Polytomies and phylogenetically independent contrasts: examination of the bounded degrees of freedom approach

We examined the effect of soft polytomies on the performance (Type I error rate and bias) of Felsenstein's (1985; Am. Nat. 125:1-15) method of phylogenetically independent contrasts for estimating a bivariate correlation. We specifically tested the adequacy of bounding degrees of freedom, as suggested by Purvis and Garland (1993; Syst. Biol. 42:569-575). We simulated bivariate character evolution under Brownian motion (assumed by independent contrasts) and eight other models on five phylogenetic trees. For non-Brownian motion simulations, the adequacy of branch-length standardization was checked with a simple diagnostic (Garland et al., 1992; Syst. Biol. 41:18-32), and transformations were applied as indicated. Surprisingly, soft polytomies tended to have negligible effects on Type I error rates when models other than Brownian motion were used. Overall, and irrespective of evolutionary model, degrees of freedom were appropriately bounded for hypothesis testing, and unbiased estimates of the correlation coefficient were obtained. Our results, along with those of previous simulation studies, suggest that independent contrasts can reliably be applied to real data, even with phylogenetic uncertainty.