In their letter, Halanych et al. criticize our recent assertion that the phylogenetic placement of ctenophores as the sister group to all other animals (the Ctenophora-sister hypothesis) in three previous studies was an artifact caused by undetected systematic error. Halanych et al. claim we used no “objective approaches” to identify sources of systematic error. In fact, we used an objective comparison of Bayesian cross-validation scores to select the best-fitting substitution model, because poorly fitting models are a frequent source of systematic error. Halanych et al. point out that this comparison did not include partitioned site-homogeneous models. However, they do not mention that only one of the studies we address used this approach, and that multiple site-homogeneous partitions still do not account for within-partition site-heterogeneous biochemical constraints, which our results show had a major impact on model fit and the tree topology.