Universal COI primers for DNA barcoding amphibians

The efficacy of DNA barcoding in the classification, genetic differentiation, and biodiversity assessment of benthic macroinvertebrates

Macroinvertebrates have been recognized as key ecological indicators of aquatic environment and are the most commonly used approaches for water quality assessment. However, species identification of macroinvertebrates (especially of aquatic insects) proves to be very difficult due to the lack of taxonomic expertise in some regions and can become time-consuming. In this study, we evaluated the feasibility of DNA barcoding for the classification of benthic macroinvertebrates and investigated the genetic differentiation in seven orders (Insecta: Ephemeroptera, Plecoptera, Trichoptera, Diptera, Hemiptera, Coleoptera, and Odonata) from four large transboundary rivers of northwest China and further explored its potential application to biodiversity assessment. A total of 1,144 COI sequences, belonging to 176 species, 112 genera, and 53 families were obtained and analyzed. The barcoding gap analysis showed that COI gene fragment yielded significant intra- and interspecific divergences and obvious barcoding gaps. NJ phylogenetic trees showed that all species group into monophyletic species clusters whether from the same population or not, except two species (Polypedilum. laetum and Polypedilum. bullum). The distance-based (ABGD) and tree-based (PTP and MPTP) methods were utilized for grouping specimens into Operational Taxonomic Units (OTUs) and delimiting species. The ABGD, PTP, and MPTP analysis were divided into 177 (p = .0599), 197, and 195 OTUs, respectively. The BIN analysis generated 186 different BINs. Overall, our study showed that DNA barcoding offers an effective framework for macroinvertebrate species identification and sheds new light on the biodiversity assessment of local macroinvertebrates. Also, the construction of DNA barcode reference library of benthic macroinvertebrates in Eurasian transboundary rivers provides a solid backup for bioassessment studies of freshwater habitats using modern high-throughput technologies in the near future.

Multiple lines of evidence reveal a new species of Krait (Squamata, Elapidae, Bungarus) from Southwestern China and Northern Myanmar

Kraits of the genus Bungarus Daudin 1803 are widely known venomous snakes distributed from Iran to China and Indonesia. Here, we use a combination of mitochondrial DNA sequence data and morphological data to describe a new species from Yingjiang County, Yunnan Province, China: Bungarussuzhenaesp. nov. Phylogenetically, this species forms a monophyletic lineage sister to the Bungaruscandidus/multicinctus/wanghaotingi complex based on cyt b and ND4 genes but forms a sister species pair with the species B.magnimaculatus Wall & Evans, 1901 based on COI gene fragments. Morphologically, B.suzhenaesp. nov. is similar to the B.candidus/multicinctus/wanghaotingi complex but differs from these taxa by a combination of dental morphology, squamation, coloration pattern, as well as hemipenial morphology. A detailed description of the cranial osteology of the new species is given based on micro-CT tomography images. We revised the morphological characters of B.candidus/multicinctus/wanghaotingi complex and verified the validity of three species in this complex. The distribution of these species was revised; the records of B.candidus in China should be attributed to B.wanghaotingi. We also provide an updated key to species of Bungarus.

An integrative approach to infer systematic relationships and define species groups in the shrub frog genus Raorchestes, with description of five new species from the Western Ghats, India

The genus Raorchestes is a large radiation of Old World tree frogs for which the Western Ghats in Peninsular India is the major center for origin and diversification. Extensive studies on this group during the past two decades have resolved long-standing taxonomic confusions and uncovered several new species, resulting in a four-fold increase in the number of known Raorchestes frogs from this region. Our ongoing research has revealed another five new species in the genus, formally described as Raorchestes drutaahu sp. nov., Raorchestes kakkayamensis sp. nov., Raorchestes keirasabinae sp. nov., Raorchestes sanjappai sp. nov., and Raorchestes vellikkannan sp. nov., all from the State of Kerala in southern Western Ghats. Based on new collections, we also provide insights on the taxonomic identity of three previously known taxa. Furthermore, since attempts for an up-to-date comprehensive study of this taxonomically challenging genus using multiple integrative taxonomic approaches have been lacking, here we review the systematic affinities of all known Raorchestes species and define 16 species groups based on evidence from multi-gene (2,327 bp) phylogenetic analyses, several morphological characters (including eye colouration and pattern), and acoustic parameters (temporal and spectral properties, as well as calling height). The results of our study present novel insights to facilitate a better working taxonomy for this rather speciose and morphologically conserved radiation of shrub frogs. This will further enable proper field identification, provide momentum for multi-disciplinary studies, as well as assist conservation of one of the most colourful and acoustically diverse frog groups of the Western Ghats biodiversity hotspot.

Mitochondrial DNA revealed the validation of Quasipaa robertingeri (Amphibia: Anura: Dicroglossidae) and its population genetic diversity

The spiny frog Quasipaa robertingeri is endemic to a narrow region of southwest China and its taxonomic validation is still controversial. Based on COI gene sequences of 110 individuals from seven populations of Q. robertingeri and its related species, we investigated the phylogenetic position and population genetic structure of the species. Phylogenetic analyses indicated that Q. robertingeri was deeply genetically separated from its closely related species Q. boulengeri, indicating the validation of the species. All samples of Q. robertingeri were clustered into two divergent lineages. Haplotype network, AMOVA, and genetic distance estimations also supported the separations of the two groups. Neutrality tests indicated that one lineage has been likely independently experienced a recent population expansion, leading to a secondary contact area between the two lineages.

Revisiting the phylogenetic predicament of the genus Huia (Amphibia: Ranidae) using molecular data and tadpole morphology

Despite a considerable amount of research, the systematics of the ranid genus Huia have remained unresolved, mostly owing to insufficient sampling and morphological similarities. As currently circumscribed, Huia consists of five species, but multiple studies have consistently demonstrated that it is not a monophyletic genus. However, no study has approached the problem with adequate data and provided a systematically sound solution, leaving the genus to languish in a classification that is phylogenetically incoherent. We generated the most comprehensive sampling of Huia to date, based on extensive fieldwork in Java and Sumatra. Using an integrative taxonomy framework, we analysed four mitochondrial and two nuclear markers and, in conjunction with tadpole morphology, investigated the phylogenetics of Huia and its congeners. Corroborating previous studies, Huia is recovered as a paraphyletic group. Huia cavitympanum emerges as the sister taxon to Meristogenys. The remaining members of Huia form a monophyletic group, sister to the H. cavitympanum + Meristogenys clade. Our extensive geographical sampling in Sumatra and Java reveals multiple highly divergent lineages that potentially represent undescribed species. Using our expanded molecular and morphological dataset, we resolve the paraphyly of Huia by restricting the genus to its type species and propose a new genus to accommodate the strongly supported clade of Sumatran and Javan populations previously belonging to Huia.

