1
|
Arzelier A, De Belvalet H, Pemonge MH, Garberi P, Binder D, Duday H, Deguilloux MF, Pruvost M. Ancient DNA sheds light on the funerary practices of late Neolithic collective burial in southern France. Proc Biol Sci 2024; 291:rspb20241215. [PMID: 39191285 DOI: 10.1098/rspb.2024.1215] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2024] [Revised: 06/26/2024] [Accepted: 07/22/2024] [Indexed: 08/29/2024] Open
Abstract
The Aven de la Boucle (Corconne, Gard, southern France) is a karst shaft used as a collective burial between 3600 and 2800 cal BCE. The site encompasses the skeletal remains of approximately 75 individuals comprising a large majority of adult individuals, represented by scattered and commingled remains. To date, few studies have explored the potential of ancient DNA to tackle the documentation of Neolithic collective burials, and the funerary selection rules within such structures remain largely debated. In this study, we combine genomic analysis of 37 individuals with archaeo-anthropological data and Bayesian modelling of radiocarbon dates. Through this multidisciplinary approach, we aim to characterize the identity of the deceased and their relationships, as well as untangle the genetic diversity and funerary dynamics of this community. Genomic results identify 76% of male Neolithic individuals, suggesting a marked sex-biased selection. Available data emphasize the importance of biological relatedness and a male-mediated transmission of social status, as the affiliation to a specific male-lineage appears as a preponderant selection factor. The genomic results argue in favour of 'continuous' deposits between 3600 and 2800 BCE, carried out by the same community, despite cultural changes reflected by the ceramic material.
Collapse
Affiliation(s)
- Ana Arzelier
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Harmony De Belvalet
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Marie-Hélène Pemonge
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Pauline Garberi
- Université Côte d'Azur, CNRS, Cultures, Environnements. Préhistoire, Antiquité, Moyen-Âge (CEPAM UMR 7264) , Nice 06300, France
| | - Didier Binder
- Université Côte d'Azur, CNRS, Cultures, Environnements. Préhistoire, Antiquité, Moyen-Âge (CEPAM UMR 7264) , Nice 06300, France
| | - Henri Duday
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Marie-France Deguilloux
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| | - Mélanie Pruvost
- Université de Bordeaux, CNRS, De la Préhistoire à l'Actuel: Culture, Environnement et Anthropologie (PACEA UMR 5199) , Pessac Cedex 33615, France
| |
Collapse
|
2
|
Primorac D, Šarac J, Havaš Auguštin D, Novokmet N, Bego T, Pinhasi R, Šlaus M, Novak M, Marjanović D. Y Chromosome Story-Ancient Genetic Data as a Supplementary Tool for the Analysis of Modern Croatian Genetic Pool. Genes (Basel) 2024; 15:748. [PMID: 38927684 PMCID: PMC11202852 DOI: 10.3390/genes15060748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Revised: 05/25/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Due to its turbulent demographic history, marked by extensive settlement and gene flow from diverse regions of Eurasia, Southeastern Europe (SEE) has consistently served as a genetic crossroads between East and West and a junction for the migrations that reshaped Europe's population. SEE, including modern Croatian territory, was a crucial passage from the Near East and even more distant regions and human populations in this region, as almost any other European population represents a remarkable genetic mixture. Modern humans have continuously occupied this region since the Upper Paleolithic era, and different (pre)historical events have left a distinctive genetic signature on the historical narrative of this region. Our views of its history have been mostly renewed in the last few decades by extraordinary data obtained from Y-chromosome studies. In recent times, the international research community, bringing together geneticists and archaeologists, has steadily released a growing number of ancient genomes from this region, shedding more light on its complex past population dynamics and shaping the genetic pool in Croatia and this part of Europe.
Collapse
Affiliation(s)
- Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- Regiomed Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- National Forensic Sciences University, Gandhinagar 382007, India
| | - Jelena Šarac
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
| | - Dubravka Havaš Auguštin
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
| | - Natalija Novokmet
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
| | - Tamer Bego
- Faculty of Pharmacy, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
- Department of Archaeology and Heritage, Faculty of Humanities, University of Primorska, 6000 Koper, Slovenia
| | - Damir Marjanović
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
- International Burch University, 71000 Sarajevo, Bosnia and Herzegovina
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
| |
Collapse
|
3
|
Havaš Auguštin D, Šarac J, Reidla M, Tamm E, Grahovac B, Kapović M, Novokmet N, Rudan P, Missoni S, Marjanović D, Korolija M. Refining the Global Phylogeny of Mitochondrial N1a, X, and HV2 Haplogroups Based on Rare Mitogenomes from Croatian Isolates. Genes (Basel) 2023; 14:1614. [PMID: 37628665 PMCID: PMC10454736 DOI: 10.3390/genes14081614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 07/28/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Mitochondrial DNA (mtDNA) has been used for decades as a predominant tool in population genetics and as a valuable addition to forensic genetic research, owing to its unique maternal inheritance pattern that enables the tracing of individuals along the maternal lineage across numerous generations. The dynamic interplay between evolutionary forces, primarily genetic drift, bottlenecks, and the founder effect, can exert significant influence on genetic profiles. Consequently, the Adriatic islands have accumulated a subset of lineages that exhibits remarkable absence or rarity within other European populations. This distinctive genetic composition underscores the islands' potential as a significant resource in phylogenetic research, with implications reaching beyond regional boundaries to contribute to a global understanding. In the initial attempt to expand the mitochondrial forensic database of the Croatian population with haplotypes from small isolated communities, we sequenced mitogenomes of rare haplogroups from different Croatian island and mainland populations using next-generation sequencing (NGS). In the next step and based on the obtained results, we refined the global phylogeny of haplogroup N1a, HV2, and X by analyzing rare haplotypes, which are absent from the current phylogenetic tree. The trees were based on 16 novel and 52 previously published samples, revealing completely novel branches in the X and HV2 haplogroups and a new European cluster in the ancestral N1a variant, previously believed to be an exclusively African-Asian haplogroup. The research emphasizes the importance of investigating geographically isolated populations and their unique characteristics within a global context.
Collapse
Affiliation(s)
- Dubravka Havaš Auguštin
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jelena Šarac
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Maere Reidla
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | - Erika Tamm
- Institute of Genomics, University of Tartu, 50090 Tartu, Estonia
| | | | | | | | - Pavao Rudan
- Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Saša Missoni
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Faculty of Dental Medicine and Health, J. J. Strossmayer University, 31000 Osijek, Croatia
| | - Damir Marjanović
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Ljudevita Gaja 32, 10000 Zagreb, Croatia; (D.H.A.)
- Institute for Anthropological Research, 10000 Zagreb, Croatia
- Genetics and Bioengineering Department, International Burch University, 71000 Sarajevo, Bosnia and Herzegovina
| | - Marina Korolija
- Forensic Science Centre “Ivan Vučetić”, Ministry of the Interior, 10000 Zagreb, Croatia
| |
Collapse
|
4
|
Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave. Commun Biol 2022; 5:1262. [DOI: 10.1038/s42003-022-04190-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Accepted: 10/31/2022] [Indexed: 11/19/2022] Open
Abstract
AbstractRecent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.
