Echolocation call frequency variation in horseshoe bats: molecular basis revealed by comparative transcriptomics

Abstract

Recently diverged taxa with contrasting phenotypes offer opportunities for unravelling the genetic basis of phenotypic variation in nature. Horseshoe bats are a speciose group that exhibit a derived form of high-duty cycle echolocation in which the inner ear is finely tuned to echoes of the narrowband call frequency. Here, by focusing on three recently diverged subspecies of the intermediate horseshoe bat ( Rhinolophus affinis ) that display divergent echolocation call frequencies, we aim to identify candidate loci putatively involved in hearing frequency variation. We used de novo transcriptome sequencing of two mainland taxa ( himalayanus and macrurus ) and one island taxon ( hainanus ) to compare expression profiles of thousands of genes. By comparing taxa with divergent call frequencies (around 15 kHz difference), we identified 252 differentially expressed genes, of which six have been shown to be involved in hearing or deafness in human/mouse. To obtain further validation of these results, we applied quantitative reverse transcription–PCR to the candidate gene FBXL15 and found a broad association between the level of expression and call frequency across taxa. The genes identified here represent strong candidate loci associated with hearing frequency variation in bats.

Comparative transcriptome analysis provides insights into the molecular mechanisms of high-frequency hearing differences between the sexes of Odorrana tormota

“…There is increasing evidence that the potassium ion channel encoding gene ( KCNQ4 ), motor protein ( Prestin ) and other key genes involved in the sound signal transduction (i.e., TMC1 , CDH23 , Pcdh15 and Otof ) undergone adaptive evolution in echolocation bats, and were strongly associated with the high-frequency hearing [ 24 , 27 , 55 – 57 ]. However, these genes exhibited no significant expression difference between the sexes of O. tormota .…”

“…In addition, recent high-throughput RNA-Sequencing (RNA-Seq) technologies provided us a large-scale platform to address the molecular mechanisms underlying the adaptive evolution of particular phenotypes in non-model organisms [ 26 – 28 ]. For example, Sun et al (2020) found that the expression level of FBXL15 gene played an important role in changing the call frequency of horseshoe bats based on comparative transcriptome analysis [ 27 ].…”

Geographic variation in the skulls of the horseshoe bats,Rhinolophus simulatorandR. cf. simulator: Determining the relative contributions of adaptation and drift using geometric morphometrics

“…This raises the question of how they can maintain such divergent and non‐overlapping echolocation frequencies. The answer to this question requires evolutionary development studies to identify the loci which code for echolocation frequency (e.g., Sun et al ( 2020 )) and how these loci are assorted during gamete formation.…”

Geographic variation in the skulls of the horseshoe bats, Rhinolophus simulator and R. cf. simulator: determining the relative contributions of adaptation and drift using geometric morphometrics.

“…This raises the question of how they can maintain such divergent and non-overlapping echolocation frequencies. The answer to this question requires evolutionary development studies to identify the loci which code for echolocation frequency (e.g., Sun et al (Sun et al , 2020)) and how these loci are assorted during gamete formation.…”