Neuroprotective Effect of Protaetia brevitarsis seulensis' Water Extract on Trimethyltin-Induced Seizures and Hippocampal Neurodegeneration

This study aimed to investigate whether the Protaetia brevitarsis seulensis (PB)’ water extract (PBWE) ameliorates trimethyltin (TMT)-induced seizures and hippocampal neurodegeneration. To investigate the potential neuroprotective effect of the PBWE in vitro, a lactate dehydrogenase (LDH) assay was conducted in TMT-treated primary cultures of mouse hippocampal neurons. In TMT-treated adult C57BL/6 mice, behavioral and histopathological changes were evaluated by seizure scoring and Fluoro-Jade C staining, respectively. In our in vitro assay, we observed that pretreating mice hippocampal neuron cultures with the PBWE reduced TMT-induced cytotoxicity, as indicated by the decreased LDH release. Furthermore, pretreatment with the PBWE alleviated seizures and hippocampal neurodegeneration in TMT-treated mice. The antioxidant activity of the PBWE increased in a dose-dependent manner; moreover, pretreatment with the PBWE mitigated the TMT-induced Nrf2 stimulation. In addition, six major compounds, including adenine, hypoxanthine, uridine, adenosine, inosine, and benzoic acid, were isolated from the PBWE, and among them, inosine and benzoic acid have been confirmed to have an essential antioxidative activity. In conclusion, the PBWE ameliorated TMT-induced toxicity in hippocampal neurons in both in vitro and in vivo assays, through a potential antioxidative effect. Our findings suggest that the PBWE may have pharmacotherapeutic potential in neurodegenerative diseases such as seizures or epilepsy.

Description of a new horned toad of Megophrys Kuhl & Van Hasselt, 1822 (Amphibia, Megophryidae) from Zhejiang Province, China

A new species of the Asian horned toad genus Megophrys is described from Zhejiang Province, China, based on multiple data. Molecular phylogenetic analyses based on mitochondrial DNA indicated the new species as an independent clade deeply clustered into the Megophrys clade. The new species is identified from its congeners by a combination of the following characters: body size small (SVL 28.4-32.4 mm in males); vomerine teeth absent; tongue not notched behind; tympanum distinctly visible, oval; a small horn-like tubercle present at the edge of each upper eyelid; two metacarpal tubercles distinctly visible in hand; toes without webbing; heels overlapped when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level to middle of eye when leg stretched forward; an internal single subgular vocal sac in male; in breeding male, the nuptial pads present on the dorsal base of the first two fingers.

Description of a new Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from Guizhou Province, China

A new species of the genus Megophrys is described from Guizhou Province, China. Molecular phylogenetic analyses based on mitochondrial DNA indicated the new species as a clade clustered into the Megophrys clade. The new species can be distinguished from its congeners by a combination of the following characters: body size moderate (SVL 40.0-45.5 mm in males and 48.9-51.2 mm in females); vomerine teeth absent; tongue not notched behind; tympanum distinctly visible, oval; a small horn-like tubercle at the edge of each upper eyelid; two metacarpal tubercles in hand; toes with rudimentary webbing; heels overlapping when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level of mid-eye when leg stretched forward; in breeding males, an internal single subgular vocal sac present and brownish nuptial pads, made up of black nuptial spines, present on the dorsal base of the first two fingers.

A powerful long metabarcoding method for the determination of complex diets from faecal analysis of the European pond turtle (Emys orbicularis, L. 1758)

High‐throughput sequencing has become an accurate method for the identification of species present in soil, water, faeces, gut or stomach contents. However, information at the species level is limited due to the choice of short barcodes and based on the idea that DNA is too degraded to allow longer sequences to be amplified. We have therefore developed a long DNA metabarcoding method based on the sequencing of short reads followed by de novo assembly, which can precisely identify the taxonomic groups of organisms associated with complex diets, such as omnivorous individuals. The procedure includes 11 different primer pairs targeting the COI gene, the large subunit of the ribulose‐1,5‐bisphosphate carboxylase gene, the maturase K gene, the 28S rRNA and the trnL‐trnF chloroplastic region. We validated this approach using 32 faeces samples from an omnivorous reptile, the European pond turtle (Emys orbicularis, L. 1758). This metabarcoding approach was assessed using controlled experiments including mock communities and faecal samples from captive feeding trials. The method allowed us to accurately identify prey DNA present in the diet of the European pond turtles to the species level in most of the cases (82.4%), based on the amplicon lengths of multiple markers (168–1,379 bp, average 546 bp), and produced by de novo assembly. The proposed approach can be adapted to analyse various diets, in numerous conservation and ecological applications. It is consequently appropriate for detecting fine dietary variations among individuals, populations and species as well as for the identification of rare food items.

Xela DS2 and Xela VS2: Two novel skin epithelial-like cell lines from adult African clawed frog (Xenopus laevis) and their response to an extracellular viral dsRNA analogue

The skin epithelial layer acts as an important immunological barrier against pathogens and is capable of recognizing and responding to pathogen-associated molecular patterns (PAMPs) in human and mouse models. Although presumed, it is unknown whether amphibian skin epithelial cells exhibit the ability to respond to PAMPs such as viral double-stranded RNA (dsRNA). To address this, two cell lines from the dorsal skin (Xela DS2) and ventral skin (Xela VS2) of the African clawed frog (Xenopus laevis) were established. Xela DS2 and Xela VS2 cells have an epithelial-like morphology, express genes associated with epithelial cells, and lack senescence-associated beta-galactosidase activity. Cells grow optimally in 70% Leibovitz's L-15 medium supplemented with 15% fetal bovine serum at 26 °C. Upon treatment with poly(I:C), a synthetic analogue of viral dsRNA and known type I interferon inducer, Xela DS2 and Xela VS2 exhibit marked upregulation of key antiviral and pro-inflammatory transcripts suggesting frog epithelial cells participate in the recognition of extracellular viral dsRNA and production of local inflammatory signals; similar to human and mouse models. Currently, these are the only known Xenopus laevis skin epithelial-like cell lines and will be important for future research in amphibian epithelial cell biology, initial host-pathogen interactions, and rapid screening of the effects of environmental stressors, including contaminants, on frog skin epithelial cells.

