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Fig. 2 in Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics
Fig. 2 Geographic sampling for the genetic analyses presented by this study. The white circles denote the locations of one or more specimens represented solely by mitochondrial sequences (cyt-b), the half-filled circles indicate specimens or groups represented only by nuclear intron sequences, and the black circles identify locations where samples with both mitochondrial and nuclear sequences were acquired
Fig. 4 a in Molecular phylogenetics of the African horseshoe bats (Chiroptera: Rhinolophidae): expanded geographic and taxonomic sampling of the Afrotropics
Fig. 4 a Bayesian phylogeny of Rhinolophus based on four nuclear introns. The phylogeny was inferred in MRBAYES and its topology closely resembled the maximum likelihood phylogeny calculated in IQ-TREE. Filled black circles on nodes denote bootstrap values (BS) ≥ 70% and Bayesian posterior probabilities (PP) ≥ 0.95, left-half-filled black circles indicate BS ≥ 70% and PP <0.95, and unmarked nodes indicate BS <70% and PP <0.95. b–d enlarged sections of the complete nuclear intron tree showing individual relationships. Branch colors indicate individual clade membership; species groups are from [13]. Specimen localities include counties for Kenya. Museum acronyms are defined in Additional file 1
Figures 1-2 from: Novaes RLM, Alves FM, Souza RF, Laurindo RS, Moratelli R (2020) Bats used as hosts by Amblyomma sculptum (Acari: Ixodidae) in Northeastern Brazil and its implications on tick-borne diseases. Zoologia 37: 1-4. https://doi.org/10.3897/zoologia.37.e56795
Figures 1-2 (1) Individual of Myotis lavali (MN 75191) parasitized by an engorged Amblyomma sculptum in the xerophytic caatinga from Northeastern Brazil. Photo: Carlos Cândido. (2) Individual of Noctilio albiventris (MN 79943) parasitized by some sub-adult individuals of hard tick Amblyomma sculptum and soft tick Ornithodoros sp. in the xerophytic caatinga from Northeastern Brazil. Photo: Roberto Leonan M. Novaes.
Data from: eDNA metabarcoding reveals a core and secondary diets of the greater horseshoe bat with strong spatio-temporal plasticity
<p><strong>ABSTRACT</strong></p> <p>Dietary plasticity is an important issue for conservation biology as it may be essential for species to cope with environmental changes. However, it still remains scarcely addressed in the literature, potentially because diet studies have long been constrained by methodological limits. The advent of molecular approaches now makes it possible to get a precise picture of diet and its plasticity, even for endangered and elusive species. Here we focused on the greater horseshoe bat (<em>Rhinolophus ferrumequinum</em>) in Western France, where this insectivorous species has been classified as ‘Vulnerable’ on the Regional Red List (2016). We applied an eDNA metabarcoding approach on 1986 fecal samples collected in six maternity colonies at three sampling dates. We described its diet and investigated whether the landscape surrounding colonies and the different phases of the maternity cycle influenced the diversity and the composition of this diet. We showed that <em>R. ferrumequinum</em> feed on a highly more diverse spectrum of prey than expected from previous studies, therefore highlighting how eDNA metabarcoding can help improving diet knowledge of a flying elusive endangered species. Our approach also revealed that <em>R. ferrumequinum</em> diet is composed of two distinct features: the core diet consisting in a few preferred taxa shared by all the colonies (25% of the occurrences) and the secondary diet consisting in numerous rare prey that were highly different between colonies and sampling dates (75% of the occurrences). Energetic needs and constraints associated with the greater horseshoe bat life-cycle, as well as insect phenology and landscape features, strongly influenced the diversity and composition of both the whole and core diets. Further research should now explore the relationships between <em>R. ferrumequinum</em> dietary plasticity and fitness, to better assess the impact of core prey decline on <em>R. ferrumequinum</em> populations viability.</p> <p> </p> <p><strong>FILE DESCRIPTION</strong></p> <p><strong>Information concerning the samples and the positive and negative controls multiplexed in the MiSeq Runs 5 to 9</strong></p> <p>This XLSX file contains the sample IDs, the sample types, the PCR IDs, the PCR replicate numbers, the locality names, the predator species and the fastq file names for each PCR products multiplexed in the five different Illumina MiSeq runs.