1
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Sharko FS, Boulygina ES, Tsygankova SV, Slobodova NV, Rastorguev SM, Krasivskaya AA, Belinsky AB, Härke H, Kadieva AA, Demidenko SV, Malashev VY, Shvedchikova TY, Dobrovolskaya MV, Reshetova IK, Korobov DS, Nedoluzhko AV. Koban culture genome-wide and archeological data open the bridge between Bronze and Iron Ages in the North Caucasus. Eur J Hum Genet 2024:10.1038/s41431-023-01524-4. [PMID: 38177408 DOI: 10.1038/s41431-023-01524-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 10/05/2023] [Accepted: 12/07/2023] [Indexed: 01/06/2024] Open
Abstract
The North Caucasus played a key role during the ancient colonization of Eurasia and the formation of its cultural and genetic ancestry. Previous archeogenetic studies described a relative genetic and cultural continuity of ancient Caucasus societies, since the Eneolithic period. The Koban culture, which formed in the Late Bronze Age on the North Caucasian highlands, is considered as a cultural "bridge" between the ancient and modern autochthonous peoples of the Caucasus. Here, we discuss the place of this archeological culture and its representatives in the genetic orbit of Caucasian cultures using genome-wide SNP data from five individuals of the Koban culture and one individual of the early Alanic culture as well as previously published genomic data of ancient and modern North Caucasus individuals. Ancient DNA analysis shows that an ancient individual from Klin-Yar III, who was previously described as male, was in fact a female. Additional studies on well-preserved ancient human specimens are necessary to determine the level of local mobility and kinship between individuals in ancient societies of North Caucasus. Further studies with a larger sample size will allow us gain a deeper understanding of this topic.
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Affiliation(s)
- Fedor S Sharko
- European University at St. Petersburg, 6/1A Gagarinskaya Street, 191187, St. Petersburg, Russia
- Institute of Bioengineering, Research Center of Biotechnology of the Russian Academy of Sciences. 33, bld. 2 Leninsky Ave., Moscow, 119071, Russia
- National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia
| | - Eugenia S Boulygina
- National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia
| | - Svetlana V Tsygankova
- National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia
| | - Natalia V Slobodova
- National Research Center "Kurchatov Institute", Kurchatov sq. 1, Moscow, 123182, Russia
- HSE University, Profsoyuznaya st. 33, bld. 4, Moscow, 117418, Russia
| | - Sergey M Rastorguev
- N. I. Pirogov Russian National Research Medical University of the Ministry of Health of the Russian Federation Ostrovityanova st. 1, Moscow, 117997, Russia
| | - Anna A Krasivskaya
- Skolkovo Institute of Science and Technology, Bolshoy Boulevard 30, bld. 1, Moscow, 121205, Russia
| | - Andrej B Belinsky
- Limited liability company Nasledie, K. Marx av., 56, Stavropol', 355017, Russia
| | - Heinrich Härke
- Centre for Classical and Oriental Archaeology, National Research University Higher School of Economics, ul. Staraya Basmannaya 21/4c1, Moscow, 105066, Russia
- Department of Medieval Archaeology, University of Tübingen, Schloss Hohentübingen, D-72070, Tübingen, Germany
| | - Anna A Kadieva
- Department of Archaeology, State Historical Museum, Krasnaya pl., 1, Moscow, 109012, Russia
| | - Sergej V Demidenko
- Department of Scythian and Sarmatian Archaeology, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Vladimir Yu Malashev
- Department of Scythian and Sarmatian Archaeology, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Tatiana Yu Shvedchikova
- Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Maria V Dobrovolskaya
- Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Irina K Reshetova
- Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia
| | - Dmitry S Korobov
- Department of Theory and Methods, Institute of Archaeology, Russian Academy of Sciences, Dm. Uljanova str., 19, Moscow, 117292, Russia.
| | - Artem V Nedoluzhko
- European University at St. Petersburg, 6/1A Gagarinskaya Street, 191187, St. Petersburg, Russia.
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2
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The genetic legacy of the Hunyadi descendants. Heliyon 2022; 8:e11731. [DOI: 10.1016/j.heliyon.2022.e11731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2022] [Revised: 10/11/2022] [Accepted: 11/11/2022] [Indexed: 11/18/2022] Open
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3
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Exchanging fluids The sociocultural implications of microbial, cultural, and ethnic admixture in Latin America. Politics Life Sci 2021; 39:56-86. [PMID: 32697057 DOI: 10.1017/pls.2020.4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Knowledge of evolutionary influences on patterns of human mating, social interactions, and differential health is increasing, yet these insights have rarely been applied to historical analyses of human population dynamics. The genetic and evolutionary forces behind biases in interethnic mating and in the health of individuals of different ethnic groups in Latin America and the Caribbean since the European colonization of America are still largely ignored. We discuss how historical and contemporary sociocultural interactions and practices are strongly influenced by population-level evolutionary forces. Specifically, we discuss the historical implications of functional (de facto) polygyny, sex-biased admixture, and assortative mating in Latin America. We propose that these three evolutionary mechanisms influenced mating patterns, shaping the genetic and cultural landscape across Latin America and the Caribbean. Further, we discuss how genetic differences between the original populations that migrated at different times into Latin America contributed to their accommodation to and survival in the different local ecologies and interethnic interactions. Relevant medical and social implications follow from the genetic and cultural changes reviewed.
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4
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Clemente F, Unterländer M, Dolgova O, Amorim CEG, Coroado-Santos F, Neuenschwander S, Ganiatsou E, Cruz Dávalos DI, Anchieri L, Michaud F, Winkelbach L, Blöcher J, Arizmendi Cárdenas YO, Sousa da Mota B, Kalliga E, Souleles A, Kontopoulos I, Karamitrou-Mentessidi G, Philaniotou O, Sampson A, Theodorou D, Tsipopoulou M, Akamatis I, Halstead P, Kotsakis K, Urem-Kotsou D, Panagiotopoulos D, Ziota C, Triantaphyllou S, Delaneau O, Jensen JD, Moreno-Mayar JV, Burger J, Sousa VC, Lao O, Malaspinas AS, Papageorgopoulou C. The genomic history of the Aegean palatial civilizations. Cell 2021; 184:2565-2586.e21. [PMID: 33930288 PMCID: PMC8127963 DOI: 10.1016/j.cell.2021.03.039] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 09/17/2020] [Accepted: 03/18/2021] [Indexed: 12/30/2022]
Abstract
The Cycladic, the Minoan, and the Helladic (Mycenaean) cultures define the Bronze Age (BA) of Greece. Urbanism, complex social structures, craft and agricultural specialization, and the earliest forms of writing characterize this iconic period. We sequenced six Early to Middle BA whole genomes, along with 11 mitochondrial genomes, sampled from the three BA cultures of the Aegean Sea. The Early BA (EBA) genomes are homogeneous and derive most of their ancestry from Neolithic Aegeans, contrary to earlier hypotheses that the Neolithic-EBA cultural transition was due to massive population turnover. EBA Aegeans were shaped by relatively small-scale migration from East of the Aegean, as evidenced by the Caucasus-related ancestry also detected in Anatolians. In contrast, Middle BA (MBA) individuals of northern Greece differ from EBA populations in showing ∼50% Pontic-Caspian Steppe-related ancestry, dated at ca. 2,600-2,000 BCE. Such gene flow events during the MBA contributed toward shaping present-day Greek genomes.
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Affiliation(s)
- Florian Clemente
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Martina Unterländer
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece; Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Olga Dolgova
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain
| | - Carlos Eduardo G Amorim
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Francisco Coroado-Santos
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Samuel Neuenschwander
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Vital-IT, Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Elissavet Ganiatsou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diana I Cruz Dávalos
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Lucas Anchieri
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Frédéric Michaud
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Jens Blöcher
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Yami Ommar Arizmendi Cárdenas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Eleni Kalliga
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Angelos Souleles
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Ioannis Kontopoulos
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark
| | | | - Olga Philaniotou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece
| | - Dimitra Theodorou
- Ephorate of Antiquities of Kozani, Hellenic Ministry of Culture and Sports, 50004 Kozani, Greece
| | - Metaxia Tsipopoulou
- Ephor Emerita of Antiquities, Hellenic Ministry of Culture and Sports, 10682 Athens, Greece
| | - Ioannis Akamatis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Paul Halstead
- Department of Archaeology, University of Sheffield, Minalloy House, 10-16 Regent St., Sheffield S1 3NJ, UK
| | - Kostas Kotsakis
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Dushka Urem-Kotsou
- Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece
| | - Diamantis Panagiotopoulos
- Institute of Classical Archaeology, University of Heidelberg, Marstallhof 4, 69117 Heidelberg, Germany
| | - Christina Ziota
- Ephorate of Antiquities of Florina, Hellenic Ministry of Culture and Sports, 53100 Florina, Greece
| | - Sevasti Triantaphyllou
- Department of History and Archaeology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Jeffrey D Jensen
- School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - J Víctor Moreno-Mayar
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland; Center for GeoGenetics, GLOBE Institute, University of Copenhagen, 1350 Copenhagen, Denmark; National Institute of Genomic Medicine (INMEGEN), 14610 Mexico City, Mexico
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution, Johannes Gutenberg University of Mainz, 55099 Mainz, Germany
| | - Vitor C Sousa
- CE3C, Centre for Ecology, Evolution and Environmental Changes, Faculty of Sciences of the University of Lisbon, 1749-016 Lisbon, Portugal
| | - Oscar Lao
- CNAG-CRG, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Baldiri Reixac 4, 08028 Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Anna-Sapfo Malaspinas
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland; Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, 69100 Komotini, Greece.
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5
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Ancient genomes from present-day France unveil 7,000 years of its demographic history. Proc Natl Acad Sci U S A 2020; 117:12791-12798. [PMID: 32457149 DOI: 10.1073/pnas.1918034117] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Genomic studies conducted on ancient individuals across Europe have revealed how migrations have contributed to its present genetic landscape, but the territory of present-day France has yet to be connected to the broader European picture. We generated a large dataset comprising the complete mitochondrial genomes, Y-chromosome markers, and genotypes of a number of nuclear loci of interest of 243 individuals sampled across present-day France over a period spanning 7,000 y, complemented with a partially overlapping dataset of 58 low-coverage genomes. This panel provides a high-resolution transect of the dynamics of maternal and paternal lineages in France as well as of autosomal genotypes. Parental lineages and genomic data both revealed demographic patterns in France for the Neolithic and Bronze Age transitions consistent with neighboring regions, first with a migration wave of Anatolian farmers followed by varying degrees of admixture with autochthonous hunter-gatherers, and then substantial gene flow from individuals deriving part of their ancestry from the Pontic steppe at the onset of the Bronze Age. Our data have also highlighted the persistence of Magdalenian-associated ancestry in hunter-gatherer populations outside of Spain and thus provide arguments for an expansion of these populations at the end of the Paleolithic Period more northerly than what has been described so far. Finally, no major demographic changes were detected during the transition between the Bronze and Iron Ages.
