%0 Journal Article
%T On the phylogenetic position of Myzostomida: can 77 genes get it wrong?
%A Christoph Bleidorn
%A Lars Podsiadlowski
%A Min Zhong
%A Igor Eeckhaut
%A Stefanie Hartmann
%A Kenneth M Halanych
%A Ralph Tiedemann
%J BMC Evolutionary Biology
%D 2009
%I BioMed Central
%R 10.1186/1471-2148-9-150
%X 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.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.Molecular phylogenies based on a single or a few genes often lead to apparently conflicting signals. Violation of orthology assumption, biases leading to non-phylogenetic signal, and stochastic error related to gene length might be problematic [1]. Use of phylogenomics (molecular phylogenetic studies using a genome-scale approach) has been thought to overcome these problems, and "ending incongruence" was in sight [2]. However, poor taxon sampling [3] and systematic error that is positively misleading [4] can cause phylogenomic analyses to yield incorrect trees with high support.Use of phylogenomic analyses to address deep metazoan relationships has recently increased. Many of these analyses consist of concatenated sets of ribosomal proteins (RP) [5-8] or of data sets dominated by RP data [3]. RP genes are highly expressed and therefor
%U http://www.biomedcentral.com/1471-2148/9/150