1
|
Kırdök E, Kashuba N, Damlien H, Manninen MA, Nordqvist B, Kjellström A, Jakobsson M, Lindberg AM, Storå J, Persson P, Andersson B, Aravena A, Götherström A. Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals. Sci Rep 2024; 13:22125. [PMID: 38238372 PMCID: PMC10796427 DOI: 10.1038/s41598-023-48762-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 11/30/2023] [Indexed: 01/22/2024] Open
Abstract
Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.
Collapse
Affiliation(s)
- Emrah Kırdök
- Department of Biotechnology, Faculty of Science, Mersin University, 33100 Yenişehir, Mersin, Turkey.
| | - Natalija Kashuba
- Department of Archaeology and Ancient History, Uppsala University, Engelska Parken, Thunbergsvägen 3H Box 626, 751 26, Uppsala, Sweden
| | - Hege Damlien
- Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway
| | - Mikael A Manninen
- PAES, Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences and Helsinki Institute of Sustainability Science, University of Helsinki, Viikinkaari 1, P.O. Box 65, Helsinki, Finland
| | - Bengt Nordqvist
- Foundation War-Booty Site Finnestorp, Klarinettvägen 75, 434 75, Kungsbacka, Sweden
| | - Anna Kjellström
- Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Mattias Jakobsson
- Department of Organismal Biology, Human Evolution, Uppsala University, Evolutionsbiologiskt Centrum EBC Norbyvägen 18 A, Uppsala, Sweden
| | - A Michael Lindberg
- Department of Chemistry and Biomedical Sciences, Faculty of Health and Life Sciences, Linnaeus University, Hus Vita, 44018, Kalmar, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Osteoarchaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| | - Per Persson
- Museum of Cultural History, University of Oslo, St. Olavs Plass, P.O. Box 6762, NO-0130, Oslo, Norway
| | - Björn Andersson
- Department of Cell and Molecular Biology (CMB), Karolinska Insitutet, P.O. Box 285, 171 77, Stockholm, Sweden
| | - Andrés Aravena
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Vezneciler, 34134, Istanbul, Turkey
| | - Anders Götherström
- Centre for Palaeogenetics, Svante Arrhenius Väg 20C, 106 91, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Archaeological Research Laboratory, Stockholm University, Stockholm, Sweden
| |
Collapse
|
2
|
Allentoft ME, Sikora M, Fischer A, Sjögren KG, Ingason A, Macleod R, Rosengren A, Schulz Paulsson B, Jørkov MLS, Novosolov M, Stenderup J, Price TD, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Sørensen L, Nielsen PO, Rasmussen P, Jensen TZT, Refoyo-Martínez A, Irving-Pease EK, Barrie W, Pearson A, Sousa da Mota B, Demeter F, Henriksen RA, Vimala T, McColl H, Vaughn A, Vinner L, Renaud G, Stern A, Johannsen NN, Ramsøe AD, Schork AJ, Ruter A, Gotfredsen AB, Henning Nielsen B, Brinch Petersen E, Kannegaard E, Hansen J, Buck Pedersen K, Pedersen L, Klassen L, Meldgaard M, Johansen M, Uldum OC, Lotz P, Lysdahl P, Bangsgaard P, Petersen PV, Maring R, Iversen R, Wåhlin S, Anker Sørensen S, Andersen SH, Jørgensen T, Lynnerup N, Lawson DJ, Rasmussen S, Korneliussen TS, Kjær KH, Durbin R, Nielsen R, Delaneau O, Werge T, Kristiansen K, Willerslev E. 100 ancient genomes show repeated population turnovers in Neolithic Denmark. Nature 2024; 625:329-337. [PMID: 38200294 PMCID: PMC10781617 DOI: 10.1038/s41586-023-06862-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 11/13/2023] [Indexed: 01/12/2024]
Abstract
Major migration events in Holocene Eurasia have been characterized genetically at broad regional scales1-4. However, insights into the population dynamics in the contact zones are hampered by a lack of ancient genomic data sampled at high spatiotemporal resolution5-7. Here, to address this, we analysed shotgun-sequenced genomes from 100 skeletons spanning 7,300 years of the Mesolithic period, Neolithic period and Early Bronze Age in Denmark and integrated these with proxies for diet (13C and 15N content), mobility (87Sr/86Sr ratio) and vegetation cover (pollen). We observe that Danish Mesolithic individuals of the Maglemose, Kongemose and Ertebølle cultures form a distinct genetic cluster related to other Western European hunter-gatherers. Despite shifts in material culture they displayed genetic homogeneity from around 10,500 to 5,900 calibrated years before present, when Neolithic farmers with Anatolian-derived ancestry arrived. Although the Neolithic transition was delayed by more than a millennium relative to Central Europe, it was very abrupt and resulted in a population turnover with limited genetic contribution from local hunter-gatherers. The succeeding Neolithic population, associated with the Funnel Beaker culture, persisted for only about 1,000 years before immigrants with eastern Steppe-derived ancestry arrived. This second and equally rapid population replacement gave rise to the Single Grave culture with an ancestry profile more similar to present-day Danes. In our multiproxy dataset, these major demographic events are manifested as parallel shifts in genotype, phenotype, diet and land use.
Collapse
Affiliation(s)
- Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia.
