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.