Multiple data revealed two new species of the Asian horned toad Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from the eastern corner of the Himalayas

Multiple disciplines can help to discover cryptic species and resolve taxonomic confusions. The Asian horned toad genus Megophrys sensu lato as a diverse group was proposed to contain dozens of cryptic species. Based on molecular phylogenetics, morphology, osteology, and bioacoustics data, the species profiles of Megophrys toads in the eastern corner of Himalayas in Medog County, Tibet Autonomous Region, China was investigated. The results indicated that this small area harbored at least four Megophrys species, i.e., M. medogensis, M. pachyproctus, Megophrys zhoui sp. nov., and Megophrys yeae sp. nov., the latter two being described in this study. Additionally, the mitochondrial DNA trees nested the low-middle-elevation and high-elevation groups of M. medogensis into a monophyletic group, being in discordance with the paraphyletic relationship between them revealed in the nuclear DNA trees. The findings highlighted the underestimated biodiversity in Himalayas, and further indicated that the Megophrys toads here have been probably experienced complicated evolutionary history, for example, introgression between clades or incomplete lineage sorting and niche divergences in microhabitats. Anyway, it is urgent for us to explore the problems because these toads are suffering from increasing threats from human activities and climatic changes.

Description of a new horned toad of Megophrys Kuhl & Van Hasselt, 1822 (Anura, Megophryidae) from southwest China

A new species of the genus Megophrys is described from Guizhou Province, China. Molecular phylogenetic analyses supported the new species as an independent clade nested into the Megophrys. The new species could be distinguished from its congeners by a combination of the following characters: body size moderate (SVL 49.3–58.2 mm in males); vomerine ridges present distinctly, vomerine teeth present; tongue feebly notched behind; tympanum distinctly visible, oval; two metacarpal tubercles in hand; toes with one-third webbing and wide lateral fringes; heels overlapped when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level between tympanum and eye when leg stretched forward; an internal single subgular vocal sac present in male; in breeding male, the nuptial pads with large and sparse black nuptial spines present on the dorsal bases of the first two fingers.

Divergence, gene flow, and the origin of leapfrog geographic distributions: The history of colour pattern variation in Phyllobates poison-dart frogs

The geographic distribution of phenotypic variation among closely related populations is a valuable source of information about the evolutionary processes that generate and maintain biodiversity. Leapfrog distributions, in which phenotypically similar populations are disjunctly distributed and separated by one or more phenotypically distinct populations, represent geographic replicates for the existence of a phenotype, and are therefore especially informative. These geographic patterns have mostly been studied from phylogenetic perspectives to understand how common ancestry and divergent evolution drive their formation. Other processes, such as gene flow between populations, have not received as much attention. Here, we investigate the roles of divergence and gene flow between populations in the origin and maintenance of a leapfrog distribution in Phyllobates poison frogs. We found evidence for high levels of gene flow between neighbouring populations but not over long distances, indicating that gene flow between populations exhibiting the central phenotype may have a homogenizing effect that maintains their similarity, and that introgression between 'leapfroging' taxa has not played a prominent role as a driver of phenotypic diversity in Phyllobates. Although phylogenetic analyses suggest that the leapfrog distribution was formed through independent evolution of the peripheral (i.e. leapfrogging) populations, the elevated levels of gene flow between geographically close populations poise alternative scenarios, such as the history of phenotypic change becoming decoupled from genome-averaged patterns of divergence, which we cannot rule out. These results highlight the importance of incorporating gene flow between populations into the study of geographic variation in phenotypes, both as a driver of phenotypic diversity and as a confounding factor of phylogeographic inferences.

A new species of the genus Acanthosaura (Squamata, Agamidae) from Yunnan, China, with comments on its conservation status

A new species of Acanthosaura from Yunnan, China, is described based on morphological and genetic data. The new species can be separated from all other species of the genus by having a different shape of the black eye patch, a different coloration of the postorbital and occipital spines and nuchal crest, and a different color of the gular pouch. Genetically, uncorrected sequence divergences of COI between the new species and investigated congeners ranged from 16.12% to 24.11%. The conservation status of the new species is also discussed.

Review of the genus Brachytarsophrys (Anura: Megophryidae), with revalidation of Brachytarsophrys platyparietus and description of a new species from China

The genus-level recognition of monophyletic short-legged toads (Brachytarsophrys) has been recently implicated in the taxonomic debate of Megophrys sensu lato. In the present study, Brachytarsophrys is reasonably regarded as a distinct genus based on significant morphological differentiations and recent molecular analyses. Furthermore, a comprehensive review of this genus is performed, with two species groups proposed based on morphological differences and phylogenetic relationships. Particularly, Brachytarsophrys platyparietus is removed as a synonym of Brachytarsophrys carinense and considered a valid species due to significant genetic divergence and distinct morphological differences. In addition, a new species, Brachytarsophrys orientalissp. nov., is described based on a series of specimens collected from southeastern China. This work takes the member species of the genus Brachytarsophrys to seven, suggesting that the diversity of Brachytarsophrys is underestimated. In addition, the genus levels of other monophyletic groups within the subfamily Megophryinae are discussed.

Mantidis Oötheca (mantis egg case) original species identification via morphological analysis and DNA barcoding

ETHNOPHARMACOLOGICAL RELEVANCE

Mantidis Oötheca (mantis egg case; sangpiaoxiao) is a medicine from an insect source, which has been widely used in Asian countries. However, misidentification due to a lack of information given variations in the medicinal portion of the ootheca and morphological similarities of the ootheca as an egg chamber.

AIM OF THE STUDY

Thus, this study aims to provide the first comprehensive data for discriminating authentic of Mantidis Oötheca. Here, we provide detailed ootheca morphology and their molecular information to accurately identify Mantidis Oötheca.

MATERIALS AND METHODS

Oothecae of Tenodera angustipennis (Saussure, 1869), Tenodera sinensis (Saussure, 1871), Hierodula patellifera Serville, 1839, and Hierodula sp. were used in the comparative morphological, principal component analysis, and DNA barcoding.

RESULTS

The morphological analyses revealed that the emergence area, outline, angle of distal end, width of air-filled layer, and weight are useful diagnostic characters. Using these quantitative and qualitative characteristics, we developed the effective identification key. Furthermore, our CO1 sequences from all individuals were monophyletic with high bootstrap values at genus and species levels. Moreover, morphological identification using our developed key among all studied individuals agreed with molecular identification results using CO1 barcoding data.

CONCLUSIONS

These multilateral approaches, including morphological, statistical, and DNA barcoding methods are highly reliable identification tools. Moreover, our diagnostic key characteristics and molecular barcoding should aid in the accurate identification, authentication, and quality control of Mantidis Oötheca medicinal materials.

