12
views
0
recommends
+1 Recommend
0 collections
    0
    shares
      • Record: found
      • Abstract: found
      • Article: not found

      A global catalog of whole-genome diversity from 233 primate species

      1 , 2 , 2 , 3 , 1 , 4 , 5 , 1 , 6 , 7 , 8 , 9 , 1 , 7 , 10 , 7 , 11 , 12 , 13 , 13 , 13 , 3 , 3 , 14 , 14 , 15 , 16 , 17 , 18 , 19 , 20 , 21 , 22 , 1 , 22 , 2 , 23 , 24 , 25 , 26 , 24 , 27 , 28 , 29 , 30 , 31 , 9 , 32 , 24 , 33 , 34 , 34 , 34 , 35 , 36 , 37 , 37 , 37 , 38 , 39 , 40 , 41 , 42 , 41 , 42 , 43 , 41 , 44 , 45 , 46 , 47 , 48 , 1 , 49 , 50 , 1 , 51 , 52 , 53 , 54 , 55 , 56 , 55 , 57 , 58 , 57 , 58 , 59 , 60 , 61 , 62 , 63 , 13 , 64 , 65 , 66 , 15 , 67 , 7 , 3 , 8 , 9 , 68 , 3 , 14 , 2 , 1 , 13 , 49 , 51
      Science
      American Association for the Advancement of Science (AAAS)

      Read this article at

      ScienceOpenPublisherPubMed
      Bookmark
          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          Abstract

          The rich diversity of morphology and behavior displayed across primate species provides an informative context in which to study the impact of genomic diversity on fundamental biological processes. Analysis of that diversity provides insight into long-standing questions in evolutionary and conservation biology and is urgent given severe threats these species are facing. Here, we present high-coverage whole-genome data from 233 primate species representing 86% of genera and all 16 families. This dataset was used, together with fossil calibration, to create a nuclear DNA phylogeny and to reassess evolutionary divergence times among primate clades. We found within-species genetic diversity across families and geographic regions to be associated with climate and sociality, but not with extinction risk. Furthermore, mutation rates differ across species, potentially influenced by effective population sizes. Lastly, we identified extensive recurrence of missense mutations previously thought to be human specific. This study will open a wide range of research avenues for future primate genomic research.

          Related collections

          Most cited references181

          • Record: found
          • Abstract: not found
          • Article: not found

          Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing

            Bookmark
            • Record: found
            • Abstract: found
            • Article: found
            Is Open Access

            BEDTools: a flexible suite of utilities for comparing genomic features

            Motivation: Testing for correlations between different sets of genomic features is a fundamental task in genomics research. However, searching for overlaps between features with existing web-based methods is complicated by the massive datasets that are routinely produced with current sequencing technologies. Fast and flexible tools are therefore required to ask complex questions of these data in an efficient manner. Results: This article introduces a new software suite for the comparison, manipulation and annotation of genomic features in Browser Extensible Data (BED) and General Feature Format (GFF) format. BEDTools also supports the comparison of sequence alignments in BAM format to both BED and GFF features. The tools are extremely efficient and allow the user to compare large datasets (e.g. next-generation sequencing data) with both public and custom genome annotation tracks. BEDTools can be combined with one another as well as with standard UNIX commands, thus facilitating routine genomics tasks as well as pipelines that can quickly answer intricate questions of large genomic datasets. Availability and implementation: BEDTools was written in C++. Source code and a comprehensive user manual are freely available at http://code.google.com/p/bedtools Contact: aaronquinlan@gmail.com; imh4y@virginia.edu Supplementary information: Supplementary data are available at Bioinformatics online.
              Bookmark
              • Record: found
              • Abstract: found
              • Article: not found

              ModelFinder: Fast Model Selection for Accurate Phylogenetic Estimates

              Model-based molecular phylogenetics plays an important role in comparisons of genomic data, and model selection is a key step in all such analyses. We present ModelFinder, a fast model-selection method that greatly improves the accuracy of phylogenetic estimates. The improvement is achieved by incorporating a model of rate-heterogeneity across sites not previously considered in this context, and by allowing concurrent searches of model-space and tree-space.
                Bookmark

