Reference genomes and fossils revise bat family phylogeny and biogeography
Abstract
Bats are extraordinary among mammals, having uniquely evolved powered flight and laryngeal echolocation, along with disease resistance, extended healthspans and the ability to hibernate 1 . However, the evolutionary history of bats and the understanding of these adaptations remain unresolved. We analysed chromosome-level, long-read genome assemblies from 103 bat species, including 42 new assemblies, representing all 21 bat families. This dataset, expanded in scope and assembly quality, yielded a new bat phylogeny. We placed Myzopodidae as the earliest branch within Vespertilionoidea, and resolved yangochiropteran relationships, identifying Emballonuroidea and Vespertilionoidea as sister groups. Our analysis revealed a mosaic evolutionary history across bats and explained why previous phylogenetic studies were misled. Chromosomal ancestral-state reconstructions supported 26 ancestral bat chromosomes. We integrated a morphological dataset of 699 characters for 65 species, including 44 pre-Quaternary fossils and representatives of most living bat families, with neutrally evolving genomic sites. Fossilized birth–death and dispersal–extinction cladogenesis analyses showed that bats, and thus powered flight, probably originated in Europe in the late Palaeocene, refuting African and North American origins. Placement of the fossil † Vielasia in the oldest ‘Eochiroptera’ clade indicates that laryngeal echolocation predates crown-bat diversification. Total evidence dating, including the fossil taxa, significantly reduced unrepresented basal branch lengths compared with molecular-only divergence estimates. By integrating comprehensive genomic and morphological datasets, analysed using innovative methods, we resolve long-standing controversies in bat biology and provide new insights into the evolutionary history and trait diversification of bats.
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BibTeX
@article{morales2026reference,
title = {{Reference genomes and fossils revise bat family phylogeny and biogeography}},
author = {Ariadna Morales and Yan Liang and William Thomas and Evgeny Leushkin and Francisco Castellanos and Denis Larkin and Tom Brown and Bastian Fromm and Suzanne Hand and Zixia Huang and Graham Hughes and Matthew Jones and Burton Lim and Meike Mai and Eugene Myers and Martin Pippel and Sebastien Puechmaille and Nancy Simmons and Linelle Ann L. Abueg and Nadav Ahituv and Zahran Alabdulsalam and Ine Alvarez van Tussenbroek and Dineilys Aparicio and Lina Arcila Hernández and Alexander Ben Hamadou and Petr Benda and Mark Blaxter and Alex Borisenko and Jorge Brocca and Nair Cabezón and Lucia Carbone and Jose Carvajal and Wharton Chan and Paul Davis and Dina Dechmann and Annette Denzinger and Judith Eger and Seth Eiseb and David Enard and Mark Engstrom and Nicole Foley and Giulio Formenti and Jackson Fuller and Ismael Galván and Akshamal Gamage and Neil Gemmell and Joanne Gillum and Alejandro Gonzales-Irribarren and Mailyn Gonzalez and Steven Goodman and Jonathan Gray and Carola Greve and Michael Guernsey and Edgar Gutiérrez and Yelena Guttman and Michael Hackenberg and Elena Hilario and Leon Hilgers and Thomas Horsley and Melissa de Waal},
journal = {Nature},
year = {2026},
month = sep,
doi = {10.1038/s41586-026-11007-3},
url = {https://hal.science/hal-05772698v1},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Reference genomes and fossils revise bat family phylogeny and biogeography
AU - Ariadna Morales
AU - Yan Liang
AU - William Thomas
AU - Evgeny Leushkin
AU - Francisco Castellanos
AU - Denis Larkin
AU - Tom Brown
AU - Bastian Fromm
AU - Suzanne Hand
AU - Zixia Huang
AU - Graham Hughes
AU - Matthew Jones
AU - Burton Lim
AU - Meike Mai
AU - Eugene Myers
AU - Martin Pippel
AU - Sebastien Puechmaille
AU - Nancy Simmons
AU - Linelle Ann L. Abueg
AU - Nadav Ahituv
AU - Zahran Alabdulsalam
AU - Ine Alvarez van Tussenbroek
AU - Dineilys Aparicio
AU - Lina Arcila Hernández
AU - Alexander Ben Hamadou
AU - Petr Benda
AU - Mark Blaxter
AU - Alex Borisenko
AU - Jorge Brocca
AU - Nair Cabezón
AU - Lucia Carbone
AU - Jose Carvajal
AU - Wharton Chan
AU - Paul Davis
AU - Dina Dechmann
AU - Annette Denzinger
AU - Judith Eger
AU - Seth Eiseb
AU - David Enard
AU - Mark Engstrom
AU - Nicole Foley
AU - Giulio Formenti
AU - Jackson Fuller
AU - Ismael Galván
AU - Akshamal Gamage
AU - Neil Gemmell
AU - Joanne Gillum
AU - Alejandro Gonzales-Irribarren
AU - Mailyn Gonzalez
AU - Steven Goodman
AU - Jonathan Gray
AU - Carola Greve
AU - Michael Guernsey
AU - Edgar Gutiérrez
AU - Yelena Guttman
AU - Michael Hackenberg
AU - Elena Hilario
AU - Leon Hilgers
AU - Thomas Horsley
AU - Melissa de Waal
PY - 2026
DA - 2026/09/23
JO - Nature
DO - 10.1038/s41586-026-11007-3
UR - https://hal.science/hal-05772698v1
AB - Bats are extraordinary among mammals, having uniquely evolved powered flight and laryngeal echolocation, along with disease resistance, extended healthspans and the ability to hibernate 1 . However, the evolutionary history of bats and the understanding of these adaptations remain unresolved. We analysed chromosome-level, long-read genome assemblies from 103 bat species, including 42 new assemblies, representing all 21 bat families. This dataset, expanded in scope and assembly quality, yielded a new bat phylogeny. We placed Myzopodidae as the earliest branch within Vespertilionoidea, and resolved yangochiropteran relationships, identifying Emballonuroidea and Vespertilionoidea as sister groups. Our analysis revealed a mosaic evolutionary history across bats and explained why previous phylogenetic studies were misled. Chromosomal ancestral-state reconstructions supported 26 ancestral bat chromosomes. We integrated a morphological dataset of 699 characters for 65 species, including 44 pre-Quaternary fossils and representatives of most living bat families, with neutrally evolving genomic sites. Fossilized birth–death and dispersal–extinction cladogenesis analyses showed that bats, and thus powered flight, probably originated in Europe in the late Palaeocene, refuting African and North American origins. Placement of the fossil † Vielasia in the oldest ‘Eochiroptera’ clade indicates that laryngeal echolocation predates crown-bat diversification. Total evidence dating, including the fossil taxa, significantly reduced unrepresented basal branch lengths compared with molecular-only divergence estimates. By integrating comprehensive genomic and morphological datasets, analysed using innovative methods, we resolve long-standing controversies in bat biology and provide new insights into the evolutionary history and trait diversification of bats.
SN - 0028-0836
SN - 1476-4687
ER -