Rhinolophus Research Articles

Modelling the functional connectivity of landscapes for greater horseshoe bats Rhinolophus ferrumequinum at a local scale

ContextThe importance of habitat connectivity for wildlife is widely recognised. However, assessing the movement of species tends to rely on radio-tracking or GPS evidence, which is difficult and costly to gather.ObjectivesTo examine functional connectivity of greater horseshoe bats (GHS, Rhinolophus ferrumequinum) at a local scale using Circuitscape software; comparing our results against expert opinion ‘fly ways’.MethodsExpert opinions were used to rank and score five environmental layers influencing GHS movement, generating resistance scores. The slope and resistance scores of these layers were varied, and validated against independent ground truthed GHS activity data, until a unimodal peak in correlation was identified for each layer. The layers were combined into a multivariate model and re-evaluated. Radio-tracking studies were used to further validate the model, and the transferability was tested at other roost locations.ResultsFunctional connectivity models could be created using bat activity data. Models had the ability to be transferred between roost locations, although site-specific validation is strongly recommended. For all other bat species recorded, markedly more (125%) bat passes occurred in the top quartile of functional connectivity compared to any of the lower three quartiles.ConclusionThe model predictions identify areas of key conservation importance to habitat connectivity for GHS that are not recognised by expert opinion. By highlighting landscape features that act as barriers to movement, this approach can be used by decision-makers as a tool to inform local management strategies.

Ambient temperature correlates with geographic variation in body size of least horseshoe bats.

Geographic variation in body size is common within many animal species. The causes of this pattern, however, remain largely unexplored in most vertebrate groups. Bats are widely distributed globally owing to their ability of powered flight. Most bat species encounter a variety of climatic conditions across their distribution range, making them an ideal taxon for the study of ecogeographic patterns in body size. Here, we used adult least horseshoe bats, Rhinolophus pusillus, to test whether geographic variation in body size was determined by heat conservation, heat dissipation, climatic seasonality, or primary productivity. We measured body mass and head-body length for 246 adult bats from 12 allopatric colonies in China. We quantified the ecological conditions inhabited by each colony, including mean maximum temperature of the warmest month, mean minimum temperature of the coldest month, temperature seasonality, precipitation seasonality, and annual net primary productivity (ANPP). Body mass and head-body length, 2 of the most reliable indicators of body size, exhibited marked differences between colonies. After controlling for spatial autocorrelation, the mean minimum temperature of the coldest month explained most of the variation in body size among colonies, regardless of sex. The mean maximum temperature, climatic seasonality, and ANPP had limited power in predicting body size of males or females in comparison with mean minimum temperature. These results support the heat conservation hypothesis and suggest adaptive responses of body size to cold climates in cave-dwelling bats.

Environmental variables do not explain the high size fluctuations in Rhinolophus euryale pre-hibernating aggregation

The Mediterranean horseshoe bat, Rhinolophus euryale, creates in the pre-hibernation period an aggregation in the Domica cave (Slovakia) and despite the harsh winter conditions displays a certain amount of flying activity. The goal of the study was to find out whether some environmental factors influence these conspicuous aggregation dynamics. We used image and statistical analysis of pictures of the aggregation taken automatically in the cave along with atmospheric pressure, humidity, outside and inside cave temperature and oxygen and carbon dioxide contents in the cave. These environmental variables were assumed to explain the observed activity. We hypothesised that the number of bats in particular time periods would correlate with some of these variables, but this was not confirmed. The only significant relations confirmed were those between bat numbers and humidity and carbon dioxide values in the cave. No trend in the spatial positioning of the bats was observed, and no environmental factors influenced the numbers, movements or groupings of bats. On the contrary, bats by their presence (breathing), activity and production of excrements may significantly influence the microclimate of the cave environment.

