Cryptic anuran biodiversity in Bangladesh revealed by mitochondrial 16S rRNA gene sequences

Vocal repertoire of Microhyla nilphamariensis from Delhi and comparison with closely related M. ornata populations from the western coast of India and Sri Lanka

Advertisement calls in frogs have evolved to be species-specific signals of recognition and are therefore considered an essential component of integrative taxonomic approaches to identify species and delineate their distribution range. The species rich genus Microhyla is a particularly challenging group for species identification, discovery and conservation management due to the small size, conserved morphology and wide distribution of its members, necessitating the need for a thorough description of their vocalization. In this study, we provide quantitative description of the vocal behaviour of Microhyla nilphamariensis, a widely distributed south Asian species, from Delhi, India, based on call recordings of 18 individuals and assessment of 21 call properties. Based on the properties measured acrossed 360 calls, we find that a typical advertisement call of M. nilphamariensis lasts for 393.5 ±  57.5 ms, has 17 pulses on average and produce pulses at rate of 39 pulses/s. The overall call dominant frequency was found to be 2.8 KHz and the call spectrum consisted of two dominant frequency peaks centered at 1.6 KHz and 3.6 KHz, ranging between 1.5-4.1 KHz. Apart from its typical advertisement call, our study also reveals the presence of three 'rare' call types, previously unreported in this species. We describe variability in call properties and discuss their relation to body size and temperature. We found that overall dominant frequency 1 (spectral property) was found to be correlated with body size, while first pulse period (temporal property) was found to be correlated with temperature. Further, we compare the vocal repertoire of M. nilphamariensis with that of the congener Microhyla ornata from the western coast of India and Sri Lanka and also compare the call properties of these two populations of M. ornata to investigate intra-specific call variation. We find statistically significant differentiation in their acoustic repertoire in both cases. Based on 18 call properties (out of 20), individuals of each locality clearly segregate on PCA factor plane forming separate groups. Discriminant function analysis (DFA) using PCA factors shows 100% classification success with individuals of each locality getting classified to a discrete group. This confirms significant acoustic differentiation between these species as well as between geographically distant conspecifics. The data generated in this study will be useful for comparative bioacoustic analysis of Microhyla species and can be utilized to monitor populations and devise conservation management plan for threatened species in this group.

Numerous uncertainties in the multifaceted global trade in frogs’ legs with the EU as the major consumer

The commercial trade in frogs and their body parts is global, dynamic and occurs in extremely large volumes (in the thousands of tonnes/yr or billions of frogs/yr). The European Union (EU) remains the single largest importer of frogs’ legs, with most frogs still caught from the wild. Amongst the many drivers of species extinction or population decline (e.g. due to habitat loss, climate change, disease etc.), overexploitation is becoming increasingly more prominent. Due to global declines and extinctions, new attention is being focused on these markets, in part to try to ensure sustainability. While the trade is plagued by daunting realities of data deficiency and uncertainty and the conflicts of commercial interests associated with these data, it is clear is that EU countries are most responsible for the largest portion of the international trade in frogs’ legs of wild species. Over decades of exploitation, the EU imports have contributed to a decline in wild frog populations in an increasing number of supplying countries, such as India and Bangladesh, as well as Indonesia, Turkey and Albania more recently. However, there have been no concerted attempts by the EU and present export countries to ensure sustainability of this trade. Further work is needed to validate species identities, secure data on wild frog populations, establish reasonable monitored harvest/export quotas and disease surveillance and ensure data integrity, quality and security standards for frog farms. Herein, we call upon those countries and their representative governments to assume responsibility for the sustainability of the trade. The EU should take immediate action to channel all imports through a single centralised database and list sensitive species in the Annexes of the EU Wildlife Trade Regulation. Further, listing in CITES (the Convention on International Trade in Endangered Species of Wild Fauna and Flora) can enforce international trade restrictions. More joint efforts are needed to improve regional monitoring schemes before the commercial trade causes irreversible extinctions of populations and species of frogs.

