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Bergfeldt N, Kırdök E, Oskolkov N, Mirabello C, Unneberg P, Malmström H, Fraser M, Sanchez-Quinto F, Jorgensen R, Skar B, Lidén K, Jakobsson M, Storå J, Götherström A. Identification of microbial pathogens in Neolithic Scandinavian humans. Sci Rep 2024; 14:5630. [PMID: 38453993 PMCID: PMC10920878 DOI: 10.1038/s41598-024-56096-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 03/01/2024] [Indexed: 03/09/2024] Open
Abstract
With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.
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Affiliation(s)
- Nora Bergfeldt
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden.
- Department of Zoology, Stockholm University, Stockholm, Sweden.
- Department of Bioinformatics and Genetics, Swedish Museum of Natural History, Stockholm, Sweden.
| | - Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, Mersin, Turkey
| | - Nikolay Oskolkov
- Science for Life Laboratory, Department of Biology, National Bioinformatics Infrastructure Sweden, Lund University, Lund, Sweden
| | - Claudio Mirabello
- Science for Life Laboratory, Department of Physics, Chemistry and Biology, National Bioinformatics Infrastructure Sweden, Linköping University, Linköping, Sweden
| | - Per Unneberg
- Science for Life Laboratory, Department of Cell and Molecular Biology, National Bioinformatics Infrastructure Sweden, Uppsala University, Uppsala, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Magdalena Fraser
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | | | - Roger Jorgensen
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Birgitte Skar
- Department of Archaeology and Cultural History, NTNU University Museum, Trondheim, Norway
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organism Biology, Uppsala University, Uppsala, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
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2
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Ginja C, Guimarães S, da Fonseca RR, Rasteiro R, Rodríguez-Varela R, Simões LG, Sarmento C, Belarte MC, Kallala N, Torres JR, Sanmartí J, Arruda AM, Detry C, Davis S, Matos J, Götherström A, Pires AE, Valenzuela-Lamas S. Iron age genomic data from Althiburos - Tunisia renew the debate on the origins of African taurine cattle. iScience 2023; 26:107196. [PMID: 37485357 PMCID: PMC10359934 DOI: 10.1016/j.isci.2023.107196] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2022] [Revised: 12/22/2022] [Accepted: 06/20/2023] [Indexed: 07/25/2023] Open
Abstract
The Maghreb is a key region for understanding the dynamics of cattle dispersal and admixture with local aurochs following their earliest domestication in the Fertile Crescent more than 10,000 years ago. Here, we present data on autosomal genomes and mitogenomes obtained for four archaeological specimens of Iron Age (∼2,800 cal BP-2,000 cal BP) domestic cattle from the Eastern Maghreb, i.e. Althiburos (El Kef, Tunisia). D-loop sequences were obtained for an additional eight cattle specimens from this site. Maternal lineages were assigned to the elusive R and ubiquitous African-T1 haplogroups found in two and ten Althiburos specimens, respectively. Our results can be explained by post-domestication hybridization of Althiburos cattle with local aurochs. However, we cannot rule out an independent domestication in North Africa considering the shared ancestry of Althiburos cattle with the pre-domestic Moroccan aurochs and present-day African taurine cattle.
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Affiliation(s)
- Catarina Ginja
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Silvia Guimarães
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Rute R. da Fonseca
- Center for Global Mountain Biodiversity, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rita Rasteiro
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | | | - Luciana G. Simões
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Cindy Sarmento
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
| | - Maria Carme Belarte
- ICREA, Institut Català de Recerca i Estudis Avançats, Barcelona, Spain
- ICAC, Institut Català d'Arqueologia Clàssica, Tarragona, Spain
| | - Nabil Kallala
- INP, Institut National du Patrimoine, Tunis, Tunisia
- Faculté des Sciences Humaines et Sociales, Université de Tunis, Tunis, Tunisia
| | | | - Joan Sanmartí
- In memoriam, Departament de Prehistòria, Història Antiga i Arqueologia, Universitat de Barcelona, Barcelona, Spain
| | - Ana Margarida Arruda
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Cleia Detry
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
| | - Simon Davis
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- LARC/DGPC, Laboratório de Arqueociências, Direcção Geral do Património Cultural, Lisboa, Portugal
| | - José Matos
- Unidade Estratégica de Investigação e Serviços de Biotecnologia e Recursos Genéticos, Instituto Nacional de Investigação Agrária e Veterinária, I.P, Oeiras, Portugal
- CE3C, Centro de Ecologia, Evolução e Alterações Ambientais, Universidade de Lisboa, Lisboa, Portugal
| | | | - Ana Elisabete Pires
- BIOPOLIS-CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos - ArchGen group, Universidade do Porto, Vairão, Portugal
- Faculdade de Medicina Veterinária, Universidade Lusófona, Lisboa, Portugal
| | - Silvia Valenzuela-Lamas
- UNIARQ, Centro de Arqueologia da Universidade de Lisboa, Faculdade de Letras da Universidade de Lisboa, Lisboa, Portugal
- Archaeology of Social Dynamics, Consejo Superior de Investigaciones Científicas-Institució Milà i Fontanals d'Humanitats (CSIC-IMF), Barcelona, Spain
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3
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Kristjansson D, Schurr TG, Bohlin J, Jugessur A. Phylogeographic history of mitochondrial haplogroup J in Scandinavia. AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY 2023; 180:298-315. [PMID: 36790764 PMCID: PMC10100211 DOI: 10.1002/ajpa.24666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 09/10/2022] [Accepted: 11/13/2022] [Indexed: 11/25/2022]
Abstract
BACKGROUND Mitochondrial DNA haplogroup J is the third most frequent haplogroup in modern-day Scandinavia, although it did not originate there. To infer the genetic history of haplogroup J in Scandinavia, we examined worldwide mitogenome sequences using a maximum-likelihood phylogenetic approach. METHODS Haplogroup J mitogenome sequences were gathered from GenBank (n = 2245) and aligned against the ancestral Reconstructed Sapiens Reference Sequence. We also analyzed haplogroup J Viking Age sequences from the European Nucleotide Archive (n = 54). Genetic distances were estimated from these data and projected onto a maximum likelihood rooted phylogenetic tree to analyze clustering and branching dates. RESULTS Haplogroup J originated approximately 42.6 kya (95% CI: 30.0-64.7), with several of its earliest branches being found within the Arabian Peninsula and Northern Africa. J1b was found most frequently in the Near East and Arabian Peninsula, while J1c occurred most frequently in Europe. Based on phylogenetic dating, subhaplogroup J1c has its early roots in the Mediterranean and Western Balkans. Otherwise, the majority of the branches found in Scandinavia are younger than those seen elsewhere, indicating that haplogroup J dispersed relatively recently into Northern Europe, most plausibly with Neolithic farmers. CONCLUSIONS Haplogroup J appeared when Scandinavia was transitioning to agriculture over 6 kya, with J1c being the most common lineage there today. Changes in the distribution of haplogroup J mtDNAs were likely driven by the expansion of farming from West Asia into Southern Europe, followed by a later expansion into Scandinavia, with other J subhaplogroups appearing among Scandinavian groups as early as the Viking Age.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Method Development and Analytics, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
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4
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Översti S, Palo JU. Variation in the substitution rates among the human mitochondrial haplogroup U sublineages. Genome Biol Evol 2022; 14:6613373. [PMID: 35731946 PMCID: PMC9250076 DOI: 10.1093/gbe/evac097] [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] [Accepted: 06/16/2022] [Indexed: 11/22/2022] Open
Abstract
Resolving the absolute timescale of phylogenetic trees stipulates reliable estimates for the rate of DNA sequence evolution. For this end, various calibration methods have been developed and studied intensively. Intraspecific rate variation among distinct genetic lineages, however, has gained less attention. Here, we have assessed lineage-specific molecular rates of human mitochondrial DNA (mtDNA) by performing tip-calibrated Bayesian phylogenetic analyses. Tip-calibration, as opposed to traditional nodal time stamps from dated fossil evidence or geological events, is based on sample ages and becoming ever more feasible as ancient DNA data from radiocarbon-dated samples accumulate. We focus on subhaplogroups U2, U4, U5a, and U5b, the data including ancient mtDNA genomes from 14C-dated samples (n = 234), contemporary genomes (n = 301), and two outgroup sequences from haplogroup R. The obtained molecular rates depended on the data sets (with or without contemporary sequences), suggesting time-dependency. More notable was the rate variation between haplogroups: U4 and U5a stand out having a substantially higher rate than U5b. This is also reflected in the divergence times obtained (U5a: 17,700 years and U5b: 29,700 years), a disparity not reported previously. After ruling out various alternative causes (e.g., selection, sampling, and sequence quality), we propose that the substitution rates have been influenced by demographic histories, widely different among populations where U4/U5a or U5b are frequent. As with the Y-chromosomal subhaplogroup R1b, the mitochondrial U4 and U5a have been associated with remarkable range extensions of the Yamnaya culture in the Bronze Age.
