title: Phylogenetic methods come of age: testing hypotheses in an evolutionary context.
abstract: The use of molecular phylogenies to examine evolutionary questions has become commonplace with the automation of DNA sequencing and the availability of efficient computer programs to perform phylogenetic analyses. The application of computer simulation and likelihood ratio tests to evolutionary hypotheses represents a recent methodological development in this field. Likelihood ratio tests have enabled biologists to address many questions in evolutionary biology that have been difficult to resolve in the past, such as whether host-parasite systems are cospeciating and whether models of DNA substitution adequately explain observed sequences.
authors.affiliation: Department of Integrative Biology, University of California, Berkeley, CA 94720, USA. john@mws4.biol.berkeley.edu
authors.forename: J P
authors.initials: JP
authors.lastname: Huelsenbeck
authors.forename: B
authors.initials: B
authors.lastname: Rannala
mesh_terms: D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D003198:Computer Simulation; D004247:DNA / Q000235:genetics; D003576:Electron Transport Complex IV / Q000235:genetics; D019143:Evolution, Molecular; D006476:Orthohantavirus / Q000235:genetics; D016013:Likelihood Functions; D009154:Mutation; D008003:Phthiraptera / Q000235:genetics; D010802:Phylogeny; D012367:RNA, Viral / Q000235:genetics; D012377:Rodentia / Q000235:genetics
chemical_list: D012367:RNA, Viral; D004247:DNA; D003576:Electron Transport Complex IV