A new species of Rana from the Dabie Mountains in eastern China (Anura, Ranidae)

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 the Genus Achalinus (Squamata: Xenodermidae) from the Dabie Mountains, Anhui, China

A new species of Xenodermid snake, Achalinus dabieshanensissp. nov., was described based on three specimens (two female and one male) collected from the Dabie Mountains of western Anhui Province. It can be distinguished from known congeners by a significant genetic divergence in the mitochondrial gene fragment COI (p-distance ≥ 9.4%) and the following combination of characteristics: (1) length of the suture between the internasals being distinctly shorter than between the prefrontals; (2) a single loreal; (3) dorsal scales strongly keeled, in 23 rows throughout the body; (4) two pairs of prefrontals; (5) six supralabials; (6) five infralabials; (7) temporals 2 + 2 + 3 (or 2 + 2 + 4); (8) 141-155 ventrals; (9) 45-55 subcaudals, unpaired; (10) anal entire; (11) weakly iridescent tinged, uniform, brown to black dorsum with vertebral scales and about three adjacent dorsal scales dark brown forming a longitudinal vertebral line from posterior margin of parietals to tail tip; (12) light brown venter, ventral shields wide, visible on both sides, light brown flanks, giving the appearance of a black subcaudal streak. The recognition of the new species increases the number of described Achalinus species to 22.

Comparative Mitogenomics of True Frogs (Ranidae, Anura), and Its Implications for the Phylogeny and Evolutionary History of Rana

Simple Summary

The true frogs of the genus Rana are a complex and diverse group. Many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana were not well understood. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.

Abstract

The true frogs of the genus Rana are a complex and diverse group, containing approximately 60 species with wide distribution across Eurasia and the Americas. Recently, many new species have been discovered with the help of molecular markers and morphological traits. However, the evolutionary history in Rana was not well understood and might be limited by the absence of mitogenome information. In this study, we sequenced and annotated the complete mitochondrial genome of R. longicrus and R. zhenhaiensis, containing 22 tRNAs, 13 protein-coding genes, two ribosomal RNAs, and a non-coding region, with 17,502 bp and 18,006 bp in length, respectively. In 13 protein codon genes, the COI was the most conserved, and ATP8 had a fast rate of evolution. The Ka/Ks ratio analysis among Rana indicated the protein-coding genes were suffering purify selection. There were three kinds of gene arrangement patterns found. The mitochondrial gene arrangement was not related to species diversification, and several independent shifts happened in evolutionary history. Climate fluctuation and environmental change may have played an essential role in species diversification in Rana. This study provides mitochondrial genetic information, improving our understanding of mitogenomic structure and evolution, and recognizes the phylogenetic relationship and taxonomy among Rana.

Assessment of Amphibians Vulnerability to Climate Change in China

Global climate change is considered to be one of the main threats to organisms. As poikilothermic animals, amphibians are in particular sensitive because they cannot adapt to the dramatic climate change through active physiological regulation. Using 104 representative species, the present study conducted an assessment of amphibians vulnerability to climate change in China through the combination of two approaches. Specifically, 18 vulnerability criteria belonging to five categories (i.e., thermal tolerance, individual reproductive, population diffusion and diversity, food and habitat, and climate conditions) were first selected and scored based on literatures and experts opinions. Species were then ranked into three levels of climate change vulnerability (i.e., high, moderate, and low) by calculating vulnerability scores and conducting natural breaks analyses, as well as performing a principal coordinate analysis (PCoA) and k-means cluster analyses, respectively. To integrate the two results, a matrix with the ranks from each result was developed to produce a final integrated list. Our results indicated that the 104 amphibian species were classified into three types by natural breaks, with 54 low vulnerable species, 41 moderately vulnerable species, and nine highly vulnerable species. Based on the results of PCoA and k-means cluster analyses, five species were highly vulnerable, 38 species were moderately vulnerable, and 61 species were low vulnerable. The combination of the two ranks suggested that 36 species such as Hyla tsinlingensis and Liangshantriton taliangensis were of low vulnerability, 54 species such as Echinotriton chinhaiensis and Hynobius chinensis were of moderate vulnerability, and 14 species such as Ichthyophis kohtaoensis and Zhangixalus prasinatus were of high vulnerability. Overall, our results indicated that climate change could have strong potential effects on amphibians in China. And the highly vulnerable species such as Ichthyophis kohtaoensis, Zhangixalus prasinatus, and Theloderma corticale should be the priority in future conservation activities.

