PT - JOURNAL ARTICLE AU - Felipe Zapata AU - Freya E. Goetz AU - Stephen A. Smith AU - Mark Howison AU - Stefan Siebert AU - Samuel H. Church AU - Steven M Sanders AU - Cheryl Lewis Ames AU - Catherine S. McFadden AU - Scott C. France AU - Marymegan Daly AU - Allen G. Collins AU - Steven H.D. Haddock AU - Casey W. Dunn AU - Paulyn Cartwright TI - Phylogenomic analyses support traditional relationships within Cnidaria AID - 10.1101/017632 DP - 2015 Jan 01 TA - bioRxiv PG - 017632 4099 - http://biorxiv.org/content/early/2015/04/06/017632.short 4100 - http://biorxiv.org/content/early/2015/04/06/017632.full AB - Cnidaria, the sister group to Bilateria, is a highly diverse group of animals in terms of morphology, lifecycles, ecology, and development. How this diversity originated and evolved is not well understood because phylogenetic relationships among major cnidarian lineages are unclear, and recent studies present contrasting phylogenetic hypotheses. Here, we use transcriptome data from 15 newly-sequenced species in combination with 26 publicly available genomes and transcriptomes to assess phylogenetic relationships among major cnidarian lineages. Phylogenetic analyses using different partition schemes and models of molecular evolution, as well as topology tests for alternative phylogenetic relationships, support the monophyly of Medusozoa, Anthozoa, Octocorallia, Hydrozoa, and a clade consisting of Staurozoa, Cubozoa, and Scyphozoa. Support for the monophyly of Hexacorallia is weak due to the equivocal position of Ceriantharia. Taken together, these results further resolve deep cnidarian relationships, largely support traditional phylogenetic views on relationships, and provide a historical framework for studying the evolutionary processes involved in one of the most ancient animal radiations.