Sponges or Ctenophores? A Synthesis of Evidence on the Root of the Animal Phylogeny

The root of the animal tree—whether sponges (Porifera) or ctenophores (Ctenophora) represent the earliest-branching lineage—remains a key unresolved question in evolutionary biology. This review synthesizes evidence from molecular sequences, rare genomic events, morphology, embryology, and paleontology. While molecular sequence data provide extensive coverage, they are susceptible to methodological errors and confounding evolutionary processes. Rare molecular events, such as chromosomal fusion-with-mixing, provide deeper resolution due to their low convergence potential and high irreversibility. Morphological and embryological traits, historically underestimated, benefit from advances in imaging and comparative gene expression. Fossil records, though direct, remain fragmentary and biased. To explain persistent conflicts among data types, we propose the concepts of a Resolution Limit and the Deep Basal Problem, which formalize why early divergences are so difficult to resolve. We introduce Highly Anti-Convergent and Highly Irreversible Marginal Instances (HACHIMIs) as a promising class of phylogenetic signals. In conclusion, while traditional datasets tend to support the Porifera-sister hypothesis, high-resolution data increasingly favor Ctenophora-sister. More broadly, this review argues that resolving deep phylogenies requires integrative methodological frameworks, not just more data.