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Affiliation(s)
- Sanni Översti
- Transmission, Infection, Diversification and Evolution Group, Max-Planck Institute for the Science of Human History, Jena, Germany Kahlaische Straße 10, 07745, Jena, Germany.,Organismal and Evolutionary Biology Research Programme, Faculty of Biological Sciences, University of Helsinki, Helsinki, Finland P.O. Box 56, FI-00014, Helsinki, Finland
| | - Jukka U Palo
- Department of Forensic Medicine, Faculty of Medicine, University of Helsinki, Helsinki, Finland P.O. Box 40, FI-00014, Helsinki, Finland.,Forensic Chemistry Unit, Forensic Genetics Team, Finnish Institute for Health and Welfare, Helsinki, Finland P.O. Box 30, FI-00271, Helsinki, Finland
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5
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Juras A, Ehler E, Chyleński M, Pospieszny Ł, Spinek AE, Malmström H, Krzewińska M, Szostek K, Pasterkiewicz W, Florek M, Wilk S, Mnich B, Kruk J, Szmyt M, Kozieł S, Götherström A, Jakobsson M, Dabert M. Maternal genetic origin of the late and final Neolithic human populations from present-day Poland. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:223-236. [PMID: 34308549 DOI: 10.1002/ajpa.24372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 06/22/2021] [Accepted: 07/07/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE We aim to identify maternal genetic affinities between the Middle to Final Neolithic (3850-2300 BC) populations from present-day Poland and possible genetic influences from the Pontic steppe. MATERIALS AND METHODS We conducted ancient DNA studies from populations associated with Złota, Globular Amphora, Funnel Beaker, and Corded Ware cultures (CWC). We sequenced genomic libraries on Illumina platform to generate 86 complete ancient mitochondrial genomes. Some of the samples were enriched for mitochondrial DNA using hybridization capture. RESULTS The maternal genetic composition found in Złota-associated individuals resembled that found in people associated with the Globular Amphora culture which indicates that both groups likely originated from the same maternal genetic background. Further, these two groups were closely related to the Funnel Beaker culture-associated population. None of these groups shared a close affinity to CWC-associated people. Haplogroup U4 was present only in the CWC group and absent in Złota group, Globular Amphora, and Funnel Beaker cultures. DISCUSSION The prevalence of mitochondrial haplogroups of Neolithic farmer origin identified in Early, Middle and Late Neolithic populations suggests a genetic continuity of these maternal lineages in the studied area. Although overlapping in time - and to some extent - in cultural expressions, none of the studied groups (Złota, Globular Amphora, Funnel Beaker), shared a close genetic affinity to CWC-associated people, indicating a larger extent of cultural influence from the Pontic steppe than genetic exchange. The higher frequency of haplogroup U5b found in populations associated with Funnel Beaker, Globular Amphora, and Złota cultures suggest a gradual maternal genetic influx from Mesolithic hunter-gatherers. Moreover, presence of haplogroup U4 in Corded Ware groups is most likely associated with the migrations from the Pontic steppe at the end of the Neolithic and supports the observed genetic distances.
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Affiliation(s)
- Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Edvard Ehler
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the ASCR, v. v. i, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK.,Institute of Archaeology and Ethnology, Polish Academy of Sciences, Poznań, Poland
| | - Anna Elżbieta Spinek
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Maja Krzewińska
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, Warszawa, Poland
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Skłodowska University, Lublin, Poland
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, Kraków, Poland.,The Karkonosze Museum in Jelenia Góra, Jelenia Góra, Poland
| | - Barbara Mnich
- Department of Anthropology, Institute of Zoology and Biomedical Research, Jagiellonian University in Kraków, Kraków, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, Kraków, Poland
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland.,Archaeological Museum, Poznań, Poland
| | - Sławomir Kozieł
- Department of Anthropology, Hirszfeld Institute of Immunology and Experimental Therapy, Polish Academy of Sciences, Wroclaw, Poland
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden.,Centre for Palaeogenetics, Stockholm, Sweden
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, University of Johannesburg, Johannesburg, South Africa
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Poznań, Poland
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6
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Kristjansson D, Bohlin J, Jugessur A, Schurr TG. Matrilineal diversity and population history of Norwegians. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2021; 176:120-133. [PMID: 34110627 DOI: 10.1002/ajpa.24345] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Revised: 05/19/2021] [Accepted: 05/23/2021] [Indexed: 11/06/2022]
Abstract
BACKGROUND While well known for its Viking past, Norway's population history and the influences that have shaped its genetic diversity are less well understood. This is particularly true with respect to its demography, migration patterns, and dialectal regions, despite there being curated historical records for the past several centuries. In this study, we undertook an analysis of mitochondrial DNA (mtDNA) diversity within the country to elaborate this history from a matrilineal genetic perspective. METHODS We aggregated 1174 partial modern Norwegian mtDNA sequences from the published literature and subjected them to detailed statistical and phylogenetic analysis by dialectal regions and localities. We further contextualized the matrilineal ancestry of modern Norwegians with data from Mesolithic, Iron Age, and historic period populations. RESULTS Modern Norwegian mtDNAs fell into eight West Eurasian (N, HV, JT, I, U, K, X, W), five East Eurasian (A, F, G, N11, Z), and one African (L2) haplogroups. Pairwise analysis of molecular variance (AMOVA) estimates for all Norwegians indicated they were differentiated from each other at 1.68% (p < 0.001). Norwegians within the same dialectal region also showed genetic similarities to each other, although differences between subpopulations within dialectal regions were also observed. In addition, certain mtDNA lineages in modern Norwegians were also found among prehistoric and historic period populations, suggesting some level of genetic continuity over hundreds to many thousands of years. CONCLUSIONS This analysis of mtDNA diversity provides a detailed picture of the genetic variation within Norway in light of its topography, settlement history, and historical migrations over the past several centuries.