Can animals like bats, pangolins, and ticks would be considered as long-term reservoirs of severe acute respiratory syndrome coronavirus 2

In December 2019, there was an outbreak of pneumonia with an unknown cause in Wuhan, Hubei province, China. Within less than 3–4 months, the virus has spread to more than 200 countries. The virus rapidly transmitted from different places of the world with various cultural traditions. Thereby, the question is remained to be resolved about the main intermediate carrier of diseases in different animals. Studied showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was originated from horseshoe bats, but its intermediate hosts are still largely unknown. Therefore, the possibility of horseshoe bat infection by ticks is high during the flight between plants or when resting in these places. Female ticks can either feed on horseshoe bat blood for 5–7 days before shedding or can form large aggregations by laying several thousand eggs in the right places or on them. Once they feed on horseshoe bat blood containing SARS-CoV-2, they can transfer the infection to the next generations without the need to reuse infections from the reservoir host. With all the potential features that this creature has, it is mandatory to investigate the presence or absences of SARS-CoV-2, especially when we know that ticks co-exist with that horseshoe bats. These factors highlight the importance of studying the viral epidemiology in the tick population. Thereby, based on the wide distribution of ticks and their co-existence with horseshoe bat, we suggest further studies on ticks that might act as one of the main intermediate hosts in different animals.

Comparative echolocation and foraging ecology of horseshoe bats (Rhinolophidae) and Old World leaf-nosed bats (Hipposideridae)

Horseshoe (Rhinolphidae) and Old World leaf-nosed (Hipposideridae) bats are high duty cycle (HDC) echolocators sharing a suite of adaptations including long duration signals relative to their signal periods, peak energy concentrated in a narrow spectral band dominated by a constant frequency (CF) component, ‘auditory fovea’ (over-representation and sharp tuning of neurons responsible for frequencies at or around the CF) and ability to compensate for Doppler shifts in echoes. HDC bats separate signals from returning echoes in the frequency domain. Rhinolophids are more specialised neurobiologically than hipposiderids, producing longer duration signals at higher duty cycles, and have narrowly tuned auditory fovea and almost full Doppler shift compensation. Here, I examine whether these differences have produced ecological divergence between the families by testing predictions of differences in prey perception, prey capture behaviour, foraging habitat and diet. I found no discernible differences in these variables between the two families. Rhinolophids and hipposiderids both forage close to vegetation, capture prey by aerial hawking and gleaning from surfaces, and consume mostly flying insects with spiders and terrestrial, flightless arthropods taken occasionally. The data presented here show that the two families are similar in foraging ecology despite differences in echolocation and audition.

A biomimetic soft robotic pinna for emulating dynamic reception behavior of horseshoe bats

Encoding of sensory information is fundamental to closing the performance gap between man-made and biological sensing. It has been hypothesized that the coupling of sensing and actuation, a phenomenon observed in bats among other species, is critical to accomplishing this. Using horseshoe bats as a model, we have developed a biomimetic pinna model with a soft actuation system along with a prototype strain sensor for enabling motor feedback. The actuation system used three individually controlled pneumatic actuators per pinna which actuated different portions of the baffle. This prototype produced eight different possible motions that were shown to have significant effects on incoming sound and could hence function as a substrate for adaptive sensing. The range of possible motions could be expanded by adjusting the fill and release parameters of the actuation system. Additionally, the strain sensor was able to represent the deformation of the pinna as measurements from this sensor were highly correlated with deformation estimates based on stereo vision. However, the relationship between displacements of points on the pinna and the sensor output was nonlinear. The improvements embodied in the system discussed here could lead to enhancements in the ability of autonomous systems to encode relevant information about the real world.

Conservation analysis of SARS-CoV-2 spike suggests complicated viral adaptation history from bat to human.

BackgroundThe current coronavirus disease 2019 (COVID-19) pandemic, caused by severe acute respiratory syndrome (SARS)-CoV-2, has become the most devastating public health emergency in the 21st century and one of the most influential plagues in history. Studies on the origin of SARS-CoV-2 have generally agreed that the virus probably comes from bat, closely related to a bat CoV named BCoV-RaTG13 taken from horseshoe bat (Rhinolophus affinis), with Malayan pangolin (Manis javanica) being a plausible intermediate host. However, due to the relatively low number of SARS-CoV-2-related strains available in public domain, the evolutionary history remains unclear.MethodologyNine hundred ninety-five coronavirus sequences from NCBI Genbank and GISAID were obtained and multiple sequence alignment was carried out to categorize SARS-CoV-2 related groups. Spike sequences were analyzed using similarity analysis and conservation analyses. Mutation analysis was used to identify variations within receptor-binding domain (RBD) in spike for SARS-CoV-2-related strains.ResultsWe identified a family of SARS-CoV-2-related strains, including the closest relatives, bat CoV RaTG13 and pangolin CoV strains. Sequence similarity analysis and conservation analysis on spike sequence identified that N-terminal domain, RBD and S2 subunit display different degrees of conservation with several coronavirus strains. Mutation analysis on contact sites in SARS-CoV-2 RBD reveals that human-susceptibility probably emerges in pangolin.Conclusion and implicationWe conclude that the spike sequence of SARS-CoV-2 is the result of multiple recombination events during its transmission from bat to human, and we propose a framework of evolutionary history that resolve the relationship of BCoV-RaTG13 and pangolin coronaviruses with SARS-CoV-2.Lay SummaryThis study analyses whole-genome and spike sequences of coronavirus from NCBI using phylogenetic and conservation analyses to reconstruct the evolutionary history of severe acute respiratory syndrome (SARS)-CoV-2 and proposes an evolutionary history of spike in the progenitors of SARS-CoV-2 from bat to human through mammal hosts before they recombine into the current form.

