The role of DNA barcodes in understanding and conservation of mammal diversity in southeast Asia

Endemic species analysis: Foliar epidermal anatomical characters of Aster glehnii F. Schmidt (Asteraceae)

The classification and identification of Aster glehnii F. Schmidt are determined from its foliar epidermal anatomical features. Scanning electronic microscopy has been used to determine the foliar epidermal anatomical characteristics of the species in detail. This study compared the qualitative and quantitative characteristics of the leaf epidermis of A. glehnii for taxonomic identification to be used as a reference for future studies on the species. A. glehnii has smooth, thin cuticles, depressed anomocytic stomata dispersed randomly throughout the leaf surface, polygonal epidermal cells with straight to slightly curved anticlinal walls, and no trichomes. There are obvious veins containing thick-walled bundle sheath cells. The stomatal density is between 100 and 150 stomata per millimeter. The vein density ranges from five to 10 veins per millimeter, and the epidermal cells are 10 to 20 μm long and 5 to 10 μm in width. Understanding the connections between the different A. glehnii species and categorizing and identifying them depend heavily on these foliar epidermal structural features. Taxonomy and conservation are closely intertwined because the former serves as the basis for comprehending and safeguarding biodiversity. RESEARCH HIGHLIGHTS: Optical microscopy of the A. glehnii leaf epidermis for taxonomic identification SEM was used to identify and authenticate endemic species Microscopic identification of endemic species can assist in the conservation.

Barcoding Brazilian mammals to monitor biological diversity and threats: Trends, perspectives, and knowledge gaps

DNA barcoding and environmental DNA (eDNA) represent significant advances for biomonitoring the world's biodiversity and its threats. However, these methods are highly dependent on the presence of species sequences on molecular databases. Brazil is one of the world's largest and most biologically diverse countries. However, many knowledge gaps still exist for describing, identifying, and monitoring of mammalian biodiversity using molecular methods. We aimed to unravel the patterns of the presence of Brazilian mammal species on molecular databases to improve our understanding of how effectively it would be to monitor them using DNA barcoding and environmental DNA, and contribute to mammalian conservation. We foundt many gaps in molecular databases, with many taxa being poorly represented, particularly from Amazonia, the order Lagomorpha, and arboreal, gomivorous, near extinct, and illegally traded species. Moreover, our analyses revealed that species description year was the most important factor determining the probability of a species to being sequenced. Primates are the group with the highest number of species considered a priority for sequencing due to their high level of combined threats. We highlight where investments are needed to fill knowledge gaps and increase the representativity of species on molecular databases to enable a better monitoring ability of Brazilian mammals encompassing different traits using DNA barcoding and environmental DNA.

DNA barcoding of indigenous fowl of Manipur, Kaunayen (Gallus gallus domesticus)

The jungle fowl (Gallus gallus) is a tropical bird with important hereditary and phenotypical traits like disease resistance and resistance to harsh conditions and can often survive with scanty diet. However, as commercial chicken breeds replace them, their population is dwindling, which poses a significant threat to fowl genetic resources. There is minimal information on the variety of Indian poultry, mainly native chicken from Northeast India. As a result, the record of the fowl's genetic diversity is essential for its preservation and formulation of conservation strategies. The current study sought to identify indigenous chicken, Kaunayen (Gallus gallus domesticus), from Manipur using barcoding based on DNA sequences. A total of 5 CO1 DNA barcodes from several indigenous chickens were sequenced and compared to the previous data of diverse taxa of Phasianidae using the conventional methodology and were recognized as Gallus gallus. The Phasianid birds that were researched were accurately classified into their appropriate species. There is a minuscule genomic difference between G. gallus and G. varius (1.2%) and the highest between Arborophila rufipectus and Tympanuchus pallidicinctus (22.5%). The phylogenetic relationship established on the NJ tree revealed a coherent gathering of indigenous fowl with G. gallus and unique to all other species studied, showing their taxonomic classification. Nonetheless, the investigation offered a genetic identity tag for indigenous chicken for the first time. It will be a potential guide for identifying distinctive and genetically unique poultry sequences for later requirements.

Creating, curating and evaluating a mitogenomic reference database to improve regional species identification using environmental DNA

Species detection using eDNA is revolutionizing global capacity to monitor biodiversity. However, the lack of regional, vouchered, genomic sequence information-especially sequence information that includes intraspecific variation-creates a bottleneck for management agencies wanting to harness the complete power of eDNA to monitor taxa and implement eDNA analyses. eDNA studies depend upon regional databases of mitogenomic sequence information to evaluate the effectiveness of such data to detect and identify taxa. We created the Oregon Biodiversity Genome Project to create a database of complete, nearly error-free mitogenomic sequences for all of Oregon's fishes. We have successfully assembled the complete mitogenomes of 313 specimens of freshwater, anadromous and estuarine fishes representing 24 families, 55 genera and 129 species and lineages. Comparative analyses of these sequences illustrate that many regions of the mitogenome are taxonomically informative, that the short (~150 bp) mitochondrial 'barcode' regions typically used for eDNA assays do not consistently diagnose for species and that complete single or multiple genes of the mitogenome are preferable for identifying Oregon's fishes. This project provides a blueprint for other researchers to follow as they build regional databases, illustrates the taxonomic value and limits of complete mitogenomic sequences and offers clues as to how current eDNA assays and environmental genomics methods of the future can best leverage this information.