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Anders Fischer
- Cluster of Excellence ROOTS, Kiel University, Kiel, Germany
- Sealand Archaeology, Kalundborg, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, Gothenburg University, Göteborg, Sweden
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | - Ruairidh Macleod
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
| | | | | | - Maria Novosolov
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - T Douglas Price
- Laboratory for Archaeological Chemistry, Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA
| | | | | | | | | | | | | | | | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Alice Pearson
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Eco-anthropologie (EA), Dpt ABBA, Muséum National d'Histoire Naturelle, CNRS, Université Paris Cité, Musée de l'Homme, Paris, France
| | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Vaughn
- Center for Computational Biology, University of California, Berkeley, USA
| | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aaron Stern
- Center for Computational Biology, University of California, Berkeley, USA
| | | | - Abigail Daisy Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrew Joseph Schork
- Laboratory of Biological Anthropology, University of Copenhagen, Copenhagen, Denmark
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anthony Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anne Birgitte Gotfredsen
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | | | | | | | - Morten Meldgaard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Health and Nature, University of Greenland, Nuuk, Greenland
| | | | | | - Per Lotz
- Museum Nordsjælland, Hillerød, Denmark
- Museum Vestsjælland, Holbæk, Denmark
| | - Per Lysdahl
- Vendsyssel Historiske Museum, Hjørring, Denmark
| | - Pernille Bangsgaard
- Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Rikke Maring
- Department of Archaeology and Heritage Studies, Aarhus University, Aarhus, Denmark
- Museum Østjylland, Randers, Denmark
| | - Rune Iversen
- The Saxo Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | | | | | - Niels Lynnerup
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Simon Rasmussen
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen N, Denmark
| | | | - Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology and Statistics, UC Berkeley, Berkeley, CA, USA
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Center Sct. Hans, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, Gothenburg University, Göteborg, Sweden
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
| |
Collapse
|
3
|
Allentoft ME, Sikora M, Refoyo-Martínez A, Irving-Pease EK, Fischer A, Barrie W, Ingason A, Stenderup J, Sjögren KG, Pearson A, Sousa da Mota B, Schulz Paulsson B, Halgren A, Macleod R, Jørkov MLS, Demeter F, Sørensen L, Nielsen PO, Henriksen RA, Vimala T, McColl H, Margaryan A, Ilardo M, Vaughn A, Fischer Mortensen M, Nielsen AB, Ulfeldt Hede M, Johannsen NN, Rasmussen P, Vinner L, Renaud G, Stern A, Jensen TZT, Scorrano G, Schroeder H, Lysdahl P, Ramsøe AD, Skorobogatov A, Schork AJ, Rosengren A, Ruter A, Outram A, Timoshenko AA, Buzhilova A, Coppa A, Zubova A, Silva AM, Hansen AJ, Gromov A, Logvin A, Gotfredsen AB, Henning Nielsen B, González-Rabanal B, Lalueza-Fox C, McKenzie CJ, Gaunitz C, Blasco C, Liesau C, Martinez-Labarga C, Pozdnyakov DV, Cuenca-Solana D, Lordkipanidze DO, En'shin D, Salazar-García DC, Price TD, Borić D, Kostyleva E, Veselovskaya EV, Usmanova ER, Cappellini E, Brinch Petersen E, Kannegaard E, Radina F, Eylem Yediay F, Duday H, Gutiérrez-Zugasti I, Merts I, Potekhina I, Shevnina I, Altinkaya I, Guilaine J, Hansen J, Aura Tortosa JE, Zilhão J, Vega J, Buck Pedersen K, Tunia K, Zhao L, Mylnikova LN, Larsson L, Metz L, Yepiskoposyan L, Pedersen L, Sarti L, Orlando L, Slimak L, Klassen L, Blank M, González-Morales M, Silvestrini M, Vretemark M, Nesterova MS, Rykun M, Rolfo MF, Szmyt M, Przybyła M, Calattini M, Sablin M, Dobisíková M, Meldgaard M, Johansen M, Berezina N, Card N, Saveliev NA, Poshekhonova O, Rickards O, Lozovskaya OV, Gábor O, Uldum OC, Aurino P, Kosintsev P, Courtaud P, Ríos P, Mortensen P, Lotz P, Persson P, Bangsgaard P, de Barros Damgaard P, Vang Petersen P, Martinez PP, Włodarczak P, Smolyaninov RV, Maring R, Menduiña R, Badalyan R, Iversen R, Turin R, Vasilyev S, Wåhlin S, Borutskaya S, Skochina S, Sørensen SA, Andersen SH, Jørgensen T, Serikov YB, Molodin VI, Smrcka V, Merts V, Appadurai V, Moiseyev V, Magnusson Y, Kjær KH, Lynnerup N, Lawson DJ, Sudmant PH, Rasmussen S, Korneliussen TS, Durbin R, Nielsen R, Delaneau O, Werge T, Racimo F, Kristiansen K, Willerslev E. Population genomics of post-glacial western Eurasia. Nature 2024; 625:301-311. [PMID: 38200295 PMCID: PMC10781627 DOI: 10.1038/s41586-023-06865-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 11/14/2023] [Indexed: 01/12/2024]
Abstract
Western Eurasia witnessed several large-scale human migrations during the Holocene1-5. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.
