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Doronicheva EV, Golovanova LV, Doronichev VB, Kurbanov RN. Archaeological evidence for two culture diverse Neanderthal populations in the North Caucasus and contacts between them. PLoS One 2023; 18:e0284093. [PMID: 37053172 PMCID: PMC10101426 DOI: 10.1371/journal.pone.0284093] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 03/23/2023] [Indexed: 04/14/2023] Open
Abstract
Neanderthals were widespread during the Middle Palaeolithic (MP) across Europe and Asia, including the Caucasus Mountains. Occupying the border between eastern Europe and West Asia, the Caucasus is important region regarding the Neanderthal occupation of Eurasia. On current radiometric estimates, the MP is represented in the Caucasus between about 260-210 ka and about 40 ka. Archaeological record indicates that several culture diverse MP hominin populations inhabited the Caucasus, but the region complex population history during this period remains poorly understood. In this paper, we identify for the first time the archaeological evidence indicating contacts between two culture diverse MP Neanderthal populations in the North Caucasus and discuss the nature of these contacts. Basing on the lithic assemblages that we excavated at Mezmaiskaya cave in the north-western Caucasus (Kuban River basin) and Saradj-Chuko grotto in the north-central Caucasus (Terek River basin), dating from MIS 5 to MIS 3, and comparative data from other MP sites in the Caucasus, we identify two large cultural regions that existed during the late MP in the North Caucasus. The distinctive toolkits and stone knapping technologies indicate that the MP assemblages from Mezmaiskaya cave and other sites in the west of North Caucasus represent a Caucasian variant of the Eastern Micoquian industry that was wide spread in central and eastern Europe, while the assemblages from Saradj-Chuko Grotto and other sites in the east of North Caucasus closely resemble the Zagros Mousterian industry that was wide spread in the Armenian Highlands, Lesser Caucasus and Zagros Mountains. The archaeological evidence implies that two culture diverse populations of Neanderthals settled the North Caucasus during the Late Pleistocene from two various source regions: from the Armenian Highlands and Lesser Caucasus along the Caspian Sea coast, and from Russian plain along the Sea of Azov coast.
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Affiliation(s)
- Ekaterina V Doronicheva
- Autonomous Nonprofit Organization in the Field of Humanitarian and Scientific Research «Laboratory of Prehistory», St. Petersburg, Russia
| | - Liubov V Golovanova
- Autonomous Nonprofit Organization in the Field of Humanitarian and Scientific Research «Laboratory of Prehistory», St. Petersburg, Russia
| | - Vladimir B Doronichev
- Autonomous Nonprofit Organization in the Field of Humanitarian and Scientific Research «Laboratory of Prehistory», St. Petersburg, Russia
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2
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Andreeva TV, Manakhov AD, Gusev FE, Patrikeev AD, Golovanova LV, Doronichev VB, Shirobokov IG, Rogaev EI. Genomic analysis of a novel Neanderthal from Mezmaiskaya Cave provides insights into the genetic relationships of Middle Palaeolithic populations. Sci Rep 2022; 12:13016. [PMID: 35906446 PMCID: PMC9338269 DOI: 10.1038/s41598-022-16164-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/05/2022] [Indexed: 11/09/2022] Open
Abstract
The Mezmaiskaya cave is located on the North Caucasus near the border that divides Europe and Asia. Previously, fossil remains for two Neanderthals were reported from Mezmaiskaya Cave. A tooth from the third archaic hominin specimen (Mezmaiskaya 3) was retrieved from layer 3 in Mezmaiskaya Cave. We performed genome sequencing of Mezmaiskaya 3. Analysis of partial nuclear genome sequence revealed that it belongs to a Homo sapiens neanderthalensis female. Based on a high-coverage mitochondrial genome sequence, we demonstrated that the relationships of Mezmaiskaya 3 to Mezmaiskaya 1 and Stajnia S5000 individuals were closer than those to other Neanderthals. Our data demonstrate the close genetic connections between the early Middle Palaeolithic Neanderthals that were replaced by genetically distant later group in the same geographic areas. Based on mitochondrial DNA (mtDNA) data, we suggest that Mezmaiskaya 3 was the latest Neanderthal individual from the early Neanderthal’s branches. We proposed a hierarchical nomenclature for the mtDNA haplogroups of Neanderthals. In addition, we retrieved ancestral mtDNA mutations in presumably functional sites fixed in the Neanderthal clades, and also provided the first data showing mtDNA heteroplasmy in Neanderthal specimen.
