A combined approach of mitochondrial DNA and anchored nuclear phylogenomics sheds light on unrecognized diversity, phylogeny, and historical biogeography of the torrent frogs, genus Amolops (Anura: Ranidae)

Contrasting nidification behaviors facilitate diversification and colonization of the Music frogs under a changing paleoclimate

In order to cope with the complexity and variability of the terrestrial environment, amphibians have developed a wide range of reproductive and parental behaviors. Nest building occurs in some anuran species as parental care. Species of the Music frog genus Nidirana are known for their unique courtship behavior and mud nesting in several congeners. However, the evolution of these frogs and their nidification behavior has yet to be studied. With phylogenomic and phylogeographic analyses based on a wide sampling of the genus, we find that Nidirana originated from central-southwestern China and the nidification behavior initially evolved at ca 19.3 Ma but subsequently lost in several descendants. Further population genomic analyses suggest that the nidification species have an older diversification and colonization history, while N. adenopleura complex congeners that do not exhibit nidification behavior have experienced a recent rapid radiation. The presence and loss of the nidification behavior in the Music frogs may be associated with paleoclimatic factors such as temperature and precipitation. This study highlights the nidification behavior as a key evolutionary innovation that has contributed to the diversification of an amphibian group under past climate changes.

Genomic analysis reveals deep population divergence in the water snake Trimerodytes percarinatus (Serpentes, Natricidae)

Although several phylogeographic studies of Asian snakes have been conducted, most have focused on pitvipers, with non-venomous snakes, such as colubrids or natricids, remaining poorly studied. The Chinese keelback water snake (Trimerodytes percarinatus Boulenger) is a widespread, semiaquatic, non-venomous species occurring in China and southeastern Asia. Based on mitochondrial DNA (mtDNA) and single nucleotide polymorphism (SNP) data, we explored the population genetic structure, genetic diversity, and evolutionary history of this species. MtDNA-based phylogenetic analysis showed that T. percarinatus was composed of five highly supported and geographically structured lineages. SNP-based phylogenetic analysis, principal component analysis, and population structure analysis consistently revealed four distinct, geographically non-overlapping lineages, which was different from the mtDNA-based analysis in topology. Estimation of divergence dates and ancestral area of origin suggest that T. percarinatus originated ~12.68 million years ago (95% highest posterior density: 10.36-15.96 Mya) in a region covering southwestern China and Vietnam. Intraspecific divergence may have been triggered by the Qinghai-Xizang Plateau uplift. Population demographics and ecological niche modeling indicated that the effective population size fluctuated during 0.5 Mya and 0.002 Mya. Based on the data collected here, we also comment on the intraspecific taxonomy of T. percarinatus and question the validity of the subspecies T. p. suriki.

A new species of Amolops (Amphibia, Anura, Ranidae) from Guizhou Province, China

The Torrent frogs of the genus Amolops are widely distributed in Nepal and northern India eastwards to southern China and southwards to Malaysia. The genus currently contains 84 species. Previous studies indicated underestimated species diversity in the genus. In the context, a new species occurring from the mountains in the northwestern Guizhou Province, China is found and described based on morphological comparisons and molecular phylogenetic analyses, Amolopsdafangensissp. nov. Phylogenetic analyses based on DNA sequences of the mitochondrial 16S rRNA and COI genes supported the new species as an independent lineage. The uncorrected genetic distances between the 16S rRNA and COI genes in the new species and its closest congener were 0.7% and 2.6%, respectively, which are higher than or at the same level as those among many pairs of congeners. Morphologically, the new species can be distinguished from its congeners by a combination of the following characters: body size moderate (SVL 43.2-46.8 mm in males); head length larger than head width slightly; tympanum distinct, oval; vocal sacs absent; vomerine teeth present; dorsolateral folds weak formed by series of glands; nuptial pads present on the base of finger I; heels overlapping when thighs are positioned at right angles to the body; tibiotarsal articulation reaching the level far beyond the tip of the snout when leg stretched forward.