Collapse
Affiliation(s)
- Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia.
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
| | - Alba Refoyo-Martínez
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Evan K Irving-Pease
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Anders Fischer
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Sealand Archaeology, Kalundborg, Denmark
| | - William Barrie
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Institute of Biological Psychiatry, Mental Health Services, Copenhagen University Hospital, Roskilde, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Karl-Göran Sjögren
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Alice Pearson
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Bárbara Sousa da Mota
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | | | - Alma Halgren
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Ruairidh Macleod
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
- Department of Archaeology, University of Cambridge, Cambridge, UK
| | | | - Fabrice Demeter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Muséum National d'Histoire Naturelle, CNRS, Université de Paris, Musée de l'Homme, Paris, France
| | | | | | - Rasmus A Henriksen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Tharsika Vimala
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
| | - Melissa Ilardo
- Anthropology Department, University of Utah, Salt Lake City, UT, USA
| | - Andrew Vaughn
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | | | | | | | | | | | - Lasse Vinner
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriel Renaud
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Aaron Stern
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | | | - Gabriele Scorrano
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hannes Schroeder
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Per Lysdahl
- Vendsyssel Historiske Museum, Hjørring, Denmark
| | - Abigail Daisy Ramsøe
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Andrew Joseph Schork
- Department of Genetics, University of Cambridge, Cambridge, UK
- Neurogenomics Division, The Translational Genomics Research Institute (TGEN), Phoenix, AZ, USA
| | - Anders Rosengren
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Anthony Ruter
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alan Outram
- Department of Archaeology, University of Exeter, Exeter, UK
| | - Aleksey A Timoshenko
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Alexandra Buzhilova
- Department of Anthropology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Alfredo Coppa
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
| | - Alisa Zubova
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Ana Maria Silva
- CIAS, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- UNIARQ, University of Lisbon, Lisbon, Portugal
| | - Anders J Hansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Andrey Gromov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Andrey Logvin
- Kostanay Regional University A. Baitursynov, Kostanay, Kazakhstan
| | - Anne Birgitte Gotfredsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Borja González-Rabanal
- Grupo EvoAdapta, Departamento de Ciencias Históricas, Universidad de Cantabria, Santander, Spain
| | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
- Natural Sciences Museum of Barcelona (MCNB), Barcelona, Spain
| | | | - Charleen Gaunitz
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Concepción Blasco
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Corina Liesau
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | | | - Dmitri V Pozdnyakov
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - David Cuenca-Solana
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Banco Santander, Gobierno de Cantabria, Santander, Spain
- Centre de Recherche en Archéologie, Archeosciences, Histoire (CReAAH), UMR-6869 CNRS, Rennes, France
| | - David O Lordkipanidze
- Georgian National Museum, Tbilisi, Georgia
- Tbilisi State University, Tbilisi, Georgia
| | - Dmitri En'shin
- IPND, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences, Tyumen, Russian Federation
| | - Domingo C Salazar-García
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
- Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - T Douglas Price
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
- Laboratory for Archaeological Chemistry, Department of Anthropology, University of Wisconsin-Madison, Madison, WI, USA
| | - Dušan Borić
- Department of Environmental Biology, Sapienza University of Rome, Rome, Italy
- Department of Anthropology, New York University, New York, NY, USA
| | - Elena Kostyleva
- Institute of Humanities, Ivanovo State University, Ivanovo, Russian Federation
| | - Elizaveta V Veselovskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russian Federation
| | - Emma R Usmanova
- Saryarka Archaeological Institute, Buketov Karaganda University, Karaganda, Kazakhstan
- South Ural State University, Chelyabinsk, Russia
- A. Kh. Khalikov Institute of Archeology of the Academy of Sciences of the Republic of Tatarstan, Kazan, Russia
- Margulan Institute of Archaeology, Committee of Science of the Ministry of Science and Higher Education of the Republic of Kazakhstan, Almaty, Kazakhstan
| | - Enrico Cappellini
- Section for Evolutionary Genomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Francesca Radina
- Soprintendenza Archeologia Belle Arti e Paesaggio per la Città Metropolitana di Bari, Bari, Italy
| | - Fulya Eylem Yediay
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Henri Duday
- UMR 5199 PACEA, CNRS, Université de Bordeaux, Pessac, France
| | - Igor Gutiérrez-Zugasti
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Banco Santander, Gobierno de Cantabria, Santander, Spain
| | - Ilya Merts
- A.Kh. Margulan Institute of Archaeology, Almaty, Kazakhstan
| | - Inna Potekhina
- Institute of Archaeology, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- National University of Kyiv-Mohyla Academy, Kyiv, Ukraine
| | - Irina Shevnina
- Kostanay Regional University A. Baitursynov, Kostanay, Kazakhstan
| | - Isin Altinkaya
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | | | - Joan Emili Aura Tortosa
- Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain
| | - João Zilhão
- UNIARQ, University of Lisbon, Lisbon, Portugal
- ICREA, University of Barcelona, Barcelona, Spain
| | | | | | - Krzysztof Tunia
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Lei Zhao
