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Concept: Rhinolophidae


There are two subspecies of Rhinolophus ferrumequinum currently recognized in South Korea. The Korean greater horseshoe bat subspecies, Rhinolophus ferrumequinum quelpartis, is distributed only in Jeju Island. The complete mitochondrial genome of the island subspecies was determined and revealed 99.7% similarity to the mainland subspecies Rhinolophus ferrumequinum korai. If d-loop region is excluded, similarity of the two genomes was 99.9%.

Concepts: DNA, Genome, South Korea, Korean language, Jeju-do, Rhinolophus, Rhinolophidae, Greater Horseshoe Bat


The phylogenetic and taxonomic relationships among the Old Wold leaf-nosed bats (Hipposideridae) and the closely related horseshoe bats (Rhinolophidae) remain unresolved. In this study, we generated a novel ~10 kb molecular dataset of 19 nuclear exon and intron gene fragments for 40 bat species to elucidate the phylogenetic relationships within the families Rhinolophidae and Hipposideridae. We estimated divergence times and explored potential reasons for any incongruent phylogenetic signal. We demonstrated the effects of outlier taxa and genes on phylogenetic reconstructions and compared the relative performance of intron and exon data to resolve phylogenetic relationships. Phylogenetic analyses produced a well-resolved phylogeny, supporting the familial status of Hipposideridae and demonstrated the paraphyly of the largest genus, Hipposideros. A fossil-calibrated timetree and biogeographical analyses estimated that Rhinolophidae and Hipposideridae diverged in Africa during the Eocene 42 mya. The phylogram, the timetree and a unique retrotransposon insertion supported the elevation of the subtribe Rhinonycterina to family level and which is diagnosed herein. Comparative analysis of diversification rates showed that the speciose genera Rhinolophus and Hipposideros underwent diversification during the Mid-Miocene Climatic Optimum. The intron versus exon analyses demonstrated the improved nodal support provided by introns for our optimal tree, an important finding for large-scale phylogenomic studies which typically rely on exon data alone. With the recent outbreak of Middle East Respiratory Syndrome (MERS), caused by a novel coronavirus, the study of these species is urgent as they are considered the natural reservoir for emergent SARS-like coronaviruses. It has been shown that host phylogeny is the primary factor that determines a virus’s persistence, replicative ability and can act as a predictor of new emerging disease. Therefore, this newly resolved phylogeny can be used to direct future assessments of viral diversity and to elucidate the origin and development of SARS like coronaviruses in mammals.

Concepts: Biology, Species, Severe acute respiratory syndrome, Phylogenetic tree, Phylogenetics, Rhinolophidae, Horseshoe bat, Hipposiderinae


To examine the level of genetic differentiation in the sequences of the mitochondrial D-loop gene of Rhinolophus ferrumequinum, and to evaluate the current taxonomic status of this species, 50 tissue samples of greater horseshoe bats were collected in 2011-2015 from 21 different localities in northwest, northeast, west, central, and south regions of Iran. Twenty-two published D-loop sequences from Europe (Switzerland, United Kingdom, Bulgaria, and Tunisia), and Anatolia (south, west, and east Turkey) were downloaded from GenBank. Molecular genetic analyses revealed remarkable variation among populations of R. ferrumequinum. Two major clades with strong support were identified within the greater horseshoe bat. One of these clades consists of individuals of R. ferrumequinum from Iran and eastern Turkey, and is further subdivided into two subclades. A second clade includes samples from western Turkey and Europe. The two subclades from Iran and Turkey and the second clade from western Turkey and Europe represent three diagnosable categories, which most probably warrant three subspecies for the species. Thus, based on genetic differences, it is clear that two subspecific populations are found in Iran: R. f. irani (southern Iran) and R. f. proximus (northern Iran).

Concepts: DNA, Turkey, Microbat, Bats, Rhinolophus, Rhinolophidae, Greater Horseshoe Bat, Mendip Hills


Climatic variables are often considered when studying environmental impacts on population dynamics of terrestrial species. However, the temporal resolution considered varies depending on studies, even among studies of the same taxa. Most studies interested in climatic impacts on populations tend to average climatic data across timeframes covering life cycle periods of the organism in question or longer, even though most climatic databases provide at least a monthly resolution. We explored the impact of climatic variables on lesser horseshoe bat (Rhinolophus hipposideros) demography based on count data collected at 94 maternity colonies from 2000 to 2014 in Britanny, France. Meteorological data were considered using different time resolutions (month, life cycle period and year) to investigate their adequacy. Model averaging was used to detect significant predictors for each temporal resolution. Our results show that the finest temporal resolution, e.g. month, was more informative than coarser ones. Precipitation predictors were particularly decisive, with a negative impact on colony sizes when rainfall occurred in October, and a positive impact for June precipitations. Fecundity was influenced by April weather. This highlights the strong impact of climatic conditions during crucial but short time periods on the population dynamics of bats. We demonstrate the importance of choosing an appropriate time resolution and suggest that analogous studies should consider fine-scale temporal resolution (e.g. month) to better grasp the relationship between population dynamics and climatic conditions.

