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18S核糖体DNA（18S ribosomal DNA, rDNA，85个样本）、28S rDNA（28S ribosomal DNA，52个样本）的核苷酸序列以及形态特征的分支分类分析，推断全变态昆虫目之间的系统发育关系。外类群样本包括弹尾目（Collembola，1条序列）、石蛃目（Archaeognatha，1条）、蜉蝣目（Ephemerida，1条）、蜻蜓目（Odonata，2条）、襀翅目（Plecoptera，2条）、蜚蠊目（Blattodea，1条）、螳螂目（Mantodea，1条）、革翅目（Dermaptera，1条）、直翅目（Orthoptera，1条）、竹节虫目（Phasmatodea，1条）、纺足目（Embioptera，1条）、啮虫目（Psocoptera，1条）、虱目（Phthiraptera，1条）、半翅目（Hemiptera，4条）以及缨翅目（Thysanoptera，1条）。内类群样本包括：鞘翅目（Coleoptera）：原鞘亚目（Archostemata，1个）、肉食亚目（Adephaga，2个）以及多食亚目（Polyphaga，7个）；广翅目（Megaloptera，1个）；蛇蛉目（Raphidioptera，1个）；狭义脉翅目（Neuroptera sensu stricto，即广翅亚目Planipennia）：螳蛉总科（Mantispoidea，2个）、褐蛉总科（Hemerobioidea，2个）以及蚁蛉总科（Myrmeleontoidea，2个）；膜翅目（Hymenoptera）：广腰亚目（Symphyta，4个）以及细腰亚目（Apocrita，19个）；毛翅目（Trichoptera）：纹石蛾总科（Hydropsychoidea，1个）以及石蛾总科（Limnephiloidea，2个）；鳞翅目（Lepidoptera）：双孔亚目（Ditrysia，3个）；蚤目（Siphonaptera）：蚤总科（Pulicoidea，1个）以及角叶蚤总科（Ceratophylloidea，2个）；长翅目（Mecoptera）：美蝎蛉科（Meropeidae，1个）、雪蝎蛉科（Boreidae，1个）、蝎蛉科（Panorpidae，1个）以及蚊蝎蛉科（Bittacidae，2个）；双翅目（Diptera）：长角亚目（Nematocera，1个）、短角亚目（Brachycera，2个）以及环裂亚目（Cyclorrhapha，1个）；捻翅目（Strepsiptera）：原蜂虱科（Corioxenidae，1个）、蚁形蜂科（Myrmecolacidae，1个）、蝙越蜂科（Elenchidae，1个）以及捻翅科（Stylopidae，3个）。本研究分析了约1kb的18S rDNA序列，其起始位点位于5'端下游398个核苷酸处，以及28S rDNA扩张段D3区域的约400bp序列。18S和28S序列的多重比对分别得到1116个核苷酸位点（含24个插入区）和398个核苷酸位点（含14个插入区）。所有捻翅目与脉翅目类群在18S和28S序列中均存在较大插入区。18S插入区23的二级结构由长茎构成，基部类群的捻翅目该区域富含GC碱基，而演化程度更高的捻翅目类群则富含AT碱基。本研究针对全变态昆虫目构建了包含176个形态特征的矩阵并开展分析。不一致长度差异检验结果显示，28S序列与形态数据集存在显著不一致，但28S+18S、18S+形态以及28S+18S+形态这三种组合均未拒绝同质性假设。系统发育树通过简约法分析生成，分支稳健性通过分支长度、Bremer支持度（Bremer support）、迫使类群成为并系所需的额外步骤百分比，以及以下参数的敏感性分析进行评估：间隙权重、形态特征权重、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，以下类群被鉴定为单系群：全变态类（Holometabola）、多食亚目（Polyphaga）、广翅目+蛇蛉目、脉翅目、膜翅目、毛翅目、鳞翅目、双孔总目（Amphiesmenoptera，毛翅目+鳞翅目）、蚤目、蚤目+长翅目、捻翅目、双翅目，以及捻翅目+双翅目（即平衡翅类Halteria）。在多数总证据分析中得到支持的类群包括：吻角类（Antliophora，长翅目+双翅目+蚤目+捻翅目）、蝎蛉总目（Mecopterida，吻角类+双孔总目），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）常被置于蚤类的姊妹群位置，因此蚤目可能嵌套于长翅目之内。Priacma（鞘翅目：原鞘亚目）、Colpocaccus（鞘翅目：肉食亚目）、Agulla（蛇蛉目）以及Corydalus（广翅目）的18S序列几乎完全一致，且仅当移除这两个甲虫类群的序列时，脉翅总目（Neuropterida）才被鉴定为单系群。因此，在几乎所有参数组合下，鞘翅目均为并系群。平衡翅类与双孔总目具有较高的Bremer支持度和较长的分支长度。本研究数据不支持捻翅目位于全变态类之外，也不支持其为鞘翅目的姊妹群。我们拒绝“平衡翅类的单系性源于长枝吸引”这一观点，因为捻翅目与双翅目并非分支最长的类群，且在整个参数空间内的分子数据之间、以及形态与分子数据之间均存在系统发育同质性。