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How insect communities are assembled in nature remains largely unknown. In particular, whether habitat filtering or competition serves as the main mechanism in forming insect communities is rarely subject to an in-depth investigation. One bottleneck lies in the difficulty of species identification when dealing with a large number of diverse insects. However, high-throughput sequencing technology coupled with classic DNA barcoding offers a great opportunity to infer community assembly for this speciose group. In this study, using 13,909 full-length barcodes obtained by Sanger sequencing or the full-length metabarcoding method (SOAPBarcode), we showed that competition was the main assembly mechanism for the moth communities in the younger Taihang Mountain, while habitat filtering for those in the old Yanshan Mountain. The two sequencing methods showed highly consistent results with regards to both diversity composition and community assembly mechanism. Significant phylogenetic signals and structure suggested that the focal moth communities were the result of the non-neutral assembly process, which was further confirmed by results of neutral assembly test that accounted for immigration and speciation rates. Our study showed that the full-length metabarcoding method can facilitate community assembly inferences, even for speciose taxonomic groups.

Interactions between plants and insects are among the most important life functions for all organism at a particular natural community. Usually a large number of samples are required to identify insect diets in food web studies. Previously, Sanger sequencing and next generation sequencing (NGS) with short DNA barcodes were used, resulting in low species-level identification; meanwhile the costs of Sanger sequencing are expensive for metabarcoding together with more samples. Here, we present a fast and effective sequencing strategy to identify larvae of Lepidoptera and their diets at the same time without increasing the cost on Illumina platform in a single HiSeq run, with long-multiplex-metabarcoding (COI for insects, rbcL, matK, ITS and trnL for plants) obtained by Trinity assembly (SHMMT). Meanwhile, Sanger sequencing (for single individuals) and NGS (for polyphagous) were used to verify the reliability of the SHMMT approach. Furthermore, we show that SHMMT approach is fast and reliable, with most high-quality sequences of five DNA barcodes of 63 larvae individuals (54 species) recovered (full length of 100% of the COI gene and 98.3% of plant DNA barcodes) using Trinity assembly (up-sized to 1015 bp). For larvae diets identification, 95% are reliable; the other 5% failed because their guts were empty. The diets identified by SHMMT approach are 100% consistent with the host plants that the larvae were feeding on during our collection. Our study demonstrates that SHMMT approach is reliable and cost-effective for insect-plants network studies. This will facilitate insect-host plant studies that generally contain a huge number of samples.

Urbanization has resulted in the loss of natural habitat for many bat species, often placing bats in close proximity to humans. Bats are generally perceived as agricultural and medical pest...

The higher‐level phylogeny of Pentatomomorpha, the second largest infraorder of true bugs (Hemiptera: Heteroptera), which includes many important agriculture and forestry pests, has been debated for decades. To investigate the phylogeny and evolutionary history of Pentatomomorpha, we assembled new mitochondrial genomes for 46 species through next‐generation sequencing of pooled genomic DNA. Based on a much broader taxon sampling than available previously, Bayesian analyses using a site‐heterogeneous mixture model (CAT+GTR) resolved the higher‐level phylogeny of Pentatomomorpha as (Aradoidea + (Pentatomoidea + (Coreoidea + (Lygaeoidea + Pyrrhocoroidea)))). There was a transition from trnT/trnP to trnP/trnT in the common ancestor of Pyrrhocoroidea, which indicates that this gene rearrangement could be an autapomorphy for Pyrrhocoroidea. Divergence time analyses estimated that Pentatomomorpha originated c. 242 Ma in the Middle Triassic, and most of the recognized superfamilies originated during the Middle Jurassic to Early Cretaceous. The diversification of families within Pentatomomorpha largely coincided with the radiation of angiosperms during the Early Cretaceous.

After escaping from the burning East Indiaman Fame, but losing all of his possessions, Sir Stamford Raffles, the Lieutenant-Governor of Bencoolen, hastily re-collected as many natural history specimens and drawings as he could before leaving Sumatra in April 1824. On his return to England Raffles was elected a Fellow of the Linnean Society and, with Lord Edward Smith Stanley and others, founded the Zoological Society of London. In 1825 Raffles gave 21 Sumatran birds to Stanley. Upon his death in 1851, Stanley (then 13th Earl of Derby) bequeathed his collection to the people of Liverpool, founding what is now the World Museum, National Museums Liverpool. Here I record these birds, 11 of which are still extant in the collection, including links to: the names and types from Raffles' (1822) ‘descriptive catalogue' of a zoological collection from Sumatra; Raffles' post-Fame zoological drawings; and Nicholas Aylward Vigors' catalogue of Raffles' specimens in the Zoological Society Museum, published in Lady Sophia Raffles’ memoir in 1830.

For residents of East-Southeast Asia’s megacities, interactions with “nature” may be largely limited to interactions taking place in urban parks. Urban parks provide refuges for ecologically-important biodiversity, such as insect pollinators. While residents may be unlikely to notice small insects, butterflies are more likely to be noticed and to provide positive human-“nature” interactions. Engaging residents and city planners in promoting habitat for butterflies is valid conservation practice and has well-understood educational and well-being benefits. Surveying and monitoring is an essential activity to corroborate, improve and communicate the outcomes of conservation practices amongst city governments, scientists and other stakeholders. Here we present the data from a survey of butterflies in urban parks in the megacity of the Bangkok Metropolitan Region as part of the "Urban biodiversity and human well-being in East-Southeast Asia's megacities" project organised by the "Urban Butterflies in Asia Research Network". We recorded 51 species of butterflies from ten urban parks in the Bangkok Metropolitan Region. This was more than double the 25 species reported in Bangkok's City Biodiversity Index application. However, this was lower than that recorded in other megacities in Southeast Asia, such as Kuala Lumpur at 60 species. Most of the butterflies recorded were common and widespread species. DNA barcodes are provided for most of the butterflies sampled.

The study assessed a decade long changes of the coral community structure in the Palk Bay region using multivariate analysis based on observed coral life-forms and its diversity between the years, 2002 and 2018. A total of 11 study sites were selected from Rameswaram Island to Mandapam coast. Live coral cover was found to be 27% (21% non-Acropora and 6% Acropora corals) during the study period 2002–2005. Principal component analysis (PCA) showed that there was a significant variability (PC1: 39.5% variance) in coral cover between the study site, Bison House and the rest of the study sites. In the study of 2014–2018, live coral cover observed was 17% and this included 11% non-Acropora and 6% Acropora corals. PCA showed that the contribution of live coral cover gradually reduced towards the northern part of Rameswaram Island. Metric multi-dimensional Scaling (MDS) showed that there were four clusters formed between the sites with 80% similarity as observed based on the life-form categories. There were three major clusters with 70% similarity observed based on coral diversity. The highest diversity index (Shannon-wiener) was observed at Olaikudah and Villunditheertham as 1.906 and 1.864 respectively. As of 2014–2018, the live coral status showed 37% less than that found during 2002–2005 study period. Variation of reef flat composition was studied using Depth-Invariant Index for the study period 2002–2005. This study has helped to understand the longitudinal gradient of incidence, temporal variations, and distribution pattern of coral reef community categories in the Palk Bay region.