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Liudmila N Mylnikova
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Lars Larsson
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Laure Metz
- Aix-Marseille Université, CNRS, Min. Culture, UMR 7269, LAMPEA, Maison Méditerranéenne des Sciences de l'Homme, Aix-en-Provence, France
| | - Levon Yepiskoposyan
- Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia
- Russian-Armenian University, Yerevan, Armenia
| | | | - Lucia Sarti
- Department of History and Cultural Heritage, University of Siena, Siena, Italy
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5500, Université Paul Sabatier, Toulouse, France
| | - Ludovic Slimak
- Centre d'Anthropobiologie et de Génomique de Toulouse, CNRS UMR 5500, Université Paul Sabatier, Toulouse, France
| | | | - Malou Blank
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Manuel González-Morales
- Instituto Internacional de Investigaciones Prehistóricas de Cantabria, Universidad de Cantabria, Banco Santander, Gobierno de Cantabria, Santander, Spain
| | - Mara Silvestrini
- Soprintendenza per i Beni Archeologici delle Marche, Ancona, Italy
| | | | - Marina S Nesterova
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Marina Rykun
- Cabinet of Anthropology, Tomsk State University, Tomsk, Russian Federation
| | - Mario Federico Rolfo
- Department of History, Humanities and Society, University of Rome Tor Vergata, Rome, Italy
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, Poznań, Poland
| | - Marcin Przybyła
- Institute of Archaeology, Jagiellonian University, Kraków, Poland
| | - Mauro Calattini
- Department of History and Cultural Heritage, University of Siena, Siena, Italy
| | - Mikhail Sablin
- Zoological Institute of Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | - Miluše Dobisíková
- Department of Anthropology, Czech National Museum, Prague, Czech Republic
| | - Morten Meldgaard
- Department of Health and Nature, University of Greenland, Nuuk, Greenland
| | | | - Natalia Berezina
- Department of Anthropology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Nick Card
- Archaeology Institute, University of Highlands and Islands, Orkney, UK
| | - Nikolai A Saveliev
- Scientific Research Center "Baikal region", Irkutsk State University, Irkutsk, Russian Federation
| | - Olga Poshekhonova
- IPND, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences, Tyumen, Russian Federation
| | - Olga Rickards
- Department of Biology, University of Rome Tor Vergata, Rome, Italy
| | - Olga V Lozovskaya
- Laboratory for Experimental Traceology, Institute for the History of Material Culture of the Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | | | | | - Paola Aurino
- Soprintendenza Archeologia, Belle Arti e Paesaggio per la provincia di Cosenza, Cosenza, Italy
| | - Pavel Kosintsev
- Paleoecology Laboratory, Institute of Plant and Animal Ecology, Ural Branch of the Russian Academy of Sciences, Ekaterinburg, Russian Federation
- Department of History of the Institute of Humanities, Ural Federal University, Ekaterinburg, Russian Federation
| | | | - Patricia Ríos
- Departamento de Prehistoria y Arqueología, Universidad Autónoma de Madrid, Madrid, Spain
| | - Peder Mortensen
- Centre for the Study of Early Agricultural Societies, Department of Cross-Cultural and Regional Studies, University of Copenhagen, Copenhagen, Denmark
| | - Per Lotz
- Museum Nordsjælland, Hillerød, Denmark
- Museum Vestsjælland, Holbæk, Denmark
| | - Per Persson
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Pernille Bangsgaard
- ArchaeoScience, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Pilar Prieto Martinez
- Department of History, University of Santiago de Compostela, Santiago de Compostela, Spain
| | - Piotr Włodarczak
- Institute of Archaeology and Ethnology, Polish Academy of Sciences, Kraków, Poland
| | - Roman V Smolyaninov
- Lipetsk Regional Scientific Public Organisation "Archaeological Research", Lipetsk, Russian Federation
| | - Rikke Maring
- Department of Health Technology, Section of Bioinformatics, Technical University of Denmark, Kongens Lyngby, Denmark
- Museum Østjylland, Randers, Denmark
| | | | - Ruben Badalyan
- Institute of Archaeology and Ethnography, National Academy of Sciences, Yerevan, Armenia
| | - Rune Iversen
- The Saxo Institute, University of Copenhagen, Copenhagen, Denmark
| | | | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russian Federation
- Center for Egyptological Studies, Russian Academy of Sciences, Moscow, Russian Federation
| | | | - Svetlana Borutskaya
- Department of Anthropology, Faculty of Biology, Lomonosov Moscow State University, Moscow, Russian Federation
| | - Svetlana Skochina
- IPND, Tyumen Scientific Centre, Siberian Branch of the Russian Academy of Sciences, Tyumen, Russian Federation
| | | | | | | | - Yuri B Serikov
- Nizhny Tagil State Socio-Pedagogical Institute, Nizhny Tagil, Russia
| | - Vyacheslav I Molodin
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russian Federation
| | - Vaclav Smrcka
- Institute for History of Medicine, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Victor Merts
- Centre for Archaeological Research, Toraighyrov University, Pavlodar, Kazakhstan
| | - Vivek Appadurai
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, Saint Petersburg, Russian Federation
| | | | - Kurt H Kjær
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Niels Lynnerup
- Laboratory of Biological Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- Institute of Statistical Sciences, School of Mathematics, University of Bristol, Bristol, UK
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA, USA
- Center for Computational Biology, University of California, Berkeley, CA, USA
| | - Simon Rasmussen
- Novo Nordisk Foundation Centre for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Richard Durbin
- Department of Genetics, University of Cambridge, Cambridge, UK
- Wellcome Sanger Institute, Hinxton, UK
| | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Olivier Delaneau
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, University of Lausanne, Lausanne, Switzerland
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Genetics, University of Cambridge, Cambridge, UK
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
| | - Kristian Kristiansen
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Department of Historical Studies, University of Gothenburg, Gothenburg, Sweden
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, Globe Institute, University of Copenhagen, Copenhagen, Denmark.