Integrated phylogenetic analyses reveal the evolutionary, biogeographic, and diversification history of Asian warty treefrog genus Theloderma (Anura, Rhacophoridae)

Asian warty treefrogs, genus Theloderma, are morphologically variable arboreal frogs endemic to Southeast Asia and Southern China. However, integrated systematic studies are lacking, and knowledge of the genus in terms of diversity, origin, and historical diversification remains limited. To address these knowledge gaps, we used three mitochondrial and five nuclear gene fragments to reconstruct the Theloderma phylogeny, estimate divergence times, and examine the biogeography of the genus. Phylogenetic and species delimitation analyses suggest that the genus Theloderma comprises three major clades corresponding to two subgenera and seven species groups, and mPTP identified at least 12 putative cryptic species, suggesting that species diversity has been underestimated. Biogeographic analyses indicated that most recent common ancestor of Theloderma originated in the Indochina Peninsula during the Middle Oligocene (ca. 27.77 Ma) and the splitting of Clade A to C occurred in the Late Oligocene (ca. 23.55-25.57 Ma). Current biogeographic patterns result from two distinct processes: in situ diversification in the Indochina Peninsula and dispersal in multiple areas, namely southward dispersal to the Malay Peninsula and Borneo, northeastward dispersal to Southern China, northward dispersal to the Himalayas, and dispersal from Southern China to the Indochina Peninsula. Ancestral character reconstruction suggests that the ancestor of Theloderma may have possessed a small body size, rough dorsal skin, and absence of vomerine teeth and hand webbing, and that these four characters have undergone multiple evolutions. Principal component analysis based on eight bioclimatic variables did not clearly distinguish the three major clades of Theloderma, suggesting that species in these clades may occupy similar climatic ecological niches. Our research highlights the importance of orogeny and paleoclimatic changes, in shaping amphibian biodiversity in mountain ecosystems.

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.

Characterization and Comparison of the Two Mitochondrial Genomes in the Genus Rana

The mitochondrial genome (mitogenome) possesses several invaluable attributes, including limited recombination, maternal inheritance, a fast evolutionary rate, compact size, and relatively conserved gene arrangement, all of which make it particularly useful for applications in phylogenetic reconstruction, population genetics, and evolutionary research. In this study, we aimed to determine the complete mitogenomes of two morphologically similar Rana species (Rana hanluica and Rana longicrus) using next-generation sequencing. The entire circular mitogenome was successfully identified, with a length of 19,395 bp for R. hanluica and 17,833 bp for R. longicrus. The mitogenomes of both species contained 37 genes, including 13 protein-coding genes (PCGs), two ribosomal RNA genes, 22 transfer RNA genes, and one control region; mitogenome size varied predominantly with the length of the control region. The two synonymous codon usages in 13 PCGs showed that T and A were used more frequently than G and C. The ratios of non-synonymous to synonymous substitutions of all 13 PCGs were <1 in the Rana species, indicating that the PCGs were under purifying selection. Finally, phylogenetic relationship analyses suggested that R. hanluica and R. longicrus were classified in the R. japonica group. Our study provides valuable reference material for the taxonomy of the genus Rana.

A new species of cascade frog (Anura: Ranidae: Amolops) from central Yunnan, China

A new species of the genus Amolops, Amolops ailao sp. nov., is described from central Yunnan, China. The new species belongs to the A. mantzorum species group. Phylogenetic analyses based on the combination of mitochondrial 16S rRNA, COI, and cytb genes revealed that the new species is the sister taxon to Amolops ottorum with strong support. Genetically, the new species differs from A. ottorum by 5.0% in cytb sequences. Morphologically, the new species can be distinguished from known congeners by the combination of the following characters: true dorsolateral folds absent, but dorsolateral folds formed by series of glands present; circummarginal groove on tip of first finger absent; body size small (males SVL 33.0-35.1 mm and female SVL 41.3 mm); HW/SVL 0.32‒0.35; UEW/SVL 0.08‒0.10; THL/SVL 0.52‒0.56; vomerine teeth absent; interorbital distance narrower than internarial distance; tympanum distinct, less than half eye diameter; supratympanic fold present, indistinct; a pair of large tubercles on sides of cloaca; tibiotarsal articulation reaching beyond anterior corner of eye; and vocal sac absent. The cladogenesis events within the A. mantzorum group rapidly occurred from Pliocene 4.23 Mya to Pleistocene 1.2 Mya, coinciding with the recent intensive uplift of the Qinghai-Tibetan Plateau since the Pliocene. Combining findings in this study with the most recent taxonomic progress, we consider that there are 20 known Amolops species in Yunnan, China, accounting for the highest proportion of amphibian diversity of Yunnan, and five of them belong to the A. mantzorum group. Among different subfauna and water systems in Yunnan, the species diversity of Amolops in northwestern Yunnan and Nu River Basin is highest.