Gene rearrangements in the mitochondrial genome (mt genome) are common in certain insect groups and can be an informative character for phylogenetic reconstruction. However, knowledge of the mechanism and biases of gene rearrangement in insect mt genomes is still limited. With an accelerated rate of gene rearrangements, Hymenoptera is an important group for mt genome rearrangements diversity and for understanding the gene rearrangement evolution in mt genomes. Here, we sequenced the complete mt genome of Aphidius gifuensis and analyzed the evolution of tRNA gene rearrangements in the mt genomes of ichneumonoid wasps. Two control regions were detected in A. gifuensis and most of the tRNA rearrangement events occurred around these control regions. tRNA gene rearrangements occurred in almost all of the sequenced mt genomes of Ichneumonoidea and the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was the main hot spot of gene rearrangement. Mapped over the backbone phylogeny of Ichneumonoidea, we found that the inversion and translocation of both trnI and trnM is likely a synapomorphic rearrangement in Braconidae. Our study also demonstrated that the gene block CR-trnI-trnQ-trnM-ND2-trnW-trnC-trnY was important for inferring the gene rearrangement dynamics in Ichneumonoidea.

Arthropod communities in the tropics are increasingly impacted by rapid changes in land use. Because species showing distinct seasonal patterns of activity are thought to be at higher risk of climate-related extirpation, global warming is generally considered a lower threat to arthropod biodiversity in the tropics than in temperate regions. To examine changes associated with land use and weather variables in tropical arthropod communities, we deployed Malaise traps at three major anthropogenic forests (secondary reserve forest, oil palm forest, and urban ornamental forest (UOF)) in Peninsular Malaysia and collected arthropods continuously for 12 months. We used metabarcoding protocols to characterize the diversity within weekly samples. We found that changes in the composition of arthropod communities were significantly associated with maximum temperature in all the three forests, but shifts were reversed in the UOF compared with the other forests. This suggests arthropods in forests in Peninsular Malaysia face a double threat: community shifts and biodiversity loss due to exploitation and disturbance of forests which consequently put species at further risk related to global warming. We highlight the positive feedback mechanism of land use and temperature, which pose threats to the arthropod communities and further implicates ecosystem functioning and human well-being. Consequently, conservation and mitigation plans are urgently needed.

Mitochondrial phylogenomics is often controversial, in particular for inferring deep relationships. The recent rapid increase of mitochondrial genome data provides opportunities for better phylogenetic estimates and assessment of potential biases resulting from heterogeneity in nucleotide composition and mutation rates. Here, we gathered 76 mitochondrial genome sequences for Heteroptera representing all seven infraorders, including 17 newly sequenced mitochondrial genomes. We found strong heterogeneity in base composition and contrasting evolutionary rates among heteropteran mitochondrial genomes, which affected analyses with various datasets and partitioning schemes under site-homogeneous models and produced false groupings of unrelated taxa exhibiting similar base composition and accelerated evolutionary rates. Bayesian analyses using a site-heterogeneous mixture CAT+GTR model showed high congruence of topologies with the currently accepted phylogeny of Heteroptera. The results confirm the monophyly of the six infraorders within Heteroptera, except for Cimicomorpha which was recovered as two paraphyletic clades. The monophyly of Terheteroptera (Cimicomorpha and Pentatomomorpha) and Panheteroptera (Nepomorpha, Leptopodomorpha and Terheteroptera) was recovered demonstrating a significant improvement over previous studies using mitochondrial genome data. Our study shows the power of the site-heterogeneous mixture models for resolving phylogenetic relationships with Heteroptera and provides one more case showing that model adequacy is critical for accurate tree reconstruction in mitochondrial phylogenomics.

The expansion of cities and agricultural plantations have unpredictable impacts on biodiversity and ecosystem services. Yet some species are capable of tolerating anthropogenic impacts and continue to provide ecological services in highly disturbed landscapes. The objective of this study was to use DNA barcoding to identify digested plant materials and seeds in the faeces of frugivorous bats (Cynopterus brachyotis) and investigate whether (1) C. brachyotis in urban and agricultural areas exploit cultivated and exotic plants as a novel food resource and as a consequence, potentially facilitate the invasion of cultivated and exotic plants, or whether (2) C. brachyotis exploit native plants and as a consequence, potentially promote forest regeneration. A native species, Ficus fistulosa, was the most frequently detected plant and the seeds were found in bat faeces from all sampling sites suggesting the potential of fruit bats in dispersing seeds. However, we also detected several exotic plants in the faeces of C. brachyotis which suggests that the fruit bats exploit novel food resources at all sites. We recorded a diverse diet of C. brachyotis at an oil palm plantation which indicated that the fruit bats are not predominantly feeding on oil palm fruits. By using DNA barcoding, we detected plants that have not been reported in previous studies of the diet of C. brachyotis, although we could not identify which part of the plant was being consumed by the fruit bats. Given the varied diet of C. brachyotis, the potential of this bat to adapt to changing landscapes is high and they are likely dispersing seeds of native pioneer plants (Ficus).

The Sharm Obhur reefs have predominantly been populated by soft corals. Notably, the highest soft coral percentages were observed in the central region of the creek at Site 9 and Site 6, where anthropogenic activities are higher. Among the scleractinian corals, more non-acroporid corals such as Porites and Goniastrea were found at all study sites and were commonly observed in the creek entrance area. More acroporid corals were found at Site 7. The sedimentation rate of Sharm Obhur strongly influences the reef ecosystem. Site 9 continuously receives murky water from stormwater drainage channels and has the highest sedimentation rate in the creek, which kills most of the corals in the vicinity. Similarly, the dead end of Sharm Obhur (Site 8) also receives drainage water from the Wadi Al Kura channel, which makes this the second highest sedimentation zone of the creek. Although anthropogenic disturbances are higher in the creek, the diversity of the scleractinian corals is found to be remarkable. In this pilot study, 13 families, 34 genera and 66 species of scleractinian corals were identified.

BackgroundPine moths,Dendrolimusspp. (Lasiocampidae), are serious economic pests of conifer forests. Six closely related species (Dendrolimus punctatus,D. tabulaeformis,D. spectabilis,D. superans,D. houi, andD. kikuchii) occur in China and cause serious damage to coniferophyte. The complete mito genomes ofDendrolimusgenus are significant to resolve the phylogenetic relationship and provide theoretical support in pest control.MethodsThe complete mitogenomes of three species (D. superans,D. houi, andD. kikuchii) were sequenced based on PCR-amplified with universal primers, which were used to amplify initial fragments. Phylogenetic analyses were carried out with 78 complete mitogenomes of lepidopteran species from 10 superfamilies.ResultsThe complete mitochondrial genomes of these three species were 15,417, 15,381, and 15,377 bp in length, separately. The phylogenetic analyses produced consistent results for sixDendrolimusspecies based on complete mitogenomes, two major clades were formed, one containingD. spectabilisclustered withD. punctatus+D. tabulaeformis, andD. superansas the sister group to this three-taxon clade, the other containingD. kikuchiiandD. houi. Comparative analyses of the congeneric mitochondrial genomes were performed, which showed that non-coding regions were more variable than the A+T rich region. The mitochondrial nucleotide diversity was more variable when compared within than among genus, and the concatenated tRNA region was the most conserved and the nd6 genes was the most variable.

Pediculosis capitis caused by Pediculus humanus capitis (De Geer) is endemic all over the world, and children are mostly affected, particularly those living in overcrowded institutions. Several studies have shown that P. h. capitis carried human pathogenic bacteria, suggesting the potential role of head lice in the transmission of pathogens to humans. In this study, we determined the genetic diversity of head lice collected from welfare homes sheltering underprivileged children by using DNA barcoding and demonstrated the presence of Acinetobacter spp., Serratia marcescens, and Staphylococcus aureus in head lice, which have never been investigated before in Malaysia. Cox1 DNA barcoding identified the head lice, P. h. capitis collected from welfare homes across two geographical areas of Peninsular Malaysia as belonging to clades A, B, and D. Acinetobacter bacteria: Acinetobacter guillouiae, Acinetobacter junii, Acinetobacter baumannii, and Acinetobacter nosocomialis were detected in head lice belonging to clades A and also D. In addition, DNA from S. marcescens and S. aureus were also detected in both clades A and D. To our knowledge, this is the first report on the genetic diversity of head lice in Malaysia through DNA barcoding, as well as the first to provide molecular evidence on the type of bacteria occurring in head lice in Malaysia. It is anticipated that the DNA barcoding technique used in this study will be able to provide rapid and accurate identification of arthropods, in particular, medically important ectoparasites.