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6
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SCHMIDT RYANW, WAKABAYASHI KEN, WAKU DAISUKE, GAKUHARI TAKASHI, KOGANEBUCHI KAE, OGAWA MOTOYUKI, KARSTEN JORDANK, SOKHATSKY MYKHAILO, OOTA HIROKI. Analysis of ancient human mitochondrial DNA from Verteba Cave, Ukraine: insights into the Late Neolithic-Chalcolithic Cucuteni–Tripolye culture. ANTHROPOL SCI 2020. [DOI: 10.1537/ase.200205] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Affiliation(s)
- RYAN W. SCHMIDT
- Department of Anatomy, Kitasato University, Sagamihara
- School of Archaeology, Earth Institute, University College Dublin, Dublin
| | | | - DAISUKE WAKU
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
| | - TAKASHI GAKUHARI
- Department of Anatomy, Kitasato University, Sagamihara
- Kanazawa University, Center for Cultural Resource Studies, Kanazawa
| | | | | | - JORDAN K. KARSTEN
- Department of Anthropology and Religious Studies, University of Wisconsin-Oshkosh, Oshkosh
| | | | - HIROKI OOTA
- Department of Anatomy, Kitasato University, Sagamihara
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo
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7
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Silva NM, Rio J, Kreutzer S, Papageorgopoulou C, Currat M. Bayesian estimation of partial population continuity using ancient DNA and spatially explicit simulations. Evol Appl 2018; 11:1642-1655. [PMID: 30344633 PMCID: PMC6183456 DOI: 10.1111/eva.12655] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2017] [Revised: 05/23/2018] [Accepted: 05/27/2018] [Indexed: 11/28/2022] Open
Abstract
The retrieval of ancient DNA from osteological material provides direct evidence of human genetic diversity in the past. Ancient DNA samples are often used to investigate whether there was population continuity in the settlement history of an area. Methods based on the serial coalescent algorithm have been developed to test whether the population continuity hypothesis can be statistically rejected by analysing DNA samples from the same region but of different ages. Rejection of this hypothesis is indicative of a large genetic shift, possibly due to immigration occurring between two sampling times. However, this approach is only able to reject a model of full continuity model (a total absence of genetic input from outside), but admixture between local and immigrant populations may lead to partial continuity. We have recently developed a method to test for population continuity that explicitly considers the spatial and temporal dynamics of populations. Here, we extended this approach to estimate the proportion of genetic continuity between two populations, using ancient genetic samples. We applied our original approach to the question of the Neolithic transition in Central Europe. Our results confirmed the rejection of full continuity, but our approach represents an important step forward by estimating the relative contribution of immigrant farmers and of local hunter-gatherers to the final Central European Neolithic genetic pool. Furthermore, we show that a substantial proportion of genes brought by the farmers in this region were assimilated from other hunter-gatherer populations along the way from Anatolia, which was not detectable by previous continuity tests. Our approach is also able to jointly estimate demographic parameters, as we show here by finding both low density and low migration rate for pre-Neolithic hunter-gatherers. It provides a useful tool for the analysis of the numerous ancient DNA data sets that are currently being produced for many different species.
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Affiliation(s)
- Nuno Miguel Silva
- AGP LabDepartment of Genetics & Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
| | - Jeremy Rio
- AGP LabDepartment of Genetics & Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
| | - Susanne Kreutzer
- Palaeogenetics GroupInstitute of AnthropologyJohannes Gutenberg UniversityMainzGermany
| | - Christina Papageorgopoulou
- Laboratory of Physical AnthropologyDepartment of History & EthnologyDemocritus University of ThraceKomotiniGreece
| | - Mathias Currat
- AGP LabDepartment of Genetics & Evolution – Anthropology UnitUniversity of GenevaGenevaSwitzerland
- Institute of Genetics and Genomics in Geneva (IGE3)GenevaSwitzerland
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8
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Prehistoric migrations through the Mediterranean basin shaped Corsican Y-chromosome diversity. PLoS One 2018; 13:e0200641. [PMID: 30067762 PMCID: PMC6070208 DOI: 10.1371/journal.pone.0200641] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Accepted: 06/30/2018] [Indexed: 02/05/2023] Open
Abstract
The rarity of human remains makes it difficult to apprehend the first settlements in Corsica. It is admitted that initial colonization could have occurred during the Mesolithic period when glaciations would have shortened the open water travel distance from the continent. Mesolithic sites in Corsica show relatively short and irregular occupation, and suggest discontinuous settling of very mobile groups probably traveling by boat. Previous genetic studies on Corsican populations showed internal differentiation and a relatively poor genetic relationship with continental populations, despite intense historical contacts, however local Mesolithic-based genetic inheritance has never been properly estimated. The aim of this study was to explore the Corsican genetic profile of Y-chromosomes in order to trace the genetic signatures back to the first migrations to Corsica. This study included 321 samples from men throughout Corsica; samples from Provence and Tuscany were added to the cohort. All samples were typed for 92 Y-SNPs, and Y-STRs were also analyzed. Results revealed highly differentiated haplogroup patterns among Corsican populations. Haplogroup G had the highest frequency in Corsica, mostly displaying a unique Y-STR profile. When compared with Provence and Tuscany, Corsican populations displayed limited genetic proximity. Corsican populations present a remarkable Y-chromosome genetic mixture. Although the Corsican Y-chromosome profile shows similarities with both Provence and to a lesser extent Tuscany, it mainly displays its own specificity. This study confirms the high level of genetic diversity in Corsican populations and backs genetic contributions from prehistoric migrations associated with the Mesolithic, Neolithic and Metal Age eras, rather than from historical movements to Corsica, respectively attested by frequencies and TMRCA of haplogroups G2a-L91 and G2a-P15, J2a-M241 and J2-DYS445 = 6, R1b-U152 and R1b-U106. These results suggest that marine routes to reach the Corsican coast in many different points may have led to such a genetic heterogeneity.
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9
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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10
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Pereira JB, Costa MD, Vieira D, Pala M, Bamford L, Harich N, Cherni L, Alshamali F, Hatina J, Rychkov S, Stefanescu G, King T, Torroni A, Soares P, Pereira L, Richards MB. Reconciling evidence from ancient and contemporary genomes: a major source for the European Neolithic within Mediterranean Europe. Proc Biol Sci 2018; 284:rspb.2016.1976. [PMID: 28330913 DOI: 10.1098/rspb.2016.1976] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/14/2017] [Indexed: 11/12/2022] Open
Abstract
Important gaps remain in our understanding of the spread of farming into Europe, due partly to apparent contradictions between studies of contemporary genetic variation and ancient DNA. It seems clear that farming was introduced into central, northern, and eastern Europe from the south by pioneer colonization. It is often argued that these dispersals originated in the Near East, where the potential source genetic pool resembles that of the early European farmers, but clear ancient DNA evidence from Mediterranean Europe is lacking, and there are suggestions that Mediterranean Europe may have resembled the Near East more than the rest of Europe in the Mesolithic. Here, we test this proposal by dating mitogenome founder lineages from the Near East in different regions of Europe. We find that whereas the lineages date mainly to the Neolithic in central Europe and Iberia, they largely date to the Late Glacial period in central/eastern Mediterranean Europe. This supports a scenario in which the genetic pool of Mediterranean Europe was partly a result of Late Glacial expansions from a Near Eastern refuge, and that this formed an important source pool for subsequent Neolithic expansions into the rest of Europe.
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Affiliation(s)
- Joana B Pereira
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal
| | - Marta D Costa
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Life and Health Sciences Research Institute (ICVS), School of Health Sciences, University of Minho, Campus de Gualtar, 4710-057 Braga, Portugal.,ICVS/3Bs-PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniel Vieira
- Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Maria Pala
- Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
| | - Lisa Bamford
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | - Nourdin Harich
- Laboratoire d'Anthropogenetique, Department de Biologie, Universite Chouaib Doukkali, El Jadida 24000, Morocco
| | - Lotfi Cherni
- Laboratory of Genetics, Immunology and Human Pathology, Faculté de Sciences de Tunis, Université de Tunis El Manar, Tunis 2092, Tunisia.,Tunis and High Institute of Biotechnology, University of Monastir, 5000 Monastir, Tunisia
| | - Farida Alshamali
- General Department of Forensic Sciences and Criminology, Dubai Police General Headquarters, Dubai 1493, United Arab Emirates
| | - Jiři Hatina
- Medical Faculty in Pilsen, Institute of Biology, Charles University, Pilsen, Czech Republic
| | | | | | - Turi King
- Department of Genetics, University of Leicester, Adrian Building, University Road, Leicester LE1 7RH, UK
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie 'L. Spallanzani', Università di Pavia, Pavia, Italy
| | - Pedro Soares
- Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Department of Biology, CBMA (Centre of Molecular and Environmental Biology), University of Minho, Braga, Portugal
| | - Luísa Pereira
- Instituto de Investigacão e Inovacão em Saúde (i3S), Universidade do Porto, Porto 4200-135, Portugal.,Instituto de Patologia e Imunologia Molecular da Universidade do Porto (IPATIMUP), Porto 4200-465, Portugal.,Faculdade de Medicina da Universidade do Porto, Porto 4200-319, Portugal
| | - Martin B Richards
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK .,Department of Biological Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK
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11
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Comparison of two Neolithic mtDNA haplotypes from a Czech excavation site with the results of mitochondrial DNA studies on European Neolithic and Mesolithic individuals. FORENSIC SCIENCE INTERNATIONAL GENETICS SUPPLEMENT SERIES 2017. [DOI: 10.1016/j.fsigss.2017.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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12
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Gerbault P, Roffet-Salque M. Histoire de l’utilisation des laitages et de la persistance du gène de la lactase. CAHIERS DE NUTRITION ET DE DIÉTÉTIQUE 2017. [DOI: 10.1016/s0007-9960(17)30195-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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13
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The maternal genetic make-up of the Iberian Peninsula between the Neolithic and the Early Bronze Age. Sci Rep 2017; 7:15644. [PMID: 29142317 PMCID: PMC5688114 DOI: 10.1038/s41598-017-15480-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2017] [Accepted: 10/27/2017] [Indexed: 01/01/2023] Open
Abstract
Agriculture first reached the Iberian Peninsula around 5700 BCE. However, little is known about the genetic structure and changes of prehistoric populations in different geographic areas of Iberia. In our study, we focus on the maternal genetic makeup of the Neolithic (~ 5500–3000 BCE), Chalcolithic (~ 3000–2200 BCE) and Early Bronze Age (~ 2200–1500 BCE). We report ancient mitochondrial DNA results of 213 individuals (151 HVS-I sequences) from the northeast, central, southeast and southwest regions and thus on the largest archaeogenetic dataset from the Peninsula to date. Similar to other parts of Europe, we observe a discontinuity between hunter-gatherers and the first farmers of the Neolithic. During the subsequent periods, we detect regional continuity of Early Neolithic lineages across Iberia, however the genetic contribution of hunter-gatherers is generally higher than in other parts of Europe and varies regionally. In contrast to ancient DNA findings from Central Europe, we do not observe a major turnover in the mtDNA record of the Iberian Late Chalcolithic and Early Bronze Age, suggesting that the population history of the Iberian Peninsula is distinct in character.