Rapid and Simple Species Identification of Cicada Exuviae Using COI-Based SCAR Assay

Cicadidae periostracum (CP), the medicinal name of cicada exuviae, is well-known insect-derived traditional medicine with various pharmacological effects, e.g., anticonvulsive, anti-inflammatory, antitussive, and anticancer effects; it is also beneficial for the treatment of Parkinson’s disease. For appropriate CP application, accurate species identification is essential. The Korean pharmacopoeia and the pharmacopoeia of the People’s Republic of China define Cryptotympana atrata as the only authentic source of CP. Species identification of commercially distributed CP based on morphological features, however, is difficult because of the combined packaging of many cicada exuviae in markets, damage during distribution, and processing into powder form. DNA-based molecular markers are an excellent alternative to morphological detection. In this study, the mitochondrial cytochrome c oxidase subunit I sequences of C. atrata, Meimuna opalifera, Platypleura kaempferi, and Hyalessa maculaticollis were analyzed. On the basis of sequence alignments, we developed sequence-characterized amplified-region (SCAR) markers for efficient species identification. These markers successfully discriminated C. atrata from the three other cicada species, and detected the adulteration of market CP samples. This SCAR assay is a rapid, simple, cheap, reliable, and reproducible method for species identification, regardless of sample form and status, and contributes to CP quality control.

The evolution of polymorphism in the warning coloration of the Amazonian poison frog Adelphobates galactonotus

While intraspecific variation in aposematic signals can be selected for by different predatory responses, their evolution is also contingent on other processes shaping genetic variation. We evaluate the relative contributions of selection, geographic isolation, and random genetic drift to the evolution of aposematic color polymorphism in the poison frog Adelphobates galactonotus, distributed throughout eastern Brazilian Amazonia. Dorsal coloration was measured for 111 individuals and genetic data were obtained from 220 individuals at two mitochondrial genes (mtDNA) and 7963 Single Nucleotide Polymorphisms (SNPs). Four color categories were described (brown, blue, yellow, orange) and our models of frog and bird visual systems indicated that each color was distinguishable for these taxa. Using outlier and correlative analyses we found no compelling genetic evidence for color being under divergent selection. A time-calibrated mtDNA tree suggests that the present distribution of dorsal coloration resulted from processes occurring during the Pleistocene. Separate phylogenies based on SNPs and mtDNA resolved the same well supported clades, each containing different colored populations. Ancestral character state analysis provided some evidence for evolutionary transitions in color type. Genetic structure was more strongly associated with geographic features, than color category, suggesting that the distribution of color is explained by localized processes. Evidence for geographic isolation together with estimates of low effective population size implicates drift as playing a key role in color diversification. Our results highlight the relevance of considering the neutral processes involved with the evolution of traits with important fitness consequences.

A new species of the Music frog Nidirana (Anura, Ranidae) from Guizhou Province, China

The Music frog genus Nidirana is widely distributed in East and South Asia. Here, a new species of the genus is described from southwestern China. Phylogenetic analyses based on the mitochondrial 16S rRNA and COI gene sequences supported the new species as a clade closely related to N. leishanensis, N. hainanensis, N. chapaensis, N. daunchina, and N. yaoica. The new species could be distinguished from its congeners by a combination of the following characters: body of medium size (SVL 41.2-43.5 mm in males and 44.7 mm in female); lateroventral groove only present on toes; relative finger lengths: II < IV < I < III; three metatarsal tubercles on palm; heels overlapping when hindlimbs flexed at right angles to axis of body; tibiotarsal articulation reaching the level of eye when leg stretched forward; a pair of subgular internal vocal sacs at corners of throat in male; nuptial pad present on the inner side of base of fingers I in breeding male; tadpole labial tooth row formula with 1:1+1/1+1:2; in males, the advertisement call contains two kinds of notes and one call contains 2-6 repeated regular notes.

A new Megophrys Kuhl & Van Hasselt (Amphibia, Megophryidae) from southeastern China

A new species of the genus Megophrys from Zhejiang Province, China is described. Molecular phylogenetic analyses supported the new taxon as an independent clade nested into the Megophrys clade and sister to M.lishuiensis. The new species could be distinguished from its congeners by a combination of the following morphological characteristics: (1) small size (SVL 31.0–36.3 mm in male and 41.6 mm in female); (2) vomerine ridge present and vomerine teeth absent; (3) tongue not notched behind; (4) a small horn-like tubercle at the edge of each upper eyelid; (5) tympanum distinctly visible, rounded; (6) two metacarpal tubercles in hand; (7) relative finger lengths: II < I < IV < III; (8) toes with rudimentary webbing at bases; (9) heels overlapping when thighs are positioned at right angles to the body; (10) tibiotarsal articulation reaching tympanum to eye when leg stretched forward; (11) an internal single subgular vocal sac in male; (12) in breeding male, the nuptial pads with black nuptial spines on the dorsal bases of the first and second fingers.

Distinguishing Anuran species by high-resolution melting analysis of the COI barcode (COI-HRM)

Taxonomic identification can be difficult when two or more species appear morphologically similar. DNA barcoding based on the sequence of the mitochondrial cytochrome c oxidase 1 gene (COI) is now widely used in identifying animal species. High-resolution melting analysis (HRM) provides an alternative method for detecting sequence variations among amplicons without having to perform DNA sequencing. The purpose of this study was to determine whether HRM of the COI barcode can be used to distinguish animal species. Using anurans as a model, we found distinct COI melting profiles among three congeners of both Lithobates spp. and Hyla spp. Sequence variations within species shifted the melting temperature of one or more melting domains slightly but do not affect the distinctness of the melting profiles for each species. An NMDS ordination plot comparing melting peak profiles among eight Anuran species showed overlapping profiles for Lithobates sphenocephala and Gastrophryne carolinensis. The COI amplicon for both species contained two melting domains with melting temperatures that were similar between the two species. The two species belong to two different families, highlighting the fact that COI melting profiles do not reveal phylogenetic relationships but simply reflect DNA sequence differences among stretches of DNA within amplicons. This study suggests that high-resolution melting analysis of COI barcodes (COI-HRM) may be useful as a simple and rapid method to distinguish animal species that appear morphologically similar.

Comparative Morphological, Ultrastructural, and Molecular Studies of Four Cicadinae Species Using Exuvial Legs

Previous studies have suggested that exuviae can be used for the identification of cicada species, but the precise characteristics that differ among species have not been determined. Thus, we performed the first comparative analyses of the leg morphology, ultrastructure, and mitochondrial DNA sequences of exuviae of four dominant cicada species in Korea, Hyalessa maculaticollis (Motschulsky, 1866), Meimuna opalifera (Walker, 1850), Platypleura kaempferi (Fabricius, 1794) and Cryptotympana atrata (Fabricius, 1775), the source of Cicadidae Periostracum, a well-known traditional medicine. A morphological analysis revealed that the profemur length, femoral tooth angle, and distance between the intermediate and last tooth of the femoral comb are useful characteristics for identification. We also evaluated the usefulness of the size, degree of reflex, and number of spines on the mid-legs and hind legs as diagnostic features. An ultrastructural study showed that Meimuna opalifera has a unique surface pattern on the legs. The sequences obtained using exuviae were identical to previously obtained sequences for adult tissues. Moreover, in a phylogenetic analysis using CO1 sequences, each species formed a monophyletic cluster with high bootstrap support. Accordingly, multiple methodological approaches using exuviae might provide highly reliable identification tools. The integrative data provide useful characteristics for the exuviae-based identification of closely related species and for further taxonomic and systematic studies of Cicadinae.

