Phylogeny of the Asian spiny frog tribe Paini (Family Dicroglossidae) sensu Dubois

A New Species of Nanorana (Anura: Dicroglossidae) from Northwestern Yunnan, China, with Comments on the Taxonomy of Nanorana arunachalensis and Allopaa

The genus Nanorana contains three subgenera, namely Nanorana, Paa, and Chaparana, and currently, there are four species known to science in Nanorana (Nanorana). In this study, we describe a new species belonging to the subgenus Nanorana from northwestern Yunnan, China. Phylogenetically, the new species, Nanorana laojunshanensissp. nov., is the sister to the clade of N. pleskei and N. ventripunctata. Morphologically, the new species can be distinguished from known congeners by the combination of following characters: present tympanum, equal fingers I and II, small body size, yellow ventral surface of limbs, distinct vomerine teeth, indistinct subarticular tubercles, head width greater than head length, slender supratympanic fold, absent dorsolateral fold, nuptial spines present on fingers I and II in adult males, absent vocal sac, and paired brown spines on the chest. Moreover, we suggest moving the genus Allopaa into Nanorana (Chaparana) and consider that N. arunachalensis is neither an Odorrana species nor a member of the subfamily Dicroglossinae (therefore Nanorana), but probably represents a distinct genus closely related to Ingerana or belongs to Ingerana, pending more data. Additionally, we consider that Nanorana minica deserves the rank of an independent subgenus, and we suggest assigning N. arnoldi, N. blanfordii, N. ercepeae, N. polunini, N. rarica, N. rostandi, N. vicina, N. xuelinensis, and N. zhaoermii into the subgenus Paa and placing N. kangxianensis, N. phrynoides, and N. sichuanensis in the subgenus Chaparana.

The identity of Nanorana yunnanensis (Anderson, 1879) from Thailand, with a description of its tadpole (Anura, Dicroglossidae)

Nanorana yunnanensis has been reported in Thailand for many years; however, no specimens have been verifiably described. To verify the identity of this species in Thailand, we observed Thai specimens formerly assigned to the species N. bourreti and N. yunnanensis. The 12S rRNA, 16S rRNA, and ND2 mitochondrial genes were used to clarify the taxonomic statuses of the Thai specimens. The results showed that our specimens formed a clade with N. yunnanensis, containing specimens from southern Yunnan and Vietnam. The respective mean sequence divergences of the 12S and 16S rRNA genes between populations from Thailand versus China were 0.59% and 1.09%, for populations from Thailand versus Vietnam were 0.57% and 0.61%, and for populations from China versus Vietnam were 0.59% and 1.09%. We provide descriptions of the tadpole and adult specimens of N. yunnanensis from Thailand.

Hidden in the jungle of Vietnam: a new species of Quasipaa (Amphibia, Anura, Dicroglossidae) from Ngoc Linh Mountain

A new species of Quasipaa is described from Ngoc Linh Mountain of the Kon Tum Massif in central Vietnam. The new species is morphologically distinguishable from its congeners on the basis of a combination of the following diagnostic characters: SVL 79.6-84.3 mm in males and 64.6-69.9 mm in females; head broader than long; vomerine teeth present; external vocal sacs absent; tympanum slightly visible; dorsum with lines of thick ridges and small round tubercles; flanks covered by oval and round tubercles; supratympanic fold present; dorsolateral fold absent; ventrolateral sides, ventral surface of arms, and all fingers with spines in males; the absence of spines on chest and belly in males; toes fully webbed to distal portion of terminal phalanx; in life, dorsum dark brown, chest and belly immaculate white. Phylogenetic analyses found that the genetic divergence of the new species and its congeners ranged from 4.2-5.1% (compared with Quasipaaboulengeri) to 7.6-8.1% (compared with Q.shini) in the 16S gene.

Diversity, distribution and molecular species delimitation in frogs and toads from the Eastern Palaearctic

Biodiversity analyses can greatly benefit from coherent species delimitation schemes and up-to-date distribution data. In this article, we have made the daring attempt to delimit and map described and undescribed lineages of anuran amphibians in the Eastern Palaearctic (EP) region in its broad sense. Through a literature review, we have evaluated the species status considering reproductive isolation and genetic divergence, combined with an extensive occurrence dataset (nearly 85k localities). Altogether 274 native species from 46 genera and ten families were retrieved, plus eight additional species introduced from other realms. Independent hotspots of species richness were concentrated in southern Tibet (Medog County), the circum-Sichuan Basin region, Taiwan, the Korean Peninsula and the main Japanese islands. Phylogeographic breaks responsible for recent in situ speciation events were shared around the Sichuan Mountains, across Honshu and between the Ryukyu Island groups, but not across shallow water bodies like the Yellow Sea and the Taiwan Strait. Anuran compositions suggested to restrict the zoogeographical limits of the EP to East Asia. In a rapidly evolving field, our study provides a checkpoint to appreciate patterns of species diversity in the EP under a single, spatially explicit, species delimitation framework that integrates phylogeographic data in taxonomic research.

A chromosomal level genome sequence for Quasipaa spinosa (Dicroglossidae) reveals chromosomal evolution and population diversity

Quasipaa spinosa is an Asian commercial Dicroglossidae species noted for its spiny chest found in adult males. Here, we report the first chromosomal level Q. spinosa genome employing PacBio long read sequencing and high-resolution chromosome conformation capture (Hi-C) technology. The total length of the final assembled genome was 2,839,292,578 bp, with contig N50 of 3.79 Mb and scaffold N50 of 327.44 Mb. Approximately 99.30% of the length of the assembled genome sequences were anchored to 13 chromosomes with the assistance of Hi-C reads. A total of 26,173 protein-coding genes were predicted, and 95.98% of the genes were functionally annotated. The annotated genes covered a total of 92.10% of the complete vertebrate core gene set according to the BUSCO pipeline evaluation. Approximately 41 million years ago, Q. spinosa began to diverge from its dicroglossid sister taxon Nanorana parkeri. The Q. spinosa genome revealed obvious chromosomal fissions compared with Xenopus tropicalis, which probably represented a specific chromosome evolutionary history within frogs. Population analysis showed that Chinese Q. spinosa could be divided into eastern and western genetic clusters, with the western population showing higher diversity than the eastern population. The effective population size of Q. spinosa showed a continuously decreasing trend from one million years ago to 10,000 years ago. In summary, this study sheds light on Q. spinosa evolution and population differentiation, providing a valuable genomic resource for further biological and genetic studies on this species, and other closely related frog taxa.