Collapse
|
5
|
Childebayeva A, Rohrlach AB, Barquera R, Rivollat M, Aron F, Szolek A, Kohlbacher O, Nicklisch N, Alt KW, Gronenborn D, Meller H, Friederich S, Prüfer K, Deguilloux MF, Krause J, Haak W. Population Genetics and Signatures of Selection in Early Neolithic European Farmers. Mol Biol Evol 2022; 39:6586604. [PMID: 35578825 PMCID: PMC9171004 DOI: 10.1093/molbev/msac108] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
Human expansion in the course of the Neolithic transition in western Eurasia has been one of the major topics in ancient DNA research in the last 10 years. Multiple studies have shown that the spread of agriculture and animal husbandry from the Near East across Europe was accompanied by large-scale human expansions. Moreover, changes in subsistence and migration associated with the Neolithic transition have been hypothesized to involve genetic adaptation. Here, we present high quality genome-wide data from the Linear Pottery Culture site Derenburg-Meerenstieg II (DER) (N = 32 individuals) in Central Germany. Population genetic analyses show that the DER individuals carried predominantly Anatolian Neolithic-like ancestry and a very limited degree of local hunter-gatherer admixture, similar to other early European farmers. Increasing the Linear Pottery culture cohort size to ∼100 individuals allowed us to perform various frequency- and haplotype-based analyses to investigate signatures of selection associated with changes following the adoption of the Neolithic lifestyle. In addition, we developed a new method called Admixture-informed Maximum-likelihood Estimation for Selection Scans that allowed us test for selection signatures in an admixture-aware fashion. Focusing on the intersection of results from these selection scans, we identified various loci associated with immune function (JAK1, HLA-DQB1) and metabolism (LMF1, LEPR, SORBS1), as well as skin color (SLC24A5, CD82) and folate synthesis (MTHFR, NBPF3). Our findings shed light on the evolutionary pressures, such as infectious disease and changing diet, that were faced by the early farmers of Western Eurasia.
Collapse
Affiliation(s)
- Ainash Childebayeva
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Adam Benjamin Rohrlach
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, Australia
| | - Rodrigo Barquera
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Maïté Rivollat
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615 Pessac, France
| | - Franziska Aron
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany
| | - András Szolek
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany.,Department of Immunology, Interfaculty Institute for Cell Biology, University of Tübingen, Tübingen, Germany
| | - Oliver Kohlbacher
- Applied Bioinformatics, Dept. of Computer Science, University of Tübingen, Tübingen, Germany.,Institute for Bioinformatics and Medical Informatics, University of Tübingen, Tübingen, Germany.,Translational Bioinformatics, University Hospital Tübingen, Tübingen, Germany.,Biomolecular Interactions, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Nicole Nicklisch
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria.,State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Kurt W Alt
- Center of Natural and Cultural Human History, Danube Private University, Krems-Stein, Austria.,State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Detlef Gronenborn
- Römisch-Germanisches Zentralmuseum, Leibniz Research Institute for Archaeology, Ernst-Ludwig-Platz 2, 55116 Mainz, Germany
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt - State Museum of Prehistory, Halle (Saale), Germany
| | - Kay Prüfer
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | | | - Johannes Krause
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| | - Wolfgang Haak
- Archaeogenetics Department, Max Planck Institute for the Science of Human History, Kahlaische Straße 10, D-07745 Jena, Germany.,Archaeogenetics Department, Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
| |
Collapse
|
6
|
Ancient DNA gives new insights into a Norman Neolithic monumental cemetery dedicated to male elites. Proc Natl Acad Sci U S A 2022; 119:e2120786119. [PMID: 35446690 PMCID: PMC9170172 DOI: 10.1073/pnas.2120786119] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
By integrating genomic and archaeological data, we provide new insights into the Neolithic French monumental site of Fleury-sur-Orne in Normandy, where a group of selected individuals was buried in impressively long monuments. The earliest individuals buried at Fleury-sur-Orne match the expected western European Neolithic genetic diversity, while three individuals, designated as genetic outliers, were buried after 4,000 calibrated BCE. We hypothesize that different, unrelated families or clans used the site over several centuries. Thirteen of 14 of the analyzed individuals were male, indicating an overarching patrilineal system. However, one exception, a female buried with a symbolically male artifact, suggests that the embodiment of the male gender in death was required to access burial at the monumental structures. The Middle Neolithic in western Europe is characterized by monumental funerary structures, known as megaliths, along the Atlantic façade. The first manifestations of this phenomenon occurred in modern-day France with the long mounds of the Cerny culture. Here, we present genome-wide data from the fifth-millennium BCE site of Fleury-sur-Orne in Normandy (France), famous for its impressively long monuments built for selected individuals. The site encompasses 32 monuments of variable sizes, containing the burials of 19 individuals from the Neolithic period. To address who was buried at the site, we generated genome-wide data for 14 individuals, of whom 13 are males, completing previously published data [M. Rivollat et al., Sci. Adv. 6, eaaz5344 (2020)]. Population genetic and Y chromosome analyses show that the Fleury-sur-Orne group fits within western European Neolithic genetic diversity and that the arrival of a new group is detected after 4,000 calibrated BCE. The results of analyzing uniparentally inherited markers and an overall low number of long runs of homozygosity suggest a patrilineal group practicing female exogamy. We find two pairs of individuals to be father and son, buried together in the same monument/grave. No other biological relationship can link monuments together, suggesting that each monument was dedicated to a genetically independent lineage. The combined data and documented father–son line of descent suggest a male-mediated transmission of sociopolitical authority. However, a single female buried with an arrowhead, otherwise considered a symbol of power of the male elite of the Cerny culture, questions a strictly biological sex bias in the burial rites of this otherwise “masculine” monumental cemetery.
Collapse
|
7
|
Fischer CE, Pemonge MH, Ducoussau I, Arzelier A, Rivollat M, Santos F, Barrand Emam H, Bertaud A, Beylier A, Ciesielski E, Dedet B, Desenne S, Duday H, Chenal F, Gailledrat E, Goepfert S, Gorgé O, Gorgues A, Kuhnle G, Lambach F, Lefort A, Mauduit A, Maziere F, Oudry S, Paresys C, Pinard E, Plouin S, Richard I, Roth-Zehner M, Roure R, Thevenet C, Thomas Y, Rottier S, Deguilloux MF, Pruvost M. Origin and mobility of Iron Age Gaulish groups in present-day France revealed through archaeogenomics. iScience 2022; 25:104094. [PMID: 35402880 PMCID: PMC8983337 DOI: 10.1016/j.isci.2022.104094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 02/17/2022] [Accepted: 03/13/2022] [Indexed: 11/17/2022] Open
Abstract
The Iron Age period occupies an important place in French history because the Gauls are regularly presented as the direct ancestors of the extant French population. We documented here the genomic diversity of Iron Age communities originating from six French regions. The 49 acquired genomes permitted us to highlight an absence of discontinuity between Bronze Age and Iron Age groups in France, lending support to a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. Genomic analyses revealed strong genetic homogeneity among the regional groups associated with distinct archaeological cultures. This genomic homogenization appears to be linked to individuals' mobility between regions and gene flow with neighbouring groups from England and Spain. Thus, the results globally support a common genomic legacy for the Iron Age population of modern-day France that could be linked to recurrent gene flow between culturally differentiated communities.