</p> <p>File name: Sample_informations.xlsx</p> <p> </p> <p><strong>MiSeq raw sequences of the COI minibarcode from the faecal pellets of bats (Run5)</strong></p> <p>This ZIP file contains the Run5 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each faecal pellet in triplicate using the MiSeq platform. The 1271 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 475 multiplexed samples and the 8 positive and 94 negative controls are provided in the following XLSX file titled: Sample_Information.xlsx.</p> <p>Note: the 186 PCR3 replicates from the localities BEA and SGE are available in the ZIP file MiSeq_Reads_COI_Bat_faecal_pellets_Run9.zip</p> <p>File name: MiSeq_Reads_COI_Bat_faecal_pellets_Run5.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the COI minibarcode from the faecal pellets of bats (Run6)</strong></p> <p>This ZIP file contains the Run6 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each faecal pellet in triplicate using the MiSeq platform. The 1440 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 466 multiplexed samples and the 8 positive and 130 negative controls are provided in the following XLSX file titled: Sample_Information.xlsx.</p> <p>File name: MiSeq_Reads_COI_Bat_faecal_pellets_Run6.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the COI minibarcode from the faecal pellets of bats (Run7)</strong></p> <p>This ZIP file contains the Run7 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each faecal pellet in triplicate using the MiSeq platform. The 1464 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 475 multiplexed samples and the 8 positive and 103 negative controls are provided in the following XLSX file titled: Sample_Information.xlsx.</p> <p>File name: MiSeq_Reads_COI_Bat_faecal_pellets_Run7.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the COI minibarcode from the faecal pellets of bats (Run8)</strong></p> <p>This ZIP file contains the Run8 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each faecal pellet in triplicate using the MiSeq platform. The 1464 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 475 multiplexed samples and the 8 positive and 103 negative controls are provided in the following XLSX file titled: Sample_Information.xlsx.</p> <p>File name: MiSeq_Reads_COI_Bat_faecal_pellets_Run8.zip</p> <p> </p> <p><strong>MiSeq raw sequences of the COI minibarcode from the faecal pellets of bats (Run9)</strong></p> <p>This ZIP file contains the Run9 FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each faecal pellet in triplicate using the MiSeq platform. The 499 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 281 multiplexed samples (including 29 samples from another project) and the 11 positive and 172 negative controls are provided in the following XLSX file titled: Sample_Information.xlsx.</p> <p>Note: the 372 PCR1 & PCR2 replicates from the localities BEA and SGE are available in the ZIP file MiSeq_Reads_COI_Bat_faecal_pellets_Run5.zip</p> <p>File name: MiSeq_Reads_COI_Bat_faecal_pellets_Run9.zip</p> <p> </p> <p><strong>Raw abundance tables of the COI minibarcode from the faecal pellets of bats before data filtering (Run5 to 9)</strong></p> <p>This ZIP file contains five TXT files showing the number of reads for each of the 17,998 distinct variants (OTUs) and each of the 6138 PCR products of the samples (<em>n</em>=2015) and controls sequenced in the MiSeq Runs 5 to 9 before the data filtering.</p> <p>File name: Raw_COI_Bat_Faecal_Pellets_abundance_Runs5to9_before_filtering.zip</p> <p> </p> <p><strong>Abundance table of the COI minibarcode from the faecal pellets of bats after data filtering (Run5 to 9)</strong></p> <p>This XLSX file contains the number of reads for each of the 7206 distinct variants (OTUs) and each of sample (<em>n</em>=2014) after the data filtering using (1) the thresholds based on the negative and positive controls (Tcc & Tfa) and (2) the validation using the three technical replicates.</p> <p>File name: COI_Bat_Faecal_Pellets_abundance_Runs5to9_after_filtering.xlsx</p> <p> </p> <p><strong>Final abundance table of the COI minibarcode for the prey of <em>Rhinolophus ferrumequinum</em> only (Run5 to 9)</strong></p> <p>This XLSX file contains the number of reads for each <em>Rhinolophus ferrumequinum</em> samples (<em>n</em>=1034) and each of the 679 validated prey taxa (OTUs) after taxonomic affiliations check and redundancy removals.</p> <p>File name: Final_COI_Rhino_Prey_abundance_Run5to9.xlsx</p> <p> </p> <p><strong>Landscape data table used to build the PCA</strong></p> <p>File name: Landscape_variables.xlsx</p>