First national record of Quasipaaverrucospinosa (Bourret, 1937) (Amphibia: Anura: Dicroglossidae) from Thailand with further comment on its taxonomic status

Background

Spiny Frog Quasipaa is a genus of frogs that belongs to a relatively poorly known group. Most of the species distribution has been recorded in China; however, a few incidences of identification have occurred in the eastern part of Indochina. To date, only one species (Quasipaafasciculispina) of Quasipaa has been recorded from Chanthaburi and Trat Provinces in south-eastern Thailand.

New information

Based on recent fieldwork conducted in northern Thailand, we report a new record of Quasipaaverrucospinosa from Doi Phu Kha National Park, Nan Province at an altitude of 900–1000 m a.s.l. Our study has demonstrated that populations of this species are paraphyletic and has revealed deep genetic differences. Therefore, it is recommended that a comprehensive study be undertaken to clarify the taxonomic and geographic distribution of this species for its suitable protection and conservation.

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.

Relict groups of spiny frogs indicate Late Paleogene-Early Neogene trans-Tibet dispersal of thermophile faunal elements

BACKGROUND

The Himalaya-Tibet orogen (HTO) presents an outstanding geologically active formation that contributed to, and fostered, modern Asian biodiversity. However, our concepts of the historical biogeography of its biota are far from conclusive, as are uplift scenarios for the different parts of the HTO. Here, we revisited our previously published data set of the tribe Paini extending it with sequence data from the most western Himalayan spiny frogs Allopaa and Chrysopaa and using them as an indirect indicator for the potential paleoecological development of Tibet.

METHODS

We obtained sequence data of two mitochondrial loci (16S rRNA, COI) and one nuclear marker (Rag1) from Allopaa samples from Kashmir Himalaya as well as Chrysopaa sequence data from the Hindu Kush available from GenBank to complement our previous data set. A Maximum likelihood and dated Bayesian gene tree were generated based on the concatenated data set. To resolve the inconsistent placement of Allopaa, we performed different topology tests.

RESULTS

Consistent with previous results, the Southeast Asian genus Quasipaa is sister to all other spiny frogs. The results further reveal a basal placement of Chrysopaa relative to Allopaa and Nanorana with an estimated age of ca. 26 Mya. Based on the topology tests, the phylogenetic position of Allopaa as a sister clade to Chaparana seems to be most likely, resulting in a paraphyletic genus Nanorana and a separation from the latter clade around 20 Mya, although a basal position of Allopaa to the genus Nanorana cannot be entirely excluded. Both, the placements of Chrysopaa and Allopaa support the presence of basal Paini lineages in the far northwestern part of the HTO, which is diametrically opposite end of the HTO with respect to the ancestral area of spiny frogs in Southeast Asia. These striking distributional patterns can be most parsimoniously explained by trans-Tibet dispersal during the late Oligocene (subtropical Chrysopaa) respectively early Miocene (warm temperate Allopaa). Within spiny frogs, only members of the monophyletic Nanorana+Paa clade are adapted to the colder temperate climates, indicating that high-altitude environments did not dominate in the HTO before ca. 15 Mya. Our results are consistent with fossil records suggesting that large parts of Tibet were characterized by subtropical to warm temperate climates at least until the early Miocene. They contradict prevalent geological models of a highly uplifted late Paleogene proto-Plateau.

A new species of Nanorana Günther, 1896 (Anura, Dicroglossidae) from Yunnan, China

A new species of Nanorana Günther, 1896 is described from Yunnan Province, China, based on morphological and molecular evidence. Morphologically, Nanoranaxuelinensissp. nov. is distinguished from its congeners by a combination of the following diagnostic characters: body size large; adult males with keratinized spines on chest, belly, lateral body, posterior dorsum, buttocks, outer side of the fore limbs, the inner metacarpal tubercle, fingers I and II, and upper eyelids; no spines on the inner side of the lower and upper arm; forelimbs strongly hypertrophied in adult males; anterior dorsum skin smooth; dorsolateral folds absent; finger I longer than finger II; webbing deeply incurved between tips of toes; present outer metacarpal tubercle and absent outer metatarsal tubercle. The new species is separated from all other congeners by uncorrected genetic distances ranging from 5.2% to 7.3% based on mitochondrial 16S rRNA gene and ranging from 3.9% to 7.6% based on mitochondrial 12S rRNA gene.

Multi-locus genetic analyses of Quasipaa from throughout its distribution

Montane frogs of the genus Quasipaa Dubois, 1992 occur from southern China to Southeast Asia (Frost 2021). Analyses of mtDNA (Cytb) and nuDNA data (Rag1, Rag2, Rhod, Tyr) for samples from 93 localities throughout its distribution yield a phylogeny. Clades A and B occur in Southeast Asia, clade C in northern Yangtze River, China, clade D in southwestern China, and clades E and F in southeastern China. Results place Q. yei within monophyletic Quasipaa and identify two new species. Based on nuDNA data, the basal split of clade A and B indicates an Indochinese origin of Quasipaa. The west-east diversification of five species across South China (Q. spinosa, Q. exilispinosa, Q. jiulongensis, Q. shini, Q. boulengeri) corresponds to topographic terrains II and III of China. Divergence of species from southeastern China (Q. shini, Q. jiulongensis, Q. spinosa, Q. exilispinosa) and southwestern China (Q. boulengeri) dates to 15.30-16.56 Ma (million years ago). A principal component analysis (PCA) and t-test involving 19 bioclimatic variables identifies significantly different environmental conditions between the two regions. Species' distribution models (SDM) for Q. spinosa and Q. boulengeri identify the best areas to be eastern and western South China, respectively. Thus, environmental variation appears to have influenced the genetic divergence and distributions of Quasipaa in South China. Mito-nuclear discordance indicates that some individuals of Q. exilispinosa and Q. spinosa hybridized historically.

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.

