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•We generate ~1500 loci sequence data from 35 individuals covering six taxa.•Concatenation and coalescent methods produce similar species tree topologies.•Three cases of mitonuclear ...discordance are observed.•R. s. septentrionalis and R. s. ssp are likely to represent full species.
Recently diverged taxa are often characterised by high rates of introgressive hybridization and incomplete lineage sorting, both of which can complicate phylogenetic reconstructions of species histories. Here we use a sequence capture approach to obtain genome-wide data to resolve the evolutionary relationships, and infer the extent and timescale of hybridization and introgression events, among six recently diverged taxa of the horseshoe bat species complexes Rhinolophus sinicus and R. thomasi. We show that two different methods of species tree reconstruction applied to a set of ~1500 nuclear loci all recover species trees with similar topologies, differing from the previous phylogeny based on two nuclear loci. By comparing the tree topology obtained from the nuclear loci with that inferred from the mitochondrial genome, we observed at least three cases of conflict, each of which likely results from past introgression. Of these, the occurrence of a highly similar mitogenome sequence shared by individuals of two taxa in a sympatric region points to very recent mtDNA introgression. The other cases are characterised by greater divergence and strong phylogeographic structure among putative introgressed individuals and their source populations, and thus likely reflect more ancient hybridization events. These results also suggest that two of the subspecies (R. s. septentrionalis and the undescribed taxon R. s. ssp) are likely to represent full species, warranting full taxonomic descriptions. This work adds a growing number of studies showing the potential problems of relying solely on mitochondrial sequences, or a limited number of loci, to infer phylogenetic relationships among recently diverged taxa.
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•Multiple evidences were used to delimit species of Rhinolophus macrotis complex.•A new taxonomic treatment is proposed for the R. osgoodi.•Evolutionary processes were reconstructed ...following species delimitation.•Hybridization and introgression have contributed to the reticulate evolution.
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.
Located within the Phong Nha-Ke Bang National Park, Central Vietnam, Son Doong Cave is the world’s largest cave and has become one of the most famous sites for caving tourists and scientists ...worldwide. It contains highly diverse landscapes and ecosystems with special value in many natural aspects including biodiversity. Bat species are usually regarded as key and fascinating dwellers in cave ecosystems. We recently conducted a bat survey in Son Doong Cave in May 2022 for an initial understanding of the bat species inhabiting this special cave. Bats were captured using mist nets. Echolocation calls were recorded and analyzed using the PCTape system and Batman and Selena software, respectively. Results from the survey confirmed that Son Doong Cave is a home for at least six echolocating bat species of five genera and four families: Hipposideridae (Aselliscus stoliczkanus, Hipposideros scutinares), Rhinolophidae (Rhinolophus thomasi), Molossidae (Mops plicatus) and Vespertilionidae (Myotis pilosus and Myotis cf. muricola). Of these five species, H. scutinares and M. pilosus are listed as globally “vulnerable” by the IUCN Red List of Threatened Species. Among the six captured and recorded species from the Son Doong Cave, each species is clearly distinguishable from the others in terms of morphological features, echolocation call structure and frequencies.
Biodiversity surveys are essential for both academic research and conservation. Integrative approaches that combine morphological, genetic and acoustic aspects for species identification can provide ...reliable information in taxonomy and evolution. This is especially relevant for those groups with a high degree of cryptic diversity such as bats.
Here, we present the results from a field survey carried out in the Cuc Phuong National Park (CPNP) during 2019 as part of the VIETBIO project and from the examination of specimen collections preserved at the museums of CPNP and the Institute of Ecology and Biological Resources (IEBR). In addition, we include an annotated species list, based on this survey and a literature review. We here confirm that CPNP is home to at least 47 bat species belonging to 23 genera and seven families. We recorded ten of these bat species during our field survey. Obtained data in genetics (sequencing a fragment of the mitochondrial gene COI) supported the morphological identification of the recorded species for which we were able to produce these data. In addition, we include echolocation recordings obtained during our field training with the hope that they may contribute valuable insights to future work concerning the surveyed species. Results from the field survey represent a relevant contribution to biodiversity assessment efforts and, thus, support conservation and management efforts to maintain bat diversity in Vietnam.
