Senckenberg-Leibniz Institution for Biodiversity and Earth System Research, Senckenberganlage, Frankfurt, GermanyAriadna 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 HillerUniversity of Montpellier–CNRS–IRD, ISEM, Montpellier, FranceAriadna E. Morales & Sebastien J. PuechmailleTree of Life, Wellcome Sanger Institute, Hinxton, Cambridge, UKYan Liang
(梁妍), Eugene W. Myers, Mark Blaxter, Paul Davis, Matthieu Muffato, Guoying Qi & Emma C. TeelingDepartment of Ecology and Evolution, Stony Brook University, New York, NY, USAWilliam R. Thomas & Liliana M. DávalosDepartment of Biological Sciences, Texas Tech University, Lubbock, TX, USAFrancisco X. Castellanos & David A. RayInstituto Nacional de Biodiversidad, Quito, EcuadorFrancisco X. CastellanosDepartment of Comparative Biomedical Sciences, Royal Veterinary College, University of London, London, UKDenis M. Larkin & Maksym PrylutskyiMax Planck Institute of Molecular Cell Biology and Genetics, Dresden, GermanyTom Brown, Eugene W. Myers, Martin Pippel, Laura Uelze & Sylke WinklerThe Arctic University Museum of Norway, UiT-The Arctic University of Norway, Tromso, NorwayBastian FrommSchool of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales, AustraliaSuzanne J. HandSchool of Biology and Environmental Science, University College Dublin, Dublin, IrelandZixia Huang, Graham M. Hughes, Sarahjane Power, Marek Uvizl & Emma C. TeelingConway Institute, University College Dublin, Dublin, IrelandGraham M. HughesSchool of Life Sciences, Arizona State University, Tempe, AZ, USAMatthew F. Jones & Nathan S. UphamDepartment of Natural History, Royal Ontario Museum, Toronto, Ontario, CanadaBurton K. Lim, Judith L. Eger, Mark D. Engstrom & Thomas W. HorsleySchool of Biology, University of St Andrews, St Andrews, UKMeike Mai, Ine Alvarez van Tussenbroek & Sonja C. VernesOkinawa Institute of Science and Technology, Okinawa, JapanEugene W. MyersSciLifeLab, National Bioinformatics Infrastructure Sweden (NBIS), Department of Cell and Molecular Biology, Uppsala University, Uppsala, SwedenMartin PippelDRESDEN concept Genome Center, Dresden, GermanyMartin Pippel, Laura Uelze & Sylke WinklerInstitut Universitaire de France, Paris, FranceSebastien J. PuechmailleDepartment of Mammalogy, Division of Vertebrate Zoology, American Museum of Natural History, New York, NY, USANancy B. Simmons & Melissa R. de WaalThe Vertebrate Genome Laboratory, The Rockefeller University, New York, NY, USALinelle Ann L. Abueg, Giulio Formenti, Erich D. Jarvis, Bonhwang Koo, Kirsty McCaffrey, Brian P. O’Toole & Sam TalbotDepartment of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USANadav Ahituv, Michael W. Guernsey & Yelena GuttmanInstitute for Human Genetics, University of California San Francisco, San Francisco, CA, USANadav Ahituv, Michael W. Guernsey & Yelena GuttmanEnvironment Authority, Muscat Governorate, OmanZahran A. AlAbdulsalamCenter of Animal Behavior, Smithsonian Tropical Research Institute, Balboa, PanamaDineilys V. Aparicio, Nair Cabezón, Dina K. N. Dechmann, Mirjam Knörnschild & Jenna E. KohlesUniversity of California Santa Cruz, Santa Cruz, CA, USALina M. Arcila HernándezEcology and Evolutionary Biology, University of Toronto, Toronto, Ontario, CanadaLina M. Arcila Hernández & Mark D. EngstromDepartment of Zoology, National Museum, Prague, Czech RepublicPetr Benda & Marek UvizlDepartment of Zoology, Faculty of Science, Charles University, Prague, Czech RepublicPetr Benda & Marek UvizlBiodetics Data Solutions, Guelph, Ontario, CanadaAlex V. BorisenkoEcological and Regulatory Solutions, University of Guelph, Guelph, Ontario, CanadaAlex V. BorisenkoSOH Conservación, Santo Domingo, Dominican RepublicJorge BroccaDepartment of Medicine, KCVI, Oregon Health & Science University, Portland, OR, USALucia Carbone & Kimberly A. NevonenDepartment of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USALucia