Solving the taxonomic identity of Hipposideros cineraceus sensu lato (Chiroptera: Hipposideridae) in the Thai-Malay Peninsula, with the description of a new species

A new species of small Hipposideros in the bicolor group is described based on specimens from Thailand and Malaysia. It can be distinguished from other small Hipposideros in Southeast Asia by a combination of external, craniodental, and bacular morphology, as well as echolocation call frequency. The new species has a distinct rounded swelling on the internarial septum of the noseleaf, with a forearm length of 35.3-42.6 mm, greatest skull length of 15.94-17.90 mm, and a call frequency of maximum energy of 132.3-144.0 kHz. Although clearly different in morphology, the new species forms a sister clade with H. kunzi and H. bicolor in the phylogenetic trees based on mitochondrial DNA. In addition, this study reports echolocation and genetic data, with a confirmed record of H. einnaythu from Thailand for the first time. The new species most closely resembles H. einnaythu. However, it differs in the details of the noseleaf and craniodental morphology, and it has a genetic distance of 9.6% and 10.4% based on mitochondrial COI and ND2, respectively. It is currently documented from five localities: two in peninsular Thailand, at Hala Forest in Yala Province, and Phru To Daeng Swamp Forest in Narathiwat Province, one from peninsular Malaysia at Krau Wildlife Reserve in Pahang, and another two in Sabah, Malaysian Borneo at Gunung Kinabalu, and near Madai Caves. However, it is likely that many previous records of "H. cineraceus" from Borneo refer to this species. Most records of the species are from lowland evergreen rainforest, though one record from Sabah was at 1800m. The roosting sites for this new species are currently unknown. Future research with a combination of data such as genetics, echolocation and morphology would be necessary to further determine the species geographic distribution in Southeast Asia.

First record of the flat-skulled woolly bat Kerivoula depressa and the Indochinese woolly bat K. dongduongana (Chiroptera, Vespertilionidae) in China

Recent studies have revealed that the Kerivoula depressa complex should be divided into two species, K. depressa distributed mainly in Myanmar, Vietnam, Laos and Cambodia, and K. dongduongana found only in the Annamite Mountains of Vietnam, Laos and Cambodia. In November 2018 and April 2019, 24 woolly bats were collected by two-band harp traps in Xishuangbanna, Yunnan, China. Based on morphological, morphometric, and phylogenetic (COI, Cytb, and RAG2 gene sequences) analyses, these bats were identified as K. depressa and K. dongduongana, representing two new species records for the country. Including the new records, six Kerivoula species have been recorded in China, namely K. depressa, K. dongduongana, K. furva, K. kachinensis, K. picta and K. titania. To facilitate their identification and biological research in the future, we have provided an up-to-date key to all Kerivoula species occurring in China.

Molecular and morphological survey of Lamiaceae species in converted landscapes in Sumatra

Molecular biodiversity surveys have been increasingly applied in hyperdiverse tropical regions as an efficient tool for rapid species assessment of partially undiscovered fauna and flora. This is done by overcoming shortfalls in knowledge or availability of reproductive structures during the sampling period, which often represents a bottleneck for accurate specimens' identification. DNA sequencing technology is intensifying species discovery, and in combination with morphological identification, has been filling gaps in taxonomic knowledge and facilitating species inventories of tropical ecosystems. This study aimed to apply morphological taxonomy and DNA barcoding to assess the occurrence of Lamiaceae species in converted land-use systems (old-growth forest, jungle rubber, rubber, and oil palm) in Sumatra, Indonesia. In this species inventory, we detected 89 specimens of Lamiaceae from 18 species distributed in seven subfamilies from the Lamiaceae group. One third of the species identified in this study lacked sequences in the reference database for at least one of the markers used (matK, rbcL, and ITS). The three loci species-tree recovered a total of 12 out of the 18 species as monophyletic lineages and can be employed as a suitable approach for molecular species assignment in Lamiaceae. However, for taxa with a low level of interspecific genetic distance in the barcode regions used in this study, such as Vitex gamosepala Griff. and V. vestita Wall. ex Walp., or Callicarpa pentandra Roxb. and C. candidans (Burm.f.) Hochr., the use of traditional taxonomy remains indispensable. A change in species composition and decline in abundance is associated with an increase in land-use intensification at the family level (i.e., Lamiaceae), and this tendency might be constant across other plant families. For this reason, the maintenance of forest genetic resources needs to be considered for sustainable agricultural production, especially in hyperdiverse tropical regions. Additionally, with this change in species composition, accurate species identification throughout molecular assignments will become more important for conservation planning.

