We present the largest morphological character set ever compiled for Holometabola. This was made possible through an optimized acquisition of data. Based on our analyses and recently published hypotheses based on molecular data, we discuss higherlevel phylogeny and evolutionary changes. We comment on the information content of different character systems and discuss the role of morphology in the age of phylogenomics. Microcomputer tomography in combination with other techniques proved highly efficient for acquiring and documenting morphological data. Detailed anatomical information (356 characters) is now available for 30 representatives of all holometabolan orders. A combination of traditional and novel techniques complemented each other and rapidly provided reliable data. In addition, our approach facilitates documenting the anatomy of model organisms. Our results show little congruence with studies based on rRNA, but confirm most clades retrieved in a recent study based on nuclear genes: Holometabola excluding Hymenoptera, Coleopterida (= Strepsiptera + Coleoptera), Neuropterida excl. Neuroptera, and Mecoptera. Mecopterida (= Antliophora + Amphiesmenoptera) was retrieved only in Bayesian analyses. All orders except Megaloptera are monophyletic. Problems in the analyses are caused by taxa with numerous autapomorphies and ⁄ or inapplicable character states due to the loss of major structures (such as wings). Different factors have contributed to the evolutionary success of various holometabolan lineages. It is likely that good flying performance, the ability to occupy different habitats as larvae and adults, parasitism, liquid feeding, and co-evolution with flowering plants have played important roles. We argue that even in the ''age of phylogenomics'', comparative morphology will still play a vital role. In addition, morphology is essential for reconstructing major evolutionary transformations at the phenotypic level, for testing evolutionary scenarios, and for placing fossil taxa.

BackgroundDespite considerable progress in systematics, a comprehensive scenario of the evolution of phenotypic characters in the mega-diverse Holometabola based on a solid phylogenetic hypothesis was still missing. We addressed this issue by de novo sequencing transcriptome libraries of representatives of all orders of holometabolan insects (13 species in total) and by using a previously published extensive morphological dataset. We tested competing phylogenetic hypotheses by analyzing various specifically designed sets of amino acid sequence data, using maximum likelihood (ML) based tree inference and Four-cluster Likelihood Mapping (FcLM). By maximum parsimony-based mapping of the morphological data on the phylogenetic relationships we traced evolutionary transformations at the phenotypic level and reconstructed the groundplan of Holometabola and of selected subgroups.ResultsIn our analysis of the amino acid sequence data of 1,343 single-copy orthologous genes, Hymenoptera are placed as sister group to all remaining holometabolan orders, i.e., to a clade Aparaglossata, comprising two monophyletic subunits Mecopterida (Amphiesmenoptera + Antliophora) and Neuropteroidea (Neuropterida + Coleopterida). The monophyly of Coleopterida (Coleoptera and Strepsiptera) remains ambiguous in the analyses of the transcriptome data, but appears likely based on the morphological data. Highly supported relationships within Neuropterida and Antliophora are Raphidioptera + (Neuroptera + monophyletic Megaloptera), and Diptera + (Siphonaptera + Mecoptera). ML tree inference and FcLM yielded largely congruent results. However, FcLM, which was applied here for the first time to large phylogenomic supermatrices, displayed additional signal in the datasets that was not identified in the ML trees.ConclusionsOur phylogenetic results imply that an orthognathous larva belongs to the groundplan of Holometabola, with compound eyes and well-developed thoracic legs, externally feeding on plants or fungi. Ancestral larvae of Aparaglossata were prognathous, equipped with single larval eyes (stemmata), and possibly agile and predacious. Ancestral holometabolan adults likely resembled in their morphology the groundplan of adult neopteran insects. Within Aparaglossata, the adult’s flight apparatus and ovipositor underwent strong modifications. We show that the combination of well-resolved phylogenies obtained by phylogenomic analyses and well-documented extensive morphological datasets is an appropriate basis for reconstructing complex morphological transformations and for the inference of evolutionary histories.

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Male genital structures of representatives of Strepsiptera, Siphonaptera and Diptera are described in detail, with special emphasis on sperm pumps. The parts involved in the apparatus are evaluated with respect to their homology. Functional interpretations are presented based on the morphological observations. The phylogenetic significance of characters related to the male genital apparatus is discussed. The sperm pumps differ strongly in Strepsiptera and Antliophora (s.s.) and are not homologous. The strepsipteran type, which lacks any sclerotized parts, has evolved independently. Autapomophies of the male genital apparatus are the compact testes, the large balloon-shaped vesicula seminalis, the strongly developed musculature of the proximal ductus ejaculatorius, the strongly simplified copulatory organ, the unusual muscles of segments VIII and IX, and the complete absence of accessory glands. The median fusion and almost globular shape of the vesicula are potential autapomorphies of Corioxenidae. The absence of the furrow separating the testes from the vesicula seminalis is a derived condition found in Xenos and Myrmecolax. A sperm pump is absent in Boreus (Mecoptera) and Culicomorpha and the functionally relevant parts and their arrangement differ strongly in Siphonaptera, Pistillifera and Diptera (excl. Culicomorpha). The presence of a functional and homologous pumping apparatus does not belong to the groundplan of Antliophora, which implies that this alleged autapomorphy of the clade is invalid. A sperm pump belongs to the groundplan of Diptera and was secondarily reduced in Culicomorpha, many representatives of Bibionomorpha, and in Diopsidae. It was very likely primarily absent in Mecoptera. However, the precise reconstruction of the groundplan depends on the position of Nannochoristidae within Mecoptera and on the possible affinities of Siphonaptera and Boreidae. Sperm pumps should be considered as a functional term and not be used as a character for phylogenetic reconstruction, unless specific similarities are included in the character definition.

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