A High-Coverage Genome Sequence from an Archaic Denisovan Individual
Matthias MeyerDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyMartin KircherThe Minerva Research Group for Bioinformatics, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck SocietyMarie-Theres GansaugeDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyHeng LiBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USAFernando RacimoDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanySwapan Mallick2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USAJoshua G. SchraiberDepartment of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USAFlora JayDepartment of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USAKay PrüferGenomes, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck SocietyCesare de FilippoDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyPeter H. SudmantDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USACan AlkanDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USAQiaomei FuCAS-MPS Joint Laboratory for Human Evolution, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 100044 Beijing, ChinaRon DoBroad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USANadin RohlandDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAArti Tandon3Department of Genetics, Harvard Medical School, Boston, MA 02115, USAMichael SiebauerDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyRichard E. GreenJack Baskin School of Engineering, University of California, Santa Cruz, Santa Cruz, CA 95064, USAKatarzyna BrycDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAAdrian W. BriggsDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAUdo StenzelThe Minerva Research Group for Bioinformatics, Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Max Planck SocietyJesse DabneyDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyJay ShendureDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USAJacob O. KitzmanDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USAMichael F. HammerArizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USAM.V. ShunkovPalaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, RussiaА. П. ДеревянкоPalaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, RussiaNick Patterson2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USAAida M. AndrésDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanyEvan E. EichlerDepartment of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USAMontgomery SlatkinDepartment of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USADavid ReichDepartment of Genetics, Harvard Medical School, Boston, MA 02115, USAJanet KelsoDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, GermanySvante PääboDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
2012en
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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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