Collapse
Affiliation(s)
- Claire-Elise Fischer
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
- Corresponding author
| | | | - Isaure Ducoussau
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Ana Arzelier
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Maïté Rivollat
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
- Department of Archaeogenetics, Max Planck Institue for Evolutionary Anthropology, Deutscher Platz 6, 04103 Leipzig, Germany
| | - Frederic Santos
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Hélène Barrand Emam
- ANTEA-Archéologie, Habsheim, France
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
| | - Alexandre Bertaud
- UMR-5607 Ausonius, Université Bordeaux Montaigne, Maison de l’Archéologie, 8 Esplanade des Antilles, 33600 Pessac, France
| | - Alexandre Beylier
- Service Archéologie Sète Agglopôle Mediterranée, 34110 Frontignan, France
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Elsa Ciesielski
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Bernard Dedet
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Sophie Desenne
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 8215 Trajectoires, CNRS, Université Paris 1 Pantheon Sorbonne, 92023 Nanterre, France
| | - Henri Duday
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Fanny Chenal
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
| | - Eric Gailledrat
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Sébastien Goepfert
- ANTEA-Archéologie, Habsheim, France
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
| | - Olivier Gorgé
- Institut de Recherche Biomédicale des Armées, Place Général Valérie André, 91220 Brétigny-sur-Orge, France
| | - Alexis Gorgues
- UMR-5607 Ausonius, Université Bordeaux Montaigne, Maison de l’Archéologie, 8 Esplanade des Antilles, 33600 Pessac, France
| | - Gertrud Kuhnle
- Landesamt für Denkmalpflege im Regierungspräsidium Stuttgart Referat 84.2, Operative Archäologie Dienstsitz Freiburg Günterstalstraße 67, 79100 Freiburg im Breisgau, Germany
| | - François Lambach
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | - Anthony Lefort
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
| | | | - Florent Maziere
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
| | - Sophie Oudry
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR-7268 ADES, CNRS, Université Aix-Marseille, EFS, 13015 Marseille, France
| | - Cécile Paresys
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 7264 CEPAM, CNRS Université Nice Sophia Antipolis, 06357 Nice Cedex 4, France
| | - Estelle Pinard
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 8215 Trajectoires, CNRS, Université Paris 1 Pantheon Sorbonne, 92023 Nanterre, France
| | - Suzanne Plouin
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
| | - Isabelle Richard
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 7264 CEPAM, CNRS Université Nice Sophia Antipolis, 06357 Nice Cedex 4, France
| | - Muriel Roth-Zehner
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
- Archéologie Alsace, 11 Rue Champollion, 67600 Sélestat, France
| | - Réjane Roure
- UMR 5140 - ASM, Université Paul Valéry Montpellier 3, CNRS, Ministère de la Culture, Inrap, 34000 Montpellier, France
| | - Corinne Thevenet
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
- UMR 8215 Trajectoires, CNRS, Université Paris 1 Pantheon Sorbonne, 92023 Nanterre, France
| | - Yohann Thomas
- UMR7044 Archimède, CNRS Université de Strasbourg et Université de Haute-Alsace, Strasbourg et Mulhouse, France
- INRAP, Institut National de Recherche Archéologiques Préventives, 75685 Paris Cedex 14, France
| | - Stéphane Rottier
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
| | | | - Mélanie Pruvost
- UMR 5199 PACEA, CNRS, Université de Bordeaux, 33615 Pessac, France
- Corresponding author
| |
Collapse
|
8
|
Contrasting maternal and paternal genetic histories among five ethnic groups from Khyber Pakhtunkhwa, Pakistan. Sci Rep 2022; 12:1027. [PMID: 35046511 PMCID: PMC8770644 DOI: 10.1038/s41598-022-05076-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 12/10/2021] [Indexed: 11/24/2022] Open
Abstract
Northwest Pakistan has served as a point of entry to South Asia for different populations since ancient times. However, relatively little is known about the population genetic history of the people residing within this region. To better understand human dispersal in the region within the broader history of the subcontinent, we analyzed mtDNA diversity in 659 and Y-chromosome diversity in 678 individuals, respectively, from five ethnic groups (Gujars, Jadoons, Syeds, Tanolis and Yousafzais), from Swabi and Buner Districts, Khyber Pakhtunkhwa Province, Pakistan. The mtDNAs of all individuals were subject to control region sequencing and SNP genotyping, while Y-chromosomes were analyzed using 54 SNPs and 19 STR loci. The majority of the mtDNAs belonged to West Eurasian haplogroups, with the rest belonging to either South or East Asian lineages. Four of the five Pakistani populations (Gujars, Jadoons, Syeds, Yousafzais) possessed strong maternal genetic affinities with other Pakistani and Central Asian populations, whereas one (Tanolis) did not. Four haplogroups (R1a, R1b, O3, L) among the 11 Y-chromosome lineages observed among these five ethnic groups contributed substantially to their paternal genetic makeup. Gujars, Syeds and Yousafzais showed strong paternal genetic affinities with other Pakistani and Central Asian populations, whereas Jadoons and Tanolis had close affinities with Turkmen populations from Central Asia and ethnic groups from northeast India. We evaluate these genetic data in the context of historical and archeological evidence to test different hypotheses concerning their origins and biological relationships.
Collapse
|
9
|
Rohrlach AB, Papac L, Childebayeva A, Rivollat M, Villalba-Mouco V, Neumann GU, Penske S, Skourtanioti E, van de Loosdrecht M, Akar M, Boyadzhiev K, Boyadzhiev Y, Deguilloux MF, Dobeš M, Erdal YS, Ernée M, Frangipane M, Furmanek M, Friederich S, Ghesquière E, Hałuszko A, Hansen S, Küßner M, Mannino M, Özbal R, Reinhold S, Rottier S, Salazar-García DC, Diaz JS, Stockhammer PW, de Togores Muñoz CR, Yener KA, Posth C, Krause J, Herbig A, Haak W. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe. Sci Rep 2021; 11:15005. [PMID: 34294811 PMCID: PMC8298398 DOI: 10.1038/s41598-021-94491-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
Collapse
Affiliation(s)
- Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Marieke van de Loosdrecht
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Murat Akar
- Department of Archaeology, Mustafa Kemal University, 31060, Alahan-Antakya, Hatay, Turkey
| | - Kamen Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | - Yavor Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | | | - Miroslav Dobeš
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | - Yilmaz S Erdal
- Department of Anthropology, Hacettepe University, 06800, Ankara, Turkey
| | - Michal Ernée
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | | | | | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
| | - Emmanuel Ghesquière
- Inrap Grand Ouest, Bourguébus, France.,Université de Rennes 1, CNRS, CReAAH-UMR, 6566, Rennes, France
| | - Agata Hałuszko
- Institute of Archaeology, University of Wrocław, Wrocław, Poland.,Archeolodzy.org Foundation, Wrocław, Poland
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archeology, Weimar, Germany
| | - Marcello Mannino
- Department of Archaeology, School of Culture and Society, Aarhus University, 8270, Højbjerg, Denmark
| | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, 34450, Istanbul, Turkey
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Stéphane Rottier
- Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Ludwig Maximilian University Munich, 80799, Munich, Germany
| | | | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, 10028, USA
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences Eberhard Karls University Tübingen, 72070, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| |
Collapse
|
10
|
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.
Collapse
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.
