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Sun KY, Bai X, Chen S, Bao S, Kapoor M, Zhang C, Backman J, Joseph T, Maxwell E, Mitra G, Gorovits A, Mansfield A, Boutkov B, Gokhale S, Habegger L, Marcketta A, Locke A, Kessler MD, Sharma D, Staples J, Bovijn J, Gelfman S, Gioia AD, Rajagopal V, Lopez A, Varela JR, Alegre J, Berumen J, Tapia-Conyer R, Kuri-Morales P, Torres J, Emberson J, Collins R, Cantor M, Thornton T, Kang HM, Overton J, Shuldiner AR, Cremona ML, Nafde M, Baras A, Abecasis G, Marchini J, Reid JG, Salerno W, Balasubramanian S. A deep catalog of protein-coding variation in 985,830 individuals. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.09.539329. [PMID: 37214792 PMCID: PMC10197621 DOI: 10.1101/2023.05.09.539329] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Coding variants that have significant impact on function can provide insights into the biology of a gene but are typically rare in the population. Identifying and ascertaining the frequency of such rare variants requires very large sample sizes. Here, we present the largest catalog of human protein-coding variation to date, derived from exome sequencing of 985,830 individuals of diverse ancestry to serve as a rich resource for studying rare coding variants. Individuals of African, Admixed American, East Asian, Middle Eastern, and South Asian ancestry account for 20% of this Exome dataset. Our catalog of variants includes approximately 10.5 million missense (54% novel) and 1.1 million predicted loss-of-function (pLOF) variants (65% novel, 53% observed only once). We identified individuals with rare homozygous pLOF variants in 4,874 genes, and for 1,838 of these this work is the first to document at least one pLOF homozygote. Additional insights from the RGC-ME dataset include 1) improved estimates of selection against heterozygous loss-of-function and identification of 3,459 genes intolerant to loss-of-function, 83 of which were previously assessed as tolerant to loss-of-function and 1,241 that lack disease annotations; 2) identification of regions depleted of missense variation in 457 genes that are tolerant to loss-of-function; 3) functional interpretation for 10,708 variants of unknown or conflicting significance reported in ClinVar as cryptic splice sites using splicing score thresholds based on empirical variant deleteriousness scores derived from RGC-ME; and 4) an observation that approximately 3% of sequenced individuals carry a clinically actionable genetic variant in the ACMG SF 3.1 list of genes. We make this important resource of coding variation available to the public through a variant allele frequency browser. We anticipate that this report and the RGC-ME dataset will serve as a valuable reference for understanding rare coding variation and help advance precision medicine efforts.
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Affiliation(s)
| | | | - Siying Chen
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Suying Bao
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Adam Locke
- Regeneron Genetics Center, Tarrytown, NY, USA
| | | | | | | | | | | | | | | | | | | | - Jesus Alegre
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jaime Berumen
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Roberto Tapia-Conyer
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Pablo Kuri-Morales
- Experimental Research Unit from the Faculty of Medicine (UIME), National Autonomous University of Mexico (UNAM)
| | - Jason Torres
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Jonathan Emberson
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
- MRC Population Health Research Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | - Rory Collins
- Clinical Trial Service Unit & Epidemiological Studies Unit, Nuffield Department of Population Health, University of Oxford, Oxford, UK
| | | | | | | | | | | | | | | | | | - Mona Nafde
- Regeneron Genetics Center, Tarrytown, NY, USA
| | - Aris Baras
- Regeneron Genetics Center, Tarrytown, NY, USA
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2
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Fleskes RE, Owsley DW, Bruwelheide KS, Barca KG, Griffith DR, Cabana GS, Schurr TG. Historical genomes elucidate European settlement and the African diaspora in Delaware. Curr Biol 2023; 33:2350-2358.e7. [PMID: 37207647 DOI: 10.1016/j.cub.2023.04.069] [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: 09/16/2022] [Revised: 02/01/2023] [Accepted: 04/24/2023] [Indexed: 05/21/2023]
Abstract
The 17th-century colonization of North America brought thousands of Europeans to Indigenous lands in the Delaware region, which comprises the eastern boundary of the Chesapeake Bay in what is now the Mid-Atlantic region of the United States.1 The demographic features of these initial colonial migrations are not uniformly characterized, with Europeans and European-Americans migrating to the Delaware area from other countries and neighboring colonies as single persons or in family units of free persons, indentured servants, or tenant farmers.2 European colonizers also instituted a system of racialized slavery through which they forcibly transported thousands of Africans to the Chesapeake region. Historical information about African-descended individuals in the Delaware region is limited, with a population estimate of less than 500 persons by 1700 CE.3,4 To shed light on the population histories of this period, we analyzed low-coverage genomes of 11 individuals from the Avery's Rest archaeological site (circa 1675-1725 CE), located in Delaware. Previous osteological and mitochondrial DNA (mtDNA) sequence analyses showed a southern group of eight individuals of European maternal descent, buried 15-20 feet from a northern group of three individuals of African maternal descent.5 Autosomal results further illuminate genomic similarities to Northwestern European reference populations or West and West-Central African reference populations, respectively. We also identify three generations of maternal kin of European ancestry and a paternal parent-offspring relationship between an adult and child of African ancestry. These findings expand our understanding of the origins and familial relationships in late 17th and early 18th century North America.
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Affiliation(s)
- Raquel E Fleskes
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA; Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA.
| | - Douglas W Owsley
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA.
| | - Karin S Bruwelheide
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | - Kathryn G Barca
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560, USA
| | | | - Graciela S Cabana
- Department of Anthropology, University of Tennessee, Knoxville, TN 37996, USA; Molecular Anthropology Laboratories, University of Tennessee, Knoxville, TN 37996, USA
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, PA 19104, USA.
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3
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Rodríguez-Varela R, Moore KHS, Ebenesersdóttir SS, Kilinc GM, Kjellström A, Papmehl-Dufay L, Alfsdotter C, Berglund B, Alrawi L, Kashuba N, Sobrado V, Lagerholm VK, Gilbert E, Cavalleri GL, Hovig E, Kockum I, Olsson T, Alfredsson L, Hansen TF, Werge T, Munters AR, Bernhardsson C, Skar B, Christophersen A, Turner-Walker G, Gopalakrishnan S, Daskalaki E, Omrak A, Pérez-Ramallo P, Skoglund P, Girdland-Flink L, Gunnarsson F, Hedenstierna-Jonson C, Gilbert MTP, Lidén K, Jakobsson M, Einarsson L, Victor H, Krzewińska M, Zachrisson T, Storå J, Stefánsson K, Helgason A, Götherström A. The genetic history of Scandinavia from the Roman Iron Age to the present. Cell 2023; 186:32-46.e19. [PMID: 36608656 DOI: 10.1016/j.cell.2022.11.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 10/14/2022] [Accepted: 11/22/2022] [Indexed: 01/07/2023]
Abstract
We investigate a 2,000-year genetic transect through Scandinavia spanning the Iron Age to the present, based on 48 new and 249 published ancient genomes and genotypes from 16,638 modern individuals. We find regional variation in the timing and magnitude of gene flow from three sources: the eastern Baltic, the British-Irish Isles, and southern Europe. British-Irish ancestry was widespread in Scandinavia from the Viking period, whereas eastern Baltic ancestry is more localized to Gotland and central Sweden. In some regions, a drop in current levels of external ancestry suggests that ancient immigrants contributed proportionately less to the modern Scandinavian gene pool than indicated by the ancestry of genomes from the Viking and Medieval periods. Finally, we show that a north-south genetic cline that characterizes modern Scandinavians is mainly due to the differential levels of Uralic ancestry and that this cline existed in the Viking Age and possibly earlier.
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Affiliation(s)
- Ricardo Rodríguez-Varela
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
| | | | - S Sunna Ebenesersdóttir
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland
| | - Gulsah Merve Kilinc
- Department of Bioinformatics, Graduate School of Health Sciences, Hacettepe University, 06100 Ankara, Turkey
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Clara Alfsdotter
- Department of Archaeology, Bohusläns Museum, Museigatan 1, 451 19 Udevalla, Sweden
| | - Birgitta Berglund
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Loey Alrawi
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Natalija Kashuba
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden; Department of Archaeology and Ancient History, Archaeology, Uppsala University, 752 38 Uppsala, Sweden; Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Verónica Sobrado
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Vendela Kempe Lagerholm
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Edmund Gilbert
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Gianpiero L Cavalleri
- School of Pharmacy and Biomolecular Sciences, RCSI, D02 YN77 Dublin, Ireland; FutureNeuro SFI Research Centre, RCSI, D02 YN77 Dublin, Ireland
| | - Eivind Hovig
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway; Centre for Bioinformatics, Department of Informatics, University of Oslo, 166 0450 Oslo, Norway
| | - Ingrid Kockum
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Tomas Olsson
- Center for Molecular Medicine, Department of Clinical Neuroscience, Neuroimmunology Unit, Karolinska Institutet, 171 76 Stockholm, Sweden
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, 171 77 Stockholm, Sweden
| | - Thomas F Hansen
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Danish Headache Center, Department of Neurology, Copenhagen University Hospital, 2600 Glostrup, Denmark
| | - Thomas Werge
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, 4000 Roskilde, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2200, Denmark; The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, 8210 Aarhus, Denmark
| | - Arielle R Munters
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Carolina Bernhardsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Axel Christophersen
- Department of Archaeology and Cultural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Gordon Turner-Walker
- Department of Archaeology and Anthropology National Museum of Natural Science, 404023 Taichung City, Taiwan
| | - Shyam Gopalakrishnan
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark
| | - Eva Daskalaki
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Patxi Pérez-Ramallo
- isoTROPIC Research Group, Department of Archaeology, Max Planck Institute for Geoanthropology, 07745 Jena, Germany; Department of Medical and Surgical Specialities, Faculty of Medicine and Nursing, University of the Basque Country (EHU), Donostia-San Sebastián 20014, Spain
| | | | - Linus Girdland-Flink
- Department of Archaeology, School of Geosciences, University of Aberdeen, AB24 3FX Aberdeen, UK; School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK
| | - Fredrik Gunnarsson
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | | | - M Thomas P Gilbert
- Center for Evolutionary Hologenomics, the GLOBE Institute, University of Copenhagen, 1353 Copenhagen, Denmark; Department of Natural History, NTNU University Museum, Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, and SciLife Lab, Uppsala University, 75236 Uppsala, Sweden
| | - Lars Einarsson
- Kronan, Marine Archaeological Department, Kalmar County Museum, Box 104, Kalmar S-39121, Sweden
| | - Helena Victor
- Department of Museum Archaeology, Kalmar County Museum, Box 104, Kalmar 39121, Sweden
| | - Maja Krzewińska
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | | | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Kári Stefánsson
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Agnar Helgason
- deCODE Genetics/AMGEN, Inc., 102 Reykjavik, Iceland; Department of Anthropology, University of Iceland, 102 Reykjavik, Iceland.
| | - Anders Götherström
- Centre for Palaeogenetics, 106 91 Stockholm, Sweden; Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden.
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4
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Korunes KL, Soares-Souza GB, Bobrek K, Tang H, Araújo II, Goldberg A, Beleza S. Sex-biased admixture and assortative mating shape genetic variation and influence demographic inference in admixed Cabo Verdeans. G3 (BETHESDA, MD.) 2022; 12:jkac183. [PMID: 35861404 PMCID: PMC9526050 DOI: 10.1093/g3journal/jkac183] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 06/21/2022] [Indexed: 11/22/2022]
Abstract
Genetic data can provide insights into population history, but first, we must understand the patterns that complex histories leave in genomes. Here, we consider the admixed human population of Cabo Verde to understand the patterns of genetic variation left by social and demographic processes. First settled in the late 1400s, Cabo Verdeans are admixed descendants of Portuguese colonizers and enslaved West African people. We consider Cabo Verde's well-studied historical record alongside genome-wide SNP data from 563 individuals from 4 regions within the archipelago. We use genetic ancestry to test for patterns of nonrandom mating and sex-specific gene flow, and we examine the consequences of these processes for common demographic inference methods and genetic patterns. Notably, multiple population genetic tools that assume random mating underestimate the timing of admixture, but incorporating nonrandom mating produces estimates more consistent with historical records. We consider how admixture interrupts common summaries of genomic variation such as runs of homozygosity. While summaries of runs of homozygosity may be difficult to interpret in admixed populations, differentiating runs of homozygosity by length class shows that runs of homozygosity reflect historical differences between the islands in their contributions from the source populations and postadmixture population dynamics. Finally, we find higher African ancestry on the X chromosome than on the autosomes, consistent with an excess of European males and African females contributing to the gene pool. Considering these genomic insights into population history in the context of Cabo Verde's historical record, we can identify how assumptions in genetic models impact inference of population history more broadly.
