title: Is congruence between data partitions a reliable predictor of phylogenetic accuracy? Empirically testing an iterative procedure for choosing among phylogenetic methods.
abstract: The relationship between phylogenetic accuracy and congruence between data partitions collected from the same taxa was explored for mitochondrial DNA sequences from two well-supported vertebrate phylogenies. An iterative procedure was adopted whereby accuracy, phylogenetic signal, and congruence were measured before and after modifying a simple reconstruction model, equally weighted parsimony. These modifications included transversion parsimony, successive weighting, and six-parameter parsimony. For the data partitions examined, there is a generally positive relationship between congruence and phylogenetic accuracy. If congruence increased without decreasing resolution or phylogenetic signal, this increased congruence was a good predictor of accuracy. If congruence increased as a result of poor resolution, the degree of congruence was not a good predictor of accuracy. For all sets of data partitions, six-parameter parsimony methods show a consistently positive relationship between congruence and accuracy. Unlike successive weighting, six-parameter parsimony methods were not strongly influenced by the starting tree.
authors.affiliation: Zoology Department, Duke University, Durham, North Carolina 27708-0325, USA. cliff@duke.edu
authors.forename: C W
authors.initials: CW
authors.lastname: Cunningham
mesh_terms: D000818:Animals; D001699:Biometry / Q000379:methods*; D003062:Codon / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D003627:Data Interpretation, Statistical; D016013:Likelihood Functions; D008957:Models, Genetic; D009115:Muridae / Q000145:classification / Q000235:genetics; D010542:Peromyscus / Q000145:classification / Q000235:genetics; D010802:Phylogeny
chemical_list: D003062:Codon; D004272:DNA, Mitochondrial