Disentangling interactions among mercury, immunity, and infection in a Neotropical bat community
<ol> <li>Contaminants such as mercury are pervasive and can have immunosuppressive effects on wildlife. Impaired immunity could be important for forecasting pathogen spillover risks, as many land-use changes that generate mercury contamination also bring wildlife into close contact with humans and domestic animals. However, the interactions among contaminants, immunity, and infection are difficult to study in natural systems, and empirical tests of possible directional relationships remain rare.</li> <li>We capitalized on extreme mercury variation in a diverse bat community in Belize to test association among contaminants, immunity, and infection. By comparing a previous dataset of bats sampled in 2014 with new data from 2017, representing a period of rapid agricultural land conversion, we first confirmed bat species more reliant on aquatic prey had higher fur mercury. Bats in the agricultural habitat also had higher mercury in recent years. We then tested covariation between mercury and cellular immunity and determined if such relationships mediated associations between mercury and common bacterial pathogens . As bat ecology can dictate exposure to mercury and pathogens, we also assessed species-specific patterns in mercury–infection relationships.</li> <li>Across the bat community, individuals with higher mercury had fewer neutrophils but not lymphocytes, suggesting stronger associations with innate immunity. However, the odds of infection for hemoplasmas and <i>Bartonella </i>spp. were generally lowest in bats with high mercury, and relationships between mercury and immunity did not mediate infection patterns. Mercury also showed species- and clade-specific relationships with infection, being associated with especially low odds for hemoplasmas in <i>Pteronotus mesoamericanus </i>and <i>Dermanura phaeotis</i>. For <i>Bartonella </i>spp., mercury was associated with particularly low odds in the genus <i>Pteronotus</i> but high odds in the Stenodermatinae.</li> <li> <i>Synthesis and application</i>: Lower general infection risk in bats with high mercury despite weaker innate defense suggests contaminant-driven loss of pathogen habitat (i.e., anemia) or vector mortality as possible causes. Greater attention to these potential pathways could help disentangle relationships among contaminants, immunity, and infection in anthropogenic habitats and help forecast disease risks. Our results also suggest contaminants may increase infection risk in some taxa but not others, emphasizing the importance of considering surveillance and management at different phylogenetic scales.</li> </ol>
Data from: Estimating population density of insectivorous bats based on stationary acoustic detectors: a case study
<p>1. Automated recording units are commonly used by consultants to assess environmental impacts and to monitor animal populations. Although estimating population density of bats using stationary acoustic detectors is key for evaluating environmental impacts, estimating densities from call activity data is only possible through recently developed numerical methods, as the recognition of calling individuals is impossible.<br> 2. We tested the applicability of generalized random encounter models (gREMs) for determining population densities of three bat species (Common pipistrelle <em>Pipistrellus pipistrellus</em>, Northern bat Eptesicus nilssonii,, and Natterer's bat Myotis nattereri) based on passively collected acoustical data. To validate the results, we compared them to (i) density estimates from the literature and to (ii) Royle-Nichols (RN) models of detection/non-detection data.<br> 3. Our estimates for M. nattereri matched both the published data and RN-model results. For E. nilssonii, the gREM yielded similar estimates to the RN-models, but the published estimates were more than twice as high. This discrepancy might be because the high-altitude flight of E. nilssonii is not accounted for in gREMs. Results of gREMs for P. pipistrellus were supported by published data but were approximately 10 times higher than those of RN-models. RN-models use detection/non-detection data and this loss of information probably affected population estimates of very active species like P. pipistrellus.<br> 4. gREM models provided realistic estimates of bat population densities based on automatically recorded call activity data. However, the average flight altitude of species should be accounted for in future analyses. We suggest including flight altitude in the calculation of the detection range to assess the detection sphere more accurately and to obtain more precise density estimates.</p>