The Times They Are A-Changin’

The photograph on the front cover of this issue of Human–Wildlife Interactions (HWI) is a horseshoe bat (Rhinolophus spp.). This genus has been identified as the wildlife reservoir for COVID-19. COVID-19 is one of an estimated 5,000 coronaviruses that naturally occur in bats. Because the virus is fairly stable, scientists studying the COVID-19 outbreak suspect that there were many more individuals infected with the disease for several months that were exhibiting mild symptoms, before more severe cases raised public alarm. © 2020,Human-Wildlife Interactions. All rights reserved.

RNA based mNGS approach identifies a novel human coronavirus from two individual pneumonia cases in 2019 Wuhan outbreak

ABSTRACT From December 2019, an outbreak of unusual pneumonia was reported in Wuhan with many cases linked to Huanan Seafood Market that sells seafood as well as live exotic animals. We investigated two patients who developed acute respiratory syndromes after independent contact history with this market. The two patients shared common clinical features including fever, cough, and multiple ground-glass opacities in the bilateral lung field with patchy infiltration. Here, we highlight the use of a low-input metagenomic next-generation sequencing (mNGS) approach on RNA extracted from bronchoalveolar lavage fluid (BALF). It rapidly identified a novel coronavirus (named 2019-nCoV according to World Health Organization announcement) which was the sole pathogens in the sample with very high abundance level (1.5% and 0.62% of total RNA sequenced). The entire viral genome is 29,881 nt in length (GenBank MN988668 and MN988669, Sequence Read Archive database Bioproject accession PRJNA601736) and is classified into β-coronavirus genus. Phylogenetic analysis indicates that 2019-nCoV is close to coronaviruses (CoVs) circulating in Rhinolophus (Horseshoe bats), such as 98.7% nucleotide identity to partial RdRp gene of bat coronavirus strain BtCoV/4991 (GenBank KP876546, 370 nt sequence of RdRp and lack of other genome sequence) and 87.9% nucleotide identity to bat coronavirus strain bat-SL-CoVZC45 and bat-SL-CoVZXC21. Evolutionary analysis based on ORF1a/1b, S, and N genes also suggests 2019-nCoV is more likely a novel CoV independently introduced from animals to humans.

Structural and Functional Analysis of the D614G SARS-CoV-2 Spike Protein Variant

The SARS-CoV-2 spike (S) protein variant D614G supplanted the ancestral virus worldwide, reaching near fixation in a matter of months. Here we show that D614G was more infectious than the ancestral form on human lung cells, colon cells, and on cells rendered permissive by ectopic expression of human ACE2 or of ACE2 orthologs from various mammals, including Chinese rufous horseshoe bat and Malayan pangolin. D614G did not alter S protein synthesis, processing, or incorporation into SARS-CoV-2 particles, but D614G affinity for ACE2 was reduced due to a faster dissociation rate. Assessment of the S protein trimer by cryo-electron microscopy showed that D614G disrupts an interprotomer contact and that the conformation is shifted toward an ACE2 binding-competent state, which is modeled to be on pathway for virion membrane fusion with target cells. Consistent with this more open conformation, neutralization potency of antibodies targeting the S protein receptor-binding domain was not attenuated.