- GeoGenetics Group, Department of Zoology, University of Cambridge, Cambridge, UK.
- MARUM Center for Marine Environmental Sciences and Faculty of Geosciences, University of Bremen, Bremen, Germany.
| |
Collapse
|
4
|
Mattila TM, Svensson EM, Juras A, Günther T, Kashuba N, Ala-Hulkko T, Chyleński M, McKenna J, Pospieszny Ł, Constantinescu M, Rotea M, Palincaș N, Wilk S, Czerniak L, Kruk J, Łapo J, Makarowicz P, Potekhina I, Soficaru A, Szmyt M, Szostek K, Götherström A, Storå J, Netea MG, Nikitin AG, Persson P, Malmström H, Jakobsson M. Genetic continuity, isolation, and gene flow in Stone Age Central and Eastern Europe. Commun Biol 2023; 6:793. [PMID: 37558731 PMCID: PMC10412644 DOI: 10.1038/s42003-023-05131-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 07/10/2023] [Indexed: 08/11/2023] Open
Abstract
The genomic landscape of Stone Age Europe was shaped by multiple migratory waves and population replacements, but different regions do not all show similar patterns. To refine our understanding of the population dynamics before and after the dawn of the Neolithic, we generated and analyzed genomic sequence data from human remains of 56 individuals from the Mesolithic, Neolithic, and Eneolithic across Central and Eastern Europe. We found that Mesolithic European populations formed a geographically widespread isolation-by-distance zone ranging from Central Europe to Siberia, which was already established 10,000 years ago. We found contrasting patterns of population continuity during the Neolithic transition: people around the lower Dnipro Valley region, Ukraine, showed continuity over 4000 years, from the Mesolithic to the end of the Neolithic, in contrast to almost all other parts of Europe where population turnover drove this cultural change, including vast areas of Central Europe and around the Danube River.
Collapse
Affiliation(s)
- Tiina M Mattila
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden.
| | - Emma M Svensson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Anna Juras
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Torsten Günther
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Natalija Kashuba
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Department of Archaeology and Ancient History, Uppsala University, 75126, Uppsala, Sweden
| | - Terhi Ala-Hulkko
- Geography Research Unit, University of Oulu, 90014, Oulu, Finland
- Kerttu Saalasti Institute, University of Oulu, 90014, Oulu, Finland
| | - Maciej Chyleński
- Institute of Human Biology & Evolution, Faculty of Biology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - James McKenna
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
| | - Łukasz Pospieszny
- Department of Anthropology and Archaeology, University of Bristol, Bristol, UK
- Institute of Archaeology, University of Gdańsk, 80-851, Gdańsk, Poland
| | - Mihai Constantinescu
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, 050711, Bucharest, Romania
- Faculty of History, University of Bucharest, 030167, Bucharest, Romania
| | - Mihai Rotea
- National History Museum of Transylvania, Cluj-Napoca, Romania
| | - Nona Palincaș
- Vasile Pârvan Institute of Archaeology, Bucharest, Romania
| | - Stanisław Wilk
- Institute of Archaeology, Jagiellonian University, 31-007, Kraków, Poland
- Karkonosze Museum, 58-500, Jelenia Góra, Poland
| | - Lech Czerniak
- Institute of Archaeology, University of Gdańsk, 80-851, Gdańsk, Poland
| | - Janusz Kruk
- Polish Academy of Sciences, Institute of Archaeology and Ethnology, 31-016, Kraków, Poland
| | - Jerzy Łapo
- Museum of Folk Culture, 11-600, Węgorzewo, Poland
| | - Przemysław Makarowicz
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210, Kyiv, Ukraine
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, 3008, Bern, Switzerland
| | - Andrei Soficaru
- "Francisc I. Rainer" Institute of Anthropology, Romanian Academy, 050711, Bucharest, Romania
| | - Marzena Szmyt
- Faculty of Archaeology, Adam Mickiewicz University in Poznań, 61-614, Poznań, Poland
- Archaeological Museum, 61-781, Poznań, Poland
| | - Krzysztof Szostek
- Institute of Biological Sciences, Cardinal Stefan Wyszyński University in Warsaw, 01-938, Warszawa, Poland
| | - Anders Götherström
- Centre for Palaeogenetics, Stockholm University and the Swedish Museum of Natural History, 106 91, Stockholm, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, 106 91, Stockholm, Sweden
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, 106 91, Stockholm, Sweden
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, 6525, HP, Nijmegen, the Netherlands
- Department for Genomics & Immunoregulation, Life and Medical Sciences Institute (LIMES), University of Bonn, 53115, Bonn, Germany
| | - Alexey G Nikitin
- Grand Valley State University, Department of Biology, Allendale, MI, 49401, USA
| | - Per Persson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Museum of Cultural History, University of Oslo, 0130, Oslo, Norway
| | - Helena Malmström
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa
| | - Mattias Jakobsson
- Human Evolution, Department of Organismal Biology, Uppsala University, 75105, Uppsala, Sweden.
