Modelos de distribución de especies y estado de conservación de murciélagos amenazados en la región tumbesina de Ecuador y Perú / Species distribution models and conservation status of threatened bats in the Tumbesian region of Ecuador and Perú

Resumen Introducción: La biodiversidad se está perdiendo a un ritmo acelerado como resultado del cambio global. Herramientas como los modelos de distribución de especies (MDEs) han sido ampliamente usados para mejorar el conocimiento sobre el estado de conservación de las especies y ayudar a desarrollar estrategias de gestión para mitigar la pérdida de biodiversidad. Objetivo: Determinar cómo la distribución potencial predicha por los MDEs para ocho especies de murciélagos amenazados difiere de los mapas de distribución reportados por la UICN. También, inferir el área de distribución y estado de endemismo de cada especie, y evaluar la importancia de la región tumbesina para su conservación. Métodos: Basados en registros de presencia del rango global de las especies, usamos MDEs para evaluar el estado de conservación de estas ocho especies en la región tumbesina de Ecuador y Perú. Resultados: Las áreas estimadas por los MDEs eran 35-78 % más pequeñas para cuatro especies (Eptesicus innoxius, Lophostoma occidentale, Platalina genovensium y Lonchophylla hesperia) y 26-1 600 % más grandes para tres especies (Amorphochilus schnablii, Promops davisoni y Rhogeessa velilla) que aquellas reportadas por la UICN. Para Tomopeas ravus, el área estimada por el MDE y la UICN fue similar, pero difirió en la distribución espacial. Los MDEs coincidieron con áreas de endemismo informadas por autores previos para E. innoxius, R. velilla y T. ravus, pero fueron diferentes para A. schnablii, P. genovensium, P. davisoni y L. hesperia, debido en parte a las distribuciones proyectadas para estas últimas especies en valles secos interandinos según los MDEs. Conclusiones: La región tumbesina representa una porción significativa (40-96 %) de la distribución predicha de siete de las ocho especies estudiadas, subrayando la importancia de esta región para la conservación de murciélagos. Nuestros resultados muestran las probables distribuciones para estas especies y proporcionan una base importante para identificar vacíos de investigación y desarrollar medidas de conservación para murciélagos amenazados en el punto caliente de biodiversidad de Tumbes.

Abstract Introduction: Biodiversity is being lost at an accelerating rate because of global change. Tools such as species distribution models (SDMs) have been widely used to improve knowledge about species' conservation status and help develop management strategies to mitigate biodiversity loss. SDMs are especially important for species with restricted distributions, such as endemic species. Objective: To determine how potential distribution predicted by SDMs for eight threatened bat species differed from the distribution maps reported by the IUCN. Also, to infer the area of distribution and state of endemism of each specie, and to evaluate the importance of the Tumbesian region for their conservation. Methods: Based on presence records across the species' entire ranges, we used SDMs to assess the conservation status of these eight species in the Tumbesian region of Ecuador and Peru. Results: The areas estimated by SDMs were 35-78 % smaller for four species (Eptesicus innoxius, Lophostoma occidentale, Platalina genovensium and Lonchophylla hesperia) and 26-1 600 % larger for three species (Amorphochilus schnablii, Promops davisoni and Rhogeessa velilla) than those reported by the IUCN. For Tomopeas ravus, the area estimated by the SDM and IUCN was similar but differed in spatial distribution. SDMs coincided with areas of endemism reported by previous authors for E. innoxius, R. velilla, and T. ravus, but were different for A. schnablii, P. genovensium, P. davisoni, and L. hesperia, due in part to projected distributions for these latter species in dry inter-Andean valleys according to the SDMs. Conclusions: The Tumbesian region represents a significant portion (40-96 %) of the predicted distribution of seven of the eight species studied, underscoring the importance of this region for bat conservation. Our results show likely distributions for these species and provide an important basis for identifying research gaps and developing conservation measures for threatened bats in the Tumbes biodiversity hotspot.

The genome sequence of the endemic Mexican common mustached Bat, Pteronotus mexicanus. Miller, 1902 [Mormoopidae; Pteronotus].