The capital of China, Beijing, has a history of more than 800 years of urbanization, representing a unique site for studies of urban ecology. Urbanization can severely impact butterfly communities, yet there have been no reports of the species richness and distribution of butterflies in urban parks in Beijing. Here, we conducted the first butterfly survey in ten urban parks in Beijing and estimated butterfly species richness. Subsequently, we examined the distribution pattern of butterfly species and analyzed correlations between butterfly species richness with park variables (age, area and distance to city center), and richness of other bioindicator groups (birds and plants). We collected 587 individual butterflies belonging to 31 species from five families; 74% of the species were considered cosmopolitan. The highest butterfly species richness and abundance was recorded at parks located at the edge of city and species richness was significantly positively correlated with distance from city center (p p > 0.05). Our study provides the first data of butterfly species in urban Beijing, and serves as a baseline for further surveys and conservation efforts.

Freshwater mussels (Bivalvia, Unionida) fulfil important ecosystem functions and are one of the most threatened freshwater taxa globally. Knowledge of freshwater mussel diversity, distribution and ecology in Peninsular Malaysia is extremely poor, and the conservation status of half of the species presumed to occur in the region has yet to be assessed. We conducted the first comprehensive assessment of Peninsular Malaysia's freshwater mussels based on species presence/absence and environmental data collected from 155 sites spanning all major river catchments and diverse habitat types. Through an integrative morphological-molecular approach we recognised nine native and one widespread non-native species, i.e. Sinanodonta woodiana. Two species, i.e. Pilsbryoconcha compressa and Pseudodon cambodjensis, had not been previously recorded from Malaysia, which is likely a result of morphological misidentifications of historical records. Due to their restriction to single river catchments and declining distributions, Hyriopsis bialata, possibly endemic to Peninsular Malaysia, Ensidens ingallsianus, possibly already extinct in the peninsula, and Rectidens sumatrensis, particularly require conservation attention. Equally, the Pahang, the Perak and the north-western river catchments are of particular conservation value due to the presence of a globally unique freshwater mussel fauna. Statistical relationships of 15 water quality parameters and mussel presence/absence identified acidification and nutrient pollution (eutrophication) as the most important anthropogenic factors threatening freshwater mussel diversity in Peninsular Malaysia. These factors can be linked to atmospheric pollution, deforestation, oil-palm plantations and a lack of functioning waste water treatment, and could be mitigated by establishing riparian buffers and improving waste water treatment for rivers running through agricultural and residential land., This project was funded by grants of the Mohamed bin Zayed Species Conservation Fund (Project 152510591) to A.Z., the Conchologists of America (2015) to P.Y.N. and the Kenyir Research Institute, University Malaysia Terengganu to S.W. A.Z. is supported by a Postdoctoral Fellowship from the University of Nottingham Malaysia Campus., info:eu-repo/semantics/publishedVersion

Certain species of Phlebotomine sandflies (Diptera: Psychodidae) are vectors of the protozoa which causes leishmaniasis. Sandflies are found breeding in enclosed places like caves. Thailand is a popular tourist destination, including for ecotourism activities like caving, which increases the risk of contact between tourists and sandflies. Surveillance of sandflies is important for monitoring this risk but identification of species based on morphology is challenged by phenotypic plasticity and cryptic diversity. DNA barcodes have been used for the identification of sandflies in Thailand. We collected sandflies using CDC light trap from four tourist caves in Northern Thailand. Female sandflies were provisionally sorted into 13 morphospecies and 19 unidentified specimens. DNA was extracted from the thorax and legs of sandflies and the DNA barcode region of cytochrome c oxidase I mtDNA amplified and sequenced. The specimens were sorted into 22 molecular operational taxonomic units (MOTU) based on the 145 DNA barcodes, which is significantly more than the morphospecies. Several of the taxa thought to be present in multiple caves, based on morphospecies sorting, split into cave-specific MOTU which likely represent cryptic species. Several MOTU reported in an earlier study from Wihan Cave, Thailand, were also found in these caves. This supports the use of DNA barcodes to investigate species diversity of sandflies and their useful role in surveillance of sandflies in Thailand.

Adamowicz, Sarah J. et al., The two special issues—Barcodes to Biomes—mark the one-year anniversary of the 6th International Barcode of Life Conference held in Guelph, Canada. The 6th Conference brought together 601 delegates from 51 nations. The diversity of talks and poster presentations revealed that the global DNA barcoding community has expanded from its original focus on building libraries of reference sequences to a more diversified community, presenting research on themes ranging from systematics to food web ecology to wildlife forensics. Based on a comparison with an earlier conference, marked trends were observed in the increasing breadth of topics and in the pronounced rise of contributions employing DNA barcoding for diverse socio-economically important applications, including pest management, invasive species detection, and monitoring of environmental health (Adamowicz 2015a, 2015b). One year ago, Genome published a special open-access issue containing the abstracts from the 6th Conference (Adamowicz 2015b); that compilation highlighted the breadth of research topics and leading-edge research directions. The current open-access special issues feature 24 full articles. Part 1 includes two reviews that expand upon conference presentations and themes and 10 additional research articles associated with conference presentations, four of which are first authored by winners of a postdoctoral or graduate student prize at the 6th Conference (Beet et al. 2016; Mark et al. 2016; Saitoh et al. 2016; Sing et al. 2016). Part 2 includes 12 additional articles—three reviews, eight research articles, and one opinion piece—that cover topics ranging from a review of the field of fungal DNA barcoding (Xu 2016) to applications of DNA barcoding for biosecurity (Hodgetts et al. 2016) to multiple novel methods of species detection (discussed below). A large virtual special issue to be published online in 2017 will collate all conference-associated papers published across multiple issues of Genome. These special issues of Genome complement a special collection of 16 articles in Philosophical Transactions of the Royal Society B (Hebert et al. 2016). Together, these issues showcase the progress that has been made in applying DNA barcoding in diverse ways and outline exciting future prospects for discovery.

Over the past 50 years, Tropical East Asia has lost more biodiversity than any tropical region. Tropical East Asia is a megadiverse region with an acute taxonomic impediment. DNA barcodes are short standardized DNA sequences used for taxonomic purposes and have the potential to lessen the challenges of biodiversity inventory and assessments in regions where they are most needed. We reviewed DNA barcoding efforts in Tropical East Asia relative to other tropical regions. We suggest DNA barcodes (or metabarcodes from next-generation sequencers) may be especially useful for characterizing and connecting species-level biodiversity units in inventories encompassing taxa lacking formal description (particularly arthropods) and in large-scale, minimal-impact approaches to vertebrate monitoring and population assessments through secondary sources of DNA (invertebrate derived DNA and environmental DNA). We suggest interest and capacity for DNA barcoding are slowly growing in Tropical East Asia, particularly among the younger generation of researchers who can connect with the barcoding analogy and understand the need for new approaches to the conservation challenges being faced.

