Data from: Reanalyzing the Palaeoptera problem - the origin of insect flight remains obscure

The phylogenetic relationships of the winged insect lineages – mayflies (Ephemeroptera), damselflies and dragonflies (Odonata), and all other winged insects (Neoptera) – are still controversial with three hypotheses supported by different datasets: Palaeoptera, Metapterygota and Chiastomyaria. Here, we reanalyze available phylogenomic data with a focus on detecting confounding and alternative signal. In this context, we provide a framework to quantitatively evaluate and assess incongruent molecular phylogenetic signal inherent in phylogenomic datasets. Despite overall support for the Palaeoptera hypothesis, we also found considerable signal for Chiastomyaria, which is not easily detectable by standardized tree inference approaches. Analyses of the accumulation of signal across gene partitions showed that signal accumulates gradually. However, even in case signal only slightly supported one over the other hypothesis, topologies inferred from large datasets switch from statistically strongly supported Palaeoptera to strongly supported Chiastomyaria. From a morphological point of view, Palaeoptera currently appears to be the best-supported hypothesis; however, recent analyses were restricted to head characters. Phylogenetic approaches covering all organ systems including analyses of potential functional or developmental convergence are still pending so that the Palaeoptera problem has to be considered an open question in insect systematics.有翅昆虫支系的系统发育关系——涵盖蜉蝣目（Ephemeroptera）、蜻蛉目（Odonata，包含豆娘与蜻蜓）以及其余所有有翅昆虫类群的新翅下纲（Neoptera）——目前仍存在争议，现有三类不同数据集分别支持古翅类（Palaeoptera）、间翅亚纲（Metapterygota）与交错翅类（Chiastomyaria）三种假说。本研究重新分析了公开可用的系统发育组学数据，重点关注混淆信号与替代信号的检测。在此研究框架下，我们构建了一套可定量评估与分析系统发育组学数据中内在不一致分子系统发育信号的分析框架。尽管整体分析结果支持古翅类假说，但本研究同时发现了大量支持交错翅类（Chiastomyaria）假说的信号——这类信号难以通过标准化树推断方法有效检出。针对基因分区的信号积累分析显示，系统发育信号呈现逐步累积的特征。即便单个基因仅对某一假说存在微弱支持，基于大型数据集推导得到的系统发育拓扑结构，仍会从统计学上显著支持的古翅类，转变为显著支持交错翅类。从形态学视角来看，古翅类假说目前是证据最为充分的假说，但过往相关分析仅局限于头部形态特征。当前仍缺乏覆盖所有器官系统的系统发育分析，以及针对潜在功能或发育趋同现象的研究，因此古翅类争议问题仍是昆虫分类学领域尚未解决的开放性课题。