Arizona State University School of Life Sciences paleontologist, assistant professor and presidential postdoctoral fellow, Matthew Jones helped provide a key piece of a landmark Nature study that revises scientists’ understanding of where bats came from, how their major families are related and when defining traits such as flight and echolocation emerged.
Published today in Nature , the study brought together 137 researchers from 64 countries through the Bat1K consortium. The team combined genomic and fossil evidence to show that bats, and thus mammalian flight, most likely originated in Europe around 65 million years ago.
Jones, an ASU author on the paper, contributed to the project’s fossil and biogeography work. His role centered on the evidence that genomes alone cannot provide: the bones of extinct bats. Because genomes can only be sequenced from living species in this study, the fossil record was essential for bringing extinct bats into the analysis and anchoring the family tree in deep time. Jones helped score fossil bats for anatomical traits, such as teeth and limb bones, so extinct species could be placed into the same evolutionary framework as living bats whose genomes were sequenced.
“For the living bats, we have the genomes,” Jones said. “But for the fossil bats, we do not have genomic data. We just have the bones. Scoring those anatomical characters lets us put the fossils into the tree and use them to understand the deep time dynamics of bat evolution.”
Jones worked with paleontologists Sue Hand and Nancy Simmons as part of the core fossil team. Their work helped the study go beyond a snapshot of living bat diversity and incorporate extinct species that lived tens of millions of years ago.
“The living bats are what we can observe in this very specific time slice,” Jones said. “Adding fossils gives us a lot more data right at the beginning of the radiation of bats. Because we know where fossils were found and how old they are, they help us reconstruct where bats originated and when they originated.”
The results overturn earlier hypotheses proposing Asian, African or North American origins. The earliest bat descendants then dispersed into Africa, establishing a Europe-Africa hub from which bats later expanded into Asia, the Americas and Australia.
The team assembled the largest collection of high-quality bat genomes to date, covering 103 species and representing every one of the currently recognized 21 living bat families. “We combined state-of-the-art DNA sequencing and computational methods to generate and compare these genomes and identify the genes they contain,” said Prof. Michael Hiller of the Senckenberg Research Institute in Frankfurt, a senior author. The team combined those genomes with 44 fossil bats from across the globe to reconstruct the evolutionary history of the world’s only flying mammals.
This is where the fossil work was essential. The study included 44 pre-Quaternary fossil taxa and 699 morphological characters scored across 65 species, including 21 living and 44 extinct taxa. That fossil framework helped constrain the timing of the earliest bat branches and strengthened the study’s reconstruction of where bats originated and how they spread.
Bats are among the most extraordinary mammals on Earth. They are the only mammals capable of true powered flight, and most orient and hunt in complete darkness using sound alone. With more than 1,500 species distributed across the globe, bats account for one fifth of all living mammals and play vital roles in healthy ecosystems by pollinating plants, dispersing seeds and consuming vast numbers of insect pests.
Many bat species also show remarkable resistance to disease and live exceptionally long lives for their size. The genomic resource built for this study gives scientists the first robust evolutionary framework to investigate the genes behind these traits. This work could eventually inform human research into aging, immunity and disease resistance.
Yet despite their extraordinary biology and ecological importance, scientists have struggled for decades to answer fundamental questions about bat evolution: Where did bats come from? How are the bat families related? When did flight and echolocation emerge? And how did bats evolve the unusual traits that set them apart from other mammals? This study provides answers to many of those long-standing questions.
Building the dataset required samples collected over decades from bats across the world, including representatives of some of the rarest and most unusual bat families, found in remote locations.
Among them are the tiny bumblebee bats of Thailand and Myanmar, widely considered Earth’s smallest mammal; the remarkable sucker-footed bats of Madagascar, which have suction cups on their wrists and ankles that they use to cling to smooth leaves; and one of New Zealand’s only native mammals, the lesser short-tailed bat, which “walks” along the forest floor using its folded wings as forelegs.
Jones noted that the Malagasy sucker-footed bats have been especially difficult to place on the bat family tree. The new study provides stronger support that they belong near the group that includes vesper bats and free-tailed bats, familiar lineages in North America and around the world.
The fossil evidence also provides important clues about another long-standing mystery: when bats first evolved echolocation.
The placement of the fossil bat Vielasia within the oldest branch of the bat family tree indicates that echolocation predates the diversification of modern bats. The finding suggests that two of the defining characteristics of bat biology, echolocation and powered flight, were established near the origin of the group itself, helping explain the extraordinary evolutionary success of bats over the subsequent 65 million years.
The team also reconstructed the genome of the bat ancestor, showing what the first genome of a mammal capable of flight would have looked like.
“This resource for the community of scientists allows them to investigate the different types of genomic variation, from single base changes to hundreds or thousands of bases missing from one lineage but present in another, that have given rise to the huge variety of bats that we share the planet with, and the origins of their unique characteristics,” said Prof. David Ray of Texas Tech University, a senior author.
This gives scientists a genomic map for how one lineage of mammals evolved powered flight, advanced biosonar, exceptional longevity and unusual disease resistance, creating a foundation to trace the genetic basis of these traits with relevance well beyond bats.
Topic
Detail
ASU role
Matthew Jones contributed to the fossil and biogeography work, including scoring fossil bats for anatomical characters used to place extinct species in the bat family tree.
Fossil evidence
The study incorporated 44 fossil bat species and 699 morphological characters, allowing researchers to use extinct species to reconstruct deep bat history.
Scale
103 bat genomes and 44 fossil taxa analyzed by 137 researchers from 64 countries.
Origin
Bats most likely arose in Europe around 65 million years ago, rather than Asia, Africa or North America as previously proposed.
Evolution
Flight and echolocation appear to have evolved early in bat history.
Future research
The genomic resource supports future studies of bat longevity, immunity and disease resistance.
Area
Additional technical detail
Genomes
103 bat species analyzed, including 42 new chromosome-level genome assemblies representing 41 distinct species; 26 of the new assemblies are haplotype-resolved. All 21 currently recognized bat families are represented. The study identified 188 conserved microRNA families, a clear relationship between genome size and transposable element content, distinct mobile DNA accumulations in each bat lineage and 26 chromosomes reconstructed for the bat common ancestor.
Fossils and biogeography
699 morphological characters scored across 65 species, including 21 living and 44 extinct taxa. The study includes 44 pre-Quaternary fossil taxa and infers a European origin in the late Paleocene, with a major superfamily radiation around the Paleocene-Eocene Thermal Maximum, about 56 million years ago.
Revised relationships
The enigmatic Madagascan sucker-footed bats are more closely related to the pan-global superfamily Vespertilionoidea than to the superfamily containing the New Zealand and South American endemic families, changing current understanding of bat biogeography.
Why the tree was hard to resolve
Bat genomes contain a mosaic of evolutionary histories. Different regions, and even different chromosomes, support different relationships among the major lineages. This pattern is most consistent with extensive ancient gene flow between lineages early in bat evolution. A region of the X chromosome retained a signal of the true species relationships and was key to resolving decades of conflicting phylogenies.
Ancestral genome
The team computationally reconstructed the genome of the last common ancestor of all living bats, offering a preliminary view of what a genome capable of powered flight may have looked like approximately 65 million years ago.
Nature
Computational simulation/modeling
Animals
Reference genomes and fossils revise bat family phylogeny and biogeography
23-Sep-2026
“The authors declare no competing interests.”