Mapping global conservation priorities and habitat vulnerabilities for cave-dwelling bats in a changing world

Research and media attention is disproportionately focused on taxa and ecosystems perceived as charismatic, while other equally diverse systems such as caves and subterranean ecosystems are often neglected in biodiversity assessments and prioritisations. Highlighting the urgent need for protection, an especially large fraction of cave endemic species may be undescribed. Yet these more challenging systems are also vulnerable, with karsts for example losing a considerable proportion of their area each year. Bats are keystone to cave ecosystems making them potential surrogates to understand cave diversity patterns and identify conservation priorities. On a global scale, almost half (48 %) of known bat species use caves for parts of their life histories, with 32 % endemic to a single country, and 15 % currently threatened. We combined global analysis of cave bats from the IUCN spatial data with site-specific analysis of 1930 bat caves from 46 countries to develop global priorities for the conservation of the most vulnerable subterranean ecosystems. Globally, 28 % of caves showed high bat diversity and were highly threatened. The highest regional concentration of conservation priority caves was in the Palearctic and tropical regions (except the Afrotropical, which requires more intensive cave data sampling). Our results further highlight the importance of prioritising bat caves by incorporating locally collected data and optimising parameter selection (i.e., appropriate landscape features and threats). Finally, to protect and conserve these ecosystems it is crucial that we use frameworks such as this to identify priorities in species and habitat-level and map vulnerable underground habitats with the highest biodiversity and distinctiveness.

Taxonomic boundaries in Lesser Treeshrews (Scandentia, Tupaiidae: Tupaia minor )

The Lesser Treeshrew, Tupaia minor  Günther, 1876, is a small mammal from Southeast Asia with four currently recognized subspecies: T. m. minor from Borneo; T. m. malaccana from the Malay Peninsula; T. m. humeralis from Sumatra; and T. m. sincepis from Singkep Island and Lingga Island. A fifth subspecies, T. m. caedis, was previously synonymized with T. m. minor; it was thought to occur in northern Borneo and on the nearby islands of Banggi and Balambangan. These subspecies were originally differentiated based on pelage color, a plastic feature that has proven to be an unreliable indicator of taxonomic boundaries in treeshrews and other mammals. To explore infraspecific variation among T. minor populations across the Malay Peninsula, Borneo, Sumatra, and smaller islands, we conducted multivariate analyses of morphometric data collected from the hands and skulls of museum specimens. Principal component and discriminant function analyses reveal limited differentiation in manus and skull proportions among populations of T. minor from different islands. We find no morphometric support for the recognition of the four allopatric subspecies and no support for the recognition of T. m. caedis as a separate subspecies on Borneo.

The evolutionary history and ancestral biogeographic range estimation of old-world Rhinolophidae and Hipposideridae (Chiroptera)

BACKGROUND

Family Rhinolophidae (horseshoe bats), Hipposideridae (leaf-nosed bats) and Rhinonycteridae (trident bats) are exclusively distributed in the Old-World, and their biogeography reflects the complex historic geological events throughout the Cenozoic. Here we investigated the origin of these families and unravel the conflicting family origin theories using a high resolution tree covering taxa from each zoogeographic realm from Africa to Australia. Ancestral range estimations were performed using a probabilistic approach implemented in BioGeoBEARS with subset analysis per biogeographic range [Old-World as whole, Australia-Oriental-Oceania (AOO) and Afrotropical-Madagascar-Palearctic (AMP)].

RESULT

Our result supports an Oriental origin for Rhinolophidae, whereas Hipposideridae originated from the Oriental and African regions in concordance with fossil evidence of both families. The fossil evidence indicates that Hipposideridae has diversified across Eurasia and the Afro-Arabian region since the Middle Eocene. Meanwhile, Rhinonycteridae (the sister family of Hipposideridae) appears to have originated from the Africa region splitting from the common ancestor with Hipposideridae in Africa. Indomalaya is the center of origin of Rhinolophidae AOO lineages, and Indomalayan + Philippines appears to be center of origin of Hipposideridae AOO lineage indicating allopatric speciation and may have involved jump-dispersal (founder-event) speciation within AOO lineage. Wallacea and the Philippines may have been used as stepping stones for dispersal towards Oceania and Australia from the Oriental region. Multiple colonization events via different routes may have occurred in the Philippines (i.e., Palawan and Wallacea) since the Late Miocene. The colonization of Rhinolophidae towards Africa from Asia coincided with the estimated time of Tethys Ocean closure around the Oligocene to Miocene (around 27 Ma), allowing species to disperse via the Arabian Peninsula. Additionally, the number of potential cryptic species in Rhinolophidae in Southeast Asia may have increased since Plio-Pleistocene and late Miocene.

CONCLUSION

Overall, we conclude an Oriental origin for Rhinolophidae, and Oriental + African for Hipposideridae. The result demonstrates that complex historical events, in addition to species specific ecomorphology and specialization of ecological niches may shape current distributions.