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14
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Koczur LM, Williford D, DeYoung RW, Ballard BM. Bringing back the dead: Genetic data from avian carcasses. WILDLIFE SOC B 2017. [DOI: 10.1002/wsb.823] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Lianne M. Koczur
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Damon Williford
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Randy W. DeYoung
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
| | - Bart M. Ballard
- Caesar Kleberg Wildlife Research Institute; Texas A&M University-Kingsville; Kingsville TX 78363 USA
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15
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Yardumian A, Shengelia R, Chitanava D, Laliashvili S, Bitadze L, Laliashvili I, Villanea F, Sanders A, Azzam A, Groner V, Edleson K, Vilar MG, Schurr TG. Genetic diversity in Svaneti and its implications for the human settlement of the Highland Caucasus. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2017; 164:837-852. [PMID: 29076141 DOI: 10.1002/ajpa.23324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Revised: 07/19/2017] [Accepted: 09/10/2017] [Indexed: 11/11/2022]
Abstract
OBJECTIVES In this study, we characterized genetic diversity in the Svans from northwestern Georgia to better understand the phylogeography of their genetic lineages, determine whether genetic diversity in the highland South Caucasus has been shaped by language or geography, and assess whether Svan genetic diversity was structured by regional residence patterns. MATERIALS AND METHODS We analyzed mtDNA and Y-chromosome variation in 184 individuals from 13 village districts and townlets located throughout the region. For all individuals, we analyzed mtDNA diversity through control region sequencing, and, for males, we analyzed Y-chromosome diversity through SNP and STR genotyping. The resulting data were compared with those for populations from the Caucasus and Middle East. RESULTS We observed significant mtDNA heterogeneity in Svans, with haplogroups U1-U7, H, K, and W6 being common there. By contrast, ∼78% of Svan males belonged to haplogroup G2a, with the remainder falling into four other haplogroups (J2a1, I2, N, and R1a). While showing a distinct genetic profile, Svans also clustered with Caucasus populations speaking languages from different families, suggesting a deep common ancestry for all of them. The mtDNA data were not structured by geography or linguistic affiliation, whereas the NRY data were influenced only by geography. DISCUSSION These patterns of genetic variation confirm a complex set of geographic sources and settlement phases for the Caucasus highlands. Such patterns may also reflect social and cultural practices in the region. The high frequency and antiquity of Y-chromosome haplogroup G2a in this region further points to its emergence there.
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Affiliation(s)
- Aram Yardumian
- Department of History and Social Sciences, Bryn Athyn College, Pennsylvania 19009.,Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Ramaz Shengelia
- Department of the History of Medicine and Bioethics, Tbilisi State Medical University, Tbilisi 01747, Georgia
| | - David Chitanava
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Shorena Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Lia Bitadze
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Irma Laliashvili
- Laboratory for Anthropologic Studies, Ivane Javakhishvili Institute of History and Ethnology, Tbilisi 0102, Georgia
| | - Fernando Villanea
- Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Akiva Sanders
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Andrew Azzam
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Victoria Groner
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Kristi Edleson
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
| | - Miguel G Vilar
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104.,Grant Programs, Science and Exploration, National Geographic Society, Washington, DC 20036
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania 19104
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16
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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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17
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Affiliation(s)
- Laure Ségurel
- Laboratoire Éco-Anthropologie et Ethnobiologie, UMR 7206 CNRS – Muséum national d'Histoire naturelle – Univ Paris Diderot, Sorbonne Paris Cité, F-75016 Paris, France;,
| | - Céline Bon
- Laboratoire Éco-Anthropologie et Ethnobiologie, UMR 7206 CNRS – Muséum national d'Histoire naturelle – Univ Paris Diderot, Sorbonne Paris Cité, F-75016 Paris, France;,
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18
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Ethier J, Bánffy E, Vuković J, Leshtakov K, Bacvarov K, Roffet-Salque M, Evershed RP, Ivanova M. Earliest expansion of animal husbandry beyond the Mediterranean zone in the sixth millennium BC. Sci Rep 2017; 7:7146. [PMID: 28769118 PMCID: PMC5541088 DOI: 10.1038/s41598-017-07427-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 06/26/2017] [Indexed: 11/18/2022] Open
Abstract
Since their domestication in the Mediterranean zone of Southwest Asia in the eighth millennium BC, sheep, goats, pigs and cattle have been remarkably successful in colonizing a broad variety of environments. The initial steps in this process can be traced back to the dispersal of farming groups into the interior of the Balkans in the early sixth millennium BC, who were the first to introduce Mediterranean livestock beyond its natural climatic range. Here, we combine analysis of biomolecular and isotopic compositions of lipids preserved in prehistoric pottery with faunal analyses of taxonomic composition from the earliest farming sites in southeast Europe to reconstruct this pivotal event in the early history of animal husbandry. We observe a marked divergence between the (sub)Mediterranean and temperate regions of Southeast Europe, and in particular a significant increase of dairying in the biochemical record coupled with a shift to cattle and wild fauna at most sites north of the Balkan mountain range. The findings strongly suggest that dairying was crucial for the expansion of the earliest farming system beyond its native bioclimatic zone.
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Affiliation(s)
- Jonathan Ethier
- Institut für Ur- und Frühgeschichte und Vorderasiatische Archäologie, Universität Heidelberg, Marstallhof 4, 69117, Heidelberg, Germany
| | - Eszter Bánffy
- Römisch-Germanische Kommission des Deutschen Archäologischen Instituts, Palmengartenstr. 10-12, 60325, Frankfurt, Germany
| | - Jasna Vuković
- Department of Archaeology, Faculty of Philosophy, University of Belgrade, Čika Ljubina 18-20, 11000, Belgrade, Serbia
| | - Krassimir Leshtakov
- Department of Archaeology, Faculty of History, Sofia University St. Kliment Ohridski, 15 Tzar Osvoboditel Boulevard, 1504, Sofia, Bulgaria
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, 2 Saborna St., 1000, Sofia, Bulgaria
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Richard P Evershed
- Organic Geochemistry Unit, School of Chemistry, University of Bristol, Cantock's Close, Bristol, BS8 1TS, United Kingdom
| | - Maria Ivanova
- Institut für Ur- und Frühgeschichte und Vorderasiatische Archäologie, Universität Heidelberg, Marstallhof 4, 69117, Heidelberg, Germany.
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19
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Origin and spread of human mitochondrial DNA haplogroup U7. Sci Rep 2017; 7:46044. [PMID: 28387361 PMCID: PMC5384202 DOI: 10.1038/srep46044] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 03/07/2017] [Indexed: 01/17/2023] Open
Abstract
Human mitochondrial DNA haplogroup U is among the initial maternal founders in Southwest Asia and Europe and one that best indicates matrilineal genetic continuity between late Pleistocene hunter-gatherer groups and present-day populations of Europe. While most haplogroup U subclades are older than 30 thousand years, the comparatively recent coalescence time of the extant variation of haplogroup U7 (~16–19 thousand years ago) suggests that its current distribution is the consequence of more recent dispersal events, despite its wide geographical range across Europe, the Near East and South Asia. Here we report 267 new U7 mitogenomes that – analysed alongside 100 published ones – enable us to discern at least two distinct temporal phases of dispersal, both of which most likely emanated from the Near East. The earlier one began prior to the Holocene (~11.5 thousand years ago) towards South Asia, while the later dispersal took place more recently towards Mediterranean Europe during the Neolithic (~8 thousand years ago). These findings imply that the carriers of haplogroup U7 spread to South Asia and Europe before the suggested Bronze Age expansion of Indo-European languages from the Pontic-Caspian Steppe region.
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20
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Chyleński M, Juras A, Ehler E, Malmström H, Piontek J, Jakobsson M, Marciniak A, Dabert M. Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5 th millennium BC. BMC Evol Biol 2017; 17:80. [PMID: 28302068 PMCID: PMC5356262 DOI: 10.1186/s12862-017-0924-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/23/2017] [Indexed: 11/29/2022] Open
Abstract
Background Recent aDNA studies are progressively focusing on various Neolithic and Hunter - Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities. Results Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK. Conclusions We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0924-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614, Poznań, Poland.
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Edvard Ehler
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland.,Department of Biology and Environmental Studies, Faculty of Education, Charles University in Prague, Magdalény Rettigové 4, 116 39, Prague, Czech Republic
| | - Helena Malmström
- Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Mattias Jakobsson
- Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - Arkadiusz Marciniak
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614, Poznań, Poland
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland
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21
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Nikitin AG, Potekhina I, Rohland N, Mallick S, Reich D, Lillie M. Mitochondrial DNA analysis of eneolithic trypillians from Ukraine reveals neolithic farming genetic roots. PLoS One 2017; 12:e0172952. [PMID: 28235025 PMCID: PMC5325568 DOI: 10.1371/journal.pone.0172952] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/13/2017] [Indexed: 01/14/2023] Open
Abstract
The agricultural revolution in Eastern Europe began in the Eneolithic with the Cucuteni-Trypillia culture complex. In Ukraine, the Trypillian culture (TC) existed for over two millennia (ca. 5,400-2,700 BCE) and left a wealth of artifacts. Yet, their burial rituals remain a mystery and to date almost nothing is known about the genetic composition of the TC population. One of the very few TC sites where human remains can be found is a cave called Verteba in western Ukraine. This report presents four partial and four complete mitochondrial genomes from nine TC individuals uncovered in the cave. The results of this analysis, combined with the data from previous reports, indicate that the Trypillian population at Verteba carried, for the most part, a typical Neolithic farmer package of mitochondrial DNA (mtDNA) lineages traced to Anatolian farmers and Neolithic farming groups of central Europe. At the same time, the find of two specimens belonging to haplogroup U8b1 at Verteba can be viewed as a connection of TC with the Upper Paleolithic European populations. At the level of mtDNA haplogroup frequencies, the TC population from Verteba demonstrates a close genetic relationship with population groups of the Funnel Beaker/ Trichterbecker cultural complex from central and northern Europe (ca. 3,950-2,500 BCE).
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Affiliation(s)
- Alexey G. Nikitin
- Biology Department, Grand Valley State University, Allendale, Michigan, United States of America
- * E-mail:
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, Ukrainian Academy of Sciences, Kyiv, Ukraine
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Malcolm Lillie
- School of Environmental Sciences (Geography), University of Hull, Hull, England
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22
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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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23
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Carreras-Torres R, Ferran A, Zanetti D, Esteban E, Varesi L, Pojskic N, Coia V, Chaabani H, Via M, Moral P. Population structure from NOS genes correlates with geographical differences in coronary incidence across Europe. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:634-645. [PMID: 27500977 DOI: 10.1002/ajpa.23063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Revised: 06/19/2016] [Accepted: 07/26/2016] [Indexed: 11/05/2022]
Abstract
OBJECTIVES The population analysis of cardiovascular risk and non-risk genetic variation can help to identify adaptive or random demographic processes that shaped coronary incidence variation across geography. MATERIAL AND METHODS In this study, 114 single nucleotide polymorphisms and 17 tandem repeat polymorphisms from Nitric Oxide Synthases (NOS) regions were analyzed in 1686 individuals from 35 populations from Europe, North Africa, and the Middle East. NOS genes encode for key enzymes on nitric oxide availability, which is involved in several cardiovascular processes. These genetic variations were used to test for selection and to infer the population structure of NOS regions. Moreover, we tested whether the variation in the incidence of coronary events and in the levels of classical risk factors in 11 of these European populations could be explained by the population structure estimates. RESULTS Our results supported, first, the absence of clear signs of selection for NOS genetic variants associated with cardiovascular diseases, and second, the presence of a continuous genetic pattern of variation across European and North African populations without a Mediterranean barrier for gene flow. Finally, population structure estimates from NOS regions are closely correlated with coronary event rates and classical risk parameters (explaining 39-98%) among European populations. CONCLUSION Our results reinforce the hypothesis that genetic bases of cardiovascular diseases and associated complex phenotypes could be geographically shaped by random demographic processes.