Phylogeny of spiny frogs Nanorana (Anura: Dicroglossidae) supports a Tibetan origin of a Himalayan species group

Recent advances in the understanding of the evolution of the Asian continent challenge the long-held belief of a faunal immigration into the Himalaya. Spiny frogs of the genus Nanorana are a characteristic faunal group of the Himalaya-Tibet orogen (HTO). We examine the phylogeny of these frogs to explore alternative biogeographic scenarios for their origin in the Greater Himalaya, namely, immigration, South Tibetan origin, strict vicariance. We sequenced 150 Nanorana samples from 62 localities for three mitochondrial (1,524 bp) and three nuclear markers (2,043 bp) and complemented the data with sequence data available from GenBank. We reconstructed a gene tree, phylogenetic networks, and ancestral areas. Based on the nuDNA, we also generated a time-calibrated species tree. The results revealed two major clades (Nanorana and Quasipaa), which originated in the Lower Miocene from eastern China and subsequently spread into the HTO (Nanorana). Five well-supported subclades are found within Nanorana: from the East, Central, and Northwest Himalaya, the Tibetan Plateau, and the southeastern Plateau margin. The latter subclade represents the most basal group (subgenus Chaparana), the Plateau group (Nanorana) represents the sister clade to all species of the Greater Himalaya (Paa). We found no evidence for an east-west range expansion of Paa along the Himalaya, nor clear support for a strict vicariance model. Diversification in each of the three Himalayan subclades has probably occurred in distinct areas. Specimens from the NW Himalaya are placed basally relative to the highly diverse Central Himalayan group, while the lineage from the Tibetan Plateau is placed within a more terminal clade. Our data indicate a Tibetan origin of Himalayan Nanorana and support a previous hypothesis, which implies that a significant part of the Himalayan biodiversity results from primary diversification of the species groups in South Tibet before this part of the HTO was uplifted to its recent heights.

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.

Intrasexually selected weapons

We propose a practical concept that distinguishes the particular kind of weaponry that has evolved to be used in combat between individuals of the same species and sex, which we term intrasexually selected weapons (ISWs). We present a treatise of ISWs in nature, aiming to understand their distinction and evolution from other secondary sex traits, including from 'sexually selected weapons', and from sexually dimorphic and monomorphic weaponry. We focus on the subset of secondary sex traits that are the result of same-sex combat, defined here as ISWs, provide not previously reported evolutionary patterns, and offer hypotheses to answer questions such as: why have only some species evolved weapons to fight for the opposite sex or breeding resources? We examined traits that seem to have evolved as ISWs in the entire animal phylogeny, restricting the classification of ISW to traits that are only present or enlarged in adults of one of the sexes, and are used as weapons during intrasexual fights. Because of the absence of behavioural data and, in many cases, lack of sexually discriminated series from juveniles to adults, we exclude the fossil record from this review. We merge morphological, ontogenetic, and behavioural information, and for the first time thoroughly review the tree of life to identify separate evolution of ISWs. We found that ISWs are only found in bilateral animals, appearing independently in nematodes, various groups of arthropods, and vertebrates. Our review sets a reference point to explore other taxa that we identify with potential ISWs for which behavioural or morphological studies are warranted. We establish that most ISWs come in pairs, are located in or near the head, are endo- or exoskeletal modifications, are overdeveloped structures compared with those found in females, are modified feeding structures and/or locomotor appendages, are most common in terrestrial taxa, are frequently used to guard females, territories, or both, and are also used in signalling displays to deter rivals and/or attract females. We also found that most taxa lack ISWs, that females of only a few species possess better-developed weapons than males, that the cases of independent evolution of ISWs are not evenly distributed across the phylogeny, and that animals possessing the most developed ISWs have non-hunting habits (e.g. herbivores) or are faunivores that prey on very small prey relative to their body size (e.g. insectivores). Bringing together perspectives from studies on a variety of taxa, we conceptualize that there are five ways in which a sexually dimorphic trait, apart from the primary sex traits, can be fixed: sexual selection, fecundity selection, parental role division, differential niche occupation between the sexes, and interference competition. We discuss these trends and the factors involved in the evolution of intrasexually selected weaponry in nature.

Species groups distributed across elevational gradients reveal convergent and continuous genetic adaptation to high elevations

Although many cases of genetic adaptations to high elevations have been reported, the processes driving these modifications and the pace of their evolution remain unclear. Many high-elevation adaptations (HEAs) are thought to have arisen in situ as populations rose with growing mountains. In contrast, most high-elevation lineages of the Qinghai-Tibetan Plateau appear to have colonized from low-elevation areas. These lineages provide an opportunity for studying recent HEAs and comparing them with ancestral low-elevation alternatives. Herein, we compare four frogs (three species of Nanorana and a close lowland relative) and four lizards (Phrynocephalus) that inhabit a range of elevations on or along the slopes of the Qinghai-Tibetan Plateau. The sequential cladogenesis of these species across an elevational gradient allows us to examine the gradual accumulation of HEA at increasing elevations. Many adaptations to high elevations appear to arise gradually and evolve continuously with increasing elevational distributions. Numerous related functions, especially DNA repair and energy metabolism pathways, exhibit rapid change and continuous positive selection with increasing elevations. Although the two studied genera are distantly related, they exhibit numerous convergent evolutionary changes, especially at the functional level. This functional convergence appears to be more extensive than convergence at the individual gene level, although we found 32 homologous genes undergoing positive selection for change in both high-elevation groups. We argue that species groups distributed along a broad elevational gradient provide a more powerful system for testing adaptations to high-elevation environments compared with studies that compare only pairs of high-elevation versus low-elevation species.

Examining the interglacial high-elevation refugia scenario in East Asian subtropical mountain systems with the frog species Leptobrachium liui

The effects of Quaternary climatic oscillations on the distributions of organisms in different parts of the world are not equally well understood, limiting the ability to understand the determinants of biodiversity. Compared with the mountain regions in southern Europe and southwestern North America, such effects on high-elevation species in the East Asian subtropical mountain systems located in southern and southeastern China have seldom been addressed. In this study, using Leptobrachium liui (Megophryidae), we made one of the earliest attempts to examine the interglacial high-elevation refugia scenario in these Asian mountains. Based on our current understanding of the study system, we formulated a hypothesis that these frogs of western origin were distributed more widely and continuously during glacial phases, allowing eastward dispersal, and that they are currently isolated in interglacial refugia at higher elevations. Microsatellite data and mitochondrial and nuclear sequence data were obtained with extensive sampling followed by the synthesis of phylogeographic and population genetic analyses and modeling of the species distribution. The analyses revealed a sequential eastward divergence of microsatellite clusters and gene lineages accompanied by a decline in genetic diversity. Molecular dating estimates revealed divergence events in the Pleistocene, and a reduction in local populations was inferred to have occurred at a time comparable to the end of the last glacial. Strong genetic isolation by distance reflecting a more continuous historical distribution was detected. Furthermore, environmental niche models inferred a wide planar distribution during the last glacial maximum, providing further support for the hypothesis.