Postmating isolation and evolutionary relationships among Fejervarya species from Lesser Sunda, Indonesia and other Asian countries revealed by crossing experiments and mtDNA Cytb sequence analyses

To evaluate the degree of postmating isolation and the evolutionary relationships among frog species in the genus Fejervarya from Indonesia (Lesser Sunda), Bangladesh, China, and Japan, crossing experiments and molecular phylogenetic analyses were carried out. Crossing experiments revealed that reciprocal hybrids among F. iskandari, F. verruculosa, and F. sp. large type and between F. multistriata and F. kawamurai are viable through metamorphosis, while those between the F. iskandari group and F. limnocharis group were completely or partially inviable at the tadpole stage and those between Southeast Asian and South Asian Fejervarya groups were completely inviable at the embryonic stage. The mature reciprocal hybrids between F. iskandari and F. verruculosa from Lesser Sunda, Indonesia, showed some degree of abnormality in spermatogenesis. In phylogenetic analyses based on mtDNA Cytb sequences, F. iskandari formed a sister clade with F. verruculosa from Lesser Sunda, Indonesia, with 8.1% sequence divergence. F. multistriata from China formed a clade with populations of F. limnocharis in Thailand, Malaysia, and Indonesia (topotype), and these taxa showed sister relationships to F. kawamurai from Japan with 8.9% sequence divergence. Fejervarya sp. small type from Bangladesh formed a clade with the other South Asian members of the Fejervarya group and formed a sister clade with the Southeast Asian Fejervarya group, with 23.1% sequence divergence in the Cytb gene. These results showed that the degree of postmating isolation reflects molecular phylogenetic relationships and that F. iskandari and F. verruculosa from Indonesia (Lesser Sunda) are reproductively isolated by abnormalities in spermatogenesis and show genetic differentiation.

An insight into molecular taxonomy of bufonids, microhylids, and dicroglossid frogs: First genetic records from Pakistan

The current study was focused on documentation of amphibian assemblage in North Punjab and Islamabad Capital Territory, Pakistan, by using mitochondrial gene sequences of 16S rRNA. Our study entailed 37% of the known amphibian species of the country. We provided a phylogenetic analysis based on 74 newly generated mitochondrial 16S rRNAs from nine species of genus Microlyla, Duttaphrynus, Allopaa, Nanorana, Sphaerotheca, Minervarya, Hoplobatrachus, and Euphlyctis. We employed the maximum-likelihood inference and Bayesian analysis to assess the taxonomic status of the samples obtained from Pakistan, with respect to other congeneric species from surrounding regions. Our findings confirmed the taxonomic status of South Asian anuran species Duttaphrynus stomaticus, Duttaphrynus melanostictus, Microhyla nilphamariensis, Allopaa hazarensis, Nanorana vicina, Sphaerotheca maskeyi (synonym: S. pashchima), Minervarya pierrei, Hoplobatrachus tigerinus, and Euphlyctis kalasgramensis in Pakistan. We have reported new country records of genus Minervarya ( M. pierrei). Minervarya pierrei was previously misidentified as Fejervarya limnocharis, due to dearth of genetic information. We provided the first genetic records of our endemic species N. vicina. The results revealed the taxonomic placement of N. vicina with respect to its congeners and validated the taxonomic status of N. vicina from its type locality (Murree) for the first time. The findings of the present study also indicated the paraphyletic relationship of A.- hazarensis with Nanorana species. So, based on our phylogenetic inferences, morphological characters, and habitat preferences, validity of generic status of A. hazarensis is undecided. As our data were not enough to resolve this issue, we suggest sequencing of additional mitochondrial and nuclear genes in the future studies to get a better resolution. We recommend carrying out extensive surveys throughout the country for proper scientific documentation of amphibians of Pakistan. Many new species, some of them might be endemic to Pakistan, are expected to be discovered, and taxonomic status of other species would be resolved.

Two new cryptic species of Microhyla Tschudi, 1838 (Amphibia, Anura, Microhylidae) related to the M. heymonsi group from central Vietnam

The Microhyla heymonsi species complex from central Vietnam was examined, and based upon morphological and molecular evidence, two new species are described. The discovery of Microhyla daklakensis sp. nov. and Microhyla ninhthuanensis sp. nov. brings the total number of known species in the genus to 46 and the species number of Microhyla in Vietnam to 13. The Truong Son Range harbors the highest diversity of the genus Microhyla with 11 recorded species so far. However, this apparent micro-endemic diversity is at risk because of habitat loss by deforestation, which highlights the necessity of further research leading to improved conservation measures.

