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In Redmond and McLysaght 1 (R&M) we integrated precomputed siteheterogeneous amino acid substitution models and amino acid recoding into partitioned phylogenomics and showed that this improved model-fit and resistance to long-branch attraction (LBA; a common phylogenetic error). These better fitting modelling strategies revealed a shift in support away from Ctenophora (comb jellies), and towards Porifera (sponges), as sister to all other animals 1. Whelan and Halanych 2 (W&H) criticised our recoded analyses and interpretations on the placement of Porifera and Ctenophora in the animal phylogeny. Here we counter these criticisms, and bolster evidence for Porifera as sister to all other animals.

W&H claim we did not adequately consider well-accepted relationships (called ‘generally accepted topologies’ in R&M 1) when assessing the performance of new approaches in R&M 2. The siteheterogeneous …