Ribosomal RNA Phylogeny Derived from a Correlation Model of Sequence Evolution

Present-day stochastic models of DNA sequence evolution assume independent and identically distributed nucleotide sites. However, it is well known that there exists correlation among nucleotides in a DNA sequence. We present a stochastic model of sequence evolution that takes into account the correlation of non—overlapping pairs of nucleotides. This model enables us to estimate the number of substitutions per nucleotide. As a biological example we re—analyze the phylogenetic tree of Metazoa based on small ribosomal subunit RNA.