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RESEARCH ARTICLE · Science · 2010

A Draft Sequence of the Neandertal Genome

Richard Edward Green, Johannes Krause, Adrian W. Briggs, Tomislav Maričić, Udo Stenzel, Martin Kircher, Nick J. Patterson, Heng Li, Weiwei Zhai, Markus Hsi-Yang Fritz, Nancy Fisher Hansen, Eric Y. Durand, Anna‐Sapfo Malaspinas, Jeffrey D. Jensen, Tomàs Marquès‐Bonet, Can Alkan, Kay Prüfer, Matthias Meyer, Hernán A. Burbano, Jeffrey Martin Good, Rigo Schultz, Ayinuer Aximu‐Petri, Anne Butthof, Barbara Höber, Barbara Höffner, Madlen Siegemund, Antje Weihmann, Chad Nusbaum, Eric S. Lander, Carsten Russ, Nathaniel Novod, Jason P. Affourtit, Michael Egholm, Christine Verna, Pavao Rudan, Dejana Brajković, Željko Kućan, Ivan Gušic, Vladimir Borisovich Doronichev, Liubov Vitalievna Golovanova, Carles Lalueza‐Fox, Marco de la Rasilla Vives, Javier Fortea, Antonio Rosas, Ralf W. Schmitz, Philip L. F. Johnson, Evan E. Eichler, Daniel Falush, Ewan Birney, James C. Mullikin, Montgomery Slatkin, Rasmus Nielsen, Janet F. Kelso, Michael Lachmann, David Reich, Svante Pääbo