Suppressed Recombination of Sex Chromosomes Is Not Caused by Chromosomal Reciprocal Translocation in Spiny Frog (Quasipaa boulengeri)

Chromosome rearrangements (CRs) are perceived to be related to sex chromosome evolution, but it is a matter of controversy whether CRs are the initial causative mechanism of suppressed recombination for sex differentiation. The early stages of sex chromosome evolution in amphibians may represent intermediate states of differentiation, and if so, they potentially shed light on the ultimate cause of suppressed recombination and the role of CRs in sex chromosome differentiation. In this paper, we showed that sex determination differs among 16 populations of spiny frog (Quasipaa boulengeri), in which individuals have normal and rearranged chromosomes caused by reciprocal translocation. In eastern areas, without translocation, genetic differentiation between sexes was relatively low, suggesting unrestricted recombination. In comparison, in western populations that have both normal and translocated chromosomes, a male-heterogametic system and lack of X-Y recombination were identified by male-specific alleles and heterozygote excess. However, such genetic differentiation between sexes in western populations was not directly related to karyotypes, as it was found in individuals with both normal and translocated karyotypes. In the western Sichuan Basin, male-specific and translocation-specific allelic frequency distributions suggested that recombination of sex-differentiation ceased in all populations, but recombination suppression caused by translocation did not exist in some populations. Combined with phylogenetic inference, this indicated that the establishment of sex-linkage had taken place independently of reciprocal translocation, and translocation was not the ultimate cause of sex chromosome differentiation. Furthermore, comparison of the genetic diversity of alleles on Y chromosomes, X chromosomes, and autosomes in western populations showed a reduction of effective population size on sex chromosomes, which may be caused by reciprocal translocation. It indicates that, although it is not the ultimate cause of recombination suppression, reciprocal translocation may enhance sex chromosome differentiation.

The first complete mitochondrial genome sequence of Nanorana parkeri and Nanorana ventripunctata (Amphibia: Anura: Dicroglossidae), with related phylogenetic analyses

Members of the Nanorana genus (family Dicroglossidae) are often referred to as excellent model species with which to study amphibian adaptations to extreme environments and also as excellent keystone taxa for providing insights into the evolution of the Dicroglossidae. However, a complete mitochondrial genome is currently only available for Nanorana pleskei. Thus, we analyzed the complete mitochondrial genomes of Nanorana parkeri and Nanorana ventripunctata to investigate their evolutionary relationships within Nanorana and their phylogenetic position in the family Dicroglossidae. Our results showed that the genomes of N. parkeri (17,837 bp) and N. ventripunctata (18,373 bp) encode 13 protein‐coding genes (PCGs), two ribosomal RNA genes, 23 transfer RNA (tRNA) genes, and a noncoding control region. Overall sequences and genome structure of the two species showed high degree of similarity with N. pleskei, although the motif structures and repeat sequences of the putative control region showed clear differences among these three Nanorana species. In addition, a tandem repeat of the tRNA‐Met gene was found located between the tRNA‐Gln and ND2 genes. On both the 5′ and 3′‐sides, the control region possessed distinct repeat regions; however, the CSB‐2 motif was not found in N. pleskei. Based on the nucleotide sequences of 13 PCGs, our phylogenetic analyses, using Bayesian inference and maximum‐likelihood methods, illustrate the taxonomic status of Nanorana with robust support showing that N. ventripunctata and N. pleskei are more closely related than they are to N. parkeri. In conclusion, our analyses provide a more robust and reliable perspective on the evolutionary history of Dicroglossidae than earlier analyses, which used only a single species (N. pleskei).

Complete mitochondrial genomes of Nanorana taihangnica and N. yunnanensis (Anura: Dicroglossidae) with novel gene arrangements and phylogenetic relationship of Dicroglossidae

BACKGROUND

Complete mitochondrial (mt) genomes have been used extensively to test hypotheses about microevolution and to study population structure, phylogeography, and phylogenetic relationships of Anura at various taxonomic levels. Large-scale mt genomic reorganizations have been observed among many fork-tongued frogs (family Dicroglossidae). The relationships among Dicroglossidae and validation of the genus Feirana are still problematic. Hence, we sequenced the complete mt genomes of Nanorana taihangnica (=F. taihangnica) and N. yunnanensis as well as partial mt genomes of six Quasipaa species (dicroglossid taxa), two Odorrana and two Amolops species (Ranidae), and one Rhacophorus species (Rhacophoridae) in order to identify unknown mt gene rearrangements, to investigate the validity of the genus Feirana, and to test the phylogenetic relationship of Dicroglossidae.

RESULTS

In the mt genome of N. taihangnica two trnM genes, two trnP genes and two control regions were found. In addition, the trnA, trnN, trnC, and trnQ genes were translocated from their typical positions. In the mt genome of N. yunnanensis, three control regions were found and eight genes (ND6, trnP, trnQ, trnA, trnN, trnC, trnY and trnS genes) in the L-stand were translocated from their typical position and grouped together. We also found intraspecific rearrangement of the mitochondrial genomes in N. taihangnica and Quasipaa boulengeri. In phylogenetic trees, the genus Feirana nested deeply within the clade of genus Nanorana, indicating that the genus Feirana may be a synonym to Nanorana. Ranidae as a sister clade to Dicroglossidae and the clade of (Ranidae + Dicroglossidae) as a sister clade to (Mantellidae + Rhacophoridae) were well supported in BI analysis but low bootstrap in ML analysis.

