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Updated: Dec 9, 2025

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

Haijian Sun1, Wenli Chen1, Jiaying Wang2

  • 1School of Ecological and Environmental Sciences, East China Normal University, Shanghai 200062, People's Republic of China.

Proceedings. Biological Sciences
|September 9, 2020
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Summary

Researchers studied hearing frequency variation in horseshoe bats by comparing gene expression. They identified several candidate genes, including FBXL15, linked to differences in echolocation calls, offering insights into auditory evolution.

Keywords:
adaptationhearing genemammalsphenotypic variationtranscriptomics

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Area of Science:

  • Genomics and Evolutionary Biology
  • Auditory Neuroscience
  • Bioacoustics

Background:

  • Recently diverged taxa with contrasting phenotypes are valuable for studying the genetic basis of natural variation.
  • Horseshoe bats possess a specialized high-duty cycle echolocation system, requiring precise inner ear tuning to their narrowband call frequencies.

Purpose of the Study:

  • To identify candidate genes associated with hearing frequency variation in three recently diverged subspecies of the intermediate horseshoe bat (Rhinolophus affinis).
  • To investigate the genetic underpinnings of divergent echolocation call frequencies within this bat species.

Main Methods:

  • De novo transcriptome sequencing was performed on two mainland subspecies (himalayanus, macrurus) and one island subspecies (hainanus).
  • Gene expression profiles were compared between taxa with divergent echolocation call frequencies (approximately 15 kHz difference).
  • Quantitative reverse transcription-PCR (qRT-PCR) was used to validate expression levels of candidate genes, specifically FBXL15.

Main Results:

  • Comparison of gene expression profiles identified 252 differentially expressed genes between taxa with divergent call frequencies.
  • Six of these differentially expressed genes have known associations with hearing or deafness in humans and mice.
  • FBXL15 showed a significant association between its expression level and echolocation call frequency across the studied subspecies.

Conclusions:

  • The study identified strong candidate gene loci potentially involved in regulating hearing frequency variation in bats.
  • These findings contribute to understanding the genetic mechanisms underlying auditory adaptations in echolocating mammals.
  • FBXL15 is highlighted as a key gene associated with hearing frequency differences in Rhinolophus affinis.