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A Draft Sequence of the Neandertal GenomeOriginalThe NIH Human Microbiome Project2098The UCSC Genome Browser database: update 20111811Genetic history of an archaic hominin group from Denisova Cave in Siberia1983The real cost of sequencing: higher than you think!373Initial impact of the sequencing of the human genome1042Testing for Ancient Admixture between Closely Related Populations1365Human-specific loss of regulatory DNA and the evolution of human-specific traits535Hunter-gatherer genomic diversity suggests a southern African origin for modern humans502A framework for variation discovery and genotyping using next-generation DNA sequencing data11464g:Profiler—a web server for functional interpretation of gene lists (2011 update)504Inference of human population history from individual whole-genome sequences2625The Shaping of Modern Human Immune Systems by Multiregional Admixture with Archaic Humans537Assemblathon 1: A competitive assessment of de novo short read assembly methods507Bayesian inference of ancient human demography from individual genome sequences597An Aboriginal Australian Genome Reveals Separate Human Dispersals into Asia783Denisova Admixture and the First Modern Human Dispersals into Southeast Asia and Oceania655Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform1101Insights into hominid evolution from the gorilla genome sequence754Molecular phylogenetics: principles and practice754A “Copernican” Reassessment of the Human Mitochondrial DNA Tree from its Root528Origins and Genetic Legacy of Neolithic Farmers and Hunter-Gatherers in Europe613Evolution of Human-Specific Neural SRGAP2 Genes by Incomplete Segmental Duplication407Butterfly genome reveals promiscuous exchange of mimicry adaptations among species1189The bonobo genome compared with the chimpanzee and human genomes579Polar and brown bear genomes reveal ancient admixture and demographic footprints of past climate change353Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers342Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution636A High-Coverage Genome Sequence from an Archaic Denisovan Individual1961Ancient Admixture in Human History2839Revising the human mutation rate: implications for understanding human evolution605Genomic Variation in Seven Khoe-San Groups Reveals Adaptation and Complex African History469The Date of Interbreeding between Neandertals and Modern Humans460The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils630The great human expansion404Analyses of pig genomes provide insight into porcine demography and evolution1387Inference of Population Splits and Mixtures from Genome-Wide Allele Frequency Data2720Multiplex Targeted Sequencing Identifies Recurrently Mutated Genes in Autism Spectrum Disorders1239Geologic Life: Prehistory, Climate, Futures in the Anthropocene399On the antiquity of language: the reinterpretation of Neandertal linguistic capacities and its consequences436Variable NK cell receptors and their MHC class I ligands in immunity, reproduction and human evolution476DNA analysis of an early modern human from Tianyuan Cave, China608Towards practical, high-capacity, low-maintenance information storage in synthesized DNA1215Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium465Single-stranded DNA library preparation for the sequencing of ancient or damaged DNA540mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters1666Inferring Phylogeny and Introgression using RADseq Data: An Example from Flowering Plants (Pedicularis: Orobanchaceae)514The Genomic Signature of Crop-Wild Introgression in Maize346Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse841Accurate sex identification of ancient human remains using DNA shotgun sequencing511Adaptive introgression in animals: examples and comparison to new mutation and standing variation as sources of adaptive variation704Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments1442Genome-wide evidence for speciation with gene flow in Heliconius butterflies648The genetic causes of convergent evolution815Complete Mitochondrial Genomes of Ancient Canids Suggest a European Origin of Domestic Dogs526Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans961The complete genome sequence of a Neanderthal from the Altai Mountains2248Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico508Genome Sequencing Highlights the Dynamic Early History of Dogs624Derived immune and ancestral pigmentation alleles in a 7,000-year-old Mesolithic European362Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal498The genomic landscape of Neanderthal ancestry in present-day humans1105Resurrecting Surviving Neandertal Lineages from Modern Human Genomes561The Systems View of Life1346Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX536Population Genomics Reveal Recent Speciation and Rapid Evolutionary Adaptation in Polar Bears409Inferring human population size and separation history from multiple genome sequences1070The timing and spatiotemporal patterning of Neanderthal disappearance895Ancient human genomes suggest three ancestral populations for present-day Europeans1351Evaluating the Use of ABBA–BABA Statistics to Locate Introgressed Loci744ANGSD: Analysis of Next Generation Sequencing Data2971The UCSC Genome Browser database: 2015 update874Extensive introgression in a malaria vector species complex revealed by phylogenomics651Evolution of Darwin’s finches and their beaks revealed by genome sequencing983Massive migration from the steppe was a source for Indo-European languages in Europe1941Mountain gorilla genomes reveal the impact of long-term population decline and inbreeding470Complete Genomes Reveal Signatures of Demographic and Genetic Declines in the Woolly Mammoth376Evidence for archaic adaptive introgression in humans520Ancient Wolf Genome Reveals an Early Divergence of Domestic Dog Ancestors and Admixture into High-Latitude Breeds377An early modern human from Romania with a recent Neanderthal ancestor799Targeted capture in evolutionary and ecological genomics352Genetic evidence for two founding populations of the Americas456Genomic evidence for the Pleistocene and recent population history of Native Americans537Global diversity, population stratification, and selection of human copy-number variation345Linked selection and recombination rate variation drive the evolution of the genomic landscape of differentiation across the speciation continuum of Ficedula flycatchers403Upper Palaeolithic genomes reveal deep roots of modern Eurasians416Genomic islands of speciation separate cichlid ecomorphs in an East African crater lake420How reticulated are species?589Ancient DNA and the rewriting of human history: be sparing with Occam’s razor1923Ancient gene flow from early modern humans into Eastern Neanderthals576A genomic perspective on hybridization and speciation554Phylogenomics Reveals Three Sources of Adaptive Variation during a Rapid Radiation432Nuclear DNA sequences from the Middle Pleistocene Sima de los Huesos hominins583Excavating Neandertal and Denisovan DNA from the genomes of Melanesian individuals458The Combined Landscape of Denisovan and Neanderthal Ancestry in Present-Day Humans465EAGER: efficient ancient genome reconstruction522The Genetic Cost of Neanderthal Introgression419Cerebral cortex expansion and folding: what have we learned?361The genetic history of Ice Age Europe956The discovery of fire by humans: a long and convoluted process414Characterization of Greater Middle Eastern genetic variation for enhanced disease gene discovery375Genomic insights into the origin of farming in the ancient Near East955Palaeoproteomic evidence identifies archaic hominins associated with the Châtelperronian at the Grotte du Renne360Genomic analyses inform on migration events during the peopling of Eurasia455The Simons Genome Diversity Project: 300 genomes from 142 diverse populations1584Genomic insights into the peopling of the Southwest Pacific414Hybridization in Plants: Old Ideas, New Techniques357Robust and scalable inference of population history from hundreds of unphased whole genomes940Tracing the peopling of the world through genomics728Ancient hybridization fuels rapid cichlid fish adaptive radiations732Neanderthal behaviour, diet, and disease inferred from ancient DNA in dental calculus582Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly1183Neandertal and Denisovan DNA from Pleistocene sediments465Evolution of the Human Nervous System Function, Structure, and Development515Interpreting the genomic landscape of speciation: a road map for finding barriers to gene flow531Reconstructing Prehistoric African Population Structure426A high-coverage Neandertal genome from Vindija Cave in Croatia718Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers343DNA sequencing at 40: past, present and future1095On the origin of modern humans: Asian perspectives467Terminal Pleistocene Alaskan genome reveals first founding population of Native Americans423The evolution of modern human brain shape389Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza571Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life343Analysis of Human Sequence Data Reveals Two Pulses of Archaic Denisovan Admixture381Natural selection interacts with recombination to shape the evolution of hybrid genomes412The first horse herders and the impact of early Bronze Age steppe expansions into Asia425Whole-genome resequencing reveals world-wide ancestry and adaptive introgression events of domesticated cattle in East Asia401The prehistoric peopling of Southeast Asia516The genome of the offspring of a Neanderthal mother and a Denisovan father539Early human dispersals within the Americas368Assembly of a pan-genome from deep sequencing of 910 humans of African descent365Whole-genome sequences of Malawi cichlids reveal multiple radiations interconnected by gene flow578Multiple Deeply Divergent Denisovan Ancestries in Papuans345Exome sequencing highlights the role of wild-relative introgression in shaping the adaptive landscape of the wheat genome357Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype14902A method for genome-wide genealogy estimation for thousands of samples504Genomic architecture and introgression shape a butterfly radiation609Pan-genomics in the human genome era360The major genetic risk factor for severe COVID-19 is inherited from Neanderthals636Dsuite ‐ Fast D ‐statistics and related admixture evidence from VCF files993Triticum population sequencing provides insights into wheat adaptation374Origins of modern human ancestry416Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program2198Ancient DNA analysis414Million-year-old DNA sheds light on the genomic history of mammoths342A complete reference genome improves analysis of human genetic variation433Segmental duplications and their variation in a complete human genome347The Human Pangenome Project: a global resource to map genomic diversity493Genome evolution and diversity of wild and cultivated potatoes367The Allen Ancient DNA Resource (AADR) a curated compendium of ancient human genomes385

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