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      The complete genome sequence of a Neandertal from the Altai Mountains

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      1 ,   2 , 3 , 2 , 3 , 1 , 1 , 1 , 5 , 1 , 3 , 3 , 4 , 1 , 1 , 16 , 1 , 5 , 1 , 1 , 1 , 1 , 1 , 1 , 3 , 4 , 4 , 4 , 6 , 7 , 7 , , 9 , 10 , 10 , 5 , 5 , 5 , 11 , 12 , 12 , 13 , 13 , 14 , 14 , 15 , 2 , 3 , 4 ,   1 , 1

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          Abstract

          We present a high-quality genome sequence of a Neandertal 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 Neandertal 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 Neandertals, 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 Neandertal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neandertals and Denisovans.

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          Most cited references 31

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          A high-coverage genome sequence from an archaic Denisovan individual.

          We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of "missing evolution" in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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            Analysis of genetic inheritance in a family quartet by whole-genome sequencing.

            We analyzed the whole-genome sequences of a family of four, consisting of two siblings and their parents. Family-based sequencing allowed us to delineate recombination sites precisely, identify 70% of the sequencing errors (resulting in > 99.999% accuracy), and identify very rare single-nucleotide polymorphisms. We also directly estimated a human intergeneration mutation rate of approximately 1.1 x 10(-8) per position per haploid genome. Both offspring in this family have two recessive disorders: Miller syndrome, for which the gene was concurrently identified, and primary ciliary dyskinesia, for which causative genes have been previously identified. Family-based genome analysis enabled us to narrow the candidate genes for both of these Mendelian disorders to only four. Our results demonstrate the value of complete genome sequencing in families.
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              Patterns of damage in genomic DNA sequences from a Neandertal.

              High-throughput direct sequencing techniques have recently opened the possibility to sequence genomes from Pleistocene organisms. Here we analyze DNA sequences determined from a Neandertal, a mammoth, and a cave bear. We show that purines are overrepresented at positions adjacent to the breaks in the ancient DNA, suggesting that depurination has contributed to its degradation. We furthermore show that substitutions resulting from miscoding cytosine residues are vastly overrepresented in the DNA sequences and drastically clustered in the ends of the molecules, whereas other substitutions are rare. We present a model where the observed substitution patterns are used to estimate the rate of deamination of cytosine residues in single- and double-stranded portions of the DNA, the length of single-stranded ends, and the frequency of nicks. The results suggest that reliable genome sequences can be obtained from Pleistocene organisms.
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                Author and article information

                Journal
                0410462
                6011
                Nature
                Nature
                Nature
                0028-0836
                1476-4687
                18 April 2014
                18 December 2013
                2 January 2014
                02 July 2014
                : 505
                : 7481
                : 43-49
                Affiliations
                [1 ]Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
                [2 ]Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
                [3 ]Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
                [4 ]Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
                [5 ]Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
                [6 ]Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
                [7 ]Department of Biomolecular Engineering, University of California, Santa Cruz 95064, USA
                [8 ]Ludwig-Maximilians-Universität München, Martinsried 82152, Munich, Germany
                [9 ]Department of Biology, Emory University, Atlanta, Georgia 30322, USA
                [10 ]Fondation Jean Dausset, Centre d’Étude du Polymorphisme Humain (CEPH), Paris, France
                [11 ]Howard Hughes Medical Institute, Seattle, WA 98195, USA
                [12 ]Allen Institute for Brain Science, Seattle, Washington 98103, USA
                [13 ]ANO Laboratory of Prehistory 14 Linia 3-11, St. Petersburg, 1990 34, Russia
                [14 ]Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
                [15 ]Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
                [16 ]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
                Author notes
                [* ]Correspondence to: Montgomery Slatkin, David Reich and Svante Pääbo
                Article
                NIHMS541101
                10.1038/nature12886
                4031459
                24352235

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