First national record of Microhylahmongorum Hoang, Nguyen, Phan, Pham, Ninh, Wang, Jiang, Ziegler and Nguyen, 2022 (Anura, Microhylidae, Microhyla) in China

Background

To date, 10 species of the genus Microhyla have been recorded in China, of which six were distributed in Yunnan Province. Microhylahmongorum Hoang, Nguyen, Phan, Pham, Ninh, Wang, Jiang, Ziegler, and Nguyen, 2022 was also speculated to be distributed in Xishuangbana, Yunnan Province, China. However, there is no evidence of documentation of M.hmongorum.

New information

We report the first country record of Microhylahmongorum, based on specimens collected from Yunnan border region. Morphologically, the specimen was consistent with the original descriptions of M.hmongorum. Phylogenetically, the sequences of the specimens from China clustered with the sequence of type specimens of M.hmongorum from Vietnam, with uncorrected pairwise distances of 0.9% at the 16S gene fragment analysed. Therefore, we report M.hmongorum as a new record species in China.

Unrecognized diversity, genetic structuring, and phylogeography of the genus Triplophysa (Cypriniformes: Nemacheilidae) sheds light on two opposite colonization routes during Quaternary glaciation that occurred in the Qilian Mountains

In recent years, the influence of historical geological and climatic events on the evolution of flora and fauna in the Tibetan Plateau has been a hot research topic. The Qilian Mountain region is one of the most important sources of biodiversity on the Qinghai-Tibet Plateau. Many species existed in the region during the Pleistocene glacial oscillation, and the complex geographical environment provided suitable conditions for the survival of local species. The shrinkage, expansion, and transfer of the distribution range and population size of species have significant effects on genetic diversity and intraspecific differentiation. To reveal the effects of geological uplift and climate oscillation on the evolution of fish populations in the Qilian Mountains, we investigated the genetic structure, phylogenetic relationship, and phylogeographical characteristics of genus Triplophysa species in the Qilian Mountains using the mitochondrial DNA gene (COI), three nuclear genes (RAG1, sRH, and Myh6) and 11 pairs of nuclear microsatellite markers. We collected 11 species of genus Triplophysa living in the Qilian Mountains, among which Triplophysa hsutschouensis and Triplophysa papillosolabiata are widely distributed in the rivers on the northern slope of the Qilian Mountains. There was a high degree of lineage differentiation among species, and the genetic diversity of endemic species was low. The different geographical groups of T. papillosolabiata presented some allogeneic adaptation and differentiation, which was closely related to the changes in the river system. Except for the population expansion event of T. hsutschouensis during the last glacial period of the Qinghai-Tibet Plateau (0.025 MYA), the population sizes of other plateau loach species remained stable without significant population expansion. Starting from the east and west sides of the Qilian Mountains, T. hsutschouensis, and T. papillosolabiata showed two species colonization routes in opposite directions. The geological events of the uplift of the Qinghai-Tibet Plateau and the climatic oscillation of the Quaternary glaciation had a great influence on the genetic structure of the plateau loach in the Qilian Mountains, which promoted the genetic differentiation of the plateau loach and formed some unique new species. The results of this study have important guiding significance for fish habitat protection in the Qilian Mountains.

A cryptic species of the Amolopsricketti species group (Anura, Ranidae) from China-Vietnam border regions

It was supposed that the current records of Amolopsricketti might be a species complex composed of multiple species. In this study, on the basis of wide sampling, we found that the records of A.ricketti from Yunnan, China, and northern Vietnam actually represent a cryptic species based on morphological and molecular evidence. Amolopsshihaitaoi sp. nov. can be distinguished from other members of the A.ricketti species group by its moderate body size (SVL 35.5‒37.3 mm in males and 39.2‒45.7 mm in females); white spines on the temporal region, loreal region, snout, and lips in breeding males but absent in females; overlapping heels; tibiotarsal articulation reaching tip of snout; indistinct longitudinal glandular folds on the skin of the shoulders; presence of supernumerary tubercles below the base of fingers II‒IV, distinct pineal body; presence of vomerine teeth; and absence of vocal sacs. Phylogenetic analysis supports that the new species is sister to Amolopsyatseni and the populations from Jingxi, Guangxi and Lào Cai, Vietnam previously reported as A.yatesni also belong to it. Additionally, our results indicate that more cryptic species may exist within the A.ricketti species group, implying that more studies are needed to achieve a complete understanding of the species diversity of this group.