| |
Collapse
|
11
|
Goude G, Salazar-García DC, Power RC, Rivollat M, Gourichon L, Deguilloux MF, Pemonge MH, Bouby L, Binder D. New insights on Neolithic food and mobility patterns in Mediterranean coastal populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 173:218-235. [PMID: 32557548 DOI: 10.1002/ajpa.24089] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2019] [Revised: 05/12/2020] [Accepted: 05/14/2020] [Indexed: 12/22/2022]
Abstract
OBJECTIVES The aims of this research are to explore the diet, mobility, social organization, and environmental exploitation patterns of early Mediterranean farmers, particularly the role of marine and plant resources in these foodways. In addition, this work strives to document possible gendered patterns of behavior linked to the neolithization of this ecologically rich area. To achieve this, a set of multiproxy analyses (isotopic analyses, dental calculus, microremains analysis, ancient DNA) were performed on an exceptional deposit (n = 61) of human remains from the Les Bréguières site (France), dating to the transition of the sixth to the fifth millennium BCE. MATERIALS AND METHODS The samples used in this study were excavated from the Les Bréguières site (Mougins, Alpes-Maritimes, France), located along the southeastern Mediterranean coastline of France. Stable isotope analyses (C, N) on bone collagen (17 coxal bones, 35 craniofacial elements) were performed as a means to infer protein intake during tissue development. Sulfur isotope ratios were used as indicators of geographical and environmental points of origin. The study of ancient dental calculus helped document the consumption of plants. Strontium isotope analysis on tooth enamel (n = 56) was conducted to infer human provenance and territorial mobility. Finally, ancient DNA analysis was performed to study maternal versus paternal diversity within this Neolithic group (n = 30). RESULTS Stable isotope ratios for human bones range from -20.3 to -18.1‰ for C, from 8.9 to 11.1‰ for N and from 6.4 to 15‰ for S. Domestic animal data range from -22.0 to -20.2‰ for C, from 4.1 to 6.9‰ for N, and from 10.2 to 12.5‰ for S. Human enamel 87 Sr/86 Sr range from 0.7081 to 0.7102, slightly wider than the animal range (between 0.7087 and 0.7096). Starch and phytolith microremains were recovered as well as other types of remains (e.g., hairs, diatoms, fungal spores). Starch grains include Triticeae type and phytolith includes dicotyledons and monocot types as panicoid grasses. Mitochondrial DNA characterized eight different maternal lineages: H1, H3, HV (5.26%), J (10.53%), J1, K, T (5.2%), and U5 (10.53%) but no sample yielded reproducible Y chromosome SNPs, preventing paternal lineage characterization. DISCUSSION Carbon and nitrogen stable isotope ratios indicate a consumption of protein by humans mainly focused on terrestrial animals and possible exploitation of marine resources for one male and one undetermined adult. Sulfur stable isotope ratios allowed distinguishing groups with different geographical origins, including two females possibly more exposed to the sea spray effect. While strontium isotope data do not indicate different origins for the individuals, mitochondrial lineage diversity from petrous bone DNA suggests the burial includes genetically differentiated groups or a group practicing patrilocality. Moreover, the diversity of plant microremains recorded in dental calculus provide the first evidence that the groups of Les Bréguières consumed a wide breadth of plant foods (as cereals and wild taxa) that required access to diverse environments. This transdisciplinary research paves the way for new perspectives and highlights the relevance for novel research of contexts (whether recently discovered or in museum collections) excavated near shorelines, due to the richness of the biodiversity and the wide range of edible resources available.
Collapse
Affiliation(s)
- Gwenaëlle Goude
- Aix Marseille Univ, CNRS, Minist. Culture, LAMPEA, Aix-en-Provence, France
| | - Domingo C Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Aix Marseille Univ, IMERA, Marseille, France.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - Robert C Power
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Bordeaux University, Pessac, France
| | | | | | | | - Laurent Bouby
- ISEM-Université Montpellier, CNRS, EPHE, IRD, Montpellier, France
| | | |
Collapse
|
12
|
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
| |
Collapse
|
13
|
Grugni V, Raveane A, Colombo G, Nici C, Crobu F, Ongaro L, Battaglia V, Sanna D, Al-Zahery N, Fiorani O, Lisa A, Ferretti L, Achilli A, Olivieri A, Francalacci P, Piazza A, Torroni A, Semino O. Y-chromosome and Surname Analyses for Reconstructing Past Population Structures: The Sardinian Population as a Test Case. Int J Mol Sci 2019; 20:E5763. [PMID: 31744094 PMCID: PMC6888588 DOI: 10.3390/ijms20225763] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2019] [Revised: 11/11/2019] [Accepted: 11/14/2019] [Indexed: 11/17/2022] Open
Abstract
Many anthropological, linguistic, genetic and genomic analyses have been carried out to evaluate the potential impact that evolutionary forces had in shaping the present-day Sardinian gene pool, the main outlier in the genetic landscape of Europe. However, due to the homogenizing effect of internal movements, which have intensified over the past fifty years, only partial information has been obtained about the main demographic events. To overcome this limitation, we analyzed the male-specific region of the Y chromosome in three population samples obtained by reallocating a large number of Sardinian subjects to the place of origin of their monophyletic surnames, which are paternally transmitted through generations in most of the populations, much like the Y chromosome. Three Y-chromosome founding lineages, G2-L91, I2-M26 and R1b-V88, were identified as strongly contributing to the definition of the outlying position of Sardinians in the European genetic context and marking a significant differentiation within the island. The present distribution of these lineages does not always mirror that detected in ancient DNAs. Our results show that the analysis of the Y-chromosome gene pool coupled with a sampling method based on the origin of the family name, is an efficient approach to unravelling past heterogeneity, often hidden by recent movements, in the gene pool of modern populations. Furthermore, the reconstruction and comparison of past genetic isolates represent a starting point to better assess the genetic information deriving from the increasing number of available ancient DNA samples.
Collapse
Affiliation(s)
- Viola Grugni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Raveane
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Giulia Colombo
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Carmen Nici
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Francesca Crobu
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche (CNR), 09042 Monserrato, Italy
| | - Linda Ongaro
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Estonian Biocentre, Institute of Genomics, Riia 23, 51010 Tartu, Estonia
- Department of Evolutionary Biology, Institute of Molecular and Cell Biology, Riia 23, 51010 Tartu, Estonia
| | - Vincenza Battaglia
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Daria Sanna
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
- Dipartimento di Scienze Biomediche, Università di Sassari, 07100 Sassari, Italy
| | - Nadia Al-Zahery
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Fiorani
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Antonella Lisa
- Istituto di Genetica Molecolare “L.L. Cavalli-Sforza”, Consiglio Nazionale delle Ricerche (CNR), 27100 Pavia, Italy; (O.F.); (A.L.)
| | - Luca Ferretti
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Paolo Francalacci
- Dipartimento di Scienza della Vita e dell’Ambiente, Università di Cagliari, 09123 Cagliari, Italy;
| | - Alberto Piazza
- Dipartimento di Scienze Mediche, Scuola di Medicina, Università di Torino, 10124 Torino, Italy;
| | - Antonio Torroni
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| | - Ornella Semino
- Dipartimento di Biologia e Biotecnologie “L. Spallanzani”, Università di Pavia, 27100 Pavia, Italy; (V.G.); (A.R.); (G.C.); (C.N.); (F.C.); (L.O.); (V.B.); (D.S.); (N.A.-Z.); (L.F.); (A.A.); (A.O.); (A.T.)
| |
Collapse
|
14
|
Infant funerary behavior and kinship in Pleistocene hunter-gatherers from Morocco. J Hum Evol 2019; 135:102637. [DOI: 10.1016/j.jhevol.2019.07.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 07/02/2019] [Accepted: 07/03/2019] [Indexed: 11/21/2022]
|
15
|
Fischer CE, Lefort A, Pemonge MH, Couture-Veschambre C, Rottier S, Deguilloux MF. The multiple maternal legacy of the Late Iron Age group of Urville-Nacqueville (France, Normandy) documents a long-standing genetic contact zone in northwestern France. PLoS One 2018; 13:e0207459. [PMID: 30521562 PMCID: PMC6283558 DOI: 10.1371/journal.pone.0207459] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2018] [Accepted: 10/31/2018] [Indexed: 11/18/2022] Open
Abstract
The compilation of archaeological and genetic data for ancient European human groups has provided persuasive evidence for a complex series of migrations, population replacements and admixture until the Bronze Age. If the Bronze-to-Iron Age transition has been well documented archaeologically, ancient DNA (aDNA) remains rare for the latter period and does not precisely reflect the genetic diversity of European Celtic groups. In order to document the evolution of European communities, we analysed 45 individuals from the Late Iron Age (La Tène) Urville-Nacqueville necropolis in northwestern France, a region recognized as a major cultural contact zone between groups from both sides of the Channel. The characterization of 37 HVS-I mitochondrial sequences and 40 haplogroups provided the largest maternal gene pool yet recovered for the European Iron Age. First, descriptive analyses allowed us to demonstrate the presence of substantial amounts of steppe-related mitochondrial ancestry in the community, which is consistent with the expansion of Bell Beaker groups bearing an important steppe legacy in northwestern Europe at approximately 2500 BC. Second, maternal genetic affinities highlighted with Bronze Age groups from Great Britain and the Iberian Peninsula regions tends to support the idea that the continuous cultural exchanges documented archaeologically across the Channel and along the Atlantic coast (during and after the Bronze Age period) were accompanied by significant gene flow. Lastly, our results suggest a maternal genetic continuity between Bronze Age and Iron Age groups that would argue in favour of a cultural transition linked to progressive local economic changes rather than to a massive influx of allochthone groups. The palaeogenetic data gathered for the Urville-Nacqueville group constitute an important step in the biological characterization of European Iron age groups. Clearly, more numerous and diachronic aDNA data are needed to fully understand the complex relationship between the cultural and biological evolution of groups from the period.