We describe here the first characterization of the genome of the bat Pteronotus mexicanus, an endemic species of Mexico, as part of the Mexican Bat Genome Project which focuses on the characterization and assembly of the genomes of endemic bats in Mexico. The genome was assembled from a liver tissue sample of an adult male from Jalisco, Mexico provided by the Texas Tech University Museum tissue collection. The assembled genome size was 1.9 Gb. The assembly of the genome was fitted in a framework of 110,533 scaffolds and 1,659,535 contigs. The ecological importance of bats such as P. mexicanus, and their diverse ecological roles, underscores the value of having complete genomes in addressing information gaps and facing challenges regarding their function in ecosystems and their conservation.

Complete mitochondrial genomes of three vulnerable cave bat species and their phylogenetic relationships within the order Chiroptera.

The IUCN Red List of Threatened Species contains 175 Brazilian bat species that are threatened by extinction in some degree. From this perspective, it is essential to expand the knowledge about the genetic diversity of vulnerable bats. Genomic sequencing can be useful to generate robust and informative genetic references, increasing resolution when analyzing relationships among populations, species, or higher taxonomic levels. In this study, we sequenced and characterized in detail the first complete mitochondrial genomes of Furipterus horrens, Lonchorhina aurita, and Natalus macrourus, and investigated their phylogenetic position based on amino acid sequences of protein-coding genes (PCGs). The mitogenomes of these species are 16,516, 16,697, and 16,668 bp in length, respectively, and each comprises 13 PCGs, 22 tRNA genes, two rRNA genes, and a putative control region (CR). In the three species, genes were arranged similarly to all other previously described bat mitogenomes, and nucleotide composition was also consistent with the reported range. The length and arrangement of rrnS and rrnL were also consistent with those of other bat species, showing a positive AT-skew and a negative GC-skew. Except for trnS1, for which we did not observe the DHU arm, all other tRNAs showed the cloverleaf secondary structure in the three species. In addition, the mitogenomes showed minor differences in start and stop codons, and in all PCGs, codons ending in adenine were more common compared to those ending in guanine. We found that PCGs of the three species use multiple codons to encode each amino acid, following the previously documented pattern. Furthermore, all PCGs are under purifying selection, with atp8 experiencing the most relaxed purifying selection. Considering the phylogenetic reconstruction, F. horrens was recovered as sister to Noctilio leporinus, L. aurita and Tonatia bidens shared a node within Phyllostomidae, and N. macrourus appeared as sister to Molossidae and Vespertilionidae.

Buzzfindr: Automating the detection of feeding buzzes in bat echolocation recordings.

Quantification of bat communities and habitat heavily rely on non-invasive acoustic bat surveys the scope of which has greatly amplified with advances in remote monitoring technologies. Despite the unprecedented amount of acoustic data being collected, analysis of these data is often limited to simple species classification which provides little information on habitat function. Feeding buzzes, the rapid sequences of echolocation pulses emitted by bats during the terminal phase of prey capture, have historically been used to evaluate foraging habitat quality. Automated identification of feeding buzzes in recordings could benefit conservation by helping identify critical foraging habitat. I tested if detection of feeding buzzes in recordings could be automated with bat recordings from Ontario, Canada. Data were obtained using three different recording devices. The signal detection method involved sequentially scanning narrow frequency bands with the "Bioacoustics" R package signal detection algorithm, and extracting temporal and signal strength parameters from detections. Buzzes were best characterized by the standard deviation of the time between consecutive pulses, the average pulse duration, and the average pulse signal-to-noise ratio. Classification accuracy was highest with artificial neural networks and random forest algorithms. I compared each model's receiver operating characteristic curves and random forest provided better control over the false-positive rate so it was retained as the final model. When tested on a new dataset, buzzfindr's overall accuracy was 93.4% (95% CI: 91.5%- 94.9%). Overall accuracy was not affected by recording device type or species frequency group. Automated detection of feeding buzzes will facilitate their integration in the analytical workflow of acoustic bat studies to improve inferences on habitat use and quality.

Optimal inventorying and monitoring of taxonomic, phylogenetic and functional diversity.