Assessment of the threat status of the amphibians in Vietnam - Implementation of the One Plan Approach

The current decline in global biodiversity is most evident in amphibians with 41% percent of all species worldwide classified as threatened with extinction. Hence, a major challenge in amphibian conservation is the high number of threatened species, leading to a common approach of identifying priority species and regions for conservation efforts. As a part of one of 36 globally designated biodiversity hotspots, Vietnam is considered to be of particular importance for conservation action. To improve amphibian conservation in Vietnam, this study provides an updated species list and assesses their threat status by compiling data from a variety of sources. Furthermore, a Zoological Information Management System (ZIMS) analysis was conducted to determine the representation of extant amphibians from Vietnam in zoos worldwide. The batrachofauna of Vietnam is characterized by a high level of species richness and local endemism as well as a high rate of new discoveries, with more than half of the endemic species reported exclusively from their type locality, making them especially vulnerable to extinction. Up to 18% of all amphibians extant in Vietnam and 28% of endemic species are classified as threatened with extinction by the IUCN. In many cases, the IUCN Red List status is either missing or outdated, highlighting the urgent need of action. Around 14% of endemic amphibian species have been recorded exclusively from unprotected areas, suggesting prioritization for further research and conservation measures. The continuing decline in many species remains an unresolved problem. As a guide for future research and conservation measures, a list of the top 57 species was compiled. In addition, according to the ZIMS analysis, only 8% of threatened and 3% of endemic amphibian taxa from Vietnam are currently kept in zoos worldwide, and a richness analysis revealed that the highest density of husbandries is found in Europe and North America. To achieve maximum outcome for the conservation of threatened species, this study recommends a general shift by zoos towards maintaining species in greater need of captive assurance populations and breeding programs to support integrative strategies that combine in situ and ex situ conservation efforts following the IUCN’s One Plan Approach.

Distribution extension of Leptobrachella eos (Ohler, Wollenberg, Grosjean, Hendrix, Vences, Ziegler & Dubois, 2011): first record from Thailand

We report the first country record of Leptobrachella eos (Ohler, Wollenberg, Grosjean, Hendrix, Vences, Ziegler &amp; Dubois, 2011) from Thailand, based on one specimen collected from Chom poo Phuka nature trail, Bo Kluea District. Morphologically, the specimen displayed good agreement with the original descriptions provided for L. eos. Phylogenetically, the specimens clustered according to the sequences of type locality of L. eos. Notably, our discovery increases the number of Leptobrachella species known to occur in Thailand to nine.

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.

Molecular phylogeny and historical biogeography of the cave fish genus Sinocyclocheilus (Cypriniformes: Cyprinidae) in southwest China

Modern accumulations of genetic data offer unprecedented opportunities for understanding the systematic classification and origins of specific groups of organisms. The genus Sinocyclocheilus is among the most cave abundant genera in Cyprinidae, with 76 recognized species, belonging to four species groups. Recent phylogenetic studies have shown that the classification of species groups within the genus Sinocyclocheilus remains controversial. In this study, we constructed a sequence supermatrix of 26 species from four species groups of the genus Sinocyclocheilus using the mitochondrial genome to reveal phylogenetic relationships, historical biogeography and patterns of species diversification in the genus Sinocyclocheilus. Phylogenetic analysis strongly supports the monophyletic groups of the three species groups (S. jii, S. cyphotergous, and S. tingi groups) except the S. angularis group. Phylogenetic analysis showed that S. anshuiensis and S. microphthalmus, which were recognized as numbers of S. angularis group, formed a strongly supported independent clade. Therefore, we propose a new species group, the S. microphthalmus group, which contains S. anshuiensis and S. microphthalmus. Biogeographic reconstruction suggests that the living Sinocyclocheilus may have originated in north-central Guangxi at the late Eocene and dispersed outward after a vicariance at 32.31 Million years ago (Ma). Early diversification is focused on the late Oligocene (ca. 25 Ma), which is related to the second uplift of the Qinghai-Tibetan Plateau and the lateral extrusion of the Indochina at the Oligocene/Miocene boundary. Our results suggest that two uplifts of the Qinghai-Tibetan Plateau and climate change in the Miocene may have influenced the diversification of the Sinocyclocheilus lineage. This article is protected by copyright. All rights reserved.