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Affiliation(s)
- Dana Kristjansson
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Jon Bohlin
- Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Infection Epidemiology and Modelling, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Department of Genetics and Bioinformatics, Norwegian Institute of Public Health, Oslo, Norway.,Center of Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.,Department of Global Public Health and Primary Care, Faculty of Medicine, University of Bergen, Bergen, Norway
| | - Theodore G Schurr
- Department of Anthropology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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7
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Coutinho A, Günther T, Munters AR, Svensson EM, Götherström A, Storå J, Malmström H, Jakobsson M. The Neolithic Pitted Ware culture foragers were culturally but not genetically influenced by the Battle Axe culture herders. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2020; 172:638-649. [PMID: 32497286 DOI: 10.1002/ajpa.24079] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Revised: 03/26/2020] [Accepted: 04/17/2020] [Indexed: 12/14/2022]
Abstract
OBJECTIVES In order to understand contacts between cultural spheres in the third millennium BC, we investigated the impact of a new herder culture, the Battle Axe culture, arriving to Scandinavia on the people of the sub-Neolithic hunter-gatherer Pitted Ware culture. By investigating the genetic make-up of Pitted Ware culture people from two types of burials (typical Pitted Ware culture burials and Battle Axe culture-influenced burials), we could determine the impact of migration and the impact of cultural influences. METHODS We sequenced and analyzed the genomes of 25 individuals from typical Pitted Ware culture burials and from Pitted Ware culture burials with Battle Axe culture influences in order to determine if the different burial types were associated with different gene-pools. RESULTS The genomic data show that all individuals belonged to one genetic population-a population associated with the Pitted Ware culture-irrespective of the burial style. CONCLUSION We conclude that the Pitted Ware culture communities were not impacted by gene-flow, that is, via migration or exchange of mates. These different cultural expressions in the Pitted Ware culture burials are instead a consequence of cultural exchange.
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Affiliation(s)
- Alexandra Coutinho
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Arielle R Munters
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Anders Götherström
- Archaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Jan Storå
- Osteoarchaeological Research Laboratory, Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa
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8
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Mallory J, Dybo A, Balanovsky O. The Impact of Genetics Research on Archaeology and Linguistics in Eurasia. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795419120081] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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9
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Interactions between earliest Linearbandkeramik farmers and central European hunter gatherers at the dawn of European Neolithization. Sci Rep 2019; 9:19544. [PMID: 31863024 PMCID: PMC6925266 DOI: 10.1038/s41598-019-56029-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2019] [Accepted: 12/01/2019] [Indexed: 01/19/2023] Open
Abstract
Archaeogenetic research over the last decade has demonstrated that European Neolithic farmers (ENFs) were descended primarily from Anatolian Neolithic farmers (ANFs). ENFs, including early Neolithic central European Linearbandkeramik (LBK) farming communities, also harbored ancestry from European Mesolithic hunter gatherers (WHGs) to varying extents, reflecting admixture between ENFs and WHGs. However, the timing and other details of this process are still imperfectly understood. In this report, we provide a bioarchaeological analysis of three individuals interred at the Brunn 2 site of the Brunn am Gebirge-Wolfholz archeological complex, one of the oldest LBK sites in central Europe. Two of the individuals had a mixture of WHG-related and ANF-related ancestry, one of them with approximately 50% of each, while the third individual had approximately all ANF-related ancestry. Stable carbon and nitrogen isotope ratios for all three individuals were within the range of variation reflecting diets of other Neolithic agrarian populations. Strontium isotope analysis revealed that the ~50% WHG-ANF individual was non-local to the Brunn 2 area. Overall, our data indicate interbreeding between incoming farmers, whose ancestors ultimately came from western Anatolia, and local HGs, starting within the first few generations of the arrival of the former in central Europe, as well as highlighting the integrative nature and composition of the early LBK communities.
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10
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Human mitochondrial DNA lineages in Iron-Age Fennoscandia suggest incipient admixture and eastern introduction of farming-related maternal ancestry. Sci Rep 2019; 9:16883. [PMID: 31729399 PMCID: PMC6858343 DOI: 10.1038/s41598-019-51045-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Accepted: 09/19/2019] [Indexed: 11/16/2022] Open
Abstract
Human ancient DNA studies have revealed high mobility in Europe’s past, and have helped to decode the human history on the Eurasian continent. Northeastern Europe, especially north of the Baltic Sea, however, remains less well understood largely due to the lack of preserved human remains. Finland, with a divergent population history from most of Europe, offers a unique perspective to hunter-gatherer way of life, but thus far genetic information on prehistoric human groups in Finland is nearly absent. Here we report 103 complete ancient mitochondrial genomes from human remains dated to AD 300–1800, and explore mtDNA diversity associated with hunter-gatherers and Neolithic farmers. The results indicate largely unadmixed mtDNA pools of differing ancestries from Iron-Age on, suggesting a rather late genetic shift from hunter-gatherers towards farmers in North-East Europe. Furthermore, the data suggest eastern introduction of farmer-related haplogroups into Finland, contradicting contemporary genetic patterns in Finns.
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11
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Mitochondrial DNA analysis of a Viking age mass grave in Sweden. Forensic Sci Int Genet 2019; 42:268-274. [DOI: 10.1016/j.fsigen.2019.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2019] [Revised: 06/05/2019] [Accepted: 06/06/2019] [Indexed: 01/12/2023]
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12
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Re-integrating Archaeology: A Contribution to aDNA Studies and the Migration Discourse on the 3rd Millennium BC in Europe. ACTA ACUST UNITED AC 2019. [DOI: 10.1017/ppr.2019.4] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Since aDNA research suggested a marked gene influx from Eastern into Central Europe in the 3rd millenniumbc, outdated, simplistic narratives of massive migrations of closed populations have re-appeared in archaeological discussions. A more sophisticated model of migration from the steppes was proposed recently by Kristiansenet al. As a reaction to that proposal, this paper aims to contribute to this ongoing debate by refining the latter model, better integrating archaeological data and anthropological knowledge. It is argued that a polythetic classification of the archaeological material in Central Europe in the 3rd millennium reveals the presence of a new complex of single grave burial rituals which transcends the traditional culture labels. Genetic steppe ancestry is mainly connected to this new kind of burials, rather than to Corded Ware or Bell Beaker materials. Here it is argued that a polythetic view on the archaeological record suggests more complicated histories of migration, population mixtures and interaction than assumed by earlier models, and ways to better integrate detailed studies of archaeological materials with a deeper exploration of anthropological models of mobility and social group composition and the molecular biological data are explored.
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Mitochondrial Gene Sequence ( COI) Reveals the Genetic Structure and Demographic History of Lymantria dispar (Lepidoptera: Erebidae: Lymantriinae) in and around China. INSECTS 2019; 10:insects10050146. [PMID: 31121918 PMCID: PMC6572239 DOI: 10.3390/insects10050146] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 05/16/2019] [Accepted: 05/18/2019] [Indexed: 11/17/2022]
Abstract
The gypsy moth, Lymantria dispar, is among the most destructive quarantine pests of forests. Here, we reconstructed the genetic structure and determined the population differentiation of gypsy moths across its distribution range at different times. This information could be used to both improve the prevention and detection of gypsy moths in the field. Using 31 newly designed species-specific primers targeting fragments of 216-1102 bp, we identified 103 full-length cytochrome oxidase subunit I (COI) gene sequences from eight fresh samples and 95 L. dispar specimens collected between 1955 and 1996, mainly in China. Combining 103 full-length COI gene sequences with 146 COI gene sequences from Genbank or DNA barcode libraries, we analyzed the genetic differentiation, gene flow and haplotypes between gypsy moth populations in order to reflect the genetic structure and population dynamics of gypsy moths. We discovered 25 previously unknown haplotypes from old gypsy moth specimens. We found that the genetic diversity among gypsy moth populations (collected in the same region at different time points) was relatively high. Furthermore, the genetic structure of Chinese geographical populations (Heilongjiang, Liaoning, Beijing) in different years was distinct. Our results suggested that some gypsy moths in China showed the genetic affinity with European gypsy moths (a sub-species of gypsy moths found mainly in Europe).
