Molecular Phylogenetics and Systematics of Bat Taxa

Molecular phylogenetics has transformed our understanding of bat diversity by providing a framework for reconstructing evolutionary relationships among lineages that often lack clear morphological distinctions. By combining mitochondrial and nuclear DNA sequences with transcriptome‐scale data, researchers have resolved both deep and recent divergences within Chiroptera, identified cryptic species, and elucidated the timing and drivers of major radiations. Integrative systematics further incorporates acoustic, morphological and ecological datasets to corroborate molecular hypotheses, revealing patterns of convergent echolocation, adaptive shifts in skull morphology, and the role of geographic isolation in speciation. These advances have global significance for biodiversity assessment, conservation prioritisation and the study of zoonotic disease reservoirs. Applied outcomes range from refining species boundaries for legal protection to mapping the evolutionary origins of echolocation and identifying refugia that buffer bat lineages against climate change.

Research from Nature Portfolio

Recent transcriptome‐based analyses have leveraged RNA‐seq data from multiple bat taxa to test subordinal classifications, providing strong support for the Yinpterochiroptera–Yangochiroptera split and estimating their divergence at approximately 63 million years ago. Genome‐scale orthologue sampling improved resolution across contentious nodes and confirmed that sampling breadth rather than analytical method is key to robust phylogenies. In parallel, studies of the bumblebee bat (Craseonycteris thonglongyai) have combined population genomics with echolocation analyses to show that geographic isolation in Myanmar and Thailand preceded sensory divergence, with restricted gene flow creating conditions for local adaptation of sonar calls. These findings underscore the interplay between demographic history and phenotypic evolution in driving speciation among bats.

Molecular Phylogenetics and Systematics of Bat Taxa publication trend

The graph below shows the total number of articles in molecular phylogenetics and systematics of bat taxa across all publications each year (not limited to Nature Index journals).

Technical terms

Molecular phylogenetics: Reconstruction of evolutionary relationships using sequence data from DNA or RNA.

Systematics: Discipline that integrates taxonomy, phylogeny and biogeography to classify organisms and infer their evolutionary history.

Transcriptome sequencing: High‐throughput profiling of expressed genes (RNA) to generate broad sets of phylogenetically informative characters.

Ultraconserved elements (UCEs): Highly conserved nuclear DNA regions used as markers for resolving relationships at multiple taxonomic depths.

Laryngeal echolocation: Biological sonar produced by the larynx, enabling bats to navigate and forage in darkness.

Mito-nuclear discordance: Conflict between phylogenetic trees inferred from mitochondrial genomes and those from nuclear loci.

Coalescent lineage delimitation: Statistical approach that infers species boundaries by modelling gene tree histories under the coalescent process.

References

1. Phylogenomic analyses of bat subordinal relationships based on transcriptome data. Scientific Reports (2016).
2. The evolution of sensory divergence in the context of limited gene flow in the bumblebee bat. Nature Communications (2011).
3. Southern Africa's Great Escarpment as an amphitheater of climate‐driven diversification and a buffer against future climate change in bats. Global Change Biology (2024).
4. Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics. BMC Ecology and Evolution (2019).
5. Conflicting Evolutionary Histories of the Mitochondrial and Nuclear Genomes in New World Myotis Bats. Systematic Biology (2017).