title: The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data.
abstract: BACKGROUND
  Despite 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.
  
  
  RESULTS
  In 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.
  
  
  CONCLUSIONS
  Our 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.
authors.forename: Ralph S
authors.initials: RS
authors.lastname: Peters
authors.forename: Karen
authors.initials: K
authors.lastname: Meusemann
authors.forename: Malte
authors.initials: M
authors.lastname: Petersen
authors.forename: Christoph
authors.initials: C
authors.lastname: Mayer
authors.forename: Jeanne
authors.initials: J
authors.lastname: Wilbrandt
authors.forename: Tanja
authors.initials: T
authors.lastname: Ziesmann
authors.forename: Alexander
authors.initials: A
authors.lastname: Donath
authors.forename: Karl M
authors.initials: KM
authors.lastname: Kjer
authors.forename: Ulrike
authors.initials: U
authors.lastname: Aspöck
authors.forename: Horst
authors.initials: H
authors.lastname: Aspöck
authors.forename: Andre
authors.initials: A
authors.lastname: Aberer
authors.forename: Alexandros
authors.initials: A
authors.lastname: Stamatakis
authors.forename: Frank
authors.initials: F
authors.lastname: Friedrich
authors.forename: Frank
authors.initials: F
authors.lastname: Hünefeld
authors.forename: Oliver
authors.initials: O
authors.lastname: Niehuis
authors.forename: Rolf G
authors.initials: RG
authors.lastname: Beutel
authors.affiliation: Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung (zmb), Adenauerallee 160, 53113 Bonn, Germany. b.misof.zfmk@uni-bonn.de.
authors.forename: Bernhard
authors.initials: B
authors.lastname: Misof
mesh_terms: D000818:Animals; D005075:Biological Evolution; D001517:Coleoptera / Q000033:anatomy & histology / Q000235:genetics; D017344:Genes, Insect; D006927:Hymenoptera / Q000033:anatomy & histology / Q000235:genetics; D007313:Insecta / Q000033:anatomy & histology / Q000145:classification* / Q000235:genetics* / Q000254:growth & development; D007814:Larva / Q000033:anatomy & histology; D010058:Oviposition; D010802:Phylogeny; D059467:Transcriptome