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Affiliation(s)
| | | | - Katherine Bobrek
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
| | - Hua Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Isabel Inês Araújo
- Faculdade de Ciências e Tecnologia, Universidade de Cabo Verde (Uni-CV), Praia, Ilha de Santiago CP 379C, Cabo Verde
| | - Amy Goldberg
- Evolutionary Anthropology, Duke University, Durham, NC 27705, USA
| | - Sandra Beleza
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
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5
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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, Davtyan R. A genetic probe into the ancient and medieval history of Southern Europe and West Asia. Science 2022; 377:940-951. [PMID: 36007020 PMCID: PMC10019558 DOI: 10.1126/science.abq0755] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Literary and archaeological sources have preserved a rich history of Southern Europe and West Asia since the Bronze Age that can be complemented by genetics. Mycenaean period elites in Greece did not differ from the general population and included both people with some steppe ancestry and others, like the Griffin Warrior, without it. Similarly, people in the central area of the Urartian Kingdom around Lake Van lacked the steppe ancestry characteristic of the kingdom's northern provinces. Anatolia exhibited extraordinary continuity down to the Roman and Byzantine periods, with its people serving as the demographic core of much of the Roman Empire, including the city of Rome itself. During medieval times, migrations associated with Slavic and Turkic speakers profoundly affected the region.
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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, 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
| | - Ruben Davtyan
- Institute of Archaeology and Ethnography, NAS RA, 0025 Yerevan, Armenia
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6
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Wangkumhang P, Greenfield M, Hellenthal G. An efficient method to identify, date, and describe admixture events using haplotype information. Genome Res 2022; 32:1553-1564. [PMID: 35794007 PMCID: PMC9435750 DOI: 10.1101/gr.275994.121] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 06/28/2022] [Indexed: 11/24/2022]
Abstract
We present fastGLOBETROTTER, an efficient new haplotype-based technique to identify, date, and describe admixture events using genome-wide autosomal data. With simulations, we show how fastGLOBETROTTER reduces computation time by an order of magnitude relative to the related technique GLOBETROTTER without suffering loss of accuracy. We apply fastGLOBETROTTER to a cohort of more than 6000 Europeans from 10 countries, revealing previously unreported admixture signals. In particular, we infer multiple periods of admixture related to East Asian or Siberian-like sources, starting >2000 yr ago, in people living in countries north of the Baltic Sea. In contrast, we infer admixture related to West Asian, North African, and/or Southern European sources in populations south of the Baltic Sea, including admixture dated to ∼300-700 CE, overlapping the fall of the Roman Empire, in people from Belgium, France, and parts of Germany. Our new approach scales to analyzing hundreds to thousands of individuals from a putatively admixed population and, hence, is applicable to emerging large-scale cohorts of genetically homogeneous populations.
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Affiliation(s)
- Pongsakorn Wangkumhang
- University College London Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
- National Biobank of Thailand, National Science and Technology Development Agency, Pathum Thani 12120, Thailand
| | - Matthew Greenfield
- University College London Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
| | - Garrett Hellenthal
- University College London Genetics Institute (UGI), Department of Genetics, Evolution and Environment, University College London, London, WC1E 6BT, United Kingdom
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7
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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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8
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Shirsekar G, Devos J, Latorre SM, Blaha A, Queiroz Dias M, González Hernando A, Lundberg DS, Burbano HA, Fenster CB, Weigel D. Multiple Sources of Introduction of North American Arabidopsis thaliana from across Eurasia. Mol Biol Evol 2021; 38:5328-5344. [PMID: 34499163 PMCID: PMC8662644 DOI: 10.1093/molbev/msab268] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Large-scale movement of organisms across their habitable range, or migration, is an important evolutionary process that can shape genetic diversity and influence the adaptive spread of alleles. Although human migrations have been studied in great detail with modern and ancient genomes, recent anthropogenic influence on reducing the biogeographical constraints on the migration of nonnative species has presented opportunities in several study systems to ask the questions about how repeated introductions shape genetic diversity in the introduced range. We present an extensive overview of population structure of North American Arabidopsis thaliana by studying a set of 500 whole-genome sequenced and over 2,800 RAD-seq genotyped individuals in the context of global diversity represented by Afro-Eurasian genomes. We use methods based on haplotype and rare-allele sharing as well as phylogenetic modeling to identify likely sources of introductions of extant N. American A. thaliana from the native range in Africa and Eurasia. We find evidence of admixture among the introduced lineages having increased haplotype diversity and reduced mutational load. We also detect signals of selection in immune-system-related genes that may impart qualitative disease resistance to pathogens of bacterial and oomycete origin. We conclude that multiple introductions to a nonnative range can rapidly enhance the adaptive potential of a colonizing species by increasing haplotypic diversity through admixture. Our results lay the foundation for further investigations into the functional significance of admixture.
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Affiliation(s)
- Gautam Shirsekar
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jane Devos
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Sergio M Latorre
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Andreas Blaha
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | | | | | - Derek S Lundberg
- Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Hernán A Burbano
- Max Planck Institute for Developmental Biology, Tübingen, Germany
- Centre for Life’s Origin and Evolution, University College London, London, United Kingdom
| | - Charles B Fenster
- Oak Lake Field Station, Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - Detlef Weigel
- Max Planck Institute for Developmental Biology, Tübingen, Germany
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9
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Ferreira JC, Alshamali F, Montinaro F, Cavadas B, Torroni A, Pereira L, Raveane A, Fernandes V. Projecting Ancient Ancestry in Modern-Day Arabians and Iranians: A Key Role of the Past Exposed Arabo-Persian Gulf on Human Migrations. Genome Biol Evol 2021; 13:6364187. [PMID: 34480555 PMCID: PMC8435661 DOI: 10.1093/gbe/evab194] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/17/2021] [Indexed: 02/07/2023] Open
Abstract
The Arabian Peninsula is strategic for investigations centered on the early structuring of modern humans in the wake of the out-of-Africa migration. Despite its poor climatic conditions for the recovery of ancient human DNA evidence, the availability of both genomic data from neighboring ancient specimens and informative statistical tools allow modeling the ancestry of local modern populations. We applied this approach to a data set of 741,000 variants screened in 291 Arabians and 78 Iranians, and obtained insightful evidence. The west-east axis was a strong forcer of population structure in the Peninsula, and, more importantly, there were clear continuums throughout time linking western Arabia with the Levant, and eastern Arabia with Iran and the Caucasus. Eastern Arabians also displayed the highest levels of the basal Eurasian lineage of all tested modern-day populations, a signal that was maintained even after correcting for a possible bias due to a recent sub-Saharan African input in their genomes. Not surprisingly, eastern Arabians were also the ones with highest similarity with Iberomaurusians, who were, so far, the best proxy for the basal Eurasians amongst the known ancient specimens. The basal Eurasian lineage is the signature of ancient non-Africans who diverged from the common European-eastern Asian pool before 50,000 years ago, prior to the later interbred with Neanderthals. Our results appear to indicate that the exposed basin of the Arabo-Persian Gulf was the possible home of basal Eurasians, a scenario to be further investigated by searching ancient Arabian human specimens.
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Affiliation(s)
- Joana C Ferreira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.,ICBAS-Instituto de Ciências Biomédicas Abel Salazar, Universidade do Porto, Portugal
| | - Farida Alshamali
- Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai, United Arab Emirates
| | - Francesco Montinaro
- Department of Biology-Genetics, University of Bari, Italy.,Estonian Biocentre, Institute of Genomics, University of Tartu, Estonia
| | - Bruno Cavadas
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Antonio Torroni
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy
| | - Luisa Pereira
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
| | - Alessandro Raveane
- Department of Biology and Biotechnology "L. Spallanzani", University of Pavia, Italy.,Laboratory of Haematology-Oncology, European Institute of Oncology IRCCS, Milan, Italy
| | - Veronica Fernandes
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Portugal.,IPATIMUP-Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal
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10
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Archaeogenetics and Landscape Dynamics in Sicily during the Holocene: A Review. SUSTAINABILITY 2021. [DOI: 10.3390/su13179469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The Mediterranean islands and their population history are of considerable importance to the interpretation of the population history of Europe as a whole. In this context, Sicily, because of its geographic position, represents a bridge between Africa, the Near East, and Europe that led to the stratification of settlements and admixture events. The genetic analysis of extant and ancient human samples has tried to reconstruct the population dynamics associated with the cultural and demographic changes that took place during the prehistory and history of Sicily. In turn, genetic, demographic and cultural changes need to be understood in the context of the environmental changes that took place over the Holocene. Based on this framework, this paper aims to discuss the cultural and demographic dimension of the island by reviewing archaeogenetic studies, and lastly, we discuss the ecological constraints related to human peopling in times of change in landscapes that occurred on the island in various periods. Finally, possible directions for future archaeogenetic studies of Sicily are discussed. Despite its long human history, Sicily is still one of the world’s biodiversity hotspots. The lessons we learn from the past use of landscape provide models for sustainable future management of the Mediterranean’s landscapes.
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11
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Yang XY, Rakha A, Chen W, Hou J, Qi XB, Shen QK, Dai SS, Sulaiman X, Abdulloevich NT, Afanasevna ME, Ibrohimovich KB, Chen X, Yang WK, Adnan A, Zhao RH, Yao YG, Su B, Peng MS, Zhang YP. Tracing the Genetic Legacy of the Tibetan Empire in the Balti. Mol Biol Evol 2021; 38:1529-1536. [PMID: 33283852 PMCID: PMC8042757 DOI: 10.1093/molbev/msaa313] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The rise and expansion of Tibetan Empire in the 7th to 9th centuries AD affected the course of history across East Eurasia, but the genetic impact of Tibetans on surrounding populations remains undefined. We sequenced 60 genomes for four populations from Pakistan and Tajikistan to explore their demographic history. We showed that the genomes of Balti people from Baltistan comprised 22.6–26% Tibetan ancestry. We inferred a single admixture event and dated it to about 39–21 generations ago, a period that postdated the conquest of Baltistan by the ancient Tibetan Empire. The analyses of mitochondrial DNA, Y, and X chromosome data indicated that both ancient Tibetan males and females were involved in the male-biased dispersal. Given the fact that the Balti people adopted Tibetan language and culture in history, our study suggested the impact of Tibetan Empire on Baltistan involved dominant cultural and minor demic diffusion.
