Likelihood (ln) scores for gene trees and AU test P values comparing gene tree topologies estimated with RAxML against the concatenation topology (from Fig. 3, pruned to only include taxa in the subset), calculated under homogeneous (RAxML) and non-homogeneous (nhPhyML) optimization. The nhPhyML model used unlimited base equilibrium frequencies. Values in bold highlight cases in which the concatenation topology resulted in either better or non-significantly worse likelihood scores