We report an unusual cause of gastrointestinal infection occurring in a 1-year-old infant patient who was brought to a public hospital in Kuala Lumpur, Malaysia. Larvae passed out in the patient's feces were confirmed by DNA barcoding as belonging to the species, Lasioderma serricorne (F.), known as the cigarette beetle. We postulate that the larvae were acquired from contaminated food and were responsible for gastrointestinal symptoms in the patient. To our knowledge, this the first report of human canthariasis caused by larvae of L. serricorne.

Three species of sponges and a tunicate were collected from Obhur creek of Jeddah coast for this bioactivity study. In order to assess the antifouling efficacy of selected marine organisms, methanolic extracts of these organisms were tested against different fouling bacterial forms and II-instar stage of the barnacle, Balanus amphitrite. Antibiosis, bioactivity and followed by multivariate analyses were carried out to check the efficacy of antifouling effect of the selected marine organisms. Principal component analysis revealed the exemplary antifouling efficacy of the sponge extracts of Stylissa sp. observed followed by Hyrtios sp. against bacterial forms in the laboratory study. De-trended correspondence analysis confirmed that the contribution of antifouling efficacy of the selected sponge extracts was observed to be more towards Bacillus sp., Vibrio sp. and Alteromonas sp. Moreover, the efficacy of Hyrtios sp. extract (20.430 μg mL−1) followed by Stylissa sp. (30.945 μg mL−1) showed higher against barnacle instar compared with other extracts in the bioactivity assay. Bray-Curtis cluster analysis under paired linkage categorized all the sponge extracts into one major cluster with 75% similarity, and one outlier tunicate. More than 80% similarity observed between Hyrtios sp. and Stylissa sp. Fourier transform infrared spectroscopy (FTIR) showed that the contribution of major peaks found in the marine organisms were towards sulfones, sulfoxides, cyanates and ketones.

Mosquitoes are vectors of various human diseases in the tropics including yellow fever, dengue, malaria and West Nile virus. Mosquitoes can act as vectors between wildlife and humans, which is particularly important for diseases where wild animals serve as reservoirs of parasites in the absence of human infections. Research has mainly focused on the medical impacts of Anopheles, Aedes, Mansonia and Culex, however, very little attention has been directed towards other mosquito genera, especially those which act as vectors of diseases of wildlife. We have observed adults of Mimomyia (Etorleptiomyia) luzonensis (Ludlow, 1905) feeding on a toad, Ingerophrynus parvus, near an oil palm plantation settlement in Setia Alam, Selangor state, Peninsular Malaysia. Mimomyia is known to feed on reptiles and amphibians, and is a documented vector of several arboviruses, including West Nile virus. The observation of Mimomyia feeding on a common toad near a human settlement highlights a need to understand the relationships between mosquitoes, toads and humans from an ecological perspective. We report on-site observations of the feeding habit of Mimomyia; the first records from Malaysia.

This open-access special issue features 12 full articles representing emerging trends from the international DNAbarcoding community. Several articles highlight how DNA-based techniques are elucidating the species diversity,biogeography, and conservation status of Africas biodiversity. Another prominent theme is the movementtowards big biodiversity data using high-throughput, individual-based DNA barcoding methods, which preservevoucher specimens and abundance data, as well as bulk sample-based metabarcoding. Methodological developments are enhancing the detection of specific species and whole communities using environmental DNA(eDNA) barcoding and metabarcoding. Data are also expanding in terms of genetic coverage; in this issue, a newdatabase is established for a secondary fungalDNAbarcode marker, and multi-kingdom, multi-marker biodiversitysurveys are gaining traction. DNA barcode sequence data, often combined with complementary markers or taxonomic information, are increasingly contributing to large-scale phylogenetic projects, with implications for understanding evolutionary history, community structure, and conservation priorities. Fil: Adamowicz, Sarah J.. University of Guelph; Canadá Fil: Boatwright, James S.. University of The Western Cape; Sudáfrica Fil: Chain, Frédéric. University of Massachusetts; Estados Unidos Fil: Fisher, Brian L.. California Academy Of Sciences.; Estados Unidos Fil: Hogg, Ian D.. Polar Knowledge Canada; Canadá Fil: Leese, Florian. Universitat Essen; Alemania Fil: Lijtmaer, Dario Alejandro. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"; Argentina Fil: Mwale, Monica. South African National Biodiversity Institute; Sudáfrica Fil: Naaum, Amanda M.. The Queens University of Belfast; Irlanda Fil: Pochon, Xavier. University of Auckland; Nueva Zelanda Fil: Schubert, Dirk W.. University of Guelph; Canadá Fil: Wilson, John James. National Museums Liverpool; Reino Unido Fil: Wood, Susanna. Cawthron Institute; Nueva Zelanda Fil: Xu, Jianping. Mcmaster University; Canadá Fil: Xu, Sen. University of Texas at Arlington; Estados Unidos Fil: Zhou, Xin. China Agricultural University; China Fil: Van Der Bank, Michelle. University of Johannesburg; Sudáfrica

Reduviidae is the second largest family of Heteroptera and most of them are important natural enemies of agricultural and forest pests. Most of the sequenced mitochondrial (mt) genomes in this family have the typical gene arrangement of insects and encode 37 coding genes (13 protein-coding genes, 22 tRNA genes and two rRNA genes). In the present study, we sequenced the mt genome of Phalantus geniculatus from the subfamily Peiratinae through high-throughput sequencing and encountered the duplication of tRNA genes for the first time in this subfamily. We identified 23 tRNA genes, including 22 tRNAs commonly found in insect mt genomes and an extra trnT (trnT2), which has high sequence similarity (96.9%) to trnT1. The presence of a “pseudo-trnP” in the non-coding region between trnT1 and trnT2 supports the hypothesis that the presence of an extra trnT can be explained by the tandem duplication-random loss (TDRL) model. Phylogenetic results inferred from mt genome sequences supported a sister relationship between Phymatinae and the remaining sampled subfamilies, as well as a paraphyletic Reduviinae. The present study highlights the utility of mt genomes in the phylogenetic study of Reduviidae based on the large scale taxon sampling in the future.

Background. Intense landscaping often alters the plant composition in urban areas. Knowing which plant species that pollinators are visiting in urban areas is necessary for understanding how landscaping impacts biodiversity and associated ecosystem services. The cave nectar bat, Eonycteris spelaea, is an important pollinator for many plants and is often recorded in human-dominated habitats. Previous studies of the diet of E. spelaea relied on morphological identification of pollen grains found in faeces and on the body of bats and by necessity disregarded other forms of digested plant material present in the faeces (i.e., plant juice and remnants). The main objective of this study was to examine the diet of the nectarivorous bat, E. spelaea, roosting in an urban cave at Batu Caves, Peninsular Malaysia by identifying the plant material present in the faeces of bats using DNA metabarcoding. Methods. Faeces were collected under the roost of E. spelaea once a week from December 2015 to March 2016. Plant DNA was extracted from the faeces, PCR amplified at ITS2 and rbcL regions and mass sequenced. The resultant plant OTU were searched against NCBI GenBank for identification. Results. A total of 55 species of plants were detected from faeces of E. spelaea including Artocarpus heterophyllus, Duabanga grandiflora and Musa spp. which are likely to be important food resources for the cave nectar bat. Discussion. Many native plant species that had not been reported in previous dietary studies of E. spelaea were detected in this study including Bauhinia strychnoidea and Urophyllum leucophlaeum, suggesting that E. spelaea remains a crucial pollinator for these plants even in highly disturbed habitats. The detection of many introduced plant species in the bat faeces indicates that E. spelaea are exploiting them, particularly Xanthostemon chrysanthus, as food resources in urban area. Commercial food crops were detected from all of the faecal samples, suggesting that E. spelaea feed predominantly on the crops particularly jackfruit and banana and play a significant role in pollination of economically important plants. Ferns and figs were also detected in the faeces of E. spelaea suggesting future research avenues to determine whether the “specialised nectarivorous” E. spelaea feed opportunistically on other parts of plants.