CONCLUSIONS

We found that the gene arrangements of N. taihangnica and N. yunnanensis differed from other published dicroglossid mt genomes. The gene arrangements in N. taihangnica and N. yunnanensis could be explained by the Tandem Duplication and Random Loss (TDRL) and the Dimer-Mitogenome and Non-Random Loss (DMNR) models, respectively. The invalidation of the genus Feirana is supported in this study.

Interspecies introgressive hybridization in spiny frogs Quasipaa (Family Dicroglossidae) revealed by analyses on multiple mitochondrial and nuclear genes

Introgression may lead to discordant patterns of variation among loci and traits. For example, previous phylogeographic studies on the genus Quasipaa detected signs of genetic introgression from genetically and morphologically divergent Quasipaa shini or Quasipaa spinosa. In this study, we used mitochondrial and nuclear DNA sequence data to verify the widespread introgressive hybridization in the closely related species of the genus Quasipaa, evaluate the level of genetic diversity, and reveal the formation mechanism of introgressive hybridization. In Longsheng, Guangxi Province, signs of asymmetrical nuclear introgression were detected between Quasipaa boulengeri and Q. shini. Unidirectional mitochondrial introgression was revealed from Q. spinosa to Q. shini. By contrast, bidirectional mitochondrial gene introgression was detected between Q. spinosa and Q. shini in Lushan, Jiangxi Province. Our study also detected ancient hybridizations between a female Q. spinosa and a male Q. jiulongensis in Zhejiang Province. Analyses on mitochondrial and nuclear genes verified three candidate cryptic species in Q. spinosa, and a cryptic species may also exist in Q. boulengeri. However, no evidence of introgressive hybridization was found between Q. spinosa and Q. boulengeri. Quasipaa exilispinosa from all the sampling localities appeared to be deeply divergent from other communities. Our results suggest widespread introgressive hybridization in closely related species of Quasipaa and provide a fundamental basis for illumination of the forming mechanism of introgressive hybridization, classification of species, and biodiversity assessment in Quasipaa.

Phylogeographic investigation and ecological niche modelling of the endemic frog species Nanorana pleskei revealed multiple refugia in the eastern Tibetan Plateau

The largest plateau Tibetan Plateau supplied an excellent opportunity to investigate the influence of the Pleistocene events on the high-elevation species. To test for the alternative hypotheses of Pleistocene glacial refugia, we used partial sequences of two mitochondrial genes and one nuclear gene to examine the phylogeographic patterns of the endemic frog species Nanorana pleskei across its known range in the eastern Tibetan Plateau, and conducted species distribution modelling (SDM) to explore changes of its distribution range through current and paleo periods. In all data sets, the species was divided into lineage north occupying open plateau platform and lineage south colonizing the mountainous plateau. The divergence of two major clades was estimated at the early Pleistocene. In mtDNA, lineage north contained northeastern and northwestern sublineages, and lineage south had two overlapping-distributed sublineages. Different lineages possessed distinct demographic characteristics, i.e., subdivision in the northeastern sublineage, historical bottleneck effects and recent expansions in the northwestern sublineage and the southeastern sublineage. SDMs depicted that stable suitable habitats had existed in the upper-middle streams of the Yellow River, Dadu River, Jinsha River and Yalong River. These regions were also recognized as the ancestral areas of different lineages. In conclusion, Nanorana pleskei lineages have probably experienced long-term separations. Stable suitable habitats existing in upper-middle streams of major rivers on the eastern Tibetan Plateau and distinct demographic dynamics of different lineages indicated that the lineages possessed independent evolutionary processes in multiple glacial refugia. The findings verified the profound effects of Pleistocene climatic fluctuations on the plateau endemic species.

Next-generation sequencing of mixed genomic DNA allows efficient assembly of rearranged mitochondrial genomes in Amolops chunganensis and Quasipaa boulengeri

Recent improvements in next-generation sequencing (NGS) technologies can facilitate the obtainment of mitochondrial genomes. However, it is not clear whether NGS could be effectively used to reconstruct the mitogenome with high gene rearrangement. These high rearrangements would cause amplification failure, and/or assembly and alignment errors. Here, we choose two frogs with rearranged gene order, Amolops chunganensis and Quasipaa boulengeri, to test whether gene rearrangements affect the mitogenome assembly and alignment by using NGS. The mitogenomes with gene rearrangements are sequenced through Illumina MiSeq genomic sequencing and assembled effectively by Trinity v2.1.0 and SOAPdenovo2. Gene order and contents in the mitogenome of A. chunganensis and Q. boulengeri are typical neobatrachian pattern except for rearrangements at the position of "WANCY" tRNA genes cluster. Further, the mitogenome of Q. boulengeri is characterized with a tandem duplication of trnM. Moreover, we utilize 13 protein-coding genes of A. chunganensis, Q. boulengeri and other neobatrachians to reconstruct the phylogenetic tree for evaluating mitochondrial sequence authenticity of A. chunganensis and Q. boulengeri. In this work, we provide nearly complete mitochondrial genomes of A. chunganensis and Q. boulengeri.

Integrative taxonomy helps to reveal the mask of the genus Gynandropaa (Amphibia: Anura: Dicroglossidae)

Species of the genus Gynandropaa within the family Dicroglossidae are typical spiny frogs whose taxonomic status has long been in doubt. We used integrative methods, involving morphological and molecular analyses, to elucidate the phylogenetic relationships, and to determine identities and the geographic distribution of each valid species. We obtained DNA sequence data of 5 species of Gynandropaa (complete sequences of the mitochondrial NADH dehydrogenase subunit 2 [ND2] gene, and 890 bp of 12S rRNA and 16S rRNA partial sequences) from 37 localities (including the topotypes of 5 described species) and constructed Bayesian and maximum-likelihood trees to examine the patterns of phylogeography. A total of 28 morphological variables were taken on 624 specimens. Three clades with clear geographic patterns were recognized: clade C (from south-western Sichuan Province and central Yunnan Province), clade E (western Guizhou Province and eastern to central Yunnan Province) and clade W (western to southern Yunnan Province). Integrating morphological characteristics and distribution information, the clades W, E and C represent Gynandropaa yunnanensis, G. phrynoides and G. sichuanensis, respectively. We draw the following conclusions: (i) the taxon G. phrynoides, formerly evaluated as a junior synonym of G. yunnanensis, is revalidated herein at the rank of species; (ii) G. liui is a junior synonym of G. sichuanensis; and (iii) G. yunnanensis is a valid species while G. bourreti is probably a subspecies of G. yunnanensis, with the distribution range from Vietnam to southern Yunnan Province. This study clears up the taxonomic status of Gynandropaa and provides important information for understanding the evolution and conservation of these spiny frogs.

