Phylogenomics provides a robust topology of the major cnidarian lineages and insights on the origins of key organismal traits

Background: The phylogeny of Cnidaria has been a source of debate for decades, during which nearly all possible relationships among the major lineages have been proposed The ecological success of Cnidaria is predicated on several fascinating organismal innovations including stinging cells, symbiosis, colonial body plans and elaboiate life histories However, understanding the origins and subsequent diversification of these traits remains difficult due to persistent uncertainty surrounding the evolutionary/ relationships within Cnidaria. While recent phylogenomic studies have advanced our knowledge of the cnidarian tree of life, no analysis to date has included genome scale data for each major cnidarian lineage. Results: Here we describe a well supported hypothesis for cnidarian phylogeny based on phylogenomic analyses of new and existing genome scale data that includes representatives of all cnidarian classes Our results are robust to alternative modes of phylogenetic estimation and phylogenomic dataset construction We show that two popular phylogenomic matrix construction pipelines yield profoundly different datasets, both in the identities and in the functional classes of the loci they include, but resolve the same topology We then level age our phylogenetic resolution of Cnidaria to understand the character histones of several critical organismal traits Ancestral state reconstruction analyses based on our phylogeny establish several notable oiganismal transitions in the evolutionary history of Cnidaria and depict the ancestral cnidarian as a solitary/, non symbiotic polyp that lacked a medusa stage In addition, Bayes factor tests strongly suggest that symbiosis has evolved multiple times independently across the cnidarian radiation. Conclusions: Cnidaria have experienced more than 600 million years of independent evolution and in the process generated an array of organismal innovations Our results add significant clarification on the cnidarian tree of life and the histories of some of these innovations Further, we confirm the existence of Acraspeda (staurozoans plus scyphozoans and cubozoans),, thus reviving an evolutionary hypothesis put forward more than a century ago.