Figure 4

The basal-protostome branching of chætognaths is confirmed through improved inference methods and expanded taxon sampling. A RP alignment of 11,730 positions (after GBlock filtration; see Additional data file 4) was analyzed using two classes of models. (a) Site-homogeneous model (WAG) implemented in a maximum-likelihood framework (PhyML [80] and Treefinder [81]). Similar topology and maximal posterior probabilities were obtained with Bayesian analyses using the same model (MrBayes). (b) Site-heterogeneous model (CAT) implemented in a bayesian framework (Phylobayes [79]). Plain colored circles denote nodes for which significant support values were obtained (likelihood ratio statistics based on expected-likelihood weights (LR-ELW) >0.95 for site-homogenous and PP >0.95 for site-heterogenous). Support values are indicated for selected nodes: LR-ELW statistics and bootstrap (bold type) for maximum likelihood (ML) using the WAG model and posterior probabilities for Bayesian inference using the CAT model.