Dataset: Tropical bats counter heat by combining torpor with adaptive hyperthermia
<p>Many tropical mammals are vulnerable to heat because their water budget limits the use of evaporative cooling for heat compensation. Further increasing temperatures and aridity might consequently exceed their thermoregulatory capacities. Here, we describe two novel modes of torpor, a response usually associated with cold or resource bottlenecks, as efficient mechanisms to counter heat. We conducted a field study on the Malagasy bat <i>Macronycteris commersoni</i> resting in foliage during the hot season, unprotected from environmental extremes. On warm days, the bats alternated between remarkably short micro-torpor-bouts and normal resting metabolism within few minutes. On hot days, the bats extended their torpor bouts over the hottest time of the day while tolerating body temperatures up to 42.9°C. Adaptive hyperthermia combined with lowered metabolic heat production from torpor allows higher heat storage from the environment, negates the need for evaporative cooling and thus increases heat tolerance. However, it is a high-risk response as the torpid bats cannot defend body temperature if ambient temperature increases above a critical/lethal threshold. Torpor coupled with hyperthermia and micro-torpor-bouts broaden our understanding of the basic principles of thermal physiology and demonstrate how mammals can perform near their upper thermal limits in an increasingly warmer world.</p>
FIG. 16 in Diversity, morphological phylogeny, and distribution of bats of the genus Molossus E. Geoffroy, 1805 (Chiroptera, Molossidae) in Brazil
FIG. 16. — Molossus currentium Thomas, 1901 skull: A, dorsal view; B, ventral view; C, posterior view; D, frontal view. Scale bar: 1 mm.
Data from: Loss of sweet taste despite the conservation of sweet receptor genes in insectivorous bats
<p>The evolution of taste perception is usually associated with the ecology and dietary changes of organisms. However, mismatches between feeding ecology and taste receptor evolution have been identified in some vertebrate animals. One example is the sweet taste receptor gene <em>Tas1r2</em>. Previous analysis of partial sequences has revealed that <em>Tas1r2</em> has undergone equally strong purifying selection between insectivorous and frugivorous bats. To test whether the sweet taste function is also important in bats with contrasting diets, we examined the complete coding sequences of both sweet taste receptor genes (<em>Tas1r2</em> and <em>Tas1r3</em>) in 34 representative bat species. Although these two genes are highly conserved between frugivorous and insectivorous bats at the sequence level, our behavioral experiments revealed that an insectivorous bat (<em>Myotis ricketti</em>) showed no preference for natural sugars, whereas the frugivorous species (<em>Rousettus leschenaultii</em>) showed strong preferences for sucrose and fructose. Furthermore, while both sweet taste receptor genes are expressed in the taste tissue of insectivorous and frugivorous bats, our cell-based assays revealed striking functional divergence: the sweet taste receptors of frugivorous bats are able to respond to natural sugars whereas those of insectivorous bats are not, which is consistent with the behavioral preference tests, suggesting that functional evolution of sweet taste receptors is closely related to diet. This comprehensive study suggests that using sequence conservation alone could be misleading in inferring protein and physiological function, and highlights the power of combining behavioral experiments, expression analysis, and functional assays in molecular evolutionary studies. </p>
Seasonal dietary niche contraction in coexisting Neotropical frugivorous bats (Stenodermatinae)