Impact of the Miocene orogenesis on Kaloula spp. radiation and implication of local refugia on genetic diversification

The phylogeography of the Kaloula genus in East Asia is still poorly understood. One of the difficulties is the absence of fossils to corroborate molecular dating estimates. Here, we examined the mitochondrial structure of Kaloula spp. in East Asia and focused on the impact of glaciations on the northernmost species: Kaloula borealis. We determined the phylogenetic relationships, molecular dating, and genetic connectivity assessments within the genus from 1211 bp of concatenated mitochondrial 12S and 16S. The relaxed clock analyses reveal the emergence of Kaloula spp. common ancestor in East and Southeast Asia between the Eocene and Oligocene, c. 38.47 Ma (24.69-53.65). The genetic diversification of lineages then increased on the East Asian Mainland during the Lower Miocene, c. 20.10 (8.73-30.65), most likely originating from the vicariance and radiation triggered by the orogeny of the Qinghai-Tibetan Plateau. Later, the dispersal towards the North East Asian Mainland during the Upper Miocene drove the population diversification of K. borealis c. 9.01 Ma (3.66-15.29). Finally, the central mainland population became isolated following orogenesis events and diverged into K. rugifera during the Pliocene, c. 3.06 Ma (0.02-10.90). The combination of population genetic and barrier analyses revealed a significant genetic isolation between populations of Kaloula spp. matching with the massive Qinling-Daba Mountain chain located in south-central China. Finally, we highlight a young divergence within the Eastern Mainland population of K. borealis, possibly attributed to refugia in south eastern China from which populations later expanded.

A little frog leaps a long way: compounded colonizations of the Indian Subcontinent discovered in the tiny Oriental frog genus Microhyla (Amphibia: Microhylidae)

Frogs of the genus Microhyla include some of the world's smallest amphibians and represent the largest radiation of Asian microhylids, currently encompassing 50 species, distributed across the Oriental biogeographic region. The genus Microhyla remains one of the taxonomically most challenging groups of Asian frogs and was found to be paraphyletic with respect to large-sized fossorial Glyphoglossus. In this study we present a time-calibrated phylogeny for frogs in the genus Microhyla, and discuss taxonomy, historical biogeography, and morphological evolution of these frogs. Our updated phylogeny of the genus with nearly complete taxon sampling includes 48 nominal Microhyla species and several undescribed candidate species. Phylogenetic analyses of 3,207 bp of combined mtDNA and nuDNA data recovered three well-supported groups: the Glyphoglossus clade, Southeast Asian Microhyla II clade (includes M. annectens species group), and a diverse Microhyla I clade including all other species. Within the largest major clade of Microhyla are seven well-supported subclades that we identify as the M. achatina, M. fissipes, M. berdmorei, M. superciliaris, M. ornata, M. butleri, and M. palmipes species groups. The phylogenetic position of 12 poorly known Microhyla species is clarified for the first time. These phylogenetic results, along with molecular clock and ancestral area analyses, show the Microhyla-Glyphoglossus assemblage to have originated in Southeast Asia in the middle Eocene just after the first hypothesized land connections between the Indian Plate and the Asian mainland. While Glyphoglossus and Microhyla II remained within their ancestral ranges, Microhyla I expanded its distribution generally east to west, colonizing and diversifying through the Cenozoic. The Indian Subcontinent was colonized by members of five Microhyla species groups independently, starting with the end Oligocene-early Miocene that coincides with an onset of seasonally dry climates in South Asia. Body size evolution modeling suggests that four groups of Microhyla have independently achieved extreme miniaturization with adult body size below 15 mm. Three of the five smallest Microhyla species are obligate phytotelm-breeders and we argue that their peculiar reproductive biology may be a factor involved in miniaturization. Body size increases in Microhyla-Glyphoglossus seem to be associated with a burrowing adaptation to seasonally dry habitats. Species delimitation analyses suggest a vast underestimation of species richness and diversity in Microhyla and reveal 15-33 undescribed species. We revalidate M. nepenthicola, synonymize M. pulverata with M. marmorata, and provide insights on taxonomic statuses of a number of poorly known species. Further integrative studies, combining evidence from phylogeny, morphology, advertisement calls, and behavior will result in a better systematic understanding of this morphologically cryptic radiation of Asian frogs.

