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More than ten species of the genus Sinocyclocheilus (Cyprinidae: Barbinae) have been found to exhibit striking variation related to cave-dwelling traits. Until now, the molecular phylogeny and evolutionary history of this genus have remained unclear. To understand the molecular phylogeny and biogeographic evolution of Sinocyclocheilus, we analyzed the complete mitogenomes of 12 Sinocyclocheilus species based on Bayesian Inference (BI) and Maximum Likelihood (ML) analyses. The results of phylogenetic analyses strongly suggest that the genus Sinocyclocheilus is a monophyletic group, and S. jii is the most basal species. Molecular clock estimates showed that the diversification of this genus occurred in the late Miocene (about 6.49 Ma), which was associated with the intensive uplift of the Tibetan Plateau. Selective pressure analyses showed the dN/dS ratios of all Sinocyclocheilus species were < 1, indicating that this genus suffered strong purifying selection on its mitochondrial function, and then adapted to the contrasting environments. [ABSTRACT FROM AUTHOR]

Light is completely absent in cave habitats, causing a shortage or lack of autochthonous photosynthesis. Thus, understanding the mechanisms underlying the ability of organisms to adapt to the unique cave habitat is of great interest. We used high-throughput sequencing of the 16S ribosomal RNA gene of intestinal microorganisms from 11 Sinocyclocheilus (Cypriniformes: Cyprinidae) species, to explore the characteristics of intestinal microorganisms and the adaptive mechanisms of Sinocyclocheilus cavefish and surface fish. We found that the α-diversity and richness of the intestinal microbiome were much higher in cavefish than in surface fish. Principal coordinate analysis showed that cavefish and surface fish formed three clusters because of different dominant gut microorganisms which are generated by different habitats. Based on PICRUSt-predicted functions, harmful substance degradation pathways were much more common in cavefish intestinal microorganisms than in those from surface fish. The intestinal microbiota of surface fish group 1 had a higher capacity for carbohydrate metabolism, whereas protein and amino acid metabolism and digestive pathways were more abundant in microorganisms from the cavefish group and surface fish group 2. Combined analysis of the intestinal microbial composition and functional predictions further revealed the structures and functions of intestinal microbial communities in Sinocyclocheilus cave and surface species. Moreover, based on their habits and intestinal microbial composition and intestinal microbial functional predictions, we inferred that the three fish groups were all omnivorous; however, surface fish group 1 preferred feeding on plants, while surface fish group 2 and cavefish preferred meat. This study improves our understanding of mechanisms of adaptation in cave habitats and may contribute to the protection of these habitats from water pollution. [ABSTRACT FROM AUTHOR]

Cave animals possess remarkable phenotypes associated with existence in their dark environments. The Chinese cavefish Sinocyclocheilus tileihornes shows substantial eye degeneration, a trait shared by most cave species. The extent to which independent evolution of troglomorphic traits uses convergent molecular genetic mechanisms is as yet unknown. We performed transcriptome-wide gene expression profiling in S. tileihornes eyes and compared results with those from the closely related surface species S. angustiporus and an independently derived congeneric cavefish, S. anophthalmus. In total, 52.85 million 100 bp long paired-end clean reads were generated for S. tileihornes, and we identified differentially expressed genes between the three possible pairs of species. Functional analysis of genes differentially expressed between S. tileihornes and S. angustiporus revealed that phototransduction (KEGG id: dre04744) was the most significantly enriched pathway, indicating the obvious differences in response to captured photons between the cavefish S. tileihornes and the surface species S. angustiporus. Analysis of key genes regulating eye development showed complete absence of otx5b (orthodenticle homolog 5) expression in S. tileihornes eyes, probably related to degradation of rods, but normal expression of crx (cone-rod homeobox). The enriched pathways and Otx5 are involved in phototransduction, photoreceptor formation, and regulation of photoreceptor-related gene expression. Unlike the S. tileihornes reported here, S. anophthalmus has reduced crx and otx5 expression. These results show that different species of cavefish within the same genus that independently evolved troglodyte characteristics can have different genetic mechanisms of eye degeneration. [ABSTRACT FROM AUTHOR]

Sinocyclocheilus cyphotergous was described by Dai in 1988 as Gibbibarbus cyphotergous based on a single specimen collected in Luodian County, Guizhou Province, China. The holotype (the only one type specimen) has been lost and the original description was vague and was published in a report with limited circulation. A specimen collected from the type locality in 2015 was the basis for a detailed redescription of the species and designation of a neotype. Sinocyclocheilus cyphotergous can be distinguished from all other congeners by the following combination of characters: a humpback profile with a fleshy dorsal projection; a hard last unbranched ray of dorsal fin with a serrated rear edge; and nearly straight lateral line. This species is the only member of the genus with a fleshy dorsal projection composed of adipose tissue (either a bony projection located on the nape or fleshy humpback is present in all other species). The conservation status of S. cyphotergous is uncertain and most likely critical due to its limited distribution, apparent rarity (based on low frequency of detection), and the potential for increased impacts to its habitat due to diminished quantity and quality of groundwater. [ABSTRACT FROM AUTHOR]

