Figure 3

Species trees inferred from the 248 individual maximum likelihood (ML) gene trees using a pseudo-ML approach. Maximum pseudo-likelihood for estimating species trees (MP-EST) bootstrap consensus species tree obtained for (a) the amino-acid and (b) the nucleotide dataset. (a) This consensus tree was computed from the species trees estimated by the MP-EST method for 100 bootstrap datasets of the 248 ML gene trees inferred under the LG + G8 model. (b) This consensus tree was computed from the species trees estimated by the MP-EST method for 100 bootstrap datasets of the 248 ML gene trees inferred under the GTR + G8 model. Values at nodes indicate bootstrap percentages obtained with 100 replicates. Note the strong incongruence between the two species trees concerning the position of turtles.