Evolutionary history and systematics of European blind mole rats (Rodentia: Spalacidae: Nannospalax): Multilocus phylogeny and species delimitation in a puzzling group.

Species delimitation is a powerful approach to assist taxonomic decisions in challenging taxa where species boundaries are hard to establish. European taxa of the blind mole rats (genus Nannospalax) display small morphological differences and complex chromosomal evolution at a shallow evolutionary divergence level. Previous analyses led to the recognition of 25 'forms' in their distribution area. We provide a comprehensive framework to improve knowledge on the evolutionary history and revise the taxonomy of European blind mole rats based on samples from all but three of the 25 forms. We sequenced two nuclear-encoded genetic regions and the whole mitochondrial cytochrome b gene for phylogenetic tree reconstructions using concatenation and coalescence-based species-tree estimations. The phylogenetic analyses confirmed that Aegean N. insularis belongs to N. superspecies xanthodon, and that it represents the second known species of this superspecies in Europe. Mainland taxa reached Europe from Asia Minor in two colonisation events corresponding to two superspecies-level taxa: N. superspecies monticola (taxon established herewith) reached Europe c. 2.1 million years ago (Mya) and was followed by N. superspecies leucodon (re-defined herewith) c. 1.5 Mya. Species delimitation allowed the clarification of the taxonomic contents of the above superspecies. N. superspecies monticola contains three species geographically confined to the western periphery of the distribution of blind mole rats, whereas N. superspecies leucodon is more speciose with six species and several additional subspecies. The observed geographic pattern hints at a robust peripatric speciation process and rapid chromosomal evolution. The present treatment is thus regarded as the minimum taxonomic content of each lineage, which can be further refined based on other sources of information such as karyological traits, crossbreeding experiments, etc. The species delimitation models also allowed the recognition of a hitherto unnamed blind mole rat taxon from Albania, described here as a new subspecies.

Detection and sequence analysis of Canine morbillivirus in multiple species of the Mustelidae family.

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.

Species delimitation and evolutionary reconstruction within an integrative taxonomic framework: A case study on Rhinolophus macrotis complex (Chiroptera: Rhinolophidae).

Species delimitation and evolutionary reconstruction remain challenging for non-model species that have experienced reticulate evolution and exhibit conflicting patterns of differentiation among multiple lines of evidence, such as mitochondrial and nuclear data and phenotypes. Here, we applied an integrative taxonomic approach to a case study of Rhinolophus macrotis complex, whose taxonomic status remains controversial, to provide insight into the systematics and evolutionary history of these species. By integrating traditional genetic markers with different modes of inheritance, genome-wide SNPs as well as phenotypic characteristics, we clarified the presence of three closely related species, R. episcopus, R. siamensis, and R. osgoodi, within this complex, and proposed a new taxonomic treatment for R. osgoodi. Our results suggested that hybridization and introgression are the main causes of low mtDNA divergence in these species. Combined with the demographic inference, we deduced that glacial-interglacial cycles drove geographic isolation and secondary contacts of these species, then promoted hybridization and lineage fusion among them, finally resulting in a reticulate evolutionary pattern. Overall, our study highlights the importance of combining multiple types of data to delimit species, especially those with conserved morphology, and to reveal the sophisticated processes of speciation.

Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data.

Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and Murina recondita are both endemic to Taiwan and are putative sister species. To test for nonallopatric divergence and gene flow in these taxa, we generated sequences using Sanger and next-generation sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita; however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species Murina eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *beast and isolation-with-migration and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.

Thumb-pads up-a new species of thick-thumbed bat from Sumatra (Chiroptera: Vespertilionidae: Glischropus).

To date, three species of the genus Glischropus are recognized from the Indomalayan zoogeographic region-G. bucephalus from the Indochinese subregion, G. tylopus from the Sundaic subregion (Peninsular Thailand and Malaysia, Borneo, Sumatra, Moluccas) and G. javanus, restricted to Java. The investigation of the holotype and three topotype specimens of G. batjanus supported the view that the name was previously correctly regarded as the junior subjective synonym of G. tylopus. During review of material recently collected in southwestern Sumatra, Indonesia, one specimen of a yet undescribed species of Thick-thumbed bat was identified. G. aquilus n. sp. markedly differs from its congeners by its dark brown pelage, nearly black ear and tragus, and in skull proportions. The phylogenetic analysis based on cytb sequences also supports the specific distinctness of G. aquilus n. sp. Its discovery brings the count to 88 species of bats known from Sumatra.

New records of Harpiolaisodon (Chiroptera, Vespertilionidae) from the Chinese mainland.