First record of Euphlyctis kalasgramensis (Anura: Dicroglossidae) from Punjab, Pakistan

The present study documented the first record of Euphlyctis kalasgramensis from Punjab, Pakistan. The specimens were collected during field visits from June through August 2018. Various morphometric measurements of E. kalasgramensis were taken and compared with Euphlyctis cyanophlyctis. Snout-vent length (SVL) was 38.11 ± 0.87 mm (n = 5), snout length was 3% of SVL, foot length was 55% of SVL, head length was 32% of SVL and weight was 8.01 ± 0.12 g (n = 5). A few specimens (n = 2) were euthanized and preserved for molecular analysis through mitochondrial 16S rRNA gene sequences. The newly obtained DNA sequences of E. kalasgramensis were submitted to GenBank and accession numbers were obtained (MK881165.1 and MK920114.1). The Maximum likelihood and Neighbor-joining trees based on Kimura 2-parameter distance resulted in similar phylogenetic trees. Euphlyctis kalasgramensis was out group in both phylogenetic trees. The interspecific divergence of E. kalasgramensis and E. cyanophlyctis was high ranging from 4% to 6% as compared to low intraspecific divergence 0% and 1%. The diversity and distribution ranges of many amphibians species are not well known in Pakistan due to lack of taxonomic information. In our recommendation, a large scale DNA barcoding is required to report more cryptic or new species from Pakistan.

Species delimitation of crab-eating frogs (Fejervarya cancrivora complex) clarifies taxonomy and geographic distributions in mainland Southeast Asia

The taxonomy and geographic distributions of species of crab-eating frogs (Fejervaryacancrivora complex) in mainland Southeast Asia have been highly uncertain. Three taxonomic names are used in recent literature (F.cancrivora, F.raja, and F.moodiei) but the applications of these names to localities has been inconsistent, especially owing to the lack of available molecular data for F.raja. Morphometric and mitochondrial DNA variation was examined in these frogs, including name-bearing types and topotypes of all three species. Findings corroborate evidence for the existence of two species in coastal mainland Southeast Asia, with F.moodiei having a wide geographic distribution and F.cancrivora sensu stricto occurring only in extreme southern Thailand and peninsular Malaysia. Fejervaryaraja is shown to be only a large-bodied population of F.cancrivora sensu stricto and is synonymized with that species. Revised descriptions of F.moodiei and F.cancrivora sensu stricto are provided.

On the road to Mandalay: contribution to the Microhyla Tschudi, 1838 (Amphibia: Anura: Microhylidae) fauna of Myanmar with description of two new species

We present a morphological and molecular assessment of the Microhyla fauna of Myanmar based on new collections from central (Magway Division) and northern (Kachin State) parts of the country. In total, six species of Microhyla are documented, including M. berdmorei, M. heymonsi, M. butleri, M. mukhlesuri and two new species described from the semi-arid savanna-like plains of the middle part of the Irrawaddy (Ayeyarwady) River Valley. We used a 2 481 bp long 12S rRNA-16S rRNA fragment of mtDNA to hypothesize genealogical relationships within Microhyla. We applied an integrative taxonomic approach combining molecular, morphological, and acoustic lines of evidence to evaluate the taxonomic status of Myanmar Microhyla. We demonstrated that the newly discovered populations of Microhyla sp. from the Magway Division represent two yet undescribed species. These two new sympatric species are assigned to the M. achatina species group, with both adapted to the seasonally dry environments of the Irrawaddy Valley. Microhyla fodiens sp. nov. is a stout-bodied species with a remarkably enlarged shovel-like outer metatarsal tubercle used for burrowing and is highly divergent from other known congeners (P-distance≥8.8%). Microhyla irrawaddy sp. nov. is a small-bodied slender frog reconstructed as a sister species to M. kodial from southern India (P-distance=5.3%); however, it clearly differs from the latter both in external morphology and advertisement call parameters. Microhyla mukhlesuri is reported from Myanmar for the first time. We further discuss the morphological diagnostics and biogeography of Microhyla species recorded in Myanmar.