The phylogenetic and taxonomic relationships among the Old World leaf-nosed bats (Hipposideridae) and the closely related horseshoe bats (Rhinolophidae) remain unresolved. In this study, we generated ...a novel approximately 10-kb molecular data set of 19 nuclear exon and intron gene fragments for 40 bat species to elucidate the phylogenetic relationships within the families Rhinolophidae and Hipposideridae. We estimated divergence times and explored potential reasons for any incongruent phylogenetic signal. We demonstrated the effects of outlier taxa and genes on phylogenetic reconstructions and compared the relative performance of intron and exon data to resolve phylogenetic relationships. Phylogenetic analyses produced a well-resolved phylogeny, supporting the familial status of Hipposideridae and demonstrated the paraphyly of the largest genus, Hipposideros. A fossil-calibrated timetree and biogeographical analyses estimated that Rhinolophidae and Hipposideridae diverged in Africa during the Eocene approximately 42 Ma. The phylogram, the timetree, and a unique retrotransposon insertion supported the elevation of the subtribe Rhinonycterina to family level and which is diagnosed herein. Comparative analysis of diversification rates showed that the speciose genera Rhinolophus and Hipposideros underwent diversification during the Mid-Miocene Climatic Optimum. The intron versus exon analyses demonstrated the improved nodal support provided by introns for our optimal tree, an important finding for large-scale phylogenomic studies, which typically rely on exon data alone. With the recent outbreak of Middle East respiratory syndrome, caused by a novel coronavirus, the study of these species is urgent as they are considered the natural reservoir for emergent severe acute respiratory syndrome (SARS)-like coronaviruses. It has been shown that host phylogeny is the primary factor that determines a virus's persistence, replicative ability, and can act as a predictor of new emerging disease. Therefore, this newly resolved phylogeny can be used to direct future assessments of viral diversity and to elucidate the origin and development of SARS-like coronaviruses in mammals.
AIM: The goals of our study were to assess the population history and genetic structure of the widespread bat Hipposideros armiger, and to evaluate the effect of palaeoclimatic changes and dispersal ...patterns on this species. LOCATION: South China, mainland Southeast Asia and the South Himalayas. METHODS: We amplified two mitochondrial DNA (mtDNA) regions (cyt b and D‐loop) and seven nuclear microsatellite loci (nSSRs) from 216 individuals of H. armiger. To examine the evolutionary history of this species, we constructed maximum likelihood and Bayesian phylogenetic trees based on the two mtDNA regions. From the mtDNA and/or nSSR data, we assessed population genetic structure using analysis of molecular variance (AMOVA) and median‐joining network and structure analyses. We also estimated demographic history and gene flow using a Bayesian skyline plot and the program IMa2. RESULTS: Phylogenetic and median‐joining network analyses revealed that H. armiger comprises two distinct mtDNA clades divided into seven subclades. The results of AMOVA suggested strong population genetic structure based on mtDNA, but weak structure based on nSSRs. structure analysis identified three population clusters and also showed weak genetic structure at the nuclear level. Demographic analyses revealed two population expansion events c. 0.62 Ma and c. 0.25 Ma. The basic phylogeographical structure of H. armiger was established by 0.24 Ma. IMa2 analysis demonstrated that substantial gene flow has occurred between different regions since then. Additionally, non‐significant population structure and significant gene flow were detected between Taiwan and Hainan island populations and those from mainland China. MAIN CONCLUSIONS: Our results suggest that divergence and population expansion of H. armiger occurred in association with Pleistocene climatic changes and that multiple refugia may have existed for this species. Post‐glacial male‐biased dispersal was likely to be the primary contributor to the contemporary genetic structure of H. armiger populations. Gene flow may have contributed greatly to the genetic structure of insular populations and populations from mainland China.