Rapid economic development has accelerated urbanisation and biodiversity loss in Southeast Asia. Studies of urban ecology have suggested urban parks can be effective refuges for wildlife in temperate regions, but their effectiveness as refuges in rapidly urbanising tropical regions is understudied. We examined the species diversity of butterflies in urban parks in the Federal Territory of Kuala Lumpur and investigated the relationships between butterfly species richness and three park variables: i) park size, ii) distance from the central business district and iii) park age. Standardised butterfly sampling was conducted across different microhabitat types at each park: i) groves, ii) hedges, iii) flowerbeds and iv) unmanaged areas. We recorded 572 butterflies belonging to 60 species (97 % considered common) from five families. Although species richness was positively correlated with park size and age and negatively correlated with distance from the central business district; the correlations were weak and not statistically significant. However, species richness of host-specialist species was significantly positively correlated with park size and age. The highest species richness (65 % of observed species) was recorded in the unmanaged microhabitat. It is likely that both park planting scheme and the presence of early successional plants in unmanaged microhabitat led to highest butterfly species richness in parks that contained all four microhabitat types. Whether a diverse planting scheme and increased size and number of unmanaged areas in urban parks can improve the ability of parks to sustain populations of rare butterflies in the face of future urbanisation remains to be seen.

Metabarcoding, the coupling of DNA-based species identification and high-throughput sequencing, offers enormous promise for arthropod biodiversity studies but factors such as cost, speed and ease-of-use of bioinformatic pipelines, crucial for making the leapt from demonstration studies to a real-world application, have not yet been adequately addressed. Here, four published and one newly designed primer sets were tested across a diverse set of 80 arthropod species, representing 11 orders, to establish optimal protocols for Illumina-based metabarcoding of tropical Malaise trap samples. Two primer sets which showed the highest amplification success with individual specimen polymerase chain reaction (PCR, 98%) were used for bulk PCR and Illumina MiSeq sequencing. The sequencing outputs were subjected to both manual and simple metagenomics quality control and filtering pipelines. We obtained acceptable detection rates after bulk PCR and high-throughput sequencing (80–90% of input species) but analyses were complicated by putative heteroplasmic sequences and contamination. The manual pipeline produced similar or better outputs to the simple metagenomics pipeline (1.4 compared with 0.5 expected:unexpected Operational Taxonomic Units). Our study suggests that metabarcoding is slowly becoming as cheap, fast and easy as conventional DNA barcoding, and that Malaise trap metabarcoding may soon fulfill its potential, providing a thermometer for biodiversity.

Chinese knotweed (Persicaria chinensis) is of ecological and economic importance as a high-risk invasive species and a traditional medicinal herb. However, the insects associated with P. chinensis pollination have received scant attention. As a widespread invasive plant we would expect P. chinensis to be associated with a diverse group of insect pollinators, but lack of taxonomic identification capacity is an impediment to confirm this expectation. In the present study we aimed to elucidate the insect pollinators of P. chinensis in peninsular Malaysia using DNA barcoding. Forty flower visitors, representing the range of morphological diversity observed, were captured at flowers at Ulu Kali, Pahang, Malaysia. Using Automated Barcode Gap Discovery, 17 morphospecies were assigned to 23 species representing at least ten families and four orders. Using the DNA barcode library (BOLD) 30% of the species could be assigned a species name, and 70% could be assigned a genus name. The insects visiting P. chinensis were broadly similar to those previously reported as visiting Persicaria japonica, including honey bees (Apis), droneflies (Eristalis), blowflies (Lucilia) and potter wasps (Eumedes), but also included thrips and ants.

Consensus on the optimal high-throughput sequencing (HTS) approach to examine biodiversity in mixed terrestrial arthropod samples has not been reached. Metatranscriptomics could increase the proportion of taxonomically informative mitochondrial reads in HTS outputs but has not been investigated for terrestrial arthropod samples. We compared the efficiency of 16S rRNA metabarcoding, metagenomics and metatranscriptomics for detecting species in a mixed terrestrial arthropod sample (pooled DNA/RNA from 38 taxa). 16S rRNA metabarcoding and nuclear rRNA-depleted metatranscriptomics had the highest detection rate with 97% of input species detected. Based on cytochrome c oxidase I, metagenomics had the highest detection rate with 82% of input species detected, but metatranscriptomics produced a larger proportion of reads matching (Sanger) reference sequences. Metatranscriptomics with nuclear rRNA depletion may offer advantages over metabarcoding through reducing the number of spurious operational taxonomic units while retaining high detection rates, and offers natural enrichment of mitochondrial sequences which may enable increased species detection rates compared with metagenomics.

DNA barcoding, based on a fragment of cytochrome c oxidase I (COI) mtDNA, is as an effective molecular tool for identification, discovery, and biodiversity assessment for most animals. However, multiple gene markers coupled with more sophisticated analytical approaches may be necessary to clarify species boundaries in cases of cryptic diversity or morphological plasticity. Using 339 moths collected from mountains surrounding Beijing, China, we tested a pipeline consisting of two steps: (1) rapid morphospecies sorting and screening of the investigated fauna with standard COI barcoding approaches; (2) additional analyses with multiple molecular markers for those specimens whose morphospecies and COI barcode grouping were incongruent. In step 1, 124 morphospecies were delimited into 116 barcode units, with 90% of the conflicts being associated with specimens identified to the genus Hypena. In step 2, 55 individuals representing all 12 Hypena morphospecies were analysed using COI, COII, 28S, EF-1a, Wgl sequences or their combinations with the BPP (Bayesian Phylogenetics and Phylogeography) multigene species delimitation method. The multigene analyses supported the delimitation of 5 species, consistent with the COI analysis. We conclude that a two-step barcoding analysis pipeline is able to rapidly characterize insect biodiversity and help to elucidate species boundaries for taxonomic complexes without jeopardizing overall project efficiency by substantially increasing analytical costs.

Environmental DNA detection has emerged as a powerful tool to monitor aquatic species without the need for capture or visual identification and is particularly useful for rare or elusive species. Our objective was to develop an eDNA approach for detecting the southern river terrapin (Batagur affinis) in Malaysia. We designed species-specific primers for a fragment of B. affinis mtDNA and evaluated their effectiveness in silico, in vitro and in situ. The primers amplified 110 bp of the cytochrome b mtDNA sequence of B. affinis from aquarium water samples housing nine juvenile B. affinis. We also successfully detected B. affinis eDNA from river samples taken from a site where turtles were known to be in the vicinity. Prospects and challenges of using an eDNA approach to help determine the distribution of B. affinis, essential information for an effective conservation plan, are discussed.