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Affiliation(s)
- Tatiana V Andreeva
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192.
| | - Andrey D Manakhov
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Fedor E Gusev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340.,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333.,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192
| | - Anton D Patrikeev
- Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333
| | | | | | - Ivan G Shirobokov
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Sciences, St. Petersburg, Russia, 199034
| | - Evgeny I Rogaev
- Center for Genetics and Life Science, Sirius University of Science and Technology, Sochi, Russia, 354340. .,Laboratory of Evolutionary Genomics, Department of Genomics and Human Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 119333. .,Faculty of Biology, Centre for Genetics and Genetic Technologies, Lomonosov Moscow State University, Moscow, Russia, 119192. .,Department of Psychiatry, University of Massachusetts Medical School, Worcester, MA, 01604, USA.
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3
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Petr M, Hajdinjak M, Fu Q, Essel E, Rougier H, Crevecoeur I, Semal P, Golovanova LV, Doronichev VB, Lalueza-Fox C, de la Rasilla M, Rosas A, Shunkov MV, Kozlikin MB, Derevianko AP, Vernot B, Meyer M, Kelso J. The evolutionary history of Neanderthal and Denisovan Y chromosomes. Science 2020; 369:1653-1656. [PMID: 32973032 DOI: 10.1126/science.abb6460] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/06/2020] [Indexed: 12/31/2022]
Abstract
Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.
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Affiliation(s)
- Martin Petr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,The Francis Crick Institute, NW1 1AT London, UK
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Hélène Rougier
- Department of Anthropology, California State University, Northridge, Northridge, CA 91330-8244, USA
| | | | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | | | | | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - Marco de la Rasilla
- Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Antonio Rosas
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoli P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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4
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Hajdinjak M, Fu Q, Hübner A, Petr M, Mafessoni F, Grote S, Skoglund P, Narasimham V, Rougier H, Crevecoeur I, Semal P, Soressi M, Talamo S, Hublin JJ, Gušić I, Kućan Ž, Rudan P, Golovanova LV, Doronichev VB, Posth C, Krause J, Korlević P, Nagel S, Nickel B, Slatkin M, Patterson N, Reich D, Prüfer K, Meyer M, Pääbo S, Kelso J. Reconstructing the genetic history of late Neanderthals. Nature 2018; 555:652-656. [PMID: 29562232 PMCID: PMC6485383 DOI: 10.1038/nature26151] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2017] [Accepted: 01/24/2018] [Indexed: 12/19/2022]
Abstract
Although it is known that Neandertals contributed DNA to modern humans1,2, not much is known about the genetic diversity of Neandertals or the relationship between late Neandertal populations at the time when their last interactions with early modern humans occurred and before they eventually disappeared. Our ability to retrieve DNA from a larger number of Neandertal individuals has been limited by poor preservation of endogenous DNA3 and large amounts of microbial and present-day human DNA that contaminate Neandertal skeletal remains3–5. Here we use hypochlorite treatment6 of as little as 9 mg of bone or tooth powder to generate between 1- and 2.7-fold genomic coverage of five 39,000- to 47,000-year-old Neandertals (i.e. late Neandertals), thereby doubling the number of Neandertals for which genome sequences are available. Genetic similarity among late Neandertals is well predicted by their geographical location, and comparison to the genome of an older Neandertal from the Caucasus2,7 indicates that a population turnover is likely to have occurred, either in the Caucasus or throughout Europe, towards the end of Neandertal history. We find that the bulk of Neandertal gene flow into early modern humans originated from one or more source populations that diverged from the Neandertals studied here at least 70,000 years ago, but after they split from a previously sequenced Neandertal from Siberia2 ~150,000 years ago. Although four of these Neandertals post-date the putative arrival of early modern humans into Europe, we do not detect any recent gene flow from early modern humans in their ancestry.