<p>Tropical dry forests are characterized by punctuated seasonal precipitation patterns that drive primary production and the availability of fruits, seeds, flowers, and insects throughout the year. In environments in which the quantity and quality of food resources varies seasonally, consumers should adjust their foraging behavior to maximize energy intake while minimizing overlap with competitors during periods of low food availability. Here, we investigated how the diets of frugivorous bats in tropical dry forests of NW Mexico varied in response to seasonal availability and how this affected dietary overlap of morphologically similar species. We performed stable isotope analyses to understand temporal and interspecific patterns of overall isotopic niche breadth, trophic position, and niche overlap in the diet of six frugivorous species of closely related New World Leaf-nosed Bats (family Phyllostomidae, subfamily Stenodermatinae). We estimated seasonal changes in resource abundance in two complementary ways: 1) vegetative phenology based on long-term remote-sensing data, and 2) observational data on food availability from previously published insect and plant fruiting surveys. In all species, there was a consistent pattern of reduced isotopic niche breadth during periods of low food availability. However, patterns of niche overlap varied between morphologically similar species. Overall, results from our study and others suggest that seasonal food availability likely determines overall dietary niche breadth in Phyllostomidae and that despite morphological specialization, it is likely that other mechanisms, such as opportunistic foraging and spatiotemporal niche segregation may play a role in maintaining coexistence rather than simply dietary displacement.</p>
MHC variation is similar in little brown bats before and after white-nose syndrome outbreak
<p>White-nose syndrome (WNS), caused by the fungal pathogen <i>Pseudogymnoascus destructans</i><i> </i>(Pd), has driven alarming declines in North American hibernating bats, such as little brown bat (<i>Myotis lucifugus</i>). During hibernation, infected little brown bats are able to initiate anti-Pd immune responses, indicating pathogen-mediated selection on the major histocompatibility complex (MHC) genes. However, such immune responses may not be protective as they interrupt torpor, elevate energy costs, and potentially lead to higher mortality rates. To assess whether WNS drives selection on MHC genes, we compared the MHC <i>DRB</i> gene in little brown bats pre- (Wisconsin) and post- (Michigan, New York, Vermont, and Pennsylvania) WNS (detection spanning 2014-2015). We genotyped 131 individuals and found 45 nucleotide alleles (27 amino acid alleles) indicating a maximum of 3 loci (1-5 alleles per individual). We observed high allelic admixture and a lack of genetic differentiation both among sampling sites and between pre- and post-WNS populations, indicating no signal of selection on MHC genes. However, post-WNS populations exhibited decreased allelic richness, reflecting effects from bottleneck and drift following rapid population declines. We propose that mechanisms other than adaptive immunity are more likely driving current persistence of little brown bats in affected regions.</p>
Data from: Social call divergence in bats: a comparative analysis
Acoustic signals mediate important life history events in a variety of species, providing new vistas for understanding speciation. It has been proposed that animal acoustic signals undergo complex interactions among morphology, ecology, social pressure, and phylogenetic history. Yet, the relative importance of these factors in shaping acoustic divergence is rarely assessed within a comparative framework. Herein, we aim to investigate the key determinants of social call divergence across 31 bat species from 5 families. We compiled a wide data set on bat aggressive calls, body size, foraging habitats, foraging modes, climatic conditions, colony size, and phylogenetic components. We identified remarkable interspecific divergence versus within-species variation in aggressive vocalizations. Despite weak effects of ecological factors, colony size, body size, and phylogenetic components accounted for the majority of variation in call parameters among species. The colony size and body size played a major role in influencing spectral parameters, whereas phylogenetic relationships determined call duration and minimum frequency. Together, our findings constitute convincing evidence that sociality, morphological constraint, and phylogenetic constraint mold social call divergence in bats. This study expands our limited knowledge of the evolution of bat social calls, and highlights the importance of sociality in driving acoustic phenotype diversity.
