Phylogenies from restriction sites: a maximum-likelihood approach

Abstract

Restriction sites data can be analyzed by maximum likelihood to obtain estimates of phylogenies. The likelihood methods of Smouse and Li, who were able to compute likelihoods for up to four species under a simplified model of base change, can be extended numerically to deal with any number of species. The resulting algorithms take multiple gains and losses of restriction sites fully into account, unlike parsimony methods. Analysis of published five-species hominoid data confirms that a chimpanzee-gorilla clade is favored, but not statistically significantly over other tree topologies. -from Author