Bats are among the most unusual mammals alive. They are the only mammals capable of powered flight, many navigate through darkness using sophisticated echolocation, and their biology includes exceptional longevity, disease tolerance and extraordinary ecological diversity. Yet the deeper history of how the roughly 1,500 living bat species are related, and where their common ancestor first emerged, has remained surprisingly difficult to resolve.
A major genomic study published in Nature has now produced one of the most comprehensive reconstructions of bat evolution to date. Researchers assembled and analysed chromosome-level genomes from 103 bat species representing all 21 recognised living bat families, then integrated those molecular data with evidence from 44 fossils. The resulting evolutionary tree revises several long-disputed relationships and points strongly to Europe as the geographical origin of bats in the late Paleocene, roughly 60 million to 65 million years ago.
A genome set spanning every living bat family
The scale and quality of the genomic dataset are central to the study. The team used long-read and Hi-C sequencing to generate 42 new reference-quality chromosome-level assemblies representing 41 species. Twenty-six of these new genomes were haplotype resolved, allowing researchers to distinguish the two chromosome sets inherited from an animal’s parents. These new assemblies were combined with existing high-quality genomes to produce a dataset covering 103 species and every recognised bat family.
This broad coverage matters because evolutionary relationships can be distorted when analyses contain only a small or uneven sample of lineages. Bats diversified rapidly early in their history, leaving relatively short intervals between some major branching events. Over tens of millions of years, mutations, incomplete lineage sorting and other genomic processes can obscure those early signals.
Rather than relying on a single class of genetic evidence, the researchers compared multiple genomic signals. Their analyses resolved relationships that had remained unstable across earlier studies. In particular, they placed Myzopodidae as the earliest branch within Vespertilionoidea and identified Emballonuroidea and Vespertilionoidea as sister groups. The study also showed that different parts of the genome can preserve conflicting evolutionary histories, helping explain why previous molecular studies sometimes produced different bat family trees.
Fossils changed the timing as well as the tree
Genomes alone cannot reveal the full history of an ancient radiation. The researchers therefore integrated 44 fossil bats into a total-evidence dating framework that combined molecular and morphological information. This approach allowed extinct species to contribute directly to estimates of evolutionary timing rather than serving only as external calibration points.
The analysis substantially reduced the amount of evolutionary history inferred to be missing from the known fossil record. Earlier work had estimated that an average of 73% of molecular branch length was unrepresented by fossils. In the new analysis, the estimated missing proportion fell to about 48.7% to 50.8%, depending on the fossil boundary used. The reduction was statistically significant across families.
Including fossil species also changed estimates of how rapidly bats diversified and disappeared. The researchers estimated a mean speciation rate of 0.314 species per million years, around three times earlier single-rate estimates. The estimated extinction rate was 0.270 species per million years, about nine times higher than previous estimates. Together, these figures imply considerably more evolutionary turnover in bat history than analyses focused mainly on living species had suggested.
The strongest signal points to a European origin
The geographical birthplace of bats has been debated for decades. Different methods have previously pointed to North America, Africa or Asia. The problem is unusually difficult because the bat fossil record is incomplete and flight gives bats exceptional dispersal ability. A lineage capable of crossing large distances can rapidly erase the geographical signal of where it began.
To address this, the researchers used a biogeographical model that incorporated dispersal and extinction, changing distances between landmasses through geological time, and the unusually high mobility of flying mammals. When the fossil and genomic evidence were analysed together, the model assigned a 99.2% posterior probability to a European origin for the common ancestor of living bats in the late Paleocene.
The reconstruction suggests that descendants of this early European lineage most probably dispersed into Africa. Europe and Africa then acted as an important early hub from which separate bat lineages expanded into Asia, the Americas and Australia. Much of the diversification into the four major bat superfamilies occurred within a relatively narrow interval during the early Eocene.
For one major lineage, Yinpterochiroptera, the analysis estimated an African origin about 57.1 million years ago. Later ancestors associated with horseshoe bats and related families expanded toward Asia by the middle Eocene. The broader picture is therefore not a simple outward migration from a single point, but a rapid sequence of dispersal and diversification events after the earliest bats appeared.
Chromosomes preserve another record of deep history
The chromosome-level assemblies also allowed the researchers to reconstruct the likely organisation of the ancestral bat genome. Their final reconstruction contained 26 ancestral chromosomes. Comparisons among modern families revealed extensive chromosome rearrangement over evolutionary time, while still preserving enough shared structure to recover aspects of the ancestral karyotype.
This is more than a technical addition to the bat family tree. Chromosome rearrangements can affect gene regulation, recombination and reproductive isolation. A high-quality map across every living family gives future researchers a framework for investigating whether particular genomic changes accompanied the emergence of distinctive bat traits.
Why resolving the bat family tree matters
A reliable evolutionary tree is the foundation for comparative biology. Researchers interested in why bats live unusually long for their body size, tolerate viruses that can be dangerous to other mammals, navigate by echolocation or evolved specialised diets need to know whether similarities arose once in a common ancestor or independently in separate lineages.
The new genomic resource makes those comparisons substantially more powerful. Because all 21 living families are represented by chromosome-level genomes, scientists can more confidently identify genetic changes associated with traits and distinguish lineage-specific adaptations from features inherited from deeper ancestors.
The findings also illustrate why expanding a dataset can change apparently settled evolutionary conclusions. Previous disagreements were not simply the result of inadequate analytical techniques. The study found a mosaic of evolutionary signals across bat genomes, meaning different genomic regions can support different histories. Denser taxonomic sampling and higher-quality assemblies helped the researchers identify and account for those conflicts rather than allowing one signal to dominate the reconstruction.
Important uncertainties remain
The study does not eliminate uncertainty from bat evolution. The fossil record remains incomplete, particularly near the earliest stages of bat history, and the researchers’ own estimates indicate that roughly half of family-level branch length is still not represented by known fossils. Biogeographical reconstructions also depend on assumptions about dispersal, extinction, continental geography and how fossil locations relate to ancestral ranges.
The 99.2% posterior probability for Europe is therefore strong support within the researchers’ model, not direct observation of the first bat population. Future fossil discoveries, especially from the Paleocene and earliest Eocene, could refine the timing and geography further. Likewise, 103 genomes represent extraordinary family-level coverage but still sample only a fraction of living bat species.
Even with those limitations, the study substantially narrows several long-running uncertainties. By combining high-quality genomes, fossils, chromosome reconstruction and time-aware biogeography, it provides a coherent account in which bats emerged in Europe near the end of the Paleocene, rapidly diversified through an early Europe-Africa hub and subsequently spread across the world.
Source Information
Study: Reference genomes and fossils revise bat family phylogeny and biogeography
Journal: Nature, volume 658, pages 141-152 (2026)
Published: 23 September 2026
DOI: 10.1038/s41586-026-11007-3
Research focus: Bat phylogeny, comparative genomics, fossil-informed evolutionary dating and historical biogeography