Concepts: Demography, Population, Precipitation, Climate, Menstrual cycle, Rhinolophus, Rhinolophidae, Lesser horseshoe bat


Many animals produce alarm or distress calls when they encounter predators. Previous studies have shown that the distress calls of some birds can also signal the quality of the bird as prey to predators. In this case, both predator and prey may benefit from sharing information about prey’s ability to escape. However, little is known about whether echolocation pulses and distress calls in bats convey size and quality information in distress situations. This study investigates the relationship between echolocation, distress calls, and the health of the callers to determine whether these signals are reliable indicators of sender’s attributes and quality. The spectro-temporal structure of echolocation pulses and distress calls from captured greater horseshoe bats, Rhinolophus ferrumequinum, were found to be correlated to their body size, body condition, and T-cell-mediated immunocompetence. The peak frequency of echolocation pulses was found to be positively correlated with the bats' forearm length. However, regression analysis has shown that no significant relationship exists between distress calls and overall body size, or between distress calls and overall health. These results suggest that the peak frequency of echolocation pulses may be a reliable index signal to attract conspecifics, but distress calls of bats may not convey information about their size or overall quality as conspecifics or prey. These results indicate that distress calls in bats may only convey their emotional state, to attract conspecifics and facilitate estimation of predation risk.

Concepts: Predation, Rhinolophus, Rhinolophidae, Greater Horseshoe Bat


The emission of biosonar pulses in horseshoe bats (family Rhinolophidae) differs from technical sonar in that it has dynamic features at the interface to the free field. When the horseshoe bats emit their biosonar pulses through the nostrils, the walls of a horn-shaped baffle (anterior leaf) are in motion while diffracting the outgoing ultrasonic wave packets. Here, biomimetic reproductions of the dynamic emission shapes of horseshoe bats have been studied for their ability to impose time-variant signatures onto the outgoing pulses. It was found that an elliptical sound outlet with rotating baffles that were attached along the direction of the major axis can be well suited for this purpose. Most importantly, concave baffle shapes were found to produce strongly time-dependent devices characteristics that could reach a root-mean-square-difference between beampatterns of almost 6 dB within a rotation angle of 10°. In contrast to this, a straight baffle shape needs to be rotated over 60° for a similar result. When continuously rotated in synchrony with the emitted pulses, the concave biomimetic baffles produced time-variant device characteristics that depended jointly on direction, frequency, and time. Since such device properties are so easily produced, it appears well worthwhile to explore their use in engineering.

Concepts: Ultrasound, Bat, Rotation, Sonar, Microbat, Bats, Rhinolophidae, Horseshoe bat


Echolocating greater horseshoe bats (Rhinolophus ferrumequinum) emit their biosonar pulses nasally, through nostrils surrounded by fleshy appendages (‘noseleaves’) that diffract the outgoing ultrasonic waves. Movements of one noseleaf part, the lancet, were measured in live bats using two synchronized high speed video cameras with 3D stereo reconstruction, and synchronized with pulse emissions recorded by an ultrasonic microphone. During individual broadcasts, the lancet briefly flicks forward (flexion) and is then restored to its original position. This forward motion lasts tens of milliseconds and increases the curvature of the affected noseleaf surfaces. Approximately 90% of the maximum displacements occurred within the duration of individual pulses, with 70% occurring towards the end. Similar lancet motions were not observed between individual pulses in a sequence of broadcasts. Velocities of the lancet motion were too small to induce Doppler shifts of a biologically-meaningful magnitude, but the maximum displacements were significant in comparison with the overall size of the lancet and the ultrasonic wavelengths. Three finite element models were made from micro-CT scans of the noseleaf post mortem to investigate the acoustic effects of lancet displacement. The broadcast beam shapes were found to be altered substantially by the observed small lancet movements. These findings demonstrate that-in addition to the previously described motions of the anterior leaf and the pinna-horseshoe bat biosonar has a third degree of freedom for fast changes that can happen on the time scale of the emitted pulses or the returning echoes and could provide a dynamic mechanism for the encoding of sensory information.

