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We also conducted simulations in which the effect of increasing elapsed time on phylogenetic accuracy was measured, using trees in which all branches are proportionally scaled as time span increases. Results from these simulations show that most internodes are resolved near 100% accuracy, irrespective of time span simulated (fig. 56 and table 58). These results, combined with the lack of resolution within superclades of the metazoan tree, argue against models of metazoan radiation in which the temporal window of diversification is much larger (48).
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A goodness-of-fit test using parametric bootstrapping (15) showed that even the best-fit model of sequence evolution does not adequately describe the evolution of the sequence data from these 32 fungal and metazoan taxa (fig. 58).
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49
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note
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We thank D. Arendt for providing RNA for Platynereis dumerilii; C. Ané for providing the modified version of the Seq-Gen simulation software with an implementation of a covarion model; and B. Prud'homme, B. Williams, and T. Rokas for comments on the manuscript. A.R. was funded by a Human Frontier Science Program Long-Term Fellowship. This work was funded by the Howard Hughes Medical Institute.
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