Reference genomes and fossils revise bat family phylogeny and biogeography

Nature & Environment

September 23, 2026

Reference genomes and fossils revise bat family phylogeny and biogeography

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.

Source link