title: On the phylogenetic position of Myzostomida: can 77 genes get it wrong?
abstract: BACKGROUND
  Phylogenomic analyses recently became popular to address questions about deep metazoan phylogeny. Ribosomal proteins (RP) dominate many of these analyses or are, in some cases, the only genes included. Despite initial hopes, phylogenomic analyses including tens to hundreds of genes still fail to robustly place many bilaterian taxa.
  
  
  RESULTS
  Using the phylogenetic position of myzostomids as an example, we show that phylogenies derived from RP genes and mitochondrial genes produce incongruent results. Whereas the former support a position within a clade of platyzoan taxa, mitochondrial data recovers an annelid affinity, which is strongly supported by the gene order data and is congruent with morphology. Using hypothesis testing, our RP data significantly rejects the annelids affinity, whereas a platyzoan relationship is significantly rejected by the mitochondrial data.
  
  
  CONCLUSIONS
  We conclude (i) that reliance of a set of markers belonging to a single class of macromolecular complexes might bias the analysis, and (ii) that concatenation of all available data might introduce conflicting signal into phylogenetic analyses. We therefore strongly recommend testing for data incongruence in phylogenomic analyses. Furthermore, judging all available data, we consider the annelid affinity hypothesis more plausible than a possible platyzoan affinity for myzostomids, and suspect long branch attraction is influencing the RP data. However, this hypothesis needs further confirmation by future analyses.
authors: Unit of Evolutionary Biology/Systematic Zoology, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Haus 26, D-14476 Potsdam-Golm, Germany. Bleidorn@uni-potsdam.de
authors: Christoph
authors: C
authors: Bleidorn
authors: Lars
authors: L
authors: Podsiadlowski
authors: Min
authors: M
authors: Zhong
authors: Igor
authors: I
authors: Eeckhaut
authors: Stefanie
authors: S
authors: Hartmann
authors: Kenneth M
authors: KM
authors: Halanych
authors: Ralph
authors: R
authors: Tiedemann
mesh_terms: D000818:Animals; D000845:Annelida / Q000235:genetics; D001499:Bayes Theorem; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D015723:Gene Library; D023061:Gene Order; D050259:Genes, Mitochondrial; D005819:Genetic Markers; D054629:Genome, Mitochondrial; D008957:Models, Genetic; D010802:Phylogeny; D012269:Ribosomal Proteins / Q000235:genetics*; D017422:Sequence Analysis, DNA
chemical_list: D004272:DNA, Mitochondrial; D005819:Genetic Markers; D012269:Ribosomal Proteins