How to Accurately Delineate Morphologically Conserved Taxa and Diagnose Their Phenotypic Disparities: Species Delimitation in Cryptic Rhinolophidae (Chiroptera)

Systematics and taxonomy are the backbone of all components of biology and ecology, yet cryptic species present a major challenge for accurate species identification. This is especially problematic as they represent a substantial portion of undiscovered biodiversity, and have implications for not only species conservation, but even assaying potential risk of zoonotic spillover. Here, we use integrative approaches to delineate potential cryptic species in horseshoe bats (Rhinolophidae), evaluate the phenotypic disparities between cryptic species, and identify key traits for their identification. We tested the use of multispecies coalescent models (MSC) using Bayesian Phylogenetic and Phylogeography (BPP) and found that BPP was useful in delineating potential cryptic species, and consistent with acoustic traits. Our results show that around 40% of Asian rhinolophid species are potentially cryptic and have not been formally described. In order to avoid potential misidentification and allow species to be accurately identified, we identified quantitative noseleaf sella and acoustic characters as the most informative traits in delineating between potential cryptic species in Rhinolophidae. This highlights the physical differences between cryptic species that are apparent in noseleaf traits which often only qualitatively described but rarely measured. Each part of the noseleaf including the sella, lateral lappets, and lancet furrows, play roles in focusing acoustic beams and thus, provide useful characteristics to identify cryptic Rhinolophus species. Finally, species delimitation for cryptic species cannot rely on genetic data alone, but such data should be complemented by other evidence, including phenotypic, acoustic data, and geographic distributions to ensure accurate species identification and delineation.

Range extension and species confirmation of Rhyneptesicus nasutus (Sind Serotine Bat) (Mammalia:Chiroptera) from Bajaur Agency, FATA, Pakistan

BACKGROUND

The lack of morphological differentiation among chiropteran species and cryptic speciation impedes species identification. DNA-based approaches help species identification and contribute to the discovery of additional species. Rhyneptesicus nasutus (Sind Serotine Bat) is a rare and poorly studied species in Pakistan.

METHODS

This study explores the range extension of Sind Bat within the territorial limits of Pakistan from Sind and Baluchistan to Federally Administered Areas of Pakistan. No molecular record exists for the species in Pakistan. In the present study, we for the first time confirm species identification of Rhyneptesicus nasutus from Pakistan using a genetic marker (cytochrome b) along with morphometric analysis. A neighbor-joining tree based on Kimura-2 parameters was created to infer phylogenetic relationships. We sequenced the cytochrome b gene segment and conducted a phylogenetic analysis with previously published data from other countries.

RESULTS

Sequences from Pakistan formed a clade with Iranian Rhyneptesicus nasutus specimens suggesting a common ancestry. Various morphometric parameters (mean values) were measured, including Head and Body length (44.3 mm), Tail length (43.4 mm), Hindfoot length (8.3 mm), Forearm length (35.7 mm), and Ear length 36 mm while 5th Metacarpal Length, 4th Metacarpal Length, and 3rd Metacarpal Lengths were 33.2 mm, 34.7 mm, and 35.3 mm. Approaches based on DNA barcoding reveal a high diversity of bat species in the study area.

CONCLUSION

The data will enable researchers to build an improved evolutionary framework of the Serotine Bats from this region and subsequently reconstruct a detailed evolutionary history of the genus. Further research is required to test other molecular markers to support the findings of the current study in Pakistan.

W, Bacus M, Labrador C, Numeron AM, Gamalo LE, Murao LA. The first complete mitochondrial genome sequence of Cynopterus brachyotis (Chiroptera, Pteropodidae) from the Philippines

The technical limitations of capillary sequencing in providing insights on phylogeny have been greatly aided in recent years by the implementation of next generation sequencing platforms which can generate whole mitochondrial genome (mitogenome) sequences. In this study, enriched mitochondrial DNA of Cynopterusbrachyotis from Mindanao, Philippines was sequenced using the Illumina MiSeq platform. A total of 653,967 clean paired-end reads was assembled using a MIRA-MITObim pipeline, resulting in a consensus mitogenome sequence length of 17,382 bases and a GC content of 41.48%, which is consistent with other published mitogenomes in fruit bats. The assembled C.brachyotis mitogenome was annotated using the MITOS online server and was able to resolve all mitochondrial genes, except for one transfer RNA gene (trnT) which may be further resolved by additional capillary sequencing of the region. Sequence analysis showed that the Philippine C.brachyotis is only 90%-91% homologous with other Cynopterus spp., based on its full mitogenome sequence. Phylogenetic analysis of fruit bat mitogenomes, deposited in online repositories, revealed that the Philippine C.brachyotis in this study has diverged from Asian Cynopterus, namely Cynopterusbrachyotis and Cynopterussphinx from other parts of Asia (100% bootstrap support) with the latter two forming a separate clade. This divergence at the species level was consistent with phylogentic inference using cytochrome oxidase 1 (CO1) and cytochrome B (cytb) gene markers. Our results strengthen the previously reported hypothesis that the Cynopteruscf.brachyotis in the Philippines is distinct from its Asian counterparts and should be, therefore, treated as a new species.

Discovery of Kerivoula kachinensis and a validity of K. titania (Chiroptera: Vespertilionidae) in China

In April 2019, 15 (10♂, 5♀) Kerivoula bats were collected by harp traps from Xishuangbanna, Yunnan Province, China. External and craniodental examination, multivariate statistical analyses and molecular phylogenetic inference (CoI, Cytb and Rag2 gene markers) indicated they are Kerivoula kachinensis and Kerivoula titania, respectively. Former represents a new chiropteran record from China, while the latter is a valid occurrence of K. titania in this region because recent study indicate a misidentification of “K. titania” in Guangdong, Guangxi and Hainan, China. All specimens are presently preserved at Key Laboratory of Conservation and Application in Biodiversity of South China in Guangzhou University, Guangzhou, China. Nowadays, four woolly bats occur in China including, Kerivoula furva, K. kachinensis, Kerivoula picta and K. titania, whilst there is a risk of underestimation the actual species diversity in China region when comparing those of neighboring region such as Vietnam. Supports for field survey need to be continued in future.

