EVOLUTIONARY RELATIONSHIPS OF EUKARYOTIC KINGDOMS

The evolutionary relationships of four eukaryotic kingdoms-Animalia, P lantae, Fungi, and Protista-remain unclear. In particular, statistical support for the closeness of animals to fungi rather than to plants i s lacking, and a preferred branching order of these and other eukaryot ic lineages is still controversial even though molecular sequences fro m diverse eukaryotic taxa have been analyzed. We report a statistical analysis of 214 sequences of nuclear small-subunit ribosomal RNA (srRN A) gene undertaken to clarify these evolutionary relationships. We hav e considered the variability of substitution rates and the nonindepend ence of nucleotide substitution across sites in the srRNA gene in test ing alternative hypotheses regarding the branching pat terns of eukary ote phylogeny. We find that the rates of evolution among sites in the srRNA sequences vary substantially and are approximately gamma distrib uted with size and shape parameter equal to 0.76. Our results suggest that (1) the animals and true fungi are indeed closer to each other th an to any other ''crown'' group in the eukaryote tree, (2) red algae a re the closest relatives of animals, true fungi, and green plants, and (3) the heterokonts and alveolates probably evolved prior to the dive rgence of red algae and animal-fungus-green-plant Lineages. Furthermor e, our analyses indicate that the branching order of the eukaryotic li neages that diverged prior to the evolution of alveolates may be gener ally difficult to resolve with the srRNA sequence data.