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Halanych et al.(1) claim we used no “objective approaches” to identify sources of systematic error. In fact, we used an objective comparison of Bayesian crossvalidation 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 (3) 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. Halanych et al.(1) also incorrectly suggest that our model-selection procedure relied on circular assumptions about the position of sponges. No such assumptions were made to demonstrate the better fit of site-heterogeneous models …