Bat selfies: photographic surveys of flying bats

The recent pandemic and other environmental concerns have resulted in restrictions on research and surveys involving capture and handling bats. While acoustic surveys have been widely used as an alternative survey method, in this study, we show how photographic surveys can offer an important contribution to study and survey bats. We outline approaches, using high speed flash and automated trip beams to obtain photos of flying bats of sufficient quality for reliable identification of species. We show, through a series of examples of setups and photographs, that photography is effective for surveying bats at a variety of sites, where bats roost, drink, and forage. We note, however, that photographic surveys cannot replace capture in all situations. In addition, although photographing bats is less invasive than capturing them, it can involve disturbance, so we stress the importance of minimizing the impact of such operations on bats.

Supplementary Information

The online version contains supplementary material available at 10.1007/s42991-022-00233-7.

Genetic variations and phylogenetic relationship of genus Uromastyx from Punjab Pakistan

During the present study, specimens were collected from selected sites of Cholistan desert and Kalabagh Game Reserve, Punjab province, Pakistan. Each captured specimen was tagged with voucher number and morphometric measurements were taken. The average snout to vent length was 172.559±1.40 mm and average weight was 92.1±1.30 g. The DNA of Uromastyx hardwickii was amplified and sequenced using 16S rRNA primer set. The obtained DNA sequence has shown reliable and clear species identification. After trimming ambiguous bases, the obtained 16S rRNA fragment was 520 bp while 16S rRNA fragments aligned with closely matched sequence from NCBI comprised of 510 bp. Closely matched sequences of genus Uromastyx were retrieved from NCBI in blast searches. Neighbour-joining tree of genus Uromastyx was constructed based on p-distance using MEGA X. The mean intraspecific variation was 0.095±0.01 while intraspecific variation was ranging from 0-1%. Similarly, interspecific variation of Uromastyx hardwikii with Saara asmussi, Uromastyx alfredschmidti, Uromastyx geyri, Uromastyx thomasi, Uromastyx alfredschmidti was 0-12%, 0-19%, 0-19%, 0-20%, 12-19% respectively. The newly produced DNA was submitted to NCBI and accession number was obtained (MW052563.1). Results of current study provided information about the molecular and morphological identification of Genus Uromastyx. In our recommendation, comprehensive molecular based identification of Pakistan's reptiles is required to report any new or subspecies from country.

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.

Molecular identification of genus Pipistrellus (Mammalia: Chiroptera) from Fata region, Pakistan

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 (MN 719478 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.

Molecular classification and comparative phylogeographic study of insectivorous bat species (Pipisitrellus coromandra) from Punjab, Pakistan

Molecular based identification of bat fauna in Pakistan has been relatively less explored. The current study was therefore planned to report for the first time the molecular classification of insectivorous bats (Pipistrellus coromandra) based on mitochondrion gene (COI) from Punjab, Pakistan. Specimens were collected from five different locations followed by DNA extraction with subsequent gene amplification and sequencing. All samples in the study had shown close identity matches with species (Pipistrellus coromandra) from India and (Pipistrellus tenuis) from Vietnam with percentage identity score of 96.11 and 95.58 respectively except one sequence which only revealed 86.78% identity match on Basic Local Alignment Search Tool (BLAST) and could only be assigned to genus level Pipistrellus sp. The results indicated negligible intra-population genetic distance among collected samples whereas the comparison with species from other countries had shown high intraspecific (P. coromandra) and interspecific (P. tenuis) mean genetic distances. The current study hence successfully proved the efficiency of COI gene as a molecular marker for species identification and in analyzing the patterns of genetic variation with species from other countries.

Not the Cryptic Species: Diversity of Hipposideros gentilis (Chiroptera: Hipposideridae) in Indochina

We present here the result of phylogenetic analysis for Vietnamese Hipposideros gentilis specimens using 7 nuclear genes and one mitochondrial gene. The complex distribution of divergent mitochondrial DNA lineages contradicts, at least in part, nuclear and morphological data. The most likely explanation for this discordance is the historical hybridization between ancestral populations of H. gentilis and H. rotalis/H. khaokhouayensis. Our data supports the species status of H. gentilis, while only partially corroborating its previously proposed subspecies delimitation. We suggest the lowland forest populations from south Vietnam may correspond to their own subspecies. At the same time, the close phylogenetic relationship and morphological similarity of mountain forms from south and central Vietnam to the north Vietnamese populations make doubtful the subspecies status of H. gentilis sinensis.

