Evaluating hypotheses of basal animal phylogeny using complete sequences of large and small subunit rRNA

We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA se quences for 23 taxa. After identifying competing hypotheses, we performed m aximum likelihood searches for trees conforming to each hypothesis. Kishino -Hase-gawa tests were used to determine whether the data (LSU, SSU, and com bined) reject any of the competing hypotheses. We also conducted unconstrai ned tree searches, compared the resulting topologies, and calculated bootst rap indices. Shimodaira-Hase-gawa tests were applied to determine whether t he data reject any of the topologies resulting from the constrained and unc onstrained tree searches. LSU, SSU, and the combined data strongly contradi ct two assertions pertaining to sponge phylogeny. Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera or the siste r group to all other animals. Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea. it remains unclear, o n the basis of these data alone, whether the calcarean sponges are more clo sely related to Silicea or to nonsponge animals. The SSU and combined data reject the hypothesis that Bilateria is more closely related to Ctenophora than it is to Cnidaria, whereas LSU data alone do not refute either hypothe sis. LSU and SSU data agree in supporting the monophyly of Bilateria, Cnida ria, Ctenophora, and Metazoa. LSU sequence data reveal phylogenetic structu re in a data set with limited taxon sampling. Continued accumulation of LSU sequences should increase our understanding of animal phylogeny.