title: Phylogenomic Analyses Support Traditional Relationships within Cnidaria.
abstract: 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.
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Felipe
authors.initials: F
authors.lastname: Zapata
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Freya E
authors.initials: FE
authors.lastname: Goetz
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Stephen A
authors.initials: SA
authors.lastname: Smith
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America; Computing and Information Services, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Mark
authors.initials: M
authors.lastname: Howison
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Stefan
authors.initials: S
authors.lastname: Siebert
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Samuel H
authors.initials: SH
authors.lastname: Church
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America.
authors.forename: Steven M
authors.initials: SM
authors.lastname: Sanders
authors.affiliation: Department of Invertebrate Zoology, Smithsonian Museum of Natural History, Washington District of Columbia, United States of America; Biological Sciences Graduate Program, University of Maryland, College Park, Maryland, United States of America.
authors.forename: Cheryl Lewis
authors.initials: CL
authors.lastname: Ames
authors.affiliation: Department of Biology, Harvey Mudd College, Claremont, California, United States of America.
authors.forename: Catherine S
authors.initials: CS
authors.lastname: McFadden
authors.affiliation: Department of Biology, The University of Louisiana at Lafayette, Lafayette, Louisiana, United States of America.
authors.forename: Scott C
authors.initials: SC
authors.lastname: France
authors.affiliation: Department of Evolution, Ecology and Organismal Biology, Ohio State University, Columbus, Ohio, United States of America.
authors.forename: Marymegan
authors.initials: M
authors.lastname: Daly
authors.affiliation: Department of Invertebrate Zoology, Smithsonian Museum of Natural History, Washington District of Columbia, United States of America; National Systematics Laboratory of NOAA's Fisheries Service, National Museum of Natural History, Washington, District of Columbia, United States of America.
authors.forename: Allen G
authors.initials: AG
authors.lastname: Collins
authors.affiliation: Monterey Bay Aquarium Research Institute, Moss Landing, California, United States of America.
authors.forename: Steven H D
authors.initials: SH
authors.lastname: Haddock
authors.affiliation: Department of Ecology and Evolutionary Biology, Brown University, Providence, Rhode Island, United States of America.
authors.forename: Casey W
authors.initials: CW
authors.lastname: Dunn
authors.affiliation: Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, Kansas, United States of America.
authors.forename: Paulyn
authors.initials: P
authors.lastname: Cartwright
mesh_terms: D000818:Animals; D037421:Anthozoa / Q000145:classification* / Q000235:genetics; D001499:Bayes Theorem; D005075:Biological Evolution; D037462:Cubozoa / Q000145:classification* / Q000235:genetics; D037402:Hydrozoa / Q000145:classification* / Q000235:genetics; D055764:Myxozoa / Q000145:classification* / Q000235:genetics; D010802:Phylogeny; D037401:Scyphozoa / Q000145:classification* / Q000235:genetics; D059467:Transcriptome