Delineating Microhyla ornata (Anura, Microhylidae): mitochondrial DNA barcodes resolve century-old taxonomic misidentification

Microhyla ornata, a species originally described from the southwest coast of India in 1841, was long reported to be wide-ranging throughout South, Southeast, and East Asia. Although the name M. ornata is restricted to populations from South Asia, the species is still considered to occur widely in India and its neighboring regions. To clarify the identity and geographical distribution of M. ‘ornata’, we performed DNA barcoding using a fragment of the mitochondrial 16S rRNA gene from 62 newly obtained samples. Our results show that this taxon is restricted to Peninsular India and Sri Lanka, whereas, populations from the other parts represent three different species – M. mukhlesuri, M. mymensinghensis, and M. nilphamariensis, creating new country records for India. Our work reemphasizes the benefits of DNA barcoding for rapidly identifying populations of widespread species and provides insights into the patterns of genetic differentiation in the M. ‘ornata’ species complex of South Asia.

Filling the BINs of life: Report of an amphibian and reptile survey of the Tanintharyi (Tenasserim) Region of Myanmar, with DNA barcode data

Despite threats of species extinctions, taxonomic crises, and technological advances in genomics and natural history database informatics, we are still distant from cataloguing all of the species of life on earth. Amphibians and reptiles are no exceptions; in fact new species are described nearly every day and many species face possible extinction. The number of described species continues to climb as new areas of the world are explored and as species complexes are examined more thoroughly. The use of DNA barcoding provides a mechanism for rapidly estimating the number of species at a given site and has the potential to record all of the species of life on Earth. Though DNA barcoding has its caveats, it can be useful to estimate the number of species in a more systematic and efficient manner, to be followed in combination with more traditional, morphology-based identifications and species descriptions. Herein, we report the results of a voucher-based herpetological expedition to the Tanintharyi (Tenasserim) Region of Myanmar, enhanced with DNA barcode data. Our main surveys took place in the currently proposed Tanintharyi National Park. We combine our results with photographs and observational data from the Chaung-nauk-pyan forest reserve. Additionally, we provide the first checklist of amphibians and reptiles of the region, with species based on the literature and museum. Amphibians, anurans in particular, are one of the most poorly known groups of vertebrates in terms of taxonomy and the number of known species, particularly in Southeast Asia. Our rapid-assessment program combined with DNA barcoding and use of Barcode Index Numbers (BINs) of voucher specimens reveals the depth of taxonomic diversity in the southern Tanintharyi herpetofauna even though only a third of the potential amphibians and reptiles were seen. A total of 51 putative species (one caecilian, 25 frogs, 13 lizards, 10 snakes, and two turtles) were detected, several of which represent potentially undescribed species. Several of these species were detected by DNA barcode data alone. Furthermore, five species were recorded for the first time in Myanmar, two amphibians (Ichthyophis cf. kohtaoensis and Chalcorana eschatia) and three snakes (Ahaetulla mycterizans, Boiga dendrophila, and Boiga drapiezii).

Inter- and intra-specific genetic divergence of Asian tiger frogs (genus Hoplobatrachus), with special reference to the population structure of H. tigerinus in Bangladesh

The five frog species of the genus Hoplobatrachus are widely distributed in Asia and Africa, with Asia being considered the genus' origin. However, the evolutionary relationships of Asian Hoplobatrachus species remain ambiguous. Additionally, genetic diversity and fundamental differentiation processes within species have not been studied. We conducted molecular phylogenetic analysis on Asian Hoplobatrachus frogs and population genetic analysis on H. tigerinus in Bangladesh using the mitochondrial CYTB gene and 21 microsatellite markers. The resultant phylogenetic tree revealed monophyly in each species, notwithstanding the involvement of cryptic species in H. chinensis and H. tigerinus, which are evident from the higher genetic divergence between populations. Bayesian inference of population structure revealed genetic divergence between western and eastern H. tigerinus populations in Bangladesh, suggesting restricted gene flow caused by barriers posed by major rivers. However, genetic distances among populations were generally low. A discrete population is located in the low riverine delta region, which likely reflects long-distance dispersal. These results strongly suggest that the environment specific to this river system has maintained the population structure of H. tigerinus in this region.

