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Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus Sinocyclocheilus (Pisces: Cypriniformes)

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Abstract

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.

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Acknowledgments

We extend our sincerest gratitude to Jun-bing Li, Zai-yun Li, Zi-ming Chen, Bao-cheng Guo, and Jin-neng Tao for assistance in species collection or providing tissue samples and Ming Chen for helpful discussion and suggestions. We are very grateful to Zuo-gang Peng, Qiong-ying Tang, and Simon Y. W. Ho for their kind help in reading the manuscript. Liming Li (University of Northwestern) and Manyuan Long (University of Chicago) are gratefully acknowledged for critically reading this manuscript. We also thank Associate Editor and the anonymous referees for useful comments on earlier versions of this manuscript. This research was supported by the grants from National Natural Science Foundation of China (NSFC) 2007CB411600 and 30530120 to S. H.

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Authors and Affiliations

  1. Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, People’s Republic of China

    Zhiqiang Li & Shunping He

  2. Graduate School of Chinese Academy of Sciences, Beijing, 100039, People’s Republic of China

    Zhiqiang Li

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  1. Zhiqiang Li
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  2. Shunping He
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Correspondence to Shunping He.

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Handling editor: Christian Sturmbauer

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Li, Z., He, S. Relaxed purifying selection of rhodopsin gene within a Chinese endemic cavefish genus Sinocyclocheilus (Pisces: Cypriniformes). Hydrobiologia 624, 139–149 (2009). https://doi.org/10.1007/s10750-008-9688-2

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  • DOI: https://doi.org/10.1007/s10750-008-9688-2

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