation defects and hair color variation. Here, we analyzed several publicly available genome variation data sets and identified multiple variations in the TPC2 protein in distinct human populations. Surprisingly, one variation, L564P, was found to be the predominant TPC2 isoform on a global scale. By applying endo-lysosomal patch-clamp electrophysiology, we found that L564P is a prerequisite for the previously described M484L gain-of-function effect that is associated with blond hair. Additionally, other gain-of-function variants with distinct geographical and ethnic distribution were discovered and functionally characterized. A meta-analysis of genome-wide association studies was performed, finding the polymorphisms to be associated with both distinct and overlapping traits. In sum, we present the first systematic analysis of variations in TPC2. We functionally characterized the most common variations and assessed their association with various disease traits. With TPC2 emerging as a novel drug target for the treatment of various diseases, this study provides valuable insights into ethnic and geographical distribution of TPC2 polymorphisms and their effects on channel activity.
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Affiliation(s)
- Julia Böck
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Einar Krogsaeter
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Marcel Passon
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Yu-Kai Chao
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
| | - Sapna Sharma
- Helmholtz Zentrum–Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epidemiology, Neuherberg, Germany
| | - Harald Grallert
- Helmholtz Zentrum–Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epidemiology, Neuherberg, Germany
| | - Annette Peters
- Helmholtz Zentrum–Deutsches Forschungszentrum für Gesundheit und Umwelt (GmbH), Institute of Epidemiology, Neuherberg, Germany
| | - Christian Grimm
- Walther Straub Institute of Pharmacology and Toxicology, Faculty of Medicine, Ludwig-Maximilians-Universität, Munich, Germany
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Skourtanioti E, Erdal YS, Frangipane M, Balossi Restelli F, Yener KA, Pinnock F, Matthiae P, Özbal R, Schoop UD, Guliyev F, Akhundov T, Lyonnet B, Hammer EL, Nugent SE, Burri M, Neumann GU, Penske S, Ingman T, Akar M, Shafiq R, Palumbi G, Eisenmann S, D'Andrea M, Rohrlach AB, Warinner C, Jeong C, Stockhammer PW, Haak W, Krause J. Genomic History of Neolithic to Bronze Age Anatolia, Northern Levant, and Southern Caucasus. Cell 2020; 181:1158-1175.e28. [PMID: 32470401 DOI: 10.1016/j.cell.2020.04.044] [Citation(s) in RCA: 53] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 03/18/2020] [Accepted: 04/22/2020] [Indexed: 12/22/2022]
Abstract
Here, we report genome-wide data analyses from 110 ancient Near Eastern individuals spanning the Late Neolithic to Late Bronze Age, a period characterized by intense interregional interactions for the Near East. We find that 6th millennium BCE populations of North/Central Anatolia and the Southern Caucasus shared mixed ancestry on a genetic cline that formed during the Neolithic between Western Anatolia and regions in today's Southern Caucasus/Zagros. During the Late Chalcolithic and/or the Early Bronze Age, more than half of the Northern Levantine gene pool was replaced, while in the rest of Anatolia and the Southern Caucasus, we document genetic continuity with only transient gene flow. Additionally, we reveal a genetically distinct individual within the Late Bronze Age Northern Levant. Overall, our study uncovers multiple scales of population dynamics through time, from extensive admixture during the Neolithic period to long-distance mobility within the globalized societies of the Late Bronze Age. VIDEO ABSTRACT.
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Affiliation(s)
- Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Yilmaz S Erdal
- Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | | | - K Aslıhan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Frances Pinnock
- Department of Classics, Sapienza University of Rome, Rome 00185, Italy
| | - Paolo Matthiae
- Department of Classics, Sapienza University of Rome, Rome 00185, Italy
| | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, Istanbul 34450, Turkey
| | - Ulf-Dietrich Schoop
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Farhad Guliyev
- Institute of Archaeology and Ethnography, Azerbaijan National Academy of Sciences, Baku AZ1073, Azerbaijan
| | - Tufan Akhundov
- Institute of Archaeology and Ethnography, Azerbaijan National Academy of Sciences, Baku AZ1073, Azerbaijan
| | - Bertille Lyonnet
- PROCLAC/UMR Laboratory, French National Centre for Scientific Research, UMR 7192, Paris 75005, France
| | - Emily L Hammer
- Near Eastern Languages and Civilizations, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Selin E Nugent
- School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX2 6PE, UK
| | - Marta Burri
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Tara Ingman
- Department of Archaeology and History of Art, Koç University, Istanbul 34450, Turkey
| | - Murat Akar
- Department of Archaeology, Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - Rula Shafiq
- History Department, Ibn Haldun University, Istanbul 34494, Turkey
| | - Giulio Palumbi
- Université Nice Sophia Antipolis, CEPAM (Cultures et Environnements. Préhistoire, Antiquité, Moyen Âge), CNRS-UMR 7264, Nice 06357, France
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Marta D'Andrea
- Department of Classics, Sapienza University of Rome, Rome 00185, Italy
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; ARC Centre of Excellence for the Mathematical and Statistical Frontiers, The University of Adelaide, Adelaide, SA 5005, Australia
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Department of Anthropology, Harvard University, Cambridge, MA 02138, USA.
| | - Choongwon Jeong
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Biological Sciences, Seoul National University, Seoul 08826, Republic of Korea.
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University, Munich 80539, Germany.
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany.
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Kinship and social organization in Copper Age Europe. A cross-disciplinary analysis of archaeology, DNA, isotopes, and anthropology from two Bell Beaker cemeteries. PLoS One 2020; 15:e0241278. [PMID: 33196640 PMCID: PMC7668604 DOI: 10.1371/journal.pone.0241278] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 10/12/2020] [Indexed: 11/28/2022] Open
Abstract
We present a high-resolution cross-disciplinary analysis of kinship structure and social institutions in two Late Copper Age Bell Beaker culture cemeteries of South Germany containing 24 and 18 burials, of which 34 provided genetic information. By combining archaeological, anthropological, genetic and isotopic evidence we are able to document the internal kinship and residency structure of the cemeteries and the socially organizing principles of these local communities. The buried individuals represent four to six generations of two family groups, one nuclear family at the Alburg cemetery, and one seemingly more extended at Irlbach. While likely monogamous, they practiced exogamy, as six out of eight non-locals are women. Maternal genetic diversity is high with 23 different mitochondrial haplotypes from 34 individuals, whereas all males belong to one single Y-chromosome haplogroup without any detectable contribution from Y-chromosomes typical of the farmers who had been the sole inhabitants of the region hundreds of years before. This provides evidence for the society being patrilocal, perhaps as a way of protecting property among the male line, while in-marriage from many different places secured social and political networks and prevented inbreeding. We also find evidence that the communities practiced selection for which of their children (aged 0–14 years) received a proper burial, as buried juveniles were in all but one case boys, suggesting the priority of young males in the cemeteries. This is plausibly linked to the exchange of foster children as part of an expansionist kinship system which is well attested from later Indo-European-speaking cultural groups.
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