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Vanhanen S, Gustafsson S, Ranheden H, Björck N, Kemell M, Heyd V. Maritime Hunter-Gatherers Adopt Cultivation at the Farming Extreme of Northern Europe 5000 Years Ago. Sci Rep 2019; 9:4756. [PMID: 30894607 PMCID: PMC6426860 DOI: 10.1038/s41598-019-41293-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 03/05/2019] [Indexed: 12/17/2022] Open
Abstract
The dynamics of the origins and spread of farming are globally debated in anthropology and archaeology. Lately, numerous aDNA studies have turned the tide in favour of migrations, leaving only a few cases in Neolithic Europe where hunter-gatherers might have adopted agriculture. It is thus widely accepted that agriculture was expanding to its northern extreme in Sweden c. 4000 BC by migrating Funnel Beaker Culture (FBC) farmers. This was followed by intense contacts with local hunter-gatherers, leading to the development of the Pitted Ware Culture (PWC), who nonetheless relied on maritime prey. Here, we present archaeobotanical remains from Sweden and the Åland archipelago (Finland) showing that PWC used free-threshing barley and hulled and free-threshing wheat from c. 3300 BC. We suggest that these hunter-gatherers adopted cultivation from FBC farmers and brought it to islands beyond the 60th parallel north. Based on directly dated grains, land areas suitable for cultivation, and absence of signs of exchange with FBC in Sweden, we argue that PWC cultivated crops in Åland. While we have isotopic and lipid-biomarker proof that their main subsistence was still hunting/fishing/gathering, we argue small-scale cereal use was intended for ritual feasts, when cereal products could have been consumed with pork.
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Affiliation(s)
- Santeri Vanhanen
- Archaeology, Department of Cultures, University of Helsinki, P.O. Box 59, Unioninkatu 38, Helsinki, 00014, Finland.
| | | | - Håkan Ranheden
- Arkeologerna, Statens historiska museer, Instrumentvägen 19, Hägersten, 126 53, Sweden
| | - Niclas Björck
- Arkeologerna, Statens historiska museer, Hållnäsgatan 11, Uppsala, 752 28, Sweden
| | - Marianna Kemell
- Department of Chemistry, University of Helsinki, 00014, Helsinki, Finland
| | - Volker Heyd
- Archaeology, Department of Cultures, University of Helsinki, P.O. Box 59, Unioninkatu 38, Helsinki, 00014, Finland
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Fort J, Mercè Pareta M, Sørensen L. Estimating the relative importance of demic and cultural diffusion in the spread of the Neolithic in Scandinavia. J R Soc Interface 2018; 15:20180597. [PMID: 30464058 PMCID: PMC6283996 DOI: 10.1098/rsif.2018.0597] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/29/2018] [Indexed: 12/05/2022] Open
Abstract
Using a database of early farming sites in Scandinavia, we estimate that the spread rate of the Neolithic was in the range 0.44-0.66 km yr-1 This is substantially slower (by about 50%) than the rate in continental Europe. We interpret this result in the framework of a new mathematical model that includes horizontal cultural transmission (acculturation), vertical cultural transmission (interbreeding) and demic diffusion (reproduction and dispersal of farmers). To parametrize the model, we estimate reproduction rates of early farmers using archaeological data (sum-calibrated probabilities for the dates of early Neolithic Scandinavian sites) and use them in a wave-of-advance model for the first time. Comparing the model with the archaeological data, we find that the percentage of the spread rate due to cultural diffusion is below 50% (except for very extreme parameter values, and even for them it is below 54%). This strongly suggests that the spread of the Neolithic in Scandinavia was driven mainly by demic diffusion. This conclusion, obtained from archaeological data, agrees qualitatively with the implications of ancient genetic data, but the latter are yet too few in Scandinavia to produce any quantitative percentage for the spread rate due to cultural diffusion. We also find that, on average, fewer than eight hunter-gatherers were incorporated in the Neolithic communities by each group of 10 pioneering farmers, via horizontal and/or vertical cultural transmission.
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Affiliation(s)
- Joaquim Fort
- Complex Systems Laboratory, University of Girona, C/. Maria Aurèlia Capmany 61, 17003 Girona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), C/. Lluís Companys 23, 08010 Barcelona, Spain
| | - Maria Mercè Pareta
- Complex Systems Laboratory, University of Girona, C/. Maria Aurèlia Capmany 61, 17003 Girona, Spain
| | - Lasse Sørensen
- Ancient Cultures of Denmark and the Mediterranean, The National Museum of Denmark, Frederiksholms Kanal 12, 1220 Copenhagen K, Denmark
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16
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Brandl M, Martinez MM, Hauzenberger C, Filzmoser P, Nymoen P, Mehler N. A multi-technique analytical approach to sourcing Scandinavian flint: Provenance of ballast flint from the shipwreck "Leirvigen 1", Norway. PLoS One 2018; 13:e0200647. [PMID: 30089119 PMCID: PMC6082525 DOI: 10.1371/journal.pone.0200647] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 06/30/2018] [Indexed: 11/26/2022] Open
Abstract
Although Scandinavian flint is one of the most important materials used for prehistoric stone tool production in Northern and Central Europe, a conclusive method for securely differentiating between flint sources, geologically bound to northern European chalk formations, has never been achieved. The main problems with traditional approaches concern the oftentimes high similarities of SiO2 raw materials (i.e. chert and flint) on different scales due to similar genetic conditions and higher intra- than inter-source variation. Conventional chert and flint provenance studies chiefly concentrate on visual, petrographic or geochemical investigations. Hence, attempts to generate characteristic fingerprints of particular chert raw materials were in most cases unsatisfying. Here we show that the Multi Layered Chert Sourcing Approach (MLA) achieves a clear differentiation between primary sources of Scandinavian flint. The MLA combines visual comparative studies, stereo-microscopic analyses of microfossil inclusions, geochemical trace element analyses applying LA-ICP-MS (Laser Ablation Inductively Coupled Plasma Mass Spectrometry) and statistical analyses through CODA (Compositional Data Analysis). For archaeologists, provenance studies are the gateway to advance interpretations of economic behavior expressed in resource management strategies entailing the procurement, use and distribution of lithic raw materials. We demonstrate the relevance of our results for archaeological materials in a case study in which we were able to differentiate between Scandinavian flint sources and establish the provenance of historic ballast flint from a shipwreck found near Kristiansand close to the shore of southern Norway from a beach source in Northern Jutland, the Vigsø Bay.