Southeast Asia as One of World’s Primary Sources of Biotic Recolonization Following Anthropocene Extinctions

The plight of Southeast Asia’s animals, plants and ecosystems in the face of unsustainable exploitation and habitat destruction has been illustrated in several recent studies, despite often falling outside the global discourse on global conservation priorities. Here, we collate biogeographic and phylogenetic information to argue that this beleaguered region is one of world’s primary macrorefugia, and possibly its best chance of regaining its natural biodiversity distribution patterns after the current Anthropocene upheaval. The region uniquely combines top diversity values in (a) ancient lineage diversity and (b) cosmopolitan lineage diversity, suggesting that it has acted in the past as a biodiversity museum and source of global colonization. This is at least partly due to the interplay between latitudinal diversity gradients and continental connectivity patterns. However, the peak values in South China/North Indochina for cosmopolitan tetrapods and their sister lineages suggest that a key feature is also the availability of diverse climatic conditions. In particular, the north-south orientation of the mountain ranges here has allowed for rapid recolonization within the region following past climatic changes, resulting in high survival values and overall exceptional relict lineage diversity. From this starting point, global colonization occurred on multiple occasions. It is hoped that, with urgent action, the region can once again fulfill this function.

Molecular and morphological revision of small Myotinae from the Himalayas shed new light on the poorly known genus Submyotodon (Chiroptera: Vespertilionidae)

The systematics status of the constituent species of the M. mystacinus morphogroup in the Himalayan region has long been marred by uncertainty. Lack of integrative studies combining morphological and genetic data from specimens recently collected in this region has hampered our understanding of cryptic variations in this complex taxonomic group. To address this issue, new material from the Himalayan region of India and Nepal was obtained and vouchered specimens in the holdings of various museums were also re-examined. As comparative material, a large series of relevant specimens from South and Southeast Asia were also included in this revision. Using a combination of multivariate analysis of craniodental characters and molecular reconstructions, we critically evaluated the systematic position of the small Myotinae in the Himalayas. We establish that M. nipalensis forms a very distinct lineage (which also includes the recently described M. annatessae) and refute previous taxonomic suggestions that it is related to M. davidii. Our study also conclusively proved the common occurrence of the poorly known genus Submyotodon in the Himalayan region (Afghanistan, Pakistan, India, Nepal and China) and evidenced species-level divergences within that genus. Submyotodon species share nyctalodont or semi-nyctalodont lower molar configuration with few other small and unrelated Myotinae from Asia suggesting that these unusual dental characters are homoplasious in this subfamily. We also noticed a very confused taxonomic situation associated with many DNA sequences of Asian Myotis deposited in public repositories and call for possibilities of better data curation.

Heterogeneous taxonomic resolution of cytochrome b gene identification of bats from Argentina: Implications for field studies

Bats are among the most diverse, widespread, and abundant mammals. In Argentina, 67 species of bats have been recorded, belonging to 5 families and 29 genera. These high levels of biodiversity are likely to complicate identification at fieldwork, especially between closely related species, where external morphology-based approaches are the only immediate means for a priori species assignment. The use of molecular markers can enhance species identification, and acquires particular relevance in capture-release studies. In this study, we discuss the extent of the use of the mitochondrial cytochrome b gene for species identification, comparing external morphology identification with a molecular phylogenetic classification based on this marker, under the light of current bat systematics. We analyzed 33 samples collected in an eco-epidemiological survey in the province of Santa Fe (Argentina). We further sequenced 27 museum vouchers to test the accuracy of cytochrome b -based phylogenies in taxonomic identification of bats occurring in the Pampean/Chacoan regions of Argentina. The cytochrome b gene was successfully amplified in all Molossid and Vespertilionid species except for Eptesicus, for which we designed a new reverse primer. The resulting Bayesian phylogeny was congruent with current systematics. Cytochrome b proved useful for species-level delimitation in non-conflicting genera (Eumops, Dasypterus, Molossops) and has infrageneric resolution in more complex lineages (Eptesicus, Myotis, Molossus). We discuss four sources of incongruence that may act separately or in combination: 1) molecular processes, 2) biology, 3) limitations in identification, and 4) errors in the current taxonomy. The present study confirms the general applicability of cytochrome b -based phylogenies in eco-epidemiological studies, but its resolution and reliability depend mainly, but not solely, on the level of genetic differentiation within each bat genus.

An Attempt to Reconstruct the Phylogeny of the Hipposideros Leaf-nosed Bats Based on Nuclear Gene Markers

The genus Hipposideros is one of the largest bat genera. The latest research on its Asian representatives has been done only with mitochondrial or sole nuclear markers. In the present study we compare the results of phylogenetic reconstructions, based on mitochondrial, on single nuclear genes and on multiple nuclear markers analyzed using the MRP algorithm (Matrix representation with parsimony) for representative species from all the main species groups. MRP analysis provides the most supported and well-interpretable phylogeny. Our data indicate monophyly of the large Asian leaf-nosed bats which suggests they are an independent taxon of the subgenus rank, as well as monophyly of several species complexes which are paraphyletic according to mtDNA analysis.