Long-term effects of grating derelict mines on bat emergence activity, abundance and behaviour

In Australia, there are at least 50 000 derelict mines, many of which provide habitat for cave-roosting bats. Grating of derelict mines, be it horizontal (adits) or vertical (shafts) drives, is commonly undertaken to prevent human access, though longer-term responses of bats are largely unknown. We assessed the long-term (2–20 years) effects of grating on bats by documenting trends in emergence activity and bat abundance at grated and ungrated derelict mines and quantified behavioural responses of bats in autumn and winter. Emergence activity was dominated by the eastern horseshoe bat (Rhinolophus megaphyllus) with limited activity of other less manoeuvrable species. Both emergence activity and minimum colony size at horizontal adits were 8–9 times greater than at vertical shafts, with bats observed emerging from only 2 of 13 shafts. Emergence activity and minimum colony size were 7–10 times greater at adits with ‘bat friendly’ grating (horizontal bars with spacing >125 mm) than at other treatments (ungrated adits and adits with standard grating). In winter, there were 4–11 times more aborted exit attempts per bat at adits with ‘bat friendly’ grating compared with other treatments, which corresponded to greater emergence activity. Emergence activity and minimum colony size were not related to spacing between bars or time since grating, indicating rapid habituation by R. megaphyllus. However, circling at grates continued for many years and bentwing bats (Miniopterus spp.) made little use of these sites. Bat-friendly grates appear to be an effective management option for R. megaphyllus, but alternatives need to be trialled for other species.

Genetic diversity of Italian greater horseshoe bats ( Rhinolophus ferrumequinum ) and distinction of the Sardinian colonies

Genetic diversity of Italian greater horseshoe bats ( Rhinolophus ferrumequinum ) and distinction of the Sardinian colonies

Complementary bat (Mammalia: Chiroptera) survey techniques uncover two new country records for Nigeria

Knowledge of the bat fauna in Nigeria is limited due to use of outdated collection techniques, and infrequent sampling effort. To advance knowledge of bat diversity in the country, a survey of bats from three localities:—Emu, Okomu National Park (ONP), and Ososo—in southern Nigeria was conducted using mist nets set at canopy and at ground level from February–September 2011. During 28 capture nights involving a total of 202.7 mist net/nights, 239 individuals belonging to 27 bat species in eight families (Emballonuridae, Hipposideridae, Megadermatidae, Molossidae, Nycteridae, Pteropodidae, Rhinolophidae, and Vespertilionidae) were recorded. A total of 130, 64, 45 individuals of 8, 13 and 11 species were recorded from Emu, Okomu, and Ososo, respectively. Two new country records, Casinycteris campomaanensis and Chaerephon aloysiisabaudiae, both collected from Okomu National Park, are reported for Nigeria. Whereas the former species was collected in a canopy high stacked mist net setup, the latter was collected in a ground level mist net, demonstrating the value of employing contemporary and complementary sampling techniques especially in such understudied regions of Africa.

Performance of Doppler shift compensation in bats varies with species rather than with environmental clutter

The performance of vocal motor control is crucial for vocal communication; however, its evolution and ecological drivers are largely unknown. Doppler shift compensation (DSC), which has been found only in bats, represents an excellent model for studying the mechanisms and evolution of vocal control. We tested whether species that are more dependent on DSC for pulse–echo separation have a more precise DSC and whether changes in environmental clutter would result in adjustments in DSC performance. We recorded the echolocation and flight behaviour of the greater horseshoe bat, Rhinolophus ferrumequinum, and the great leaf-nosed bat, Hipposideros armiger, flying through a corridor and a window in turn. The DSC precision in H. armiger was significantly lower than that of R. ferrumequinum; the offset between the reference frequency and resting frequency, however, was not significantly different between the two species. We also studied the DSC of H. armiger flying through windows of different sizes. Their flight speed decreased significantly with reduced window size. However, DSC precision and the offset did not vary significantly with window size. Our results suggest that DSC is more precise in rhinolophids, which have a higher demand for pulse–echo separation by DSC, than in hipposiderids. Changes in environmental clutter do not necessarily result in adjustments of DSC performance. Functional importance associated with high-performance vocal control may be critical in shaping the precision of vocal control in the course of evolution. Instead, habitat clutter encountered by vocalizing animals may not play an important role.

