title: Nearly complete 28S rRNA gene sequences confirm new hypotheses of sponge evolution.
abstract: The highly collaborative research sponsored by the NSF-funded Assembling the Porifera Tree of Life (PorToL) project is providing insights into some of the most difficult questions in metazoan systematics. Our understanding of phylogenetic relationships within the phylum Porifera has changed considerably with increased taxon sampling and data from additional molecular markers. PorToL researchers have falsified earlier phylogenetic hypotheses, discovered novel phylogenetic alliances, found phylogenetic homes for enigmatic taxa, and provided a more precise understanding of the evolution of skeletal features, secondary metabolites, body organization, and symbioses. Some of these exciting new discoveries are shared in the papers that form this issue of Integrative and Comparative Biology. Our analyses of over 300 nearly complete 28S ribosomal subunit gene sequences provide specific case studies that illustrate how our dataset confirms new hypotheses of sponge evolution. We recovered monophyletic clades for all 4 classes of sponges, as well as the 4 major clades of Demospongiae (Keratosa, Myxospongiae, Haploscleromorpha, and Heteroscleromorpha), but our phylogeny differs in several aspects from traditional classifications. In most major clades of sponges, families within orders appear to be paraphyletic. Although additional sampling of genes and taxa are needed to establish whether this pattern results from a lack of phylogenetic resolution or from a paraphyletic classification system, many of our results are congruent with those obtained from 18S ribosomal subunit gene sequences and complete mitochondrial genomes. These data provide further support for a revision of the traditional classification of sponges.
authors.affiliation: *Department of Biology, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294-1170, USA; Department of Biology, University of Richmond, Richmond, VA, USA; Department of Invertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; National Systematics Laboratory of NOAA's Fisheries Service, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; School of Biological Sciences, MBC, 97 Lisburn Road, Queen's University, Belfast BT9 7BL, UK; Museo Marino de Margarita, Boulevard de Boca Del Rio, Boca del Rio, Nueva Esparta, Venezuela; **Department of Computer and Information Sciences, University of Alabama at Birmingham, 1300 University Boulevard, Birmingham, AL 35294-1170, USA.
authors.forename: Robert W
authors.initials: RW
authors.lastname: Thacker
authors.forename: April L
authors.initials: AL
authors.lastname: Hill
authors.forename: Malcolm S
authors.initials: MS
authors.lastname: Hill
authors.forename: Niamh E
authors.initials: NE
authors.lastname: Redmond
authors.forename: Allen G
authors.initials: AG
authors.lastname: Collins
authors.forename: Christine C
authors.initials: CC
authors.lastname: Morrow
authors.forename: Lori
authors.initials: L
authors.lastname: Spicer
authors.forename: Cheryl A
authors.initials: CA
authors.lastname: Carmack
authors.forename: Megan E
authors.initials: ME
authors.lastname: Zappe
authors.forename: Deborah
authors.initials: D
authors.lastname: Pohlmann
authors.forename: Chelsea
authors.initials: C
authors.lastname: Hall
authors.forename: Maria C
authors.initials: MC
authors.lastname: Diaz
authors.forename: Purushotham V
authors.initials: PV
authors.lastname: Bangalore
mesh_terms: D000818:Animals; D001483:Base Sequence; D001499:Bayes Theorem; D017931:DNA Primers / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D008969:Molecular Sequence Data; D010176:Panama; D010802:Phylogeny; D011161:Porifera / Q000145:classification* / Q000235:genetics*; D012339:RNA, Ribosomal, 28S / Q000235:genetics*; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity; D013056:Spectrophotometry, Ultraviolet
chemical_list: D017931:DNA Primers; D012339:RNA, Ribosomal, 28S