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Affiliation(s)
- Robert Carreras-Torres
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Albert Ferran
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Daniela Zanetti
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain
| | - Esther Esteban
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
| | - Laurent Varesi
- Laboratoire de virologie, Faculté des Sciences et Techniques, Université de Corse, France
| | - Naris Pojskic
- Laboratory for Molecular Genetics of Natural Resources, Institute for Genetic Engineering and Biotechnology, University of Sarajevo, Bosnia and Herzegovina
| | - Valentina Coia
- Accademia Europea di Bolzano (EURAC), Istituto per le Mummie e l'Iceman, Bolzano, Italy
| | - Hassen Chaabani
- Laboratory of Human Genetics and Anthropology, Faculty of Pharmacy, University of Monastir, Tunisia
| | - Marc Via
- Departament Psicologia Clínica i Psicobiologia and Institute of Neurosciences (UBNEURO), Universitat de Barcelona, Spain.,Institut de Recerca Pediàtrica Hospital Sant Joan de Déu (IRP_HSJD), Barcelona, Spain
| | - Pedro Moral
- Departament Biologia Animal, Unitat d'Antropologia, Facultat de Biologia, Universitat de Barcelona, Spain.,Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona, Spain
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24
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Simón M, Díaz N, Solórzano E, Montiel R, Francalacci P, Malgosa A. Dissecting mitochondrial dna variability of balearic populations from the bronze age to the current era. Am J Hum Biol 2016; 29. [PMID: 27292871 DOI: 10.1002/ajhb.22883] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2015] [Revised: 05/15/2016] [Accepted: 05/17/2016] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVES To determine ancient population influences on ancient and current Balearic populations and to reconstruct their mitochondrial DNA (mtDNA) gene pool evolution. METHODS We analyzed 239 individuals belonging to five archaeological populations from Majorca and Minorca, four dating to the transition between the Bronze Age and the Iron Age, and one Late Roman Majorcan population. Six additional individuals from Santa Teresa di Gallura from the Nuragic period were characterized and added to the existing samples from that culture to make comparisons with Talaiotic populations. RESULTS We characterized the haplogroups of 138 individuals and obtained 69 sequences from mtDNA hypervariable region I. In the intra-island study, the apparent differences in social and funerary rites between two contiguous Majorcan necropolises were correlated with genetic characteristics. Also, the likely occurrence of consanguinity in a population with a very particular burial pattern was supported by genetic data. Despite the uniqueness of each necropolis, the global comparison of the five necropolises revealed no significant differences between them, or between ancient and modern populations from the islands. Ancient Balearics showed a similar mtDNA gene pool to Ancient Catalans, had a Near Eastern component, and showed continuity with European populations since at least the Bronze Age. CONCLUSION We characterized five Balearic necropolises in the context of their geographic and cultural characteristics. The similarity between ancient Balearic and ancient Catalan gene pools reinforces their known historic interactions, while the lack of a consistent genetic continuity with Ancient Sardinians suggests that Talaiotic and Nuragic cultures arose in differentiated populations. Am. J. Hum. Biol. 29:e22883, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Marc Simón
- Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - Nancy Díaz
- Universidad de los Andes. Avenida 3, Independencia. Edificio el Rectorado, Mérida, 5101, Venezuela
| | - Eduvigis Solórzano
- Universidad de los Andes. Avenida 3, Independencia. Edificio el Rectorado, Mérida, 5101, Venezuela
| | - Rafael Montiel
- Laboratorio Nacional de Genómica para la Biodiversidad, Unidad de Genómica Avanzada, CINVESTAV-IPN. Km. 9.6 Libramiento Norte Carretera Irapuato, Irapuato, 36821, Mexico
| | - Paolo Francalacci
- Universitá di Sassari, Piazza D'Armi, 17, Sassari, SS, 07100, Italia
| | - Assumpció Malgosa
- Unitat d'Antropologia Biològica, Departament BABVE, Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
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25
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Šarac J, Šarić T, Havaš Auguštin D, Novokmet N, Vekarić N, Mustać M, Grahovac B, Kapović M, Nevajda B, Glasnović A, Missoni S, Rootsi S, Rudan P. Genetic heritage of Croatians in the Southeastern European gene pool-Y chromosome analysis of the Croatian continental and Island population. Am J Hum Biol 2016; 28:837-845. [PMID: 27279290 DOI: 10.1002/ajhb.22876] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Revised: 03/22/2016] [Accepted: 05/10/2016] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVES The research objective of this study is to enlarge and deepen the Y chromosome research on the Croatian population and enable additional insights into the population diversity and historic events that shaped the current genetic landscape of Croatia and Southeastern Europe (SEE). MATERIALS AND METHODS A high-resolution phylogenetic and phylogeographic analysis of 66 biallelic (SNPs) and 17 microsatellite (STRs) markers of the Y chromosome was performed using 720 Croatian samples. The obtained results were placed in a wider European context by comparison with ∼4450 samples from a number of other European populations. RESULTS A high diversity of haplogroups was observed in the overall Croatian sample, and all typical European Y chromosome haplogroups with corresponding clinal patterns were observed. Three distinct genetic signals were identifiable in the Croatian paternal gene pool - I2a1b-M423, R1a1a1b1a*-M558, and E1b1b1a1b1a-V13 haplogroups. DISCUSSION The analyses of the dominant and autochthonous I2a1b-M423 lineage (>30%) suggest that SEE had a significant role in the Upper Paleolithic, the R1a1a1b1a*-M558 lineage (19%) represents a signal from present day Slavic populations of Central Europe in the Croatian population, and the phylogeography of the E1b1b1a1b1a-V13 clade (around 9%) implies cultural diffusion of agriculture into Europe via the Balkan Peninsula. Am. J. Hum. Biol., 2016. © 2016 Wiley Periodicals, Inc. Am. J. Hum. Biol. 28:837-845, 2016. © 2016Wiley Periodicals, Inc.
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Affiliation(s)
- Jelena Šarac
- Institute for Anthropological Research, 10000, Zagreb, Croatia
| | - Tena Šarić
- Institute for Anthropological Research, 10000, Zagreb, Croatia
| | | | | | - Nenad Vekarić
- Institute for Historical Sciences, Croatian Academy of Sciences and Arts, 20000, Dubrovnik, Croatia
| | - Mate Mustać
- Occupational Health Clinic, 23000, Zadar, Croatia
| | - Blaženka Grahovac
- Department of Pathology and Pathological Anatomy, School of Medicine, University of Rijeka, 51000, Rijeka, Croatia
| | - Miljenko Kapović
- Department of Biology and Medical Genetics, School of Medicine, University of Rijeka, 51000, Rijeka, Croatia
| | | | | | - Saša Missoni
- Institute for Anthropological Research, 10000, Zagreb, Croatia.,"Josip Juraj Strossmayer" University of Osijek, School of Medicine, Osijek, Croatia
| | - Siiri Rootsi
- Estonian Biocentre and Institute for Molecular and Cell Biology, Department of Evolutionary Biology, , University of Tartu, 51010, Tartu, Estonia
| | - Pavao Rudan
- Institute for Anthropological Research, 10000, Zagreb, Croatia.,Anthropological Center of the Croatian Academy of Sciences and Arts, 10000, Zagreb, Croatia
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Voskarides K, Mazières S, Hadjipanagi D, Di Cristofaro J, Ignatiou A, Stefanou C, King RJ, Underhill PA, Chiaroni J, Deltas C. Y-chromosome phylogeographic analysis of the Greek-Cypriot population reveals elements consistent with Neolithic and Bronze Age settlements. INVESTIGATIVE GENETICS 2016; 7:1. [PMID: 26870315 PMCID: PMC4750176 DOI: 10.1186/s13323-016-0032-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2015] [Accepted: 02/02/2016] [Indexed: 12/15/2022]
Abstract
Background The archeological record indicates that the permanent settlement of Cyprus began with pioneering agriculturalists circa 11,000 years before present, (ca. 11,000 y BP). Subsequent colonization events followed, some recognized regionally. Here, we assess the Y-chromosome structure of Cyprus in context to regional populations and correlate it to phases of prehistoric colonization. Results Analysis of haplotypes from 574 samples showed that island-wide substructure was barely significant in a spatial analysis of molecular variance (SAMOVA). However, analyses of molecular variance (AMOVA) of haplogroups using 92 binary markers genotyped in 629 Cypriots revealed that the proportion of variance among the districts was irregularly distributed. Principal component analysis (PCA) revealed potential genetic associations of Greek-Cypriots with neighbor populations. Contrasting haplogroups in the PCA were used as surrogates of parental populations. Admixture analyses suggested that the majority of G2a-P15 and R1b-M269 components were contributed by Anatolia and Levant sources, respectively, while Greece Balkans supplied the majority of E-V13 and J2a-M67. Haplotype-based expansion times were at historical levels suggestive of recent demography. Conclusions Analyses of Cypriot haplogroup data are consistent with two stages of prehistoric settlement. E-V13 and E-M34 are widespread, and PCA suggests sourcing them to the Balkans and Levant/Anatolia, respectively. The persistent pre-Greek component is represented by elements of G2-U5(xL30) haplogroups: U5*, PF3147, and L293. J2b-M205 may contribute also to the pre-Greek strata. The majority of R1b-Z2105 lineages occur in both the westernmost and easternmost districts. Distinctively, sub-haplogroup R1b- M589 occurs only in the east. The absence of R1b- M589 lineages in Crete and the Balkans and the presence in Asia Minor are compatible with Late Bronze Age influences from Anatolia rather than from Mycenaean Greeks. Electronic supplementary material The online version of this article (doi:10.1186/s13323-016-0032-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Konstantinos Voskarides
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Stéphane Mazières
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Despina Hadjipanagi
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | | | - Anastasia Ignatiou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Charalambos Stefanou
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
| | - Roy J King
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA USA
| | - Peter A Underhill
- Department of Genetics, Stanford University, Stanford, California 94305 USA
| | - Jacques Chiaroni
- Aix Marseille Université, ADES UMR7268, CNRS, EFS-AM, Marseille, France
| | - Constantinos Deltas
- Molecular Medicine Research Center and Laboratory of Molecular and Medical Genetics, Department of Biological Sciences, University of Cyprus, Kallipoleos 75, 1678 Nicosia, Cyprus
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Alt KW, Zesch S, Garrido-Pena R, Knipper C, Szécsényi-Nagy A, Roth C, Tejedor-Rodríguez C, Held P, García-Martínez-de-Lagrán Í, Navitainuck D, Arcusa Magallón H, Rojo-Guerra MA. A Community in Life and Death: The Late Neolithic Megalithic Tomb at Alto de Reinoso (Burgos, Spain). PLoS One 2016; 11:e0146176. [PMID: 26789731 PMCID: PMC4720281 DOI: 10.1371/journal.pone.0146176] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 12/13/2015] [Indexed: 11/19/2022] Open
Abstract
The analysis of the human remains from the megalithic tomb at Alto de Reinoso represents the widest integrative study of a Neolithic collective burial in Spain. Combining archaeology, osteology, molecular genetics and stable isotope analysis (87Sr/86Sr, δ15N, δ13C) it provides a wealth of information on the minimum number of individuals, age, sex, body height, pathologies, mitochondrial DNA profiles, kinship relations, mobility, and diet. The grave was in use for approximately one hundred years around 3700 cal BC, thus dating from the Late Neolithic of the Iberian chronology. At the bottom of the collective tomb, six complete and six partial skeletons lay in anatomically correct positions. Above them, further bodies represented a subsequent and different use of the tomb, with almost all of the skeletons exhibiting signs of manipulation such as missing skeletal parts, especially skulls. The megalithic monument comprised at least 47 individuals, including males, females, and subadults, although children aged 0-6 years were underrepresented. The skeletal remains exhibited a moderate number of pathologies, such as degenerative joint diseases, healed fractures, cranial trauma, and a low intensity of caries. The mitochondrial DNA profiles revealed a pattern pointing to a closely related local community with matrilineal kinship patterns. In some cases adjacent individuals in the bottom layer showed familial relationships. According to their strontium isotope ratios, only a few individuals were likely to have spent their early childhood in a different geological environment, whilst the majority of individuals grew up locally. Carbon and nitrogen isotope analysis, which was undertaken to reconstruct the dietary habits, indicated that this was a homogeneous group with egalitarian access to food. Cereals and small ruminants were the principal sources of nutrition. These data fit in well with a lifestyle typical of sedentary farming populations in the Spanish Meseta during this period of the Neolithic.