Vaginal plug formation and release in female hibernating Korean greater horseshoe bat, Rhinolophus ferrumequinum korai (Chiroptera: Rhinolophidae) during the annual reproductive cycle

The objective of this study was to investigate morphological characteristics and functional roles of vaginal plug formation and release in female hibernating Korean greater horseshoe bat (Rhinolophus ferrumequinum korai) using optical microscope and scanning electron microscope. Vaginal plug formation begins by part of semen first jetted from cervical region and secretions of vaginal epithelium immediately after mating (at the end of August). These secretions are gradually solidified, accumulated, and moved toward the vaginal introitus while filling the vaginal lumen. This formation process continues through the copulation period and the hibernation period (from end of October to middle of March), maintaining vaginal plug throughout the next pregnancy period (from end of March to end of May). Finally, vaginal plug is discharged to the outside of vagina immediately before giving birth. Normal vaginal structures are taken from the nurturing period (from the beginning of June to the middle of August) and before mating period. Therefore, vaginal plug generated immediately after mating is important as a protective barrier to prevent re-mating with male. In addition, vaginal plug during pregnancy can protect fetus in the uterus from physical stimulation by preventing re-mating with male as a kind of defense mechanism to maintain healthy development of fetus in uterus.

First insights into the population genetic structure and the phylogeographic status of the Mehely’s horseshoe bat Rhinolophus mehelyi (Chiroptera: Rhinolophidae) in Iran inferred from mitochondrial genes

Mehely’s horseshoe bat, Rhinolophus mehelyi Matschie 1901, is a medium-sized rhinolophid with a discontinuous distribution from North Africa and southern Europe through Asia Minor, Anatolia, to Transcaucasia and Iran. Here, we present a detailed study of the phylogeography and population genetics of this species using 745 bp of the mitochondrial cytochrome b and 522 bp of the mitochondrial D-loop genes in 46 bats in eight localities in western and southwesternIran. Based on the mtDNA sequences, we found a low degree of genetic diversity in the Iranian populations of R. mehelyi (π = 0.0032 for Cytb and π = 0.0064 for D-loop gene), that show a close relationship among the haplotypes. With a K2P genetic distance (0.38%–0.97% on D-loop and 0.22%–0.69% on Cytb), and the phylogenetic reconstruction in the Eurasia lineage two major clades are introduced. Here, the phylogenetic trees and statistical parsimony network showed all Iranian samples were grouped in the same clade, but southern Europe and North Africa samples belonged to another clade. The average genetic divergence between reciprocally monophyletic clade of the R. mehelyi group in Iran and southern Europe and North Africa were 0.69% for Cytb and 4.09% for D-Loop respectively. The analysis of population structure suggests an incongruent pattern of genetic differentiation. Mismatch distributions and neutrality tests showed recent historical demographic events as indicated by significant deviations in Fu’s FS from neutrality. The hypothesis of sudden-expansion was not rejected by analyses of mismatch distribution as the Raggedness and SSD were insignificant (p(r) = 0.11 and p (SSD) = 0.07). Similarly, the Bayesian skyline plot suggested a population expansion scenario that took place in the past 4.000 years.

Species identification of Late Pleistocene bat bones using collagen fingerprinting

AbstractBats form the second most diverse mammalian order (Chiroptera), after rodents, and vary widely in their physiology and ecology. Those species that live in temperate climates are generally insectivorous and nocturnal or crepuscular, sheltering in tree hollows, caves, or buildings during the day. They are potentially valuable ecological indicators, due to their dependence on suitable roosting sites and arthropod food, both of which are commonly affected by human activities. Identification of bats from ancient assemblages that are found in caves could therefore provide useful data for palaeoenvironmental reconstructions and show the effect of habitat loss. Here, we apply the recently developed approach of collagen fingerprinting by soft ionisation mass spectrometry to the identification of ancient bat remains in an archaeological assemblage from Pin Hole Cave (Derbyshire, England). Our results show that a simple set of markers can distinguish all seven genera of bats known to be present in either modern or ancient Britain (Myotis, Nyctalus, Pipistrellus, Barbastella, Plecotus, Eptesicus, and Rhinolophus). Further analysis indicates that species‐level determination is possible in some of these taxa, but it would more readily be achieved using the more advanced methods of collagen sequence analysis by liquid chromatography coupled with tandem mass spectrometry. Within our assemblage yielding ~6,800 ancient bone collagen fingerprints, we identified only ~1% that derived from chiropterans, and these were predominantly derived from Myotis (two apparent Brandt's bat fingerprints but the majority indistinguishable between the whiskered, Daubenton's and Natterer's bats), Barbastella (the western barbastelle being the only member of this genus known within Europe), and Rhinolophus (identified as the lesser horsehoe bat R. hipposideros rather than the rare greater horseshoe bat R. ferrumequinum). We infer that the site was likely used by roosting bats throughout the year, and the accumulation of these remains was probably not the result of predator activity. More importantly, the peptide biomarkers provided here could proove valuable in the more systematic analysis of microfaunal remains across many European archaeological and palaeontological sites, preferably those that are collected with well curated stratigraphical information and chronological frameworks.