                Author and article information

                Contributors
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                (View ORCID Profile)
                Journal
                Science
                Science
                American Association for the Advancement of Science (AAAS)
                0036-8075
                1095-9203
                June 02 2023
                June 02 2023
                : 380
                : 6648
                : 906-913
                Affiliations
                [1 ]IBE, Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra. PRBB, C. Doctor Aiguader N88, 08003 Barcelona, Spain.
                [2 ]Illumina Artificial Intelligence Laboratory, Illumina Inc., Foster City, CA 94404, USA.
                [3 ]School of Science, Engineering & Environment, University of Salford, Salford M5 4WT, UK.
                [4 ]Department of Evolutionary Anthropology, University of Vienna, Djerassiplatz 1, 1030 Vienna, Austria.
                [5 ]Human Evolution and Archaeological Sciences (HEAS), University of Vienna, Austria.
                [6 ]Département d’anthropologie, Université de Montréal, 3150 Jean-Brillant, Montréal, QC H3T 1N8, Canada.
                [7 ]Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark.
                [8 ]Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
                [9 ]Laboratory for the Conservation of Endangered Species, CSIR-Centre for Cellular and Molecular Biology, Hyderabad 500007, India.
                [10 ]Section for Ecoinformatics and Biodiversity, Department of Biology, Aarhus University, Aarhus, Denmark.
                [11 ]Research Group on Primate Biology and Conservation, Mamirauá Institute for Sustainable Development, Estrada da Bexiga 2584, CEP 69553-225, Tefé, Amazonas, Brazil.
                [12 ]Evolutionary Biology and Ecology (EBE), Département de Biologie des Organismes, Université libre de Bruxelles (ULB), Av. Franklin D. Roosevelt 50, CP 160/12, B-1050 Brussels Belgium.
                [13 ]CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri I Reixac 4, 08028 Barcelona, Spain.
                [14 ]Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
                [15 ]Department of Ecology and Genetics, Animal Ecology, Uppsala University, SE-75236 Uppsala, Sweden.
                [16 ]Tanzania National Parks, Arusha, Tanzania.
                [17 ]North Carolina Museum of Natural Sciences, Raleigh, NC 27601, USA.
                [18 ]Department of Biological and Biomedical Sciences, North Carolina Central University, Durham, NC 27707, USA.
                [19 ]Department of Biological Sciences, North Carolina State University, Raleigh, NC 27695, USA.
                [20 ]Department of Evolutionary Anthropology, Duke University, Durham, NC 27708, USA.
                [21 ]Renaissance Computing Institute, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
                [22 ]Copenhagen Zoo, 2000 Frederiksberg, Denmark.
                [23 ]Universidade Federal de Viçosa, Viçosa, Brazil.
                [24 ]Universidade Federal do Amazonas, Departamento de Genética, Laboratório de Evolução e Genética Animal (LEGAL), Manaus, Amazonas 69080-900, Brazil.
                [25 ]Department of Anthropology, University of Utah, Salt Lake City. UT 84102, USA.
                [26 ]Universidade Federal do Para, Bragança, Para, Brazil.
                [27 ]Research Group on Terrestrial Vertebrate Ecology, Mamirauá Institute for Sustainable Development, Tefé, Amazonas, Brazil.
                [28 ]Rede de Pesquisa para Estudos sobre Diversidade, Conservação e Uso da Fauna na Amazônia – RedeFauna, Manaus, Amazonas, Brazil
                [29 ]Comunidad de Manejo de Fauna Silvestre en la Amazonía y en Latinoamérica – ComFauna, Iquitos, Loreto, Peru.
                [30 ]Universidade Federal de Rondônia, Porto Velho, Rondônia, Brazil.
                [31 ]Instituto Nacional de Pesquisas da Amazônia, Manaus, AM, Brazil.
                [32 ]Instituto de Biociências, Universidade Federal do Mato Grosso, Cuiabá, MT, Brazil.
                [33 ]Department of Biology, Trinity University, San Antonio, TX 78212, USA.
                [34 ]Life Sciences and Environment, Technology and Environment of Mahajanga, University of Mahajanga, Mahajanga, Madagascar.
                [35 ]Department of Anthropology, New York University, New York, NY 10003, USA.