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Affiliation(s)
- Kurt W. Alt
- Danube Private University, Krems, Austria
- Institute for Prehistory and Archaeological Science and Hightech Research Center, Basel University, Basel, Switzerland
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
- * E-mail:
| | - Stephanie Zesch
- German Mummy Project, Reiss-Engelhorn-Museen, Mannheim, Germany
| | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Madrid, Spain
| | - Corina Knipper
- Curt Engelhorn Centre Archaeometry gGmbH, Mannheim, Germany
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Christina Roth
- Institute of Anthropology, Mainz University, Mainz, Germany
| | | | - Petra Held
- Department of Applied and Analytical Paleontology, Mainz University, Mainz, Germany
| | - Íñigo García-Martínez-de-Lagrán
- Department of Prehistory, University of the Basque Government, Vitoria, Spain
- Laboratoire TRACES UMR5608, Université de Toulouse, Toulouse, France
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Coia V, Cipollini G, Anagnostou P, Maixner F, Battaggia C, Brisighelli F, Gómez-Carballa A, Destro Bisol G, Salas A, Zink A. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman. Sci Rep 2016; 6:18932. [PMID: 26764605 PMCID: PMC4725900 DOI: 10.1038/srep18932] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/01/2015] [Indexed: 01/01/2023] Open
Abstract
The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps - putatively in genetic continuity with the Tyrolean Iceman-and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp.
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Affiliation(s)
- V Coia
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - G Cipollini
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - P Anagnostou
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy
| | - F Maixner
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - C Battaggia
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy
| | - F Brisighelli
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - A Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - G Destro Bisol
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy.,Istituto Italiano di Antropologia, Roma, Italy
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - A Zink
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
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Singh S, Singh A, Rajkumar R, Sampath Kumar K, Kadarkarai Samy S, Nizamuddin S, Singh A, Ahmed Sheikh S, Peddada V, Khanna V, Veeraiah P, Pandit A, Chaubey G, Singh L, Thangaraj K. Dissecting the influence of Neolithic demic diffusion on Indian Y-chromosome pool through J2-M172 haplogroup. Sci Rep 2016; 6:19157. [PMID: 26754573 PMCID: PMC4709632 DOI: 10.1038/srep19157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Accepted: 10/08/2015] [Indexed: 11/24/2022] Open
Abstract
The global distribution of J2-M172 sub-haplogroups has been associated with Neolithic demic diffusion. Two branches of J2-M172, J2a-M410 and J2b-M102 make a considerable part of Y chromosome gene pool of the Indian subcontinent. We investigated the Neolithic contribution of demic dispersal from West to Indian paternal lineages, which majorly consists of haplogroups of Late Pleistocene ancestry. To accomplish this, we have analysed 3023 Y-chromosomes from different ethnic populations, of which 355 belonged to J2-M172. Comparison of our data with worldwide data, including Y-STRs of 1157 individuals and haplogroup frequencies of 6966 individuals, suggested a complex scenario that cannot be explained by a single wave of agricultural expansion from Near East to South Asia. Contrary to the widely accepted elite dominance model, we found a substantial presence of J2a-M410 and J2b-M102 haplogroups in both caste and tribal populations of India. Unlike demic spread in Eurasia, our results advocate a unique, complex and ancient arrival of J2a-M410 and J2b-M102 haplogroups into Indian subcontinent.
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Affiliation(s)
- Sakshi Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Ashish Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Raja Rajkumar
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | | | - Sheikh Nizamuddin
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Amita Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Vidya Peddada
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | - Vinee Khanna
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
| | | | - Aridaman Pandit
- Theoretical Biology and Bioinformatics, Utrecht University, Utrecht, Netherlands
| | | | - Lalji Singh
- CSIR-Centre for Cellular and Molecular Biology, Uppal Road, Hyderabad, India
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30
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31
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Szécsényi-Nagy A, Brandt G, Haak W, Keerl V, Jakucs J, Möller-Rieker S, Köhler K, Mende BG, Oross K, Marton T, Osztás A, Kiss V, Fecher M, Pálfi G, Molnár E, Sebők K, Czene A, Paluch T, Šlaus M, Novak M, Pećina-Šlaus N, Ősz B, Voicsek V, Somogyi K, Tóth G, Kromer B, Bánffy E, Alt KW. Tracing the genetic origin of Europe's first farmers reveals insights into their social organization. Proc Biol Sci 2015; 282:rspb.2015.0339. [PMID: 25808890 DOI: 10.1098/rspb.2015.0339] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Farming was established in Central Europe by the Linearbandkeramik culture (LBK), a well-investigated archaeological horizon, which emerged in the Carpathian Basin, in today's Hungary. However, the genetic background of the LBK genesis is yet unclear. Here we present 9 Y chromosomal and 84 mitochondrial DNA profiles from Mesolithic, Neolithic Starčevo and LBK sites (seventh/sixth millennia BC) from the Carpathian Basin and southeastern Europe. We detect genetic continuity of both maternal and paternal elements during the initial spread of agriculture, and confirm the substantial genetic impact of early southeastern European and Carpathian Basin farming cultures on Central European populations of the sixth-fourth millennia BC. Comprehensive Y chromosomal and mitochondrial DNA population genetic analyses demonstrate a clear affinity of the early farmers to the modern Near East and Caucasus, tracing the expansion from that region through southeastern Europe and the Carpathian Basin into Central Europe. However, our results also reveal contrasting patterns for male and female genetic diversity in the European Neolithic, suggesting a system of patrilineal descent and patrilocal residential rules among the early farmers.
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Affiliation(s)
- Anna Szécsényi-Nagy
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany Laboratory of Archaeogenetics, Hungarian Academy of Sciences, Budapest 1014, Hungary
| | - Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Earth and Environmental Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Victoria Keerl
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany
| | - János Jakucs
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary
| | - Sabine Möller-Rieker
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany
| | - Kitti Köhler
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary
| | - Balázs Gusztáv Mende
- Laboratory of Archaeogenetics, Hungarian Academy of Sciences, Budapest 1014, Hungary
| | - Krisztián Oross
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary
| | - Tibor Marton
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary
| | - Anett Osztás
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary
| | - Viktória Kiss
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary
| | - Marc Fecher
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany
| | - György Pálfi
- Department of Biological Anthropology, University of Szeged, Szeged 6726, Hungary
| | - Erika Molnár
- Department of Biological Anthropology, University of Szeged, Szeged 6726, Hungary
| | - Katalin Sebők
- Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary
| | - András Czene
- Salisbury Archaeological Ltd, Budaörs 2040, Hungary
| | | | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, Zagreb 10000, Croatia
| | - Mario Novak
- School of Archaeology, University College Dublin, Dublin 4, Ireland
| | - Nives Pećina-Šlaus
- Department of Biology, School of Medicine, University of Zagreb, Zagreb 10000, Croatia
| | - Brigitta Ősz
- Department Pécs, National Heritage Protection Centre of the Hungarian National Museum, Pécs 7621, Hungary
| | - Vanda Voicsek
- Department Pécs, National Heritage Protection Centre of the Hungarian National Museum, Pécs 7621, Hungary
| | - Krisztina Somogyi
- Institute of Archaeological Sciences, Eötvös Loránd University, Budapest 1088, Hungary
| | - Gábor Tóth
- Biology Department, University of West Hungary, Szombathely 9700, Hungary
| | - Bernd Kromer
- Curt-Engelhorn-Centre for Archaeometry, Mannheim 68159, Germany
| | - Eszter Bánffy
- Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest 1014, Hungary German Archaeological Institute, Roman-Germanic Commission, Frankfurt am Main 0325, Germany
| | - Kurt W Alt
- Institute of Anthropology, Johannes Gutenberg University of Mainz, Mainz 55128, Germany Institute for Integrative Prehistory and Archaeological Science, University of Basel, Basel 4003, Switzerland Center of Natural and Cultural History of Teeth, Danube Private University, Krems 3500, Austria
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32
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Olalde I, Schroeder H, Sandoval-Velasco M, Vinner L, Lobón I, Ramirez O, Civit S, García Borja P, Salazar-García DC, Talamo S, María Fullola J, Xavier Oms F, Pedro M, Martínez P, Sanz M, Daura J, Zilhão J, Marquès-Bonet T, Gilbert MTP, Lalueza-Fox C. A Common Genetic Origin for Early Farmers from Mediterranean Cardial and Central European LBK Cultures. Mol Biol Evol 2015; 32:3132-42. [PMID: 26337550 PMCID: PMC4652622 DOI: 10.1093/molbev/msv181] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The spread of farming out of the Balkans and into the rest of Europe followed two distinct routes: An initial expansion represented by the Impressa and Cardial traditions, which followed the Northern Mediterranean coastline; and another expansion represented by the LBK (Linearbandkeramik) tradition, which followed the Danube River into Central Europe. Although genomic data now exist from samples representing the second migration, such data have yet to be successfully generated from the initial Mediterranean migration. To address this, we generated the complete genome of a 7,400-year-old Cardial individual (CB13) from Cova Bonica in Vallirana (Barcelona), as well as partial nuclear data from five others excavated from different sites in Spain and Portugal. CB13 clusters with all previously sequenced early European farmers and modern-day Sardinians. Furthermore, our analyses suggest that both Cardial and LBK peoples derived from a common ancient population located in or around the Balkan Peninsula. The Iberian Cardial genome also carries a discernible hunter–gatherer genetic signature that likely was not acquired by admixture with local Iberian foragers. Our results indicate that retrieving ancient genomes from similarly warm Mediterranean environments such as the Near East is technically feasible.