A new species of the Asian music frog genus Nidirana (Amphibia, Anura, Ranidae) from Southwestern China

The Asian music frog genus Nidirana is widely distributed in East and Southeastern Asia. Systematic profiles of the group remain on debate, and cryptic species are expected especially in the species with wide distributional range. Here, we describe a new species of the genus from Southwestern China. Phylogenetic analyses based on mitochondrial DNA and nuclear DNA supported the new species as an independent clade nested into the Nidirana clade and sister to N. hainanensis. Morphologically, the new species could be distinguished from its congeners by a combination of the following characters: a large body size in males (SVL > 49 mm); the presence of lateroventral grooves both on fingers and toes; relative finger lengths: II < IV < I < III; tibiotarsal articulation reaching the level between eye and nostril when leg stretched forward; a pair of subgular internal vocal sacs at corners of throat in males; nuptial pad present on the inner side of base of fingers I and II in males in breading season; webbing formula: I 2 –21/3 II 2 –22/3 III 31/2 –32/3 IV 32/3 –3V. The findings provided a better knowledge on phylogenetic assignments of the genus Nidirana, and indicated future deeper investigations necessarily for exploring systematic settings of the group.

A new species of the endemic Himalayan genus Liurana (Anura, Ceratobatrachidae) from southeastern Tibet, China, with comments on the distribution, reproductive biology, and conservation of the genus

A new species of the genus Liurana Dubois, 1986 is described from Medog County, Tibet, China, based on morphological and molecular data. The new species can be differentiated from all other congeners by the following combination of characters: (1) head wider than long; (2) tympanum distinct and large; (3) hindlimb long, tibiotarsal articulation beyond tip of snout when adpressed; (4) belly with flat tubercles, cloacal region with small tubercles; (5) transverse bands distinctly on dorsal limbs, four bands on thigh and three on tibia; and, (6) dark brown marbled patterns or speckles on white belly. Here, we also discuss the distribution pattern of Liurana in the East Himalaya region, the role of the Yarlung Tsangpo River in the speciation and genetic isolation of congeners, the direct developmental mode of reproduction, and the two different ecotypes of the genus. Lastly, we provide conservation recommendations for the genus in southeastern Tibet.

Genetic diversity and population structure of goliath frogs (Conraua goliath) from Cameroon

The goliath frog (Conraua goliath) is an Endangered species exclusively found in Cameroon and Equatorial Guinea. Climate change, deforestation and overhunting are principal causes driving this species to extinction. Therefore, a better understanding of the genetic diversity and population structure of this species is necessary to improve conservation efforts. Here we used two mitochondrial genes (Cytochrome Oxidase subunit 1 (COI) and 16S) extracted from 54 C. goliath individuals from six localities in Cameroon to examine their genetic diversity. The result shows a low DNA substitution between the sequences. There were four 16S and two COI haplotypes in total. Overall, genetic diversity was very low for all the genes with nucleotide diversity of 0.00106 and 0.00007 for 16S and COI respectively. The Tajima D and Fu Fs statistics were negative. The TCS haplotype network revealed a predominant and ancestral haplotype (H1) for these genes which is distributed in the 6 populations. Pairwise genetic differentiation (F_ST) generated between these populations using 16S revealed very high differentiation between populations from Nkam and Mungo Administrative Divisions in Cameroon. In contrast, we observed low differentiation among the geographically clustered Mungo and Nkam populations. Overall, human activities and perhaps climate change can appear to have depleted genetic diversity in the scattered populations that remain of this amphibian. To sustain the Goliath frog, we suggest to the Cameroonian government to implement more effective strategies to conserve and manage remnant populations of this iconic species through more effort against poaching which contribute to reduce the genetic diversity.

Reconciling the Mitonuclear Compatibility Species Concept with Rampant Mitochondrial Introgression

The mitonuclear compatibility species concept defines a species as a population that is genetically isolated from other populations by uniquely coadapted mitochondrial (mt) and nuclear genes. A key prediction of this hypothesis is that the mt genotype of each species will be functionally distinct and that introgression of mt genomes will be prevented by mitonuclear incompatibilities that arise when heterospecific mt and nuclear genes attempt to cofunction to enable aerobic respiration. It has been proposed, therefore, that the observation of rampant introgression of mt genotypes from one species to another constitutes a strong refutation of the mitonuclear speciation. The displacement of a mt genotype from a nuclear background with which it co-evolved to a foreign nuclear background will necessarily lead to fitness loss due to mitonuclear incompatibilities. Here I consider two potential benefits of mt introgression between species that may, in some cases, overcome fitness losses arising from mitonuclear incompatibilities. First, the introgressed mt genotype may be better adapted to the local environment than the native mt genotype such that higher fitness is achieved through improved adaptation via introgression. Second, if the mitochondria of the recipient taxa carry a high mutational load, then introgression of a foreign, less corrupt mt genome may enable the recipient taxa to escape its mutational load and gain a fitness advantage. Under both scenarios, fitness gains from novel mt genotypes could theoretically compensate for the fitness that is lost via mitonuclear incompatibility. I also consider the role of endosymbionts in non-adaptive rampant introgression of mt genomes. I conclude that rampant introgression is not necessarily evidence against the idea of tight mitonuclear coadaptation or the mitonuclear compatibility species concept. Rampant mt introgression will typically lead to erasure of species but in some cases could lead to hybrid speciation.

Cryptic diversity in Lithobateswarszewitschii (Amphibia, Anura, Ranidae)

Lithobateswarszewitschii is a species of ranid frog distributed from southern Honduras to Panama. This species suffered severe population declines at higher elevations (above 500 m a.s.l.) from the 1980s to early 1990s, but there is more recent evidence of recovery in parts of its range. Here we advocate for the status of Lithobateswarszewitschii as a candidate cryptic species complex based on sequence data from mitochondrial genes CO1 and 16S. Using concatenated phylogenies, nucleotide diversity (K2P-π), net between group mean distance (NBGMD) (πnet) and species delimitation methods, we further elucidate cryptic diversity within this species. All phylogenies display polyphyletic lineages within Costa Rica and Panama. At both loci, observed genetic polymorphism (K2P-π) is also high within and between geographic populations, surpassing proposed species threshold values for amphibians. Additionally, patterns of phylogeographic structure are complicated for this species, and do not appear to be explained by geographic barriers or isolation by distance. These preliminary findings suggest L.warszewitschii is a wide-ranging species complex. Therefore, we propose further research within its wider range, and recommend integrative taxonomic assessment is merited to assess species status.

