On the phylogenetic position of Myzostomida: can 77 genes get it wrong?
1 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
2 Institute of Evolutionary Biology and Ecology, Rheinische Friedrich-Wilhelms-Universität Bonn, An der Immenburg 1, D-53121 Bonn, Germany
3 Department of Biological Sciences, Auburn University, 101 Life Science Building, AL 36849, USA
4 Marine Biology Laboratory, Natural Sciences Building, University of Mons-Hainaut, Av. Champs de Mars 6, B-7000 Mons, Belgium
5 Unit of Bioinformatics, Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Strasse 24-25, Haus 26, D-14476 Potsdam-Golm, Germany
BMC Evolutionary Biology 2009, 9:150 doi:10.1186/1471-2148-9-150Published: 1 July 2009
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.
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.