Dynamic echo signatures created by a biomimetic sonar head

Certain bat species (e.g. horseshoe bats, family Rhinolophidae) are known for conspicuous deformations of the emission baffles (noseleaves) and reception baffles (ears). Previously reported numerical studies and experiments with biomimetic reproductions of these baffles have shown that such deformations can result in time-variant emitter/receiver characteristics. However, it has not been investigated whether these time-variant characteristics could also manifest themselves in likewise time-variant properties in echoes from targets of varying complexity. To investigate this question, a biomimetic sonar head complete with deformable emission and reception baffles has been used to ensonify targets with different simple geometries (sphere, cylinder, and cube) as well as random, more natural target geometries (artificial plants) from distances of about 1 meter. Time-variant echo signatures were found in all these cases, i.e. irrespective of target complexity and whether the time-variance was injected into the emission, the reception, or into both. This demonstrates that although the time-variant emission/reception characteristics had been previously measured only under careful conditions, they are capable of impacting real-world echoes. Even targets with distributed clouds of scattering facets did not obscure the effects of the changing conformation states. Hence these changes in ear position created by baffle deformations could serve the animals or man-made sonar systems that mimic them to encode additional echo information through time-variant echo signatures.

Integrating population genetics to define conservation units from the core to the edge of Rhinolophus ferrumequinum western range.

The greater horseshoe bat (Rhinolophus ferrumequinum) is among the most widespread bat species in Europe but it has experienced severe declines, especially in Northern Europe. This species is listed Near Threatened in the European IUCN Red List of Threatened Animals, and it is considered to be highly sensitive to human activities and particularly to habitat fragmentation. Therefore, understanding the population boundaries and demographic history of populations of this species is of primary importance to assess relevant conservation strategies. In this study, we used 17 microsatellite markers to assess the genetic diversity, the genetic structure, and the demographic history of R. ferrumequinum colonies in the western part of its distribution. We identified one large population showing high levels of genetic diversity and large population size. Lower estimates were found in England and northern France. Analyses of clustering and isolation by distance suggested that the Channel and the Mediterranean seas could impede R. ferrumequinum gene flow. These results provide important information to improve the delineation of R. ferrumequinum management units. We suggest that a large management unit corresponding to the population ranging from Spanish Basque Country to northern France must be considered. Particular attention should be given to mating territories as they seem to play a key role in maintaining high levels of genetic mixing between colonies. Smaller management units corresponding to English and northern France colonies must also be implemented. These insular or peripheral colonies could be at higher risk of extinction in the near future.

Integrated approaches to identifying cryptic bat species in areas of high endemism: The case of Rhinolophus andamanensis in the Andaman Islands.

The diversity of bats worldwide includes large numbers of cryptic species, partly because divergence in acoustic traits such as echolocation calls are under stronger selection than differences in visual appearance in these nocturnal mammals. Island faunas often contain disproportionate numbers of endemic species, and hence we might expect cryptic, endemic species to be discovered relatively frequently in bats inhabiting islands. Species are best defined when multiple lines of evidence supports their diagnosis. Here we use morphometric, acoustic, and molecular phylogenetic data to show that a horseshoe bat in the Andaman Islands is distinct in all three aspects, supporting its status as a distinct species. We recommend investigation into possible new and endemic bat species on islands by using integrated approaches that provide independent lines of evidence for taxonomic distinctiveness. We provide a formal redescription of the taxon newly raised to species level, Rhinolophus andamanensis Dobson, 1872.