Genetic variation and cryptic lineage diversity of the Nigerian red-headed rock agama Agama agama associate with eco-geographic zones

Nigeria is an Afrotropical region with considerable ecological heterogeneity and levels of biotic endemism. Among its vertebrate fauna, reptiles have broad distributions, thus, they constitute a compelling system for assessing the impact of ecological variation and geographic isolation on species diversification. The red-headed rock agama, Agama agama, lives in a wide range of habitats and, thus, it may show genetic structuring and diversification. Herein, we tested the hypothesis that ecology affects its genetic structure and population divergence. Bayesian inference phylogenetic analysis of a mitochondrial DNA (mtDNA) gene recovered four well-supported matrilines with strong evidence of genetic structuring consistent with eco-geographic regions. Genetic differences among populations based on the mtDNA also correlated with geographic distance. The ecological niche model for the matrilines had a good fit and robust performance. Population divergence along the environmental axes was associated with climatic conditions, and temperature ranked highest among all environmental variables for forest specialists, while precipitation ranked highest for the forest/derived savanna, and savanna specialists. Our results cannot reject the hypothesis that niche conservatism promotes geographic isolation of the western populations of Nigerian A. agama. Thus, ecological gradients and geographic isolation impact the genetic structure and population divergence of the lizards. This species might be facing threats due to recent habitat fragmentation, especially in western Nigeria. Conservation actions appear necessary.

New microhylid frog genus from Peninsular India with Southeast Asian affinity suggests multiple Cenozoic biotic exchanges between India and Eurasia

Anurans in Peninsular India exhibit close biogeographical links with Gondwana as well as Laurasia, often explainable by the geological history of the Indian subcontinent; its breakup from Gondwanan landmasses followed by long isolation that resulted in diversification of endemic lineages, and subsequent land connections with Asia that enabled dispersal of widespread groups. Although widely distributed, the frog subfamily Microhylinae mostly comprises of geographically restricted genera found either in Southeast and East Asia or Peninsular India and Sri Lanka. Here we report a previously unknown microhylid from the Western Ghats in Peninsular India with closest relatives found over 2,000 km away in Southeast Asia. Based on integrated evidence from mitochondrial and nuclear DNA, adult and tadpole morphology, hand musculature, male advertisement call, and geographical distance, we recognize this enigmatic frog as a distinct new species and genus endemic to the Western Ghats. The discovery of Mysticellus franki gen. et sp. nov. and its close evolutionary relationship with the Southeast Asian genus Micryletta also provide insights on the biogeography of Microhylinae. Genus-level divergences within the subfamily suggest multiple Cenozoic biotic exchange events between India and Eurasia, particularly through postulated Eocene land bridges via Southeast Asia prior to accretion of the two landmasses.

Barcoding the Neotropical freshwater fish fauna using a new pair of universal COI primers with a discussion of primer dimers and M13 primer tails

Designing primers for DNA barcoding is a significant challenge for the rich Neotropical fish fauna, which is comprised of ∼6000 species. Previously, researchers required multiple pairs of PCR primers or primer cocktails to obtain standard COI (i.e., mitochondrial cytochrome c oxidase subunit I) barcode sequences from assemblages of freshwater fish in this region. To simplify DNA barcoding and metabarcoding studies of Neotropical freshwater fish, we present a new pair of COI primers, which have yielded high quality barcodes across six teleost orders-Characiformes, Cichliformes, Cyprinodontiformes, Gymnotiformes, Siluriformes, and Synbranchiformes-native to South America. Following previous fish barcoding studies, we also tailed our primers with M13 forward and reverse primers to facilitate the DNA sequencing process. Although this practice generates primer dimers, we obtained complete and high quality COI barcode sequences for all samples. We discuss the problem of primer dimers and suggest strategies for neutralizing their influence on data quality.

Description of two cryptic species of the Amolopsricketti group (Anura, Ranidae) from southeastern China

Two cryptic species, which were previously reported as Amolopsricketti, are revealed on the basis of significant morphological and genetic divergences. Amolopssinensissp. n. from central Guangdong, northeastern Guangxi and southwestern Hunan can be distinguished by the longitudinal glandular folds on the skin of the shoulders and other character combinations. Amolopsyatsenisp. n. from the coastal hills of west Guangdong can be distinguished by the dense tiny round translucent, or white, spines on the dorsal skin of the body, dorsal and dorsolateral skin of the limbs, and other character combinations. The phylogenetic interrelationships of the A.ricketti group have been inferred as (A.wuyiensis + A.ricketti) + (A.yunkaiensis + (A.albispinus + (A.sinensissp. n. + A.yatsenisp. n.))). This work indicates that the current records of A.ricketti might be a species complex composed of multiple species, and further work is needed to figure out this puzzle.

Past vicariance promoting deep genetic divergence in an endemic frog species of the Espinhaço Range in Brazil: The historical biogeography of Bokermannohyla saxicola (Hylidae)

The highland endemic frog Bokermannohyla saxicola occurs within the Espinhaço Range, the most extensive and continuous orogenic belt of the Brazilian territory, located in southeastern Brazil. We used mitochondrial DNA markers to test for spatial structure, to investigate the likely influence of past vicariant events, to evaluate demographic dynamics along the species range, and to understand the role of habitat discontinuities in promoting connectivity and diversity along the range. We found four major monophyletic lineages, each one associated with distinct mountain tops. The divergence time found between the four main clades clearly pre-dated the Pleistocene, except for the most recent separation. We observed no signs of population expansion for most of the sampling sites along the range, and a higher genetic diversity in the most continuous and central highland plateau, compared to smaller marginal regions. The Espinhaço Range harbors four deeply divergent lineages of B. saxicola within areas restricted by barriers for millions of years. These relatively isolated populations were kept apart by discontinuities represented by lowland habitats between mountain tops. Most of the lineage divergences occurred earlier than the Pleistocene, thus they cannot be solely explained by climatic oscillations of this epoch. However, within-lineage divergence times were all dated from the Pleistocene, suggesting an important effect in population dynamics. We also suggest that some marginal populations like those from Serra Negra and Serra de Itacambira can be the result of recent colonization events. Finally, in the southern Espinhaço region, the most continuous central highland area shows greater genetic diversity than the marginal discontinuous areas, where we have also observed a significant correlation between genetic and geographic distances. Bokermannohyla saxicola is a good model to study the biogeography of the Espinhaço Range because its high genetic structure reflects ancient as well as recent geological/climatic events, with important implications for conservation.

