INTRASPECIFIC CLADOGRAM ESTIMATION - ACCURACY AT HIGHER LEVELS OF DIVERGENCE

Because phylogenies play a central role in many evolutionary and popul ation genetic questions, it is vital to have confidence in phylogeny r econstructions for particular data sets. An algorithm recently introdu ced by Templeton et al. (1992, Genetics 132:619-633) simultaneously es timates cladograms from a given set of restriction site or nucleotide sequence data and calculates a confidence set of alternatives while al lowing for the possibility of recombination within the data set. This method was developed for use at the intraspecific level, where mutatio nal differences between operational taxonomic units are few. Because o f the strengths of this method, it would be desirable to use it at hig her levels of phylogenetic analysis. I tested the accuracy of the meth od of Templeton et al. using a known phylogeny from bacteriophage T7, which simulates higher levels of diversification. This method has grea ter statistical power and more accurately reconstructs phylogenetic re lationships than does maximum parsimony when few molecular characters are available for analysis, even at higher levels of diversification.