                [36 ]Department of Neuroscience, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, USA.
                [37 ]Keeling Center for Comparative Medicine and Research, MD Anderson Cancer Center, Bastrop TX 78602, USA.
                [38 ]Department of Anthropology, Yale University, New Haven, CT 06511, USA.
                [39 ]School of Mathematical and Natural Sciences, Arizona State University, Phoenix, AZ 85004, USA.
                [40 ]Guinea Worm Eradication Program, The Carter Center Ethiopia, Addis Ababa, Ethiopia.
                [41 ]State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China.
                [42 ]Center for Evolutionary and Organismal Biology, Zhejiang University School of Medicine, Hangzhou 310058, China.
                [43 ]Villum Centre for Biodiversity Genomics, Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark.
                [44 ]Liangzhu Laboratory, Zhejiang University Medical Center, 1369 West Wenyi Road, Hangzhou 311121, China.
                [45 ]Women’s Hospital, School of Medicine, Zhejiang University, 1 Xueshi Road, Shangcheng District, Hangzhou 310006, China.
                [46 ]Tanzania Wildlife Research Institute (TAWIRI), Head Office, P.O. Box 661, Arusha, Tanzania.
                [47 ]Institute of International Animal Health/One Health, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, 17493 Greifswald–Insel Riems, Germany.
                [48 ]Department of Environmental Ecology, Faculty of Environmental Sciences, University of Science and Central Institute for Natural Resources and Environmental Studies, Vietnam National University, Hanoi, Vietnam.
                [49 ]Institut Català de Paleontologia Miquel Crusafont, Universitat Autònoma de Barcelona, Barcelona, Spain.
                [50 ]Department of Zoology, State Museum of Natural History Stuttgart, Stuttgart, Germany.
                [51 ]Institució Catalana de Recerca i Estudis Avançats (ICREA) and Universitat Pompeu Fabra. Pg. Luís Companys 23, 08010 Barcelona, Spain.
                [52 ]Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Av. Doctor Aiguader, N88, 08003 Barcelona, Spain.
                [53 ]BarcelonaBeta Brain Research Center, Pasqual Maragall Foundation, C. Wellington 30, 08005 Barcelona, Spain.
                [54 ]Cuc Phuong Commune, Nho Quan District, Ninh Binh Province, Vietnam.
                [55 ]Genome Institute of Singapore, Agency for Science, Technology and Research, Singapore.
                [56 ]Mandai Nature, 80 Mandai Lake Road, Singapore.
                [57 ]SingHealth Duke-NUS Institute of Precision Medicine (PRISM), Singapore.
                [58 ]Cancer and Stem Cell Biology Program, Duke-NUS Medical School, Singapore
                [59 ]SingHealth Duke-NUS Genomic Medicine Centre, Singapore.
                [60 ]Department of Natural Sciences, National Museums Scotland, Chambers Street, Edinburgh EH1 1JF, UK, and School of Geosciences, Drummond Street, Edinburgh EH8 9XP, UK.
                [61 ]Cognitive Ethology Laboratory, Germany Primate Center, Leibniz Institute for Primate Research, 37077 Göttingen, Germany.
                [62 ]Department of Primate Cognition, Georg-August-Universität Göttingen, 37077 Göttingen, Germany.
                [63 ]Leibniz ScienceCampus Primate Cognition, 37077 Göttingen, Germany.
                [64 ]Department of Anthropology and Archaeology, University of Calgary, 2500 University Dr NW, Calgary, AB T2N 1N4, Canada.
                [65 ]Department of Medical Genetics, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada.
                [66 ]Alberta Children’s Hospital Research Institute, University of Calgary, 3330 Hospital Drive NW, HMRB 202, Calgary, AB T2N 4N1, Canada.
                [67 ]Institute of Ecology and Evolution, School of Biological Sciences, University of Edinburgh, Edinburgh, UK.
                [68 ]Gene Bank of Primates and Primate Genetics Laboratory, German Primate Center, Leibniz Institute for Primate Research, Kellnerweg 4, 37077 Göttingen, Germany.
                Article
                10.1126/science.abn7829
                37262161
                bb35dbad-a781-4893-957b-1dcd0f2ef9b1
                © 2023

                Free to read

                History

                Comments

                Comment on this article