Gene Ontology-Based Comparative Transcriptomics Provides Evidence of Genetic Adaptations in the Rhinolophus macrotis Group (Chiroptera: Rhinolophidae).

Understanding adaptive evolution has long fascinated evolutionary biologists. Adaptive phenotypic divergence is often driven by modifications to protein-coding sequences. The Rhinolophus macrotis group exhibits relatively lower echolocation frequencies relative to body size compared with other rhinolophids, implying distinct evolutionary trajectories. Transcriptomes bridge genotypes and phenotypes. Here, we sequenced brain, liver and cochlea transcriptomes from one individual per species representing five taxa of the macrotis group. We performed comparative transcriptomic analyses and detected signals of positive selection. Seven hearing-related genes (CRYM, FOXM1, MAP6, PYCARD, SLC35A2, WRB and SPRY2) were under positive selection. Unexpectedly, we also identified five vision-associated positively selected genes (ARRDC3, LZTFL1, RAB8A, IGFBPL1 and TRNT1) in taxa with relatively lower echolocation frequencies within the macrotis group, indicating selection on sensory genes. Furthermore, candidate positively selected genes were significantly enriched in metabolism-related GO terms such as catalytic and oxidoreductase activity. Our study offers valuable transcriptomic resources for unraveling adaptive genetic mechanisms in horseshoe bats.