New research into bat evolutionary history has fundamentally rewritten the timeline and geography of how these extraordinary mammals came to be. In a massive study published on September 23, 2026, in the journal Nature, an international consortium of scientists revealed that bats—the only mammals capable of sustained powered flight—most likely originated in Europe during the late Palaeocene. This discovery refutes decades of competing theories that placed the origin of the order Chiroptera in North America, Africa, or Asia.
Key Takeaways
- European Origins: Advanced dispersal models suggest bats originated in Europe in the late Palaeocene before spreading to Africa and eventually the rest of the world.
- Redefined Family Tree: The study provides a new phylogeny, placing the enigmatic Myzopodidae family within the Vespertilionoidea superfamily.
- Echolocation Timeline: The placement of the fossil †Vielasia suggests that laryngeal echolocation evolved before the diversification of modern crown bats.
- Genomic Scale: The Bat1K consortium analyzed 103 chromosome-level genome assemblies, representing all 21 known bat families.
- Chromosomal Evolution: Research shows that bat evolution is characterized by the fusion of ancestral chromosomes rather than fissions or translocations.
- High Evolutionary Turnover: The study found that both speciation and extinction rates in bats were significantly higher than previously estimated.
- For Conservationists: Understanding the precise evolutionary lineages and geographic origins of bats is vital for prioritizing conservation efforts. If certain lineages are more ancient or have unique evolutionary histories, they may represent more critical nodes of biodiversity that require protection.
- For Medical Researchers: Bats are known to be reservoirs for various viruses. By understanding their evolutionary history and the genomic adaptations that allow them to tolerate these pathogens, scientists may find new insights into human immunology and disease resistance.
- For the Scientific Community: The Bat1K dataset serves as a massive, high-quality resource for benchmarking genomic alignment methods and exploring other complex evolutionary questions in different taxonomic groups.
- www.nature.com
What Happened: The Bat1K Breakthrough
For years, the evolutionary path of bats has been one of the most contentious subjects in mammalian biology. Because bats are highly mobile and their fossil record is notoriously sparse, scientists have struggled to pin down where they came from and how their unique traits—such as flight and echolocation—emerged.
To resolve these mysteries, the Bat1K consortium launched a massive undertaking to generate reference-quality, chromosome-level genome assemblies for every living bat species. On September 23, 2026, the researchers announced the completion of phase 1 of this project, which included 103 high-quality genome assemblies. This dataset, which includes 42 entirely new assemblies, covers all 21 recognized bat families, including rare and regionally endemic groups like the Craseonycteridae of Thailand and the Myzopodidae of Madagascar.
By combining these high-resolution genomic datasets with a massive morphological dataset of 699 characters from 65 species—including 44 pre-Quaternary fossils—the team employed “total evidence dating” (TED). This innovative approach allowed them to integrate molecular data with physical fossil evidence to create a much more accurate picture of the past than molecular-only studies could ever achieve.
Why It Matters: Resolving a Biological Mystery
This research does more than just update a textbook; it solves fundamental questions about how complex biological traits are acquired and maintained. Bats are biological marvels: they possess unique immune adaptations that allow them to host various viruses without falling ill, they exhibit extreme longevity for their size, and they have mastered the physics of powered flight.
Understanding the bat evolutionary history provides a roadmap for how mammals can adapt to extreme ecological niches. For instance, the study’s finding that laryngeal echolocation predates the diversification of modern bats suggests that the sensory ability to navigate in the dark was a foundational requirement for the radiation of the group. Furthermore, by identifying the specific genomic drivers of their unique traits, scientists can better understand the evolutionary trade-offs involved in specialized lifestyles, such as flight and nocturnal foraging.
The Genomic Revolution: Mapping the ‘Dark Genome’
One of the most significant technical achievements of this study was the ability to look past the functional genes to the “dark genome.” While protein-coding genes make up only about 2% of the genome, they can often be misleading in evolutionary studies due to selection pressures.
According to the researchers, previous phylogenetic studies were often misled because they relied too heavily on these protein-coding regions. The Bat1K team utilized neutrally evolving genomic sites—regions of the DNA that are not under heavy selection—to build a more accurate tree. By using methods like CASTER, which accounts for incomplete lineage sorting and rate heterogeneity, they were able to bypass the “noise” created by rapid speciation events and introgression (the movement of genes between species).
This approach revealed that the evolutionary history of bats is a mosaic. Different parts of the genome actually tell different stories. For example, the study found that widespread phylogenetic incongruence among chromosomes indicates that pervasive introgression has shaped the history of the suborder Yangochiroptera. This means that as different bat lineages diverged, they occasionally interbred, leaving a complex trail of genetic signatures across their chromosomes.
The Myzopodidae Mystery Explained
For a long time, the placement of the Myzopodidae—the unique, sucker-footed bats endemic to Madagascar—was a major headache for taxonomists. Because of their unique morphology and long evolutionary branch, different studies had placed them in various parts of the bat tree, often within the Noctilionoidea superfamily.
