1. Introduction
Ever since the book “On the Origin of Species by Means of Natural
Selection” was published by Charles Darwin 160 years ago
(Darwin, 1859), adaptive evolution has
become an important research question
(Tian et al., 2017). Understanding the
driving forces of speciation processes is a primary goal of evolutionary
biology (Feldmeyer et al., 2015;
Marie Curie et al., 2012). And inferring
the patterns and processes that accompany the generation of phenotypic
diversity and new species is a primary goal of evolutionary biology
(Mason and Taylor, 2015). The development
of high-throughput sequencing technology provided more genetic
information of evolutionary history
(Lemmon and Lemmon, 2013;
Mccormack et al., 2013), adaptive traits
(Ma et al., 2023;
Sun et al., 2023;
Yu et al., 2023), and the evolution of
phenotypic diversity and speciation (Mason
and Taylor, 2015).
Thereinto
transcriptome analysis has been widely used in the study to reveal the
species evolutionary mechanisms (Dong et
al., 2013; Hao et al., 2019;
Koenig et al., 2013;
Naumenko et al., 2017;
Shao et al., 2015). Comparative
evolutionary approaches can address whether interspecific differences
are the result of neutral divergence over evolutionary history or
whether they are the result of nonrandom processes, such as adaptation
to different environmental conditions
(Marra et al., 2014). Thus comparative
transcriptomics was usually used to study the genetic basis of
evolutionary differences among species.
Bats belong to the order Chiroptera. Due to the constant changes in
external and internal factors during bat evolution, different bat
species have evolved different adaptive mechanisms to adapt to the
environment in the process of natural selection. Evolution is typically
thought to proceed through the divergence of genes, proteins, and
ultimately phenotypes (Clark et al., 2007;
Hughes et al., 2010;
Soskine and Tawfik, 2010). The changes in
phenotype can reflect the changes in genes. The new phenotype or
biological character of bats reflected the changes in the molecular
level of genetic material under selective pressure fundamentally.
Echolocation is an important phenotype in bats, and it is a complex
phenotypic trait, which involves the production, reception, and auditory
processing of ultrasonic pulses for obstacle avoidance, orientation, and
hunting (Au and Simmons, 2007;
Marianne et al., 2004). Rhinolophid bats
possess the most sophisticated echolocation
systems(Jones and Teeling, 2006), and
detected the positive selection of auditory genes in the study of genome
data (Dong et al., 2016). It revealed the
adaptation of auditory sensory perception in the rhinolophid bat
lineages (Dong et al., 2016;
Wang et al., 2019;
Zhao et al., 2019). Current studies into
the evolution of bat acoustic have been conducted at the population
level or in bats with different echolocation types, the molecular
mechanisms underlying acoustic differences between closely related bat
species are rare.
The Rhinolophus macrotis group, belonging to the family
Rhinolophidea, is a specific species group among the genusRhinolophus . The macrotis group currently includes six
species, namely R. episcopus ; R. siamensis ; R. rex ;R. osgoodi ; R. marshalli ; and R. schnitzleri(Liu et al., 2019;
Zhang et al., 2018). These species are
closely related species, and experienced recent and rapid
diversification during the Pleistocene
(Zhang et al., 2018). Compared with otherRhinolophus species, the echolocation frequencies for the species
within the macrotis group exhibits differences except R.
osgoodi , which were lower relative to their body size
(Zhang et al., 2009). Although some
acoustic related genes showed sequence convergence in echolocation bats
(Davies et al., 2012;
Li et al., 2008;
Li et al., 2010;
Liu et al., 2012;
Liu et al., 2011), different echolocation
characters among closely related species may indicated they have
undergone different evolutionary processes, which may reflected at the
genome level. Previous studies on morphology and behavior for this
special phenomenon showed that both pinna and nasal capsule size were
better predictors of echolocation call frequencies than forearm length
(Wu et al., 2015). Studies using
transcriptomics for R. episcopus and R. siamensis found
differentially expressed genes relevant to the variation in echolocation
frequency (Li et al., 2022a), and the
expression variation related to acoustic signals (resting frequency) and
body size (forearm length) was widely governed by natural selection
(Li et al., 2022b). However, little is
known about the molecular basis on gene sequences for this specific
phenomenon, which will help us to understand the evolution mode for the
auditory system in bats.
The species within the macrotis group are closely related withR. pusillus . Species in the macrotis group (exceptR. osgoodi ) have low frequencies relative to body size
(specieslow), whereas R. osgoodi and R.
pusillus emit echolocation with normal frequencies
(speciesnormal). The difference in echolocation
frequency provides the basis for understanding adaptations in their
evolutionary history. The whole-genome sequence of these species is not
available yet. Transcriptome analysis will help us to determine the
molecular genetics for the adaptation of the macrotis group. In
this study, we performed a comparative transcriptome analysis and
obtained the sequence for multi-tissues of specieslowand speciesnormal for the first time, to (1) identify
genes under positive selection and GO categories significantly enriched
involved in the adaptation; (2) characterize the sequence differences
between specieslow and speciesnormal;
and (3) uncover the potential genetic mechanism underlying the
adaptation for specieslow.