Collapse
Affiliation(s)
- Claire-Elise Fischer
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
- * E-mail:
| | - Anthony Lefort
- Inrap Grand-Ouest, Boulevard de l’Europe, Bourguébus, France
| | - Marie-Hélène Pemonge
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
| | - Christine Couture-Veschambre
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
| | - Stéphane Rottier
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
| | - Marie-France Deguilloux
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie–UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac Cedex, France
| |
Collapse
|
16
|
Hendy J, Colonese AC, Franz I, Fernandes R, Fischer R, Orton D, Lucquin A, Spindler L, Anvari J, Stroud E, Biehl PF, Speller C, Boivin N, Mackie M, Jersie-Christensen RR, Olsen JV, Collins MJ, Craig OE, Rosenstock E. Ancient proteins from ceramic vessels at Çatalhöyük West reveal the hidden cuisine of early farmers. Nat Commun 2018; 9:4064. [PMID: 30283003 PMCID: PMC6170438 DOI: 10.1038/s41467-018-06335-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 08/28/2018] [Indexed: 02/08/2023] Open
Abstract
The analysis of lipids (fats, oils and waxes) absorbed within archaeological pottery has revolutionized the study of past diets and culinary practices. However, this technique can lack taxonomic and tissue specificity and is often unable to disentangle signatures resulting from the mixing of different food products. Here, we extract ancient proteins from ceramic vessels from the West Mound of the key early farming site of Çatalhöyük in Anatolia, revealing that this community processed mixes of cereals, pulses, dairy and meat products, and that particular vessels may have been reserved for specialized foods (e.g., cow milk and milk whey). Moreover, we demonstrate that dietary proteins can persist on archaeological artefacts for at least 8000 years, and that this approach can reveal past culinary practices with more taxonomic and tissue-specific clarity than has been possible with previous biomolecular techniques.
Collapse
Affiliation(s)
- Jessica Hendy
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.
| | - Andre C Colonese
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Ingmar Franz
- Institute of Prehistoric and Protohistoric Archaeology, Christian-Albrechts-Universität zu Kiel, D-24098, Kiel, Germany
| | - Ricardo Fernandes
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,School of Archaeology, University of Oxford, Oxford, OX1 2PG, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford, OX3 7FZ, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Alexandre Lucquin
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Luke Spindler
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,Oxford Radiocarbon Accelerator Unit, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK
| | - Jana Anvari
- Institute of Prehistoric Archaeology, Freie Universität Berlin, 14195, Berlin, Germany
| | - Elizabeth Stroud
- School of Archaeology, University of Oxford, Oxford, OX1 2PG, UK
| | - Peter F Biehl
- Department of Anthropology, University at Buffalo, Buffalo, NY, 14261-0026, USA
| | - Camilla Speller
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,Department of Anthropology, The University of British Columbia, Vancouver, BC, V6T 1Z1, Canada
| | - Nicole Boivin
- Department of Archaeology, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Meaghan Mackie
- EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Rosa R Jersie-Christensen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Jesper V Olsen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, 2200, Copenhagen, Denmark
| | - Matthew J Collins
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.,EvoGenomics, Natural History Museum of Denmark, University of Copenhagen, 2100, Copenhagen, Denmark
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5DD, UK.
| | - Eva Rosenstock
- Institute of Prehistoric Archaeology, Freie Universität Berlin, 14195, Berlin, Germany.
| |
Collapse
|
17
|
Hollard C, Zvénigorosky V, Kovalev A, Kiryushin Y, Tishkin A, Lazaretov I, Crubézy E, Ludes B, Keyser C. New genetic evidence of affinities and discontinuities between bronze age Siberian populations. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 167:97-107. [PMID: 29900529 DOI: 10.1002/ajpa.23607] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2017] [Revised: 04/10/2018] [Accepted: 04/26/2018] [Indexed: 11/12/2022]
Abstract
OBJECTIVES This work focuses on the populations of South Siberia during the Eneolithic and Bronze Age and specifically on the contribution of uniparental lineage and phenotypical data to the question of the genetic affinities and discontinuities between western and eastern populations. MATERIALS AND METHODS We performed molecular analyses on the remains of 28 ancient humans (10 Afanasievo (3600-2500 BC) and 18 Okunevo (2500-1800 BC) individuals). For each sample, two uniparentally inherited systems (mitochondrial DNA and Y-chromosome DNA) were studied, in order to trace back maternal and paternal lineages. Phenotype-informative SNPs (Single Nucleotide Polymorphisms) were also analyzed, along with autosomal STRs (Short Tandem Repeats). RESULTS Most of the Afanasievo men submitted to analysis belonged to a single sub-haplogroup, R1b1a1a, which reveals the predominance of this haplogroup in these early Bronze Age populations. Conversely, Okunevo individuals carried more diverse paternal lineages that mostly belonged to Asian/Siberian haplogroups. These differences are also apparent, although less strongly, in mitochondrial lineage composition and phenotype marker variant frequencies. DISCUSSION This study provides new elements that contribute to our understanding of the genetic interactions between populations in Eneolithic and Bronze Age southern Siberia. Our results support the hypothesis of a genetic link between Afanasievo and Yamnaya (in western Eurasia), as suggested by previous studies of other markers. However, we found no Y-chromosome lineage evidence of a possible Afanasievo migration to the Tarim Basin. Moreover, the presence of Y-haplogroup Q in Okunevo individuals links them to Native American populations, as was suggested by whole-genome sequencing.
Collapse
Affiliation(s)
- Clémence Hollard
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France
| | - Vincent Zvénigorosky
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France.,Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France
| | - Alexey Kovalev
- Institute of Archaeology, Russian Academy of Sciences, Moscow, Russia
| | - Yurii Kiryushin
- The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Alexey Tishkin
- The Laboratory of Interdisciplinary Studies in Archaeology of Western Siberia and Altai, Department of Archaeology, Ethnography and Museology, Altai State University, Barnaul, Russia
| | - Igor Lazaretov
- Institute of the History of Material Culture, Russian Academy of Sciences, St. Petersburg, Russia
| | - Eric Crubézy
- Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France
| | - Bertrand Ludes
- Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France.,Institut Médico-légal de Paris, Paris, France.,Université Paris Descartes, Paris, France
| | - Christine Keyser
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France.,Laboratoire AMIS, CNRS UMR 5288, Université de Toulouse, Toulouse, France
| |
Collapse
|
18
|
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: 37] [Impact Index Per Article: 6.2] [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.
