Phylogenetic relationships of Nemacheilidae cavefish (<i>Heminoemacheilus</i>, <i>Oreonectes</i>, <i>Yunnanilus</i>, <i>Paranemachilus</i>, and <i>Troglonectes</i>) revealed by analysis of mitochondrial genome and seven nuclear genes
T. Luo, 贵州师范大学生命科学学院, 贵州 贵阳 550025, 中国, Qin Yang, Li-Wei Wu, Yali Wang, Jia-Jun Zhou, Huaiqing Deng, Ning Xiao, Jiang Zhou, 贵州师范大学喀斯特研究院, 贵州 贵阳 550001, 中国, 浙江省森林资源监测中心, 浙江 杭州 310020, 中国, 浙江省林业勘测规划设计有限公司, 浙江 杭州 310020, 中国, 贵州康养职业大学, 贵州 贵阳 550081, 中国
Abstract
Cave loaches within the family Nemacheilidae are among the most diverse group of cavefish in southwestern China. Although certain species have been included in previous phylogenetic studies, the intergeneric and interspecific relationships of Chinese cave loaches in Nemacheilidae remain poorly investigated due to insufficient sampling. In this study, a total of 45 samples from 37 recognized species and two unidentified species of cave loaches were collected, accounting for 87.5% of the eight recognized genera of cave loaches within the family Nemacheilidae in China. The complete mitochondrial genome (mitogenome) and seven nuclear genes were sequenced, and the phylogenetic tree of Chinese cave loaches was reconstructed. Both Bayesian inference and maximum-likelihood analyses resolved the phylogenetic relationships at the generic and species levels, suggesting the effectiveness of this multilocus marker system in determining phylogenetic relationships in Chinese cave loaches. Phylogenetic analysis not only confirmed previous taxonomic hypotheses based on morphological data but also provided new insights into the relationships of many cave loaches at the genus and species levels as well as suggestions for the current taxonomy of cave loaches within the family Nemacheilidae.条鳅科的洞穴鳅类是中国西南喀斯特区域洞穴鱼类中最具多样化的类群之一。尽管一些物种已被纳入到先前的系统发育研究，但由于采样不足，中国条鳅科内洞穴鳅类的属间和种间关系仍未得到充分研究。该研究共收集了条鳅科洞穴鳅类的37个公认种和2个待定种的45个样本，占中国条鳅科洞穴鳅类8个有效属的87.5%。我们对线粒体基因组和7个核基因进行了测序，并分别重建了条鳅科洞穴鳅类的系统发育树。贝叶斯推断和最大似然分析都解决了在属和种水平的系统发育关系，这表明该多位点标记系统在确定中国洞穴泥鳅系统发育关系方面的有效性。系统发育分析结果不仅证实了以前传统上基于形态学数据提出的分类假说，并且对许多洞穴鳅类在属和种水平上的系统发育关系有了新的认识，也为目前条鳅科洞穴鳅类的分类提出了建议。.