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Comparative Study
, 98 (17), 9707-12

Evaluating Hypotheses of Basal Animal Phylogeny Using Complete Sequences of Large and Small Subunit rRNA

Affiliations
Comparative Study

Evaluating Hypotheses of Basal Animal Phylogeny Using Complete Sequences of Large and Small Subunit rRNA

M Medina et al. Proc Natl Acad Sci U S A.

Abstract

We studied the evolutionary relationships among basal metazoan lineages by using complete large subunit (LSU) and small subunit (SSU) ribosomal RNA sequences for 23 taxa. After identifying competing hypotheses, we performed maximum likelihood searches for trees conforming to each hypothesis. Kishino-Hasegawa tests were used to determine whether the data (LSU, SSU, and combined) reject any of the competing hypotheses. We also conducted unconstrained tree searches, compared the resulting topologies, and calculated bootstrap indices. Shimodaira-Hasegawa tests were applied to determine whether the data reject any of the topologies resulting from the constrained and unconstrained tree searches. LSU, SSU, and the combined data strongly contradict two assertions pertaining to sponge phylogeny. Hexactinellid sponges are not likely to be the basal lineage of a monophyletic Porifera or the sister group to all other animals. Instead, Hexactinellida and Demospongia form a well-supported clade of siliceous sponges, Silicea. It remains unclear, on the basis of these data alone, whether the calcarean sponges are more closely 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 hypothesis. LSU and SSU data agree in supporting the monophyly of Bilateria, Cnidaria, Ctenophora, and Metazoa. LSU sequence data reveal phylogenetic structure in a data set with limited taxon sampling. Continued accumulation of LSU sequences should increase our understanding of animal phylogeny.

Figures

Figure 1
Figure 1
Comparison of ML SSU and LSU trees (A and B, respectively). ML bootstrap (100 replicates) values are shown at the nodes. < indicates bootstrap less than 50%. (Bar = 0.1 substitutions per site.)
Figure 2
Figure 2
Comparison of ML tree and strict consensus of two MP trees based on combined SSU and LSU data (Left and Right, respectively). ML bootstrap values are shown at the nodes of the ML tree. MP bootstrap values and Bremer support indices are shown at the nodes of the MP tree. < indicates bootstrap of less than 50%. (Bar = 0.1 substitutions per site.)

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