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Affiliation(s)
- Xing-Yan Yang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China
| | - Allah Rakha
- Department of Forensic Sciences, University of Health Sciences, Lahore, Pakistan.,Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Wei Chen
- College of Agronomy and Biotechnology, Yunnan Agricultural University, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, Yunnan Agricultural University, Kunming, China
| | - Juzhi Hou
- Key Laboratory of Alpine Ecology (LAE), Institute of Tibetan Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Xue-Bin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Quan-Kuan Shen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Shan-Shan Dai
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China
| | - Xierzhatijiang Sulaiman
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | | | - Manilova Elena Afanasevna
- E.N. Pavlovsky Institute of Zoology and Parasitology, Academy of Sciences of Republic of Tajikistan, Dushanbe, Tajikistan
| | | | - Xi Chen
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Wei-Kang Yang
- Research Center for Ecology and Environment of Central Asia, Chinese Academy of Sciences, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Atif Adnan
- Department of Human Anatomy, School of Basic Medicine, China Medical University, Shenyang, China
| | - Ruo-Han Zhao
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Yong-Gang Yao
- Key Laboratory of Animal Models and Human Disease Mechanisms of the Chinese Academy of Sciences and Yunnan Province, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
| | - Min-Sheng Peng
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan, School of Life Sciences, Yunnan University, Kunming, China.,Kunming College of Life Science, University of Chinese Academy of Sciences, Kunming, China.,KIZ-CUHK Joint Laboratory of Bioresources and Molecular Research in Common Diseases, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, China.,Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, China
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12
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Saupe T, Montinaro F, Scaggion C, Carrara N, Kivisild T, D'Atanasio E, Hui R, Solnik A, Lebrasseur O, Larson G, Alessandri L, Arienzo I, De Angelis F, Rolfo MF, Skeates R, Silvestri L, Beckett J, Talamo S, Dolfini A, Miari M, Metspalu M, Benazzi S, Capelli C, Pagani L, Scheib CL. Ancient genomes reveal structural shifts after the arrival of Steppe-related ancestry in the Italian Peninsula. Curr Biol 2021; 31:2576-2591.e12. [PMID: 33974848 DOI: 10.1016/j.cub.2021.04.022] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 11/28/2020] [Accepted: 04/09/2021] [Indexed: 12/30/2022]
Abstract
Across Europe, the genetics of the Chalcolithic/Bronze Age transition is increasingly characterized in terms of an influx of Steppe-related ancestry. The effect of this major shift on the genetic structure of populations in the Italian Peninsula remains underexplored. Here, genome-wide shotgun data for 22 individuals from commingled cave and single burials in Northeastern and Central Italy dated between 3200 and 1500 BCE provide the first genomic characterization of Bronze Age individuals (n = 8; 0.001-1.2× coverage) from the central Italian Peninsula, filling a gap in the literature between 1950 and 1500 BCE. Our study confirms a diversity of ancestry components during the Chalcolithic and the arrival of Steppe-related ancestry in the central Italian Peninsula as early as 1600 BCE, with this ancestry component increasing through time. We detect close patrilineal kinship in the burial patterns of Chalcolithic commingled cave burials and a shift away from this in the Bronze Age (2200-900 BCE) along with lowered runs of homozygosity, which may reflect larger changes in population structure. Finally, we find no evidence that the arrival of Steppe-related ancestry in Central Italy directly led to changes in frequency of 115 phenotypes present in the dataset, rather that the post-Roman Imperial period had a stronger influence, particularly on the frequency of variants associated with protection against Hansen's disease (leprosy). Our study provides a closer look at local dynamics of demography and phenotypic shifts as they occurred as part of a broader phenomenon of widespread admixture during the Chalcolithic/Bronze Age transition.
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Affiliation(s)
- Tina Saupe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia.
| | - Francesco Montinaro
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology-Genetics, University of Bari, Via E. Orabona, 4, Bari 70124, Italy
| | - Cinzia Scaggion
- Department of Geosciences, University of Padova, Via Gradenigo 6, Padova 35131, Italy
| | - Nicola Carrara
- Museum of Anthropology, University of Padova, Palazzo Cavalli, via Giotto 1, Padova 35121, Italy
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 49 3000, Belgium
| | - Eugenia D'Atanasio
- Institute of Molecular Biology and Pathology, CNR, Piazzale Aldo Moro 5, Rome 00185, Italy
| | - Ruoyun Hui
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Anu Solnik
- Core Facility, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Ophélie Lebrasseur
- Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK; Palaeogenomics & Bio-Archaeology Research Network, School of Archaeology, University of Oxford, 1 South Parks Road, Oxford OX1 3TG, UK
| | - Greger Larson
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Luca Alessandri
- Groningen Institute of Archaeology, University of Groningen, Poststraat 6, Groningen 9712, the Netherlands
| | - Ilenia Arienzo
- Istituto Nazionale di Geofisica e Vulcanologia, Osservatorio Vesuviano, Via Diocleziano 328, Naples 80125, Italy
| | - Flavio De Angelis
- Centre of Molecular Anthropology for Ancient DNA Studies, Department of Biology, University of Rome "Tor Vergata," Via della Ricerca Scientifica 1, Rome 00133, Italy
| | - Mario Federico Rolfo
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Lower Mountjoy, South Road, Durham DH1 3LE, UK
| | - Letizia Silvestri
- Department of History, Culture and Society, University of Rome "Tor Vergata," Via Columbia 1, Rome 00133, Italy
| | | | - Sahra Talamo
- Department of Chemistry "Giacomo Ciamician," University of Bologna, Via Selmi 2, Bologna 40126, Italy; Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig 04103, Germany
| | - Andrea Dolfini
- School of History, Classics and Archaeology, Newcastle University, Newcastle upon Tyne NE1 7RU, UK
| | - Monica Miari
- Superintendency of Archeology, Fine Arts and Landscape for the metropolitan city of Bologna and the provinces of Modena, Reggio Emilia and Ferrara, Comune di Bologna, Sede Via Belle Arti n. 52, Bologna 40126, Italy
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia
| | - Stefano Benazzi
- Department of Cultural Heritage, University of Bologna, Via degli Ariani, 1, Ravenna 40126, Italy
| | - Cristian Capelli
- Department of Zoology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Dipartimento di Scienze Chimiche, della Vita e della Sostenibilità Ambientale, University of Parma, Parco Area delle Scienze 17/A, Parma 43124, Italy
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, Via U. Bassi, 58/B, Padova 35122, Italy
| | - Christiana L Scheib
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; St. John's College, University of Cambridge, St. John's Street, Cambridge CB2 1TP, UK.
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13
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Hamid I, Korunes KL, Beleza S, Goldberg A. Rapid adaptation to malaria facilitated by admixture in the human population of Cabo Verde. eLife 2021; 10:e63177. [PMID: 33393457 PMCID: PMC7815310 DOI: 10.7554/elife.63177] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 01/04/2021] [Indexed: 12/20/2022] Open
Abstract
Humans have undergone large migrations over the past hundreds to thousands of years, exposing ourselves to new environments and selective pressures. Yet, evidence of ongoing or recent selection in humans is difficult to detect. Many of these migrations also resulted in gene flow between previously separated populations. These recently admixed populations provide unique opportunities to study rapid evolution in humans. Developing methods based on distributions of local ancestry, we demonstrate that this sort of genetic exchange has facilitated detectable adaptation to a malaria parasite in the admixed population of Cabo Verde within the last ~20 generations. We estimate that the selection coefficient is approximately 0.08, one of the highest inferred in humans. Notably, we show that this strong selection at a single locus has likely affected patterns of ancestry genome-wide, potentially biasing demographic inference. Our study provides evidence of adaptation in a human population on historical timescales.
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Affiliation(s)
- Iman Hamid
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
| | | | - Sandra Beleza
- Department of Genetics and Genome Biology, University of LeicesterLeicesterUnited Kingdom
| | - Amy Goldberg
- Department of Evolutionary Anthropology, Duke UniversityDurhamUnited States
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14
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Anagnostou P, Dominici V, Battaggia C, Boukhchim N, Ben Nasr J, Boussoffara R, Cancellieri E, Marnaoui M, Marzouki M, Bel Haj Brahim H, Bou Rass M, di Lernia S, Destro Bisol G. Berbers and Arabs: Tracing the genetic diversity and history of Southern Tunisia through genome wide analysis. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:697-708. [PMID: 32936953 DOI: 10.1002/ajpa.24139] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 06/11/2020] [Accepted: 08/02/2020] [Indexed: 01/09/2023]
Abstract
OBJECTIVES Tunisia has been a crossroads for people from Africa, Europe, and the Middle East since prehistoric times. At present, it is inhabited by two main ethnic groups, Arabs and Berbers, and several minorities. This study aims to advance knowledge regarding their genetic structure using new population samplings and a genome-wide approach. MATERIALS AND METHODS We investigated genomic variation, estimated ancestry components and dated admixture events in three Berber and two Arab populations from Southern Tunisia, mining a dataset including Middle Eastern, sub-Saharan, and European populations. RESULTS Differences in the proportion of North African, Arabian, and European ancestries and the varying impact of admixture and isolation determined significant heterogeneity in the genetic structure of Southern Tunisian populations. Admixture time estimates show a multilayer pattern of admixture events, involving both ethno-linguistic groups, which started around the mid XI century and lasted for nearly five centuries. DISCUSSION Our study provides evidence that the relationships between genetic and cultural diversity of old and new inhabitants of North Africa in southern Tunisia follow different patterns. The Berbers seem to have preserved a significant part of their common genomic heritage despite Islamization, Arab cultural influence, and linguistic diversity. Compared to Morocco and Algeria, southern Tunisian Arabs have retained a higher level of Arabian ancestry. This is more evident in the semi-nomad R'Baya, who have kept their original Bedouin lifestyle, than in the population from Douz, who have undergone multiple events of stratification and admixture.
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Affiliation(s)
- Paolo Anagnostou
- Dipartimento di Biologia Ambientale, Università di Roma "La Sapienza", Italy.,Istituto Italiano di Antropologia, Italy
| | - Valentina Dominici
- Dipartimento di Biologia Ambientale, Università di Roma "La Sapienza", Italy
| | - Cinzia Battaggia
- Dipartimento di Biologia Ambientale, Università di Roma "La Sapienza", Italy
| | - Nouri Boukhchim
- Faculté des Lettres et Sciences Humaines, Université de Kairouan, Kairouan, Tunisia.,Laboratoire LMAIM, LR99ES01, Université de Tunis, Tunisia
| | - Jaâfar Ben Nasr
- Département d'Archéologie (FLSHK), LR 13 ES 11/ UR 16 ES 01, Université de Kairouan, Tunisia
| | | | | | - Marwa Marnaoui
- Dipartimento di Scienze dell'Antichità, Università di Roma "La Sapienza", Italy
| | - Meriem Marzouki
- Higher institute of fine arts, Department of Space Design, University of Sousse, Sousse, Tunisia
| | | | | | - Savino di Lernia
- Dipartimento di Scienze dell'Antichità, Università di Roma "La Sapienza", Italy.,GAES, University of Witwatersrand, Johannesburg, South Africa
| | - Giovanni Destro Bisol
- Dipartimento di Biologia Ambientale, Università di Roma "La Sapienza", Italy.,Istituto Italiano di Antropologia, Italy
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15
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Arauna LR, Hellenthal G, Comas D. Dissecting human North African gene-flow into its western coastal surroundings. Proc Biol Sci 2020; 286:20190471. [PMID: 31039721 DOI: 10.1098/rspb.2019.0471] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
North African history and populations have exerted a pivotal influence on surrounding geographical regions, although scant genetic studies have addressed this issue. Our aim is to understand human historical migrations in the coastal surroundings of North Africa. We built a refined genome-wide dataset of North African populations to unearth the fine-scale genetic structure of the region, using haplotype information. The results suggest that the gene-flow from North Africa into the European Mediterranean coast (Tuscany and the Iberian Peninsula) arrived mainly from the Mediterranean coast of North Africa. In Tuscany, this North African admixture date estimate suggests the movement of peoples during the fall of the Roman Empire around the fourth century. In the Iberian Peninsula, the North African component probably reflects the impact of the Arab expansion since the seventh century and the subsequent expansion of the Christian Kingdoms. By contrast, the North African component in the Canary Islands has a source genetically related to present-day people from the Atlantic North African coast. We also find sub-Saharan gene-flow from the Senegambia region in the Canary Islands. Specifically, we detect a complex signal of admixture involving Atlantic, Senegambian and European sources intermixing around the fifteenth century, soon after the Castilian conquest. Our results highlight the differential genetic influence of North Africa into the surrounding coast and show that specific historical events have not only had a socio-cultural impact but additionally modified the gene pool of the populations.