Comparable data is essential to understand biodiversity patterns. While assemblage or community inventorying requires comprehensive sampling, monitoring focuses on as few components as possible to detect changes. Quantifying species, their evolutionary history, and the way they interact requires studying changes in taxonomic (TD), phylogenetic (PD) and functional diversity (FD). Here we propose a method for the optimization of sampling protocols for inventorying and monitoring assemblages or communities across these three diversity dimensions taking sampling costs into account. We used Iberian spiders and Amazonian bats as two case-studies. The optimal combination of methods for inventorying and monitoring required optimizing the accumulation curve of α-diversity and minimizing the difference between sampled and estimated ß-diversity (bias), respectively. For Iberian spiders, the optimal combination for TD, PD and FD allowed sampling at least 50% of estimated diversity with 24 person-hours of fieldwork. The optimal combination of six person-hours allowed reaching a bias below 8% for all dimensions. For Amazonian bats, surveying all the 12 sites with mist-nets and 0 or 1 acoustic recorders was the optimal combination for almost all diversity types, resulting in >89% of the diversity and <10% bias with roughly a third of the cost. Only for phylogenetic α-diversity, the best solution was less clear and involved surveying both with mist nets and acoustic recorders. The widespread use of optimized and standardized sampling protocols and regular repetition in time will radically improve global inventory and monitoring of biodiversity. We strongly advocate for the global adoption of sampling protocols for both inventory and monitoring of taxonomic, phylogenetic and functional diversity.

Parameter estimation of the hyperbolic frequency-modulated bat calls using hyperbolic scale transform.

Echolocating bats are known to vary their waveforms at the phases of searching, approaching, and capturing the prey. It is meaningful to estimate the parameters of the calls for bat species identification and the technological improvements of the synthetic systems, such as radar and sonar. The type of bat calls is species-related, and many calls can be modeled as hyperbolic frequency- modulated (HFM) signals. To obtain the parameters of the HFM-modeled bat calls, a reversible integral transform, i.e., hyperbolic scale transform (HST), is proposed to transform a call into two-dimensional peaks in the "delay-scale" domain, based on which harmonic separation and parameter estimation are realized. Compared with the methods based on time-frequency analysis, the HST-based method does not need to extract the instantaneous frequency of the bat calls, only searching for peaks. The verification results show that the HST is suitable for analyzing the HFM-modeled bat calls containing multiple harmonics with a large energy difference, and the estimated parameters imply that the use of the waveforms from the searching phase to the capturing phase is beneficial to reduce the ranging bias, and the trends in parameters may be useful for bat species identification.

Old World Fruit Bats (Pteropodidae, Chiroptera) from the Pleistocene of Vietnam.

Isolated teeth of a lesser short-nosed fruit bat Cynopterus brachyotis (Müller, 1838), a fulvous fruit bat Rousettus leschenaultii (Desmarest, 1820), and a dawn bat Eonycteris spelaea (Dobson, 1871) are described from the Middle Pleistocene Tham Hai cave locality in northern Vietnam (Lang Son Province). These are the first fossil findings of the Old World fruit bats in Vietnam. The Middle Pleistocene association of Pteropodidae from the Tham Hai locality may largely reflect the composition of species that roosted in local caves.

Automated echolocation classifiers vary in accuracy for northeastern U.S. bat species.

Acoustic surveys of bat echolocation calls are an important management tool for determining presence and probable absence of threatened and endangered bat species. In the northeastern United States, software programs such as Bat Call Identification (BCID), Kaleidoscope Pro (KPro), and Sonobat can automatically classify ultrasonic detector sound files, yet the programs' accuracy in correctly classifying calls to species has not been independently assessed. We used 1,500 full-spectrum reference calls with known identities for nine northeastern United States bat species to test the accuracy of these programs using calculations of Positive Predictive Value (PPV), Negative Predictive Value (NPV), Sensitivity (SN), Specificity (SP), Overall Accuracy, and No Information Rate. We found that BCID performed less accurately than other programs, likely because it only operates on zero-crossing data and may be less accurate for recordings converted from full-spectrum to zero-crossing. NPV and SP values were high across all species categories for SonoBat and KPro, indicating these programs' success at avoiding false positives. However, PPV and SN values were relatively low, particularly for individual Myotis species, indicating these programs are prone to false negatives. SonoBat and KPro performed better when distinguishing Myotis species from non-Myotis species. We expect less accuracy from these programs for acoustic recordings collected under normal working conditions, and caution that a bat acoustic expert should verify automatically classified files when making species-specific regulatory or conservation decisions.