Phoniscus atrox Miller, 1905 Phoniscus atrox Miller, 1905: 230; vicinity of the Kateman River, east Sumatra, INDONE- SIA (Dr. W. L. Abbott, collector; USNM 123141) [183]. Common English name: Lesser Groove-toothed Bat Barcode Index Number: There are no DNA barcodes recorded under this name on BOLD. IUCN status: Near Threatened Recorded at: Pahang: Krau Wildlife Reserve [11, 41, 42], Bukit Ibam, Kemasul and Gunung Aais [100]; Terengganu: Pasir Raja-Dungun [15], Gunung Tebu Forest Reserve [101]; Selangor: Ulu Gombak [23, 52, 54]; Negeri Sembilan: Pasoh Forest Reserve [45]; Perak: Temengor Forest Reserve [46, 47, 111], Royal Belum State Park [66]; Kelantan: Air Panas-Gua Musang [61]; Johor: Labis Forest Reserve [100]. P. atrox has been recorded in primary lowland forests and disturbed areas near primary forest, and found roosting in abandoned hanging bird nests [11, 14]., Published as part of Voon-Ching Lim, Rosli Ramli, Subha Bhassu & John-James Wilson, 2017, A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library, pp. 1-65 in PLoS ONE 12 (7) on pages 41-42, DOI: 10.1371/journal.pone.0179555, http://zenodo.org/record/4251352, {"references":["183. Miller GS. A new genus of bats from Sumatra. In Proceedings of Biological Society 18. Washington; 1905. pp. 229 - 230.","11. Kingston T, Lim BL, Akbar Z. Bats of Krau wildlife reserve. Penerbit Universiti Kebangsaan Malaysia; 2006.","41. Zubaid A. A comparison of the bat fauna between a primary and fragmented secondary forest in Peninsular Malaysia. Mammalia. 1993; 57 (2): 201 - 206.","42. Anan S, Rashdi AM, Abdul J, Lim BL. A survey of small mammals at Sungai Chenderoh, Perlok, Krau Wildlife Reserve, Pahang. Journal of Wildlife and Parks. 1998; 16: 104 - 109.","100. Lim LS, Mohd-Adnan A, Zubaid A, Struebig MJ, Rossiter SJ. Diversity of Malaysian insectivorous bat assemblages revisited. J Trop Ecol. 2014; 30 (02): 111 - 121.","15. Wilson JJ, Sing KW, Halim MR, Ramli R, Hashim R, Sofian-Azirun M. Utility of DNA barcoding for rapid and accurate assessment of bat diversity in Malaysia in the absence of formally described species. Genet Mol Res 2014; 13 (1): 920 - 5. https: // doi. org / 10.4238 / 2014. February. 19.2 PMID: 24634112","101. Joann CL, Fletcher C, Rahman KA. Spatial effects of virgin jungle reserves (VJR) on the community of insectivorous bats in Peninsular Malaysia. J Trop For Sci. 2013; 25 (1): 118 - 130.","23. Medway L. The wild mammals of Malaya. London: Oxford University Press. 1969.","52. Medway L. The Ulu Gombak Field Studies Centre. Malayan Scientist. 1966; 2: 1 - 6.","54. Heller KG, Volleth MA. Fledermause aus Malaysia. 1. Beobachtungen zur Biologie, Morphologie und Taxonomie. Senckenb Biol. 1989; 69 (4 - 6): 243 - 76.","45. Francis CM. Trophic structure of bat communities in the understorey of lowland dipterocarp rain forest in Malaysia. J Trop Ecol. 1990; 6: 421 - 431.","46. Francis CM. The diversity of bats in Temengor Forest Reserve, Hulu Perak, Malaysia. Mal Nat J. 1995; 48: 403 - 408.","47. Shahfiz MA, Shahrul-Anuar MA, Kaviarasu M, Fauzi MZ, Rizal MR. Preliminary checklist of mammals at Sungai Enam in Temengor Forest Reserve, Perak, Peninsular Malaysia In: Mohamed AL, Krishnapillay DB, Kasim Z, Khushairi ZA, Ismail NI, Rezan EFN, Sadali A, Mohammad MS, Hassan MN, Aznan ARY, editors. Proceedings of the 2 nd Temengor Scientific Expedition 2012, 22 - 25 August 2013. Pulau Banding Foundation, Malaysia; 2013.","111. Joann CL, Fletcher C, Salim HMW, Abdul-Rahman K, Harrison RD, Potts MD. Insectivorous bat assemblage in the hill dipterocarp forest of Temengor Forest Reserve, Peninsular Malaysia. Mal Nat J. 2011; 63 (3): 569 - 576.","66. Shahfiz MA, Sahrul-Anuar MS, Zalipah MN, Nurul-Ain E, Pan KA, Muin MA, et al. Surveys of small mammals at selected sites in Royal Belum State Park. In: Rahman A, Koh HL, Mohd-Paiz K, Muhamad A, Latiff A, editors). Proceedings for Forestry Department of Peninsular Malaysia, 3 - 5 August 2008. Department of Wildlife and National Parks, Malaysia; 2008. pp. 299 - 308.","61. Hasan NH, Khan K, Senawi J, Ketol B, Sait I, Abdullah MT. A report on bats survey at Air Panas-Gua Musang, Kelantan, Malaysia. J Trop Biol Conserv. 2012; 9 (2): 156 - 162.","14. Francis CM. A field guide to the mammals of South-East Asia. New Holland Publishers; 2008."]}

Hesperoptenus tomesi Thomas, 1905 Hesperoptenus tomesi Thomas, 1905: 575; Malacca = Melaka, MALAYSIA (Collector unknown; Originally No. 190Ain the collection of Mr. R. F. Tomes but currently as BM(NH) 1907.1.1.428) [208]. Common English name: Tome’s False-serotine Barcode Index Number: There are no DNA barcodes recorded under this name on BOLD. IUCN status: Vulnerable Recorded at: Melaka: Unspecified [208]; Selangor: Ulu Gombak [53, 54]. H. tomesi has been recorded in mature lowland forest [14]., Published as part of Voon-Ching Lim, Rosli Ramli, Subha Bhassu & John-James Wilson, 2017, A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library, pp. 1-65 in PLoS ONE 12 (7) on page 49, DOI: 10.1371/journal.pone.0179555, http://zenodo.org/record/4251352, {"references":["208. Thomas O. A new genus and two new species of bats. Annals Mag Nat Hist. 1905; 16: 572 - 576.","53. Heller KG, Volleth M. Taxonomic position of \" Pipistrellus societatis \" Hill, 1972 and the karyological characteristics of the genus Eptesicus (Chiroptera: Vespertilionidae). J Zoolog Syst Evol Res. 1984; 22 (1): 65 - 77.","54. Heller KG, Volleth MA. Fledermause aus Malaysia. 1. Beobachtungen zur Biologie, Morphologie und Taxonomie. Senckenb Biol. 1989; 69 (4 - 6): 243 - 76.","14. Francis CM. A field guide to the mammals of South-East Asia. New Holland Publishers; 2008."]}

