Syst. Biol. 55(1):97–115, 2006 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150500433615 Medusozoan Phylogeny and Character Evolution Clarified by New Large and Small Subunit rDNA Data and an Assessment of the Utility of Phylogenetic Mixture Models ALLEN G. COLLINS,1 PETER SCHUCHERT,2 ANTONIO C. MARQUES,3 THOMAS JANKOWSKI,4 MONICA´ MEDINA,5 AND BERND SCHIERWATER6 1NMFS, National Systematics Laboratory, National Museum of Natural History, MRC-153, Smithsonian Institution, P.O. Box 37012, Washington, DC 20013-7012, USA; E-mail:
[email protected] (A.G.C.) 2Museum´ d’Histoire Naturelle, 1 route Malagnou, CH-1211 Geneve,` Switzerland 3Department of Zoology, Institute of Biosciences, University of Sao˜ Paulo, Sao˜ Paulo, Brazil 4W&T,Swiss Federal Institute of Aquatic Science and Technology (EAWAG-ETH), Ueberlandstrasse 133, CH-8600 Duebendorf, Switzerland 5DOE Joint Genome Institute, 2800 Mitchell Drive, Walnut Creek, California 94598, USA 6ITZ, Ecology & Evolution, TiHo Hannover, Bunteweg¨ 17d, D-30559 Hannover, Germany Abstract.—A newly compiled data set of nearly complete sequences of the large subunit of the nuclear ribosome (LSU or 28S) sampled from 31 diverse medusozoans greatly clarifies the phylogenetic history of Cnidaria. These data have substantial power to discern among many of the competing hypotheses of relationship derived from prior work. Moreover, LSU data provide strong support at key nodes that were equivocal based on other molecular markers. Combining LSU sequences with those of the small subunit of the nuclear ribosome (SSU or 18S), we present a detailed working hypothesis of medusozoan relationships and discuss character evolution within this diverse clade.