• Senckenberg-Leibniz Institution for Biodiversity and Earth System Research, Senckenberganlage, Frankfurt, Germany

    Ariadna E. Morales, Evgeny V. Leushkin, Alexander Ben Hamadou, Alejandro Gonzales-Irribarren, Carola Greve, Leon Hilgers, Dimitrios-Georgios Kontopoulos, Shenglin Liu, Yury V. Malovichko, Tilman Schell & Michael Hiller

  • University of Montpellier–CNRS–IRD, ISEM, Montpellier, France

    Ariadna E. Morales & Sebastien J. Puechmaille

  • Tree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UK

    Yan Liang 
    (梁妍), Eugene W. Myers, Mark Blaxter, Paul Davis, Matthieu Muffato, Guoying Qi & Emma C. Teeling

  • Department of Ecology and Evolution, Stony Brook University, New York, NY, USA

    William R. Thomas & Liliana M. Dávalos

  • Department of Biological Sciences, Texas Tech University, Lubbock, TX, USA

    Francisco X. Castellanos & David A. Ray

  • Instituto Nacional de Biodiversidad, Quito, Ecuador

    Francisco X. Castellanos

  • Department of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UK

    Denis M. Larkin & Maksym Prylutskyi

  • Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany

    Tom Brown, Eugene W. Myers, Martin Pippel, Laura Uelze & Sylke Winkler

  • The Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromso, Norway

    Bastian Fromm

  • School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, Australia

    Suzanne J. Hand

  • School of Biology and Environmental Science, University College Dublin, Dublin, Ireland

    Zixia Huang, Graham M. Hughes, Sarahjane Power, Marek Uvizl & Emma C. Teeling

  • Conway Institute, University College Dublin, Dublin, Ireland

    Graham M. Hughes

  • School of Life Sciences, Arizona State University, Tempe, AZ, USA

    Matthew F. Jones & Nathan S. Upham

  • Department of Natural History, Royal Ontario Museum, Toronto, Ontario, Canada

    Burton K. Lim, Judith L. Eger, Mark D. Engstrom & Thomas W. Horsley

  • School of Biology, University of St Andrews, St Andrews, UK

    Meike Mai, Ine Alvarez van Tussenbroek & Sonja C. Vernes

  • Okinawa Institute of Science and Technology, Okinawa, Japan

    Eugene W. Myers

  • SciLifeLab, National Bioinformatics Infrastructure Sweden (NBIS), Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden

    Martin Pippel

  • DRESDEN concept Genome Center, Dresden, Germany

    Martin Pippel, Laura Uelze & Sylke Winkler

  • Institut Universitaire de France, Paris, France

    Sebastien J. Puechmaille

  • Department of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USA

    Nancy B. Simmons & Melissa R. de Waal

  • The Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USA

    Linelle Ann L. Abueg, Giulio Formenti, Erich D. Jarvis, Bonhwang Koo, Kirsty McCaffrey, Brian P. O’Toole & Sam Talbot

  • Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA

    Nadav Ahituv, Michael W. Guernsey & Yelena Guttman

  • Institute for Human Genetics, University of California San Francisco, San Francisco, CA, USA

    Nadav Ahituv, Michael W. Guernsey & Yelena Guttman

  • Environment Authority, Muscat Governorate, Oman

    Zahran A. AlAbdulsalam

  • Center of Animal Behavior, Smithsonian Tropical Research Institute, Balboa, Panama

    Dineilys V. Aparicio, Nair Cabezón, Dina K. N. Dechmann, Mirjam Knörnschild & Jenna E. Kohles

  • University of California Santa Cruz, Santa Cruz, CA, USA

    Lina M. Arcila Hernández

  • Ecology and Evolutionary Biology, University of Toronto, Toronto, Ontario, Canada

    Lina M. Arcila Hernández & Mark D. Engstrom

  • Department of Zoology, National Museum, Prague, Czech Republic

    Petr Benda & Marek Uvizl

  • Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic

    Petr Benda & Marek Uvizl

  • Biodetics Data Solutions, Guelph, Ontario, Canada

    Alex V. Borisenko

  • Ecological and Regulatory Solutions, University of Guelph, Guelph, Ontario, Canada

