Integrative phylogenomics positions sponges at the root of the animal tree.

Determining whether sponges or ctenophores root the animal tree has important implications for understanding early animal evolution. Here, we examined support for these competing hypotheses by constructing large and highly informative data matrices containing sequences from sponges, ctenophores, cnidarians, bilaterians, and diverse animal relatives. The new data matrices and 10 published datasets were analyzed in 785 topology tests conducted using integrative phylogenomics, a method that unifies concatenation and coalescence to identify genes with a consistent phylogenetic signal. All 490 statistically significant tests supported the sponge-sister hypothesis and none supported the ctenophore-sister hypothesis; the remaining 295 tests were inconclusive. These results provide compelling evidence for the sponge-sister hypothesis and suggest that integrative phylogenomics provides a robust and powerful approach for disentangling branches in the tree of life. Editor's summary: The increased availability of high-quality genomes and improved phylogenetic methods have led to researchers revisiting many taxon relationships. Steenwyk and King took on a highly contested debate: whether sponges or comb jellies (ctenophores) were the first lineage to diverge among animals (see the Perspective by Mulhair and Redmond). Using data from 100 genomes and transcriptomes enriched for sponges, ctenophores, and cnidarians, the authors used an integrative phylogenomic approach to determine which of the nearly universal single-copy genes consistently supported either lineage as a sister taxon. Most tests conducted with this set of genes supported sponges as the sister taxon, and none supported ctenophores. This work supports early trees constructed using morphology, although it is likely not the final word in this debate. —Corinne Simonti [ABSTRACT FROM AUTHOR]