Cryptic hybridization between the ancient lineages of Natterer's bat (Myotis nattereri).

Studying hybrid zones that form between morphologically cryptic taxa offers valuable insights into the mechanisms of cryptic speciation and the evolution of reproductive barriers. Although hybrid zones have long been the focus of evolutionary studies, the awareness of cryptic hybrid zones increased recently due to rapidly growing evidence of biological diversity lacking obvious phenotypic differentiation. The characterization of cryptic hybrid zones with genome-wide analysis is in its early stages and offers new perspectives for studying population admixture and thus the impact of gene flow. In this study, we investigate the population genomics of the Myotis nattereri complex in one of its secondary contact zones, where a putative hybrid zone is formed between two of its cryptic lineages. By utilizing a whole-genome shotgun sequencing approach, we aim to characterize this cryptic hybrid zone in detail. Demographic analysis suggests that the cryptic lineages diverged during the Pliocene, c. 3.6 million years ago. Despite this ancient separation, the populations in the contact zone exhibit mitochondrial introgression and a considerable amount of mixing in nuclear genomes. The genomic structure of the populations corresponds to geographic locations and the genomic admixture changes along a geographic gradient. These findings suggest that there is no effective hybridization barrier between both lineages, nevertheless, their population structure is shaped by dispersal barriers. Our findings highlight how such deeply diverged cryptic lineages can still readily hybridize in secondary contact.

Abundance of the bat Sturnira lilium (Phyllostomidae) in relation Solanum mauritianum (Solanaceae) diaspores in an Atlantic Forest fragment of southern Brazil.

Frugivore bats are important seed dispersers in forests and their abundance are associated with the presence of zoochoric plants. In this context, the aim of our study was to investigate the association of the frugivore bat S. lilium with the diaspores of the zoochoric plant S. mauritianum, a common arboreal species present in forest fragments of southern Brazil. We also investigated the diet of the species based on seed content present in feces of individuals. Bats were mist-netted from November 2017 to April 2018 in a fragment of Atlantic Forest. The proportion of immature and mature diaspores of S. mauritianum was estimated in the same area where bats were sampled, and feces were sampled from captured individuals. In total, 61 individuals of S. lilium were captured, and 795 seeds were sampled from their feces. The abundance of S. lilium was significantly associated with the proportion of immature diaspores of S. mauritianum. We identified seeds of two botanical families: Solanaceae (89%) and Moraceae (11%) in the fecal samples. Our findings support the view that S. lilium is a legitimate disperser of S. mauritianum, and that its ecological function is probably a result of co-adaptation.

Bat2Web: A Framework for Real-Time Classification of Bat Species Echolocation Signals Using Audio Sensor Data.

Bats play a pivotal role in maintaining ecological balance, and studying their behaviors offers vital insights into environmental health and aids in conservation efforts. Determining the presence of various bat species in an environment is essential for many bat studies. Specialized audio sensors can be used to record bat echolocation calls that can then be used to identify bat species. However, the complexity of bat calls presents a significant challenge, necessitating expert analysis and extensive time for accurate interpretation. Recent advances in neural networks can help identify bat species automatically from their echolocation calls. Such neural networks can be integrated into a complete end-to-end system that leverages recent internet of things (IoT) technologies with long-range, low-powered communication protocols to implement automated acoustical monitoring. This paper presents the design and implementation of such a system that uses a tiny neural network for interpreting sensor data derived from bat echolocation signals. A highly compact convolutional neural network (CNN) model was developed that demonstrated excellent performance in bat species identification, achieving an F1-score of 0.9578 and an accuracy rate of 97.5%. The neural network was deployed, and its performance was evaluated on various alternative edge devices, including the NVIDIA Jetson Nano and Google Coral.

Plecotus macrobullaris sarmaticus subsp. nov. (Vespertilionidae, Chiroptera) from the Early Pleistocene of Crimea.