CarboneDivision of Genetics, Oregon National Primate Research Center, Beaverton, OR, USALucia CarboneNew Cultivar Innovation, New Zealand Institute for Bioeconomy Science Limited, Auckland, New ZealandJose I. Carvajal & Elena HilarioProgramme for Emerging Infectious Diseases, Duke-NUS Medical School, Singapore, SingaporeWharton O. Y. Chan, Akshamal M. Gamage & Lin-Fa WangMax Planck Institute of Animal Behavior, Radolfzell, GermanyDina K. N. Dechmann & Jenna E. KohlesUniversity of Konstanz, Konstanz, GermanyDina K. N. Dechmann & Jenna E. KohlesInstitute for Neurobiology, University of Tübingen, Tübingen, GermanyAnnette DenzingerDepartment of Environmental Science, School of Science, University of Namibia, Windhoek, NamibiaSeth J. EisebNational Museum of Namibia, Windhoek, NamibiaSeth J. EisebDepartment of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, USADavid Enard & M. Elise LauterburVeterinary Integrative Biosciences, Texas A&M University, College Station, TX, USANicole M. Foley & William J. MurphyCenter for Comparative Genomics, Texas A&M AgriLife Research, College Station, TX, USANicole M. Foley & William J. MurphyDepartment of National Parks and Wildlife, Research and Development Section, Lilongwe, MalawiJackson Fuller & William O. MgoolaDepartment of Evolutionary Ecology, National Museum of Natural Sciences, CSIC, Madrid, SpainIsmael GalvánDepartment of Anatomy, Faculty of Biomedical Sciences, University of Otago, Otago, New ZealandNeil J. Gemmell, Joanne E. Gillum & William S. PearmanInstituto de Investigación de Recursos Biológicos Alexander von Humboldt, Bogota, ColombiaMailyn A. GonzalezNegaunee Integrative Research Center, Field Museum of Natural History, Chicago, IL, USASteven M. GoodmanAssociation Vahatra, Antananarivo, MadagascarSteven M. GoodmanParatus Sciences, New York, NY, USAJonathan Gray & Ning ZhangDepartment of Biological Sciences, California State University Stanislaus, Turlock, CA, USAMichael W. GuernseyLaboratorio de Bioconservación y Manejo, Escuela Nacional de Ciencias Biológicas, IPN, Mexico City, MexicoEdgar G. Gutiérrez & Jorge OrtegaDepartment of Genetics, University of Granada, Granada, SpainMichael HackenbergBioinformatics Laboratory, Biotechnology Institute & Biomedical Research Centre (CIBM), Granada, SpainMichael HackenbergInstitute of Cell Biology and Neuroscience, Faculty of Biosciences, Goethe University Frankfurt, Frankfurt, GermanyLeon Hilgers, Shenglin Liu, Yury V. Malovichko & Michael HillerDepartment of Biological Sciences, Fairleigh Dickinson University, Teaneck, NJ, USAMelissa R. de WaalCobra Collective Guyana, Georgetown, GuyanaDeirdre M. JafferallyHughes Medical Institute, Chevy Chase, MD, USAErich D. JarvisAmazon Conservation Team, Paramaribo, SurinameSahieda A. JoemratieInstitute for Biology, Humboldt-Universität zu Berlin, Berlin, GermanyMirjam Knörnschild & York WinterMuseum für Naturkunde-Leibniz Institute for Evolution and Biodiversity Science, Berlin, GermanyMirjam Knörnschild & Martina NagyDepartment of Ecology and Evolutionary Biology, University of California, Los Angeles, CA, USADimitrios-Georgios KontopoulosDepartment of Biology, University of Vermont, Burlington, VT, USAM. Elise LauterburPaul G. Allen School for Global Health, College of Veterinary Medicine, Washington State University, Pullman, WA, USAMichael Letko & Stephanie N. SeifertJulie Ann Wrigley Global Futures Laboratory, Walton Center for Planetary Health, Arizona State University, Tempe, AZ, USAHarris A. LewinDepartment of Molecular Medicine, Aarhus University Hospital (AUH), Aarhus, DenmarkShenglin LiuDepartment of Clinical Medicine, Aarhus University, Aarhus, DenmarkShenglin LiuBragato Research Institute, Lincoln, New ZealandDarrell K. LizamoreScience and Research Directorate, Department of Conservation, Wellington, New ZealandBrian D. LloydMedical Affairs Organization, Illumina, San Diego, CA, USALivia