RT Journal Article SR Electronic T1 Phylogenomic analyses support traditional relationships within Cnidaria JF bioRxiv FD Cold Spring Harbor Laboratory SP 017632 DO 10.1101/017632 A1 Felipe Zapata A1 Freya E. Goetz A1 Stephen A. Smith A1 Mark Howison A1 Stefan Siebert A1 Samuel H. Church A1 Steven M Sanders A1 Cheryl Lewis Ames A1 Catherine S. McFadden A1 Scott C. France A1 Marymegan Daly A1 Allen G. Collins A1 Steven H.D. Haddock A1 Casey W. Dunn A1 Paulyn Cartwright YR 2015 UL http://biorxiv.org/content/early/2015/04/06/017632.abstract 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.