Reference genomes and fossils revise bat family phylogeny and biogeography

Summary

Bats are unusual animals. They can fly, use sound to find their way, live for a long time and carry some viruses without getting very sick. Scientists have wanted to understand how bats developed these special abilities, but their family history has been difficult to work out.

In this study, researchers compared the DNA of 103 bat species, covering all 21 bat families. They also studied bat fossils and physical features. This gave them a clearer picture of how bats are related to each other and how they changed over millions of years.

The researchers found that bats most likely first appeared in Europe about 55 million years ago. They also found evidence that bats were using echolocation very early in their history. By comparing the DNA of different bats, they reconstructed what the earliest bat chromosomes may have looked like.

The study provides a large new collection of bat genomes that can help scientists study bats and their unusual biology.

Keywords

Bats, genomics, bat genomes, DNA, evolution, phylogeny, fossils, echolocation, chromosomes, comparative genomics, biogeography, Bat1K

Abstract

Bats are extraordinary among mammals, having uniquely evolved powered flight and laryngeal echolocation, along with disease resistance, extended healthspans and the ability to hibernate1. 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.