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Background In genus Rhinolophus , species in the Rhinolophus philippinensis and R. macrotis groups are unique because the horseshoe bats in these group have relatively low echolocation frequencies and flight speeds compared with other horseshoe bats with similar body size. The different characteristics among bat species suggest particular evolutionary processes may have occurred in this genus. To study the adaptive evidence in the mitochondrial genomes (mitogenomes) of rhinolophids, especially the mitogenomes of the species with low echolocation frequencies, we sequenced eight mitogenomes and used them for comparative studies of molecular phylogeny and adaptive evolution. Results Phylogenetic analysis using whole mitogenome sequences produced robust results and provided phylogenetic signals that were better than those obtained using single genes. The results supported the recent establishment of the separate macrotis group. The signals of adaptive evolution discovered in the Rhinolophus species were tested for some of the codons in two genes ( ND2 and ND6 ) that encode NADH dehydrogenases in oxidative phosphorylation system complex I. These genes have a background of widespread purifying selection. Signals of relaxed purifying selection and positive selection were found in ND2 and ND6 , respectively, based on codon models and physicochemical profiles of amino acid replacements. However, no pronounced overlap was found for non-synonymous sites in the mitogenomes of all the species with low echolocation frequencies. A signal of positive selection for ND5 was found in the branch-site model when R. philippinensis was set as the foreground branch. Conclusions The mitogenomes provided robust phylogenetic signals that were much more informative than the signals obtained using single mitochondrial genes. Two mitochondrial genes that encoding proteins in the oxidative phosphorylation system showed some evidence of adaptive evolution in genus Rhinolophus and the positive selection signals were tested for ND5 in R. philippinensis . These results indicate that mitochondrial protein-coding genes were targets of adaptive evolution during the evolution of Rhinolophus species, which might have contributed to a diverse range of acoustic adaptations in this genus.

Accurate species delimitation is fundamental yet challenging, particularly in recently diverged, phenotypically conservative taxa such as bats. The \" group\" represents one of the most taxonomically contentious groups among horseshoe bats. During field surveys in Southwest China, we discovered an unidentified sp. occurring sympatrically with and , sharing broad morphological affinities with recognized species of the \" group.\" To explore its taxonomic status, we employed an integrative approach combining morphological, acoustic, and multi-locus genetic (mitogenomic and nuclear) data. Phenotypically, sp. closely resembles but can be distinguished by its divergent echolocation resting frequency. Genetically, while mitochondrial data deeply nested sp. within with a shallow divergence time, phylogenies based on two nuclear introns positioned it closer to two other species, and . Species delimitation based on these genetic markers revealed a pattern of mitochondrial subdivision contrasted by overly conservative nuclear signals. Such mito-nuclear discordance suggests a complex evolutionary history that complicates taxonomic assignments. Given that only three specimens of sp. were available, which precludes a robust assessment of intraspecific variation, we provisionally designate it as a candidate lineage within the \" group,\" warranting future validation with additional comprehensive evidence. This study highlights the indispensable utility of integrative taxonomy in uncovering hidden diversity and provides insights into chiropteran evolutionary history.

Bats play a vital role in ecosystems through providing essential functions and services, such as pollination and pest control, but they face many threats from anthropogenic activities, climate change, and diseases. While establishing protected areas can be a conservation measure to mitigate bats’ population declines and habitats loss, the effectiveness of current protected areas in conserving bat species remains poorly understood. Using Vietnam as a case, this study aims to evaluate the representation of the existing protected area network for bats in terms of the proportion of their distribution ranges covered and the number of well-covered species. We also identified areas that would improve the representation using the spatial prioritization approach. Our results showed that while Vietnam’s protected area network provides better representation than random allocation, it currently only covers 6.12% of bat distribution ranges on average, leaving the distribution areas of more than 78 (96%) of the 81 species examined in this study insufficiently represented. Through the spatial prioritization, the forests in Central Highlands, western Central Coast, and Northwest were identified as the key regions for bats. Expanding the current network to cover 9% and 30% of the land under the national and global targets could improve the range coverage to 11.89% and 41.99%, respectively, reducing the number of poorly represented bats to 10–23 (12.3–28.4%) species. These findings offer critical insights for conservation practitioners and policymakers into prioritizing resources and efforts for improving conservation of not only bats in Vietnam but also biodiversity in general in other places.

