SUCCESS OF PHYLOGENETIC METHODS IN THE 4-TAXON CASE

The success of 16 methods of phylogenetic inference was examined using consistency and simulation analysis. Success-the frequency with which a tree-making method correctly identified the true phylogeny-was exam ined for an unrooted four-taxon tree. In this study, tree-making metho ds were examined under a large number of branch-length conditions and under three models of sequence evolution. The results are plotted to f acilitate comparisons among the methods. The consistency analysis indi cated which methods converge on the correct tree given infinite sample size. General parsimony, transversion parsimony, and weighted parsimo ny are inconsistent over portions of the graph space examined, althoug h the area of inconsistency varied. Lake's method of invariants consis tently estimated phylogeny over all of the graph space when the model of sequence evolution matched the assumptions of the invariants method . However, when one of the assumptions of the invariants method was vi olated, Lake's method of invariants became inconsistent over a large p ortion of the graph space. In general, the distance methods (neighbor joining, weighted least squares, and unweighted least squares) consist ently estimated phylogeny over all of the graph space examined when th e assumptions of the distance correction matched the model of evolutio n used to generate the model trees. When the assumptions of the distan ce methods were violated, the methods became inconsistent over portion s of the graph space. UPGMA was inconsistent over a large area of the graph space, no matter which distance was used. The simulation analysi s showed how tree-making methods perform given limited numbers of char acter data. In some instances, the simulation results differed quantit atively from the consistency analysis. The consistency analysis indica ted that Lake's method of invariants was consistent over all of the gr aph space under some conditions, whereas the simulation analysis showe d that Lake's method of invariants performs poorly over most of the gr aph space for up to 500 variable characters. Parsimony, neighbor-joini ng, and the least-squares methods performed well under conditions of l imited amount of character change and branch-length variation. By weig hting the more slowly evolving characters or using distances that corr ect for multiple substitution events, the area in which tree-making me thods are misleading can be reduced. Good performance at high rates of change was obtained only by giving increased weight to slowly evolvin g characters (e.g., transversion parsimony, weighted parsimony). UPGMA performed well only when branch lengths were close in length.