The northwestern part of Guangxi is a typical karst landform. There are about ten species of the genus Sinocyclocheilus distributed in the region. To investigate the phylogenetic relationships and resolve the taxonomic status of these species, we determined nucleotide sequences of complete mitochondrial cytochrome b gene of 11 ingroup species and one outgroup species Barbodes laticeps. Phylogenetic trees were reconstructed using maximum parsimony and maximum likelihood analyses. Phylogenetic results showed that these species cluster as one clade with strong support. The 95% credibility interval (CI) of the divergence time between the species in the northwest part of Guangxi and other species in the genus Sinocyclocheilus is 8.28-12.40Mya. For the karst environment, these species show marked, recent genetic differentiation. From the overall consideration of morphology and molecular data Sinocyclocheilus tianeensis should be a valid species. [ABSTRACT FROM AUTHOR]

We investigated the molecular evolution of duplicated color vision genes ( LWS-1 and SWS2) within cyprinid fish, focusing on the most cavefish-rich genus— Sinocyclocheilus. Maximum likelihood-based codon substitution approaches were used to analyze the evolution of vision genes. We found that the duplicated color vision genes had unequal evolutionary rates, which may lead to a related function divergence. Divergence of LWS-1 was strongly influenced by positive selection causing an accelerated rate of substitution in the proportion of pocket-forming residues. The SWS2 pigment experienced divergent selection between lineages, and no positively selected site was found. A duplicate copy of LWS-1 of some cyprinine species had become a pseudogene, but all SWS2 sequences remained intact in the regions examined in the cyprinid fishes examined in this study. The pseudogenization events did not occur randomly in the two copies of LWS-1 within Sinocyclocheilus species. Some cave species of Sinocyclocheilus with numerous morphological specializations that seem to be highly adapted for caves, retain both intact copies of color vision genes in their genome. We found some novel amino acid substitutions at key sites, which might represent interesting target sites for future mutagenesis experiments. Our data add to the increasing evidence that duplicate genes experience lower selective constraints and in some cases positive selection following gene duplication. Some of these observations are unexpected and may provide insights into the effect of caves on the evolution of color vision genes in fishes. [ABSTRACT FROM AUTHOR]

The endemic Chinese cavefish genus Sinocyclocheilus possesses very rich species diversity. Specimens of this genus collected from Guilin, Guangxi, China, were originally described in an unpublished document in 1982. Later, they were recognized as Sinocyclocheilus jii. Comparison to the type specimens of S. jii leads to the conclusion that, though similar, they represent two different species. Herein we describe them as a new species, Sinocyclocheilus guilinensis sp. nov. It can be distinguished from all congeners by its possession of soft, unbranched dorsal ray without serrations, 19–20 (11–12) scale rows above (below) the lateral line, 34–36 circumpeduncular scales and 8–9 pre-dorsal vertebrae. Sinocyclocheilus guilinensis sp. nov. is most similar to S. jii. In addition to the scale count differences, a morphometrics-based principal component analysis (PCA) also supports designation of S. guilinensis and S. jii as two distinct species. [ABSTRACT FROM AUTHOR]

A new species of the cavefish genus Sinocyclocheilus is described based on six specimens collected from a subterranean river in Du’an County in the Guangxi Zhuang Autonomous Region of southern China. Sinocyclocheilus brevibarbatus sp. nov. can be distinguished from all congeners by the following combination of characteristics: a completely scaled body with well-developed eyes and a strongly-humped back; an almost straight lateral line possessing 49–51 perforated scales; seven soft rays on the dorsal fin; a relatively large eyeball (3.3–5.7% of SL) and short maxillary and rictal barbels (1.7–5.7% and 4.5–7.0% of SL, respectively). [ABSTRACT FROM AUTHOR]

The cyprinid fish genus Sinocyclocheilus, as the most cavefish rich genus, includes many species showing striking adaptation to caves and convergent reduction or even loss of eyes and pigmentation. RH1 is responsible for dim vision. In order to explore the evolution of RH1 gene in this genus, we sequenced the complete gene from 28 individuals of 16 representative species of Sinocyclocheilus, with cave and surface species included. Phylogenetic analyses supported the monophyly of Sinocyclocheilus and polyphyly of the cave species. Codon models implemented in PAML were used to infer the evolution of RH1. We found that Sinocyclocheilus had a significantly higher evolutionary rate for amino acids than other cyprinid fishes compared, which might be the result of relaxation of purifying selection and could be ascribed to cave habit of this genus. In contrast to previous hypotheses, both cave and surface lineages exhibited a similar rate of molecular evolution, so the RH1 of cave species may still be functional, although these species were highly adapted to cave environment. Two amino acid substitutions (D83G and E122V) that were not reported before were found, which may be useful for site-directed mutagenesis in the future. [ABSTRACT FROM AUTHOR]