Independent contrasts succeed where ancestor reconstruction fails in a known bacteriophage phylogeny

Methods of ancestor reconstruction are important tools for evolutionary inf erence that are difficult to test empirically because ancestral states are rarely known with certainty. We evaluated reconstruction methods for contin uous phenotypic characters using taxa from an experimentally generated bact eriophage phylogeny. Except for one slowly evolving character, the estimate d ancestral states of continuous phenotypic characters were highly inaccura te and biased, even when including a known ancestor at the root. This error was caused by a directional trend in character evolution and by rapid rate s of character evolution. Computer simulations confirmed that such factors affect reconstruction of continuous characters in general. We also used phe notypic viral characters to evaluate two methods that attempt to estimate t he correlation between characters during evolution. Whereas a nonphylogenet ic regression was relatively inaccurate and biased, independent contrasts a ccurately estimated the correlation between characters with little bias.