1
|
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.
Collapse
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
| |
Collapse
|
3
|
Prüfer K, Munch K, Hellmann I, Akagi K, Miller JR, Walenz B, Koren S, Sutton G, Kodira C, Winer R, Knight JR, Mullikin JC, Meader SJ, Ponting CP, Lunter G, Higashino S, Hobolth A, Dutheil J, Karakoç E, Alkan C, Sajjadian S, Catacchio CR, Ventura M, Marques-Bonet T, Eichler EE, André C, Atencia R, Mugisha L, Junhold J, Patterson N, Siebauer M, Good JM, Fischer A, Ptak SE, Lachmann M, Symer DE, Mailund T, Schierup MH, Andrés AM, Kelso J, Pääbo S. The bonobo genome compared with the chimpanzee and human genomes. Nature 2012; 486:527-31. [PMID: 22722832 DOI: 10.1038/nature11128] [Citation(s) in RCA: 284] [Impact Index Per Article: 23.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Accepted: 04/05/2012] [Indexed: 01/09/2023]
Abstract
Two African apes are the closest living relatives of humans: the chimpanzee (Pan troglodytes) and the bonobo (Pan paniscus). Although they are similar in many respects, bonobos and chimpanzees differ strikingly in key social and sexual behaviours, and for some of these traits they show more similarity with humans than with each other. Here we report the sequencing and assembly of the bonobo genome to study its evolutionary relationship with the chimpanzee and human genomes. We find that more than three per cent of the human genome is more closely related to either the bonobo or the chimpanzee genome than these are to each other. These regions allow various aspects of the ancestry of the two ape species to be reconstructed. In addition, many of the regions that overlap genes may eventually help us understand the genetic basis of phenotypes that humans share with one of the two apes to the exclusion of the other.
Collapse
Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|