title: Variation in the pattern of nucleotide substitution across sites.
abstract: A model of nucleotide substitution that allows the transition/transversion rate bias to vary across sites was constructed. We examined the fit of this model using likelihood-ratio tests by analyzing 13 protein coding genes and 1 pseudogene. Likelihood-ratio testing indicated that a model that allows variation in the transition/transversion rate bias across sites provided a significant improvement in fit for most protein coding genes but not for the pseudogene. When the analysis was repeated with parameters estimated separately for first, second, and third codon positions, strong heterogeneity was uncovered for the first and second codon positions; the variation in the transition/transversion rate was generally weaker at the third codon position. The transition rate bias and branch lengths are underestimated when variation in the transition/transversion rate was not accommodated, suggesting that it may be important to accommodate variation in the pattern of nucleotide substitution for accurate estimation of evolutionary parameters.
authors.affiliation: Laboratory of Molecular Systematics, Smithsonian Museum Support Center, 4210 Silver Hill Road, Suitland, MD 20746, USA. johnh@onyx.si.edu
authors.forename: J P
authors.initials: JP
authors.lastname: Huelsenbeck
authors.forename: R
authors.initials: R
authors.lastname: Nielsen
mesh_terms: D000818:Animals; D003062:Codon; D004272:DNA, Mitochondrial / Q000235:genetics; D019143:Evolution, Molecular; D005796:Genes; D014644:Genetic Variation; D006801:Humans; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D017354:Point Mutation; D011544:Pseudogenes
chemical_list: D003062:Codon; D004272:DNA, Mitochondrial