The extinct mountain long-eared bat Plecotus macrobullaris sarmaticus subsp. nov. is described on the base of jaw remains from the Lower Pleistocene of the Taurida cave in central Crimea. This is the first record of the genus Plecotus in the Lower Pleistocene of Russia and the first fossil find of P. macrobullaris Kuzyakin, 1965, documenting the early stage of the evolutionary history of the species.

Comparative mitochondrial genomics of endemic Mexican vesper yellow bats genus Rhogeessa (Chiroptera: Vespertilionidae) and insights into internal relationships in the family Vespertilionidae.

In the species-rich family Vespertilionidae, vesper yellow bats in the genus Rhogeessa include eleven species, three of them endemic to Mexico. These insectivorous bats provide important ecosystem services, including pest control. Even though some aspects of their biology are well- known, only a few genomic resources are available for these species, which limits our understanding of their biology. In this study, we assembled and annotated the mitochondrial genome of four species: R. aenea, R. genowaysi, R. mira, and R. parvula. We generated a phylomitogenomic hypothesis based on translated protein-coding genes for a total of 52 species in the family Vespertilionidae and examined the phylogenetic position of the genus Rhogeessa and species within the family. The AT-rich mitogenomes of R. aenea, R. genowaysi, R. mira, and R. parvula are 16,763, 16,781, 16,807, and 16,794 pb in length, respectively. Each studied mitogenome encodes 13 Protein Coding Genes (PCGs), 22 transfer RNA genes, and 2 rRNA genes, and contains a putative control region (CR). All tRNAs exhibit a 'cloverleaf' secondary structure, except tRNA-Serine-1 that lacked the DHU arm in all studied mitogenomes. Selective pressure analyses indicated that all protein-coding genes are exposed to purifying selection. The phylomitogenomic analysis supported the monophyletic status of the family Vespertilionidae, confirmed the placement of Rhogeessa within the tribe Antrozoini, and clarified phylogenetic relationships within and among subfamilies and tribes in this family. Our results indicate that phylomitogenomics are useful to explore the evolutionary history of vesper bats. The assembly and comprehensive analysis of mitochondrial genomes offer the potential to generate molecular references and resources beneficial for genetic analyses aimed at understanding the ecology and evolution of these remarkable bats.

Evolution of olfactory receptor superfamily in bats based on high throughput molecular modelling.

The origin of flight and laryngeal echolocation in bats is likely to have been accompanied by evolutionary changes in other aspects of their sensory biology. Of all sensory modalities in bats, olfaction is perhaps the least well understood. Olfactory receptors (ORs) function in recognizing odour molecules, with crucial roles in evaluating food, as well as in processing social information. Here we compare OR repertoire sizes across taxa and apply a new pipeline that integrates comparative genome data with protein structure modelling and then we employ molecular docking techniques with small molecules to analyse OR functionality based on binding energies. Our results suggest a sharp contraction in odorant recognition of the functional OR repertoire during the origin of bats, consistent with a reduced dependence on olfaction. We also compared bat lineages with contrasting different ecological characteristics and found evidence of differences in OR gene expansion and contraction, and in the composition of ORs with different tuning breadths. The strongest binding energies of ORs in non-echolocating fruit-eating bats were seen to correspond to ester odorants, although we did not detect a quantitative advantage of functional OR repertoires in these bats compared with echolocating insectivorous species. Overall, our findings based on molecular modelling and computational docking suggest that bats have undergone olfactory evolution linked to dietary adaptation. Our results from extant and ancestral bats help to lay the groundwork for targeted experimental functional tests in the future.

Parallel evolution in an island archipelago revealed by genomic sequencing of Hipposideros leaf-nosed bats.