Hipposideros pomona Andersen, 1918 Hipposideros pomona Andersen, 1918: 380, 381; Haleri, North Coorg, INDIA (A few miles north of Mercara, Coorg District, Karnataka) (G. C. Shortridge; BM (NH) 1918.8.3.4) [117]. Hipposideros pomona gentilis [118]. Common English name: Large-eared Roundleaf Bat Barcode Index Number: DNA barcodes recorded as H. pomona are associated with eight BINs, BOLD: AAA 4932, BOLD: AAA 4933, BOLD: AAA 4934, BOLD: AAA 4935, BOLD: AAA 4936, BOLD: AAA 4937, BOLD: AAA 4938 and BOLD: AAA 4939, but there are no DNA barcodes from Peninsular Malaysia (S3 Fig). Remarks: Andersen [117] first separated H. pomona and H. gentilis on the basis of the noseleaf of H. pomona sensu stricto being broader than the noseleaf of H. gentilis. Similarly, Corbet and Hill [9] examined ethanol-preserved specimens and commented that H. pomona sensu stricto lacked of lateral supplementary leaflets. Likewise, Douangboubpha et al. [17] suggested that H. pomona sensu stricto [9] may represents at least two species: H. pomona sensu stricto (restricted to Peninsular India) and H. gentilis (distributed from north-east India into Southeast Asia). DNA sequences of H. pomono sensu lato from two mitochondrial genes: ND2 and RAG1 fell into two distinct clades in a phylogenetic tree (see Fig 4 in [125]): (i) H. pomona, H. rotalis and H. khaokhouayensis from Laos, and (ii) H. pomona from Laos, China, Myanmar and Peninsular Malaysia. Specimens of H. pomona from both groups are morphologically similar [125]. Three subspecies of H. pomona have been reported from China: H. p. sinesis (Min- Guang coastal region), H. p. gentilis (South Yunnan region) and an undescribed subspecies (Hainan Island), showing 6.0–8.5% divergences in cytochrome b mtDNA and 5.2–8.0% divergences in COI mtDNA [144]. Due to the lack of DNA barcodes from Peninsular Malaysia and unresolved taxonomy across the whole Southeast Asia region, we tentatively retained the name H. pomona in this checklist pending further research. IUCN status: Least Concern Recorded at: Perlis: Bukit Jerneh Cave and Tumang Lembing Cave [30], Bukit Lagi [145]. H. pomona is a cave dweller and has been recorded from various forest types and disturbed areas [14]., Published as part of Voon-Ching Lim, Rosli Ramli, Subha Bhassu & John-James Wilson, 2017, A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library, pp. 1-65 in PLoS ONE 12 (7) on page 27, DOI: 10.1371/journal.pone.0179555, http://zenodo.org/record/4251352, {"references":["117. Andersen K. Diagnoses of new bats of the families Rhinolophidae and Megadermatidae. Annals Mag Nat Hist. 1918; 2: 374 - 384.","118. Hill JE, Zubaid A, Davison GWH. The taxonomy of leaf-nosed bats of the Hipposideros bicolor group (Chiroptera: Hipposideridae) from southeastern Asia. Mammalia. 1986; 50 (4): 535 - 540.","9. Corbet GB, Hill JE. The mammals of the Indomalayan region: a systematic review. Oxford: Oxford University Press; 1992.","17. Douangboubpha B, Bumrungsri S, Soisook P, Satasook C, Thomas NM, Bates PJ. A taxonomic review of the Hipposideros bicolor species complex and H. pomona (Chiroptera: Hipposideridae) in Thailand. Acta. Chiropt. 2010; 12 (2): 415 - 438.","125. Murray SW, Campbell P, Kingston T, Zubaid A, Francis CM, Kunz TH. Molecular phylogeny of hipposiderid bats from Southeast Asia and evidence of cryptic diversity. Mol Phylogenet Evol. 2012; 62 (2): 597 - 611. https: // doi. org / 10.1016 / j. ympev. 2011.10.021 PMID: 22079552","144. Zhao LZ, Bu YZ, Zhou HX, Zhou HW, Zhang ZS, Niu HX. Differences in Hipposideros pomona from three geographical regions in China based on morphology and molecular sequences data. J Mammal. 2015; 96 (6): 1305 - 1316.","30. Douangboubpha B, Bumrungsri S, Soisook P, Murray SW, Puechmaille SJ, Satasook C, et al. A taxonomic review of Hipposideros halophyllus, with additional information on H. ater and H. cineraceus (Chiroptera: Hipposideridae) from Thailand and Myanmar. Acta Chiropt. 2010; 12 (1): 29 - 50.","145. Zubaid A. Food habits of Hipposideros pomona (Chiroptera: Rhinolophidae) from Peninsular Malaysia. Mammalia. 1988; 52 (1): 134 - 136.","14. Francis CM. A field guide to the mammals of South-East Asia. New Holland Publishers; 2008."]}

Cheiromeles torquatus Horsfield, 1824 Cheiromeles torquatus Horsfield, 1824: pt 8; Pulau Pinang, MALAYSIA (John Crawfurd, Esq., collector; Type unknown) [102]. Common English name: Naked Bat Barcode Index Number: There are no DNA barcodes recorded under this name on BOLD. IUCN status: Least Concern Recorded at: Pulau Pinang: Unspecified [102]; Pahang: Pulau Tioman [9], Krau Wildlife Reserve [11, 41]; Selangor: Batu Cave [23], Bukit Kutu Wildlife Reserve [51], Ulu Gombak [52]; Perak: Temengor Forest Reserve [47]. C. torquatus has been reported roosting in caves, tree hollows and abandoned buildings, often with Mops mops [11, 14, 23]., Published as part of Voon-Ching Lim, Rosli Ramli, Subha Bhassu & John-James Wilson, 2017, A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library, pp. 1-65 in PLoS ONE 12 (7) on page 15, DOI: 10.1371/journal.pone.0179555, http://zenodo.org/record/4251352, {"references":["102. Horsfield, T. Zoological researches in Java. Kingbury, Parbury and Allen, London; 1823 - 1824.","9. Corbet GB, Hill JE. The mammals of the Indomalayan region: a systematic review. Oxford: Oxford University Press; 1992.","11. Kingston T, Lim BL, Akbar Z. Bats of Krau wildlife reserve. Penerbit Universiti Kebangsaan Malaysia; 2006.","41. Zubaid A. A comparison of the bat fauna between a primary and fragmented secondary forest in Peninsular Malaysia. Mammalia. 1993; 57 (2): 201 - 206.","23. Medway L. The wild mammals of Malaya. London: Oxford University Press. 1969.","51. Lim BL, Majid RA, Norsham Y. Studies on the mammal fauna of Bukit Kutu Wildlife reserve, Hulu Selangor. Journal of Wildlife and Parks. 1999; 17: 1 - 6.","52. Medway L. The Ulu Gombak Field Studies Centre. Malayan Scientist. 1966; 2: 1 - 6.","47. Shahfiz MA, Shahrul-Anuar MA, Kaviarasu M, Fauzi MZ, Rizal MR. Preliminary checklist of mammals at Sungai Enam in Temengor Forest Reserve, Perak, Peninsular Malaysia In: Mohamed AL, Krishnapillay DB, Kasim Z, Khushairi ZA, Ismail NI, Rezan EFN, Sadali A, Mohammad MS, Hassan MN, Aznan ARY, editors. Proceedings of the 2 nd Temengor Scientific Expedition 2012, 22 - 25 August 2013. Pulau Banding Foundation, Malaysia; 2013.","14. Francis CM. A field guide to the mammals of South-East Asia. New Holland Publishers; 2008."]}