Collapse
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
| |
Collapse
|
19
|
Yaka R, Birand A, Yılmaz Y, Caner C, Açan SC, Gündüzalp S, Parvizi P, Erim Özdoğan A, Togan İ, Somel M. Archaeogenetics of Late Iron Age Çemialo Sırtı, Batman: Investigating maternal genetic continuity in north Mesopotamia since the Neolithic. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2018; 166:196-207. [PMID: 29399779 DOI: 10.1002/ajpa.23423] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 12/13/2017] [Accepted: 01/12/2018] [Indexed: 01/25/2023]
Abstract
OBJECTIVES North Mesopotamia has witnessed dramatic social change during the Holocene, but the impact of these events on its demographic history is poorly understood. Here, we study this question by analysing genetic data from the recently excavated Late Iron Age settlement of Çemialo Sırtı in Batman, southeast Turkey. Archaeological and radiocarbon evidence indicate that the site was inhabited during the second and first millennia BCE. Çemialo Sırtı reveals nomadic items of the Early Iron Age, as well as items associated with the Late Achaemenid and subsequent Hellenistic Periods. We compare Çemialo Sırtı mitochondrial DNA profiles with earlier and later populations from west Eurasia to describe genetic continuity patterns in the region. MATERIALS AND METHODS A total of 16 Çemialo Sırtı individuals' remains were studied. PCR and Sanger sequencing were used to obtain mitochondrial DNA HVRI-HVRII sequences. We studied haplotype diversity and pairwise genetic distances using FST , comparing the Çemialo Sırtı population with ancient and modern-day populations from west Eurasia. Coalescent simulations were carried out to test continuity for specific population comparisons. RESULTS Mitochondrial DNA (mtDNA) haplotypes from 12 Çemialo Sırtı individuals reveal high haplotype diversity in this population, conspicuously higher than early Holocene west Eurasian populations, which supports the notion of increasing population admixture in west Eurasia through the Holocene. In its mtDNA composition, Çemialo Sırtı shows highest affinity to Neolithic north Syria and Neolithic Anatolia among ancient populations studied, and to modern-day southwest Asian populations. Based on population genetic simulations we cannot reject continuity between Neolithic and Iron Age, or between Iron Age and present-day populations of the region. DISCUSSION Despite the region's complex sociopolitical history and indication for increased genetic diversity over time, we find no evidence for sharp shifts in north Mesopotamian maternal genetic composition within the last 10,000 years.
Collapse
Affiliation(s)
- Reyhan Yaka
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Ayşegül Birand
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Yasemin Yılmaz
- Department of Archaeology, Düzce University, Düzce, Turkey
| | - Ceren Caner
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sinan Can Açan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Sidar Gündüzalp
- Department of Prehistory, İstanbul University, İstanbul, Turkey
| | - Poorya Parvizi
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Aslı Erim Özdoğan
- Department of Archaeology, Çanakkale Onsekiz Mart University, Çanakkale, Turkey
| | - İnci Togan
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| | - Mehmet Somel
- Department of Biological Sciences, Middle East Technical University, Ankara, Turkey
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
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]
|
22
|
Tassi F, Vai S, Ghirotto S, Lari M, Modi A, Pilli E, Brunelli A, Susca RR, Budnik A, Labuda D, Alberti F, Lalueza-Fox C, Reich D, Caramelli D, Barbujani G. Genome diversity in the Neolithic Globular Amphorae culture and the spread of Indo-European languages. Proc Biol Sci 2017; 284:20171540. [PMID: 29167359 PMCID: PMC5719168 DOI: 10.1098/rspb.2017.1540] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 10/23/2017] [Indexed: 12/31/2022] Open
Abstract
It is unclear whether Indo-European languages in Europe spread from the Pontic steppes in the late Neolithic, or from Anatolia in the Early Neolithic. Under the former hypothesis, people of the Globular Amphorae culture (GAC) would be descended from Eastern ancestors, likely representing the Yamnaya culture. However, nuclear (six individuals typed for 597 573 SNPs) and mitochondrial (11 complete sequences) DNA from the GAC appear closer to those of earlier Neolithic groups than to the DNA of all other populations related to the Pontic steppe migration. Explicit comparisons of alternative demographic models via approximate Bayesian computation confirmed this pattern. These results are not in contrast to Late Neolithic gene flow from the Pontic steppes into Central Europe. However, they add nuance to this model, showing that the eastern affinities of the GAC in the archaeological record reflect cultural influences from other groups from the East, rather than the movement of people.
Collapse
Affiliation(s)
- Francesca Tassi
- Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy
| | - Stefania Vai
- Department of Biology, University of Firenze, Firenze, Italy
| | - Silvia Ghirotto
- Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy
| | - Martina Lari
- Department of Biology, University of Firenze, Firenze, Italy
| | - Alessandra Modi
- Department of Biology, University of Firenze, Firenze, Italy
| | - Elena Pilli
- Department of Biology, University of Firenze, Firenze, Italy
| | - Andrea Brunelli
- Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy
| | - Roberta Rosa Susca
- Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy
| | - Alicja Budnik
- Department of Human Biology, Cardinal Stefan Wyszyński University, Warsaw, Poland
| | - Damian Labuda
- CHU Sainte-Justine Research Center, Department of Pediatrics, Université de Montréal, Montréal, PQ, Canada H3T 1C5
| | - Federica Alberti
- Department of Evolutionary Biology, Institute for Biochemistry and Biology, Potsdam University, Potsdam, Germany
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, University Pompeu Fabra, Barcelona, Spain
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
| | - David Caramelli
- Department of Biology, University of Firenze, Firenze, Italy
| | - Guido Barbujani
- Department of Life Sciences and Biotechnology, University of Firenze, Firenze, Italy
| |
Collapse
|
23
|
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.
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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;,
| |
Collapse
|
26
|
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.
Collapse
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.
| |
Collapse
|
27
|
Beau A, Rivollat M, Réveillas H, Pemonge MH, Mendisco F, Thomas Y, Lefranc P, Deguilloux MF. Multi-scale ancient DNA analyses confirm the western origin of Michelsberg farmers and document probable practices of human sacrifice. PLoS One 2017; 12:e0179742. [PMID: 28678860 PMCID: PMC5497962 DOI: 10.1371/journal.pone.0179742] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2017] [Accepted: 06/02/2017] [Indexed: 02/05/2023] Open
Abstract
In Europe, the Middle Neolithic is characterized by an important diversification of cultures. In northeastern France, the appearance of the Michelsberg culture has been correlated with major cultural changes and interpreted as the result of the settlement of new groups originating from the Paris Basin. This cultural transition has been accompanied by the expansion of particular funerary practices involving inhumations within circular pits and individuals in “non-conventional” positions (deposited in the pits without any particular treatment). If the status of such individuals has been highly debated, the sacrifice hypothesis has been retained for the site of Gougenheim (Alsace). At the regional level, the analysis of the Gougenheim mitochondrial gene pool (SNPs and HVR-I sequence analyses) permitted us to highlight a major genetic break associated with the emergence of the Michelsberg in the region. This genetic discontinuity appeared to be linked to new affinities with farmers from the Paris Basin, correlated to a noticeable hunter-gatherer legacy. All of the evidence gathered supports (i) the occidental origin of the Michelsberg groups and (ii) the potential implication of this migration in the progression of the hunter-gatherer legacy from the Paris Basin to Alsace / Western Germany at the beginning of the Late Neolithic. At the local level, we noted some differences in the maternal gene pool of individuals in "conventional" vs. "non-conventional" positions. The relative genetic isolation of these sub-groups nicely echoes both their social distinction and the hypothesis of sacrifices retained for the site. Our investigation demonstrates that a multi-scale aDNA study of ancient communities offers a unique opportunity to disentangle the complex relationships between cultural and biological evolution.
Collapse
Affiliation(s)
- Alice Beau
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie—UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France
| | - Maïté Rivollat
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie—UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France
- * E-mail: (MR); (PL)
| | - Hélène Réveillas
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie—UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France
- Centre d’Archéologie Préventive de Bordeaux Métropole, Direction des Bâtiments et Moyens, Esplanade Charles-de-Gaulle, Bordeaux cedex, France
- Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d’Altkirch, Strasbourg, France
| | - Marie-Hélène Pemonge
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie—UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France
| | - Fanny Mendisco
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie—UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France
| | - Yohann Thomas
- Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d’Altkirch, Strasbourg, France
| | - Philippe Lefranc
- Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d’Altkirch, Strasbourg, France
- Archéologie et Histoire Ancienne: Méditerranée/Europe–UMR 7044, Université de Strasbourg, Maison Interuniversitaire des Sciences de l’Homme d’Alsace, 5 Allée du Général Rouvillois, CS, Strasbourg cedex, France
- * E-mail: (MR); (PL)
| | - Marie-France Deguilloux
- De la Préhistoire à l’Actuel, Culture, Environnement, Anthropologie—UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS, Pessac cedex, France
| |
Collapse
|
28
|
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: 25] [Impact Index Per Article: 3.6] [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.