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Affiliation(s)
- Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Alexander Hübner
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Martin Petr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Steffi Grote
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Vagheesh Narasimham
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Hélène Rougier
- Department of Anthropology, California State University Northridge, Northridge, California 91330-8244, USA
| | | | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, 2300 RA Leiden, The Netherlands.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Jean-Jacques Hublin
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Ivan Gušić
- Croatian Academy of Sciences and Arts, HR-10000 Zagreb, Croatia
| | - Željko Kućan
- Croatian Academy of Sciences and Arts, HR-10000 Zagreb, Croatia
| | - Pavao Rudan
- Croatian Academy of Sciences and Arts, HR-10000 Zagreb, Croatia
| | | | | | - Cosimo Posth
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, Rümelin Strasse 23, 72070 Tübingen, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, Rümelin Strasse 23, 72070 Tübingen, Germany
| | - Petra Korlević
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Nick Patterson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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5
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Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 2017; 358:655-658. [PMID: 28982794 PMCID: PMC6185897 DOI: 10.1126/science.aao1887] [Citation(s) in RCA: 301] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/27/2017] [Indexed: 12/30/2022]
Abstract
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
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Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Pinghsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - David Reher
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Charlotte Hopfe
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Christoph Theunert
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Rebekah Rogers
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Pontus Skoglund
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Felix M Key
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Pavao Rudan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Željko Kućan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Ivan Gušić
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | | | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Aida M Andrés
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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6
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Soubrier J, Gower G, Chen K, Richards SM, Llamas B, Mitchell KJ, Ho SYW, Kosintsev P, Lee MSY, Baryshnikov G, Bollongino R, Bover P, Burger J, Chivall D, Crégut-Bonnoure E, Decker JE, Doronichev VB, Douka K, Fordham DA, Fontana F, Fritz C, Glimmerveen J, Golovanova LV, Groves C, Guerreschi A, Haak W, Higham T, Hofman-Kamińska E, Immel A, Julien MA, Krause J, Krotova O, Langbein F, Larson G, Rohrlach A, Scheu A, Schnabel RD, Taylor JF, Tokarska M, Tosello G, van der Plicht J, van Loenen A, Vigne JD, Wooley O, Orlando L, Kowalczyk R, Shapiro B, Cooper A. Early cave art and ancient DNA record the origin of European bison. Nat Commun 2016; 7:13158. [PMID: 27754477 PMCID: PMC5071849 DOI: 10.1038/ncomms13158] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 09/09/2016] [Indexed: 11/09/2022] Open
Abstract
The two living species of bison (European and American) are among the few terrestrial megafauna to have survived the late Pleistocene extinctions. Despite the extensive bovid fossil record in Eurasia, the evolutionary history of the European bison (or wisent, Bison bonasus) before the Holocene (<11.7 thousand years ago (kya)) remains a mystery. We use complete ancient mitochondrial genomes and genome-wide nuclear DNA surveys to reveal that the wisent is the product of hybridization between the extinct steppe bison (Bison priscus) and ancestors of modern cattle (aurochs, Bos primigenius) before 120 kya, and contains up to 10% aurochs genomic ancestry. Although undetected within the fossil record, ancestors of the wisent have alternated ecological dominance with steppe bison in association with major environmental shifts since at least 55 kya. Early cave artists recorded distinct morphological forms consistent with these replacement events, around the Last Glacial Maximum (LGM, ∼21–18 kya). The ancestry of the European bison (wisent) remains a mystery. Here, Cooper and colleagues examine ancient DNA from fossil remains of extinct bison, and reveal the wisent originated through the hybridization of the extinct Steppe bison and ancestors of modern cattle.