eDNA metabarcoding as a new surveillance approach for coastal Arctic biodiversity

Because significant global changes are currently underway in the Arctic, creating a large-scale standardized database for Arctic marine biodiversity is particularly pressing. This study evaluates the potential of aquatic environmental DNA (eDNA) metabarcoding to detect Arctic coastal biodiversity changes and characterizes the local spatio-temporal distribution of eDNA in two locations. We extracted and amplified eDNA using two COI primer pairs from ~80 water samples that were collected across two Canadian Arctic ports, Churchill and Iqaluit, based on optimized sampling and preservation methods for remote regions surveys. Results demonstrate that aquatic eDNA surveys have the potential to document large-scale Arctic biodiversity change by providing a rapid overview of coastal metazoan biodiversity, detecting nonindigenous species, and allowing sampling in both open water and under the ice cover by local northern-based communities. We show that DNA sequences of ~50% of known Canadian Arctic species and potential invaders are currently present in public databases. A similar proportion of operational taxonomic units was identified at the species level with eDNA metabarcoding, for a total of 181 species identified at both sites. Despite the cold and well-mixed coastal environment, species composition was vertically heterogeneous, in part due to river inflow in the estuarine ecosystem, and differed between the water column and tide pools. Thus, COI-based eDNA metabarcoding may quickly improve large-scale Arctic biomonitoring using eDNA, but we caution that aquatic eDNA sampling needs to be standardized over space and time to accurately evaluate community structure changes.

DNA Barcoding for the Identification and Authentication of Animal Species in Traditional Medicine

Animal-based traditional medicine not only plays a significant role in therapeutic practices worldwide but also provides a potential compound library for drug discovery. However, persistent hunting and illegal trade markedly threaten numerous medicinal animal species, and increasing demand further provokes the emergence of various adulterants. As the conventional methods are difficult and time-consuming to detect processed products or identify animal species with similar morphology, developing novel authentication methods for animal-based traditional medicine represents an urgent need. During the last decade, DNA barcoding offers an accurate and efficient strategy that can identify existing species and discover unknown species via analysis of sequence variation in a standardized region of DNA. Recent studies have shown that DNA barcoding as well as minibarcoding and metabarcoding is capable of identifying animal species and discriminating the authentics from the adulterants in various types of traditional medicines, including raw materials, processed products, and complex preparations. These techniques can also be used to detect the unlabelled and threatened animal species in traditional medicine. Here, we review the recent progress of DNA barcoding for the identification and authentication of animal species used in traditional medicine, which provides a reference for quality control and trade supervision of animal-based traditional medicine.

A new species of the genus Rana from Henan, central China (Anura, Ranidae)

A new species of brown frog Rana luanchuanensis Zhao & Yuan, sp. n. is described from Luanchuan County, western Henan, central China. The mitochondrial genealogy suggests that the new species is the sister taxon to the clade including R. amurensis and R. coreana, and is separated by uncorrected pairwise distances more than 12.5%. Morphologically, this new species differs from its congeners by a suite of characters. Analyses of partial sequences of cytochrome oxidase subunit I (COI) resolve the new species as a single matriline.

How many species and under what names? Using DNA barcoding and GenBank data for west Central African amphibian conservation

Development projects in west Central Africa are proceeding at an unprecedented rate, often with little concern for their effects on biodiversity. In an attempt to better understand potential impacts of a road development project on the anuran amphibian community, we conducted a biodiversity assessment employing multiple methodologies (visual encounter transects, auditory surveys, leaf litter plots and pitfall traps) to inventory species prior to construction of a new road within the buffer zone of Moukalaba-Doudou National Park, Gabon. Because of difficulties in morphological identification and taxonomic uncertainty of amphibian species observed in the area, we integrated a DNA barcoding analysis into the project to improve the overall quality and accuracy of the species inventory. Based on morphology alone, 48 species were recognized in the field and voucher specimens of each were collected. We used tissue samples from specimens collected at our field site, material available from amphibians collected in other parts of Gabon and the Republic of Congo to initiate a DNA barcode library for west Central African amphibians. We then compared our sequences with material in GenBank for the genera recorded at the study site to assist in identifications. The resulting COI and 16S barcode library allowed us to update the number of species documented at the study site to 28, thereby providing a more accurate assessment of diversity and distributions. We caution that because sequence data maintained in GenBank are often poorly curated by the original submitters and cannot be amended by third-parties, these data have limited utility for identification purposes. Nevertheless, the use of DNA barcoding is likely to benefit biodiversity inventories and long-term monitoring, particularly for taxa that can be difficult to identify based on morphology alone; likewise, inventory and monitoring programs can contribute invaluable data to the DNA barcode library and the taxonomy of complex groups. Our methods provide an example of how non-taxonomists and parataxonomists working in understudied parts of the world with limited geographic sampling and comparative morphological material can use DNA barcoding and publicly available sequence data (GenBank) to rapidly identify the number of species and assign tentative names to aid in urgent conservation management actions and contribute to taxonomic resolution.

Phylogenetic structure and ancestry of Korean clawed salamander, Onychodactylus koreanus (Caudata: Hynobiidae)

Onychodactylus koreanus, a hynobiid salamander species endemic to the Korean Peninsula, can be regarded as a strict ecological specialist, probably vulnerable to anthropogenic environmental modifications and climate change. We used mitochondrial cytochrome b gene to analyze the genetic diversity and phylogenetic structure of O. koreanus from 19 populations collected in an attempt to cover its major distribution within South Korea. A total of 76 haplotypes of O. koreanus obtained in our analyses could be subdivided into three phylogenetic clades, KR, NE and SE. Clade KR haplotypes occur in most of the regions throughout the Korean Peninsula with four distinct subclades (KR I-IV). Clade NE and SE haplotypes were only observed in two populations YY and YS, respectively. Haplotype sharing was scarce even among populations in geographical proximity, and most of the populations were represented by a single clade or subclade, indicating the low level of gene flow among populations. O. koreanus likely originated from the historical southward dispersal of its ancestral lineages following divergence from Chinese O. zhaoermii that was recovered as the sister of O. koreanus in our phylogenetic analysis. Our results have critical implications for the taxonomic status of O. koreanus and its long-term management plan.

