Log-correlation Distance And Fourier Transform With Kullback-Leibler Divergence Distance For Construction Of Vertebrate Phylogeny Using Complete Mitochondrial Genomes

Abstract

For vertebrate mitochondrial genomes, some phylogenies have been built by various methods with or without sequence alignment. These methods are important for the problem of classification and evolution. In this paper, we propose two approaches to analyze the phylogenetic relationship of 64 vertebrates using complete mitochondrial genomes without sequence alignment. The first approach combines discrete Fourier transform (DFT) with Kullback-Leibler divergence (KLD) distance. The second one directly uses a log-correlation distance. Both methods are based on compositional vectors of DNA sequences or protein sequences from the complete genome. The phylogenetic trees show that the mitochondrial genomes are separated into three major groups. One group corresponds to mammals; one group corresponds to fish; and the other one is Archosauria (including birds and reptiles). In particular, the structure of the tree based on log-correlation distance are roughly in agreement in topology with the current known phylogenies of vertebrates.