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Affiliation(s)
- Julien Soubrier
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Graham Gower
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kefei Chen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephen M Richards
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Kieren J Mitchell
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Simon Y W Ho
- School of Biological Sciences, University of Sydney, Sydney, New South Wales 2006, Australia
| | - Pavel Kosintsev
- Institute of Plant and Animal Ecology, Russian Academy of Sciences, 202 8 Marta Street, 620144 Ekaterinburg, Russia
| | - Michael S Y Lee
- School of Biological Sciences, Flinders University, South Australia 5001, Australia.,Earth Sciences Section, South Australian Museum, North Terrace, Adelaide, South Australia 5000, Australia
| | - Gennady Baryshnikov
- Zoological Institute RAS, Universitetskaya Naberezhnaya 1, 199034 St Petersburg, Russia
| | - Ruth Bollongino
- Palaeogenetics Group, Institute of Anthropology, University of Mainz D-55128, Mainz, Germany
| | - Pere Bover
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.,Department of Biodiversity and Conservation, Institut Mediterrani d'Estudis Avançats (CSIC-UIB), Cr. Miquel Marquès 21, 07190 Esporles, Illes Balears
| | - Joachim Burger
- Palaeogenetics Group, Institute of Anthropology, University of Mainz D-55128, Mainz, Germany
| | - David Chivall
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Evelyne Crégut-Bonnoure
- Museum Requien, 67 rue Joseph Vernet, 84000 Avignon, France.,Laboratoire TRACES UMR5608, Université Toulouse Jean Jaurès - Maison de la Recherche, 5 allée Antonio Machado, 31058 Toulouse, France
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | | | - Katerina Douka
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Damien A Fordham
- Environment Institute and School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Federica Fontana
- Dipartimento di Studi Umanistici, Università degli Studi di Ferrara, 12 Via Paradiso, 44121 Ferrara, Italy
| | - Carole Fritz
- CNRS, TRACES, UMR 5608 et CREAP, MSHS Toulouse, USR 3414, Maison de la Recherche, 5 allées Antonio Machado, 31058 Toulouse, France
| | - Jan Glimmerveen
- CERPOLEX/Mammuthus, Anna Paulownastraat 25A, NL-2518 BA Den Haag, The Netherlands
| | | | - Colin Groves
- School of Archaeology and Anthropology, Australian National University, Building 14, Canberra, Australian National University 0200, Australia
| | - Antonio Guerreschi
- Dipartimento di Studi Umanistici, Università degli Studi di Ferrara, 12 Via Paradiso, 44121 Ferrara, Italy
| | - Wolfgang Haak
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia.,Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Oxford OX1 3QY, UK
| | - Emilia Hofman-Kamińska
- Mammal Research Institute, Polish Academy of Sciences, Waszkiewicza 1c, 17-230 Białowieża, Poland
| | - Alexander Immel
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Marie-Anne Julien
- Department of Archaeology, Centre for the Archaeology of Human Origins, University of Southampton, Avenue Campus, Southampton SO17 1BF, UK.,Unité Histoire naturelle de l'Homme préhistorique (UMR 7194), Sorbonne Universités, Muséum national d'Histoire narurelle, CNRS, 1 rue René Panhard, 75013 Paris, France
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Oleksandra Krotova
- Department of Stone Age, Institute of Archaeology, National Ukrainian Academy of Science, 04210 Kiev, Ukraine
| | - Frauke Langbein
- Institute for Archaeological Sciences, Archaeo and Palaeogenetics, University of Tübingen, 72070 Tübingen, Germany
| | - Greger Larson
- Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology, Dyson Perrins Building, South Parks Road, Oxford OX1 3QY, UK
| | - Adam Rohrlach
- School of Mathematical Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Anthropology, University of Mainz D-55128, Mainz, Germany
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, Missouri 65211, USA
| | - Małgorzata Tokarska
- Mammal Research Institute, Polish Academy of Sciences, Waszkiewicza 1c, 17-230 Białowieża, Poland
| | - Gilles Tosello
- Chercheur associé, CREAP, MSHS Toulouse, URS 3414, Maison de la Recherche, 5 allées Antonio Machado, 31058 Toulouse, France
| | - Johannes van der Plicht
- Centre for Isotope Research, Radiocarbon Laboratory, University of Groningen, Nijenborg 4, NI-9747 AG Groningen, The Netherlands
| | - Ayla van Loenen
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Jean-Denis Vigne
- Centre National de la Recherche Scientifique, Muséum National d'Histoire Naturelle, Sorbonne Universités, UMR7209, 'Archéozoologie, archéobotanique: sociétés, pratiques et environnements', CP56, 55 rue Buffon, 75005 Paris, France
| | - Oliver Wooley
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, ØsterVoldgade 5-7, Copenhagen 1350K, Denmark.,Université de Toulouse, University Paul Sabatier, Laboratoire AMIS, CNRS UMR 5288, 37 Allées Jules Guesde, Toulouse 31000, France
| | - Rafał Kowalczyk
- Mammal Research Institute, Polish Academy of Sciences, Waszkiewicza 1c, 17-230 Białowieża, Poland
| | - Beth Shapiro
- UCSC Genomics Institute, University of California Santa Cruz, 1156 High Street, Santa Cruz, California 95064, USA
| | - Alan Cooper
- Australian Centre for Ancient DNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
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7
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Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2013; 505:43-9. [PMID: 24352235 PMCID: PMC4031459 DOI: 10.1038/nature12886] [Citation(s) in RCA: 1130] [Impact Index Per Article: 102.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2013] [Accepted: 11/15/2013] [Indexed: 12/13/2022]
Abstract
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
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Affiliation(s)
- Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fernando Racimo
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Flora Jay
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Sriram Sankararaman
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Susanna Sawyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Anja Heinze
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Peter H Sudmant
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Swapan Mallick
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany [2] Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Martin Kircher
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany [2] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Martin Kuhlwilm
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Ongyerth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Siebauer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christoph Theunert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Arti Tandon
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Priya Moorjani
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph Pickrell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James C Mullikin
- Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ines Hellmann