Niviventer confucianus sacer (Rodentia, Muridae) is a distinct species based on molecular, karyotyping, and morphological evidence

Niviventerconfucianussacer Thomas, 1908, which has been regarded as a subspecies of N.confucianus, was found to be a distinct species from N.confucianus based on molecular, karyotyping, and morphological characteristics in this study. Niviventerc.sacer was found to belong to a distinct phylogenetic clade in phylogenetic tree constructed using the mitochondrial gene Cytb, it clustered with N.bukit (Bonhote, 1903) from Vietnam and N.confucianus (Milne-Edwards, 1871) from Yunnan, but showed a distant relationship with N.confucianus from adjacent areas. The genetic distance between N.c.sacer and N.confucianus was more than 5.8%, reaching the level of interspecific differentiation. The species delimitation indicates that N.c.sacer is a monophyletic group. The karyotype of N.c.sacer (FN = 55, 8m+4st+32t+X(sm)Y(t)) differed from that of N.confucianus (FN = 59, 6m+4sm+2st+32t+X(sm)Y(t)). In terms of morphological features, the length of incisive foramen (LIF) and length of auditory bulla (LAB) of N.c.sacer is significantly larger than that of N.confucianus and N.bukit (P < 0.05) and the proportion of white tail tip to total tail length is significantly longer at N.c.sacer (≥ 1/3) than that at N.confucianus (≤ 1/3). Therefore, integrated analysis confirmed that N.c.sacer is a distinct species of genus Niviventer rather than a subspecies of N.confucianus or N.bukit, namely N.sacer, which is only distributed in Shandong.

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.

Twenty-six new species of Hoploscopa (Lepidoptera, Crambidae) from South-East Asia revealed by morphology and DNA barcoding

Hoploscopa Meyrick (Lepidoptera: Crambidae) is a fern-feeding genus found in montane areas of South-East Asia and Melanesia, eastwards up to the Samoan Islands. It includes sixteen described species, with at least 70 further undescribed species known from scientific collections. An iterative approach including morphological and molecular characters was used in order to explore the diversity of Hoploscopa. The hitherto described species are revised, and descriptions authored by T. Léger and M. Nuss are provided for an additional 26 new species: H.agtuuganonensissp. nov., H.albipunctasp. nov., H.albomaculatasp. nov., H.anacanthasp. nov., H.boletasp. nov., H.cynodontasp. nov., H.danaoensissp. nov., H.gombongisp. nov., H.gracilissp. nov., H.ignitamaculaesp. nov., H.isarogensissp. nov., H.jubatasp. nov., H.kelamasp. nov., H.kinabaluensissp. nov., H.mallyisp. nov., H.marijoweissaesp. nov., H.matheaesp. nov., H.niveofasciasp. nov., H.pangrangoensissp. nov., H.parvimaculasp. nov., H.pseudometacrossasp. nov., H.sepanggisp. nov., H.sumatrensissp. nov., H.titikasp. nov., H.tonsepisp. nov., H.ypsilonsp. nov. Using a protocol specific for the amplification of DNA from old museum specimens, we recovered 101 COI barcodes for all but one of the newly described species, with 76 being barcode compliant (>487 bp). Species delimitation analyses suggest cryptic diversity, with six cases reflecting allopatric divergence, and two further cases found in sympatry.

Integrated approaches to identifying cryptic bat species in areas of high endemism: The case of Rhinolophus andamanensis in the Andaman Islands

The diversity of bats worldwide includes large numbers of cryptic species, partly because divergence in acoustic traits such as echolocation calls are under stronger selection than differences in visual appearance in these nocturnal mammals. Island faunas often contain disproportionate numbers of endemic species, and hence we might expect cryptic, endemic species to be discovered relatively frequently in bats inhabiting islands. Species are best defined when multiple lines of evidence supports their diagnosis. Here we use morphometric, acoustic, and molecular phylogenetic data to show that a horseshoe bat in the Andaman Islands is distinct in all three aspects, supporting its status as a distinct species. We recommend investigation into possible new and endemic bat species on islands by using integrated approaches that provide independent lines of evidence for taxonomic distinctiveness. We provide a formal redescription of the taxon newly raised to species level, Rhinolophus andamanensis Dobson, 1872.

Research trends on bats in China: A twenty-first century review

In this century, China has sustained unparalleled economic development, leading to exponentially growing investments in scientific research. Yet, the demand for research-funding is large and tracing the current knowledge is a key step to define priority research topics. In this same span, studies on bats in China have uncovered an overlooked diversity and revealed novelties in bats’ evolutionary history and life-history aspects. All this 21st-century knowledge, however, is scattered and a large part is concealed from most of the international scientific community in Mandarin-language articles. Here, we summarize the post-millennium (2000–2017) research on bats in China and point out trends and future directions based on neglected topics, groups, and regions. In addition, we provide an up-to-date list of bat species in China. We retrieved 594 publications related to bats in China, nearly half were written in Mandarin. At least 147 bat species are present in China, which places it among the most bat-rich countries in the world. There was a significant positive trend on the number of publications, from 12.5 annual average in 2000–2005 to 46.5 in recent years, reflecting the Chinese economic-scientific development in this century. We found marked taxonomic and spatial biases. Half of the studies in this century focused on Rhinolophus, Myotis, and Hipposideros, and the southern and eastern provinces were the most studied. Systematic/taxonomy and Ecology were the predominant topics post-millennium, whereas only 10 articles have clear conservation-driven goals. Our review shows that the majority of studies were focused on the least concern, cave-dweller species, and on bat-rich provinces. Future projects should address the effects of human-modified landscapes on bat community to define proper conservation actions. We discuss some priority actions and projects that will help to enhance bat protection in China.