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Affiliation(s)
- Iñigo Olalde
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Hannes Schroeder
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark Faculty of Archaeology, Leiden University, Leiden, The Netherlands
| | - Marcela Sandoval-Velasco
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Vinner
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Irene Lobón
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Oscar Ramirez
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Sergi Civit
- Department of Statistics, Faculty of Biology, University of Barcelona, Barcelona, Spain
| | - Pablo García Borja
- Departament de Prehistòria i Arqueologia, Universitat de València, València, Spain
| | - Domingo C Salazar-García
- Departament de Prehistòria i Arqueologia, Universitat de València, València, Spain Department of Archaeology, University of Cape Town, Cape Town, South Africa LAMPEA UMR 7269, Maison Méditerranéenne des Sciences de l'Homme (MMSH), Aix-en-Provence, France Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Josep María Fullola
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Francesc Xavier Oms
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Mireia Pedro
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - Pablo Martínez
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain Col·Lectiu per a la Investigació de la Prehistòria i l'Arqueologia del Garraf-Ordal, CIPAG, Begues, Spain
| | - Montserrat Sanz
- Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal
| | - Joan Daura
- Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal GRQ, Grup de Recerca del Quaternari, Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain
| | - João Zilhão
- Seminari Estudis i Recerques Prehistòriques (SERP; SGR2014-00108), Departament de Prehistòria, H. Antiga i Arqueologia, Facultat de Geografia i Història, Universitat de Barcelona, Barcelona, Spain Centro de Arqueologia, Faculdade de Letras, Universidade de Lisboa (UNIARQ), Alameda da Universidade, Lisboa, Portugal Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Tomàs Marquès-Bonet
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
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Malmström H, Linderholm A, Skoglund P, Storå J, Sjödin P, Gilbert MTP, Holmlund G, Willerslev E, Jakobsson M, Lidén K, Götherström A. Ancient mitochondrial DNA from the northern fringe of the Neolithic farming expansion in Europe sheds light on the dispersion process. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130373. [PMID: 25487325 DOI: 10.1098/rstb.2013.0373] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The European Neolithization process started around 12 000 years ago in the Near East. The introduction of agriculture spread north and west throughout Europe and a key question has been if this was brought about by migrating individuals, by an exchange of ideas or a by a mixture of these. The earliest farming evidence in Scandinavia is found within the Funnel Beaker Culture complex (Trichterbecherkultur, TRB) which represents the northernmost extension of Neolithic farmers in Europe. The TRB coexisted for almost a millennium with hunter-gatherers of the Pitted Ware Cultural complex (PWC). If migration was a substantial part of the Neolithization, even the northerly TRB community would display a closer genetic affinity to other farmer populations than to hunter-gatherer populations. We deep-sequenced the mitochondrial hypervariable region 1 from seven farmers (six TRB and one Battle Axe complex, BAC) and 13 hunter-gatherers (PWC) and authenticated the sequences using postmortem DNA damage patterns. A comparison with 124 previously published sequences from prehistoric Europe shows that the TRB individuals share a close affinity to Central European farmer populations, and that they are distinct from hunter-gatherer groups, including the geographically close and partially contemporary PWC that show a close affinity to the European Mesolithic hunter-gatherers.
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Affiliation(s)
- Helena Malmström
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Anna Linderholm
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, South Road, Durham DH1 3LE, UK
| | - Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - Jan Storå
- Osteolarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Per Sjödin
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden
| | - M Thomas P Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350 Copenhagen, Denmark
| | - Gunilla Holmlund
- Department of Forensic Genetics and Forensic Toxicology, National Board of Forensic Medicine, Linköping University, Artillerigatan 12, 587 58, Linköping, Sweden Department of Clinical and Experimental Medicine, Linköping University, Artillerigatan 12, 587 58, Linköping, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Volgade 5-7, 1350 Copenhagen, Denmark
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kerstin Lidén
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
| | - Anders Götherström
- Department of Evolutionary Biology, Uppsala University, Norbyvägen 18D, 752 36 Uppsala, Sweden Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, 106 91 Stockholm, Sweden
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De Fanti S, Sazzini M, Giuliani C, Frazzoni F, Sarno S, Boattini A, Marasco E, Mantovani V, Franceschi C, Moral P, Garagnani P, Luiselli D. Inferring the genetic history of lactase persistence along the Italian peninsula from a large genomic interval surrounding theLCTgene. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 158:708-18. [DOI: 10.1002/ajpa.22814] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Revised: 06/19/2015] [Accepted: 07/03/2015] [Indexed: 12/15/2022]
Affiliation(s)
- Sara De Fanti
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology; University of Bologna; Bologna 40126 Italy
| | - Marco Sazzini
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology; University of Bologna; Bologna 40126 Italy
| | - Cristina Giuliani
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology; University of Bologna; Bologna 40126 Italy
| | - Federica Frazzoni
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
| | - Stefania Sarno
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
| | - Alessio Boattini
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
| | - Elena Marasco
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES); University of Bologna; Bologna 40126 Italy
| | - Vilma Mantovani
- Center for Applied Biomedical Research (CRBA); St. Orsola-Malpighi University Hospital; Bologna 40138 Italy
| | - Claudio Franceschi
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES); University of Bologna; Bologna 40126 Italy
| | - Pedro Moral
- Department of Animal Biology-Anthropology; University of Barcelona; Barcelona 08028 Spain
| | - Paolo Garagnani
- Department of Experimental, Diagnostic and Specialty Medicine (DIMES); University of Bologna; Bologna 40126 Italy
| | - Donata Luiselli
- Laboratory of Molecular Anthropology, Department of Biological, Geological and Environmental Sciences (BiGeA); University of Bologna; Bologna 40126 Italy
- Department of Biological, Geological and Environmental Sciences (BiGeA), Centre for Genome Biology; University of Bologna; Bologna 40126 Italy
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Rivollat M, Mendisco F, Pemonge MH, Safi A, Saint-Marc D, Brémond A, Couture-Veschambre C, Rottier S, Deguilloux MF. When the waves of European Neolithization met: first paleogenetic evidence from early farmers in the southern Paris Basin. PLoS One 2015; 10:e0125521. [PMID: 25928633 PMCID: PMC4415815 DOI: 10.1371/journal.pone.0125521] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 03/14/2015] [Indexed: 11/19/2022] Open
Abstract
An intense debate concerning the nature and mode of Neolithic transition in Europe has long received much attention. Recent publications of paleogenetic analyses focusing on ancient European farmers from Central Europe or the Iberian Peninsula have greatly contributed to this debate, providing arguments in favor of major migrations accompanying European Neolithization and highlighting noticeable genetic differentiation between farmers associated with two archaeologically defined migration routes: the Danube valley and the Mediterranean Sea. The aim of the present study was to fill a gap with the first paleogenetic data of Neolithic settlers from a region (France) where the two great currents came into both direct and indirect contact with each other. To this end, we analyzed the Gurgy 'Les Noisats' group, an Early/Middle Neolithic necropolis in the southern part of the Paris Basin. Interestingly, the archaeological record from this region highlighted a clear cultural influence from the Danubian cultural sphere but also notes exchanges with the Mediterranean cultural area. To unravel the processes implied in these cultural exchanges, we analyzed 102 individuals and obtained the largest Neolithic mitochondrial gene pool so far (39 HVS-I mitochondrial sequences and haplogroups for 55 individuals) from a single archaeological site from the Early/Middle Neolithic period. Pairwise FST values, haplogroup frequencies and shared informative haplotypes were calculated and compared with ancient and modern European and Near Eastern populations. These descriptive analyses provided patterns resulting from different evolutionary scenarios; however, the archaeological data available for the region suggest that the Gurgy group was formed through equivalent genetic contributions of farmer descendants from the Danubian and Mediterranean Neolithization waves. However, these results, that would constitute the most ancient genetic evidence of admixture between farmers from both Central and Mediterranean migration routes in the European Neolithization debate, are subject to confirmation through appropriate model-based approaches.
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Affiliation(s)
- Maïté Rivollat
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Fanny Mendisco
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Marie-Hélène Pemonge
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Audrey Safi
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Didier Saint-Marc
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Antoine Brémond
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Christine Couture-Veschambre
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Stéphane Rottier
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
| | - Marie-France Deguilloux
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie—UMR 5199, University of Bordeaux, Bordeaux, France
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Keller M, Rott A, Hoke N, Schwarzberg H, Regner-Kamlah B, Harbeck M, Wahl J. United in death-related by blood? Genetic and archeometric analyses of skeletal remains from the neolithic earthwork bruchsal-aue. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015; 157:458-71. [DOI: 10.1002/ajpa.22738] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Revised: 02/16/2015] [Accepted: 02/22/2015] [Indexed: 11/12/2022]
Affiliation(s)
- Marcel Keller
- Anthropology and Environmental History; Department Biology I; Ludwig-Maximilians-University Munich; D-82152 Martinsried Germany
| | - Andreas Rott
- Department of Anthropology; State Collection for Anthropology and Palaeoanatomy; D-80333 Munich Germany
| | - Nadja Hoke
- Anthropology and Environmental History; Department Biology I; Ludwig-Maximilians-University Munich; D-82152 Martinsried Germany
- Department of Anthropology; State Collection for Anthropology and Palaeoanatomy; D-80333 Munich Germany
| | - Heiner Schwarzberg
- Department of Prehistory; Bavarian State Archaeological Collection; D-80538 Munich Germany
| | - Birgit Regner-Kamlah
- Department of Archaeological Heritage Management 84.2; State Office for Cultural Heritage Management Baden-Württemberg, State Regional Authority Stuttgart; D-76133 Karlsruhe Germany
| | - Michaela Harbeck
- Department of Anthropology; State Collection for Anthropology and Palaeoanatomy; D-80333 Munich Germany
| | - Joachim Wahl
- Department of Archaeological Heritage Management 84.1; State Office for Cultural Heritage Management Baden-Württemberg, State Regional Authority Stuttgart; D-78467 Constance Germany
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37
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Regueiro M, Garcia-Bertrand R, Fadhlaoui-Zid K, Álvarez J, Herrera RJ. From Arabia to Iberia: A Y chromosome perspective. Gene 2015; 564:141-52. [PMID: 25701402 DOI: 10.1016/j.gene.2015.02.042] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 02/08/2015] [Accepted: 02/15/2015] [Indexed: 12/31/2022]
Abstract
At different times during recent human evolution, northern Africa has served as a conduit for migrations from the Arabian Peninsula. Although previous researchers have investigated the possibility of the Strait of Gibraltar as a pathway of migration from North Africa to Iberia, we now revisit this issue and theorize that although the Strait of Gibraltar, at the west end of this corridor, has acted as a barrier for human dispersal into Southwest Europe, it has not provided an absolute seal to gene flow. To test this hypothesis, here we use the spatial frequency distributions, STR diversity and expansion time estimates of Y chromosome haplogroups J1-P58 and E-M81 to investigate the genetic imprints left by the Arabian and Berber expansions into the Iberian Peninsula, respectively. The data generated indicate that Arabian and Berber genetic markers are detected in Iberia. We present evidence that suggest that Iberia has received gene flow from Northwest Africa during and prior to the Islamic colonization of 711A.D. It is interesting that the highest frequencies of Arabia and Berber markers are not found in southern Spain, where Islam remained the longest and was culturally most influential, but in Northwest Iberia, specifically Galicia. We propose that Moriscos' relocations to the north during the Reconquista, the migration of cryptic Muslims seeking refuge in a more lenient society and/or more geographic extensive pre-Islamic incursions may explain the higher frequencies and older time estimates of mutations in the north of the Peninsula. These scenarios are congruent with the higher diversities of some diagnostic makers observed in Northwest Iberia.
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Affiliation(s)
- María Regueiro
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
| | | | - Karima Fadhlaoui-Zid
- Laboratoire de Genetique, Immunologie et Pathologies Humaines, Faculte des Sciences de Tunis, Campus Universitaire El Manar II, Universite el Manar, Tunis, Tunisia
| | - Joseph Álvarez
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
| | - Rene J Herrera
- Biology Department, Colorado College, Colorado Springs, CO 80903, USA
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38
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Hagelberg E, Hofreiter M, Keyser C. Introduction. Ancient DNA: the first three decades. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130371. [PMID: 25487324 PMCID: PMC4275880 DOI: 10.1098/rstb.2013.0371] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Erika Hagelberg
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Christine Keyser
- Institut de Médecine Légale, Laboratoire AMIS, Université de Strasbourg, CNRS UMR 5288, Strasbourg, France
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39
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Major transitions in human evolution revisited: a tribute to ancient DNA. J Hum Evol 2014; 79:4-20. [PMID: 25532800 DOI: 10.1016/j.jhevol.2014.06.015] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2014] [Revised: 06/06/2014] [Accepted: 06/19/2014] [Indexed: 11/23/2022]
Abstract
The origin and diversification of modern humans have been characterized by major evolutionary transitions and demographic changes. Patterns of genetic variation within modern populations can help with reconstructing this ∼200 thousand year-long population history. However, by combining this information with genomic data from ancient remains, one can now directly access our evolutionary past and reveal our population history in much greater detail. This review outlines the main recent achievements in ancient DNA research and illustrates how the field recently moved from the polymerase chain reaction (PCR) amplification of short mitochondrial fragments to whole-genome sequencing and thereby revisited our own history. Ancient DNA research has revealed the routes that our ancestors took when colonizing the planet, whom they admixed with, how they domesticated plant and animal species, how they genetically responded to changes in lifestyle, and also, which pathogens decimated their populations. These approaches promise to soon solve many pending controversies about our own origins that are indecipherable from modern patterns of genetic variation alone, and therefore provide an extremely powerful toolkit for a new generation of molecular anthropologists.
