An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology.

A blind fish of Sinocyclocheilus (Cypriniformes: Cyprinidae) was caught in open water in the Three Gorges (Sanxia) reservoir, at a depth of 20 m in the mainstream of Yangtze River in Zigui County, Hubei Province, China. This fish can be easily distinguished from all other congeners by external morphological characteristics, and is estimated to have diverged from its sister group about 0.55 million years ago (Ma). The geologically well separated locality of this species has expanded the distribution of Sinocyclocheilus cavefish from around N25°(latitude) to above N30°. Herein, we describe this new species as Sinocyclocheilus sanxiaensis sp. nov., and discuss the possible reasons why the species appears, surprisingly, in the Three Gorges reservoir.

We describe a new species of Zhangixalus from southern Yunnan of China, Vietnam, and Thailand based on morphological and molecular evidence. The new species had been confused with Zhangixalus smaragdinus (Blyth, 1852) in the past. Zhangixalus pachyproctus sp. nov. can be distinguished from Z. smaragdinus morphologically by the protruding vent in adult males, large thick grey reticular mottles below the white stripe on flank, more oblique snout in profile and wider head, longer snout, greater internarial distance, larger tympanum and longer hindlimb. The new species can be distinguished from other species of Zhangixalus with green dorsum by the following combination of characters: body size larger (SVL of adult males: 74.2–83.3 mm; SVL of adult female: 102.4 mm); dorsum smooth; narrow white stripes along edge of the lower jaw, body sides, outer side of limbs and above the vent; absence of brown bands on canthus rostralis, upper eyelid and supratympanic fold; webbing between fingers and toes complete except between the first two fingers; and internal single subgular vocal sac. Phylogeny based on comparison of 16S rRNA sequences suggests that the new species is the sister taxon to Z. smaragdinus and the two species differ by 7.63% in the uncorrected pairwise distance of 16S sequences.

The partial nucleotide sequence of mitochondrial 12S and 16S rRNA genes was determined for 23 Chinese species of Rhacophoridae (Amphibia: Anura), representing four of the eight recognized genera. Using Buergeriinae as the outgroup, phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference) were performed in combination with already published mitochondrial 12S and 16S sequences of Rhacophorinae frogs. In all cases, Philautus romeriSmith, 1953 is recovered as the sister taxon to all other Rhacophorinae, although the support values are weak. Chirixalus doriae Boulenger, 1893 is closer to Chiromantis [Chiromantis rufescens (Günther, 1868) and Chiromantis xerampelina Peters, 1854] than to Chirixalus vittatus (Boulenger, 1887). The clade {Philautus odontotarsus Ye & Fei, 1993, [Philautus idiootocus (Kuramoto & Wang, 1987), Kurixalus eiffingeri (Boettger, 1895)]} is recovered with strong support. The monophyly of Theloderma and Rhacophorus rhodopus Liu & Hu, 1959 is not supported. It is suggested that Philautus albopunctatus Liu & Hu, 1962 should be placed into the synonymy of Theloderma asperum (Boulenger, 1886), and that Philautus rhododiscus Liu & Hu, 1962 should be assigned to Theloderma, so as to correct the paraphyly. Additionally, the monophyly of ‘Aquixalus’ is not supported, and this requires further examination. Results also indicate that the Rhacophorus leucomystax (Gravenhorst, 1829)/Rhacophorus megacephalus (Hallowell, 1861) complex needs further revision. Studies employing broader sampling and more molecular markers will be needed to resolve the deep relationships within the subfamily Rhacophorinae.

A new species of the genus Gracixalus, Gracixalus yunnanensis sp. n., is described based on a series of specimens collected from southwestern and southern Yunnan, China. This species is distinguished from all other known congeners by a combination of the following characters: relatively small body size in adult males (SVL 26.0-34.2 mm); dorsal surface yellow brown or red brown; distinctive conical asperities on dorsum; males with an external subgular vocal sac and linea masculina; throat, chest, and belly nearly immaculate; venter surface orangish with yellow spots, semi-transparent; snout rounded; supratympanic fold distinct; iris bronze; lack of white patch on temporal region; tibiotarsal projection absent; sides of body nearly smooth with no black blotch; finger webbing rudimentary; and toe webbing formula I1.5-2II1.5-2.7III. 5-3IV2.51.5V. Genetically, the new species diverges from its congeners by 2.2%-14.1% (uncorrected p-distance) and is closest to G. guangdongensis. However, the new species can morphologically be separated from G. guangdongensis by distinctive conical tubercles on dorsum (versus absent), lateral surface nearly smooth with no black blotches on ventrolateral region (versus lateral surface rough, scattered with tubercles and black blotches on ventrolateral region), snout rounded (versus triangularly pointed), iris bronze (versus iris brown), and ventral surface orangish (versus throat and chest creamy white and belly light brown).