- Centre for Anthropological Research, University of Johannesburg, Auckland Park, 2006, Johannesburg, South Africa.
- SciLifeLab, Uppsala University, 75105, Uppsala, Sweden.
| |
Collapse
|
5
|
Chintalapati M, Patterson N, Moorjani P. The spatiotemporal patterns of major human admixture events during the European Holocene. eLife 2022; 11:77625. [PMID: 35635751 PMCID: PMC9293011 DOI: 10.7554/elife.77625] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2022] [Accepted: 05/29/2022] [Indexed: 11/16/2022] Open
Abstract
Recent studies have shown that admixture has been pervasive throughout human history. While several methods exist for dating admixture in contemporary populations, they are not suitable for sparse, low coverage ancient genomic data. Thus, we developed DATES (Distribution of Ancestry Tracts of Evolutionary Signals) that leverages ancestry covariance patterns across the genome of a single individual to infer the timing of admixture. DATES provides reliable estimates under various demographic scenarios and outperforms available methods for ancient DNA applications. Using DATES on~1100 ancient genomes from sixteen regions in Europe and west Asia, we reconstruct the chronology of the formation of the ancestral populations and the fine-scale details of the spread of Neolithic farming and Steppe pastoralist-related ancestry across Europe. By studying the genetic formation of Anatolian farmers, we infer that gene flow related to Iranian Neolithic farmers occurred before 9600 BCE, predating the advent of agriculture in Anatolia. Contrary to the archaeological evidence, we estimate that early Steppe pastoralist groups (Yamnaya and Afanasievo) were genetically formed more than a millennium before the start of Steppe pastoralism. Our analyses provide new insights on the origins and spread of farming and Indo-European languages, highlighting the power of genomic dating methods to elucidate the legacy of human migrations.
Collapse
Affiliation(s)
- Manjusha Chintalapati
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Nick Patterson
- Program in Medical and Population Genetics, Broad Institute, Cambridge, United States
| | - Priya Moorjani
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| |
Collapse
|
6
|
Serrano JG, Ordóñez AC, Fregel R. Paleogenomics of the prehistory of Europe: human migrations, domestication and disease. Ann Hum Biol 2021; 48:179-190. [PMID: 34459342 DOI: 10.1080/03014460.2021.1942205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A substantial portion of ancient DNA research has been centred on understanding European populations' origin and evolution. A rchaeological evidence has already shown that the peopling of Europe involved an intricate pattern of demic and/or cultural diffusion since the Upper Palaeolithic, which became more evident during the Neolithic and Bronze Age periods. However, ancient DNA data has been crucial in determining if cultural changes occurred due to the movement of ideas or people. With the advent of next-generation sequencing and population-based paleogenomic research, ancient DNA studies have been directed not only at the study of continental human migrations, but also to the detailed analysis of particular archaeological sites, the processes of domestication, or the spread of disease during prehistoric times. With this vast paleogenomic effort added to a proper archaeological contextualisation of results, a deeper understanding of Europe's peopling is starting to emanate.
Collapse
Affiliation(s)
- Javier G Serrano
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
| | - Alejandra C Ordóñez
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain.,Departamento Geografía e Historia, Facultad de Humanidades, Universidad de La Laguna, La Laguna, Spain
| | - Rosa Fregel
- Departamento de Bioquímica, Microbiología, Biología Celular y Genética, Faculta de Ciencias, Universidad de La Laguna, La Laguna, Spain
| |
Collapse
|
7
|
Fellows Yates JA, Lamnidis TC, Borry M, Andrades Valtueña A, Fagernäs Z, Clayton S, Garcia MU, Neukamm J, Peltzer A. Reproducible, portable, and efficient ancient genome reconstruction with nf-core/eager. PeerJ 2021; 9:e10947. [PMID: 33777521 PMCID: PMC7977378 DOI: 10.7717/peerj.10947] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Accepted: 01/25/2021] [Indexed: 12/13/2022] Open
Abstract
The broadening utilisation of ancient DNA to address archaeological, palaeontological, and biological questions is resulting in a rising diversity in the size of laboratories and scale of analyses being performed. In the context of this heterogeneous landscape, we present an advanced, and entirely redesigned and extended version of the EAGER pipeline for the analysis of ancient genomic data. This Nextflow pipeline aims to address three main themes: accessibility and adaptability to different computing configurations, reproducibility to ensure robust analytical standards, and updating the pipeline to the latest routine ancient genomic practices. The new version of EAGER has been developed within the nf-core initiative to ensure high-quality software development and maintenance support; contributing to a long-term life-cycle for the pipeline. nf-core/eager will assist in ensuring that a wider range of ancient DNA analyses can be applied by a diverse range of research groups and fields.
