title: The phylogenetic utility of the codon-degeneracy model.
abstract: The codon-degeneracy model (CDM) predicts relative frequencies of substitution for any set of homologous protein-coding DNA sequences based on patterns of nucleotide degeneracy, codon composition, and the assumption of selective neutrality. However, at present, the CDM is reliant on outside estimates of transition bias. A new method by which the power of the CDM can be used to find a synonymous transition bias that is optimal for any given phylogenetic tree topology is presented. An example is illustrated that utilizes optimized transition biases to generate CDM GF-scores for every possible phylogenetic tree for pocket gophers of the genus Orthogeomys. The resulting distribution of CDM GF-scores is compared and contrasted with the results of maximum parsimony and maximum likelihood methods. Although convergence on a single tree topology by the CDM and another method indicates greater support for that particular tree, the value of CDM GF-score as the sole optimality criterion for phylogeny reconstruction remains to be determined. It is clear, however, that the a priori estimation of an optimum transition bias from codon composition has a direct application to differentiating between alternative trees.
authors.affiliation: Department of Biological Sciences and Museum of Natural Science, Louisiana State University, Baton Rouge, LA 70803, USA.
authors.forename: D A
authors.initials: DA
authors.lastname: McClellan
mesh_terms: D000818:Animals; D001699:Biometry; D003062:Codon / Q000235:genetics*; D004247:DNA / Q000235:genetics; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D012377:Rodentia / Q000235:genetics
chemical_list: D003062:Codon; D004247:DNA