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Affiliation(s)
- Michael Brandl
- Austrian Academy of Sciences, OREA-Institute, Vienna, Austria
- * E-mail:
| | - Maria M. Martinez
- The University of Texas at Austin, Department of Anthropology, Austin, Texas, United States of America
| | | | - Peter Filzmoser
- Vienna University of Technology, Institute of Statistics and Mathematical Methods in Economics, Vienna, Austria
| | | | - Natascha Mehler
- University of Vienna, Institute for Prehistory and Historical Archaeology, Vienna, Austria
- Centre for Baltic and Scandinavian Archaeology, Schleswig, Germany
- Institute of Nordic Studies, University of the Highlands and Islands, Kirkwall, Orkney
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17
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Valdiosera C, Günther T, Vera-Rodríguez JC, Ureña I, Iriarte E, Rodríguez-Varela R, Simões LG, Martínez-Sánchez RM, Svensson EM, Malmström H, Rodríguez L, Bermúdez de Castro JM, Carbonell E, Alday A, Hernández Vera JA, Götherström A, Carretero JM, Arsuaga JL, Smith CI, Jakobsson M. Four millennia of Iberian biomolecular prehistory illustrate the impact of prehistoric migrations at the far end of Eurasia. Proc Natl Acad Sci U S A 2018; 115:3428-3433. [PMID: 29531053 PMCID: PMC5879675 DOI: 10.1073/pnas.1717762115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Population genomic studies of ancient human remains have shown how modern-day European population structure has been shaped by a number of prehistoric migrations. The Neolithization of Europe has been associated with large-scale migrations from Anatolia, which was followed by migrations of herders from the Pontic steppe at the onset of the Bronze Age. Southwestern Europe was one of the last parts of the continent reached by these migrations, and modern-day populations from this region show intriguing similarities to the initial Neolithic migrants. Partly due to climatic conditions that are unfavorable for DNA preservation, regional studies on the Mediterranean remain challenging. Here, we present genome-wide sequence data from 13 individuals combined with stable isotope analysis from the north and south of Iberia covering a four-millennial temporal transect (7,500-3,500 BP). Early Iberian farmers and Early Central European farmers exhibit significant genetic differences, suggesting two independent fronts of the Neolithic expansion. The first Neolithic migrants that arrived in Iberia had low levels of genetic diversity, potentially reflecting a small number of individuals; this diversity gradually increased over time from mixing with local hunter-gatherers and potential population expansion. The impact of post-Neolithic migrations on Iberia was much smaller than for the rest of the continent, showing little external influence from the Neolithic to the Bronze Age. Paleodietary reconstruction shows that these populations have a remarkable degree of dietary homogeneity across space and time, suggesting a strong reliance on terrestrial food resources despite changing culture and genetic make-up.
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Affiliation(s)
- Cristina Valdiosera
- Department of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia;
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humanos, 28029 Madrid, Spain
| | - Torsten Günther
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden;
| | - Juan Carlos Vera-Rodríguez
- Centro de Investigación en Patrimonio Histórico, Cultural y Natural, Departamento de Historia, Geografía y Antropología, Universidad de Huelva, 21071 Huelva, Spain
| | - Irene Ureña
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humanos, 28029 Madrid, Spain
| | - Eneko Iriarte
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001 Burgos, Spain
| | - Ricardo Rodríguez-Varela
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humanos, 28029 Madrid, Spain
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - Luciana G Simões
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Rafael M Martínez-Sánchez
- Departamento de Prehistoria y Arqueología, Facultad de Filosofía y Letras, Universidad de Granada, 18071 Granada, Spain
| | - Emma M Svensson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Helena Malmström
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden
| | - Laura Rodríguez
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001 Burgos, Spain
- Facultad de Humanidades, Universidad Isabel I, 09003 Burgos, Spain
| | | | - Eudald Carbonell
- Institut Català de Paleoecologia Humana i Evolució Social, 43007 Tarragona, Spain
| | - Alfonso Alday
- Departamento de Geografía, Prehistoria y Arqueología, Universidad del País Vasco, 48940 Lejona, Vizcaya, Spain
| | | | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, 10691 Stockholm, Sweden
| | - José-Miguel Carretero
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humanos, 28029 Madrid, Spain
- Laboratorio de Evolución Humana, Departamento de Historia, Geografía y Comunicación, Universidad de Burgos, 09001 Burgos, Spain
| | - Juan Luis Arsuaga
- Centro Mixto, Universidad Complutense de Madrid-Instituto de Salud Carlos III de Evolución y Comportamiento Humanos, 28029 Madrid, Spain;
| | - Colin I Smith
- Department of Archaeology and History, La Trobe University, Melbourne, VIC 3086, Australia
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, 75236 Uppsala, Sweden;
- Centre for Anthropological Research, University of Johannesburg, Johannesburg 2006, South Africa
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18
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Mittnik A, Wang CC, Pfrengle S, Daubaras M, Zariņa G, Hallgren F, Allmäe R, Khartanovich V, Moiseyev V, Tõrv M, Furtwängler A, Andrades Valtueña A, Feldman M, Economou C, Oinonen M, Vasks A, Balanovska E, Reich D, Jankauskas R, Haak W, Schiffels S, Krause J. The genetic prehistory of the Baltic Sea region. Nat Commun 2018; 9:442. [PMID: 29382937 PMCID: PMC5789860 DOI: 10.1038/s41467-018-02825-9] [Citation(s) in RCA: 93] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 01/02/2018] [Indexed: 11/09/2022] Open
Abstract
While the series of events that shaped the transition between foraging societies and food producers are well described for Central and Southern Europe, genetic evidence from Northern Europe surrounding the Baltic Sea is still sparse. Here, we report genome-wide DNA data from 38 ancient North Europeans ranging from ~9500 to 2200 years before present. Our analysis provides genetic evidence that hunter-gatherers settled Scandinavia via two routes. We reveal that the first Scandinavian farmers derive their ancestry from Anatolia 1000 years earlier than previously demonstrated. The range of Mesolithic Western hunter-gatherers extended to the east of the Baltic Sea, where these populations persisted without gene-flow from Central European farmers during the Early and Middle Neolithic. The arrival of steppe pastoralists in the Late Neolithic introduced a major shift in economy and mediated the spread of a new ancestry associated with the Corded Ware Complex in Northern Europe.
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Affiliation(s)
- Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, 72070, Tübingen, Germany.
| | - Chuan-Chao Wang
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
- Department of Anthropology and Ethnology, Xiamen University, 361005, Xiamen, China
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, 72070, Tübingen, Germany
| | - Mantas Daubaras
- Department of Archaeology, Lithuanian Institute of History, 01108, Vilnius, Lithuania
| | - Gunita Zariņa
- Institute of Latvian History, University of Latvia, Riga, LV-1050, Latvia
| | | | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, 10130, Tallinn, Estonia
| | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russia, 199034
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, St. Petersburg, Russia, 199034
| | - Mari Tõrv
- Institute of History and Archaeology, University of Tartu, 50090, Tartu, Estonia
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, 72070, Tübingen, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Christos Economou
- Archaeological Research Laboratory, Stockholm University, 11418, Stockholm, Sweden
| | - Markku Oinonen
- Finnish Museum of Natural History - LUOMUS, University of Helsinki, 00014, Helsinki, Finland
| | - Andrejs Vasks
- Institute of Latvian History, University of Latvia, Riga, LV-1050, Latvia
| | | | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, 02142, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, 02115, USA
| | - Rimantas Jankauskas
- Department of Anatomy, Histology and Anthropology, Vilnius University, 03101, Vilnius, Lithuania
| | - 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
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, 72070, Tübingen, Germany.
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19
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Hudjashov G, Karafet TM, Lawson DJ, Downey S, Savina O, Sudoyo H, Lansing JS, Hammer MF, Cox MP. Complex Patterns of Admixture across the Indonesian Archipelago. Mol Biol Evol 2017; 34:2439-2452. [PMID: 28957506 PMCID: PMC5850824 DOI: 10.1093/molbev/msx196] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Indonesia, an island nation as large as continental Europe, hosts a sizeable proportion of global human diversity, yet remains surprisingly undercharacterized genetically. Here, we substantially expand on existing studies by reporting genome-scale data for nearly 500 individuals from 25 populations in Island Southeast Asia, New Guinea, and Oceania, notably including previously unsampled islands across the Indonesian archipelago. We use high-resolution analyses of haplotype diversity to reveal fine detail of regional admixture patterns, with a particular focus on the Holocene. We find that recent population history within Indonesia is complex, and that populations from the Philippines made important genetic contributions in the early phases of the Austronesian expansion. Different, but interrelated processes, acted in the east and west. The Austronesian migration took several centuries to spread across the eastern part of the archipelago, where genetic admixture postdates the archeological signal. As with the Neolithic expansion further east in Oceania and in Europe, genetic mixing with local inhabitants in eastern Indonesia lagged behind the arrival of farming populations. In contrast, western Indonesia has a more complicated admixture history shaped by interactions with mainland Asian and Austronesian newcomers, which for some populations occurred more than once. Another layer of complexity in the west was introduced by genetic contact with South Asia and strong demographic events in isolated local groups.