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Affiliation(s)
- Lara R Arauna
- 1 Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
| | - Garrett Hellenthal
- 2 UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London , London , UK
| | - David Comas
- 1 Departament de Ciències Experimentals i de la Salut, Institute of Evolutionary Biology (CSIC-UPF), Universitat Pompeu Fabra , Barcelona , Spain
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16
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Tamm E, Di Cristofaro J, Mazières S, Pennarun E, Kushniarevich A, Raveane A, Semino O, Chiaroni J, Pereira L, Metspalu M, Montinaro F. Genome-wide analysis of Corsican population reveals a close affinity with Northern and Central Italy. Sci Rep 2019; 9:13581. [PMID: 31537848 PMCID: PMC6753063 DOI: 10.1038/s41598-019-49901-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2019] [Accepted: 08/31/2019] [Indexed: 01/13/2023] Open
Abstract
Despite being the fourth largest island in the Mediterranean basin, the genetic variation of Corsica has not been explored as exhaustively as Sardinia, which is situated only 11 km South. However, it is likely that the populations of the two islands shared, at least in part, similar demographic histories. Moreover, the relative small size of the Corsica may have caused genetic isolation, which, in turn, might be relevant under medical and translational perspectives. Here we analysed genome wide data of 16 Corsicans, and integrated with newly (33 individuals) and previously generated samples from West Eurasia and North Africa. Allele frequency, haplotype-based, and ancient genome analyses suggest that although Sardinia and Corsica may have witnessed similar isolation and migration events, the latter is genetically closer to populations from continental Europe, such as Northern and Central Italians.
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Affiliation(s)
- Erika Tamm
- Institute of Genomics, University of Tartu, Tartu, Estonia.
| | - Julie Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.,Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | | | - Erwan Pennarun
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Alena Kushniarevich
- Institute of Genomics, University of Tartu, Tartu, Estonia.,Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, 220072, Belarus
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani" Università di Pavia, Via Ferrata 9, 27100, Pavia, Italy
| | - Jacques Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.,Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - Luisa Pereira
- i3S - Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135, Porto, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), 4200-135, Porto, Portugal
| | - Mait Metspalu
- Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Francesco Montinaro
- Institute of Genomics, University of Tartu, Tartu, Estonia. .,Department of Zoology, University of Oxford, Oxford, UK.
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17
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Raveane A, Aneli S, Montinaro F, Athanasiadis G, Barlera S, Birolo G, Boncoraglio G, Di Blasio AM, Di Gaetano C, Pagani L, Parolo S, Paschou P, Piazza A, Stamatoyannopoulos G, Angius A, Brucato N, Cucca F, Hellenthal G, Mulas A, Peyret-Guzzon M, Zoledziewska M, Baali A, Bycroft C, Cherkaoui M, Chiaroni J, Di Cristofaro J, Dina C, Dugoujon JM, Galan P, Giemza J, Kivisild T, Mazieres S, Melhaoui M, Metspalu M, Myers S, Pereira L, Ricaut FX, Brisighelli F, Cardinali I, Grugni V, Lancioni H, Pascali VL, Torroni A, Semino O, Matullo G, Achilli A, Olivieri A, Capelli C. Population structure of modern-day Italians reveals patterns of ancient and archaic ancestries in Southern Europe. SCIENCE ADVANCES 2019; 5:eaaw3492. [PMID: 31517044 PMCID: PMC6726452 DOI: 10.1126/sciadv.aaw3492] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 04/10/2019] [Accepted: 08/06/2019] [Indexed: 05/10/2023]
Abstract
European populations display low genetic differentiation as the result of long-term blending of their ancient founding ancestries. However, it is unclear how the combination of ancient ancestries related to early foragers, Neolithic farmers, and Bronze Age nomadic pastoralists can explain the distribution of genetic variation across Europe. Populations in natural crossroads like the Italian peninsula are expected to recapitulate the continental diversity, but have been systematically understudied. Here, we characterize the ancestry profiles of Italian populations using a genome-wide dataset representative of modern and ancient samples from across Italy, Europe, and the rest of the world. Italian genomes capture several ancient signatures, including a non-steppe contribution derived ultimately from the Caucasus. Differences in ancestry composition, as the result of migration and admixture, have generated in Italy the largest degree of population structure detected so far in the continent, as well as shaping the amount of Neanderthal DNA in modern-day populations.
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Affiliation(s)
- A. Raveane
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
- Department of Zoology, University of Oxford, Oxford, UK
| | - S. Aneli
- Department of Zoology, University of Oxford, Oxford, UK
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - F. Montinaro
- Department of Zoology, University of Oxford, Oxford, UK
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - G. Athanasiadis
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - S. Barlera
- Department of Cardiovascular Research, Istituto di Ricovero e Cura a Carattere Scientifico–Istituto di Ricerche Farmacologiche Mario Negri, Milan, Italy
| | - G. Birolo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - G. Boncoraglio
- Department of Cerebrovascular Diseases, IRCCS Istituto Neurologico Carlo Besta, Milan, Italy
- PhD Program in Neuroscience, University Milano-Bicocca, Monza, Italy
| | - A. M. Di Blasio
- Istituto Auxologico Italiano, IRCCS, Centro di Ricerche e Tecnologie Biomediche, Milano, Italy
| | - C. Di Gaetano
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - L. Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- APE lab, Department of Biology, University of Padua, Padua, Italy
| | - S. Parolo
- Computational Biology Unit, Institute of Molecular Genetics, National Research Council, Pavia, Italy
| | - P. Paschou
- Department of Biological Sciences, Purdue University, West Lafayette, IN, USA
| | - A. Piazza
- Department of Medical Sciences, University of Turin, Turin, Italy
- Academy of Sciences, Turin, Italy
| | - G. Stamatoyannopoulos
- Department of Medicine and Genome Sciences, University of Washington, Seattle, WA, USA
| | - A. Angius
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - N. Brucato
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - G. Hellenthal
- University College London Genetics Institute (UGI), University College London, London, UK
| | - A. Mulas
- Istituto di Ricerca Genetica e Biomedica (IRGB), CNR, Lanusei, Italy
| | - M. Peyret-Guzzon
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), Monserrato, Cagliari, Italy
| | - A. Baali
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - C. Bycroft
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - M. Cherkaoui
- Faculté des Sciences Semlalia de Marrakech (FSSM), Université Cadi Ayyad, Marrakech, Morocco
| | - J. Chiaroni
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - J. Di Cristofaro
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
- Etablissement Français du Sang PACA Corse, Biologie des Groupes Sanguins, Marseille, France
| | - C. Dina
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - J. M. Dugoujon
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - P. Galan
- Equipe de Recherche en Epidémiologie Nutritionnelle (EREN), Centre de Recherche en Epidémiologie et Statistiques, Université Paris 13/Inserm U1153/Inra U1125/ Cnam, COMUE Sorbonne Paris Cité, F-93017 Bobigny, France
| | - J. Giemza
- l’institut du thorax, INSERM, CNRS, University of Nantes, Nantes, France
| | - T. Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Department of Human Genetics, KU Leuven, Herestraat 49, box 604, Leuven 3000, Belgium
| | - S. Mazieres
- Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - M. Melhaoui
- Faculté des Sciences, Université Mohammed Premier, Oujda, Morocco
| | - M. Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - S. Myers
- The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - L. Pereira
- i3S–Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Porto, Portugal
- IPATIMUP–Instituto de Patologia e Imunologia Molecular, Universidade do Porto, Porto, Portugal
| | - F. X. Ricaut
- Evolutionary Medicine Group, Laboratoire d’Anthropologie Moléculaire et Imagerie de Synthèse, Centre National de la Recherche Scientifique (CNRS), Université de Toulouse, Toulouse, France
| | - F. Brisighelli
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - I. Cardinali
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. Grugni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - H. Lancioni
- Department of Chemistry, Biology and Biotechnology, University of Perugia, Perugia, Italy
| | - V. L. Pascali
- Section of Legal Medicine, Institute of Public Health, Catholic University of the Sacred Heart, Rome, Italy
| | - A. Torroni
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - O. Semino
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - G. Matullo
- Department of Medical Sciences, University of Turin, Turin, Italy
- IIGM (Italian Institute for Genomic Medicine), Turin, Italy
| | - A. Achilli
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - A. Olivieri
- Department of Biology and Biotechnology “L. Spallanzani”, University of Pavia, Pavia, Italy
| | - C. Capelli
- Department of Zoology, University of Oxford, Oxford, UK
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18
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Brace S, Diekmann Y, Booth TJ, van Dorp L, Faltyskova Z, Rohland N, Mallick S, Olalde I, Ferry M, Michel M, Oppenheimer J, Broomandkhoshbacht N, Stewardson K, Martiniano R, Walsh S, Kayser M, Charlton S, Hellenthal G, Armit I, Schulting R, Craig OE, Sheridan A, Parker Pearson M, Stringer C, Reich D, Thomas MG, Barnes I. Ancient genomes indicate population replacement in Early Neolithic Britain. Nat Ecol Evol 2019; 3:765-771. [PMID: 30988490 DOI: 10.1038/s41559-019-0871-9] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Accepted: 03/06/2019] [Indexed: 11/09/2022]
Abstract
The roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.
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Affiliation(s)
- Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Yoan Diekmann
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Thomas J Booth
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Lucy van Dorp
- UCL Genetics Institute, University College London, London, UK
| | - Zuzana Faltyskova
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Swapan Mallick
- UCL Genetics Institute, University College London, London, UK.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Susan Walsh
- Department of Biology, Indiana University-Purdue University Indianapolis, Indianapolis, IN, USA
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Centre Rotterdam, Rotterdam, the Netherlands
| | - Sophy Charlton
- Department of Earth Sciences, Natural History Museum, London, UK.,Bioarch, University of York, York, UK
| | | | - Ian Armit
- School of Archaeological and Forensic Sciences, University of Bradford, Bradford, UK
| | - Rick Schulting
- Institute of Archaeology, University of Oxford, Oxford, UK
| | | | | | | | - Chris Stringer
- Department of Earth Sciences, Natural History Museum, London, UK
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA.,Broad Institute of MIT and Harvard, Cambridge, MA, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, London, UK. .,UCL Genetics Institute, University College London, London, UK.
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK.
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19
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Modi A, Nesheva D, Sarno S, Vai S, Karachanak-Yankova S, Luiselli D, Pilli E, Lari M, Vergata C, Yordanov Y, Dimitrova D, Kalcev P, Staneva R, Antonova O, Hadjidekova S, Galabov A, Toncheva D, Caramelli D. Ancient human mitochondrial genomes from Bronze Age Bulgaria: new insights into the genetic history of Thracians. Sci Rep 2019; 9:5412. [PMID: 30931994 PMCID: PMC6443937 DOI: 10.1038/s41598-019-41945-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 03/20/2019] [Indexed: 11/17/2022] Open
Abstract
One of the best documented Indo-European civilizations that inhabited Bulgaria is the Thracians, who lasted for more than five millennia and whose origin and relationships with other past and present-day populations are debated among researchers. Here we report 25 new complete mitochondrial genomes of ancient individuals coming from three necropolises located in different regions of Bulgaria – Shekerdja mogila, Gabrova mogila and Bereketska mogila – dated to II-III millennium BC. The identified mtDNA haplogroup composition reflects the mitochondrial variability of Western Eurasia. In particular, within the ancient Eurasian genetic landscape, Thracians locate in an intermediate position between Early Neolithic farmers and Late Neolithic-Bronze Age steppe pastoralists, supporting the scenario that the Balkan region has been a link between Eastern Europe and the Mediterranean since the prehistoric time. Spatial Principal Component Analysis (sPCA) performed on Thracian and modern mtDNA sequences, confirms the pattern highlighted on ancient populations, overall indicating that the maternal gene pool of Thracians reflects their central geographical position at the gateway of Europe.
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Affiliation(s)
- Alessandra Modi
- Department of Biology, University of Florence, Florence, Italy
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Stefania Sarno
- Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | | | - Donata Luiselli
- Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Elena Pilli
- Department of Biology, University of Florence, Florence, Italy
| | - Martina Lari
- Department of Biology, University of Florence, Florence, Italy
| | - Chiara Vergata
- Department of Biology, University of Florence, Florence, Italy
| | - Yordan Yordanov
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | - Petar Kalcev
- The Regional Historical Museum of Stara Zagora, Stara Zagora, Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Olga Antonova
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria
| | - Angel Galabov
- The Stephan Angeloff Institute of Microbiology, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Medical University of Sofia, Sofia, Bulgaria.