A New Species of Frog (Anura: Dicroglossidae) Discovered from the Mega City of Dhaka

We describe a new species of frog of the genus Zakerana discovered from the urban core of Dhaka, Bangladesh, one of the most densely populated cities in the world. Although the new species is morphologically similar to the geographically proximate congeners in the Bangladeshi cricket frog group, we show that it can be distinguished from all congeners on the basis of morphological characters, advertisement calls and variation in two mitochondrial DNA genes (12S rRNA and 16S rRNA). Apart from several diagnostic differences in body proportions, the new species differs from other Zakerana species in having a flattened snout (from ventral view) projecting over the lower jaw, and diagnostic trapezoid-shaped red markings on the vocal sac in males. Molecular genetic analyses show that the new species is highly divergent (3.1–20.1% sequence divergence) from all congeneric species, and forms a well-supported clade with its sister species, Zakerana asmati. The discovery of a new amphibian species from the urban core of Dhaka together with several recent descriptions of new amphibian species from Bangladesh may indicate that more amphibian species remain to be discovered from this country.

Systematics and biogeography of the Hylarana frog (Anura: Ranidae) radiation across tropical Australasia, Southeast Asia, and Africa

We present an inclusive molecular phylogeny for Hylarana across its global distribution, utilizing two mitochondrial and four nuclear gene regions for 69 of the 97 currently described species. We use phylogenetic methods to test monophyly of Hylarana, determine relationships among ten putative subgenera, identify major clades, reconstruct biogeographic history, and estimate continental dispersal dates. Results support Hylarana as a monophyletic group originating approximately 26.9MYA and comprising eight clades that partly correspond to currently described subgenera plus two new groups. The African and Australasian species each form clades embedded within a paraphyletic Southeast Asian group. We estimate that Africa and Australasia were colonized by Hylarana s.l. from SE Asia approximately 18.7 and 10.8MYA, respectively. Biogeographic reconstructions also support three separate colonization events in India from Southeast Asia. Examination of museum specimens identified morphological characters useful for delineating subgenera and species. We herein elevate all supported subgenera to genus rank and formally describe two new genera to produce a revised taxonomy congruent with our new phylogenetic and biogeographic findings.

A new species of Microhyla (Anura: Microhylidae) from Nilphamari, Bangladesh

A new species of Microhyla frog from the Nilphamari district of Bangladesh is described and compared with its morphologically similar and geographically proximate congeners. Molecular phylogeny derived from mitochondrial DNA sequences revealed that although the new species--designated here as Microhyla nilphamariensis sp. nov.--forms a clade with M. ornate, it is highly divergent from M. ornata and all of its congeners, with 5.7-13.2% sequence divergence at the 16S rRNA gene. The new species can be identified phenotypically on the basis of a set of diagnostic (both qualitative and quantitative) characters as follows: head length is 77% of head width, distance from front of eyes to the nostril is roughly six times greater than nostril-snout length, internarial distance is roughly five times greater than nostril-snout length, interorbital distance is two times greater than internarial distance, and distance from back of mandible to back of the eye is 15% of head length. Furthermore, inner metacarpal tubercle is small and ovoid-shaped, whereas outer metacarpal tubercle is very small and rounded. Toes have rudimentary webbing, digital discs are absent, inner metatarsal tubercle is small and round, outer metatarsal tubercle is ovoid-shaped, minute, and indistinct.

A new species of Euphlyctis (Anura: Dicroglossidae) from Barisal, Bangladesh

A new species of the genus Euphlyctis is described from the Barisal district of Bangladesh and compared with its morphologically similar and geographically proximate congeners. The new species is highly divergent in comparison to other congeneric species on basis of sequence divergence in mitochondrial DNA gene sequences (ranging from 5.5% to 17.8% divergence). Euphlyctis kalasgramensis sp. nov. can be readily diagnosed by having the following combination of characters: snout-vent length (SVL) 30.44 – 37.88 mm, absence of mid-dorsal line, nostril–snout length 3% of SVL, nostril much closer to snout tip than eye, nostril–snout length 48% of distance from front of eyes to nostril, relative length of fingers (shortest to longest: 1 = 2 < 4 < 3), tibia length 59% of SVL, foot length 55% of SVL.