title: New weighting methods for phylogenetic tree reconstruction using multiple loci.
abstract: Efficient determination of evolutionary distances is important for the correct reconstruction of phylogenetic trees. The performance of the pooled distance required for reconstructing a phylogenetic tree can be improved by applying large weights to appropriate distances for reconstructing phylogenetic trees and small weights to inappropriate distances. We developed two weighting methods, the modified Tajima-Takezaki method and the modified least-squares method, for reconstructing phylogenetic trees from multiple loci. By computer simulations, we found that both of the new methods were more efficient in reconstructing correct topologies than the no-weight method. Hence, we reconstructed hominoid phylogenetic trees from mitochondrial DNA using our new methods, and found that the levels of bootstrap support were significantly increased by the modified Tajima-Takezaki and by the modified least-squares method.
authors.affiliation: Research Program for Computational Science, Research and Development Group for Next-generation Integrated Living Matter Simulation, Fusion of Data and Analysis Research and Development Team, RIKEN, 1-7-22 Suehiro-cho, Tsurumi, Yokohama 230-0045, Japan. kazumisawa@riken.jp
authors.forename: Kazuharu
authors.initials: K
authors.lastname: Misawa
authors.forename: Fumio
authors.initials: F
authors.lastname: Tajima
mesh_terms: D000818:Animals; D003198:Computer Simulation; D003627:Data Interpretation, Statistical; D050259:Genes, Mitochondrial; D056426:Genetic Loci; D015186:Hominidae / Q000145:classification / Q000235:genetics*; D006801:Humans; D016018:Least-Squares Analysis; D008957:Models, Genetic; D058885:Multilocus Sequence Typing; D010802:Phylogeny; D016012:Poisson Distribution; D016415:Sequence Alignment