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy.
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20
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Patterns of genetic differentiation and the footprints of historical migrations in the Iberian Peninsula. Nat Commun 2019; 10:551. [PMID: 30710075 PMCID: PMC6358624 DOI: 10.1038/s41467-018-08272-w] [Citation(s) in RCA: 43] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 12/07/2018] [Indexed: 12/31/2022] Open
Abstract
The Iberian Peninsula is linguistically diverse and has a complex demographic history, including a centuries-long period of Muslim rule. Here, we study the fine-scale genetic structure of its population, and the genetic impacts of historical events, leveraging powerful, haplotype-based statistical methods to analyse 1413 individuals from across Spain. We detect extensive fine-scale population structure at extremely fine scales (below 10 Km) in some regions, including Galicia. We identify a major east-west axis of genetic differentiation, and evidence of historical north to south population movement. We find regionally varying fractions of north-west African ancestry (0–11%) in modern-day Iberians, related to an admixture event involving European-like and north-west African-like source populations. We date this event to 860–1120 CE, implying greater genetic impacts in the early half of Muslim rule in Iberia. Together, our results indicate clear genetic impacts of population movements associated with both the Muslim conquest and the subsequent Reconquista. The Iberian Peninsula has a complex history. Here, the authors analyse the genetic structure of the modern Iberian population at fine scale, revealing historical population movements associated with the time of Muslim rule.
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21
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Bybjerg-Grauholm J, Hagen CM, Gonçalves VF, Bækvad-Hansen M, Hansen CS, Hedley PL, Kanters JK, Nielsen J, Theisen M, Mors O, Kennedy J, Als TD, Demur AB, Nordentoft M, Børglum A, Mortensen PB, Werge TM, Hougaard DM, Christiansen M. Complex spatio-temporal distribution and genomic ancestry of mitochondrial DNA haplogroups in 24,216 Danes. PLoS One 2018; 13:e0208829. [PMID: 30543675 PMCID: PMC6292624 DOI: 10.1371/journal.pone.0208829] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/23/2018] [Indexed: 02/06/2023] Open
Abstract
Mitochondrial DNA (mtDNA) haplogroups (hgs) are evolutionarily conserved sets of mtDNA SNP-haplotypes with characteristic geographical distribution. Associations of hgs with disease and physiological characteristics have been reported, but have frequently not been reproducible. Using 418 mtDNA SNPs on the PsychChip (Illumina), we assessed the spatio-temporal distribution of mtDNA hgs in Denmark from DNA isolated from 24,642 geographically un-biased dried blood spots (DBS), collected from 1981 to 2005 through the Danish National Neonatal Screening program. ADMIXTURE was used to establish the genomic ancestry of all samples using a reference of 100K+ autosomal SNPs in 2,248 individuals from nine populations. Median-joining analysis determined that the hgs were highly variable, despite being typically Northern European in origin, suggesting multiple founder events. Furthermore, considerable heterogeneity and variation in nuclear genomic ancestry was observed. Thus, individuals with hg H exhibited 95%, and U hgs 38.2% - 92.5%, Danish ancestry. Significant clines between geographical regions and rural and metropolitan populations were found. Over 25 years, macro-hg L increased from 0.2% to 1.2% (p = 1.1*E-10), and M from 1% to 2.4% (p = 3.7*E-8). Hg U increased among the R macro-hg from 14.1% to 16.5% (p = 1.9*E-3). Genomic ancestry, geographical skewedness, and sub-hg distribution suggested that the L, M and U increases are due to immigration. The complex spatio-temporal dynamics and genomic ancestry of mtDNA in the Danish population reflect repeated migratory events and, in later years, net immigration. Such complexity may explain the often contradictory and population-specific reports of mito-genomic association with disease.
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Affiliation(s)
| | - Christian M. Hagen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Christine S. Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Paula L. Hedley
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen K. Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jimmi Nielsen
- Aalborg Psychiatric Hospital. Aalborg University Hospital, Aalborg, Denmark
| | - Michael Theisen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Ole Mors
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - James Kennedy
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Thomas D. Als
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Alfonso B. Demur
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | | | - Anders Børglum
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Preben B. Mortensen
- Center for Register Research, Institute of Economics, Aarhus University, Århus, Denmark
| | - Thomas M. Werge
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | - David M. Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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22
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Hagen CM, Gonçalves VF, Hedley PL, Bybjerg-Grauholm J, Bækvad-Hansen M, Hansen CS, Kanters JK, Nielsen J, Mors O, Demur AB, Als TD, Nordentoft M, Børglum A, Mortensen PB, Kennedy J, Werge TM, Hougaard DM, Christiansen M. Schizophrenia-associated mt-DNA SNPs exhibit highly variable haplogroup affiliation and nuclear ancestry: Bi-genomic dependence raises major concerns for link to disease. PLoS One 2018; 13:e0208828. [PMID: 30532134 PMCID: PMC6287820 DOI: 10.1371/journal.pone.0208828] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 11/23/2018] [Indexed: 11/19/2022] Open
Abstract
Mitochondria play a significant role in human diseases. However, disease associations with mitochondrial DNA (mtDNA) SNPs have proven difficult to replicate. An analysis of eight schizophrenia-associated mtDNA SNPs, in 23,743 Danes without a psychiatric diagnosis and 2,538 schizophrenia patients, revealed marked inter-allelic differences in mitochondrial haplogroup affiliation and nuclear ancestry. This bi-genomic dependence could entail population stratification. Only two mitochondrial SNPs, m.15043A and m.15218G, were significantly associated with schizophrenia. However, these associations disappeared when corrected for haplogroup affiliation and nuclear ancestry. The extensive bi-genomic dependence documented here is a major concern when interpreting historic, as well as designing future, mtDNA association studies.
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Affiliation(s)
- Christian M. Hagen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | - Paula L. Hedley
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | | | - Marie Bækvad-Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Christine S. Hansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Jørgen K. Kanters
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Jimmi Nielsen
- Aalborg Psychiatric Hospital, Aalborg University Hospital, Aalborg, Denmark
| | - Ole Mors
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Alfonso B. Demur
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | - Thomas D. Als
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | | | - Anders Børglum
- Institute of Medical Genetics, Aarhus University, Aarhus, Denmark
| | - Preben B. Mortensen
- Center for Register Research, Institute of Economics, Aarhus University, Aarhus, Denmark
| | - James Kennedy
- Centre for Addiction and Mental Health, University of Toronto, Toronto, Canada
| | - Thomas M. Werge
- Mental Health Centre, Sct Hans, Capital Region of Denmark, Denmark
| | - David M. Hougaard
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
| | - Michael Christiansen
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Department of Biomedical Sciences, University of Copenhagen, Copenhagen, Denmark
- * E-mail:
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23
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Chimusa ER, Defo J, Thami PK, Awany D, Mulisa DD, Allali I, Ghazal H, Moussa A, Mazandu GK. Dating admixture events is unsolved problem in multi-way admixed populations. Brief Bioinform 2018; 21:144-155. [PMID: 30462157 DOI: 10.1093/bib/bby112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 10/12/2018] [Accepted: 10/15/2018] [Indexed: 12/12/2022] Open
Abstract
Advances in human sequencing technologies, coupled with statistical and computational tools, have fostered the development of methods for dating admixture events. These methods have merits and drawbacks in estimating admixture events in multi-way admixed populations. Here, we first provide a comprehensive review and comparison of current methods pertinent to dating admixture events. Second, we assess various admixture dating tools. We do so by performing various simulations. Third, we apply the top two assessed methods to real data of a uniquely admixed population from South Africa. Results reveal that current dating admixture models are not sufficiently equipped to estimate ancient admixtures events and to identify multi-faceted admixture events in complex multi-way admixed populations. We conclude with a discussion of research areas where further work on dating admixture-based methods is needed.
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Affiliation(s)
- Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Joel Defo
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Prisca K Thami
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa.,Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana.,Department of Biological Sciences, University of Botswana, Gaborone, Botswana
| | - Denis Awany
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Delesa D Mulisa
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | - Imane Allali
- Division of Computational Biology, Department of Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa
| | | | - Ahmed Moussa
- Abdelmalek Essaadi University ENSA, Tangier, Morocco
| | - Gaston K Mazandu
- Division of Human Genetics, Department of Pathology, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa.,Division of Computational Biology, Department of Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine,Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town, South Africa.,African Institute for Mathematical Sciences (AIMS),Muizenberg, Cape Town, South Africa
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24
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Tambets K, Yunusbayev B, Hudjashov G, Ilumäe AM, Rootsi S, Honkola T, Vesakoski O, Atkinson Q, Skoglund P, Kushniarevich A, Litvinov S, Reidla M, Metspalu E, Saag L, Rantanen T, Karmin M, Parik J, Zhadanov SI, Gubina M, Damba LD, Bermisheva M, Reisberg T, Dibirova K, Evseeva I, Nelis M, Klovins J, Metspalu A, Esko T, Balanovsky O, Balanovska E, Khusnutdinova EK, Osipova LP, Voevoda M, Villems R, Kivisild T, Metspalu M. Genes reveal traces of common recent demographic history for most of the Uralic-speaking populations. Genome Biol 2018; 19:139. [PMID: 30241495 PMCID: PMC6151024 DOI: 10.1186/s13059-018-1522-1] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2018] [Accepted: 09/03/2018] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND The genetic origins of Uralic speakers from across a vast territory in the temperate zone of North Eurasia have remained elusive. Previous studies have shown contrasting proportions of Eastern and Western Eurasian ancestry in their mitochondrial and Y chromosomal gene pools. While the maternal lineages reflect by and large the geographic background of a given Uralic-speaking population, the frequency of Y chromosomes of Eastern Eurasian origin is distinctively high among European Uralic speakers. The autosomal variation of Uralic speakers, however, has not yet been studied comprehensively. RESULTS Here, we present a genome-wide analysis of 15 Uralic-speaking populations which cover all main groups of the linguistic family. We show that contemporary Uralic speakers are genetically very similar to their local geographical neighbours. However, when studying relationships among geographically distant populations, we find that most of the Uralic speakers and some of their neighbours share a genetic component of possibly Siberian origin. Additionally, we show that most Uralic speakers share significantly more genomic segments identity-by-descent with each other than with geographically equidistant speakers of other languages. We find that correlated genome-wide genetic and lexical distances among Uralic speakers suggest co-dispersion of genes and languages. Yet, we do not find long-range genetic ties between Estonians and Hungarians with their linguistic sisters that would distinguish them from their non-Uralic-speaking neighbours. CONCLUSIONS We show that most Uralic speakers share a distinct ancestry component of likely Siberian origin, which suggests that the spread of Uralic languages involved at least some demic component.