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Affiliation(s)
- Georgi Hudjashov
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand.,Estonian Biocentre, 51010 Tartu, Estonia
| | | | - Daniel J Lawson
- School of Social and Community Medicine, University of Bristol, Bristol, United Kingdom
| | - Sean Downey
- Department of Anthropology, University of Maryland, College Park, MD
| | - Olga Savina
- ARL Division of Biotechnology, University of Arizona, Tucson, AZ
| | - Herawati Sudoyo
- Genome Diversity and Diseases Laboratory, Eijkman Institute for Molecular Biology, Jakarta, Indonesia.,Department of Medical Biology, Faculty of Medicine, University of Indonesia, Jakarta, Indonesia.,Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | | | | | - Murray P Cox
- Statistics and Bioinformatics Group, Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand
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Larruga JM, Marrero P, Abu-Amero KK, Golubenko MV, Cabrera VM. Carriers of mitochondrial DNA macrohaplogroup R colonized Eurasia and Australasia from a southeast Asia core area. BMC Evol Biol 2017; 17:115. [PMID: 28535779 PMCID: PMC5442693 DOI: 10.1186/s12862-017-0964-5] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2017] [Accepted: 05/11/2017] [Indexed: 11/21/2022] Open
Abstract
BACKGROUND The colonization of Eurasia and Australasia by African modern humans has been explained, nearly unanimously, as the result of a quick southern coastal dispersal route through the Arabian Peninsula, the Indian subcontinent, and the Indochinese Peninsula, to reach Australia around 50 kya. The phylogeny and phylogeography of the major mitochondrial DNA Eurasian haplogroups M and N have played the main role in giving molecular genetics support to that scenario. However, using the same molecular tools, a northern route across central Asia has been invoked as an alternative that is more conciliatory with the fossil record of East Asia. Here, we assess as the Eurasian macrohaplogroup R fits in the northern path. RESULTS Haplogroup U, with a founder age around 50 kya, is one of the oldest clades of macrohaplogroup R in western Asia. The main branches of U expanded in successive waves across West, Central and South Asia before the Last Glacial Maximum. All these dispersions had rather overlapping ranges. Some of them, as those of U6 and U3, reached North Africa. At the other end of Asia, in Wallacea, another branch of macrohaplogroup R, haplogroup P, also independently expanded in the area around 52 kya, in this case as isolated bursts geographically well structured, with autochthonous branches in Australia, New Guinea, and the Philippines. CONCLUSIONS Coeval independently dispersals around 50 kya of the West Asia haplogroup U and the Wallacea haplogroup P, points to a halfway core area in southeast Asia as the most probable centre of expansion of macrohaplogroup R, what fits in the phylogeographic pattern of its ancestor, macrohaplogroup N, for which a northern route and a southeast Asian origin has been already proposed.
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Affiliation(s)
- Jose M Larruga
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Patricia Marrero
- Research Support General Service, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain
| | - Khaled K Abu-Amero
- Glaucoma Research Chair, Department of Ophthalmology, College of Medicine, King Saud University, Riyadh, Saudi Arabia
| | | | - Vicente M Cabrera
- Departamento de Genética, Facultad de Biología, Universidad de La Laguna, E-38271 La Laguna, Tenerife, Spain.
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22
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Chyleński M, Juras A, Ehler E, Malmström H, Piontek J, Jakobsson M, Marciniak A, Dabert M. Late Danubian mitochondrial genomes shed light into the Neolithisation of Central Europe in the 5 th millennium BC. BMC Evol Biol 2017; 17:80. [PMID: 28302068 PMCID: PMC5356262 DOI: 10.1186/s12862-017-0924-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 02/23/2017] [Indexed: 11/29/2022] Open
Abstract
Background Recent aDNA studies are progressively focusing on various Neolithic and Hunter - Gatherer (HG) populations, providing arguments in favor of major migrations accompanying European Neolithisation. The major focus was so far on the Linear Pottery Culture (LBK), which introduced the Neolithic way of life in Central Europe in the second half of 6th millennium BC. It is widely agreed that people of this culture were genetically different from local HGs and no genetic exchange is seen between the two groups. From the other hand some degree of resurgence of HGs genetic component is seen in late Neolithic groups belonging to the complex of the Funnel Beaker Cultures (TRB). Less attention is brought to various middle Neolithic cultures belonging to Late Danubian sequence which chronologically fall in between those two abovementioned groups. We suspected that genetic influx from HG to farming communities might have happened in Late Danubian cultures since archaeologists see extensive contacts between those two communities. Results Here we address this issue by presenting 5 complete mitochondrial genomes of various late Danubian individuals from modern-day Poland and combining it with available published data. Our data show that Late Danubian cultures are maternally closely related to Funnel Beaker groups instead of culturally similar LBK. Conclusions We assume that it is an effect of the presence of individuals belonging to U5 haplogroup both in Late Danubians and the TRB. The U5 haplogroup is thought to be a typical for HGs of Europe and therefore we argue that it is an additional evidence of genetic exchange between farming and HG groups taking place at least as far back as in middle Neolithic, in the Late Danubian communities. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-0924-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614, Poznań, Poland.
| | - Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Edvard Ehler
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland.,Department of Biology and Environmental Studies, Faculty of Education, Charles University in Prague, Magdalény Rettigové 4, 116 39, Prague, Czech Republic
| | - Helena Malmström
- Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland
| | - Mattias Jakobsson
- Department of Organismal Biology and SciLifeLab, Uppsala University, Norbyvägen 18C, SE-752 36, Uppsala, Sweden
| | - Arkadiusz Marciniak
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznań, Umultowska 89D, 61-614, Poznań, Poland
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznań, Umultowska 89, 61-614, Poznań, Poland
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23
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Juras A, Krzewińska M, Nikitin AG, Ehler E, Chyleński M, Łukasik S, Krenz-Niedbała M, Sinika V, Piontek J, Ivanova S, Dabert M, Götherström A. Diverse origin of mitochondrial lineages in Iron Age Black Sea Scythians. Sci Rep 2017; 7:43950. [PMID: 28266657 PMCID: PMC5339713 DOI: 10.1038/srep43950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 01/31/2017] [Indexed: 12/27/2022] Open
Abstract
Scythians were nomadic and semi-nomadic people that ruled the Eurasian steppe during much of the first millennium BCE. While having been extensively studied by archaeology, very little is known about their genetic identity. To fill this gap, we analyzed ancient mitochondrial DNA (mtDNA) from Scythians of the North Pontic Region (NPR) and successfully retrieved 19 whole mtDNA genomes. We have identified three potential mtDNA lineage ancestries of the NPR Scythians tracing back to hunter-gatherer and nomadic populations of east and west Eurasia as well as the Neolithic farming expansion into Europe. One third of all mt lineages in our dataset belonged to subdivisions of mt haplogroup U5. A comparison of NPR Scythian mtDNA linages with other contemporaneous Scythian groups, the Saka and the Pazyryks, reveals a common mtDNA package comprised of haplogroups H/H5, U5a, A, D/D4, and F1/F2. Of these, west Eurasian lineages show a downward cline in the west-east direction while east Eurasian haplogroups display the opposite trajectory. An overall similarity in mtDNA lineages of the NPR Scythians was found with the late Bronze Age Srubnaya population of the Northern Black Sea region which supports the archaeological hypothesis suggesting Srubnaya people as ancestors of the NPR Scythians.