    Alex V. Borisenko

  • SOH Conservación, Santo Domingo, Dominican Republic

    Jorge Brocca

  • Department of Medicine, KCVI, Oregon Health & Science University, Portland, OR, USA

    Lucia Carbone & Kimberly A. Nevonen

  • Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA

    Lucia Carbone

  • Division of Genetics, Oregon National Primate Research Center, Beaverton, OR, USA

    Lucia Carbone

  • New Cultivar Innovation, New Zealand Institute for Bioeconomy Science Limited, Auckland, New Zealand

    Jose I. Carvajal & Elena Hilario

  • Programme for Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, Singapore

    Wharton O. Y. Chan, Akshamal M. Gamage & Lin-Fa Wang

  • Max Planck Institute of Animal Behavior, Radolfzell, Germany

    Dina K. N. Dechmann & Jenna E. Kohles

  • University of Konstanz, Konstanz, Germany

    Dina K. N. Dechmann & Jenna E. Kohles

  • Institute for Neurobiology, University of Tübingen, Tübingen, Germany

    Annette Denzinger

  • Department of Environmental Science, School of Science, University of Namibia, Windhoek, Namibia

    Seth J. Eiseb

  • National Museum of Namibia, Windhoek, Namibia

    Seth J. Eiseb

  • Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USA

    David Enard & M. Elise Lauterbur

  • Veterinary Integrative Biosciences, Texas A&M University, College Station, TX, USA

    Nicole M. Foley & William J. Murphy

  • Center for Comparative Genomics, Texas A&M AgriLife Research, College Station, TX, USA

    Nicole M. Foley & William J. Murphy

  • Department of National Parks and Wildlife, Research and Development Section, Lilongwe, Malawi

    Jackson Fuller & William O. Mgoola

  • Department of Evolutionary Ecology, National Museum of Natural Sciences, CSIC, Madrid, Spain

    Ismael Galván

  • Department of Anatomy, Faculty of Biomedical Sciences, University of Otago, Otago, New Zealand

    Neil J. Gemmell, Joanne E. Gillum & William S. Pearman

  • Instituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogota, Colombia

    Mailyn A. Gonzalez

  • Negaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USA

    Steven M. Goodman

  • Association Vahatra, Antananarivo, Madagascar

    Steven M. Goodman

  • Paratus Sciences, New York, NY, USA

    Jonathan Gray & Ning Zhang

  • Department of Biological Sciences, California State University Stanislaus, Turlock, CA, USA

    Michael W. Guernsey

  • Laboratorio de Bioconservación y Manejo, Escuela Nacional de Ciencias Biológicas, IPN, Mexico City, Mexico

    Edgar G. Gutiérrez & Jorge Ortega

  • Department of Genetics, University of Granada, Granada, Spain

    Michael Hackenberg

  • Bioinformatics Laboratory, Biotechnology Institute & Biomedical Research Centre (CIBM), Granada, Spain

    Michael Hackenberg

  • Institute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Frankfurt, Germany

    Leon Hilgers, Shenglin Liu, Yury V. Malovichko & Michael Hiller

  • Department of Biological Sciences, Fairleigh Dickinson University, Teaneck, NJ, USA

    Melissa R. de Waal

  • Cobra Collective Guyana, Georgetown, Guyana

    Deirdre M. Jafferally

  • Hughes Medical Institute, Chevy Chase, MD, USA

    Erich D. Jarvis

  • Amazon Conservation Team, Paramaribo, Suriname

    Sahieda A. Joemratie

  • Institute for Biology, Humboldt-Universität zu Berlin, Berlin, Germany

    Mirjam Knörnschild & York Winter

  • Museum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Berlin, Germany

    Mirjam Knörnschild & Martina Nagy

  • Department of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USA

    Dimitrios-Georgios Kontopoulos

  • Department of Biology, University of Vermont, Burlington, VT, USA

    M. Elise Lauterbur

  • Paul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USA

    Michael Letko & Stephanie N. Seifert

  • Julie Ann Wrigley Global Futures Laboratory, Walton Center for Planetary Health, Arizona State University, Tempe, AZ, USA

    Harris A. Lewin

  • Department of Molecular Medicine, Aarhus University Hospital (AUH), Aarhus, Denmark