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Affiliation(s)
- Kristiina Tambets
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia.
| | - Bayazit Yunusbayev
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Georgi Hudjashov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, 4442, New Zealand
| | - Anne-Mai Ilumäe
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Siiri Rootsi
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Terhi Honkola
- Department of Biology, University of Turku, 20014, Turku, Finland
- Institute of Estonian and General Linguistics, University of Tartu, 51014, Tartu, Estonia
| | - Outi Vesakoski
- Department of Biology, University of Turku, 20014, Turku, Finland
| | - Quentin Atkinson
- School of Psychology, University of Auckland, Auckland, 1142, New Zealand
- Department of Linguistic and Cultural Evolution, Max Planck Institute for the Science of Human History, D-07745, Jena, Germany
| | - Pontus Skoglund
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Alena Kushniarevich
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Genetics and Cytology of the National Academy of Sciences of Belarus, Minsk, 220072, Republic of Belarus
| | - Sergey Litvinov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Maere Reidla
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Ene Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Lehti Saag
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Timo Rantanen
- Department of Geography and Geology, University of Turku, 20014, Turku, Finland
| | - Monika Karmin
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Jüri Parik
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Sergey I Zhadanov
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Radiology, The Mount Sinai Medical Center, New York, NY, 10029, USA
| | - Marina Gubina
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
| | - Larisa D Damba
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Institute of Medical and Social Problems and Control of the Healthcare Department of Tuva Republic, Kyzyl, 667003, Russia
| | - Marina Bermisheva
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
| | - Tuuli Reisberg
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
| | - Khadizhat Dibirova
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Irina Evseeva
- Northern State Medical University, Arkhangelsk, 163000, Russia
- Anthony Nolan, London, NW3 2NU, UK
| | - Mari Nelis
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Janis Klovins
- Latvian Biomedical Research and Study Centre, Riga, LV-1067, Latvia
| | - Andres Metspalu
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Tõnu Esko
- Research Centre of Estonian Genome Center, Institute of Genomics, University of Tartu, 51010, Tartu, Estonia
| | - Oleg Balanovsky
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
- Vavilov Institute for General Genetics, RAS, Moscow, 119991, Russia
| | - Elena Balanovska
- Research Centre for Medical Genetics, Russian Academy of Medical Sciences, Moscow, 115478, Russia
| | - Elza K Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of RAS, Ufa, 450054, Russia
- Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, 450054, Russia
| | - Ludmila P Osipova
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
| | - Mikhail Voevoda
- Institute of Cytology and Genetics, Siberian Branch of RAS, Novosibirsk, 630090, Russia
- Novosibirsk State University, 2 Pirogova Str, Novosibirsk, 630090, Russia
- Institute of Internal Medicine, Siberian Branch of Russian Academy of Medical Sciences, Novosibirsk, 630090, Russia
| | - Richard Villems
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, 51010, Tartu, Estonia
- Department of Archaeology, University of Cambridge, Cambridge, CB2 1QH, UK
- Department of Human Genetics, KU Leuven, Leuven, 3000, Belgium
| | - Mait Metspalu
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23b, 51010, Tartu, Estonia
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25
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O’Sullivan N, Posth C, Coia V, Schuenemann VJ, Price TD, Wahl J, Pinhasi R, Zink A, Krause J, Maixner F. Ancient genome-wide analyses infer kinship structure in an Early Medieval Alemannic graveyard. SCIENCE ADVANCES 2018; 4:eaao1262. [PMID: 30191172 PMCID: PMC6124919 DOI: 10.1126/sciadv.aao1262] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 05/31/2018] [Indexed: 05/25/2023]
Abstract
From historical and archeological records, it is posited that the European medieval household was a combination of close relatives and recruits. However, this kinship structure has not yet been directly tested at a genomic level on medieval burials. The early 7th century CE burial at Niederstotzingen, discovered in 1962, is the most complete and richest example of Alemannic funerary practice in Germany. Excavations found 13 individuals who were buried with an array of inscribed bridle gear, jewelry, armor, and swords. These artifacts support the view that the individuals had contact with France, northern Italy, and Byzantium. This study analyzed genome-wide sequences recovered from the remains, in tandem with analysis of the archeological context, to reconstruct kinship and the extent of outside contact. Eleven individuals had sufficient DNA preservation to genetically sex them as male and identify nine unique mitochondrial haplotypes and two distinct Y chromosome lineages. Genome-wide analyses were performed on eight individuals to estimate genetic affiliation to modern west Eurasians and genetic kinship at the burial. Five individuals were direct relatives. Three other individuals were not detectably related; two of these showed genomic affinity to southern Europeans. The genetic makeup of the individuals shares no observable pattern with their orientation in the burial or the cultural association of their grave goods, with the five related individuals buried with grave goods associated with three diverse cultural origins. These findings support the idea that not only were kinship and fellowship held in equal regard: Diverse cultural appropriation was practiced among closely related individuals as well.
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Affiliation(s)
- Niall O’Sullivan
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Valentina Coia
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Verena J. Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
- Senckenberg Center for Human Evolution and Paleoecology, Palaeoanthropology, University of Tübingen, 72070 Tübingen, Germany
| | - T. Douglas Price
- Laboratory for Archaeological Chemistry, University of Wisconsin, 1180 Observatory Drive, Madison, WI 53706, USA
| | - Joachim Wahl
- State Office for Cultural Heritage Management Baden-Württemberg, Osteology, D-78467 Konstanz, Germany
- Institute for Archaeological Sciences, Palaeoanthropology, University of Tübingen, 72070 Tübingen, Germany
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin, Ireland
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Albert Zink
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745 Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, Rümelinstrasse 23, 72070 Tübingen, Germany
| | - Frank Maixner
- Institute for Mummy Studies, EURAC Research, Viale Druso 1, 39100 Bolzano, Italy
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26
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A finely resolved phylogeny of Y chromosome Hg J illuminates the processes of Phoenician and Greek colonizations in the Mediterranean. Sci Rep 2018; 8:7465. [PMID: 29748665 PMCID: PMC5945646 DOI: 10.1038/s41598-018-25912-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 04/25/2018] [Indexed: 11/15/2022] Open
Abstract
In order to improve the phylogeography of the male-specific genetic traces of Greek and Phoenician colonizations on the Northern coasts of the Mediterranean, we performed a geographically structured sampling of seven subclades of haplogroup J in Turkey, Greece and Italy. We resequenced 4.4 Mb of Y-chromosome in 58 subjects, obtaining 1079 high quality variants. We did not find a preferential coalescence of Turkish samples to ancestral nodes, contradicting the simplistic idea of a dispersal and radiation of Hg J as a whole from the Middle East. Upon calibration with an ancient Hg J chromosome, we confirmed that signs of Holocenic Hg J radiations are subtle and date mainly to the Bronze Age. We pinpointed seven variants which could potentially unveil star clusters of sequences, indicative of local expansions. By directly genotyping these variants in Hg J carriers and complementing with published resequenced chromosomes (893 subjects), we provide strong temporal and distributional evidence for markers of the Greek settlement of Magna Graecia (J2a-L397) and Phoenician migrations (rs760148062). Our work generated a minimal but robust list of evolutionarily stable markers to elucidate the demographic dynamics and spatial domains of male-mediated movements across and around the Mediterranean, in the last 6,000 years.
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27
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Ceballos FC, Joshi PK, Clark DW, Ramsay M, Wilson JF. Runs of homozygosity: windows into population history and trait architecture. Nat Rev Genet 2018; 19:220-234. [PMID: 29335644 DOI: 10.1038/nrg.2017.109] [Citation(s) in RCA: 382] [Impact Index Per Article: 63.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Long runs of homozygosity (ROH) arise when identical haplotypes are inherited from each parent and thus a long tract of genotypes is homozygous. Cousin marriage or inbreeding gives rise to such autozygosity; however, genome-wide data reveal that ROH are universally common in human genomes even among outbred individuals. The number and length of ROH reflect individual demographic history, while the homozygosity burden can be used to investigate the genetic architecture of complex disease. We discuss how to identify ROH in genome-wide microarray and sequence data, their distribution in human populations and their application to the understanding of inbreeding depression and disease risk.
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Affiliation(s)
- Francisco C Ceballos
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - David W Clark
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Parktown 2193, Johannesburg, South Africa.,Division of Human Genetics, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Braamfontein 2000, Johannesburg, South Africa
| | - James F Wilson
- Medical Research Council Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK.,Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH8 9AG, UK
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28
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Hudjashov G, Karafet TM, Lawson DJ, Downey S, Savina O, Sudoyo H, Lansing JS, Hammer MF, Cox MP. Complex Patterns of Admixture across the Indonesian Archipelago. Mol Biol Evol 2017; 34:2439-2452. [PMID: 28957506 PMCID: PMC5850824 DOI: 10.1093/molbev/msx196] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.
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Affiliation(s)
- Georgi Hudjashov
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Estonian Biocentre, 51010 Tartu, Estonia
| | | | - Daniel J Lawson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Sean Downey
- Department of Anthropology, University of Maryland, College Park, MD
| | - Olga Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | | | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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29
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Harris EE. Demic and cultural diffusion in prehistoric Europe in the age of ancient genomes. Evol Anthropol 2017; 26:228-241. [PMID: 29027332 DOI: 10.1002/evan.21545] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/23/2017] [Indexed: 11/10/2022]
Abstract
Ancient genomes can help us detect prehistoric migrations, population contractions, and admixture among populations. Knowing the dynamics of demography is invaluable for understanding culture change in prehistory, particularly the roles played by demic and cultural diffusion in transformations of material cultures. Prehistoric Europe is a region where ancient genome analyses can help illuminate the interplay between demography and culture change. In Europe, there is more archeological evidence, in terms of detailed studies, radiometric dates, and explanatory hypotheses that can be evaluated, than in any other region of the world. Here I show some important ways that ancient genomes have given us insights into population movements in European prehistory. I also propose that studies might be increasingly focused on specific questions of culture change, for example in evaluating the makers of "transitional" industries as well as the origins of the Gravettian and spread of the Magdalenian. I also discuss genomic evidence supporting the large role that demic expansion has played in the Neolithization of Europe and the formation of the European population during the Bronze Age.
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Affiliation(s)
- Eugene E Harris
- Department of Biological Sciences and Geology, Queensborough Community College, City University of New York, Medical Arts Building, M-213, 222-05, 56th Avenue Bayside, NY, 1136411364.,Affiliated Researcher, Center for the Study of Human Origins, New York University
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30
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Lazaridis I, Mittnik A, Patterson N, Mallick S, Rohland N, Pfrengle S, Furtwängler A, Peltzer A, Posth C, Vasilakis A, McGeorge PJP, Konsolaki-Yannopoulou E, Korres G, Martlew H, Michalodimitrakis M, Özsait M, Özsait N, Papathanasiou A, Richards M, Roodenberg SA, Tzedakis Y, Arnott R, Fernandes DM, Hughey JR, Lotakis DM, Navas PA, Maniatis Y, Stamatoyannopoulos JA, Stewardson K, Stockhammer P, Pinhasi R, Reich D, Krause J, Stamatoyannopoulos G. Genetic origins of the Minoans and Mycenaeans. Nature 2017; 548:214-218. [PMID: 28783727 PMCID: PMC5565772 DOI: 10.1038/nature23310] [Citation(s) in RCA: 118] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/25/2017] [Indexed: 01/02/2023]
Abstract
The origins of the Bronze Age Minoan and Mycenaean cultures have puzzled archaeologists for more than a century. We assembled genome-wide data from nineteen ancient individuals, including Minoans from Crete, Mycenaeans from mainland Greece, and their eastern neighbours from southwestern Anatolia. We show that Minoans and Mycenaeans were genetically similar, having at least three quarters of their ancestry from the first Neolithic farmers of western Anatolia and the Aegean1,2, and most of the remainder from ancient populations like those of the Caucasus3 and Iran4,5. However, the Mycenaeans differed from Minoans in deriving additional ancestry from an ultimate source related to the hunter-gatherers of eastern Europe and Siberia6–8, introduced via a proximal source related to either the inhabitants of either the Eurasian steppe1,6,9 or Armenia4,9. Modern Greeks resemble the Mycenaeans, but with some additional dilution of the early Neolithic ancestry. Our results support the idea of continuity but not isolation in the history of populations of the Aegean, before and after the time of its earliest civilizations.
