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.本研究依托包含3个线粒体基因区域与3个细胞核基因区域的分子数据集，构建了33种突眼蝇（stalk-eyed flies）的系统发育关系假说。对所有数据进行等权重合并分析后，获得唯一一棵最简约支序图（most parsimonious cladogram），且绝大多数节点均具备较强的支持置信度。本研究同时探讨了不同类别分子数据的系统发育效用（phylogenetic utility）：具体而言，我们在合并分析与单独分析两种框架下，采用多种效用衡量指标，重点聚焦于线粒体基因与细胞核基因、快速进化性状与慢速进化性状之间的差异。针对第一项对比，几乎所有效用衡量标准均表明，细胞核基因在解析突眼蝇科（Diopsidae）系统发育关系时的信息价值显著优于线粒体基因。细胞核基因的同塑性（homoplasy）更低，彼此之间以及与合并数据集间的拓扑冲突均更少，且相较于线粒体基因，可为合并分析的拓扑结构提供更高的支持置信度。然而第二项对比的结果却几乎未发现两类进化速率性状在效用上存在显著差异。尽管存在快速分化与序列饱和（saturation）的迹象，但细胞核与线粒体数据集中的快速进化性状仍保留了较强的系统发育信号（phylogenetic signal）。总体而言，纳入快速进化的数据可持续提升各数据分区（partitions）之间的拓扑一致性。