The marker choice: Unexpected resolving power of an unexplored CO1 region for layered DNA barcoding approaches

The potential of DNA barcoding approaches to identify single species and characterize species compositions strongly depends on the marker choice. The prominent “Folmer region”, a 648 basepair fragment at the 5’ end of the mitochondrial CO1 gene, has been traditionally applied as a universal DNA barcoding region for metazoans. In order to find a suitable marker for biomonitoring odonates (dragonflies and damselflies), we here explore a new region of the CO1 gene (CO1B) for DNA barcoding in 51 populations of 23 dragonfly and damselfly species. We compare the “Folmer region”, the mitochondrial ND1 gene (NADH dehydrogenase 1) and the new CO1 region with regard to (i) speed and reproducibility of sequence generation, (ii) levels of homoplasy and (iii) numbers of diagnostic characters for discriminating closely related sister taxa and populations. The performances of the gene regions regarding these criteria were quite different. Both, the amplification of CO1B and ND1 was highly reproducible and CO1B showed the highest potential for discriminating sister taxa at different taxonomic levels. In contrast, the amplification of the “Folmer region” using the universal primers was difficult and the third codon positions of this fragment have experienced nucleotide substitution saturation. Most important, exploring this new barcode region of the CO1 gene identified a higher discriminating power between closely related sister taxa. Together with the design of layered barcode approaches adapted to the specific taxonomic “environment”, this new marker will further enhance the discrimination power at the species level.

Rapid forest clearing in a Myanmar proposed national park threatens two newly discovered species of geckos (Gekkonidae: Cyrtodactylus)

Myanmar’s recent transition from military rule towards a more democratic government has largely ended decades of political and economic isolation. Although Myanmar remains heavily forested, increased development in recent years has been accompanied by exceptionally high rates of forest loss. In this study, we document the rapid progression of deforestation in and around the proposed Lenya National Park, which includes some of the largest remaining areas of lowland evergreen rainforest in mainland Southeast Asia. The globally unique forests in this area are rich in biodiversity and remain a critical stronghold for many threatened and endangered species, including large charismatic fauna such as tiger and Asian elephant. We also conducted a rapid assessment survey of the herpetofauna of the proposed national park, which resulted in the discovery of two new species of bent-toed geckos, genus Cyrtodactylus. We describe these new species, C. lenyasp. nov. and C. payarhtanensissp. nov., which were found in association with karst (i.e., limestone) rock formations within mature lowland wet evergreen forest. The two species were discovered less than 35 km apart and are each known from only a single locality. Because of the isolated nature of the karst formations in the proposed Lenya National Park, these geckos likely have geographical ranges restricted to the proposed protected area and are threatened by approaching deforestation. Although lowland evergreen rainforest has vanished from most of continental Southeast Asia, Myanmar can still take decisive action to preserve one of the most biodiverse places on Earth.

Phylogeny and biogeography of South Chinese brown frogs (Ranidae, Anura)

Few studies have explored the role of Cenozoic tectonic evolution in shaping the patterns and processes of extant animal distributions in and around East Asia. In this study, we selected South Chinese brown frogs as a model to examine the phylogenetic and biogeographical consequences of Miocene tectonic events within South China and its margins. We used mitochondrial and nuclear molecular data to reconstruct phylogenetic interrelationships among Chinese brown frogs using Bayesian and maximum likelihood analyses. The phylogeny results show that there are four main clades of Chinese brown frogs. Excepting the three commonly known Chinese brown frog species groups, R. maoershanensis forms an independent clade nearest to the R. japonica group. Phylogeny and P-distance analyses confirmed R. maoershanensis as a valid species. Among South Chinese brown frogs, there are four subclades associated with four geographical areas: (I) R. maoershanensis; (II) R. japonica; (III) R. chaochiaoensis; and (IV) other species of the R. longicrus species group. Divergence times, estimated using mitochondrial sequences, place the vicariance events among the four subclades in the middle to late Miocene epoch. Our results suggest that (1) South Chinese brown frogs originated due to a vicariance event separating them from the R. chensinensis species group at the time of the Geological movement (~18 million years ago, Ma) in southern Tibet and the Himalayan region; (2) the separation and speciation of R. maoershanensis from the R. japonica group occurred due to the dry climate at approximately 16 Ma; (3) South Chinese brown frogs migrated from South China to Japan at the time (~10.8 Ma) that the global sea-level fell and the East China Sea Shelf Basin was swamp facies, when a land gallery may have formed across the sea to connect the two areas; and (4) R. chaochiaoensis separated from other species of the R. longicrus species group during the uplift of the Tibetan Plateau at approximately 9.5 Ma.

Meeting the challenge of DNA barcoding Neotropical amphibians: polymerase chain reaction optimization and new COI primers

Amphibians are one of the most threatened vertebrate classes, yet at the same time new species are being described every year, demonstrating that the number of existing species is grossly underestimated. In groups such as amphibians, with high extinction rates and poorly known species boundaries, DNA barcoding is a tool that can rapidly assess genetic diversity and estimate species richness for prioritizing conservation decisions. However, reliable recovery of the 5' region of the cytochrome c oxidase subunit 1 (COI) gene is critical for the ongoing effort to gather DNA barcodes for all amphibian species. Here, we provide new PCR conditions and tested new primers that increase the efficiency of barcode recovery in amphibians. We found that a low extension temperature for PCR cycles significantly improves the efficiency of amplification for all combinations of primers. Combining low PCR extension temperature and primers AnF1 + AnR1, we were able to recover COI sequences for 100% of the species analysed (N = 161), encompassing ~15% of the species known from Brazil (representing 77 genera and 23 families), which is an important improvement over previous studies. The preliminary assessment of species diversity suggested that number of species might be underestimated by about 25%. We conclude that DNA barcoding is an efficient, simple, and standardized protocol for identifying cryptic diversity in amphibians and advocate for its use in biodiversity inventories and across widespread populations within known species.

A new species of the genus Scutiger (Anura: Megophryidae) from Medog of southeastern Tibet, China

A new species of Scutiger Theobald, 1868 is described from Medog, southeastern Tibet, China, based on morphological and molecular data. The new species was previously identified as Scutiger nyingchiensis, but it can be differentiated from the latter and all other congeners by the following combination of characters: (1) medium adult body size, SVL 50.5-55.6 mm in males and 53.8-57.2 mm in females; (2) maxillary teeth absent; (3) web rudimentary between toes; (4) prominent, conical-shaped tubercles on dorsal and lateral surfaces of body and limbs; (5) tubercles covered by black spines in both sexes in breeding condition; (6) a pair of pectoral glands and a pair of axillary glands present and covered by black spines in males in breeding condition, width of axillary gland less than 50% of pectoral gland; (7) nuptial spines present on dorsal surface of first and second fingers, and inner side of third finger in males in breeding condition; (8) spines absent on the abdominal region; (9) vocal sac absent. In addition, the distribution and conservation status of the new species are also discussed.