- 1] Max F. Perutz Laboratories, Mathematics and Bioscience Group, Campus Vienna Biocenter 5, Vienna 1030, Austria [2] Ludwig-Maximilians-Universität München, Martinsried, 82152 Munich, Germany
| | | | - Hélène Blanche
- Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France
| | - Howard Cann
- Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France
| | - Jacob O Kitzman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Trygve E Bakken
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | | | - Michael V Shunkov
- Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Anatoli P Derevianko
- Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Bence Viola
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - David Reich
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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8
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Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, Fritz MHY, Hansen NF, Durand EY, Malaspinas AS, Jensen JD, Marques-Bonet T, Alkan C, Prüfer K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, de la Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. A draft sequence of the Neandertal genome. Science 2010; 328:710-722. [PMID: 20448178 PMCID: PMC5100745 DOI: 10.1126/science.1188021] [Citation(s) in RCA: 2097] [Impact Index Per Article: 149.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Neandertals, the closest evolutionary relatives of present-day humans, lived in large parts of Europe and western Asia before disappearing 30,000 years ago. We present a draft sequence of the Neandertal genome composed of more than 4 billion nucleotides from three individuals. Comparisons of the Neandertal genome to the genomes of five present-day humans from different parts of the world identify a number of genomic regions that may have been affected by positive selection in ancestral modern humans, including genes involved in metabolism and in cognitive and skeletal development. We show that Neandertals shared more genetic variants with present-day humans in Eurasia than with present-day humans in sub-Saharan Africa, suggesting that gene flow from Neandertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
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Affiliation(s)
- Richard E. Green
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Johannes Krause
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Adrian W. Briggs
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Tomislav Maricic
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Udo Stenzel
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Martin Kircher
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Weiwei Zhai
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Markus Hsi-Yang Fritz
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - Nancy F. Hansen
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Eric Y. Durand
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Anna-Sapfo Malaspinas
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Jeffrey D. Jensen
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01655, USA
| | - Tomas Marques-Bonet
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Institute of Evolutionary Biology (UPF-CSIC), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Can Alkan
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Hernán A. Burbano
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Jeffrey M. Good
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
- Division of Biological Sciences, University of Montana, Missoula, MT 59812, USA
| | - Rigo Schultz
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Ayinuer Aximu-Petri
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Anne Butthof
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Barbara Höber
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Barbara Höffner
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Madlen Siegemund
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Antje Weihmann
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Chad Nusbaum
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Eric S. Lander
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Carsten Russ
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nathaniel Novod
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | | | - Christine Verna
- Department of Human Evolution, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Pavao Rudan
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | - Dejana Brajkovic
- Croatian Academy of Sciences and Arts, Institute for Quaternary Paleontology and Geology, Ante Kovacica 5, HR-10000 Zagreb, Croatia
| | - Željko Kucan
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | - Ivan Gušic
- Croatian Academy of Sciences and Arts, Zrinski trg 11, HR-10000 Zagreb, Croatia
| | | | | | - Carles Lalueza-Fox
- Institute of Evolutionary Biology (UPF-CSIC), Dr. Aiguader 88, 08003 Barcelona, Spain
| | - Marco de la Rasilla
- Área de Prehistoria Departamento de Historia Universidad de Oviedo, Oviedo, Spain
| | - Javier Fortea
- Área de Prehistoria Departamento de Historia Universidad de Oviedo, Oviedo, Spain
| | - Antonio Rosas
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, CSIC, Madrid, Spain
| | - Ralf W. Schmitz
- Der Landschaftverband Rheinlund–Landesmuseum Bonn, Bachstrasse 5-9, D-53115 Bonn, Germany
- Abteilung für Vor- und Frühgeschichtliche Archäologie, Universität Bonn, Germany
| | | | - Evan E. Eichler
- Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daniel Falush
- Department of Microbiology, University College Cork, Cork, Ireland
| | - Ewan Birney
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK
| | - James C. Mullikin
- Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, CA 94720, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Michael Lachmann
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
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9
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Briggs AW, Good JM, Green RE, Krause J, Maricic T, Stenzel U, Lalueza-Fox C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Schmitz R, Doronichev VB, Golovanova LV, de la Rasilla M, Fortea J, Rosas A, Pääbo S. Targeted retrieval and analysis of five Neandertal mtDNA genomes. Science 2009; 325:318-21. [PMID: 19608918 DOI: 10.1126/science.1174462] [Citation(s) in RCA: 289] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Analysis of Neandertal DNA holds great potential for investigating the population history of this group of hominins, but progress has been limited due to the rarity of samples and damaged state of the DNA. We present a method of targeted ancient DNA sequence retrieval that greatly reduces sample destruction and sequencing demands and use this method to reconstruct the complete mitochondrial DNA (mtDNA) genomes of five Neandertals from across their geographic range. We find that mtDNA genetic diversity in Neandertals that lived 38,000 to 70,000 years ago was approximately one-third of that in contemporary modern humans. Together with analyses of mtDNA protein evolution, these data suggest that the long-term effective population size of Neandertals was smaller than that of modern humans and extant great apes.