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40
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Warinner C, Hendy J, Speller C, Cappellini E, Fischer R, Trachsel C, Arneborg J, Lynnerup N, Craig OE, Swallow DM, Fotakis A, Christensen RJ, Olsen JV, Liebert A, Montalva N, Fiddyment S, Charlton S, Mackie M, Canci A, Bouwman A, Rühli F, Gilbert MTP, Collins MJ. Direct evidence of milk consumption from ancient human dental calculus. Sci Rep 2014; 4:7104. [PMID: 25429530 PMCID: PMC4245811 DOI: 10.1038/srep07104] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2014] [Accepted: 10/27/2014] [Indexed: 02/06/2023] Open
Abstract
Milk is a major food of global economic importance, and its consumption is regarded as a classic example of gene-culture evolution. Humans have exploited animal milk as a food resource for at least 8500 years, but the origins, spread, and scale of dairying remain poorly understood. Indirect lines of evidence, such as lipid isotopic ratios of pottery residues, faunal mortality profiles, and lactase persistence allele frequencies, provide a partial picture of this process; however, in order to understand how, where, and when humans consumed milk products, it is necessary to link evidence of consumption directly to individuals and their dairy livestock. Here we report the first direct evidence of milk consumption, the whey protein β-lactoglobulin (BLG), preserved in human dental calculus from the Bronze Age (ca. 3000 BCE) to the present day. Using protein tandem mass spectrometry, we demonstrate that BLG is a species-specific biomarker of dairy consumption, and we identify individuals consuming cattle, sheep, and goat milk products in the archaeological record. We then apply this method to human dental calculus from Greenland's medieval Norse colonies, and report a decline of this biomarker leading up to the abandonment of the Norse Greenland colonies in the 15th century CE.
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Affiliation(s)
- C Warinner
- 1] Department of Anthropology, University of Oklahoma, Norman, OK, USA [2] Institute of Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - J Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
| | - C Speller
- BioArCh, Department of Archaeology, University of York, York, UK
| | - E Cappellini
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - R Fischer
- Henry Wellcome Building for Cellular and Molecular Physiology, Oxford, UK
| | - C Trachsel
- Functional Genomics Center Zürich, University of Zürich/Swiss Federal Institute of Technology (ETH) Zürich, Zürich, Switzerland
| | - J Arneborg
- 1] National Museum of Denmark, Copenhagen, Denmark [2] School of GeoSciences, University of Edinburgh, Edinburgh, United Kingdom
| | - N Lynnerup
- Laboratory of Biological Anthropology, Institute of Forensic Medicine, Faculty of Health Sciences, University of Copenhagen, Denmark
| | - O E Craig
- BioArCh, Department of Archaeology, University of York, York, UK
| | - D M Swallow
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - A Fotakis
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark [2] Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - R J Christensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - J V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - A Liebert
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - N Montalva
- 1] Research Department of Genetics, Evolution and Environment, University College London, London, UK [2] Department of Anthropology, University College London, London UK
| | - S Fiddyment
- BioArCh, Department of Archaeology, University of York, York, UK
| | - S Charlton
- BioArCh, Department of Archaeology, University of York, York, UK
| | - M Mackie
- BioArCh, Department of Archaeology, University of York, York, UK
| | - A Canci
- Dipartimento di Archeologia, Università degli Studi di Padova, Padova, Italy
| | - A Bouwman
- Institute of Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - F Rühli
- Institute of Evolutionary Medicine, University of Zürich, Zürich, Switzerland
| | - M T P Gilbert
- 1] Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark [2] Trace and Environmental DNA Laboratory, Department of Environment and Agriculture, Curtin University, Perth, Australia
| | - M J Collins
- BioArCh, Department of Archaeology, University of York, York, UK
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Brandt G, Szécsényi-Nagy A, Roth C, Alt KW, Haak W. Human paleogenetics of Europe--the known knowns and the known unknowns. J Hum Evol 2014; 79:73-92. [PMID: 25467114 DOI: 10.1016/j.jhevol.2014.06.017] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Revised: 03/25/2014] [Accepted: 06/19/2014] [Indexed: 12/01/2022]
Abstract
The number of ancient human DNA studies has drastically increased in recent years. This results in a substantial record of mitochondrial sequences available from many prehistoric sites across Western Eurasia, but also growing Y-chromosome and autosomal sequence data. We review the current state of research with specific emphasis on the Holocene population events that likely have shaped the present-day genetic variation in Europe. We reconcile observations from the genetic data with hypotheses about the peopling and settlement history from anthropology and archaeology for various key regions, and also discuss the data in light of evidence from related disciplines, such as modern human genetics, climatology and linguistics.
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Affiliation(s)
- Guido Brandt
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Anna Szécsényi-Nagy
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany; Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1014 Budapest, Hungary
| | - Christina Roth
- Institute of Anthropology, Johannes Gutenberg University Mainz, Colonel-Kleinmannweg 2, D-55099 Mainz, Germany
| | - Kurt Werner Alt
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Heritage Museum, Richard-Wagner-Straße 9, D-06114 Halle, Germany; Institute for Prehistory and Archaeological Science, Basel University, Petersplatz 1, 4003 Basel, Switzerland; Danube Private University, Faculty of Medicine and Dentistry, Doktor-Karl-Dorrek-Straße 23, 3500 Krems an der Donau, Austria
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, The University of Adelaide, North Terrace Campus, SA-5005 Adelaide, Australia.
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42
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Genome flux and stasis in a five millennium transect of European prehistory. Nat Commun 2014; 5:5257. [PMID: 25334030 PMCID: PMC4218962 DOI: 10.1038/ncomms6257] [Citation(s) in RCA: 371] [Impact Index Per Article: 37.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2014] [Accepted: 09/11/2014] [Indexed: 12/19/2022] Open
Abstract
The Great Hungarian Plain was a crossroads of cultural transformations that have shaped European prehistory. Here we analyse a 5,000-year transect of human genomes, sampled from petrous bones giving consistently excellent endogenous DNA yields, from 13 Hungarian Neolithic, Copper, Bronze and Iron Age burials including two to high (~22 × ) and seven to ~1 × coverage, to investigate the impact of these on Europe’s genetic landscape. These data suggest genomic shifts with the advent of the Neolithic, Bronze and Iron Ages, with interleaved periods of genome stability. The earliest Neolithic context genome shows a European hunter-gatherer genetic signature and a restricted ancestral population size, suggesting direct contact between cultures after the arrival of the first farmers into Europe. The latest, Iron Age, sample reveals an eastern genomic influence concordant with introduced Steppe burial rites. We observe transition towards lighter pigmentation and surprisingly, no Neolithic presence of lactase persistence. Recent advances in high-throughput sequencing techniques have enabled the analysis of ancient human genomes. Here the authors sequence ancient human genomes that span a period of 5,000 years, to understand the ancestral influence on Europe's genetic landscape.
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43
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Fernández E, Pérez-Pérez A, Gamba C, Prats E, Cuesta P, Anfruns J, Molist M, Arroyo-Pardo E, Turbón D. Ancient DNA analysis of 8000 B.C. near eastern farmers supports an early neolithic pioneer maritime colonization of Mainland Europe through Cyprus and the Aegean Islands. PLoS Genet 2014; 10:e1004401. [PMID: 24901650 PMCID: PMC4046922 DOI: 10.1371/journal.pgen.1004401] [Citation(s) in RCA: 76] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 04/09/2014] [Indexed: 11/18/2022] Open
Abstract
The genetic impact associated to the Neolithic spread in Europe has been widely debated over the last 20 years. Within this context, ancient DNA studies have provided a more reliable picture by directly analyzing the protagonist populations at different regions in Europe. However, the lack of available data from the original Near Eastern farmers has limited the achieved conclusions, preventing the formulation of continental models of Neolithic expansion. Here we address this issue by presenting mitochondrial DNA data of the original Near-Eastern Neolithic communities with the aim of providing the adequate background for the interpretation of Neolithic genetic data from European samples. Sixty-three skeletons from the Pre Pottery Neolithic B (PPNB) sites of Tell Halula, Tell Ramad and Dja'de El Mughara dating between 8,700-6,600 cal. B.C. were analyzed, and 15 validated mitochondrial DNA profiles were recovered. In order to estimate the demographic contribution of the first farmers to both Central European and Western Mediterranean Neolithic cultures, haplotype and haplogroup diversities in the PPNB sample were compared using phylogeographic and population genetic analyses to available ancient DNA data from human remains belonging to the Linearbandkeramik-Alföldi Vonaldiszes Kerámia and Cardial/Epicardial cultures. We also searched for possible signatures of the original Neolithic expansion over the modern Near Eastern and South European genetic pools, and tried to infer possible routes of expansion by comparing the obtained results to a database of 60 modern populations from both regions. Comparisons performed among the 3 ancient datasets allowed us to identify K and N-derived mitochondrial DNA haplogroups as potential markers of the Neolithic expansion, whose genetic signature would have reached both the Iberian coasts and the Central European plain. Moreover, the observed genetic affinities between the PPNB samples and the modern populations of Cyprus and Crete seem to suggest that the Neolithic was first introduced into Europe through pioneer seafaring colonization.
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Affiliation(s)
- Eva Fernández
- Research Centre in Evolutionary Anthropology and Paleoecology, Liverpool John Moores University, Liverpool, United Kingdom
- Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
- * E-mail:
| | - Alejandro Pérez-Pérez
- Dpto. Biología Animal-Unidad de Antropología, Facultad de Biología, Universitat de Barcelona, Barcelona, Spain
| | - Cristina Gamba
- Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Eva Prats
- Centro de Investigación y Desarrollo, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Pedro Cuesta
- Dpto. de Apoyo a la Investigación, Servicios informáticos de la Universidad Complutense de Madrid, Madrid, Spain
| | - Josep Anfruns
- Dep. Prehistoria, Facultad de Filosofía y Letras, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Miquel Molist
- Dep. Prehistoria, Facultad de Filosofía y Letras, Universitat Autónoma de Barcelona, Bellaterra, Barcelona, Spain
| | - Eduardo Arroyo-Pardo
- Laboratorio de Genética Forense y Genética de Poblaciones, Dpto. Toxicología y Legislación Sanitaria, Facultad de Medicina, Universidad Complutense de Madrid, Madrid, Spain
| | - Daniel Turbón
- Dpto. Biología Animal-Unidad de Antropología, Facultad de Biología, Universitat de Barcelona, Barcelona, Spain
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Improved phylogenetic resolution and rapid diversification of Y-chromosome haplogroup K-M526 in Southeast Asia. Eur J Hum Genet 2014; 23:369-73. [PMID: 24896152 DOI: 10.1038/ejhg.2014.106] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 03/14/2014] [Accepted: 04/30/2014] [Indexed: 11/09/2022] Open
Abstract
The highly structured distribution of Y-chromosome haplogroups suggests that current patterns of variation may be informative of past population processes. However, limited phylogenetic resolution, particularly of subclades within haplogroup K, has obscured the relationships of lineages that are common across Eurasia. Here we genotype 13 new highly informative single-nucleotide polymorphisms in a worldwide sample of 4413 males that carry the derived allele at M526, and reconstruct an NRY haplogroup tree with significantly higher resolution for the major clade within haplogroup K, K-M526. Although K-M526 was previously characterized by a single polytomy of eight major branches, the phylogenetic structure of haplogroup K-M526 is now resolved into four major subclades (K2a-d). The largest of these subclades, K2b, is divided into two clusters: K2b1 and K2b2. K2b1 combines the previously known haplogroups M, S, K-P60 and K-P79, whereas K2b2 comprises haplogroups P and its subhaplogroups Q and R. Interestingly, the monophyletic group formed by haplogroups R and Q, which make up the majority of paternal lineages in Europe, Central Asia and the Americas, represents the only subclade with K2b that is not geographically restricted to Southeast Asia and Oceania. Estimates of the interval times for the branching events between M9 and P295 point to an initial rapid diversification process of K-M526 that likely occurred in Southeast Asia, with subsequent westward expansions of the ancestors of haplogroups R and Q.