Collapse
Affiliation(s)
- James A. Fellows Yates
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, Münich, Germany
| | - Thiseas C. Lamnidis
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxime Borry
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aida Andrades Valtueña
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Zandra Fagernäs
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Stephen Clayton
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxime U. Garcia
- National Genomics Infrastructure, Science for Life Laboratory, Stockholm, Sweden
- Barntumörbanken, Department of Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
- Institute for Bioinformatics and Medical Informatics, Eberhard-Karls University Tübingen, Tübingen, Germany
| | - Alexander Peltzer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
- Quantitative Biology Center, Eberhard-Karls University Tübingen, Tübingen, Germany
| |
Collapse
|
8
|
Jensen TZT, Sjöström A, Fischer A, Rosengren E, Lanigan LT, Bennike O, Richter KK, Gron KJ, Mackie M, Mortensen MF, Sørensen L, Chivall D, Iversen KH, Taurozzi AJ, Olsen J, Schroeder H, Milner N, Sørensen M, Collins MJ. An integrated analysis of Maglemose bone points reframes the Early Mesolithic of Southern Scandinavia. Sci Rep 2020; 10:17244. [PMID: 33057088 PMCID: PMC7560828 DOI: 10.1038/s41598-020-74258-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 09/28/2020] [Indexed: 11/09/2022] Open
Abstract
The extensive peat bogs of Southern Scandinavia have yielded rich Mesolithic archaeological assemblages, with one of the most iconic artefacts being the bone point. Although great in number they remain understudied. Here we present a combined investigation of the typology, protein-based species composition, and absolute chronology of Maglemosian bone points. The majority of the bone points are made from cervids and bovines. However, changes both in species composition and barb morphology can be directly linked to a paucity of finds lasting nearly 600 years in Southern Scandinavia around 10,300 cal BP. We hypothesize that this hiatus was climate-driven and forced hunter-gatherers to abandon the lakes. Furthermore, the marked change in bone points coincides with a change in lithic technology. We, therefore, propose that the Maglemose culture in Southern Scandinavia is fundamentally divided into an Early Complex and a Late Complex.
Collapse
Affiliation(s)
- Theis Zetner Trolle Jensen
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark. .,Department of Archaeology, BioArCh, University of York, Environment Building, Wentworth Way, York, YO10 5NG, UK.
| | - Arne Sjöström
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, Box 192, 221 00, Lund, Sweden
| | - Anders Fischer
- Sealand Archaeology, Gl. Roesnaesvej 27, 4400, Kalundborg, Denmark
| | - Erika Rosengren
- Department of Archaeology and Ancient History, Lund University, Helgonavägen 3, Box 192, 221 00, Lund, Sweden.,Historical Museum, Lund University, Krafts Torg 1, 223 50, Lund, Sweden
| | - Liam Thomas Lanigan
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - Ole Bennike
- Geological Survey of Denmark and Greenland (GEUS), Øster Voldgade 10, Copenhagen K, Denmark
| | - Kristine Korzow Richter
- Department of Archaeology, Max Planck Institute for the Science of Human History, Kahlaische Strasse 10, 07745, Jena, Germany
| | - Kurt Joseph Gron
- Department of Archaeology, Durham University, South Road, Durham, DH1 3LE, UK
| | - Meaghan Mackie
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen N, Denmark
| | - Morten Fischer Mortensen
- Department of Environmental Archaeology and Materials Science, The Danish National Museum, I.C.Modewegsvej, 2800, Lyngby, Denmark
| | - Lasse Sørensen
- The Danish National Museum, Ancient Cultures of Denmark and the Mediterranean, Ny Vestergade 10, Prinsens Palæ, 1471, København K, Denmark
| | - David Chivall
- Oxford Radiocarbon Accelerator Unit (ORAU), School of Archaeology, University of Oxford, 1 South Parks Road, Oxford, OX1 3TG, UK
| | - Katrine Højholt Iversen
- Novo Nordisk Foundation Center for Protein Research, University of Copenhagen, Blegdamsvej 3b, 2200, Copenhagen N, Denmark.,Department of Health Technology, Technical University of Denmark, Kemitorvet, 2800, Kgs. Lyngby, Denmark
| | - Alberto John Taurozzi
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - Jesper Olsen
- Department of Physics and Astronomy, Aarhus AMS Centre (AARAMS), Aarhus University, Ny Munkegade 120, 8000, Aarhus C, Denmark
| | - Hannes Schroeder
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark
| | - Nicky Milner
- Department of Archaeology, University of York, King's Manor, York, YO1 7EP, UK
| | - Mikkel Sørensen
- Department of Archaeology, The Saxo Institute, University of Copenhagen, Karen Blixens plads 8, 2300, Copenhagen S, Denmark
| | - Matthew James Collins
- Section for Evolutionary Genomics, Faculty of Health and Medical Sciences, GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353, Copenhagen, Denmark. .,McDonald Institute for Archaeological Research, University of Cambridge, West Tower, Downing St, Cambridge, CB2 3ER, UK.
| |
Collapse
|
9
|
Abstract
Here we show the bacteriome of wasted chewing gums from five different countries and the microbial successions on wasted gums during three months of outdoors exposure. In addition, a collection of bacterial strains from wasted gums was set, and the biodegradation capability of different gum ingredients by the isolates was tested. Our results reveal that the oral microbiota present in gums after being chewed, characterised by the presence of species such as Streptococcus spp. or Corynebacterium spp., evolves in a few weeks to an environmental bacteriome characterised by the presence of Acinetobacter spp., Sphingomonas spp. and Pseudomonas spp. Wasted chewing gums collected worldwide contain a typical sub-aerial biofilm bacteriome, characterised by species such as Sphingomonas spp., Kocuria spp., Deinococcus spp. and Blastococcus spp. Our findings have implications for a wide range of disciplines, including forensics, contagious disease control, or bioremediation of wasted chewing gum residues.
