Extensive Adaptive Variation in Gene Expression within and between Closely Related Horseshoe Bats (Chiroptera, Rhinolophus) Revealed by Three Organs

SIMPLE SUMMARY: The role of natural selection on evolution at the gene expression level is still not well-understood. However, it is important for better understanding the molecular mechanisms of species differentiation. By identifying differentially expressed genes with variation forced by natural selection, we found that expression variation and variation related to phenotypic divergence were extensively adaptive between both species and subspecies for three closely related horseshoe bats. In addition, despite the immune-related adaptive expression variation found both within and between species, there were different functional patterns with respect to adaptive expression variation between two taxonomic scales as well. These results could be helpful for better comprehending the role of natural selection on evolution, and providing scientific basis for the protection of bat species. ABSTRACT: In the process of species differentiation and adaption, the relative influence of natural selection on gene expression variation often remains unclear (especially its impact on phenotypic divergence). In this study, we used differentially expressed genes from brain, cochlea, and liver samples collected from two species of bats to determine the gene expression variation forced by natural selection when comparing at the interspecific (Rhinolophus siamensis and R. episcopus episcopus) and the intraspecific (R. e. episcopus and R. episcopus spp.) levels. In both cases, gene expression variation was extensively adaptive (>66.0%) and mainly governed by directional selection, followed by stabilizing selection, and finally balancing selection. The expression variation related to acoustic signals (resting frequency, RF) and body size (forearm length, FA) was also widely governed by natural selection (>69.1%). Different functional patterns of RF- or FA-related adaptive expression variation were found between the two comparisons, which manifested as abundant immune-related regulations between subspecies (indicating a relationship between immune response and phenotypic adaption). Our study verifies the extensive adaptive expression variation between both species and subspecies and provides insight into the effects of natural selection on species differentiation and adaptation as well as phenotypic divergence at the expression level.