Niche conservatism in Gynandropaa frogs on the southeastern Qinghai-Tibetan Plateau

The role of ecological niche in lineage diversification has been the subject of long-standing interest of ecologists and evolutionary biologists. Gynandropaa frogs diversified into three independent clades endemic to the southeastern Qinghai-Tibetan Plateau. Here, we address the question whether these clades kept the same niche after separation, and what it tells us about possible diversification processes. We applied predictions in geographical (G)-space and tests of niche conservatism in environmental (E)-space. Niche models in G-space indicate separate regions with high suitability for the different clades, with some potential areas of sympatry. While the pair of central and eastern clades displayed the largest niche overlap for most variables, and strict niche equivalency was rejected for all clade-pairs, we found no strong evidence for niche divergence, but rather the signature of niche conservatism compared to null models in E-space. These results suggest a common ancestral ecological niche, and as such give good support to divergence through allopatric speciation, but alternative explanations are also possible. Our findings illustrate how testing for niche conservatism in lineage diversification can provide insights into underlying speciation processes, and how this information may guide further research and conservation practices, as illustrated here for amphibians on the Qinghai-Tibetan Plateau.

Undiagnosed cryptic diversity in small, microendemic frogs (Leptolalax) from the Central Highlands of Vietnam

A major obstacle in prioritizing species or habitats for conservation is the degree of unrecognized diversity hidden within complexes of morphologically similar, "cryptic" species. Given that amphibians are one of the most threatened groups of organisms on the planet, our inability to diagnose their true diversity is likely to have significant conservation consequences. This is particularly true in areas undergoing rapid deforestation, such as Southeast Asia. The Southeast Asian genus Leptolalax is a group of small-bodied, morphologically conserved frogs that inhabit the forest-floor. We examined a particularly small-bodied and morphologically conserved subset, the Leptolalax applebyi group, using a combination of molecular, morphometric, and acoustic data to identify previously unknown diversity within. In order to predict the geographic distribution of the group, estimate the effects of habitat loss and assess the degree of habitat protection, we used our locality data to perform ecological niche modelling using MaxEnt. Molecular (mtDNA and nuDNA), acoustic and subtle morphometric differences revealed a significant underestimation of diversity in the L. applebyi group; at least two-thirds of the diversity may be unrecognised. Patterns of diversification and microendemism in the group appear driven by limited dispersal, likely due to their small body size, with several lineages restricted to watershed basins. The L. applebyi group is predicted to have historically occurred over a large area of the Central Highlands of Vietnam, a considerable portion of which has already been deforested. Less than a quarter of the remaining forest predicted to be suitable for the group falls within current protected areas. The predicted distribution of the L. applebyi group extends into unsurveyed watershed basins, each potentially containing unsampled diversity, some of which may have already been lost due to deforestation. Current estimates of amphibian diversity based on morphology alone are misleading, and accurate alpha taxonomy is essential to accurately prioritize conservation efforts.

DNA barcodes and species distribution models evaluate threats of global climate changes to genetic diversity: a case study from Nanorana parkeri (Anura: Dicroglossidae)

Anthropogenic global climate changes are one of the greatest threats to biodiversity. Distribution modeling can predict the effects of climate changes and potentially their effects on genetic diversity. DNA barcoding quickly identifies patterns of genetic diversity. As a case study, we use DNA barcodes and distribution models to predict threats under climate changes in the frog Nanorana parkeri, which is endemic to the Qinghai-Tibetan Plateau. Barcoding identifies major lineages W and E. Lineage W has a single origin in a refugium and Lineage E derives from three refugia. All refugia locate in river valleys and each greatly contributes to the current level of intraspecific genetic diversity. Species distribution models suggest that global climate changes will greatly influence N. parkeri, especially in the level of genetic diversity, because two former refugia will fail to provide suitable habitat. Our pipeline provides a novel application of DNA barcoding and has important implications for the conservation of biodiversity in southern areas of the Qinghai-Tibetan Plateau.

Complete mitochondrial genome of the Ye's spiny-vented frog Yerana yei (Anura: Dicroglossidae)

Yerana yei (Anura: Dicroglossidae) is the only one species in the genus Yerana and the taxonomy of the Y. yei remains unresolved and controversial. The complete mitochondrial genome of Yerana yei (Anura: Dicroglossidae) was sequenced in the present study, and it is a circular molecule of 17,072 bp in length and contains the 38 genes typically found in other anurans: 13 protein-coding genes, 2 ribosomal RNA genes and 23 transfer RNA genes (including an extra copy of tRNA(Met)). The order and orientation of the genes is the same as that found in other Paini species. The A + T content of the overall base composition of H-strand is 58% (T, 29.4%; C, 27.3%; A, 28.6%; G, 14.7%) and the length of control region is 1580 bp with 67% A + T content.

The complete mitochondrial genome of Feirana taihangnica (Anura: Dicroglossidae)

The complete mitochondrial genome sequence of the Feirana taihangnica (Anura: Dicroglossidae) was determined. It is a circular molecule of 17,412 bp in length, containing 13 protein-coding genes, 2 ribosomal RNAs, 22 transfer RNAs, and a control region. The tRNA(Thr) gene located in the LTPF tRNA gene cluster typically found in other anurans is absent from the F. taihangnica mtDNA and a tandem duplication of tRNA(Met) gene is observed. The A+T content of the overall base compositon of H-strand is 57.2% and the length of control region is 1972 bp with 61.8% A+T content.