LoureiroCentro de Investigaciones Tropicales, Universidad Veracruzana, Veracruz, MexicoM. Cristina MacSwiney GInstitute of Evolutionary Ecology and Conservation Genomics, Ulm University, Ulm, GermanyDominik W. Melville, Magdalena Meyer, Bismark A. Opoku & Simone SommerLaboratory of Virology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, Hamilton, MT, USAVincent J. MunsterUniversity of Caen Normandy, INSERM, Normandie University, Caen, FranceNicolas NesiDepartment of Forests, Ministry of Agriculture Rural Development and Environment, Nicosia, CyprusHaris NicolaouDepartment of Wildlife and Range Management, Kwame Nkrumah University of Science and Technology, Kumasi, GhanaEvans E. NkrumahBina Hill Institute Youth Learning Centre, Bina Hill, GuyanaZacharias NormanWildlife Conservation Society, Health Program, Bronx, NY, USASarah H. OlsonWildlife Health Program, Wildlife Conservation Society, Brazzaville, Republic of the CongoAlain OndzieSchool of Biological Sciences, University of Auckland, Auckland, New ZealandWilliam S. PearmanWest German Genome Center (WGGC), Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, GermanyFrancy J. Perez-LlanosBiological and Medical Research Center (BMFZ), Medical Faculty and University Hospital Düsseldorf, Heinrich Heine University Düsseldorf, Düsseldorf, GermanyFrancy J. Perez-LlanosDepartment of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USAKendra L. PhelpsSchool of Life and Health Sciences, University of Nicosia, Nicosia, CyprusMyrtani PieriEscuela de Ciencias e Ingeniería, Universidad del Rosario, Bogota, ColombiaPaola Pulido-SantacruzSchool of Biology and Center for Research in Biodiversity and Tropical Ecology (CIBET), University of Costa Rica, San Jose, Costa RicaBernal Rodríguez-HerreraDepartment of Natural Sciences and Mathematics, Pontificia Universidad Javeriana Cali, Cali, ColombiaDanny RojasEnvironmental Management Consultants Guyana, Ogle, East Coast Demerara, GuyanaIndranee RoopsindRupununi Wildlife Research Unit, Lethem, GuyanaIndranee RoopsindSchool of Biological and Behavioural Sciences, Queen Mary University of London, London, UKStephen J. RossiterInstitute of Biology, Freie Universitat Berlin, Berlin, GermanyConstance ScharffWildconscience, Kralendijk, Bonaire, the NetherlandsFernando SimalCARMABI Caribbean Research and Management of Biodiversity, Willemstad, CuraçaoFernando SimalPrincess Maha Chakri Sirindhorn Natural History Museum, Prince of Songkla University, Songkhla, ThailandPipat SoisookIndependent Wildlife Consultant, Muscat, OmanAndrew SpaltonBat Conservation Research Lab, Milner Research Institute, University of Bath, Bath, UKEmma L. StoneAfrican Bat Conservation, Lilongwe, MalawiEmma L. StoneDepartment of Integrative Biology, University of California Berkeley, Berkeley, CA, USAPeter H. SudmantBiodiversity Institute, University of Kansas, Lawrence, KS, USARobert M. TimmDepartment of Ecology & Evolutionary Biology, University of Kansas, Lawrence, KS, USARobert M. TimmCzech Academy of Sciences, Institute of Vertebrate Biology, Brno, Czech RepublicPeter ValloDepartment of Biology, Pennsylvania State University, University Park, PA, USAJuan M. VazquezFreshwater Quality Monitoring Division, Science and Technology Branch, Environment and Climate Change Canada, Burlington, Ontario, CanadaLinet C. WatsonAEWC Ltd/BatCRU, Fittleworth, UKDaniel WhitbyDepartment of Bioinformatics and Genomics, University of North Carolina, Charlotte, NC, USALaurel R. YoheOtago Genomics Facility, University of Otago, Dunedin, New ZealandMonika ZavodnaState Key Laboratory of Virology and Biosafety, College of Life Sciences, Wuhan University, Wuhan, ChinaHuabin ZhaoConsortium on Inter-Disciplinary Environmental Research, Institute for Advanced Computational Science, Stony Brook University, New York, NY, USALiliana M. DávalosY.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.
