Evolutionary analysis of DNA-Protein-Coding Regions based on a genetic code cube metric

The right estimation of the evolutionary distance between DNA or protein sequences is the cornerstone of the current phylogenetic analysis based on distance methods. Herein, it is demonstrated that the Manhattan distance (d_w), weighted by the evolutionary importance of the nucleotide bases in the codon, is a naturally derived metric in the standard genetic code cube inserted into the three-dimensional Euclidean space. Based on the application of distance d_w, a novel evolutionary model is proposed. This model includes insertion/deletion mutations that are very important for cancer studies, but usually discarded in classical evolutionary models. In this study, the new evolutionary model was applied to the phylogenetic analysis of the DNA protein-coding regions of 13 mammal mitochondrial genomes and of four cancer genetic-susceptibility genes (ATM, BRCA1, BRCA2 and p53) from nine mammals. The opossum (a marsupial) was used as an out-group species for both sets of sequences. The new evolutionary model yielded the correct topology, while the current models failed to separate the evolutionarily distant species of mouse and opossum.