Collapse
|
29
|
Brzobohatá K, Drozdová E, Smutný J, Zeman T, Beňuš R. Comparison of Suitability of the Most Common Ancient DNA Quantification Methods. Genet Test Mol Biomarkers 2017; 21:265-271. [DOI: 10.1089/gtmb.2016.0197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Kristýna Brzobohatá
- Laboratory of Biological and Molecular Anthropology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Eva Drozdová
- Laboratory of Biological and Molecular Anthropology, Institute of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Jiří Smutný
- Biovendor, Laboratory Medicine, Brno, Czech Republic
| | - Tomáš Zeman
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Radoslav Beňuš
- Department of Anthropology, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| |
Collapse
|
30
|
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.
Collapse
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
| |
Collapse
|
31
|
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).
Collapse
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
| |
Collapse
|
32
|
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]
|
33
|
Messina F, Finocchio A, Akar N, Loutradis A, Michalodimitrakis EI, Brdicka R, Jodice C, Novelletto A. Spatially Explicit Models to Investigate Geographic Patterns in the Distribution of Forensic STRs: Application to the North-Eastern Mediterranean. PLoS One 2016; 11:e0167065. [PMID: 27898725 PMCID: PMC5127579 DOI: 10.1371/journal.pone.0167065] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 11/08/2016] [Indexed: 11/18/2022] Open
Abstract
Human forensic STRs used for individual identification have been reported to have little power for inter-population analyses. Several methods have been developed which incorporate information on the spatial distribution of individuals to arrive at a description of the arrangement of diversity. We genotyped at 16 forensic STRs a large population sample obtained from many locations in Italy, Greece and Turkey, i.e. three countries crucial to the understanding of discontinuities at the European/Asian junction and the genetic legacy of ancient migrations, but seldom represented together in previous studies. Using spatial PCA on the full dataset, we detected patterns of population affinities in the area. Additionally, we devised objective criteria to reduce the overall complexity into reduced datasets. Independent spatially explicit methods applied to these latter datasets converged in showing that the extraction of information on long- to medium-range geographical trends and structuring from the overall diversity is possible. All analyses returned the picture of a background clinal variation, with regional discontinuities captured by each of the reduced datasets. Several aspects of our results are confirmed on external STR datasets and replicate those of genome-wide SNP typings. High levels of gene flow were inferred within the main continental areas by coalescent simulations. These results are promising from a microevolutionary perspective, in view of the fast pace at which forensic data are being accumulated for many locales. It is foreseeable that this will allow the exploitation of an invaluable genotypic resource, assembled for other (forensic) purposes, to clarify important aspects in the formation of local gene pools.
Collapse
Affiliation(s)
| | | | - Nejat Akar
- Pediatrics Department, TOBB-Economy and Technology University Hospital, Ankara, Turkey
| | | | | | - Radim Brdicka
- Institute of Haematology and Blood Transfusion, Praha, Czech Republic
| | - Carla Jodice
- Department of Biology, University "Tor Vergata", Rome, Italy
| | - Andrea Novelletto
- Department of Biology, University "Tor Vergata", Rome, Italy
- * E-mail:
| |
Collapse
|
34
|
Zvénigorosky V, Crubézy E, Gibert M, Thèves C, Hollard C, Gonzalez A, Fedorova SA, Alexeev AN, Bravina RI, Ludes B, Keyser C. The genetics of kinship in remote human groups. Forensic Sci Int Genet 2016; 25:52-62. [DOI: 10.1016/j.fsigen.2016.07.018] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Revised: 07/05/2016] [Accepted: 07/27/2016] [Indexed: 11/24/2022]
|
35
|
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.
Collapse
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
| |
Collapse
|
36
|
Rivollat M, Réveillas H, Mendisco F, Pemonge MH, Justeau P, Couture C, Lefranc P, Féliu C, Deguilloux MF. Ancient mitochondrial DNA from the middle neolithic necropolis of Obernai extends the genetic influence of the LBK to west of the Rhine. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 161:522-529. [PMID: 27447353 DOI: 10.1002/ajpa.23055] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2016] [Revised: 07/04/2016] [Accepted: 07/06/2016] [Indexed: 11/10/2022]
Abstract
OBJECTIVES The arrival of Neolithic farmers in Europe was the source of major cultural and genetic transitions. Neolithic settlers brought a new set of maternal lineages (mitochondrial DNA), recently well-characterized on the continental road, from the Balkans to West Germany (Rhine River). In the present study, the first mitochondrial DNA data from groups associated with this continental expansion wave located west of the Rhine River has been provided and their genetic affinities with contemporary groups have been discussed. MATERIAL AND METHODS The mitochondrial DNA analysis of 27 human remains originating from Obernai (5,000-4,400 cal. BC), a necropolis located in French Alsace Region and attributed to Grossgartach, Planig-Friedberg, and Roessen cultures was conducted. RESULTS AND DISCUSSION Among the 27 individuals studied, 15 HVR-I sequences and 17 mitochondrial haplogroups could be determined. The analysis of the Obernai gene pool clearly confirmed the genetic homogeneity of Linearbandkeramik (LBK) groups on both sides of the Rhine River. Notably, one N1a sequence found in Obernai is shared with LBK farmers from Central Europe, including one individual from the Flomborn site located approximately 200 km north-east of Obernai. On the whole, data gathered so far showed major genetic influence of the Danubian wave from Transdanubia to Atlantic French Coast, going by Alsace Region. However, the genetic influence of descendants from the Mediterranean Neolithic expansion and the significant hunter-gatherer admixture detected further west in the Paris Basin were not perceived in the Obernai necropolis. CONCLUSIONS Genetic homogeneity and continuity within LBK groups can be proposed on both sides of the Rhine River for the middle Neolithic groups. Nevertheless, mitochondrial data gathered so far for Neolithic groups from the entire extant French Territory clearly point out the complexity and the variability of Neolithic communities interactions that is worthy of further investigation.
Collapse
Affiliation(s)
- Maïté Rivollat
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France. ,
| | - Hélène Réveillas
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France.,Centre d'Archéologie Préventive de Bordeaux Métropole, direction des Bâtiments et Moyens, Esplanade Charles-de-Gaulle, Bordeaux Cedex, 33 076, France.,Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, 67000, France
| | - Fanny Mendisco
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France
| | - Marie-Hélène Pemonge
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France
| | - Pierre Justeau
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France
| | - Christine Couture
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France
| | - Philippe Lefranc
- Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, 67000, France.,Archéologie et Histoire Ancienne: Méditerranée/Europe - UMR 7044, Université de Strasbourg, Maison Interuniversitaire des Sciences de l'Homme d'Alsace, 5 allée du Général Rouvillois, CS 50008, Strasbourg Cedex, 67083, France
| | - Clément Féliu
- Institut National de Recherche en Archéologie Préventive, Centre Archéologique de Strasbourg, 10 rue d'Altkirch, Strasbourg, 67000, France.,Archéologie et Histoire Ancienne: Méditerranée/Europe - UMR 7044, Université de Strasbourg, Maison Interuniversitaire des Sciences de l'Homme d'Alsace, 5 allée du Général Rouvillois, CS 50008, Strasbourg Cedex, 67083, France
| | - Marie-France Deguilloux
- De la Préhistoire à l'Actuel, Culture, Environnement, Anthropologie - UMR 5199, CNRS, Université de Bordeaux, Allée Geoffroy Saint-Hilaire, CS 50023, Pessac Cedex, 33615, France
| |
Collapse
|
37
|
Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
Collapse
Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| |
Collapse
|
38
|
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.
