Construction of molecular evolutionary phylogenetic trees from DNA sequences based on minimum complexity principle.
Ever since the discovery of a molecular clock, many methods have been developed to reconstruct the molecular evolutionary phylogenetic trees. In this paper, we deal with the problem from the viewpoint of an inductive inference and apply Rissanen's minimum description length principle to extract the minimum complexity phylogenetic tree. Our method describes the complexity of the molecular phylogenetic tree by three terms which are related to the tree topology, the sum of the branch lengths and the difference between the model and the data measured by logarithmic likelihood. Five mitochondrial DNA sequences, from the human, the common chimpanzee, the pygmy chimpanzee, the gorilla and the orangutan, are used for investigating the validity of this method. It is suggested that this method might be superior to the traditional method in that it still shows good accuracy even near the root of phylogenetic trees.
Ren
F
F
Department of Information Medicine, Medical Research Institute, Tokyo Medical and Dental University, Japan.
Tanaka
H
H
Gojobori
T
T
D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D005075:Biological Evolution; D004272:DNA, Mitochondrial / Q000235:genetics; D006071:Gorilla gorilla / Q000235:genetics; D015186:Hominidae / Q000235:genetics; D006801:Humans; D016013:Likelihood Functions; D008967:Molecular Biology; D002679:Pan troglodytes / Q000235:genetics; D010363:Pattern Recognition, Automated; D010802:Phylogeny; D011148:Pongo pygmaeus / Q000235:genetics; D011323:Primates / Q000235:genetics*; D011381:Programming Languages; D015203:Reproducibility of Results; D012984:Software
D004272:DNA, Mitochondrial