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Affiliation(s)
- Iosif Lazaridis
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Alissa Mittnik
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, 72074 Tübingen, Germany
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Radcliffe Institute, Cambridge, Massachusetts 02138, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, 72074 Tübingen, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, University of Tübingen, 72074 Tübingen, Germany
| | - Alexander Peltzer
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Integrative Transcriptomics, Centre for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, 72074 Tübingen, Germany
| | - Andonis Vasilakis
- 23rd Ephorate of Prehistoric and Classical Antiquities, 71202 Herakleion, Crete
| | | | | | - George Korres
- Department of Archaeology, University of Athens, 17584 Athens, Greece
| | - Holley Martlew
- The Holley Martlew Archaeological Foundation, The Hellenic Archaeological Foundation, Tivoli House, Tivoli Road, Cheltenham GL50 2TD, UK
| | | | - Mehmet Özsait
- Erenköy, Bayar caddesi, Eser Apt. Number 7, Daire 24, Kadıköy, Istanbul, Turkey
| | - Nesrin Özsait
- Erenköy, Bayar caddesi, Eser Apt. Number 7, Daire 24, Kadıköy, Istanbul, Turkey
| | - Anastasia Papathanasiou
- Ephorate of Paleoantropology and Speleology, Greek Ministry of Culture, 11636 Athens, Greece
| | - Michael Richards
- Department of Archaeology, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia V5A 1S6, Canada
| | | | - Yannis Tzedakis
- Hellenic Archaeological Service, Samara, 27, Paleo Psychico, 15452 Athens, Greece
| | - Robert Arnott
- Green Templeton College, University of Oxford, Woodstock Road, Oxford OX2 6HG, UK
| | - Daniel M Fernandes
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.,CIAS, Department of Life Sciences, University of Coimbra, Coimbra 3000-456, Portugal
| | - Jeffery R Hughey
- Division of Mathematics, Science, and Engineering, Hartnell College, 411 Central Avenue, Salinas, California 93901, USA
| | - Dimitra M Lotakis
- Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Patrick A Navas
- Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA
| | - Yannis Maniatis
- Laboratory of Archaeometry, National Center for Scientific Research 'Demokritos', Aghia Paraskevi 153 10, Attiki, Greece
| | - John A Stamatoyannopoulos
- Department of Medicine, University of Washington, Seattle, Washington 98195, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.,Altius Institute for Biomedical Sciences, Seattle, Washington 98121, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Philipp Stockhammer
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Ludwig-Maximilians-Universität München, Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, 80799 München, Germany
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.,Department of Anthropology, University of Vienna, Althanstraße 14, 1090 Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, 72074 Tübingen, Germany
| | - George Stamatoyannopoulos
- Division of Medical Genetics, University of Washington, Seattle, Washington 98195, USA.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
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31
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Rey-González D, Gelabert-Besada M, Cruz R, Brisighelli F, Lopez-Soto M, Rasool M, Naseer M, Sánchez-Diz P, Carracedo A. Micro and macro geographical analysis of Y-chromosome lineages in South Iberia. Forensic Sci Int Genet 2017; 29:e9-e15. [DOI: 10.1016/j.fsigen.2017.04.021] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2016] [Revised: 04/27/2017] [Accepted: 04/29/2017] [Indexed: 11/25/2022]
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32
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Ancient and recent admixture layers in Sicily and Southern Italy trace multiple migration routes along the Mediterranean. Sci Rep 2017; 7:1984. [PMID: 28512355 PMCID: PMC5434004 DOI: 10.1038/s41598-017-01802-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2016] [Accepted: 04/04/2017] [Indexed: 12/12/2022] Open
Abstract
The Mediterranean shores stretching between Sicily, Southern Italy and the Southern Balkans witnessed a long series of migration processes and cultural exchanges. Accordingly, present-day population diversity is composed by multiple genetic layers, which make the deciphering of different ancestral and historical contributes particularly challenging. We address this issue by genotyping 511 samples from 23 populations of Sicily, Southern Italy, Greece and Albania with the Illumina GenoChip Array, also including new samples from Albanian- and Greek-speaking ethno-linguistic minorities of Southern Italy. Our results reveal a shared Mediterranean genetic continuity, extending from Sicily to Cyprus, where Southern Italian populations appear genetically closer to Greek-speaking islands than to continental Greece. Besides a predominant Neolithic background, we identify traces of Post-Neolithic Levantine- and Caucasus-related ancestries, compatible with maritime Bronze-Age migrations. We argue that these results may have important implications in the cultural history of Europe, such as in the diffusion of some Indo-European languages. Instead, recent historical expansions from North-Eastern Europe account for the observed differentiation of present-day continental Southern Balkan groups. Patterns of IBD-sharing directly reconnect Albanian-speaking Arbereshe with a recent Balkan-source origin, while Greek-speaking communities of Southern Italy cluster with their Italian-speaking neighbours suggesting a long-term history of presence in Southern Italy.
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33
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Joukhadar R, Daetwyler HD, Bansal UK, Gendall AR, Hayden MJ. Genetic Diversity, Population Structure and Ancestral Origin of Australian Wheat. FRONTIERS IN PLANT SCIENCE 2017; 8:2115. [PMID: 29312381 PMCID: PMC5733070 DOI: 10.3389/fpls.2017.02115] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2017] [Accepted: 11/28/2017] [Indexed: 05/22/2023]
Abstract
Since the introduction of wheat into Australia by the First Fleet settlers, germplasm from different geographical origins has been used to adapt wheat to the Australian climate through selection and breeding. In this paper, we used 482 cultivars, representing the breeding history of bread wheat in Australia since 1840, to characterize their diversity and population structure and to define the geographical ancestral background of Australian wheat germplasm. This was achieved by comparing them to a global wheat collection using in-silico chromosome painting based on SNP genotyping. The global collection involved 2,335 wheat accessions which was divided into 23 different geographical subpopulations. However, the whole set was reduced to 1,544 accessions to increase the differentiation and decrease the admixture among different global subpopulations to increase the power of the painting analysis. Our analysis revealed that the structure of Australian wheat germplasm and its geographic ancestors have changed significantly through time, especially after the Green Revolution. Before 1920, breeders used cultivars from around the world, but mainly Europe and Africa, to select potential cultivars that could tolerate Australian growing conditions. Between 1921 and 1970, a dependence on African wheat germplasm became more prevalent. Since 1970, a heavy reliance on International Maize and Wheat Improvement Center (CIMMYT) germplasm has persisted. Combining the results from linkage disequilibrium, population structure and in-silico painting revealed that the dependence on CIMMYT materials has varied among different Australian States, has shrunken the germplasm effective population size and produced larger linkage disequilibrium blocks. This study documents the evolutionary history of wheat breeding in Australia and provides an understanding for how the wheat genome has been adapted to local growing conditions. This information provides a guide for industry to assist with maintaining genetic diversity for long-term selection gains and to plan future breeding programs.
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Affiliation(s)
- Reem Joukhadar
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
- Agriculture Victoria Research, AgriBio, Centre for Agribioscience, Bundoora, VIC, Australia
- *Correspondence: Reem Joukhadar
| | - Hans D. Daetwyler
- Agriculture Victoria Research, AgriBio, Centre for Agribioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
| | - Urmil K. Bansal
- School of Life and Environmental Sciences, The University of Sydney Plant Breeding Institute, Cobbitty, NSW, Australia
| | - Anthony R. Gendall
- Department of Animal, Plant and Soil Sciences, La Trobe University, Bundoora, VIC, Australia
| | - Matthew J. Hayden
- Agriculture Victoria Research, AgriBio, Centre for Agribioscience, Bundoora, VIC, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC, Australia
- Matthew J. Hayden
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34
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Günther T, Jakobsson M. Genes mirror migrations and cultures in prehistoric Europe — a population genomic perspective. Curr Opin Genet Dev 2016; 41:115-123. [DOI: 10.1016/j.gde.2016.09.004] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2016] [Revised: 09/13/2016] [Accepted: 09/13/2016] [Indexed: 01/08/2023]
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35
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Complex Ancient Genetic Structure and Cultural Transitions in Southern African Populations. Genetics 2016; 205:303-316. [PMID: 27838627 PMCID: PMC5223510 DOI: 10.1534/genetics.116.189209] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 10/13/2016] [Indexed: 12/19/2022] Open
Abstract
The characterization of the structure of southern African populations has been the subject of numerous genetic, medical, linguistic, archaeological, and anthropological investigations. Current diversity in the subcontinent is the result of complex events of genetic admixture and cultural contact between early inhabitants and migrants that arrived in the region over the last 2000 years. Here, we analyze 1856 individuals from 91 populations, comprising novel and published genotype data, to characterize the genetic ancestry profiles of 631 individuals from 51 southern African populations. Combining both local ancestry and allele frequency based analyses, we identify a tripartite, ancient, Khoesan-related genetic structure. This structure correlates neither with linguistic affiliation nor subsistence strategy, but with geography, revealing the importance of isolation-by-distance dynamics in the area. Fine-mapping of these components in southern African populations reveals admixture and cultural reversion involving several Khoesan groups, and highlights that Bantu speakers and Coloured individuals have different mixtures of these ancient ancestries.
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36
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Novembre J, Peter BM. Recent advances in the study of fine-scale population structure in humans. Curr Opin Genet Dev 2016; 41:98-105. [PMID: 27662060 DOI: 10.1016/j.gde.2016.08.007] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Revised: 08/18/2016] [Accepted: 08/24/2016] [Indexed: 01/17/2023]
Abstract
Empowered by modern genotyping and large samples, population structure can be accurately described and quantified even when it only explains a fraction of a percent of total genetic variance. This is especially relevant and interesting for humans, where fine-scale population structure can both confound disease-mapping studies and reveal the history of migration and divergence that shaped our species' diversity. Here we review notable recent advances in the detection, use, and understanding of population structure. Our work addresses multiple areas where substantial progress is being made: improved statistics and models for better capturing differentiation, admixture, and the spatial distribution of variation; computational speed-ups that allow methods to scale to modern data; and advances in haplotypic modeling that have wide ranging consequences for the analysis of population structure. We conclude by outlining four important open challenges: the limitations of discrete population models, uncertainty in individual origins, the incorporation of both fine-scale structure and ancient DNA in parametric models, and the development of efficient computational tools, particularly for haplotype-based methods.
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Affiliation(s)
- John Novembre
- Department of Human Genetics, University of Chicago, IL 60636, United States; Department of Ecology and Evolutionary Biology, University of Chicago, IL 60636, United States
| | - Benjamin M Peter
- Department of Human Genetics, University of Chicago, IL 60636, United States
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37
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Complex interplay between neutral and adaptive evolution shaped differential genomic background and disease susceptibility along the Italian peninsula. Sci Rep 2016; 6:32513. [PMID: 27582244 PMCID: PMC5007512 DOI: 10.1038/srep32513] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2016] [Accepted: 08/08/2016] [Indexed: 01/23/2023] Open
Abstract
The Italian peninsula has long represented a natural hub for human migrations across
the Mediterranean area, being involved in several prehistoric and historical
population movements. Coupled with a patchy environmental landscape entailing
different ecological/cultural selective pressures, this might have produced peculiar
patterns of population structure and local adaptations responsible for heterogeneous
genomic background of present-day Italians. To disentangle this complex scenario,
genome-wide data from 780 Italian individuals were generated and set into the
context of European/Mediterranean genomic diversity by comparison with genotypes
from 50 populations. To maximize possibility of pinpointing functional genomic
regions that have played adaptive roles during Italian natural history, our survey
included also ~250,000 exomic markers and ~20,000
coding/regulatory variants with well-established clinical relevance. This enabled
fine-grained dissection of Italian population structure through the identification
of clusters of genetically homogeneous provinces and of genomic regions underlying
their local adaptations. Description of such patterns disclosed crucial implications
for understanding differential susceptibility to some inflammatory/autoimmune
disorders, coronary artery disease and type 2 diabetes of diverse Italian
subpopulations, suggesting the evolutionary causes that made some of them
particularly exposed to the metabolic and immune challenges imposed by dietary and
lifestyle shifts that involved western societies in the last centuries.
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38
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Nationwide Genomic Study in Denmark Reveals Remarkable Population Homogeneity. Genetics 2016; 204:711-722. [PMID: 27535931 DOI: 10.1534/genetics.116.189241] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2016] [Accepted: 07/30/2016] [Indexed: 02/07/2023] Open
Abstract
Denmark has played a substantial role in the history of Northern Europe. Through a nationwide scientific outreach initiative, we collected genetic and anthropometrical data from ∼800 high school students and used them to elucidate the genetic makeup of the Danish population, as well as to assess polygenic predictions of phenotypic traits in adolescents. We observed remarkable homogeneity across different geographic regions, although we could still detect weak signals of genetic structure reflecting the history of the country. Denmark presented genomic affinity with primarily neighboring countries with overall resemblance of decreasing weight from Britain, Sweden, Norway, Germany, and France. A Polish admixture signal was detected in Zealand and Funen, and our date estimates coincided with historical evidence of Wend settlements in the south of Denmark. We also observed considerably diverse demographic histories among Scandinavian countries, with Denmark having the smallest current effective population size compared to Norway and Sweden. Finally, we found that polygenic prediction of self-reported adolescent height in the population was remarkably accurate (R2 = 0.639 ± 0.015). The high homogeneity of the Danish population could render population structure a lesser concern for the upcoming large-scale gene-mapping studies in the country.
