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

Evaluation of partial 12S rRNA, 16S rRNA, COI and Cytb gene sequence datasets for potential single DNA barcode for hylids (Anura: Hylidae)

We evaluated the extent of intraspecific and interspecific genetic distances and the effectiveness of predefined threshold values using the main genes for estimates of biodiversity and specimens' identification in anurans. Partial sequences of the mitochondrial genes for small (12S) and large (16S) ribosomal subunits, cytochrome c oxidase subunit I (COI) and Cytochrome b (Cytb) of the family Hylidae were downloaded from GenBank and curated for length, coverage, and potential contaminations. We performed analyses for all sequences of each gene and the same species present in these datasets by distance and tree (monophyly)-based evaluations. We also evaluated the ability to identify specimens using these datasets applying "nearest neighbor" (NN), "best close match" (BCM) and "BOLD ID" tests. Genetic distance thresholds were generated by the function 'threshVal' and "localMinima" from SPIDER package and traditional threshold values (1%, 3%, 6% and 10%) were also evaluated. Coding genes, especially COI, had a better identification capacity than non-coding genes on barcoding gap and monophyly analysis and NN, BCM, BOLD ID tests. Considering the multiple factors involved in global DNA barcoding evaluations, we present a critical assessment of the use of these genes for biodiversity estimation and specimens' identification in anurans (e.g. hylids).

A regression-based QSAR-model to predict acute toxicity of aromatic chemicals in tadpoles of the Japanese brown frog (Rana japonica): Calibration, validation, and future developments to support risk assessment of chemicals in amphibians

Amphibian populations are undergoing a global decline worldwide. Such decline has been attributed to their unique physiology, ecology, and exposure to multiple stressors including chemicals, temperature, and biological hazards such as fungi of the Batrachochytrium genus, viruses such as Ranavirus, and habitat reduction. There are limited toxicity data for chemicals available for amphibians and few quantitative structure-activity relationship (QSAR) models have been developed and are publicly available. Such QSARs provide important tools to assess the toxicity of chemicals particularly in a data poor context. QSARs provide important tools to assess the toxicity of chemicals particularly when no toxicological data are available. This manuscript provides a description and validation of a regression-based QSAR model to predict, in a quantitative manner, acute lethal toxicity of aromatic chemicals in tadpoles of the Japanese brown frog (Rana japonica). QSAR models for acute median lethal molar concentrations (LC50-12 h) of waterborne chemicals using the Monte Carlo method were developed. The statistical characteristics of the QSARs were described as average values obtained from five random distributions into training and validation sets. Predictions from the model gave satisfactory results for the overall training set (R² = 0.72 and RMSE = 0.33) and were even more robust for the validation set (R² = 0.96 and RMSE = 0.11). Further development of QSAR models in amphibians, particularly for other life stages and species, are discussed.

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.

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.

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.

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

A new species Ranadabieshanensissp. n. is described from the Dabie Mountains in Anhui Province, China, based on morphological character differences and molecular analyses. The new species can be distinguished from its congeners by a combination of diagnostic characters. The results of phylogenetic analyses (based on 12s rRNA, 16s rRNA, ND2, Cyt b, RAG1, BDNF and Tyr) and genetic distances (based on Cyt b) indicate that the new species belongs to the Ranalongicrus group, and is placed as the sister taxon to R.hanluica.