title: Phylogenomic resolution of the hemichordate and echinoderm clade.
abstract: Ambulacraria, comprising Hemichordata and Echinodermata, is closely related to Chordata, making it integral to understanding chordate origins and polarizing chordate molecular and morphological characters. Unfortunately, relationships within Hemichordata and Echinodermata have remained unresolved, compromising our ability to extrapolate findings from the most closely related molecular and developmental models outside of Chordata (e.g., the acorn worms Saccoglossus kowalevskii and Ptychodera flava and the sea urchin Strongylocentrotus purpuratus). To resolve long-standing phylogenetic issues within Ambulacraria, we sequenced transcriptomes for 14 hemichordates as well as 8 echinoderms and complemented these with existing data for a total of 33 ambulacrarian operational taxonomic units (OTUs). Examination of leaf stability values revealed rhabdopleurid pterobranchs and the enteropneust Stereobalanus canadensis were unstable in placement; therefore, analyses were also run without these taxa. Analyses of 185 genes resulted in reciprocal monophyly of Enteropneusta and Pterobranchia, placed the deep-sea family Torquaratoridae within Ptychoderidae, and confirmed the position of ophiuroid brittle stars as sister to asteroid sea stars (the Asterozoa hypothesis). These results are consistent with earlier perspectives concerning plesiomorphies of Ambulacraria, including pharyngeal gill slits, a single axocoel, and paired hydrocoels and somatocoels. The resolved ambulacrarian phylogeny will help clarify the early evolution of chordate characteristics and has implications for our understanding of major fossil groups, including graptolites and somasteroideans.
authors.affiliation: Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; Department of Zoology, Naturhistoriska Riksmuseet, 104 05 Stockholm, Sweden; Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA. Electronic address: joie.cannon@gmail.com.
authors.forename: Johanna T
authors.initials: JT
authors.lastname: Cannon
authors.affiliation: Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; School of Biological Sciences, University of Queensland, Brisbane, QLD 4072, Australia; Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA.
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Kocot
authors.affiliation: Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA.
authors.forename: Damien S
authors.initials: DS
authors.lastname: Waits
authors.affiliation: Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; Department of Biological and Environmental Sciences, Georgia College and State University, Milledgeville, GA 31061, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Weese
authors.affiliation: Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA.
authors.forename: Billie J
authors.initials: BJ
authors.lastname: Swalla
authors.affiliation: Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA.
authors.forename: Scott R
authors.initials: SR
authors.lastname: Santos
authors.affiliation: Department of Biological Sciences and Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, Auburn, AL 36849, USA; Friday Harbor Laboratories, University of Washington, 620 University Road, Friday Harbor, WA 98250, USA. Electronic address: ken@auburn.edu.
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Halanych
mesh_terms: D000818:Animals; D005075:Biological Evolution; D043344:Chordata / Q000145:classification / Q000235:genetics; D002816:Chordata, Nonvertebrate / Q000145:classification / Q000235:genetics*; D016013:Likelihood Functions; D010802:Phylogeny; D059467:Transcriptome