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Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-del-Molino D, Kousathanas A, Sell C, Robson HK, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig OE, Bradley DG, Shennan S, Veeramah K, Mashkour M, Wegmann D, Hellenthal G, Burger J. Early Neolithic genomes from the eastern Fertile Crescent. Science 2016; 353:499-503. [PMID: 27417496 PMCID: PMC5113750 DOI: 10.1126/science.aaf7943] [Citation(s) in RCA: 144] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023]
Abstract
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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Affiliation(s)
- Farnaz Broushaki
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Vivian Link
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Karola Kirsanow
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Zuzana Hofmanová
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Yoan Diekmann
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - David Díez-del-Molino
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Athanasios Kousathanas
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
- Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
| | - Christian Sell
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Harry K. Robson
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jens Blöcher
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Ruth Bollongino
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Hossein Davudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | - Olivia Munoz
- UMR 7041 ArScAn -VEPMO, Maison de l’Archéologie et de l’Ethnologie, 21 allée de l’Université, 92023 Nanterre, France
| | - Mathias Currat
- Department of Genetics & Evolution-Anthropology Unit, University of Geneva, 1211 Geneva, Switzerland
| | - Kamyar Abdi
- Samuel Jordan Center for Persian Studies and Culture, University of California-lrvine, Irvine, CA 92697-3370, USA
| | - Fereidoun Biglari
- Paleolithic Department, National Museum of Iran, 113617111, Tehran, Iran
| | - Oliver E. Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Stephen Shennan
- Institute of Archaeology, University College London, London WC1H 0PY, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Marjan Mashkour
- CNRS/MNHN/SUs – UMR 7209, Archéozoologie et Archéobotanique, Sociétés, Pratiques et Environnements, Département Ecologie et Gestion de la Biodiversité, 55 rue Buffon, 75005 Paris, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland
- Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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40
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Pankratov V, Litvinov S, Kassian A, Shulhin D, Tchebotarev L, Yunusbayev B, Möls M, Sahakyan H, Yepiskoposyan L, Rootsi S, Metspalu E, Golubenko M, Ekomasova N, Akhatova F, Khusnutdinova E, Heyer E, Endicott P, Derenko M, Malyarchuk B, Metspalu M, Davydenko O, Villems R, Kushniarevich A. East Eurasian ancestry in the middle of Europe: genetic footprints of Steppe nomads in the genomes of Belarusian Lipka Tatars. Sci Rep 2016; 6:30197. [PMID: 27453128 PMCID: PMC4958967 DOI: 10.1038/srep30197] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Accepted: 06/29/2016] [Indexed: 12/04/2022] Open
Abstract
Medieval era encounters of nomadic groups of the Eurasian Steppe and largely sedentary East Europeans had a variety of demographic and cultural consequences. Amongst these outcomes was the emergence of the Lipka Tatars—a Slavic-speaking Sunni-Muslim minority residing in modern Belarus, Lithuania and Poland, whose ancestors arrived in these territories via several migration waves, mainly from the Golden Horde. Our results show that Belarusian Lipka Tatars share a substantial part of their gene pool with Europeans as indicated by their Y-chromosomal, mitochondrial and autosomal DNA variation. Nevertheless, Belarusian Lipkas still retain a strong genetic signal of their nomadic ancestry, witnessed by the presence of common Y-chromosomal and mitochondrial DNA variants as well as autosomal segments identical by descent between Lipkas and East Eurasians from temperate and northern regions. Hence, we document Lipka Tatars as a unique example of former Medieval migrants into Central Europe, who became sedentary, changed language to Slavic, yet preserved their faith and retained, both uni- and bi-parentally, a clear genetic echo of a complex population interplay throughout the Eurasian Steppe Belt, extending from Central Europe to northern China.
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Affiliation(s)
- Vasili Pankratov
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Sergei Litvinov
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia.,Estonian Biocentre, Tartu, Estonia
| | - Alexei Kassian
- Institute of Linguistics, Russian Academy of Sciences, Moscow, Russia.,School for Advanced Studies in the Humanities, Russian Presidential Academy of National Economy and Public Administration, Moscow, Russia
| | - Dzmitry Shulhin
- Belarusian State University, Faculty of Applied Mathematics and Computer Science Department of Probability Theory and Mathematical Statistics, Minsk, Belarus
| | - Lieve Tchebotarev
- Center of analytical and genetic engineering studies, Institute of Microbiology, National Academy of Sciences of Belarus, Minsk, Belarus
| | | | - Märt Möls
- Institute of Mathematical Statistics, University of Tartu, Tartu, Estonia
| | - Hovhannes Sahakyan
- Estonian Biocentre, Tartu, Estonia.,Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, 0014, Armenia
| | - Levon Yepiskoposyan
- Laboratory of Ethnogenomics, Institute of Molecular Biology, National Academy of Sciences of Armenia, Yerevan, 0014, Armenia
| | | | - Ene Metspalu
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Maria Golubenko
- The Research Institute for Medical Genetics, 634050, Tomsk, Russia
| | - Natalia Ekomasova
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia
| | - Farida Akhatova
- Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia.,Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Research Centre, RAS, Ufa, Bashkortostan, Russia.,Department of Genetics and Fundamental Medicine of Bashkir State University, Ufa, Bashkortostan, Russia
| | - Evelyne Heyer
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Université Paris Diderot, Sorbonne Universités, Muséum national d'Histoire naturelle, Musée de l'Homme, Paris, France
| | - Phillip Endicott
- Eco-Anthropologie et Ethnobiologie, UMR 7206 CNRS, MNHN, Université Paris Diderot, Sorbonne Universités, Muséum national d'Histoire naturelle, Musée de l'Homme, Paris, France
| | - Miroslava Derenko
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | - Boris Malyarchuk
- Institute of Biological Problems of the North, Russian Academy of Sciences, Magadan, Russia
| | | | - Oleg Davydenko
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus
| | - Richard Villems
- Estonian Biocentre, Tartu, Estonia.,Department of Evolutionary Biology, Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Alena Kushniarevich
- Institute of Genetics and Cytology, National Academy of Sciences of Belarus, Minsk, Belarus.,Estonian Biocentre, Tartu, Estonia
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41
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Busby GB, Band G, Si Le Q, Jallow M, Bougama E, Mangano VD, Amenga-Etego LN, Enimil A, Apinjoh T, Ndila CM, Manjurano A, Nyirongo V, Doumba O, Rockett KA, Kwiatkowski DP, Spencer CC. Admixture into and within sub-Saharan Africa. eLife 2016; 5. [PMID: 27324836 PMCID: PMC4915815 DOI: 10.7554/elife.15266] [Citation(s) in RCA: 87] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 05/17/2016] [Indexed: 12/27/2022] Open
Abstract
Similarity between two individuals in the combination of genetic markers along their chromosomes indicates shared ancestry and can be used to identify historical connections between different population groups due to admixture. We use a genome-wide, haplotype-based, analysis to characterise the structure of genetic diversity and gene-flow in a collection of 48 sub-Saharan African groups. We show that coastal populations experienced an influx of Eurasian haplotypes over the last 7000 years, and that Eastern and Southern Niger-Congo speaking groups share ancestry with Central West Africans as a result of recent population expansions. In fact, most sub-Saharan populations share ancestry with groups from outside of their current geographic region as a result of gene-flow within the last 4000 years. Our in-depth analysis provides insight into haplotype sharing across different ethno-linguistic groups and the recent movement of alleles into new environments, both of which are relevant to studies of genetic epidemiology. DOI:http://dx.doi.org/10.7554/eLife.15266.001 Our genomes contain a record of historical events. This is because when groups of people are separated for generations, the DNA sequence in the two groups’ genomes will change in different ways. Looking at the differences in the genomes of people from the same population can help researchers to understand and reconstruct the historical interactions that brought their ancestors together. The mixing of two populations that were previously separate is known as admixture. Africa as a continent has few written records of its history. This means that it is somewhat unknown which important movements of people in the past generated the populations found in modern-day Africa. Busby et al. have now attempted to use DNA to look into this and reconstruct the last 4000 years of genetic history in African populations. As has been shown in other regions of the world, the new analysis showed that all African populations are the result of historical admixture events. However, Busby et al. could characterize these events to unprecedented level of detail. For example, multiple ethnic groups from The Gambia and Mali all show signs of sharing the same set of ancestors from West Africa, Europe and Asia who mixed around 2000 years ago. Evidence of a migration of people from Central West Africa, known as the Bantu expansion, could also be detected, and was shown to carry genes to the south and east. An important next step will be to now look at the consequences of the observed gene-flow, and ask if it has contributed to spreading beneficial, or detrimental, mutations around Africa. DOI:http://dx.doi.org/10.7554/eLife.15266.002
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Affiliation(s)
- George Bj Busby
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Gavin Band
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Quang Si Le
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
| | - Muminatou Jallow
- Medical Research Council Unit, Serrekunda, The Gambia.,Royal Victoria Teaching Hospital, Banjul, The Gambia
| | - Edith Bougama
- Centre National de Recherche et de Formation sur le Paludisme, Ouagadougou, Burkina Faso
| | - Valentina D Mangano
- Dipartimento di Sanita Publica e Malattie Infettive, University of Rome La Sapienza, Rome, Italy
| | | | | | - Tobias Apinjoh
- Department of Biochemistry and Molecular Biology, University of Buea, Buea, Cameroon
| | | | - Alphaxard Manjurano
- Joint Malaria Programme, Kilimanjaro Christian Medical College, Moshi, Tanzania.,Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Vysaul Nyirongo
- Malawi-Liverpool Wellcome Trust Clinical Research Programme, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Ogobara Doumba
- Malaria Research and Training Centre, University of Bamako, Bamako, Mali
| | - Kirk A Rockett
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Dominic P Kwiatkowski
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom.,Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Chris Ca Spencer
- Wellcome Trust Centre for Human Genetics, Oxford, United Kingdom
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42
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Early farmers from across Europe directly descended from Neolithic Aegeans. Proc Natl Acad Sci U S A 2016; 113:6886-91. [PMID: 27274049 DOI: 10.1073/pnas.1523951113] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.
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43
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Schiffels S, Haak W, Paajanen P, Llamas B, Popescu E, Loe L, Clarke R, Lyons A, Mortimer R, Sayer D, Tyler-Smith C, Cooper A, Durbin R. Iron Age and Anglo-Saxon genomes from East England reveal British migration history. Nat Commun 2016; 7:10408. [PMID: 26783965 PMCID: PMC4735688 DOI: 10.1038/ncomms10408] [Citation(s) in RCA: 95] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2015] [Accepted: 12/09/2015] [Indexed: 12/14/2022] Open
Abstract
British population history has been shaped by a series of immigrations, including the early Anglo-Saxon migrations after 400 CE. It remains an open question how these events affected the genetic composition of the current British population. Here, we present whole-genome sequences from 10 individuals excavated close to Cambridge in the East of England, ranging from the late Iron Age to the middle Anglo-Saxon period. By analysing shared rare variants with hundreds of modern samples from Britain and Europe, we estimate that on average the contemporary East English population derives 38% of its ancestry from Anglo-Saxon migrations. We gain further insight with a new method, rarecoal, which infers population history and identifies fine-scale genetic ancestry from rare variants. Using rarecoal we find that the Anglo-Saxon samples are closely related to modern Dutch and Danish populations, while the Iron Age samples share ancestors with multiple Northern European populations including Britain.
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Affiliation(s)
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Pirita Paajanen
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Elizabeth Popescu
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford OX2 0ES, UK
| | - Rachel Clarke
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Richard Mortimer
- Oxford Archaeology East, 15 Trafalgar Way, Bar Hill, Cambridge CB23 8SQ, UK
| | - Duncan Sayer
- School of Forensic and Applied Sciences, University of Central Lancashire, Preston PR1 2HE, UK
| | | | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Richard Durbin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, UK
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