Data from: Combined molecular phylogenetic analysis of the Orthoptera (Arthropoda, Insecta) and implications for their higher systematics

A phylogenetic analysis of mitochondrial and nuclear rDNA sequences from species of all the superfamilies of the insect order Orthoptera (grasshoppers, crickets and relatives) confirmed that although mitochondrial sequences provided good resolution of the youngest superfamilies, nuclear rDNA sequences were necessary to separate the basal groups. To try to reconcile these data sets into a single fully resolved orthopteran phylogeny, we adopted consensus and combined data strategies. The consensus analysis produced a partially resolved tree, lacking several well-supported features of the individual analyses. However, this lack of resolution was explained by an examination of resampled data sets that identified the likely source of error as the relatively short length of the individual mitochondrial data partitions. In a subsequent comparison in which the mitochondrial sequences were initially combined, we observed less conflict. We then used two approaches to examine the validity of combining all of the data in a single analysis; comparative analysis of trees recovered from resampled data sets and the application of a randomization test. The results did not point to significant levels of heterogeneity in phylogenetic signal between the mitochondrial and nuclear data sets, and we therefore proceeded with a combined analysis. Reconstructing phylogenies under the minimum evolution and maximum likelihood optimality criteria, we examined monophyly of the major orthopteran groups using nonparametric and parametric bootstrap analysis and Kishino-Hasegawa tests. Our analysis suggests that phylogeny reconstruction under the ML criteria is the most discriminating approach for the combined sequences. The results indicate that the caeliferan Pneumoroidea and Pamphagoidea (as previously suggested) are polyphyletic. The Acridoidea is redefined to include all pamphagoid families other than the Pyrgomorphidae, which we propose should be accorded superfamily status.

本研究针对昆虫直翅目（Orthoptera）所有总科物种的线粒体（mitochondrial）与细胞核核糖体DNA（nuclear rDNA）序列开展系统发育分析（phylogenetic analysis），结果证实：尽管线粒体序列可较好解析较年轻的总科类群，但区分基部类群（basal groups）则必须依赖细胞核核糖体DNA序列。
为将两类数据集整合为一套完全解析的直翅目系统发育框架，本研究采用了一致性分析（consensus analysis）与联合数据策略（combined data strategies）两种研究方案。一致性分析得到了一棵部分解析的系统发育树，缺失了单次分析中若干高支持度的拓扑特征。后续对重采样数据集（resampled data sets）的分析表明，该分辨率不足的成因很可能是单个线粒体数据分区（data partitions）的序列长度相对较短。
在预先联合线粒体序列的后续对比分析中，我们观测到的拓扑冲突有所减少。随后，本研究采用两种方法检验单次分析中联合全部数据集的合理性：一是对重采样数据集得到的系统发育树开展比较分析，二是应用随机化检验（randomization test）。结果显示，线粒体与细胞核数据集之间的系统发育信号（phylogenetic signal）并未存在显著异质性（heterogeneity），因此我们最终开展了联合数据分析。
本研究基于最小进化（minimum evolution）与最大似然（maximum likelihood）最优准则重建系统发育树，并采用非参数自举（nonparametric bootstrap）与参数自举（parametric bootstrap）分析以及Kishino-Hasegawa检验（Kishino-Hasegawa tests），对直翅目主要类群的单系性（monophyly）进行了验证。分析结果表明，针对联合序列开展系统发育重建时，基于最大似然准则的方法分辨能力最强。
结果显示，蝗亚目（caeliferan）下的Pneumoroidea与Pamphagoidea（如前人研究所提出的）为多系群（polyphyletic group）。本研究重新定义了Acridoidea总科，将除Pyrgomorphidae之外的所有Pamphagoidea类群纳入其中，并建议将Pyrgomorphidae提升为总科级分类单元。