title: The complete genome sequence of a Neanderthal from the Altai Mountains.
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.
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Kay
authors.initials: K
authors.lastname: Prüfer
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
authors.forename: Fernando
authors.initials: F
authors.lastname: Racimo
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Nick
authors.initials: N
authors.lastname: Patterson
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
authors.forename: Flora
authors.initials: F
authors.lastname: Jay
authors.affiliation: 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Sriram
authors.initials: S
authors.lastname: Sankararaman
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Susanna
authors.initials: S
authors.lastname: Sawyer
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Anja
authors.initials: A
authors.lastname: Heinze
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Renaud
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Peter H
authors.initials: PH
authors.lastname: Sudmant
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Cesare
authors.initials: C
authors.lastname: de Filippo
authors.affiliation: Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA.
authors.forename: Heng
authors.initials: H
authors.lastname: Li
authors.affiliation: 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Swapan
authors.initials: S
authors.lastname: Mallick
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Dannemann
authors.affiliation: 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.
authors.forename: Qiaomei
authors.initials: Q
authors.lastname: Fu
authors.affiliation: 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.
authors.forename: Martin
authors.initials: M
authors.lastname: Kircher
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Martin
authors.initials: M
authors.lastname: Kuhlwilm
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Lachmann
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Meyer
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Matthias
authors.initials: M
authors.lastname: Ongyerth
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Michael
authors.initials: M
authors.lastname: Siebauer
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Christoph
authors.initials: C
authors.lastname: Theunert
authors.affiliation: 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Arti
authors.initials: A
authors.lastname: Tandon
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Priya
authors.initials: P
authors.lastname: Moorjani
authors.affiliation: Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Joseph
authors.initials: J
authors.lastname: Pickrell
authors.affiliation: Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.
authors.forename: James C
authors.initials: JC
authors.lastname: Mullikin
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Vohr
authors.affiliation: Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA.
authors.forename: Richard E
authors.initials: RE
authors.lastname: Green
authors.affiliation: 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.
authors.forename: Ines
authors.initials: I
authors.lastname: Hellmann
authors.affiliation: Department of Biology, Emory University, Atlanta, Georgia 30322, USA.
authors.forename: Philip L F
authors.initials: PL
authors.lastname: Johnson
authors.affiliation: Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France.
authors.forename: Hélène
authors.initials: H
authors.lastname: Blanche
authors.affiliation: Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France.
authors.forename: Howard
authors.initials: H
authors.lastname: Cann
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Jacob O
authors.initials: JO
authors.lastname: Kitzman
authors.affiliation: Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA.
authors.forename: Jay
authors.initials: J
authors.lastname: Shendure
authors.affiliation: 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, Seattle, Washington 98195, USA.
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.affiliation: Allen Institute for Brain Science, Seattle, Washington 98103, USA.
authors.forename: Ed S
authors.initials: ES
authors.lastname: Lein
authors.affiliation: Allen Institute for Brain Science, Seattle, Washington 98103, USA.
authors.forename: Trygve E
authors.initials: TE
authors.lastname: Bakken
authors.affiliation: ANO Laboratory of Prehistory 14 Linia 3-11, St. Petersburg 1990 34, Russia.
authors.forename: Liubov V
authors.initials: LV
authors.lastname: Golovanova
authors.affiliation: ANO Laboratory of Prehistory 14 Linia 3-11, St. Petersburg 1990 34, Russia.
authors.forename: Vladimir B
authors.initials: VB
authors.lastname: Doronichev
authors.affiliation: Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia.
authors.forename: Michael V
authors.initials: MV
authors.lastname: Shunkov
authors.affiliation: Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia.
authors.forename: Anatoli P
authors.initials: AP
authors.lastname: Derevianko
authors.affiliation: Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Bence
authors.initials: B
authors.lastname: Viola
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
authors.forename: Montgomery
authors.initials: M
authors.lastname: Slatkin
authors.affiliation: 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.
authors.forename: David
authors.initials: D
authors.lastname: Reich
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Janet
authors.initials: J
authors.lastname: Kelso
authors.affiliation: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors.forename: Svante
authors.initials: S
authors.lastname: Pääbo
mesh_terms: D000349:Africa; D000818:Animals; D059552:Caves; D056915:DNA Copy Number Variations / Q000235:genetics; D005260:Female; D005580:Fossils; D051456:Gene Flow / Q000235:genetics; D005787:Gene Frequency; D016678:Genome / Q000235:genetics*; D006579:Heterozygote; D006801:Humans; D007178:Inbreeding; D008957:Models, Genetic; D059125:Neanderthals / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D011156:Population Density; D012800:Siberia / Q000208:ethnology; D050277:Toe Phalanges / Q000033:anatomy & histology