Concepts: Ultrasound, Rhinolophus, Rhinolophidae, Greater Horseshoe Bat


Despite the identification of horseshoe bats as the reservoir of SARS-related-coronaviruses (SARSr-CoVs), the origin of SARS-CoV ORF8, which contains the 29-nt signature deletion among human strains, remains obscure. Although two SARSr-Rs-BatCoVs, RsSHC014 and Rs3367, previously detected from Chinese horseshoe bats (Rhinolophus sinicus) in Yunnan, possessed 95% genome identities to human/civet SARSr-CoVs, their ORF8 exhibited only 32.2-33% aa identities to that of human/civet SARSr-CoVs. To elucidate the origin of SARS-CoV ORF8, we sampled 348 bats of various species in Yunnan, among which diverse alphacoronaviruses and betacoronaviruses, including potentially novel CoVs, were identified, with some showing potential interspecies transmission. The genomes of two betacoronaviruses, SARSr-Rf-BatCoV YNLF_31C and YNLF_34C, from greater horseshoe bats (Rhinolophus ferrumequinum), possessed 93% nt identities to human/civet SARSr-CoV genomes. Although they displayed lower similarities to civet SARSr-CoVs than SARSr-Rs-BatCoV RsSHC014 and Rs3367 in S protein, their ORF8 demonstrated exceptionally high (80.4-81.3%) aa identities to that of human/civet SARSr-CoVs, compared to SARSr-BatCoVs from other horseshoe bats (23.2-37.3%). Potential recombination events were identified around ORF8 between SARSr-Rf-BatCoVs and SARSr-Rs-BatCoVs, leading to the generation of civet SARSr-CoVs. The expression of ORF8 subgenomic mRNA suggested that this protein may be functional in SARSr-Rf-BatCoVs. The high Ka/Ks ratio among human SARS-CoVs compared to SARSr-BatCoVs supported that ORF8 is under strong positive selection during animal-to-human transmission. Molecular clock analysis using ORF1ab showed that SARSs-Rf-BatCoV YNLF_31C and YNLF_34C diverged from civet/human SARSr-CoVs at approximately 1990. SARS-CoV ORF8 is originated from SARSr-CoVs of greater horseshoe bats through recombination, which may be important for animal-to-human transmission.

Concepts: DNA, Severe acute respiratory syndrome, SARS coronavirus, Coronavirus, Rhinolophus, Rhinolophidae, Greater Horseshoe Bat


Hibernation is one type of torpor, a hypometabolic state in heterothermic mammals, which can be used as an energy-conservation strategy in response to harsh environments, e.g. limited food resource. The liver, in particular, plays a crucial role in adaptive metabolic adjustment during hibernation. Studies on ground squirrels and bears reveal that many genes involved in metabolism are differentially expressed during hibernation. Especially, the genes involved in carbohydrate catabolism are down-regulated during hibernation, while genes responsible for lipid β-oxidation are up-regulated. However, there is little transcriptional evidence to suggest physiological changes to the liver during hibernation in the greater horseshoe bat, a representative heterothermic bat. In this study, we explored the transcriptional changes in the livers of active and torpid greater horseshoe bats using the Illumina HiSeq 2000 platform. A total of 1358 genes were identified as differentially expressed during torpor. In the functional analyses, differentially expressed genes were mainly involved in metabolic depression, shifts in the fuel utilization, immune function and response to stresses. Our findings provide a comprehensive evidence of differential gene expression in the livers of greater horseshoe bats during active and torpid states and highlight potential evidence for physiological adaptations that occur in the liver during hibernation.

Concepts: Gene, Genetics, Gene expression, Evolution, Organism, Rhinolophus, Rhinolophidae, Greater Horseshoe Bat


Rhinolophus ferrumequinum nippon and Rhinolophus ferrumequinum tragatus are two subspecies of Rhinolophus ferrumequinum currently recognized in China. In this study, their mitochondrial genomes were completely sequenced and annotated. Phylogenetic analyses indicated that R. f. nippon has a close relationship with two subspecies of R. ferrumequinum from Korea with 0.1% divergence, which indicated they are synonyms.

Concepts: Japan, Microbat, Rhinolophus, Rhinolophidae, Greater Horseshoe Bat