Background: The new species, Harpiolaisodon Kuo et al., 2006, was described from Taiwan, China. So far, no distribution of this species outside Taiwan has been reported. New information: During two field investigations of small mammals in Guanyin Mountains Provincial Nature Reserve, Yuanyang, Yunnan, China, in April 2022 and May 2023, five individuals of Harpiola were collected in the mid-montane evergreen broad-leaved forest. Our morphological and molecular results reveal that these individuals from the Chinese mainland belong to Harpiolaisodon, extending the occurrence of this species well beyond its known distributions in Taiwan, China and Vietnam.

The calls of Vietnamese bats: a major step toward the acoustic characterization of Asian bats.

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.

Conservation status of the blind mole rat populations in Hungary (Rodentia: Spalacinae: Nannospalax) revisited.

Regular reviews of long-term research and conservation programs are useful sources of information for future directions in science and for the assessment of current conservation status of taxa. In this paper, we compiled all available data from the last 10 years related to Hungarian blind mole rat populations and assessed this information according to the following main themes: systematics, distribution and threats, and conservation actions. Based on the most recent information, national and global risk assessments are provided for the three species of Nannospalax (N. montanosyrmiensis, N. hungaricus and N. syrmiensis), currently accepted as part of the Hungarian fauna.

Evolutionary co-variation of host and parasite diversity-the first test of Eichler's rule using parasitic lice (Insecta: Phthiraptera).

The taxonomic richness of lice (Phthiraptera) varies considerably among their avian and mammalian hosts. Previous studies explored some factors shaping louse diversity; however, the so-called Eichler's rule-according to which taxonomic richness of parasites co-varies with that of their hosts-has never been tested. Our study incorporates all families of birds and mammals and the whole order of lice to test this co-variation, thus we present the widest taxonomic range to test any correlates of louse richness. Louse richness data were controlled for uneven sampling effort. We used the method of independent contrasts to control for phylogenetic effects. We found a strong correlation between the species richness of avian and mammalian families and generic richness of their lice. We discuss some alternative macroevolutionary and macroecological hypotheses that may explain this phenomenon that may well be a general feature of parasitism and it seems possible that this effect contribute considerably to global biodiversity.

Typhlitis and abdominal cystic lymphangiomatosis in a Mt. Carmel blind mole rat (Nannospalax (ehrenbergi) carmeli).

An abdominal cystic lymphangiomatosis in a Mt. Carmel blind mole rat (Nannospalax (ehrenbergi) carmeli) is described. This case was most likely due to a congenital abnormality with long-term compensation by the animal. The case describes the clinical course and subsequent postmortem examination. The death in the animal was caused by an abscess in the peritoneal wall and subsequent peritonitis.

Out of Southeast Asia: A new species of thick-thumbed bat (Chiroptera: Vespertilionidae: Glischropus) from Meghalaya, north-eastern India.

Thick-thumbed bats of the genus Glischropus are currently composed of four recognized species from Southeast Asia, two of which were described in recent times. Among these species, G. aquilus is endemic to Sumatra, G. javanus is restricted to western Java, whereas G. bucephalus is widely distributed north to the Isthmus of Kra and G. tylopus is widespread south to this zoogeographic boundary. Two recently collected Glischropus specimens from Meghalaya state in north-eastern India extend the known distribution range of the genus westward into South Asia by ca. 1000 km. Morphological examination of these specimens and comparison with all known species in this genus revealed marked differences in colouration, dental characters and bacular traits. We therefore describe the Meghalaya specimens as a new species. The discovery of the new species from a forest patch adjacent to Nongkhyllem Wildlife Sanctuary from where another specialized bamboo-dwelling species (Eudiscopus denticulus) was reported recently also underscore the importance of the area from a conservation point of view.

ChiroVox: a public library of bat calls.

Recordings of bat echolocation and social calls are used for many research purposes from ecological studies to taxonomy. Effective use of these relies on identification of species from the recordings, but comparative recordings or detailed call descriptions to support identification are often lacking for areas with high biodiversity. The ChiroVox website (https://www.chirovox.org) was created to facilitate the sharing of bat sound recordings together with their metadata, including biodiversity data and recording circumstances. To date, more than 30 researchers have contributed over 3,900 recordings of nearly 200 species, making ChiroVox the largest open-access bat call library currently available. Each recording has a unique identifier that can be cited in publications; hence the acoustic analyses are repeatable. Most of the recordings available through the website are from bats whose species identities are confirmed, so they can be used to determine species in recordings where the bats were not captured or could not be identified. We hope that with the help of the bat researcher community, the website will grow rapidly and will serve as a solid source for bat acoustic research and monitoring.

Expert range maps of global mammal distributions harmonised to three taxonomic authorities.