    Shenglin Liu

  • Department of Clinical Medicine, Aarhus University, Aarhus, Denmark

    Shenglin Liu

  • Bragato Research Institute, Lincoln, New Zealand

    Darrell K. Lizamore

  • Science and Research Directorate, Department of Conservation, Wellington, New Zealand

    Brian D. Lloyd

  • Medical Affairs Organization, Illumina, San Diego, CA, USA

    Livia Loureiro

  • Centro de Investigaciones Tropicales, Universidad Veracruzana, Veracruz, Mexico

    M. Cristina MacSwiney G

  • Institute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, Germany

    Dominik W. Melville, Magdalena Meyer, Bismark A. Opoku & Simone Sommer

  • Laboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USA

    Vincent J. Munster

  • University of Caen Normandy, INSERM, Normandie University, Caen, France

    Nicolas Nesi

  • Department of Forests, Ministry of Agriculture Rural Development and Environment, Nicosia, Cyprus

    Haris Nicolaou

  • Department of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana

    Evans E. Nkrumah

  • Bina Hill Institute Youth Learning Centre, Bina Hill, Guyana

    Zacharias Norman

  • Wildlife Conservation Society, Health Program, Bronx, NY, USA

    Sarah H. Olson

  • Wildlife Health Program, Wildlife Conservation Society, Brazzaville, Republic of the Congo

    Alain Ondzie

  • School of Biological Sciences, University of Auckland, Auckland, New Zealand

    William S. Pearman

  • West German Genome Center (WGGC), Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Francy J. Perez-Llanos

  • Biological and Medical Research Center (BMFZ), Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, Germany

    Francy J. Perez-Llanos

  • Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA

    Kendra L. Phelps

  • School of Life and Health Sciences, University of Nicosia, Nicosia, Cyprus

    Myrtani Pieri

  • Escuela de Ciencias e Ingeniería, Universidad del Rosario, Bogota, Colombia

    Paola Pulido-Santacruz

  • School of Biology and Center for Research in Biodiversity and Tropical Ecology (CIBET), University of Costa Rica, San Jose, Costa Rica

    Bernal Rodríguez-Herrera

  • Department of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, Colombia

    Danny Rojas

  • Environmental Management Consultants Guyana, Ogle, East Coast Demerara, Guyana

    Indranee Roopsind

  • Rupununi Wildlife Research Unit, Lethem, Guyana

    Indranee Roopsind

  • School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK

    Stephen J. Rossiter

  • Institute of Biology, Freie Universitat Berlin, Berlin, Germany

    Constance Scharff

  • Wildconscience, Kralendijk, Bonaire, the Netherlands

    Fernando Simal

  • CARMABI Caribbean Research and Management of Biodiversity, Willemstad, Curaçao

    Fernando Simal

  • Princess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Songkhla, Thailand

    Pipat Soisook

  • Independent Wildlife Consultant, Muscat, Oman

    Andrew Spalton

  • Bat Conservation Research Lab, Milner Research Institute, University of Bath, Bath, UK

    Emma L. Stone

  • African Bat Conservation, Lilongwe, Malawi

    Emma L. Stone

  • Department of Integrative Biology, University of California Berkeley, Berkeley, CA, USA

    Peter H. Sudmant

  • Biodiversity Institute, University of Kansas, Lawrence, KS, USA

    Robert M. Timm

  • Department of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, USA

    Robert M. Timm

  • Czech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech Republic

    Peter Vallo

  • Department of Biology, Pennsylvania State University, University Park, PA, USA

    Juan M. Vazquez

  • Freshwater Quality Monitoring Division, Science and Technology Branch, Environment and Climate Change Canada, Burlington, Ontario, Canada

    Linet C. Watson

  • AEWC Ltd/BatCRU, Fittleworth, UK

    Daniel Whitby

  • Department of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USA

    Laurel R. Yohe

  • Otago Genomics Facility, University of Otago, Dunedin, New Zealand

    Monika Zavodna

  • State Key Laboratory of Virology and Biosafety, College of Life Sciences, Wuhan University, Wuhan, China

    Huabin Zhao

  • Consortium on Inter-Disciplinary Environmental Research, Institute for Advanced Computational Science, Stony Brook University, New York, NY, USA