Data from: Comparative phylogeography of mainland and insular species of Neotropical molossid bats (Molossus)
<p>Genetic structures, historical events, habitat preferences, and geographic barriers might result in distinct patterns in insular versus mainland populations. Comparison between these two biogeographic systems provides an opportunity to investigate the relative role of isolation in phylogeographic patterns and to elucidate the importance of evolution and demographic history in population structure. Herein we use a genotype by sequencing approach (GBS) to explore population structure within three species of mastiff bats (Molossus molossus, M. coibensis, and M. milleri), which represent different ecological histories and geographical distributions in the genus to explore phylogeographic patterns and better understand the role of geographic barriers in their dispersal and gene flow. We tested the hypotheses that oceanic straits serve as barriers to dispersal in Caribbean bats and that isolated island populations are more likely to experience genetic drift and bottlenecks relative to highly connected ones, which should have different phylogeographic patterns. We show that population structures vary according to general habitat preferences, to levels of population isolation, and to historical fluctuations in climate. In our dataset, mainland geographic barriers played only a small role in isolation of lineages. However, oceanic straits posed a partial barrier to the dispersal for some populations within some species (M. milleri), but do not seem to disrupt gene flow in others (M. molossus). Lineages on distant islands undergo genetic bottlenecks more frequently than island lineages closer to the mainland, which have a greater exchange of haplotypes.</p>
Data from: Early diversification trend and Asian origin for extant bat lineages
Bats are a unique mammalian group, which belong to one of the largest and most diverse mammalian radiations, but their early diversification is still poorly understood, and conflicting hypotheses have emerged regarding their biogeographic history. Understanding their diversification is crucial for untangling the enigmatic evolutionary history of bats. In this study, we elucidated the rate of diversification and the biogeographic history of extant bat lineages using genus-level chronograms. The results suggest that a rapid adaptive radiation persisted from the emergence of crown bats until the Early Eocene Climatic Optimum, whereas there was a major deceleration in diversification around 35–49 Ma. There was a positive association between changes in the palaeotemperature and the net diversification rate until 35 Ma, which suggests that the palaeotemperature may have played an important role in the regulation of ecological opportunities. By contrast, there were unexpectedly higher diversification rates around 25–35 Ma during a period characterized by intense and long-lasting global cooling, which implies that intrinsic innovations or adaptations may have released some lineages from the intense selective pressures associated with these severe conditions. Our reconstruction of the ancestral distribution suggests an Asian origin for bats, thereby indicating that the current panglobal but disjunct distribution pattern of extant bats may be related to events involving seriate cross-continental dispersal and local extinction, as well as the influence of geological events and the expansion and contraction of megathermal rainforests during the Tertiary.
Data from: Prevalence, diversity, and host associations of Bartonella strains in bats from Georgia (Caucasus)
Bartonella infections were investigated in seven species of bats from four regions of the Republic of Georgia. Of the 236 bats that were captured, 212 (90%) specimens were tested for Bartonella infection. Colonies identified as Bartonella were isolated from 105 (49.5%) of 212 bats Phylogenetic analysis based on sequence variation of the gltA gene differentiated 22 unique Bartonella genogroups. Genetic distances between these diverse genogroups were at the level of those observed between different Bartonella species described previously. Twenty-one reference strains from 19 representative genogroups were characterized using four additional genetic markers. Host specificity to bat genera or families was reported for several Bartonella genogroups. Some Bartonella genotypes found in bats clustered with those identified in dogs from Thailand and humans from Poland.
Data from: Synchronized shift of oral, fecal and urinary microbiotas in bats and natural infection dynamics during seasonal reproduction
Seasonal reproduction is a period of extreme physiological and behavioral changes, yet we know little about how it may affect host microbial communities (i.e. microbiota) and pathogen transmission. Here, we investigated shifts of the bacterial microbiota in saliva, urine and faeces during the seasonal reproduction of bats in South Africa, and test for an interaction in shedding patterns of both bacterial (Leptospira) and viral (adeno- and herpes-viruses) agents. Based on a comparative approach in two cave-dwelling bat species and high-throughput sequencing of the 16S rRNA gene, we demonstrated a clear signature in microbiota changes over the reproduction season, consistent across the multiple body habitats investigated, and associated with sex, age and reproductive condition of bats. We observed in parallel highly dynamic shedding patterns for both bacteria and viruses, but did not find a significant association between viral shedding and bacterial microbiota composition. Indeed, only Leptospira shedding was associated with alterations in both the diversity and composition of the urinary microbiota. These results illustrate how seasonal reproduction in bats substantially affects microbiota composition and infection dynamics, and have broad implications for the understanding of disease ecology in important reservoir hosts, such as bats.
Data from: Estimating colony sizes of emerging bats using acoustic recordings
The decline of bats demands more widespread monitoring of populations for conservation and management. Current censusing methods are either prone to bias or require costly equipment. Here, we report a new method using passive acoustics to determine bat count census from overall acoustic amplitude of the emerging bat stream. We recorded the video and audio of an emerging colony of Mexican free-tailed bats from two cave locations across multiple nights. Instantaneous bat counts were calculated from the video frames, and the bat stream's acoustic amplitude corresponding to each video frame was determined using three different methods for calculating acoustic intensity. We found a significant link between all three acoustic parameters and bat count, with the highest R2 of 0.742 linking RMS pressure and bat count. Additionally, the relationship between acoustics and population size at one cave location could accurately predict the population size at another cave location. The data were gathered with low-cost, easy-to-operate equipment, and the data analysis can be easily accomplished using automated scripts or with open-source acoustic software. These results are a potential first step towards creating an acoustic model to estimate bat population at large cave colonies worldwide.