Phylogeographic analyses strongly suggest cryptic speciation in the giant spiny frog (Dicroglossidae: Paa spinosa) and interspecies hybridization in Paa

Species identification is one of the most basic yet crucial issues in biology with potentially far-reaching implications for fields such as conservation, population ecology, and epidemiology. The widely distributed but threatened frog Paa spinosa has been speculated to represent a complex of multiple species. In this study, 254 individuals representing species of the genus Paa were investigated along the entire range of P. spinosa: 196 specimens of P. spinosa, 8 specimens of P. jiulongensis, 5 specimens of P. boulengeri, 20 specimens of P. exilispinosa, and 25 specimens of P. shini. Approximately 1333 bp of mtDNA sequence data (genes 12S rRNA and 16S rRNA) were used. Phylogenetic analyses were conducted using maximum parsimony, maximum likelihood and Bayesian inference. BEAST was used to estimate divergence dates of major clades. Results suggest that P. spinosa can be divided into three distinct major lineages. Each major lineage totally corresponds to geographical regions, revealing the presence of three candidate cryptic species. Isolation and differentiation among lineages are further supported by the great genetic distances between the lineages. The bifurcating phylogenetic pattern also suggests an east-west dispersal trend during historic cryptic speciation. Dating analysis estimates that P. spinosa from Western China split from the remaining P. spinosa populations in the Miocene and that P. spinosa from Eastern China diverged from Central China in the Pliocene. We also found that P. exilispinosa from Mainland China and Hong Kong might have a complex of multiple species. After identifying cryptic lineages, we then determine the discrepancy between the mtDNA and the morphotypes in several individuals. This discrepancy may have been caused by introgressive hybridization between P. spinosa and P. shini.

Phylogeographic patterns of mtDNA variation revealed multiple glacial refugia for the frog species Feirana taihangnica endemic to the Qinling Mountains

Diversification patterns and demography of montane species are affected by Pleistocene climate fluctuations. Empirical cases from the Qinling Mountains (QM) region, which is a major biogeographic divider of East Asia, are few. We used DNA sequence data of the complete mitochondrial ND2 gene to detect effects of the Pleistocene glaciations on phylogeographic profiles of a frog species, Feirana taihangnica, which is endemic to the QM. Four distinct lineages consisting of seven sublineages were revealed. The strongest signal of biogeographical structure (F(ct) = 0.971, P < 0.01) was found when populations were grouped according to these seven sublineages. One narrow secondary contact zone was detected in the middle QM between the lineage from middle QM and the lineage from eastern QM. Coalescent simulations indicated that this species colonized the QM region by a stepping-stone model. Divergences among lineages had likely been influenced by the uplift of the Tibetan Plateau during the late Miocene-to-late Pleistocene, as well as by the Pleistocene climatic cycles. Coalescent simulations also suggested that F. taihangnica populations have persisted through the Pleistocene glacial periods in multiple refugia across the QM region. Demographic analyses indicated that all lineages, except the lineage in the Funiu Mountains, have been experienced postglacial expansion of population size and distribution range. In conclusion, Pleistocene climate fluctuations and tectonic changes during the late Miocene-late Pleistocene have profoundly influenced the phylogeography and historical demography of F. taihangnica.

A de novo case of floating chromosomal polymorphisms by translocation in Quasipaa boulengeri (Anura, Dicroglossidae)

Very few natural polymorphisms involving interchromosomal reciprocal translocations are known in amphibians even in vertebrates. In this study, thirty three populations, including 471 individuals of the spiny frog Quasipaa boulengeri, were karyotypically examined using Giemsa stain or FISH. Five different karyomorphs were observed. The observed heteromorphism was autosomal but not sex-related, as the same heteromorphic chromosomes were found both in males and females. Our results indicated that the variant karyotypes resulted from a mutual interchange occurring between chromosomes 1 and 6. The occurrence of a nearly whole-arm translocation between chromosome no. 1 and no. 6 gave rise to a high frequency of alternate segregation and probably resulted in the maintenance of the translocation polymorphisms in a few populations. The translocation polymorphism is explained by different frequencies of segregation modes of the translocation heterozygote during meiosis. Theoretically, nine karyomorphs should be investigated, however, four expected karyotypes were not found. The absent karyomorphs may result from recessive lethal mutations, position effects, duplications and deficiencies. The phylogenetic inference proved that all populations of Q. boulengeri grouped into a monophyletic clade. The mutual translocation likely evolved just once in this species and the dispersal of the one karyomorph (type IV) can explain the chromosomal variations among populations.

Postglacial colonization of the Qinling Mountains: phylogeography of the swelled vent frog (Feirana quadranus)

BACKGROUND

The influence of Pleistocene climatic fluctuations on intraspecific diversification in the Qinling-Daba Mountains of East Asia remains poorly investigated. We tested hypotheses concerning refugia during the last glacial maximum (LGM) in this region by examining the phylogeography of the swelled vent frog (Feirana quadranus; Dicroglossidae, Anura, Amphibia).

METHODOLOGY/PRINCIPAL FINDINGS

We obtained complete mitochondrial ND2 gene sequences of 224 individuals from 34 populations of Feirana quadranus for phylogeographic analyses. Additionally, we obtained nuclear tyrosinase gene sequences of 68 F. quadranus, one F. kangxianensis and three F. taihangnica samples to test for mitochondrial introgression among them. Phylogenetic analyses based on all genes revealed no introgression among them. Phylogenetic analyses based on ND2 datasets revealed that F. quadranus was comprised of six lineages which were separated by deep valleys; the sole exception is that the Main Qinling and Micang-Western Qinling lineages overlap in distribution. Analyses of population structure indicated restricted gene flow among lineages. Coalescent simulations and divergence dating indicated that the basal diversification within F. quadranus may be associated with the dramatic uplifts of the Tibetan Plateau during the Pliocene. Coalescent simulations indicated that Wuling, Daba, and Western Qinling-Micang-Longmen Mountains were refugia for F. quadranus during the LGM. Demographic analyses indicated that the Daba lineage experienced population size increase prior to the LGM but the Main Qinling and the Micang-Western Qinling lineages expanded in population size and range after the LGM, and the other lineages almost have stable population size or slight slow population size decline.

CONCLUSIONS/SIGNIFICANCE

The Qinling-Daba Mountains hosted three refugia for F. quadranus during the LGM. Populations that originated in the Daba Mountains colonized the Main Qinling Mountains after the LGM. Recent sharp expansion of the Micang-Western Qinling and Main Qinling lineages probably contribute to their present-day secondary contact.

