Bats, the only mammals capable of powered flight and laryngeal echolocation, have long puzzled scientists seeking to map their evolutionary history. A collaborative effort now delivers a substantially revised family tree by merging chromosome‑level genome assemblies from 103 species with an extensive morphological fossil dataset.
New Genome Dataset Enables Refined Phylogeny
The Bat1K consortium released phase 1 of its project, providing long‑read, Hi‑C‑based assemblies for all 21 recognized bat families. Forty‑two of these assemblies are newly generated, representing 41 distinct species, and 26 of them are haplotype‑resolved. Together with 62 previously available high‑quality genomes, the collection spans the full taxonomic breadth of Chiroptera and includes eight outgroup mammals for comparative context.
Analysis of these chromosome‑level genomes uncovers a mosaic pattern of evolutionary relationships that resolves several longstanding ambiguities. The family Myzopodidae, endemic to Madagascar, emerges as the earliest diverging lineage within the superfamily Vespertilionoidea. Moreover, the study identifies Emballonuroidea and Vespertilionoidea as sister groups, clarifying the branching order among the Yangochiroptera.
Reconstruction of ancestral chromosome numbers suggests that the common ancestor of all bats possessed 26 chromosomes, a figure supported by the new high‑resolution assemblies. The comprehensive dataset also enabled a detailed survey of transposable elements. Thousands of novel consensus sequences were added to the Dfam database, confirming previous observations of recent DNA transposon bursts in several clades and a near‑complete halt of transposable‑element activity in the fruit‑bat family Pteropodidae. Patterns of LINE, Helitron, and long terminal repeat accumulation differ markedly across lineages, and a strong positive correlation (R² = 0.88) links transposable‑element load with overall genome size.
MicroRNA profiling using MirMachine identified 188 conserved families across all 103 bat genomes, providing an additional layer of functional insight into bat diversification.
Fossil Integration Shifts Bat Origin to Europe
Beyond the genomic component, researchers compiled a morphological matrix of 699 characters for 65 taxa, incorporating 44 pre‑Quaternary fossils that represent most living families. By applying fossilized birth–death and dispersal–extinction cladogenesis models, the combined evidence points to a European origin for bats and, consequently, for powered flight, during the late Palaeocene. This conclusion directly challenges earlier hypotheses that placed the cradle of bat evolution in Africa or North America.
The placement of the extinct genus †Vielasia within the oldest clade, termed “Eochiroptera,” indicates that laryngeal echolocation predates the diversification of crown‑group bats. Total‑evidence dating that integrates both fossil and genomic data markedly shortens the basal branch lengths that molecular‑only analyses had inferred, yielding a more compact timeline for early bat diversification.
Collectively, the study demonstrates how integrating high‑quality genomic resources with a robust fossil framework can resolve deep phylogenetic questions that have persisted for decades. The findings not only refine the bat family tree but also reshape our understanding of how key adaptations such as flight and echolocation emerged.
Future phases of the Bat1K initiative aim to expand sampling to the remaining bat species and to deepen functional analyses of the genomic features highlighted in this work, promising further insights into the remarkable biology of these mammals.
Norman Pearlstine is the Executive Editor and Co-Founder at News Raise. With over two decades of experience across financial journalism, corporate governance, and market analysis, Norman leads the editorial direction and ensures strict adherence to journalistic accuracy and ethics.