However, the new genomic analysis provided a definitive answer. By analyzing the whole-genome signal across multiple partitions, including the X chromosome and neutral “dark” SNPs, the researchers unambiguously placed Myzopodidae as the earliest branch within the superfamily Vespertilionoidea.
| Feature | Previous Consensus | New Bat1K Findings |
|---|---|---|
| Myzopodidae Placement | Noctilionoidea | Vespertilionoidea |
| Sister Group Relationship | Unclear/Multiple | Emballonuroidea + Vespertilionoidea |
| Primary Data Source | Morphology/Protein-coding | Neutral Genomic Windows/Dark SNPs |
| Evolutionary Signal | Conflicting/Long-branch | Robust/Genome-wide support |
This correction is a testament to the power of high-quality, chromosome-level assemblies. The study noted that while protein-coding genes suggested several different arrangements, the neutral regions provided a consistent, singular signal that aligned with morphological evidence.
A New Map of Bat Origins: From Europe to the World
Perhaps the most striking result of the study is the rejection of the long-held theories regarding the biogeographical origin of bats. For decades, the scientific community was split: some argued for an Asian origin, others for North America, and some for Africa.
The Bat1K team used a dispersal-extinction cladogenesis model that accounted for continental drift and the high mobility of bats. Their findings point to a late Palaeocene ancestor that originated in Europe. From this central Europe–Africa hub, the researchers inferred that bats underwent multiple, independent range expansions.
According to the research, the Yinpterochiroptera suborder likely originated in Africa during the early Eocene before expanding into Asia and Europe. Meanwhile, the Yangochiroptera suborder most likely emerged from a European ancestor within a similar timeframe. This expansion coincided with the Paleocene–Eocene thermal maximum (approximately 56 Ma), a period of intense global warming and environmental change that likely provided the ideal conditions for the rapid radiation of these flying mammals.
Chromosomal Architecture: The Power of Fusions
The study also provides the first comprehensive reconstruction of the ancestral bat karyotype. By comparing the 103 genome assemblies, the team identified that the common ancestor of all bats likely possessed 26 chromosomes.
Interestingly, the research shows that the evolution of bat chromosomes has been driven primarily by fusion rather than fission. In 97% of the bat genomes studied, fusions of ancestral chromosomes were the dominant mechanism of change. This finding is crucial for understanding how bats have managed to maintain some of the smallest mammalian genomes while still supporting the complex biological processes required for flight and long lifespans.
What It Means for You
While this research is deeply rooted in evolutionary biology, its implications reach further than one might expect.
Counterpoints and Open Questions
Despite the robustness of the Bat1K findings, the researchers acknowledge that several questions remain. The fossil record, while significantly improved by this study, is still described as “sparse and highly fragmented.” This means that while the researchers have significantly reduced the gaps in our knowledge, they cannot claim to have a complete picture of every transitional species.
Furthermore, the high degree of introgression observed in certain lineages suggests that the evolutionary history of bats is far more messy than a simple branching tree. This “genomic compartmentalization” means that different parts of a bat’s DNA might have different histories, which could complicate future attempts to map the evolution of specific traits like flight or echolocation with absolute certainty.
There is also the question of how much the Paleocene–Eocene thermal maximum influenced the radiation. While the correlation is strong, determining whether the environmental change was a driver or merely a facilitator of bat diversification remains a subject for future study.
What Happens Next
The Bat1K project is not over. The researchers have indicated that this study represents only “phase 1” of their mission. Future work will likely focus on deeper analysis of the remaining species and the continued refinement of the genomic datasets.
Watch for upcoming studies that apply this “total evidence” framework to other highly mobile or specialized mammalian orders. As sequencing technology improves and more fossils are discovered, the map of life will continue to be redrawn. The methodologies developed by the Bat1K team—specifically their ability to handle complex, introgressed histories using neutral genomic regions—are expected to become a standard in the field of phylogenomics.
Frequently Asked Questions
Where did bats originally come from?
According to the new research published in Nature, bats most likely originated in Europe during the late Palaeocene. From this European and African hub, they dispersed to the Americas, Asia, and Australia during the early Eocene.
What is the Bat1K project?
The Bat1K project is an international scientific consortium dedicated to generating and analyzing reference-quality, chromosome-level genome assemblies for all 103 living species of bats. Its goal is to resolve long-standing mysteries regarding bat evolution, biology, and diversity.
Why was the bat family tree so difficult to map for so long?
Mapping the bat family tree has been difficult due to several factors: a fragmented fossil record, the high mobility of bats which obscures their geographic origins, and conflicting signals in their DNA caused by rapid evolution and interbreeding (introgression) between lineages.
Did bats evolve echolocation at the same time as flight?
While the two traits are closely linked, the study suggests that laryngeal echolocation may have actually predated the diversification of modern bats. The placement of the fossil †Vielasia in the oldest bat clade indicates that the ability to echolocate was likely established before the modern groups of bats fully branched out.
The study of bat evolutionary history continues to reveal that even the most well-known animals can still hold profound secrets about the history of life on Earth
References
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