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Affiliation(s)
- Anna Juras
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University Wallenberglaboratoriet, SE-106 91 Stockholm, Sweden
| | - Alexey G Nikitin
- Biology Department, Grand Valley State University, 1 Campus Drive, Allendale, Michigan 49401, United States of America
| | - Edvard Ehler
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland.,Department of Biology and Environmental Studies, Faculty of Education, Charles University in Prague, Magdalény Rettigové 4, 116 39, Prague, Czech Republic
| | - Maciej Chyleński
- Institute of Archaeology, Faculty of History, Adam Mickiewicz University in Poznan, Umultowska 89D, 61-614 Poznan, Poland
| | - Sylwia Łukasik
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Marta Krenz-Niedbała
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Vitaly Sinika
- Taras Shevchenko University in Tiraspol, Taras Shevchenko University in Tiraspol, October Street 25, 33-00 Tiraspol, Moldova
| | - Janusz Piontek
- Department of Human Evolutionary Biology, Institute of Anthropology, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Svetlana Ivanova
- Institute of Archaeology, National Academy of Sciences of Ukraine, Lanzheronivska Street, 65026, Odessa, Ukraine
| | - Miroslawa Dabert
- Molecular Biology Techniques Laboratory, Faculty of Biology, Adam Mickiewicz University in Poznan, Umultowska 89, 61-614 Poznan, Poland
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University Wallenberglaboratoriet, SE-106 91 Stockholm, Sweden
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24
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Nikitin AG, Potekhina I, Rohland N, Mallick S, Reich D, Lillie M. Mitochondrial DNA analysis of eneolithic trypillians from Ukraine reveals neolithic farming genetic roots. PLoS One 2017; 12:e0172952. [PMID: 28235025 PMCID: PMC5325568 DOI: 10.1371/journal.pone.0172952] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2016] [Accepted: 02/13/2017] [Indexed: 01/14/2023] Open
Abstract
The agricultural revolution in Eastern Europe began in the Eneolithic with the Cucuteni-Trypillia culture complex. In Ukraine, the Trypillian culture (TC) existed for over two millennia (ca. 5,400-2,700 BCE) and left a wealth of artifacts. Yet, their burial rituals remain a mystery and to date almost nothing is known about the genetic composition of the TC population. One of the very few TC sites where human remains can be found is a cave called Verteba in western Ukraine. This report presents four partial and four complete mitochondrial genomes from nine TC individuals uncovered in the cave. The results of this analysis, combined with the data from previous reports, indicate that the Trypillian population at Verteba carried, for the most part, a typical Neolithic farmer package of mitochondrial DNA (mtDNA) lineages traced to Anatolian farmers and Neolithic farming groups of central Europe. At the same time, the find of two specimens belonging to haplogroup U8b1 at Verteba can be viewed as a connection of TC with the Upper Paleolithic European populations. At the level of mtDNA haplogroup frequencies, the TC population from Verteba demonstrates a close genetic relationship with population groups of the Funnel Beaker/ Trichterbecker cultural complex from central and northern Europe (ca. 3,950-2,500 BCE).
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Affiliation(s)
- Alexey G. Nikitin
- Biology Department, Grand Valley State University, Allendale, Michigan, United States of America
- * E-mail:
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, Ukrainian Academy of Sciences, Kyiv, Ukraine
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, United States of America
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts, United States of America
- Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, United States of America
| | - Malcolm Lillie
- School of Environmental Sciences (Geography), University of Hull, Hull, England
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25
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Nikitin AG, Ivanova S, Kiosak D, Badgerow J, Pashnick J. Subdivisions of haplogroups U and C encompass mitochondrial DNA lineages of Eneolithic-Early Bronze Age Kurgan populations of western North Pontic steppe. J Hum Genet 2017; 62:605-613. [PMID: 28148921 DOI: 10.1038/jhg.2017.12] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Revised: 01/10/2017] [Accepted: 01/11/2017] [Indexed: 01/01/2023]
Abstract
Prehistoric Europe experienced a marked cultural and economic shift around 4000 years ago, when the established Neolithic agriculture-based economy was replaced by herding-pastoralist industry. In recent years new data about the genetic structure of human communities living during this transition period began to emerge. At the same time, the genetic identities of the Eneolithic and Early Bronze Age (EBA) inhabitants from a prehistoric cultural crossroad in western North Pontic steppe region remain understudied. This report presents results of the investigation of maternal genetic lineages of individuals buried in kurgans constructed during the Eneolithic-EBA transition in the western part of the North Pontic Region (NPR). Mitochondrial DNA (mtDNA) lineages from the interments belonging to the Eneolithic as well as the EBA cultures such as Yamna (Pit Grave), Catacomb and Babino (Mnogovalikovaya or KMK) were examined. In the 12 successfully haplotyped specimens, 75% of mtDNA lineages consisted of west Eurasian haplogroup U and its U4 and U5 sublineages. Furthermore, we identified a subgroup of east Eurasian haplogroup C in two representatives of the Yamna culture in one of the studied kurgans. Our results indicate the persistence of Mesolithic hunter-gatherer mtDNA lineages in western NPR through the EBA, as well as suggesting a mtDNA lineage continuum connecting the western NPR inhabitants of the Early Metal Ages to the North Pontic Neolithic population groups.
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Affiliation(s)
- Alexey G Nikitin
- Biology Department, Grand Valley State University, Allendale, MI, USA
| | - Svetlana Ivanova
- Institute of Archaeology, National Academy of Sciences of Ukraine, Odessa, Ukraine
| | - Dmytro Kiosak
- I.I. Mechnikov Odessa National University, Odessa, Ukraine
| | - Jessica Badgerow
- Biology Department, Grand Valley State University, Allendale, MI, USA
| | - Jeff Pashnick
- Biology Department, Grand Valley State University, Allendale, MI, USA
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26
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Fine-Scale Human Population Structure in Southern Africa Reflects Ecogeographic Boundaries. Genetics 2016; 204:303-14. [PMID: 27474727 DOI: 10.1534/genetics.116.187369] [Citation(s) in RCA: 74] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 07/07/2016] [Indexed: 01/08/2023] Open
Abstract
Recent genetic studies have established that the KhoeSan populations of southern Africa are distinct from all other African populations and have remained largely isolated during human prehistory until ∼2000 years ago. Dozens of different KhoeSan groups exist, belonging to three different language families, but very little is known about their population history. We examine new genome-wide polymorphism data and whole mitochondrial genomes for >100 South Africans from the ≠Khomani San and Nama populations of the Northern Cape, analyzed in conjunction with 19 additional southern African populations. Our analyses reveal fine-scale population structure in and around the Kalahari Desert. Surprisingly, this structure does not always correspond to linguistic or subsistence categories as previously suggested, but rather reflects the role of geographic barriers and the ecology of the greater Kalahari Basin. Regardless of subsistence strategy, the indigenous Khoe-speaking Nama pastoralists and the N|u-speaking ≠Khomani (formerly hunter-gatherers) share ancestry with other Khoe-speaking forager populations that form a rim around the Kalahari Desert. We reconstruct earlier migration patterns and estimate that the southern Kalahari populations were among the last to experience gene flow from Bantu speakers, ∼14 generations ago. We conclude that local adoption of pastoralism, at least by the Nama, appears to have been primarily a cultural process with limited genetic impact from eastern Africa.