Confirmation of Leptobrachellaventripunctata (Fei, Ye, and Li, 1990), based on molecular and morphological evidence in Thailand

Background

Thailand is considered a global biodiversity hotspot that is known to harbour a striking diversity of endemic species. However, several research studies have determined that the level of amphibian diversity in the country has been significantly underestimated. The megophryid genus Leptobrachella Smith, 1925 is currently known to include 89 species that are primarily distributed throughout southern China and Southeast Asia; however, only seven species have been found in Thailand.

New information

Based on an integrative approach encompassing genetic and morphological analyses, we have concluded that the population identified from Chiang Rai Province of Thailand is conspecific with Leptobrachellaventripunctata (Fei, Ye, and Li, 1990). Importantly, this is the first confirmation record of this species, based on molecular and morphological evidence in Thailand. The discovery of this species reaffirms that the diversity within the genus has been underestimated with many species yet to be discovered. In addition, the findings of our study further highlight the lack of existing knowledge on amphibian taxonomy and an underestimation of the biodiversity that exists along these national border areas.

A new species of Torrent frog (Anura, Ranidae, Amolops) from the Coastal Hills of Southeastern China

The Amolops populations in the coastal hills in eastern Guangdong and southern Fujian, China, were controversially recorded as A. hongkongensis or A. daiyunensis before. In this study, based on the morphological examination and phylogenetic analysis of the specimens from these areas, a new species, Amolops teochew sp. nov., is described. Amolops teochew sp. nov. can be distinguished reliably from A. hongkongensis and A. daiyunensis by a combination of characteristics morphologically and distinct divergences genetically. The description of the new species highlights the Amolops diversity in the limited hilly region of southeastern China, which is remarkably higher than that in the more extensive inland region of southeastern China.

A new species of Amolops (Anura: Ranidae) from northern Myanmar

A new species of the genus Amolops, Amolops putaoensis sp. nov., is described from northern Myanmar. The new species can be distinguished from its congeners by the following characters: (1) dorsolateral fold distinct; (2) upper-lip stripe white; (3) male body size 37.6-40.2 mm; (4) ground color of dorsal surface brown, flank green, small warts on dorsum; (5) two internal subgular vocal sacs present; (6) HL slightly shorter than HW; (7) two palmar tubercles present, supernumerary tubercles and outer metatarsal tubercle absent; (8) tympanum smaller than half of eye diameter; (9) vomerine teeth present; (10) tibiotarsal articulation reaching beyond snout tip; (11) supratympanic fold indistinct; (12) pineal body present; (13) finger webbing absent, presence of circummarginal groove on tip of first finger; (14) nuptial pads present. The population from Myanmar represented a distinct maternal lineage within the Amolops monticola group and was recovered as a sister taxon to Amolops aniqiaoensis with strong support (100) based on concatenated data. Average uncorrected pairwise distances ( P-distances) between the specimens from Myanmar and other species in the genus ranged from 2.69% (vs. A. aniqiaoensis) to 12.24% (vs. A. indoburmanensis) for 16S rRNA, 6.14% (vs. A. aniqiaoensis) to 15.79% (vs. A. panhai) for COI, and 9.66% (vs. A. aniqiaoensis) to 19.52% (vs. A. afghanus) for ND2.

Development and characterization of twelve microsatellite loci for Amolops ricketti using next-generation sequencing

Amphibian populations have decreased dramatically because of human disturbance. To better conserve and manage native or wild populations of Amolops ricketti, 12 novel microsatellite loci were developed using high-throughput sequencing. The number of alleles ranged from 2 to 19, with an average of 7.67 alleles per locus. The observed and expected heterozygosity ranged from 0.42 to 1.00 (average 0.81) and from 0.51 to 0.95 (average 0.76), respectively. The polymorphism information content per locus ranged from 0.38 to 0.92 (average 0.69). These polymorphic microsatellite markers will contribute to the assessment of population structure, gene flow and genetic differentiation in A. ricketti.