Collapse
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
| |
Collapse
|
39
|
Early farmers from across Europe directly descended from Neolithic Aegeans. Proc Natl Acad Sci U S A 2016; 113:6886-91. [PMID: 27274049 DOI: 10.1073/pnas.1523951113] [Citation(s) in RCA: 222] [Impact Index Per Article: 27.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Farming and sedentism first appeared in southwestern Asia during the early Holocene and later spread to neighboring regions, including Europe, along multiple dispersal routes. Conspicuous uncertainties remain about the relative roles of migration, cultural diffusion, and admixture with local foragers in the early Neolithization of Europe. Here we present paleogenomic data for five Neolithic individuals from northern Greece and northwestern Turkey spanning the time and region of the earliest spread of farming into Europe. We use a novel approach to recalibrate raw reads and call genotypes from ancient DNA and observe striking genetic similarity both among Aegean early farmers and with those from across Europe. Our study demonstrates a direct genetic link between Mediterranean and Central European early farmers and those of Greece and Anatolia, extending the European Neolithic migratory chain all the way back to southwestern Asia.
Collapse
|
40
|
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.
Collapse
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
| |
Collapse
|
41
|
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.
Collapse
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
| | | | | | | |
Collapse
|
42
|
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.
Collapse
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
| |
Collapse
|
43
|
|
44
|
Neolithic and Bronze Age migration to Ireland and establishment of the insular Atlantic genome. Proc Natl Acad Sci U S A 2015; 113:368-73. [PMID: 26712024 DOI: 10.1073/pnas.1518445113] [Citation(s) in RCA: 118] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The Neolithic and Bronze Age transitions were profound cultural shifts catalyzed in parts of Europe by migrations, first of early farmers from the Near East and then Bronze Age herders from the Pontic Steppe. However, a decades-long, unresolved controversy is whether population change or cultural adoption occurred at the Atlantic edge, within the British Isles. We address this issue by using the first whole genome data from prehistoric Irish individuals. A Neolithic woman (3343-3020 cal BC) from a megalithic burial (10.3× coverage) possessed a genome of predominantly Near Eastern origin. She had some hunter-gatherer ancestry but belonged to a population of large effective size, suggesting a substantial influx of early farmers to the island. Three Bronze Age individuals from Rathlin Island (2026-1534 cal BC), including one high coverage (10.5×) genome, showed substantial Steppe genetic heritage indicating that the European population upheavals of the third millennium manifested all of the way from southern Siberia to the western ocean. This turnover invites the possibility of accompanying introduction of Indo-European, perhaps early Celtic, language. Irish Bronze Age haplotypic similarity is strongest within modern Irish, Scottish, and Welsh populations, and several important genetic variants that today show maximal or very high frequencies in Ireland appear at this horizon. These include those coding for lactase persistence, blue eye color, Y chromosome R1b haplotypes, and the hemochromatosis C282Y allele; to our knowledge, the first detection of a known Mendelian disease variant in prehistory. These findings together suggest the establishment of central attributes of the Irish genome 4,000 y ago.
Collapse
|
45
|
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.
Collapse
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
| |
Collapse
|
46
|
|
47
|
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.
Collapse
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
| |
Collapse
|
48
|
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.
Collapse
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
| |
Collapse
|
49
|
Zupan A, Hauptman N, Glavač D. The maternal perspective for five Slovenian regions: The importance of regional sampling. Ann Hum Biol 2015; 43:57-66. [PMID: 26065896 DOI: 10.3109/03014460.2015.1006678] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
BACKGROUND The Slovenian territory is geographically positioned between the Alps, Adriatic Sea, Pannonian basin and the Dinaric Mountains and, as such, has served as a passageway for various populations in different periods of time. Turbulent historic events and diverse geography of the region have produced a diverse contemporary population whose genetic analysis could provide insight into past demographic events. AIM The aims of this study were to characterize the Slovenian mitochondrial gene pool at the micro-geographic level and to compare it with surrounding populations. SUBJECTS AND METHODS A total of 402 individuals from five Slovenian regions were analysed in this study by typing HVR I, HVR II and coding region polymorphisms of mtDNA. RESULTS Analysis revealed 47 haplogroups and sub-haplogroups, the most common of which were H*, H1, J1c, T2 and U5a. Intra-population comparisons revealed a sharp gradient of the J1c haplogroup between Slovenian regions, with a peak frequency of 24.5% being observed in the population of the Littoral Region. CONCLUSION The sharp gradient of the J1c haplogroup between Slovenian regions is in line with the archaeological horizon known as Impressed Ware culture and could, therefore, represent a genetic trace of the early Neolithic expansion route along the East Adriatic coastal region.
Collapse
Affiliation(s)
- Andrej Zupan
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Nina Hauptman
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| | - Damjan Glavač
- a Department of Molecular Genetics , Institute of Pathology, Faculty of Medicine, University of Ljubljana , Ljubljana , Slovenia
| |
Collapse
|
50
|
Hervella M, Rotea M, Izagirre N, Constantinescu M, Alonso S, Ioana M, Lazăr C, Ridiche F, Soficaru AD, Netea MG, de-la-Rua C. Ancient DNA from South-East Europe Reveals Different Events during Early and Middle Neolithic Influencing the European Genetic Heritage. PLoS One 2015; 10:e0128810. [PMID: 26053041 PMCID: PMC4460020 DOI: 10.1371/journal.pone.0128810] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 04/30/2015] [Indexed: 01/26/2023] Open
Abstract
The importance of the process of Neolithization for the genetic make-up of European populations has been hotly debated, with shifting hypotheses from a demic diffusion (DD) to a cultural diffusion (CD) model. In this regard, ancient DNA data from the Balkan Peninsula, which is an important source of information to assess the process of Neolithization in Europe, is however missing. In the present study we show genetic information on ancient populations of the South-East of Europe. We assessed mtDNA from ten sites from the current territory of Romania, spanning a time-period from the Early Neolithic to the Late Bronze Age. mtDNA data from Early Neolithic farmers of the Starčevo Criş culture in Romania (Cârcea, Gura Baciului and Negrileşti sites), confirm their genetic relationship with those of the LBK culture (Linienbandkeramik Kultur) in Central Europe, and they show little genetic continuity with modern European populations. On the other hand, populations of the Middle-Late Neolithic (Boian, Zau and Gumelniţa cultures), supposedly a second wave of Neolithic migration from Anatolia, had a much stronger effect on the genetic heritage of the European populations. In contrast, we find a smaller contribution of Late Bronze Age migrations to the genetic composition of Europeans. Based on these findings, we propose that permeation of mtDNA lineages from a second wave of Middle-Late Neolithic migration from North-West Anatolia into the Balkan Peninsula and Central Europe represent an important contribution to the genetic shift between Early and Late Neolithic populations in Europe, and consequently to the genetic make-up of modern European populations.
Collapse
Affiliation(s)
- Montserrat Hervella
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain
| | - Mihai Rotea
- National History Museum of Transylvania, Cluj-Napoca, Romania
| | - Neskuts Izagirre
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain
| | - Mihai Constantinescu
- “Francisc I. Rainer" Institute of Anthropology, Romanian Academy, Bucharest, Romania
| | - Santos Alonso
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain
| | - Mihai Ioana
- Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
| | - Cătălin Lazăr
- National History Museum of Romania, Bucharest, Romania
| | | | | | - Mihai G. Netea
- Department of Medicine, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- Radboud Center for Infectious Diseases, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
- * E-mail: (CR); (MN)
| | - Concepcion de-la-Rua
- Department of Genetics, Physical Anthropology and Animal Physiology, University of the Basque Country UPV/EHU, Bizkaia, Spain
- * E-mail: (CR); (MN)
| |
Collapse
|