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

To survey the diversity of anuran species in Bangladesh, we compared mitochondrial 16S rRNA gene sequences (approximately 1.4 kbp) from 107 Bangladesh frog specimens. The results of genetic divergence and phylogenetic analyses incorporating data from related species revealed the occurrence of at least eight cryptic species. Hoplobatrachus tigerinus from two districts diverged considerably, indicating the involvement of a cryptic species. Two Fejervarya sp. (large and medium types) and Hylarana cf. taipehensis formed lineages distinct from related species and are probably new species. Microhyla cf. ornata differed from M. ornata with respect to type locality area and involved two distinct species. In addition, we found that Hylarana sp. and Microhyla sp. did not match congeners examined to date in either morphology or 16S rRNA sequence. The occurrence of M. fissipes was tentatively suggested. Consequently, at least, 19 species were found from Bangladesh in this study. These findings revealed a rich anuran biodiversity in Bangladesh, which is unexpected considering the rather simple topographic features of the country.

Elevational patterns of species richness, range and body size for spiny frogs

Quantifying spatial patterns of species richness is a core problem in biodiversity theory. Spiny frogs of the subfamily Painae (Anura: Dicroglossidae) are widespread, but endemic to Asia. Using spiny frog distribution and body size data, and a digital elevation model data set we explored altitudinal patterns of spiny frog richness and quantified the effect of area on the richness pattern over a large altitudinal gradient from 0-5000 m a.s.l. We also tested two hypotheses: (i) the Rapoport's altitudinal effect is valid for the Painae, and (ii) Bergmann's clines are present in spiny frogs. The species richness of Painae across four different altitudinal band widths (100 m, 200 m, 300 m and 400 m) all showed hump-shaped patterns along altitudinal gradient. The altitudinal changes in species richness of the Paini and Quasipaini tribes further confirmed this finding, while the peak of Quasipaini species richness occurred at lower elevations than the maxima of Paini. The area did not explain a significant amount of variation in total, nor Paini species richness, but it did explain variation in Quasipaini. Five distinct groups across altitudinal gradient were found. Species altitudinal ranges did not expand with an increase in the midpoints of altitudinal ranges. A significant negative correlation between body size and elevation was exhibited. Our findings demonstrate that Rapoport's altitudinal rule is not a compulsory attribute of spiny frogs and also suggest that Bergmann's rule is not generally applicable to amphibians. The study highlights a need to explore the underlying mechanisms of species richness patterns, particularly for amphibians in macroecology.

Spiny frogs (Paini) illuminate the history of the Himalayan region and Southeast Asia

Asian frogs of the tribe Paini (Anura: Dicroglossidae) range across several first-order tectono-morphological domains of the Cenozoic Indo-Asian collision that include the Tibetan Plateau, the Himalayas, and Indochina. We show how the tectonic events induced by the Indo-Asian collision affected the regional biota and, in turn, how the geological history of the earth can be viewed from a biological perspective. Our analysis of a concatenated dataset comprising four nuclear gene sequences of Paini revealed two main radiations, corresponding to the genera Nanorana (I) and Quasipaa (II). Five distinct clades are recognized: Tibetan plateau clade (I-1), Himalaya clade (I-2), environs of Himalaya-Tibetan plateau clade (I-3), South China clade (II-1), and Indochina clade (II-2). This pattern of relationships highlights the significance of geography in shaping evolutionary history. Building on our molecular dating, ancestral region reconstruction, and distributional patterns, we hypothesize a distinct geographic and climatic transition in Asia beginning in the Oligocene and intensifying in the Miocene; this stimulated rapid diversification of Paini. Vicariance explains species formation among major lineages within Nanorana. Dispersal, in contrast, plays an important role among Quasipaa, with the southern Chinese taxa originating from Indochina. Our results support the tectonic hypothesis that an uplift in the Himalaya-Tibetan plateau region resulting from crustal thickening and lateral extrusion of Indochina occurred synchronously during the transition between Oligocene and Miocene in reaction to the Indo-Asian collision. The phylogenetic history of Paini illuminates critical aspects of the timing of geological events responsible for the current geography of Southeast Asia.

Impending conservation crisis for Southeast Asian amphibians

With an understudied amphibian fauna, the highest deforestation rate on the planet and high harvesting pressures, Southeast Asian amphibians are facing a conservation crisis. Owing to the overriding threat of habitat loss, the most critical conservation action required is the identification and strict protection of habitat assessed as having high amphibian species diversity and/or representing distinctive regional amphibian faunas. Long-term population monitoring, enhanced survey efforts, collection of basic biological and ecological information, continued taxonomic research and evaluation of the impact of commercial trade for food, medicine and pets are also needed. Strong involvement of regional stakeholders, students and professionals is essential to accomplish these actions.

Molecular phylogeny and genetic identification of populations of two species of Feirana frogs (Amphibia: Anura, Ranidae, Dicroglossinae, Paini) endemic to China

Using mitochondrial 12S rRNA, 16S rRNA, and ND2 sequences, we investigated phylogenetic relationships among populations of two frog species endemic to China, both referred to the genus Feirana. A sister-group relationship between the two species was supported moderately in a maximum likelihood analysis and significantly in a Bayesian analysis, but not in a maximum parsimony analysis, of combined data for the three genes. Pending resolution of this incongruence, we provisionally maintain these species in the genus Feirana. Two major clades with a deep divergence are concordant with the species F. quadranus and "F." taihangnica. In the present work, some populations from the Qinling Mountains and all those from the Funiu and the Zhongtiao-southern Taihang Mountains are referred to "F." taihangnica rather than F. quadranus, whereas others are referred to F. quadranus. Consequently, the main body of the Qinling Mountains was identified as a large contact zone between these two species. On the basis of phylogenetic relationships and the distribution pattern of populations, we propose a hypothesis for the divergence of "F." taihangnica: the ancestral species might have inhabited the westernmost Qinling Mountains and dispersed to the main Qinling Mountains, and then to the Zhongtiao-southern Taihang and Funiu Mountains. In contrast, two alternative hypotheses are suggested for F. quadranus: if the two species are confirmed as sister groups, F. quadranus might have dispersed from the westernmost Qinling to the Longmen, Qinling, Daba, and northern Wuling Mountains; alternatively, F. quadranus might have come from the northern Wuling Mountains and then dispersed to the Daba, Qinling, and Longmen mountains.