Rhinolophus robinsoni Andersen, 1918 Rhinolophus robinsoni Andersen, 1918: 375; Khao Nawng, Bandon, THAILAND (Federated Malay States Museum, presenter; BM(NH) 1918.8.2.1) [117]. Common English name: Peninsular Horseshoe Bat Barcode Index Number: There are no DNA barcodes recorded under this name on BOLD. Remarks: R. robinsoni was previously considered to be conspecific with R. megaphyllus [9] but is now recognised as a distinct species [98]. Specimens recorded as R. megaphyllus from Peninsular Malaysia [46] should be updated to R. robinsoni. IUCN status: Near Threatened Recorded at: Pahang: Krau Wildlife Reserve [11], Fraser Hill [23, 140], Pulau Tioman [23], Kenong and Gunung Aais [100]; Johor: Pulau Aur and Pulau Pemanggil [23], Gunung Panti and Labis Forest Reserve [100]; Perlis: Wang Kelian State Park [50]; Kelantan: Gua Musang [62]; Melaka: Unspecified [68]; Negeri Sembilan: Gunung Angsi Forest Reserve [100]; Perak: Kledang Saiong Forest Reserve [100]; Pulau Pinang: Bukit Panchor [100]. Recorded as R. megaphyllus at Perak: Temengor Forest Reserve [46]. R. robinsoni inhabits forests primarily and has been recorded in lowland and hill forests roosting in rock crevices and palm leaves [11, 14]., Published as part of Voon-Ching Lim, Rosli Ramli, Subha Bhassu & John-James Wilson, 2017, A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library, pp. 1-65 in PLoS ONE 12 (7) on page 34, DOI: 10.1371/journal.pone.0179555, http://zenodo.org/record/4251352, {"references":["117. Andersen K. Diagnoses of new bats of the families Rhinolophidae and Megadermatidae. Annals Mag Nat Hist. 1918; 2: 374 - 384.","9. Corbet GB, Hill JE. The mammals of the Indomalayan region: a systematic review. Oxford: Oxford University Press; 1992.","98. Simmons NB. Order chiroptera. In: Wilson DE, Reeder DM, editors. Mammal species of the world: a taxonomic and geographic reference. Johns Hopkins University Press, Baltimore; 2005. pp. 312 - 529.","46. Francis CM. The diversity of bats in Temengor Forest Reserve, Hulu Perak, Malaysia. Mal Nat J. 1995; 48: 403 - 408.","11. Kingston T, Lim BL, Akbar Z. Bats of Krau wildlife reserve. Penerbit Universiti Kebangsaan Malaysia; 2006.","23. Medway L. The wild mammals of Malaya. London: Oxford University Press. 1969.","140. Hill JE. The Gunong Benom Expedition 1967. 4. New records of Malayan bats, with taxonomic notes and the description of a new Pipistrellus. Bull Br Mus.: Zool. 1972; 23: 21 - 42.","100. Lim LS, Mohd-Adnan A, Zubaid A, Struebig MJ, Rossiter SJ. Diversity of Malaysian insectivorous bat assemblages revisited. J Trop Ecol. 2014; 30 (02): 111 - 121.","50. Jayaraj VK, Daud SH, Azhar MI, Sah SA, Mokhtar SI, Abdullah MT. Diversity and conservation status of mammals in Wang Kelian State Park, Perlis, Malaysia. Check List. 2013; 9 (6): 1439 - 48.","62. Jayaraj VK, Khan FA, Azhar I, WeeChen E, Ali MR, Ahmad A, et al. Diversity and conservation status of small mammals in Kelantan, Malaysia. Warasan Songkhla Nakharin. 2016; 38 (2): 213 - 20.","68. Shahfiz MA, Shahrul-Anuar MA, Nor-Zalipah M, Kaviarasu M, Pan KA, Yusof MO, et al. Surveys of bats at selected sites in Melaka Forest Reserves, Peninsular Malaysia. In: Rahman A, Koh HL, Muhamad A, Yusof WKW, Latiff A, editors. Proceedings for Forestry Department of Peninsular Malaysia, 1 - 2 April 2009 2008. Department of Wildlife and National Parks, Malaysia; 2009. pp. 265 - 270.","14. Francis CM. A field guide to the mammals of South-East Asia. New Holland Publishers; 2008."]}

Cynopterus sphinx [Vahl, 1797] Vespertilio sphinx Vahl, 1797: 123; Tranquebar, Madras, INDIA (Collector unknown; Type unknown) [72]. Cynopterus sphinx [73]. Common English name: Greater Short-nosed Fruit Bat Barcode Index Number: DNA barcodes recorded as C. sphinx are associated with BIN, BOLD: AAA 3386, but there are no DNA barcodes from Peninsular Malaysia. Another BIN (BOLD: AAD 9139) contains a single DNA barcode of C. sphinx from India and DNA barcodes recorded as Pteropus vampyrus, P. lylei, and Rousettus leschenaultii, which we suspect may represent erroneous records or contamination. Remarks: C. sphinx resembles C. cf. brachyotis closely in morphology and both taxa overlap in forearm measurements [14]. However, examination of specimens from Peninsular Malaysia identified as C. sphinx, C. cf. brachyotis SUNDA and C. cf. brachyotis FOREST revealed that C. sphinx is 8.9% from C. cf. brachyotis SUNDA and 7.5% divergentfrom C. cf. brachyotis FOR- EST in mtDNA (combined control region and cytochrome b) [64]. Our examination of DWNP specimens labelled as C. sphinx and C. cf. brachyotis from Peninsular Malayia revealed that the taxa can be differentiatied by a distinctive lower last molar. Specimens labelled as C. sphinx have lower teeth which are almost uniform in size whereas specimens of C. cf. brachyotis have non-uniformed lower teeth with extremely small lower last molars [74]. IUCN status: Least Concern Recorded at: Perak: Selama [49], Taiping [64]; Kelantan: Gunung Reng and Lojing Highlands [62], Gunung Stong State Park [67]; Perlis: Wang Kelian State Park [50], Kuala Perlis, Perlis State Park and Kangar [64]; Pahang: Cameron Highland [64]. C. sphinx is commonly found in disturbed habitats and ecotones but not in the forest interior [14, 65]., Published as part of Voon-Ching Lim, Rosli Ramli, Subha Bhassu & John-James Wilson, 2017, A checklist of the bats of Peninsular Malaysia and progress towards a DNA barcode reference library, pp. 1-65 in PLoS ONE 12 (7) on pages 8-9, DOI: 10.1371/journal.pone.0179555, http://zenodo.org/record/4251352, {"references":["72. Vahl M. Beskrivelse paa tre nye Arter Flagermuse. Skrivt. Naturhist. Selskabet Kjobenhavn. 1797; 4: 121 - 38.","73. Cuvier F. Des dents des mammiferes. FG Levrault, Strasbourg, France; 1824.","14. Francis CM. A field guide to the mammals of South-East Asia. New Holland Publishers; 2008.","64. Campbell P, Schneider CJ, Adnan AM, Zubaid A, Kunz TH. Phylogeny and phylogeography of Old World fruit bats in the Cynopterus brachyotis complex. Mol Phylogenet Evol. 2004; 33 (3): 764 - 81. https: // doi. org / 10.1016 / j. ympev. 2004.06.019 PMID: 15522802","74. Boonsong L, McNeely JA. Mammals of Thailand. Association for the Conservation of Wildlife; 1977. pp. 758.","49. Shafie NJ, Sah SA, Latip NA, Azman NM, Khairuddin NL. Diversity pattern of bats at two contrasting habitat types along Kerian River, Perak, Malaysia. Trop Life Sci Res 2011; 22: 13 - 22.","62. Jayaraj VK, Khan FA, Azhar I, WeeChen E, Ali MR, Ahmad A, et al. Diversity and conservation status of small mammals in Kelantan, Malaysia. Warasan Songkhla Nakharin. 2016; 38 (2): 213 - 20.","67. Jayaraj VK, Tahir NF, Udin NA, Baharin NF, Ismail SK, Zakaria SN. Species diversity of small mammals at Gunung Stong State Park, Kelantan, Malaysia. J Threat Taxa. 2012; 4 (6): 2617 - 2628.","50. Jayaraj VK, Daud SH, Azhar MI, Sah SA, Mokhtar SI, Abdullah MT. Diversity and conservation status of mammals in Wang Kelian State Park, Perlis, Malaysia. Check List. 2013; 9 (6): 1439 - 48.","65. Campbell P, Schneider CJ, Zubaid A, Adnan AM, Kunz TH. Morphological and ecological correlates of coexistence in Malaysian fruit bats (Chiroptera: Pteropodidae). J Mamma. 2007 Feb 28; 88 (1): 105 - 18."]}