Collapse
|
10
|
Hanel A, Carlberg C. Skin colour and vitamin D: An update. Exp Dermatol 2020; 29:864-875. [PMID: 32621306 DOI: 10.1111/exd.14142] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2020] [Revised: 06/14/2020] [Accepted: 06/25/2020] [Indexed: 02/06/2023]
Abstract
Homo sapiens evolved in East Africa and had dark skin, hair, and eyes, in order to protect against deleterious consequences of intensive UV radiation at equatorial latitudes. Intensive skin pigmentation was thought to bear the risk of inefficient vitamin D3 synthesis in the skin. This initiated the hypothesis that within the past 75 000 years, in which humans migrated to higher latitudes in Asia and Europe, the need for vitamin D3 synthesis served as an evolutionary driver for skin lightening. In this review, we summarize the recent archeogenomic reconstruction of population admixture in Europe and demonstrate that skin lightening happened as late as 5000 years ago through immigration of lighter pigmented populations from western Anatolia and the Russian steppe but not primarily via evolutionary pressure for vitamin D3 synthesis. We show that variations in genes encoding for proteins being responsible for the transport, metabolism and signalling of vitamin D provide alternative mechanisms of adaptation to a life in northern latitudes without suffering from consequences of vitamin D deficiency. This includes hypotheses explaining differences in the vitamin D status and response index of European populations.
Collapse
Affiliation(s)
- Andrea Hanel
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Carsten Carlberg
- School of Medicine, Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| |
Collapse
|
11
|
Beyond broad strokes: sociocultural insights from the study of ancient genomes. Nat Rev Genet 2020; 21:355-366. [DOI: 10.1038/s41576-020-0218-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/04/2020] [Indexed: 01/01/2023]
|
12
|
Jensen TZT, Niemann J, Iversen KH, Fotakis AK, Gopalakrishnan S, Vågene ÅJ, Pedersen MW, Sinding MHS, Ellegaard MR, Allentoft ME, Lanigan LT, Taurozzi AJ, Nielsen SH, Dee MW, Mortensen MN, Christensen MC, Sørensen SA, Collins MJ, Gilbert MTP, Sikora M, Rasmussen S, Schroeder H. A 5700 year-old human genome and oral microbiome from chewed birch pitch. Nat Commun 2019; 10:5520. [PMID: 31848342 PMCID: PMC6917805 DOI: 10.1038/s41467-019-13549-9] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 11/15/2019] [Indexed: 12/18/2022] Open
Abstract
The rise of ancient genomics has revolutionised our understanding of human prehistory but this work depends on the availability of suitable samples. Here we present a complete ancient human genome and oral microbiome sequenced from a 5700 year-old piece of chewed birch pitch from Denmark. We sequence the human genome to an average depth of 2.3× and find that the individual who chewed the pitch was female and that she was genetically more closely related to western hunter-gatherers from mainland Europe than hunter-gatherers from central Scandinavia. We also find that she likely had dark skin, dark brown hair and blue eyes. In addition, we identify DNA fragments from several bacterial and viral taxa, including Epstein-Barr virus, as well as animal and plant DNA, which may have derived from a recent meal. The results highlight the potential of chewed birch pitch as a source of ancient DNA.
Collapse
Affiliation(s)
- Theis Z T Jensen
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
- BioArch, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Jonas Niemann
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
- BioArch, Department of Archaeology, University of York, York, YO10 5DD, UK
| | - Katrine Højholt Iversen
- Department of Bio and Health Informatics, Technical University of Denmark, Kongens, Lyngby, 2800, Denmark
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Anna K Fotakis
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Shyam Gopalakrishnan
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Åshild J Vågene
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Mikkel Winther Pedersen
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Mikkel-Holger S Sinding
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Martin R Ellegaard
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Morten E Allentoft
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Liam T Lanigan
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Alberto J Taurozzi
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Sofie Holtsmark Nielsen
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Michael W Dee
- Centre for Isotope Research, University of Groningen, Groningen, 9747 AG, The Netherlands
| | - Martin N Mortensen
- The National Museum of Denmark, I.C. Modewegs Vej, Brede, Kongens Lyngby, 2800, Denmark
| | - Mads C Christensen
- The National Museum of Denmark, I.C. Modewegs Vej, Brede, Kongens Lyngby, 2800, Denmark
| | - Søren A Sørensen
- Museum Lolland-Falster, Frisegade 40, Nykøbing Falster, 4800, Denmark
| | - Matthew J Collins
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
- McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, CB2 3ER, UK
| | - M Thomas P Gilbert
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
- University Museum, NTNU, 7012, Trondheim, Norway
| | - Martin Sikora
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 2200, Denmark
| | - Hannes Schroeder
- The Globe Institute, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, 1353, Denmark.
| |
Collapse
|
13
|
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.
Collapse
|