ABSTRACT
Modeling nucleotide evolution, or the substitutions of the nucleotides of a DNA sequence by other nucleotides throughout evolution, is important both conceptually and methodologically. First, measuring nucleotide substitutions provides an idea of how complex and what consequences the mutation of a particular nucleotide site has on: (a) the regulatory expression of a gene (if the mutation happens to
occur in the promoter of such a gene), (b) on the structure of a protein (if the mutation affects a protein-coding DNA sequence and yields a different amino acid sequence), and (c) on the tempo and mode of evolution of a particular species. Second, measuring nucleotide differences between species is the fi rst step in building distance matrices that are crucial to draw and understand the phylogenetic relationships between species-ultimately determining the natural history of a collection of species.
