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.

针对昆虫纲直翅目（Orthoptera）所有总科类群（涵盖蝗虫、蟋蟀及其近缘物种）的线粒体与核核糖体DNA（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新近分化的总科类群，但厘清基部类群的演化关系仍需核rDNA序列数据。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，本研究采用共识分析与联合数据两种分析策略。共识分析得到一棵部分解析的系统发育树，缺失了单次独立分析中多个高支持度的演化分支特征；进一步对重采样数据集的检验表明，该分辨率不足的根源在于线粒体数据分区的序列长度相对偏短。在后续先联合线粒体序列的比对分析中，我们观测到的演化冲突有所减少。随后，我们采用两种方法验证了将所有数据整合为单一分析集的合理性：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）。分析结果未显示线粒体与核数据集间的系统发育信号存在显著异质性，因此我们最终采用联合分析策略。基于最小进化（minimum evolution）与最大似然（maximum likelihood）两种最优准则重建系统发育树，我们通过非参数自举分析（nonparametric bootstrap analysis）、参数自举分析（parametric bootstrap analysis）以及Kishino-Hasegawa检验（Kishino-Hasegawa test），验证了直翅目主要类群的单系性。本研究结果显示，基于最大似然（ML）准则的系统发育重建方法，对联合序列数据集的区分度最高。结果表明，锥尾亚目（caeliferan）的Pneumoroidea总科与Pamphagoidea总科（如前人研究所提出）为多系群；本研究重新界定了Acridoidea总科的范围，将其扩展至除Pyrgomorphidae科之外的所有Pamphagoidea类群，并提议将Pyrgomorphidae科提升为总科级分类单元。