Body size is a key morphological attribute, often used to delimit species boundaries among closely related taxa. But body size can evolve in parallel, reaching similar final states despite independent evolutionary and geographic origins, leading to faulty assumptions of evolutionary history. Here, we document parallel evolution in body size in the widely distributed leaf-nosed bat genus Hipposideros, which has misled both taxonomic and evolutionary inference. We sequenced reduced representation genomic loci and measured external morphological characters from three closely related species from the Solomon Islands archipelago, delimited by body size. Species tree reconstruction confirms the paraphyly of two morphologically designated species. The nonsister relationship between large-bodied H. dinops lineages found on different islands indicates that large-bodied ecomorphs have evolved independently at least twice in the history of this radiation. A lack of evidence for gene flow between sympatric, closely related taxa suggests the rapid evolution of strong reproductive isolating barriers between morphologically distinct populations. Our results position Solomon Islands Hipposideros as a novel vertebrate system for studying the repeatability of parallel evolution under natural conditions. We conclude by offering testable hypotheses for how geography and ecology could be mediating the repeated evolution of large-bodied Hipposideros lineages in the Solomon Islands.

Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan / Identificação molecular do gênero Pipistrellus (Mammalia: Chiroptera) da região de Fáta, Paquistão

A total of 10 specimens were captured from selected sites of Bajaur Agency FATA, Pakistan using mist nets. The captured specimens were morphologically identified and various morphometric measurements were taken. The head and Body length (HB) of Pipistrellus coromondra and Pipistrellus kuhlii lepidus (n=10) was 43±0.11 mm and 45±1.1 respectively. Morphologically identified Pipistrellus kuhlii confirmed as Pipistrellus kuhlii lepidus based on 16S rRNA sequences. The DNA sequences were submitted to GenBank and accession numbers were obtained (MN719478 and MT430902). The available 16S rRNA gene sequences of Pipistrellus coromondra and Pipistrellus kuhlii lepidus were retrieved from NCBI and incorporated in N-J tree analysis. Overall, the interspecific genetic variations among Pipistrellus coromondra and Pipistrellus kuhlii lepidus were 8% and 1% respectively. In our recommendation, a comprehensive molecular identification of bats is need of hour to report more cryptic and new species from Pakistan.

Um total de 10 espécimes foi capturado em locais selecionados da Bajaur Agency FATA, Paquistão, usando redes de neblina. Os espécimes capturados foram identificados morfologicamente e várias medidas morfométricas foram realizadas. O comprimento da cabeça e do corpo (HB) de Pipistrellus coromondra e Pipistrellus kuhlii lepidus (n = 10) foi de 43 ± 0,11 mm e 45 ± 1,1, respectivamente. Pipistrellus kuhlii identificado morfologicamente e confirmado como Pipistrellus kuhlii lepidus com base em sequências de rRNA 16S. As sequências de DNA foram submetidas ao GenBank e os números de acesso foram obtidos (MN 719478 e MT430902). As sequências do gene 16S rRNA disponíveis de Pipistrellus coromondra e Pipistrellus kuhlii lepidus foram recuperadas do NCBI e incorporadas na análise da árvore N-J. No geral, as variações genéticas interespecíficas entre Pipistrellus coromondra e Pipistrellus kuhlii lepidus foram de 8% e 1%, respectivamente. Em nossa recomendação, uma identificação molecular abrangente de morcegos precisa de uma hora para relatar mais espécies crípticas e novas do Paquistão.

Presence of Recombinant Bat Coronavirus GCCDC1 in Cambodian Bats.

Bats have been recognized as an exceptional viral reservoir, especially for coronaviruses. At least three bat zoonotic coronaviruses (SARS-CoV, MERS-CoV and SARS-CoV-2) have been shown to cause severe diseases in humans and it is expected more will emerge. One of the major features of CoVs is that they are all highly prone to recombination. An extreme example is the insertion of the P10 gene from reoviruses in the bat CoV GCCDC1, first discovered in Rousettus leschenaultii bats in China. Here, we report the detection of GCCDC1 in four different bat species (Eonycteris spelaea, Cynopterus sphinx, Rhinolophus shameli and Rousettus sp.) in Cambodia. This finding demonstrates a much broader geographic and bat species range for this virus and indicates common cross-species transmission. Interestingly, one of the bat samples showed a co-infection with an Alpha CoV most closely related to RsYN14, a virus recently discovered in the same genus (Rhinolophus) of bat in Yunnan, China, 2020. Taken together, our latest findings highlight the need to conduct active surveillance in bats to assess the risk of emerging CoVs, especially in Southeast Asia.

