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Bayesian mixed models and divergence time estimation of Chinese cavefishes （Cyprinidae： Sinocyclocheilus）

ISSN号：1673-6273
期刊名称：《现代生物医学进展》
时间：0
分类：Q959.4[生物学—动物学]
作者机构：[1]Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China, [2]Graduate University of the Chinese Academy of Sciences, Beijing 100049, China
相关基金：Supported by the National Basic Research Program of China （Grant No. 2007CB411600） and the National Natural Science Foundation of China （Grant No. 30530120）;We are grateful to LI ZaiYun, CHEN ZiMing, TAO JinNeng for assistances in collecting specimens and providing tissues. LI WeiXian provided some species. We thank GUO XianGuang and M. C. Brandley for their kind help on the partitioned Bayesian analyses. We are also grateful to WANG XuZhen whose comments greatly improved the presentation of our manuscript.

作者： LI ZhiQiang[1,2], GUO BaoCheng[1,2], LI JunBing[1,2], HE ShunPing[1], CHEN YiYu[1]

关键词：中国洞穴鱼, 系统发育, 变异状况, 生长特点, Sinocyclocheilus, phylogeny, relaxed molecular clock

中文摘要：

类 Sinocyclocheilus 仅仅在 Yun-Gui 高原和它的包围区域是分布式的，在显示出有奇妙的改编的眼睛和色素沉着的退化的不同的度的超过 10 洞种类以内。到现在，从优先的工作出版了 Sinocyclocheilus 的词法、分子的种系发生的假设是很不同的，在类以内的关系仍然是远非清楚的。我们获得了细胞色素 b (cyt b ) 和 NADH 的序列脱氢酶子单元 4 (ND4 ) 在 Sinocyclocheilus 以内的 34 种类，它代表最采样上的稠密的税迄今为止。我们与这个数据集合执行了贝叶斯的混合模型分析。在这个种系发生的框架下面，我们在放松的分子的钟下面用不同方法估计了恢复 clades 的分叉时间。我们支持的 phyloegentic 结果 monophyly Sinocyclocheilus 并且证明这个类能被细分进 6 主要 clades。另外，一更早发现表明洞种类的 polyphyletic 并且最 S 的基础位置。jii 被支持。放松的分叉时间评价建议那 Sinocyclocheilus 发源在晚中新世，大约 1100 万年以前(妈) ，它比什么旧被假定。

英文摘要：

The genus Sinocyclocheilus is distributed in Yun-Gui Plateau and its surrounding region only, within more than 10 cave species showing different degrees of degeneration of eyes and pigmentaUon with wonderful adaptations. To present, published morphological and molecular phylogenetic hypotheses of Slnocyclocheilus from prior works are very different and the relationships within the genus are still far from clear. We obtained the sequences of cytochrome b （cyt b） and NADH dehydrogenase subunlt 4 （ND4） of 34 species within Sinocyclocheilus, which represent the most dense taxon sampling to date. We performed Bayesian mixed models analyses with this data set. Under this phylogenetic framework, we estimated the divergence times of recovered clades using different methods under relaxed molecular clock. Our phyloegentic results supported the monophyly of Sinocyclocheilus and showed that this genus could be subdivided into 6 major clades. In addition, an earlier finding demonstrating the polyphyletlc of cave species and the most basal position of S. jii was corroborated. Relaxed divergence-time estimation suggested that Sinocyclocheilus originated at the late Miocene, about 11 million years ago （Ma）, which is older than what have been assumed.

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