EFFECTS OF CHARACTER WEIGHTING AND SPECIES SAMPLING ON PHYLOGENY RECONSTRUCTION - A CASE-STUDY BASED ON DNA-SEQUENCE DATA IN CETACEANS

Different phylogenetic analyses of the same genetic data set can yield conflicting results, depending on the choice of parameter settings an d included taxa. This is particularly true in studies involving data s ets where levels of homoplasy are high and likely to obscure the phylo genetic signal. Filtering of this phylogenetic noise can be attempted, with varying degrees of success, by using different weighting schemes and ingroup/outgroup choices, but it can be difficult to decide objec tively which approach is best. Using a cytochrome b data set from ceta ceans and artiodactyls, we examined the effects of a suite of paramete r settings on the outcome of phylogenetic analyses. We tested 2968 com binations among the seven parameters that most often vary among phylog enetic studies. It is our contention that this sensitivity analysis id entifies portions of the multidimensional parameter space where phylog enetic signal is most reliably recovered, and simple rules are given t o guide the choice of settings. Portions of this data set have been us ed in previous studies with conflicting results, namely the monophyly vs. paraphyly of one of the two major recognized cetacean suborders, t he toothed whales. This analysis strongly supports the sister relation ship between sperm whales and baleen whales.