title: Exploiting gene families for phylogenomic analysis of myzostomid transcriptome data.
abstract: BACKGROUND
  In trying to understand the evolutionary relationships of organisms, the current flood of sequence data offers great opportunities, but also reveals new challenges with regard to data quality, the selection of data for subsequent analysis, and the automation of steps that were once done manually for single-gene analyses. Even though genome or transcriptome data is available for representatives of most bilaterian phyla, some enigmatic taxa still have an uncertain position in the animal tree of life. This is especially true for myzostomids, a group of symbiotic (or parasitic) protostomes that are either placed with annelids or flatworms.
  
  
  METHODS
  Based on similarity criteria, Illumina-based transcriptome sequences of one myzostomid were compared to protein sequences of one additional myzostomid and 29 reference metazoa and clustered into gene families. These families were then used to investigate the phylogenetic position of Myzostomida using different approaches: Alignments of 989 sequence families were concatenated, and the resulting superalignment was analyzed under a Maximum Likelihood criterion. We also used all 1,878 gene trees with at least one myzostomid sequence for a supertree approach: the individual gene trees were computed and then reconciled into a species tree using gene tree parsimony.
  
  
  CONCLUSIONS
  Superalignments require strictly orthologous genes, and both the gene selection and the widely varying amount of data available for different taxa in our dataset may cause anomalous placements and low bootstrap support. In contrast, gene tree parsimony is designed to accommodate multilocus gene families and therefore allows a much more comprehensive data set to be analyzed. Results of this supertree approach showed a well-resolved phylogeny, in which myzostomids were part of the annelid radiation, and major bilaterian taxa were found to be monophyletic.
authors.affiliation: Department of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.
authors.forename: Stefanie
authors.initials: S
authors.lastname: Hartmann
authors.forename: Conrad
authors.initials: C
authors.lastname: Helm
authors.forename: Birgit
authors.initials: B
authors.lastname: Nickel
authors.forename: Matthias
authors.initials: M
authors.lastname: Meyer
authors.forename: Torsten H
authors.initials: TH
authors.lastname: Struck
authors.forename: Ralph
authors.initials: R
authors.lastname: Tiedemann
authors.forename: Joachim
authors.initials: J
authors.lastname: Selbig
authors.forename: Christoph
authors.initials: C
authors.lastname: Bleidorn
mesh_terms: D000818:Animals; D000845:Annelida / Q000145:classification / Q000235:genetics; D019143:Evolution, Molecular; D007448:Invertebrates / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D010986:Platyhelminths / Q000145:classification / Q000235:genetics; D059467:Transcriptome / Q000235:genetics