Southeast Asia includes several global biodiversity hotspots and bats account for nearly one-third of mammal species currently known in the region. While acoustic methods have become widespread in bat research, basic information is often lacking on the echolocation calls produced by Asian bat species. Since such information can aid a wide variety of research and conservation initiatives, descriptions of the calls emitted by Asian bats are fundamental. The aim of our study was to provide a standardized analysis and description of the Vietnamese bat echolocation calls. We analyzed call recordings of 87 species arranged in eight families. This constitutes 74% of the echolocating bats presently known in Vietnam and includes the first call descriptions for five taxa. Our use of an open-source software and the deposition of recordings in the ChiroVox repository will facilitate comparative studies in Asia and the information we provide represents one of the most comprehensive bioacoustic databases for Asian bats to date.

Climate and land-cover changes are among major threats to biodiversity. However, the interactive effects of the two threats are often overlooked in conservation planning. Using 81 bat species occurring in Vietnam as a case, we investigated the individual and interactive effects of climate and land-cover changes, highlighting the importance of this information for conservation efforts. By using species distribution models, we predicted the potential changes in range size among species and in species richness across Vietnam by the 2050s, considering projected climate and land-cover changes under two emission scenarios. Our results revealed that both threats individually would have predominantly negative effects on bats in Vietnam. Moreover, when these threats occur simultaneously, their interactions would generally intensify the impacts by mitigating individual positive effects and/or enhancing negative effects. However, we also found large interspecific and geographic variations in the direction and magnitude of these effects. Forest specialists, insectivores and cave-roosting species were predicted to be particularly vulnerable to the negative effects, with northern and southern Vietnam being more affected. These results underscore the urgent need to incorporate both climate and land-cover changes, as well as their interactions, into conservation planning for bats in Vietnam and biodiversity in general. The species-specific and spatially-explicit information regarding the impacts of the two threats can guide conservation actions, allowing us to target more manageable and less uncertain threats, as well as prioritize the protection of more vulnerable species.

Knowledge as to the taxonomic status of enigmatic bat species often is hindered by limited availability of specimens. This is particularly true for aerial-hawking bats that are difficult to catch. One such species, “Hypsugo” joffrei, was originally described in Nyctalus due to its long and slender wings, but subsequently transferred to Pipistrellus, and most recently to Hypsugo, on the basis of morphology. Analysis of newly available material, which more than doubles the known specimens of this taxon, demonstrates that it is morphologically and genetically distinct from all other bat genera. We accordingly describe it as belonging to a new, monotypic genus. We provide a detailed description of its external and craniodental traits, measurements, and assessment of genetic relationships, including barcode sequences to facilitate its rapid identification in future. The new genus belongs to a group that includes the recently described Cassistrellus, as well as Tylonycteris, and its closest relative, Philetor. We also describe the echolocation calls emitted by members of the taxon in different situations, which may facilitate finding them in previously unsampled locations. Based on the new data, the species occurs from Nepal to North Vietnam and China, which suggests that it could be more widespread than previously thought.

The Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the coronavirus disease 2019 (COVID-19) pandemic. To date, viruses closely related to SARS-CoV-2 have been reported in four bat species: Rhinolophus acuminatus , Rhinolophus affinis , Rhinolophus malayanus , and Rhinolophus shameli . Here, we analysed 343 sequences of the mitochondrial cytochrome c oxidase subunit 1 gene ( CO1 ) from georeferenced bats of the four Rhinolophus species identified as reservoirs of viruses closely related to SARS-CoV-2. Haplotype networks were constructed in order to investigate patterns of genetic diversity among bat populations of Southeast Asia and China. No strong geographic structure was found for the four Rhinolophus species, suggesting high dispersal capacity. The ecological niche of bat viruses closely related to SARS-CoV-2 was predicted using the four localities in which bat viruses were recently discovered and the localities where bats showed the same CO1 haplotypes than virus-positive bats. The ecological niche of bat viruses related to SARS-CoV was deduced from the localities where bat viruses were previously detected. The results show that the ecological niche of bat viruses related to SARS-CoV2 includes several regions of mainland Southeast Asia whereas the ecological niche of bat viruses related to SARS-CoV is mainly restricted to China. In agreement with these results, human populations in Laos, Vietnam, Cambodia, and Thailand appear to be much less affected by the COVID-19 pandemic than other countries of Southeast Asia. In the climatic transitional zone between the two ecological niches (southern Yunnan, northern Laos, northern Vietnam), genomic recombination between highly divergent viruses is more likely to occur. Considering the limited data and the risk of recombinant bat-CoVs emergence as the source of new pandemics in humans, the bat populations in these regions should be under surveillance.

