Phylogenetic trees obtained for three subsets extracted from the Metazoa dataset. Maximum Likelihood inferences were performed with the JTT+Γ (4 categories) model by TreeFinder  on two datasets based on the Philippe et al.  Metazoa dataset and constructed as follows. The species were grouped according to 12 OTUs. Sequences with at least 90% of the total number of positions were considered as complete and sequences or chimera shorter than 10% of the total number of positions were removed. The two datasets differ on the main criteria of selection, A: longest sequence (LC) and B: smaller evolutionary distances (SC). Numbers above branches indicate bootstrap support values obtained by analysing 100 bootstrap replicates under the same conditions.