Thank you for this very thoughtful and nuanced discussion. The arguments of Pisani et al. would be more convincing if a mechanism behind the ‘undetected biases’ was investigated. At first I thought that maybe among-taxon compositional heterogeneity is the problem (our study did not explicitly address this and we didn’t have distant outgroups anyways), but Whelan et al. did look into this. What other properties/similarities of the outgroup sequences could be pulling ctenophores to the base?