title: Pancrustacean phylogeny in the light of new phylogenomic data: support for Remipedia as the possible sister group of Hexapoda.
abstract: Remipedes are a small and enigmatic group of crustaceans, first described only 30 years ago. Analyses of both morphological and molecular data have recently suggested a close relationship between Remipedia and Hexapoda. If true, the remipedes occupy an important position in pancrustacean evolution and may be pivotal for understanding the evolutionary history of crustaceans and hexapods. However, it is important to test this hypothesis using new data and new types of analytical approaches. Here, we assembled a phylogenomic data set of 131 taxa, incorporating newly generated 454 expressed sequence tag (EST) data from six species of crustaceans, representing five lineages (Remipedia, Laevicaudata, Spinicaudata, Ostracoda, and Malacostraca). This data set includes all crustacean species for which EST data are available (46 species), and our largest alignment encompasses 866,479 amino acid positions and 1,886 genes. A series of phylogenomic analyses was performed to evaluate pancrustacean relationships. We significantly improved the quality of our data for predicting putative orthologous genes and for generating data subsets by matrix reduction procedures, thereby improving the signal to noise ratio in the data. Eight different data sets were constructed, representing various combinations of orthologous genes, data subsets, and taxa. Our results demonstrate that the different ways to compile an initial data set of core orthologs and the selection of data subsets by matrix reduction can have marked effects on the reconstructed phylogenetic trees. Nonetheless, all eight data sets strongly support Pancrustacea with Remipedia as the sister group to Hexapoda. This is the first time that a sister group relationship of Remipedia and Hexapoda has been inferred using a comprehensive phylogenomic data set that is based on EST data. We also show that selecting data subsets with increased overall signal can help to identify and prevent artifacts in phylogenetic analyses.
authors: Zoologisches Forschungsmuseum Alexander Koenig, Zentrum für Molekulare Biodiversitätsforschung, Bonn, Germany. bmvr@arcor.de
authors: Bjoern M
authors: BM
authors: von Reumont
authors: Ronald A
authors: RA
authors: Jenner
authors: Matthew A
authors: MA
authors: Wills
authors: Emiliano
authors: E
authors: Dell'ampio
authors: Günther
authors: G
authors: Pass
authors: Ingo
authors: I
authors: Ebersberger
authors: Benjamin
authors: B
authors: Meyer
authors: Stefan
authors: S
authors: Koenemann
authors: Thomas M
authors: TM
authors: Iliffe
authors: Alexandros
authors: A
authors: Stamatakis
authors: Oliver
authors: O
authors: Niehuis
authors: Karen
authors: K
authors: Meusemann
authors: Bernhard
authors: B
authors: Misof
mesh_terms: D000818:Animals; D001483:Base Sequence; D016000:Cluster Analysis; D019295:Computational Biology; D003445:Crustacea / Q000235:genetics*; D020224:Expressed Sequence Tags; D007313:Insecta / Q000235:genetics*; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010802:Phylogeny; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity