Data from: Phylogenetic utility of different types of molecular data used to infer evolutionary relationships among stalk-eyed flies (Diopsidae)

A phylogenetic hypothesis of relationships among 33 species of stalk-eyed flies was generated from a molecular data set comprised of three mitochondrial and three nuclear gene regions. A combined analysis of all the data equally weighted produced a single most parsimonious cladogram with relatively strong support at the majority of nodes. The phylogenetic utility of different classes of molecular data was also examined. In particular, using a number of different measures of utility in both a combined and separate analysis framework, we focus on the distinction between mitochondrial and nuclear genes, and faster-evolving characters and slower-evolving characters. For the first comparison, by nearly any measure of utility, the nuclear genes are substantially more informative for resolving diopsid relationships than are the mitochondrial genes. The nuclear genes exhibit less homoplasy, are less incongruent both with one another and with the combined data, and contribute more support to the combined analysis topology than the mitochondrial genes. Results from the second comparison, however, provide little evidence of a clear difference in utility. Despite indications of rapid divergence and saturation, faster-evolving characters in both the nuclear and mitochondrial data sets still provide substantial phylogenetic signal. In general, inclusion of the more rapidly evolving data consistently improves the congruence among partitions.

本研究利用由3个线粒体基因区域与3个核基因区域组成的分子数据集，构建了33种柄眼蝇（stalk-eyed flies）的系统发育关系假说（phylogenetic hypothesis）。采用等权重合并所有数据的分析策略，得到了唯一一棵最简约支序图（most parsimonious cladogram），且绝大多数节点（nodes）具有较强的支持度。本研究同时检验了不同类别分子数据的系统发育信息效用（phylogenetic utility）：通过联合分析与单独分析框架下的多种效用衡量指标，重点聚焦于线粒体基因与核基因之间、快速进化特征与慢速进化特征之间的差异。针对第一项比较（线粒体基因与核基因的比较），几乎所有效用衡量指标均显示，核基因在解析柄眼蝇科的系统发育关系方面，其信息价值显著高于线粒体基因；核基因的同塑性（homoplasy）更低，彼此之间以及与合并数据集之间的冲突性更弱，且相较于线粒体基因，可为合并分析的拓扑结构（topology）提供更强的支持。然而第二项比较（快速与慢速进化特征的比较）的结果则未发现明确的效用差异。尽管存在快速进化与序列饱和（saturation）的迹象，但核与线粒体数据集中的快速进化特征仍可提供可观的系统发育信号。总体而言，纳入快速进化的数据分区（partitions），可持续提升各数据分区之间的一致性。