Mitochondrial DNA identified bat species in northeast India: electrocution mortality and biodiversity loss

Northeast India with two biodiversity hotspots is recognized as a biodiversity-rich region. However, several extant animals including chiropterans are currently at jeopardy due to habitat loss, electrocution mortality, and other anthropogenic threats. This study examines the efficacy of mitochondrial Cytochrome b (mtCytb) sequences for species-level identification of five electrocuted bat specimens from Manipur state. The similarity search results in the global database, Kimura 2 parameter (K2P) genetic distances, and neighbor-joining (NJ) tree identified all bat specimens into two species, Cynopterus sphinx and Megaerops niphanae. The detection of M. niphanae is the first record of this mammal from the state. In comparison with other Pteropodidae species, the genetic distances clearly discriminate both C. sphinx (7.9–30.2%) and M. niphanae (12.2–25.7%). In addition, the combined tree analysis of present and earlier genetic information of C. sphinx suggested the presence of cryptic lineages and sympatric population in India. This similar approach with more sampling from a wide distribution area could assist the future genetics research on chiropterans and their precise conservation.

Genetic status of indigenous poultry (red jungle fowl) from India

The global biodiversity of domesticated red jungle fowl (Gallus gallus) is gradually eroding by replacement with commercial poultry breeds and results loss of valuable genetic and physical traits like resistance to disease, extreme environment, etc. posing a threat to the poultry genetic resources. Very fewer reports exist on Indian poultry diversity, especially native chicken of India. Therefore, species identification and inventorying of the poultry genetic resource is indispensable. Thus, the present study aimed to characterize indigenous chicken from bio-diversity hotspot of Sunderban and Northeast India using DNA sequence based barcoding approach. A total of 15 CO1 (Cytochrome c Oxidase-I) DNA barcode of different indigenous chicken were newly sequenced along with 6 previously published sequences from our laboratory and compared with the available data of distinctive genera of Phasianidae as per the standard protocol and are identified as Gallus gallus. About 98.96% of the Phasianid birds were successfully delimitated into the respective species except for 12 congeneric pairs whose minimum interspecific K2P (Kimura 2-parameter) distance overlaps with the maximum intraspecific distance (3.9%). The least genetic divergence is observed between G. gallus and G. varius (0.013%) and highest between G. gallus and G. lafayettei (0.059%). The NJ tree showed a cohesive clustering of indigenous chicken with G. gallus and distinct with respect to all the different species under study, thereby revealing their taxonomic position except for few G. sonneratti that showed mixed clustering with G. gallus. This may be due to the genetic introgression between the species. Nevertheless, the study for the first time provided the molecular identification tag of indigenous poultry from biodiversity hotspot of East and Northeast India and will remain as a potential guide to recognize inimitable and valuable poultry genetic resources for future needs.

Porous barriers? Assessment of gene flow within and among sympatric long-eared bat species

Species are the basic units for measuring biodiversity and for comprehending biological interactions. Yet, their delineation is often contentious, especially in groups that are both diverse and phenotypically conservative. Three cryptic species of long-eared bats, Plecotus auritus, P. austriacus, and P. macrobullaris, co-occur over extensive areas of Western Europe. The latter is a fairly recent discovery, questioning the overall diversity of the entire Plecotus complex. Yet, high morphological and acoustic similarities compromise the reliable identification of long-eared bats in the field. We postulate that such extensive phenotypic overlap, along with the recurrent observation of morphologically intermediate individuals, may hide rampant interspecific hybridization. Based on a geographic sampling centered on areas of sympatry in the Alps and Corsica, we assessed the level of reproductive isolation of these three Plecotus species with mitochondrial and nuclear markers, looking at both inter- and intraspecific genetic population structuring. No sign of hybridization was detected between these three species that appear well separated biologically. Genetic structuring of populations, however, reflected different species-specific responses to environmental connectivity, that is, to the presence of orographic or sea barriers. While the Alpine range and the Ligurian Sea coincided with sharp genetic discontinuities in P. macrobullaris and P. austriacus, the more ubiquitous P. auritus showed no significant population structuration. There were clear phylogeographic discrepancies between microsatellite and mitochondrial markers at the intraspecific level, however, which challenges the reliance on simple barcoding approaches for the delineation of sound conservation units.

Extraction of DNA from micro-tissue for bat species identification

Bat populations are declining worldwide. Accurate identification is essential to promote species' conservation. However, minimal morphological differences and a high rate of cryptic species make identification difficult, unless voucher specimens are kept, a controversial issue today. The objective of this work was to standardize a method of extracting non-lethal DNA using bats' uropatagium micro-tissue, aiming the molecular identification of species that occur in the region of Maringá PR. The method standardized was efficient, and does not cause serious damage to bats. For future field studies, collection of micro-tissue and morphometry of the specimens will be sufficient for accurate identification.