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An ancient Mediterranean melting pot: investigating the uniparental genetic structure and population history of sicily and southern Italy. PLoS One 2014; 9:e96074. [PMID: 24788788 PMCID: PMC4005757 DOI: 10.1371/journal.pone.0096074] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Accepted: 04/03/2014] [Indexed: 11/19/2022] Open
Abstract
Due to their strategic geographic location between three different continents, Sicily and Southern Italy have long represented a major Mediterranean crossroad where different peoples and cultures came together over time. However, its multi-layered history of migration pathways and cultural exchanges, has made the reconstruction of its genetic history and population structure extremely controversial and widely debated. To address this debate, we surveyed the genetic variability of 326 accurately selected individuals from 8 different provinces of Sicily and Southern Italy, through a comprehensive evaluation of both Y-chromosome and mtDNA genomes. The main goal was to investigate the structuring of maternal and paternal genetic pools within Sicily and Southern Italy, and to examine their degrees of interaction with other Mediterranean populations. Our findings show high levels of within-population variability, coupled with the lack of significant genetic sub-structures both within Sicily, as well as between Sicily and Southern Italy. When Sicilian and Southern Italian populations were contextualized within the Euro-Mediterranean genetic space, we observed different historical dynamics for maternal and paternal inheritances. Y-chromosome results highlight a significant genetic differentiation between the North-Western and South-Eastern part of the Mediterranean, the Italian Peninsula occupying an intermediate position therein. In particular, Sicily and Southern Italy reveal a shared paternal genetic background with the Balkan Peninsula and the time estimates of main Y-chromosome lineages signal paternal genetic traces of Neolithic and post-Neolithic migration events. On the contrary, despite showing some correspondence with its paternal counterpart, mtDNA reveals a substantially homogeneous genetic landscape, which may reflect older population events or different demographic dynamics between males and females. Overall, both uniparental genetic structures and TMRCA estimates confirm the role of Sicily and Southern Italy as an ancient Mediterranean melting pot for genes and cultures.
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Skoglund P, Malmström H, Omrak A, Raghavan M, Valdiosera C, Günther T, Hall P, Tambets K, Parik J, Sjögren KG, Apel J, Willerslev E, Storå J, Götherström A, Jakobsson M. Genomic diversity and admixture differs for Stone-Age Scandinavian foragers and farmers. Science 2014; 344:747-50. [PMID: 24762536 DOI: 10.1126/science.1253448] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Prehistoric population structure associated with the transition to an agricultural lifestyle in Europe remains a contentious idea. Population-genomic data from 11 Scandinavian Stone Age human remains suggest that hunter-gatherers had lower genetic diversity than that of farmers. Despite their close geographical proximity, the genetic differentiation between the two Stone Age groups was greater than that observed among extant European populations. Additionally, the Scandinavian Neolithic farmers exhibited a greater degree of hunter-gatherer-related admixture than that of the Tyrolean Iceman, who also originated from a farming context. In contrast, Scandinavian hunter-gatherers displayed no significant evidence of introgression from farmers. Our findings suggest that Stone Age foraging groups were historically in low numbers, likely owing to oscillating living conditions or restricted carrying capacity, and that they were partially incorporated into expanding farming groups.
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Affiliation(s)
- Pontus Skoglund
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Helena Malmström
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden
| | - Maanasa Raghavan
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Cristina Valdiosera
- Department of Archaeology, Environment and Community Planning, La Trobe University, Melbourne VIC 3086, Australia
| | - Torsten Günther
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden
| | - Per Hall
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 171 77, Sweden
| | - Kristiina Tambets
- Evolutionary Biology Group, Estonian Biocentre and University of Tartu, Tartu 51010, Estonia
| | - Jüri Parik
- Evolutionary Biology Group, Estonian Biocentre and University of Tartu, Tartu 51010, Estonia
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, 405 30, Sweden
| | - Jan Apel
- Department of Archaeology and Ancient History, Lund University, Lund, 221 00, Sweden
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen 1350, Denmark
| | - Jan Storå
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden
| | - Anders Götherström
- Department of Archaeology and Classical studies, Stockholm University, Stockholm 106 91, Sweden.
| | - Mattias Jakobsson
- Department of Evolutionary Biology, Uppsala University, Uppsala 752 36, Sweden. Science for Life Laboratory, Uppsala University, Uppsala 752 36, Sweden.
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Krüttli A, Bouwman A, Akgül G, Della Casa P, Rühli F, Warinner C. Ancient DNA analysis reveals high frequency of European lactase persistence allele (T-13910) in medieval central europe. PLoS One 2014; 9:e86251. [PMID: 24465990 PMCID: PMC3900515 DOI: 10.1371/journal.pone.0086251] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 12/10/2013] [Indexed: 11/23/2022] Open
Abstract
Ruminant milk and dairy products are important food resources in many European, African, and Middle Eastern societies. These regions are also associated with derived genetic variants for lactase persistence. In mammals, lactase, the enzyme that hydrolyzes the milk sugar lactose, is normally down-regulated after weaning, but at least five human populations around the world have independently evolved mutations regulating the expression of the lactase-phlorizin-hydrolase gene. These mutations result in a dominant lactase persistence phenotype and continued lactase tolerance in adulthood. A single nucleotide polymorphism (SNP) at C/T-13910 is responsible for most lactase persistence in European populations, but when and where the T-13910 polymorphism originated and the evolutionary processes by which it rose to high frequency in Europe have been the subject of strong debate. A history of dairying is presumed to be a prerequisite, but archaeological evidence is lacking. In this study, DNA was extracted from the dentine of 36 individuals excavated at a medieval cemetery in Dalheim, Germany. Eighteen individuals were successfully genotyped for the C/T-13910 SNP by molecular cloning and sequencing, of which 13 (72%) exhibited a European lactase persistence genotype: 44% CT, 28% TT. Previous ancient DNA-based studies found that lactase persistence genotypes fall below detection levels in most regions of Neolithic Europe. Our research shows that by AD 1200, lactase persistence frequency had risen to over 70% in this community in western Central Europe. Given that lactase persistence genotype frequency in present-day Germany and Austria is estimated at 71–80%, our results suggest that genetic lactase persistence likely reached modern levels before the historic population declines associated with the Black Death, thus excluding plague-associated evolutionary forces in the rise of lactase persistence in this region. This new evidence sheds light on the dynamic evolutionary history of the European lactase persistence trait and its global cultural implications.
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Affiliation(s)
- Annina Krüttli
- Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland
- Department of Pre- and Protohistory, Institute of History, University of Zurich, Zurich, Switzerland
| | - Abigail Bouwman
- Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Gülfirde Akgül
- Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Philippe Della Casa
- Department of Pre- and Protohistory, Institute of History, University of Zurich, Zurich, Switzerland
| | - Frank Rühli
- Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland
| | - Christina Warinner
- Centre for Evolutionary Medicine, Institute of Anatomy, University of Zurich, Zurich, Switzerland
- Department of Anthropology, University of Oklahoma, Norman, Oklahoma, United States of America
- * E-mail:
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Sverrisdóttir OÓ, Timpson A, Toombs J, Lecoeur C, Froguel P, Carretero JM, Arsuaga Ferreras JL, Götherström A, Thomas MG. Direct estimates of natural selection in Iberia indicate calcium absorption was not the only driver of lactase persistence in Europe. Mol Biol Evol 2014; 31:975-83. [PMID: 24448642 DOI: 10.1093/molbev/msu049] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Lactase persistence (LP) is a genetically determined trait whereby the enzyme lactase is expressed throughout adult life. Lactase is necessary for the digestion of lactose--the main carbohydrate in milk--and its production is downregulated after the weaning period in most humans and all other mammals studied. Several sources of evidence indicate that LP has evolved independently, in different parts of the world over the last 10,000 years, and has been subject to strong natural selection in dairying populations. In Europeans, LP is strongly associated with, and probably caused by, a single C to T mutation 13,910 bp upstream of the lactase (LCT) gene (-13,910*T). Despite a considerable body of research, the reasons why LP should provide such a strong selective advantage remain poorly understood. In this study, we examine one of the most widely cited hypotheses for selection on LP--that fresh milk consumption supplemented the poor vitamin D and calcium status of northern Europe's early farmers (the calcium assimilation hypothesis). We do this by testing for natural selection on -13,910*T using ancient DNA data from the skeletal remains of eight late Neolithic Iberian individuals, whom we would not expect to have poor vitamin D and calcium status because of relatively high incident UVB light levels. None of the eight samples successfully typed in the study had the derived T-allele. In addition, we reanalyze published data from French Neolithic remains to both test for population continuity and further examine the evolution of LP in the region. Using simulations that accommodate genetic drift, natural selection, uncertainty in calibrated radiocarbon dates, and sampling error, we find that natural selection is still required to explain the observed increase in allele frequency. We conclude that the calcium assimilation hypothesis is insufficient to explain the spread of LP in Europe.
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Affiliation(s)
- Oddny Ósk Sverrisdóttir
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden
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Gerbault P, Roffet-Salque M, Evershed RP, Thomas MG. How long have adult humans been consuming milk? IUBMB Life 2013; 65:983-90. [DOI: 10.1002/iub.1227] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Revised: 11/01/2013] [Accepted: 11/04/2013] [Indexed: 01/07/2023]
Affiliation(s)
- Pascale Gerbault
- Research Department of Genetics, Evolution and Environment; University College London; London WC1E 6BT UK
| | - Mélanie Roffet-Salque
- Organic Geochemistry Unit, School of Chemistry; University of Bristol, Cantock's Close; Bristol BS8 1TS UK
| | - Richard P. Evershed
- Organic Geochemistry Unit, School of Chemistry; University of Bristol, Cantock's Close; Bristol BS8 1TS UK
| | - Mark G. Thomas
- Research Department of Genetics, Evolution and Environment; University College London; London WC1E 6BT UK
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50
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Berger B, Niederstätter H, Erhart D, Gassner C, Schennach H, Parson W. Reprint of: High resolution mapping of Y haplogroup G in Tyrol (Austria). Forensic Sci Int Genet 2013; 7:624-631. [DOI: 10.1016/j.fsigen.2013.09.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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