Data from: The Strepsiptera Problem: Phylogeny of the Holometabolous Insect Orders Inferred from 18S and 28S Ribosomal DNA Sequences and Morphology

Phylogenetic relationships among the holometabolous insect orders were inferred from cladistic analysis of nucleotide sequences of 18S ribosomal DNA (rDNA) (85 exemplars) and 28S rDNA (52 exemplars) and morphological characters. Exemplar outgroup taxa were Collembola (1 sequence), Archaeognatha (1), Ephemerida (1), Odonata (2), Plecoptera (2), Blattodea (1), Mantodea (1), Dermaptera (1), Orthoptera (1), Phasmatodea (1), Embioptera (1), Psocoptera (1), Phthiraptera (1), Hemiptera (4), and Thysanoptera (1). Exemplar ingroup taxa were Coleoptera: Archostemata (1), Adephaga (2), and Polyphaga (7); Megaloptera (1); Raphidioptera (1); Neuroptera (sensu stricto ;eq Planipennia): Mantispoidea (2), Hemerobioidea (2), and Myrmeleontoidea (2); Hymenoptera: Symphyta (4) and Apocrita (19); Trichoptera: Hydropsychoidea (1) and Limnephiloidea (2); Lepidoptera: Ditrysia (3); Siphonaptera: Pulicoidea (1) and Ceratophylloidea (2); Mecoptera: Meropeidae (1), Boreidae (1), Panorpidae (1), and Bittacidae (2); Diptera: Nematocera (1), Brachycera (2), and Cyclorrhapha (1); and Strepsiptera: Corioxenidae (1), Myrmecolacidae (1), Elenchidae (1), and Stylopidae (3). We analyzed ~1 kilobase of 18S rDNA, starting 398 nucleotides downstream of the 5' end, and ~400 bp of 28S rDNA in expansion segment D3. Multiple alignment of the 18S and 28S sequences resulted in 1,116 nucleotide positions with 24 insert regions and 398 positions with 14 insert regions, respectively. All Strepsiptera and Neuroptera have large insert regions in 18S and 28S. The secondary structure of 18S insert 23 is composed of long stems that are GC rich in the basal Strepsiptera and AT rich in the more derived Strepsiptera. A matrix of 176 morphological characters was analyzed for holometabolous orders. Incongruence length difference tests indicate that the 28S + morphological data sets are incongruent but that 28S + 18S, 18S + morphology, and 28S + 18S + morphology fail to reject the hypothesis of congruence. Phylogenetic trees were generated by parsimony analysis, and clade robustness was evaluated by branch length, Bremer support, percentage of extra steps required to force paraphyly, and sensitivity analysis using the following parameters: gap weights, morphological character weights, methods of data set combination, removal of key taxa, and alignment region. The following are monophyletic under most or all combinations of parameter values: Holometabola, Polyphaga, Megaloptera + Raphidioptera, Neuroptera, Hymenoptera, Trichoptera, Lepidoptera, Amphiesmenoptera (Trichoptera + Lepidoptera), Siphonaptera, Siphonaptera + Mecoptera, Strepsiptera, Diptera, and Strepsiptera + Diptera (Halteria). Antliophora (Mecoptera + Diptera + Siphonaptera + Strepsiptera), Mecopterida (Antliophora + Amphiesmenoptera), and Hymenoptera + Mecopterida are supported in the majority of total evidence analyses. Mecoptera may be paraphyletic because Boreus is often placed as sister group to the fleas; hence, Siphonaptera may be subordinate within Mecoptera. The 18S sequences for Priacma (Coleoptera: Archostemata), Colpocaccus (Coleoptera: Adephaga), Agulla (Raphidioptera), and Corydalus (Megaloptera) are nearly identical, and Neuropterida are monophyletic only when those two beetle sequences are removed from the analysis. Coleoptera are therefore paraphyletic under almost all combinations of parameter values. Halteria and Amphiesmenoptera have high Bremer support values and long branch lengths. The data do not support placement of Strepsiptera outside of Holometabola nor as sister group to Coleoptera. We reject the notion that the monophyly of Halteria is due to long branch attraction because Strepsiptera and Diptera do not have the longest branches and there is phylogenetic congruence between molecules, across the entire parameter space, and between morphological and molecular data.