Evolution of TRIM5 and TRIM22 in Bats Reveals a Complex Duplication Process.

The innate immunological response in mammals involves a diverse and complex network of many proteins. Over the last years, the tripartite motif-containing protein 5 (TRIM5) and 22 (TRIM22) have shown promise as restriction factors of a plethora of viruses that infect primates. Although there have been studies describing the evolution of these proteins in a wide range of mammals, no prior studies of the TRIM6/34/5/22 gene cluster have been performed in the Chiroptera order. Here, we provide a detailed analysis of the evolution of this gene cluster in several bat genomes. Examination of different yangochiroptera and yinpterochiroptera bat species revealed a dynamic history of gene expansion occurring in TRIM5 and TRIM22 genes. Multiple copies of TRIM5 were found in the genomes of several bats, demonstrating a very low degree of conservation in the synteny of this gene among species of the Chiroptera order. Our findings also reveal that TRIM22 is often found duplicated in yangochiroptera bat species, an evolutionary phenomenon not yet observed in any other lineages of mammals. In total, we identified 31 TRIM5 and 19 TRIM22 amino acids to be evolving under positive selection, with most of the residues being placed in the PRYSPRY domain, known to be responsible for binding to the viral capsid during restriction in the primate orthologous TRIM proteins. Altogether, our results help to shed light on the distinctive role of bats in nature as reservoirs of viruses, many of which have become threatening zoonotic diseases through virus spillover in the last decades.

Biological composition analysis of a natural medicine, Faeces Vespertilionis, with complex sources using DNA metabarcoding.

Faeces Vespertilionis is a commonly used fecal traditional Chinese medicine. Traditionally, it is identified relying only on morphological characters. This poses a serious challenge to the composition analysis accuracy of this complex biological mixture. Thus, for quality control purposes, an accurate and effective method should be provided for taxonomic identification of Faeces Vespertilionis. In this study, 26 samples of Faeces Vespertilionis from ten provinces in China were tested using DNA metabarcoding. Seven operational taxonomic units (OTUs) were detected as belonging to bats. Among them, Hipposideros armiger (Hodgson, 1835) and Rhinolophus ferrumequinum (Schober and Grimmberger, 1997) were the main host sources of Faeces Vespertilionis samples, with average relative abundances of 59.3% and 24.1%, respectively. Biodiversity analysis showed that Diptera and Lepidoptera were the most frequently consumed insects. At the species level, 19 taxa were clearly identified. Overall, our study used DNA metabarcoding to analyze the biological composition of Faeces Vespertilionis, which provides a new idea for the quality control of this special traditional Chinese medicine.

Genetic identification of bat species for pathogen surveillance across France.

With more than 1400 chiropteran species identified to date, bats comprise one-fifth of all mammalian species worldwide. Many studies have associated viral zoonoses with 45 different species of bats in the EU, which cluster within 5 families of bats. For example, the Serotine bats are infected by European Bat 1 Lyssavirus throughout Europe while Myotis bats are shown infected by coronavirus, herpesvirus and paramyxovirus. Correct host species identification is important to increase our knowledge of the ecology and evolutionary pattern of bat viruses in the EU. Bat species identification is commonly determined using morphological keys. Morphological determination of bat species from bat carcasses can be limited in some cases, due to the state of decomposition or nearly indistinguishable morphological features in juvenile bats and can lead to misidentifications. The overall objective of our study was to identify insectivorous bat species using molecular biology tools with the amplification of the partial cytochrome b gene of mitochondrial DNA. Two types of samples were tested in this study, bat wing punches and bat faeces. A total of 163 bat wing punches representing 22 species, and 31 faecal pellets representing 7 species were included in the study. From the 163 bat wing punches tested, a total of 159 were genetically identified from amplification of the partial cyt b gene. All 31 faecal pellets were genetically identified based on the cyt b gene. A comparison between morphological and genetic determination showed 21 misidentifications from the 163 wing punches, representing ~12.5% of misidentifications of morphological determination compared with the genetic method, across 11 species. In addition, genetic determination allowed the identification of 24 out of 25 morphologically non-determined bat samples. Our findings demonstrate the importance of a genetic approach as an efficient and reliable method to identify bat species precisely.