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.