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Affiliation(s)
- Adrian W Briggs
- Max-Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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10
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Abstract
Mezmaiskaya Cave has yielded more than 10,000 artifacts, thousands of very well preserved faunal remains, and hominin remains, found in seven Middle Paleolithic (Mousterian) and three Upper Paleolithic levels. A complete Neanderthal infant skeleton was preserved in anatomical juxtaposition lying on a large limestone block, overlain by the earliest Mousterian layer, Layer 3. Twenty-four skull fragments from a 1-2 year-old Neanderthal infant, showing post-mortem deformation, occurred in a pit originating in the Mousterian Layer 2 and penetrating into underlying layers 2A and 2B(1). Bone from Layer 2A was dated by AMS 14C at 35.8-36.3+/-0.5 kyr BP. Direct dating of Neanderthal bone from Layer 3 gave an age of 29 kyr, but that is now considered to be due to contamination by modern carbon. Fourteen large mammal teeth from Layers 2 through 3 have been dated by standard electron spin resonance (ESR). Low U concentrations in both the enamel and dentine ensure that ESR ages do not depend significantly on the U uptake model, but do depend strongly on the sedimentary dose rates. Assuming a sedimentary water concentration equal to 20 wt%, ESR ages for the Mousterian layers range from 36.2 to 73.0+/-5.0 ka.
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Affiliation(s)
- A R Skinner
- Department of Chemistry, Williams College, Williamstown, MA 01267, USA.
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11
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Blackwell BAB, Liang S, Golovanova LV, Doronichev VB, Skinner AR, Blickstein JIB. ESR at Treugol’naya Cave, Northern Caucasus Mt., Russia: Dating Russia's oldest archaeological site and paleoclimatic change in Oxygen Isotope Stage 11. Appl Radiat Isot 2005; 62:237-45. [PMID: 15607455 DOI: 10.1016/j.apradiso.2004.08.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
At 1510 m asl, Treugol'naya Cave, Russia, is the highest cave showing evidence for human occupation in eastern Europe. Layers 4-7 in the 4.5-m-thick sequence yielded many artifacts representing Lower Paleolithic pebble and flake tool industries. Abundant faunal remains include extinct Middle Pleistocene species. Palynological, paleomagnetic, and microsedimentological analyses indicate that several climatic changes of different magnitudes occurred in the sequence. To determine absolute ages for Treugol'naya, 32 independent subsamples from nine ungulate teeth collected from the Lower Paleolithic layers were dated by standard and isochron electron spin resonance (ESR) analyses. Isochron analyses indicate that the teeth experienced no significant U leaching or secondary uptake, and that linear uptake (LU) provides accurate ages. Layers 4b through 5b dated to 365+/-12-406+/-15 ka. Therefore, hominids visited the site periodically throughout Oxygen Isotope Stage (OIS) 11, indicating that they utilized resources at elevations >1000 m at least seasonally by 400 ka. ESR, paleomagnetic, palynological and paleontological analyses all indicate that the Lower Paleolithic Layers 4-5 correlate with OIS 11. The thickness of Layers 4-5 (more than 1.5 m) makes this one of the thickest OIS 11 terrestrial deposits known.
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