Background Canine morbillivirus (canine distemper virus, CDV) is a member of the Paramyxoviridae family. Canine distemper is a serious viral disease that affects many mammalian species, including members of the Mustelidae family. These animals have an elusive nature, which makes related virological studies extremely challenging. There is a significant knowledge gap about the evolution of their viruses and about the possible effects of these viruses to the population dynamics of the host animals. Spleen and lung tissue samples of 170 road-killed mustelids belonging to six species were collected between 1997 and 2022 throughout Hungary and tested for CDV with real-time RT-PCR. Results Three species were positive for viral RNA, 2 out of 64 Steppe polecats ( Mustela eversmanii ), 1 out of 36 European polecats ( Mustela putorius ) and 2 out of 36 stone martens ( Martes foina ); all 18 pine martens ( Martes martes ), 10 least weasels ( Mustela nivalis ) and 6 stoats ( Mustela erminea ) tested negative. The complete CDV genome was sequenced in five samples using pan-genotype CDV-specific, amplicon-based Nanopore sequencing. Based on the phylogenetic analysis, all five viral sequences were grouped to the Europe/South America 1 lineage and the distribution of one sequence among trees indicated recombination of the Hemagglutinin gene. We verified the recombination with SimPlot analysis. Conclusions This paper provides the first CDV genome sequences from Steppe polecats and additional complete genomes from European polecats and stone martens. The infected specimens of various species originated from distinct parts of the country over a long time, indicating a wide circulation of CDV among mustelids throughout Hungary. Considering the high virulence of CDV and the presence of the virus in these animals, we highlight the importance of conservation efforts for wild mustelids. In addition, we emphasize the importance of full genomic data acquisition and analysis to better understand the evolution of the virus. Since CDV is prone to recombination, specific genomic segment analyses may provide less representative evolutionary traits than using complete genome sequences.

Bats belonging to the subfamily Vespertilioninae are diverse and cosmopolitan, but their systematic arrangement remains a challenge. Previous molecular surveys suggested new and unexpected relationships of some members compared to more traditional, morphology-based classifications, and revealed the existence of taxonomically undefined lineages. We describe here a new genus and species corresponding to an enigmatic lineage that was previously identified within the genus Eptesicus in the Indomalayan Region. Phylogenetic reconstructions based on mitochondrial and nuclear genes relate the new taxon to Tylonycteris and Philetor, and show that specimens associated with this new genus represent 2 genetically distinct species. Although little is known about their ecology, locations of capture and wing morphology suggest that members of this new genus are tree-dwelling, open-space aerial insect predators. The new species has only been documented from Yok Don National Park in Vietnam, so its conservation status is uncertain until more surveying methods target the bat fauna of the dipterocarp forest in Southeast Asia.

Abstract In taxonomic works, the weight to be given to morphological, mitochondrial, or nuclear signals, and the assessment of differences as species or subspecies distinctions has also varied considerably over the past decades and is largely a subjective research decision. This apparent example of the “grey zone of taxonomy” underpins the need of critical studies of as many specimens as possible and of using both mitochondrial and nuclear genes in taxonomic-systematic studies, as phylogeny based on uniparentally inherited genes alone may not represent true evolutionary scenarios. Myotis sicarius , a species occurring thorough the Himalayan foothills was found for the first time out of South Asia, in North Vietnam. Analysis of topotypical and Vietnamese specimens revealed high mitochondrial heterogeneity – at the upper limit of the usual threshold of intraspecific difference – but only minute nuclear sequence and negligible morphological differences. Albeit the large geographic distance between the two records might suggest the existence of two putative reproductively isolated taxonomic units, based on the incongruent results we concluded that the split of geographic populations of M. sicarius into different taxa is unsupported. As a morphologically closely resembling species, we also reviewed the taxonomic status of the two morphological forms of M. annectans and synonymizing M. primula with M. annectans was also corroborated by our phylogenetic analyses.