Data from: Response of bats to light with different spectra: light-shy and agile bat presence is affected by white and green, but not red light
Artificial light at night has shown a remarkable increase over the past decades. Effects are reported for many species groups, and include changes in presence, behaviour, physiology and life-history traits. Among these, bats are strongly affected, and how bat species react to light is likely to vary with light colour. Different spectra may therefore be applied to reduce negative impacts. We used a unique set-up of eight field sites to study the response of bats to three different experimental light spectra in an otherwise dark and undisturbed natural habitat. We measured activity of three bat species groups around transects with light posts emitting white, green and red light with an intensity commonly used to illuminate countryside roads. The results reveal a strong and spectrum-dependent response for the slow-flying Myotis and Plecotus and more agile Pipistrellus species, but not for Nyctalus and Eptesicus species. Plecotus and Myotis species avoided white and green light, but were equally abundant in red light and darkness. The agile, opportunistically feeding Pipistrellus species were significantly more abundant around white and green light, most likely because of accumulation of insects, but equally abundant in red illuminated transects compared to dark control. Forest-dwelling Myotis and Plecotus species and more synanthropic Pipistrellus species are thus least disturbed by red light. Hence, in order to limit the negative impact of light at night on bats, white and green light should be avoided in or close to natural habitat, but red lights may be used if illumination is needed.
Data from: Combining noninvasive genetics and a new mammalian sex-linked marker provides new tools to investigate population size, structure and individual behaviour: an application to bats
Monitoring wild populations is crucial for their effective management. Noninvasive genetic methods provide robust data from individual free-ranging animals, which can be used in capture-mark-recapture (CMR) models to estimate demographic parameters without capturing or disturbing them. However, sex- and status-specific behaviour, which may lead to differences in detection probabilities, is rarely considered in monitoring. Here, we investigated population size, sex ratio, sex- and status-related behaviour in 19 Rhinolophus hipposideros maternity colonies (Northern France) with a noninvasive genetic CMR approach (using faeces) combined with parentage assignments. The use of the DDX3X/Y-Mam sexual marker designed in this study, which shows inter- and intra-chromosomal length polymorphism across placental mammals, together with 8 polymorphic microsatellite markers, produced high quality genetic data with limited genotyping errors and allowed us to reliably distinguish different categories of individuals (males, reproductive and non-reproductive females) and to estimate population sizes. We showed that visual counts represent well adult female numbers and that population composition in maternity colonies changes dynamically during the summer. Before parturition, colonies mainly harbour pregnant and non-pregnant females with a few visiting males whereas after parturition, colonies are mainly composed of mothers and their offspring with a few visiting non-mothers and males. Our approach gives deeper insight into sex- and status-specific behaviour, a prerequisite for understanding population dynamics and developing effective monitoring and management strategies. Provided sufficient samples can be obtained, this approach can be readily applied to a wide range of species.
Data from: Development of conserved microsatellite markers of high cross-species utility in bat species (Vespertilionidae, Chiroptera, Mammalia)
Comparative ecological and behavioural studies of the widespread and diverse Vespertilionidae, which comprise almost 400 of the 1,100 bat species, have been limited by the availability of markers. The potential of new methods for developing conserved microsatellite markers which possess enhanced cross-species utility has recently been illustrated in studies of birds. We have applied these methods to develop enhanced microsatellite markers for vespertilionid bats, in particular for the genus Myotis (103 species). We compared published bat microsatellites with their homologs in the genome sequence of the little brown bat, Myotis lucifugus to create consensus sequences which were used to design candidate primer sets. Primer sets were then tested for amplification and polymorphism in 22 species of bat from nine of the largest families (including 11 Vespertilionidae). Of 46 loci tested, 33 were polymorphic, on average, for each of seven Myotis species tested, 20 in each of four non-Myotis vespertilionid species, and two in 11 non-vespertilionid species.
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Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.