Bats are a major reservoir of zoonotic viruses, including coronaviruses. Since the emergence of SARS-CoV in 2002/2003 in Asia, important efforts have been made to describe the diversity of ...Coronaviridae circulating in bats worldwide, leading to the discovery of the precursors of epidemic and pandemic sarbecoviruses in horseshoe bats. We investigated the viral communities infecting horseshoe bats living in Northern Vietnam, and report here the first identification of sarbecoviruses in Rhinolophus thomasi and Rhinolophus siamensis bats. Phylogenetic characterization of seven strains of Vietnamese sarbecoviruses identified at least three clusters of viruses. Recombination and cross-species transmission between bats seemed to constitute major drivers of virus evolution. Vietnamese sarbecoviruses were mainly enteric, therefore constituting a risk of spillover for guano collectors or people visiting caves. To evaluate the zoonotic potential of these viruses, we analyzed in silico and in vitro the ability of their RBDs to bind to mammalian ACE2s and concluded that these viruses are likely restricted to their bat hosts. The workflow applied here to characterize the spillover potential of novel sarbecoviruses is of major interest for each time a new virus is discovered, in order to concentrate surveillance efforts on high-risk interfaces.
Eyndhovenia is one of the twelve genera of Spinturnicidae which are highly specialised parasites of bats. Previously known hosts of this genus comprised 17 species of Old World bats: Eptesicus ...serotinus, Hipposideros larvatus, Miniopterus schreibersi, Myotis blythi, M. emarginatus, Pipistrellus pipistrellus, P. gaisleri, Rhinolophus axillaris, R. blasii, R. clivosus, R. cornutus, R. euryale, R. ferrumequinum, R. hipposideros, R. megachyllus, R. mehelyi, R. rouxi. Within Asia, Eyndhovenia was only recorded from two countries, China and Thailand. Between 2018 and 2020, we conducted a series of bats surveys and recorded of this genus from intermediate horseshoe bat, Rhinolophus affinis, in Vietnam. The present study exhibits the new record in both parasitological and geographical aspects.
Rhinolophids (horseshoe bats) are a widespread and diverse family. Their high level of morphological convergence has made taxonomic identification and estimation of species diversity problematic. The ...Rhinolophus philippinensis group, which is characterized with huge ears and low echolocation frequency relative to body size, is a specific group among all the rhinolophid groups, but the phylogeny of this group is poorly understood. In this study, we performed integrated analyses of the morphology, acoustic and genetic data and constructed the first multilocus phylogeny for the philippinensis group using four mitochondrial genes, four autosomal introns and one Y‐linked intron in 95 specimens representing nine taxa. Phylogenies were constructed based on concatenated phylogenetic methods and a multilocus coalescence approach. The estimated phylogenies revealed the polyphyly of the philippinensis group. Except for R. philippinensis, all the other species in this group formed a monophyletic cluster, named herewith as “R. macrotis” species group. Phylogenies, genetic and phenotypic divergence, and species delimitation analyses supported the revised status of R. paradoxolophus as a subspecies of R. rex, R. cf. macrotis as a subspecies of R. macrotis, and R. huananus and R. cf. siamensis as junior synonyms of R. siamensis. Significant discordances were found between the mitochondrial and nuclear gene trees, suggesting incomplete lineage sorting or ancient introgression events within the philippinensis group. The macrotis group appeared to have undergone a rapid radiation approximately 2.57 million years ago during the early Pleistocene period due to palaeoclimatic oscillations. Reconstruction of the ancestral ranges suggested a wide distribution of the common ancestor for the philippinensis and macrotis groups.
Most of researches on wireless sensor network (WSN) are focused on how to reduce energy consumption to increase the network lifetime. There are few researches solving the problem of energy ...optimization ensuring delay constraint. Whereas, the delay is important factor for applications that require delay-sensitive data. Several works have been published to balance the energy consumption and delay. They achieved many different results but each proposal has certain limitations. Some proposals have high computational and messaging complexity. Some others have not found the optimal solution. In this study, we investigate in finding solution to improve the energy efficiency of sensor nodes satisfying end-to-end delay to transmit data from sensor nodes to sink in multi-hop WSNs. Based on Lagrange relaxation method, we propose an aggregate cost function between energy consumption and delay as well as an efficient method to find the optimal multiplier for that objective function. We provide two algorithms to find paths with least energy consumption while maintaining end-to-end delay requirement from any sensor node to sink. Besides analyzing the complexity and convergence of the algorithm, the simulation results also show that the proposed algorithm achieved good balance between energy consumption and delay compared with the previous proposals.
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