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27
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Bankoff RJ, Perry GH. Hunter-gatherer genomics: evolutionary insights and ethical considerations. Curr Opin Genet Dev 2016; 41:1-7. [PMID: 27400119 DOI: 10.1016/j.gde.2016.06.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2016] [Revised: 06/21/2016] [Accepted: 06/23/2016] [Indexed: 10/21/2022]
Abstract
Hunting and gathering societies currently comprise only a small proportion of all human populations. However, the geographic and environmental diversity of modern hunter-gatherer groups, their inherent dependence on ecological resources, and their connection to patterns of behavior and subsistence that represent the vast majority of human history provide opportunities for scientific research to deliver major insights into the evolutionary history of our species. We review recent evolutionary genomic studies of hunter-gatherers, focusing especially on those that identify and functionally characterize phenotypic adaptations to local environments. We also call attention to specific ethical issues that scientists conducting hunter-gatherer genomics research ought to consider, including potential social and economic tensions between traditionally mobile hunter-gatherers and the land ownership-based nation-states by which they are governed, and the implications of genomic-based evidence of long-term evolutionary associations with particular habitats.
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Affiliation(s)
- Richard J Bankoff
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Intercollege Program in Bioethics, Pennsylvania State University, University Park, PA 16802, USA.
| | - George H Perry
- Department of Anthropology, Pennsylvania State University, University Park, PA 16802, USA; Department of Biology, Pennsylvania State University, University Park, PA 16802, USA.
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28
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Bhatti S, Aslamkhan M, Abbas S, Attimonelli M, Aydin HH, de Souza EMS. Genetic analysis of mitochondrial DNA control region variations in four tribes of Khyber Pakhtunkhwa, Pakistan. Mitochondrial DNA A DNA Mapp Seq Anal 2016; 28:687-697. [PMID: 27159729 DOI: 10.3109/24701394.2016.1174222] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Due to its geo strategic position at the crossroad of Asia, Pakistan has gained crucial importance of playing its pivotal role in subsequent human migratory events, both prehistoric and historic. This human movement became possible through an ancient overland network of trails called "The Silk Route" linking Asia Minor, Middle East China, Central Asia and Southeast Asia. This study was conducted to analyze complete mitochondrial control region samples of 100 individuals of four major Pashtun tribes namely, Bangash, Khattak, Mahsuds and Orakzai in the province of Khyber Pakhtunkhwa, Pakistan. All Pashtun tribes revealed high genetic diversity which is comparable to the other Central Asian, Southeast Asian and European populations. The configuration of genetic variation and heterogeneity further unveiled through Multidimensional Scaling, Principal Component Analysis and phylogenetic analysis. The results revealed that Pashtun are the composite mosaic of West Eurasian ancestry of numerous geographic origin. They received substantial gene flow during different invasive movements and have a high element of the Western provenance. The most common haplogroups reported in this study are: South Asian haplogroups M (28%) and R (8%); whereas, West Asians haplogroups are present, albeit in high frequencies (67%) and widespread over all; HV (15%), U (17%), H (9%), J (8%), K (8%), W (4%), N (3%) and T (3%). Moreover, we linked the unexplored genetic connection between Ashkenazi Jews and Pashtun. The presence of specific haplotypes J1b (4%) and K1a1b1a (5%) pointed to a genetic connection of Jewish conglomeration in Khattak tribe. This was a result of an ancient genetic influx in the early Neolithic period that led to the formation of a diverse genetic substratum in present day Pashtun.
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Affiliation(s)
- Shahzad Bhatti
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Pakistan.,b Institute of Molecular Biology and Biotechnology, University of Lahore , Lahore , Pakistan
| | - M Aslamkhan
- a Department of Human Genetics and Molecular Biology , University of Health Sciences Lahore , Pakistan
| | - Sana Abbas
- b Institute of Molecular Biology and Biotechnology, University of Lahore , Lahore , Pakistan
| | - Marcella Attimonelli
- c Department of Biosciences, Biotechnologies and Biopharmaceutics , University of Bari , Italy
| | - Hikmet Hakan Aydin
- d Department of Medical Biochemistry , Ege University School of Medicine , Bornova Izmir , Turkey
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29
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Coia V, Cipollini G, Anagnostou P, Maixner F, Battaggia C, Brisighelli F, Gómez-Carballa A, Destro Bisol G, Salas A, Zink A. Whole mitochondrial DNA sequencing in Alpine populations and the genetic history of the Neolithic Tyrolean Iceman. Sci Rep 2016; 6:18932. [PMID: 26764605 PMCID: PMC4725900 DOI: 10.1038/srep18932] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2015] [Accepted: 12/01/2015] [Indexed: 01/01/2023] Open
Abstract
The Tyrolean Iceman is an extraordinarily well-preserved natural mummy that lived south of the Alpine ridge ~5,200 years before present (ybp), during the Copper Age. Despite studies that have investigated his genetic profile, the relation of the Iceman´s maternal lineage with present-day mitochondrial variation remains elusive. Studies of the Iceman have shown that his mitochondrial DNA (mtDNA) belongs to a novel lineage of haplogroup K1 (K1f) not found in extant populations. We analyzed the complete mtDNA sequences of 42 haplogroup K bearing individuals from populations of the Eastern Italian Alps - putatively in genetic continuity with the Tyrolean Iceman-and compared his mitogenome with a large dataset of worldwide K1 sequences. Our results allow a re-definition of the K1 phylogeny, and indicate that the K1f haplogroup is absent or rare in present-day populations. We suggest that mtDNA Iceman´s lineage could have disappeared during demographic events starting in Europe from ~5,000 ybp. Based on the comparison of our results with published data, we propose a scenario that could explain the apparent contrast between the phylogeographic features of maternal and paternal lineages of the Tyrolean Iceman within the context of the demographic dynamics happening in Europe from 8,000 ybp.
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Affiliation(s)
- V Coia
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - G Cipollini
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - P Anagnostou
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy
| | - F Maixner
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
| | - C Battaggia
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy
| | - F Brisighelli
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - A Gómez-Carballa
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - G Destro Bisol
- Dipartimento Biologia Ambientale, Università La Sapienza, Roma, Italy.,Istituto Italiano di Antropologia, Roma, Italy
| | - A Salas
- Unidade de Xenética, Departamento de Anatomía Patolóxica e Ciencias Forenses, and Instituto de Ciencias Forenses, Facultade de Medicina, Universidade de Santiago de Compostela, Galicia, Spain
| | - A Zink
- Accademia Europea di Bolzano (EURAC-Research), Istituto per le mummie e l´Iceman, Bolzano, Italy
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30
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Affiliation(s)
- Anna Linderholm
- Research Laboratory for Archaeology; University of Oxford; Dyson Perrins Building South Parks Road Oxford OX1 3Q UK
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31
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Hagelberg E, Hofreiter M, Keyser C. Introduction. Ancient DNA: the first three decades. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130371. [PMID: 25487324 PMCID: PMC4275880 DOI: 10.1098/rstb.2013.0371] [Citation(s) in RCA: 69] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Affiliation(s)
- Erika Hagelberg
- Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316 Oslo, Norway
| | - Michael Hofreiter
- Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany Department of Biology, University of York, Heslington, York YO10 5DD, UK
| | - Christine Keyser
- Institut de Médecine Légale, Laboratoire AMIS, Université de Strasbourg, CNRS UMR 5288, Strasbourg, France
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