Aim: Comprehensive, global information on species' occurrences is an essential biodiversity variable and central to a range of applications in ecology, evolution, biogeography and conservation. Expert range maps often represent a species' only available distributional information and play an increasing role in conservation assessments and macroecology. We provide global range maps for the native ranges of all extant mammal species harmonised to the taxonomy of the Mammal Diversity Database (MDD) mobilised from two sources, the Handbook of the Mammals of the World (HMW) and the Illustrated Checklist of the Mammals of the World (CMW). Location: Global. Taxon: All extant mammal species. Methods: Range maps were digitally interpreted, georeferenced, error-checked and subsequently taxonomically aligned between the HMW (6253 species), the CMW (6431 species) and the MDD taxonomies (6362 species). Results: Range maps can be evaluated and visualised in an online map browser at Map of Life (mol.org) and accessed for individual or batch download for non-commercial use. Main conclusion: Expert maps of species' global distributions are limited in their spatial detail and temporal specificity, but form a useful basis for broad-scale characterizations and model-based integration with other data. We provide georeferenced range maps for the native ranges of all extant mammal species as shapefiles, with species-level metadata and source information packaged together in geodatabase format. Across the three taxonomic sources our maps entail, there are 1784 taxonomic name differences compared to the maps currently available on the IUCN Red List website. The expert maps provided here are harmonised to the MDD taxonomic authority and linked to a community of online tools that will enable transparent future updates and version control.

Inferring the ecological niche of bat viruses closely related to SARS-CoV-2 using phylogeographic analyses of Rhinolophus species.

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.

Complete mitochondrial genomes reveal robust phylogenetic signals and evidence of positive selection in horseshoe bats.

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.

First record of disk-footed bat Eudiscopus denticulus (Chiroptera, Vespertilionidae) from China and resolution of phylogenetic position of the genus.

The disk-footed bat Eudiscopus denticulus(Osgood, 1932) is a rare species in Southeast Asia. During two chiropteran surveys in the summer of 1981 and 2019, eight and three small Myotis-like bats with distinct disk-like hindfeet were collected from Yunnan Province, China, respectively. External, craniodental, and phylogenetic evidence confirmed these specimens as E. denticulus, representing a new genus in China. The complete mitochondrial genome consistently showed robust support for E. denticulus as a basal lineage within Myotinae. The coding patterns and characteristics of its mitochondrial genome were similar to that of other published genomes from Myotis. The echolocation signals of the newly collected individuals were analyzed. The potential distribution range of Eudiscopus in Southeast Asia inferred using the MaxEnt model indicated its potential occurrence along the southern border region of Yunnan, China.

Tube-nosed variations-a new species of the genus Murina (Chiroptera: Vespertilionidae) from China.

During a survey in 2014, several tube-nosed bats (Vespertilionidae: Murininae: Murina) were collected in Sichuan Province. Based on morphological characters, these bats did not match any species previously recorded from China. Morphometric analyses and phylogenetic inference based on mitochondrial and nuclear gene sequences indicated that they represented a new species, named here as Murina jinchui sp. nov. Although the new species is presently known only from Wolong National Nature Reserve, it is unlikely to be a rare species in the area based on our capture frequencies.

The taxonomic reassessment of a reportedly extinct bat, Pipistrellus sturdeei (Chiroptera: Vespertilionidae).

Insular bats are among the most vulnerable mammal species whose survival are threatened by several human-mediated factors, frequently paralleled by the paucity of information and lack of adequate management plans. Pipistrellus sturdeei is known only by the holotype collected from the remote Bonin Islands more than a hundred years ago and is declared to be extinct by the Japanese authorities. However, its taxonomic validity and collection locality is regarded ambiguous by some scholars. Here we report details about its collection circumstances and provide evidence that it morphologically differs from all other pipistrelles. We would like to raise attention on the species and the importance of a detailed study on its possible survival.

A new genus of vespertilionid bat: the end of a long journey for Joffre's Pipistrelle (Chiroptera: Vespertilionidae).

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.

Molecular Identification of a Novel Hantavirus in Malaysian Bronze Tube-Nosed Bats (Murina aenea).

In the past ten years, several novel hantaviruses were discovered in shrews, moles, and bats, suggesting the dispersal of hantaviruses in many animal taxa other than rodents during their evolution. Interestingly, the coevolutionary analyses of most recent studies have raised the possibility that nonrodents may have served as the primordial mammalian host and harboured the ancestors of rodent-borne hantaviruses as well. The aim of our study was to investigate the presence of hantaviruses in bat lung tissue homogenates originally collected for taxonomic purposes in Malaysia in 2015. Hantavirus-specific nested RT-PCR screening of 116 samples targeting the L segment of the virus has revealed the positivity of two lung tissue homogenates originating from two individuals, a female and a male of the Murina aenea bat species collected at the same site and sampling occasion. Nanopore sequencing of hantavirus positive samples resulted in partial genomic data from S, M, and L genome segments. The obtained results indicate molecular evidence for hantaviruses in the M. aenea bat species. Sequence analysis of the PCR amplicon and partial genome segments suggests that the identified virus may represent a novel species in the Mobatvirus genus within the Hantaviridae family. Our results provide additional genomic data to help extend our knowledge about the evolution of these viruses.