本研究基于85个18S核糖体DNA（18S rDNA）代表类群、52个28S核糖体DNA（28S rDNA）代表类群的核苷酸序列，以及形态学特征的分支系统学分析，对全变态昆虫目级类群间的系统发育关系进行了推断。本研究选取的外类群代表类群包括：弹尾纲（Collembola，1条序列）、古尾目（Archaeognatha，1）、蜉蝣目（Ephemerida，1）、蜻蛉目（Odonata，2）、襀翅目（Plecoptera，2）、蜚蠊目（Blattodea，1）、螳螂目（Mantodea，1）、革翅目（Dermaptera，1）、直翅目（Orthoptera，1）、竹节虫目（Phasmatodea，1）、纺足目（Embioptera，1）、啮虫目（Psocoptera，1）、虱目（Phthiraptera，1）、半翅目（Hemiptera，4）以及缨翅目（Thysanoptera，1）。内类群代表类群如下：鞘翅目（Coleoptera）：原鞘亚目（Archostemata，1）、肉食亚目（Adephaga，2）与多食亚目（Polyphaga，7）；广翅目（Megaloptera，1）；蛇蛉目（Raphidioptera，1）；狭义脉翅目（sensu stricto，即原广翅蛉下目Planipennia）：螳蛉总科（Mantispoidea，2）、褐蛉总科（Hemerobioidea，2）与蚁蛉总科（Myrmeleontoidea，2）；膜翅目（Hymenoptera）：广腰亚目（Symphyta，4）与细腰亚目（Apocrita，19）；毛翅目（Trichoptera）：石蛾总科（Hydropsychoidea，1）与纹石蛾总科（Limnephiloidea，2）；鳞翅目（Lepidoptera）：双孔亚目（Ditrysia，3）；蚤目（Siphonaptera）：蚤总科（Pulicoidea，1）与角叶蚤总科（Ceratophylloidea，2）；长翅目（Mecoptera）：蝎蛉科（Meropeidae，1）、雪蝎蛉科（Boreidae，1）、蝎蛉科（Panorpidae，1）与蚊蝎蛉科（Bittacidae，2）；双翅目（Diptera）：长角亚目（Nematocera，1）、短角亚目（Brachycera，2）与环裂亚目（Cyclorrhapha，1）；捻翅目（Strepsiptera）：异角科（Corioxenidae，1）、蚁形捻翅科（Myrmecolacidae，1）、虱捻翅科（Elenchidae，1）与捻翅科（Stylopidae，3）。本研究分析了18S rDNA中5'端下游398个核苷酸位点起始的约1000 bp序列，以及28S rDNA的D3扩张段中约400 bp序列。对18S和28S序列进行多重比对后，分别得到1116个核苷酸位点（含24个插入区）与398个核苷酸位点（含14个插入区）。所有捻翅目与脉翅目类群的18S和28S rDNA均存在较大的插入区。18S rDNA的第23个插入区的二级结构由长茎环构成：基部类群的捻翅目该区域富含GC碱基，而演化地位更衍生的类群则富含AT碱基。本研究针对全变态昆虫目级类群构建了包含176个形态学特征的矩阵并进行分析。不一致长度差异检验结果显示：28S rDNA与形态学数据集之间存在显著不一致，但28S+18S、18S+形态学以及28S+18S+形态学这三种组合数据集均未拒绝同质性假说。本研究通过简约法分析构建系统发育树，并采用以下参数评估分支的稳健性：分支长度、Bremer支持值、强制形成并系群所需的额外步数占比，以及敏感性分析，具体参数包括间隙权重、形态学特征权重、数据集组合方法、关键类群移除以及比对区域。在多数或全部参数组合下，以下类群均为单系群：全变态类（Holometabola）、多食亚目、广翅目+蛇蛉目、脉翅目、膜翅目、毛翅目、鳞翅目、毛鳞总目（Amphiesmenoptera，毛翅目+鳞翅目）、蚤目、蚤目+长翅目、捻翅目、双翅目，以及平衡棒类（Halteria，捻翅目+双翅目）。在多数总证据分析中，以下类群得到支持：吻足类（Antliophora，长翅目+双翅目+蚤目+捻翅目）、蝎蛉总目（Mecopterida，吻足类+毛鳞总目），以及膜翅目+蝎蛉总目。长翅目可能为并系群，因为雪蝎蛉属（Boreus）常被置于蚤目的姊妹群位置，因此蚤目可能嵌套于长翅目内部。原鞘甲属（Priacma，鞘翅目：原鞘亚目）、鞘甲属（Colpocaccus，鞘翅目：肉食亚目）、蛇蛉属（Agulla，蛇蛉目）及星齿蛉属（Corydalus，广翅目）的18S rDNA序列几乎完全一致；且仅当移除这两个鞘翅目类群的序列时，脉翅总目（Neuropterida）才呈现单系性。因此，在几乎所有参数组合下，鞘翅目均为并系群。平衡棒类与毛鳞总目均具有较高的Bremer支持值与较长的分支长度。本研究数据不支持将捻翅目置于全变态类之外，也不支持其作为鞘翅目的姊妹群。我们拒绝‘平衡棒类的单系性由长枝吸引导致’这一观点，原因如下：其一，捻翅目与双翅目并非分支最长的类群；其二，在全部参数空间下，分子数据间均存在系统发育一致性，且形态学数据与分子数据间也存在系统发育一致性。