    Liliana M. Dávalos

    • Y.L., W.R.T., E.V.L., F.X.C., D.M.L. and T.B. are equally contributing second authors; and B.F., S.J.H., Z.H., G.M.H., M.F.J., B.K.L., M.M., E.W.M., M. Pippel, S.J.P. and N.B.S. are equally contributing third authors, listed alphabetically. This study was conceptualized and led by the five corresponding authors: E.C.T., M. Hiller, L.M.D., S.C.V. and D.A.R. who led the scientific direction, manuscript writing and editing. Together with the corresponding authors, 18 co-authors led the data analyses and interpretation detailed in the Supplementary Notes and contributed to writing and editing: A.E.M., Y.L., W.R.T., E.V.L., F.X.C., D.M.L., T.B., B.F., S.J.H., Z.H., G.M.H., M.F.J., B.K.L., M. Mai, E.W.M., M. Pippel, S.J.P. and N.B.S. All authors had the opportunity to review and edit the manuscript. Z.A.A., I.A.V.T., D.V.A., L.M.A.H., P.B., A.V.B., J.B., N.C., W.O.Y.C., L.M.D., D.K.N.D., A.D., D.E., M.D.E., I.G., A.M.G., S.M.G., E.G.G., L.H., M.R.d.W., D.M.J., S.A.J., M.K., J.E.K., M.E.L., M.L., B.K.L., B.D.L., L.L., V.J.M., N.N., H.N., E.E.N., Z.N., S.H.O., A.O., B.A.O., J.O., K.L.P., M.Pieri, S.J.P., P.P.-S., D.A.R., B.R.-H., I.R., S.J.R., C.S., S.N.S., N.B.S., A.S., E.L.S., P.H.S., R.M.T., N.S.U., J.M.V., S.C.V., L.-F.W., L.C.W., D.W., Y.W., L.R.Y., H.Z., J.L.E., S.J.E., J.F., M.A.G., T.W.H., M.C.M.G., M.N., D.R., F.S., P.S., W.O.M., E.C.T., M. Hiller, M. Mai and P.V. acquired samples and data. S.W., D.W.M., C.G., A.B.H., A.M.G., D.K.L., E.H., F.J.P.-L., J.I.C., J.E.G., K.A.N., L.C., M. Meyer, M.W.G., M.Z., N.J.G., N.Z., W.O.Y.C., W.S.P., Y.G., S.S., N.A., B.P.O., L.-F.W., S.C.V., E.C.T. and M. Hiller performed genome sequencing. T.B., E.V.L., M. Pippel, T.S., L.A.L.A., K.M., S.T., B.K., G.F., E.D.J., L.U., E.W.M., S.C.V., E.C.T., M.B., M. Hiller and B.P.O. conducted the genome assembly. A.E.M., E.V.L., D.A.R. and M. Hiller performed the assembly statistics. A.E.M., A.G.-I., Y.V.M., L.H., S.L., D.-G.K., E.V.L. and M. Hiller conducted genome annotation and pairwise genome alignments. D.A.R. and L.M.D. performed the transposable element annotation. B.F., Z.H., S.P., M.U., M. Hackenberg, M. Mai and S.C.V. conducted the microRNA analyses. A.E.M., E.V.L., F.X.C., D.A.R. and M. Hiller performed the multiple genome alignments. A.E.M., E.C.T., M. Hiller, A.G.-I., G.M.H., S.J.P., Y.L., N.M.F. and W.J.M. undertook the phylogenomics. M. Prylutskyi, A.E.M., M. Hiller, H.A.L. and D.M.L. performed the ancestral karyotype reconstruction. W.R.T., M.F.J., F.X.C., G.M.H., S.J.H., N.B.S., L.M.D. and E.C.T. contributed fossils, total evidence and node divergence times, and biogeography. A.B.H., T.B., P.D., G.F., A.G.-I., J.G., M.F.J., B.K., M.E.L., E.V.L., Y.L., M. Mai, Y.V.M., A.E.M., M. Pippel, T.S., N.B.S., W.R.T., M. Muffato, G.Q., L.U., E.C.T., M. Hiller, L.M.D., S.C.V. and D.A.R. curated the data and performed the archving.