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 new species of the genus Rana sensu lato Linnaeus, 1758 (Anura, Ranidae) from Wuyi Mountain, Fujian Province, China

A new species of the frog genus Rana sensu lato from Wuyi Mountain, Fujian Province, China is described. Molecular phylogenetic analyses clustered the new species into the R.johnsi group and indicated that it was genetically divergent from its closely related species. The new species could be distinguished from its congeners by a combination of the following characters: body size medium, SVL 41.4–45.6 mm (42.9 ± 1.9 mm, n = 4) in adult males and 47.6–50.3 mm (n = 2) in adult females; adult male with a pair of internal subgular vocal sacs; lateroventral grooves present on tip of toes; webbing on fourth toes reaching the tip of toe; transverse skin ridges distinctly present on the dorsal surface of thigh and tibia, the number large (mean 26.5 ± 2.7, range 22–29, n = 6); breeding males possess creamy white nuptial pad with tiny velvety spines on the dorsal surface of the first finger, divided into three parts.

Spatial dynamics of Chinese Muntjac related to past and future climate fluctuations

Climate fluctuations in the past and in the future are likely to result in population expansions, shifts, or the contraction of the ecological niche of many species, and potentially leading to the changes in their geographical distributions. Prediction of suitable habitats has been developed as a useful tool for the assessment of habitat suitability and resource conservation to protect wildlife. Here, we model the ancestral demographic history of the extant modern Chinese Muntjac Muntiacus reevesi populations using approximate Bayesian computation (ABC) and used the maximum entropy model to simulate the past and predict the future spatial dynamics of the species under climate oscillations. Our results indicated that the suitable habitats for the M. reevesi shifted to the Southeast and contracted during the Last Glacial Maximum, whereas they covered a broader and more northern position in the Middle Holocene. The ABC analyses revealed that the modern M. reevesi populations diverged in the Middle Holocene coinciding with the significant contraction of the highly suitable habitat areas. Furthermore, our predictions suggest that the potentially suitable environment distribution for the species will expand under all future climate scenarios. These results indicated that the M. reevesi diverged in the recent time after the glacial period and simultaneously as its habitat’s expanded in the Middle Holocene. Furthermore, the past and future climate fluctuation triggered the change of Chinese muntjac spatial distribution, which has great influence on the Chinese muntjac’s population demographic history.

The complete mitochondrial genome sequence of Rana dabieshanensis (Anura: Ranidae)

Rana dabieshanensis is a species of frog within the family Ranidae. In this study, we assembled a complete mitochondrial genome (mito-genome) for R. dabieshanensis by high-throughput sequencing technology. It is 18,291 bp and includes 13 protein-coding genes, 22 tRNA genes, two rRNA genes and one control region. The nucleotide composition is A: 27.0%, T: 28.6%, C: 29.3% and G: 15.2%. Two overlaps among the 13 protein-coding genes were found: ATP8/ATP6, ND4L/ND4. The study of phylogenetic analysis based on complete mitochondrial genome showed that there was close genetic relationship between R. dabieshanensis and R. omeimontis and it is useful for systematic analyses of genus Rana.

A new species of the Rana japonica group (Anura, Ranidae, Rana) from China, with a taxonomic proposal for the R. johnsi group

Ranajiulingensissp. nov., a new species from Hunan and Jiangxi, southeastern China, is described. The new species is assigned to the R.japonica group. The clade comprising R.jiulingensissp. nov. and R.dabieshanensis from Anhui is the sister taxon of R.omeimontis from Sichuan. Ranajiulingensissp. nov. can be distinguished by the significant divergences in the 16S and COI genes, and the combination of following morphological characters: body size medium, SVL 48.3–57.8 mm in adult males and 48.2–57.5 mm in adult females; dorsolateral fold straight; digits without circummarginal grooves; dorsal skin smooth; tibio-tarsal articulation reaching forward beyond the tip of snout; heels overlapping; webbing formula of toes: I 1⅓ – 2 II 1⅓ – 2⅓ III 1½ – 2⅔ IV 3 – 1⅓ V; absence of vocal sacs in males; and presence of creamy white nuptial pad with tiny hoar spines on the finger I and reddish tubercles on loreal and temporal regions in breeding males. Furthermore, based on our results and the previous literature, R.zhengi is synonymized with R.sangzhiensis, and a new species group, the Ranajohnsi group, is proposed for the R.johnsi and R.sangzhiensis. Currently, the Rana contains 41 recognized species, and the phylogenetic placements of several species remain unresolved.