Assessment of the accuracy of matrix representation with parsimony analysis supertree construction. Syst. Biol

Abstract.—Despite the growing popularity of supertree construction for combining phylogenetic in-formation to produce more inclusive phylogenies, large-scale performance testing of this method has not been done. Through simulation, we tested the accuracy of the most widely used supertree method, matrix representation with parsimony analysis (MRP), with respect to a (maximum parsi-mony) total evidence solution and a known model tree. When source trees overlap completely, MRP provided a reasonable approximation of the total evidence tree; agreement was usually>85%. Per-formance improved slightly when using smaller, more numerous, or more congruent source trees, and especially when elements were weighted in proportion to the bootstrap frequencies of the nodes they represented on each source tree (“weighted MRP”). Although total evidence always estimated the model tree slightly better than nonweighted MRP methods, weighted MRP in turn usually out-performed total evidence slightly. When source studies were even moderately nonoverlapping (i.e., sharing only three-quarters of the taxa), the high proportion of missing data caused a loss in resolu-tion that severely degraded the performance for all methods, including total evidence. In such cases, even combining more trees, which had positive effects elsewhere, did not improve accuracy. Instead, “seeding ” the supertree or total evidence analyses with a single largely complete study improve