OPTIMIZATION ALIGNMENT - THE END OF MULTIPLE SEQUENCE ALIGNMENT IN PHYLOGENETICS

A method is described to assess directly the number of DNA sequence tr ansformations, evolutionary events, required by a phylogenetic topolog y without the use of multiple sequence alignment. This is accomplished through a generalization of existing character optimization procedure s to include insertion and deletion events (indels) in addition to bas e substitutions. The crux of the model is the treatment of indels as p rocesses as opposed to the patterns implied by multiple sequence align ment. The results of this procedure are directly compatible with parsi mony-based tree lengths. In addition to the simplicity of the method, it appears to generate more efficient (simpler) explanations of sequen ce variation than does multiple alignment. (C) 1996 The Willi Hennig S ociety.