Patterns of base composition within and between animal mitochondrial genomes

Nucleotide composition of a DNA molecule is a product of base substitution. Variation in nucleotide composition indicates a change in the pattern of substitution at either the level of the underlying mutational spectrum or the constraints imposed by natural selection. This work explores patterns of nucleotide usage within and between animal mitochondrial genomes and the evolutionary mechanisms that have shaped these patterns. Fourfold degenerate sites are expected to reflect the underlying mutational spectrum. Three simple measures of compositional bias, taking into account the strand-specific nature of nucleotide distribution in mtDNA, reveal considerable variation among fourfold degenerate sites of metazoan mitochondrial genomes. Log-linear analysis of intramolecular compositional patterns of mammalian mtDNA demonstrates that fourfold degenerate sites from even a single strand of the genome are not homogeneous. Rather, base composition varies among codon families and around the circular genome. A companion analysis of two additional taxonomic groups, molluscs and insects, also reveals compositional variation among codon families and between strands. The observed intramolecular variation cannot be explained solely by a simple strand-specific mutational pressure, but requires either a contextual bias to the mutational process or translational level natural selection as well. First and second codon position base composition and amino acid frequencies regressed on fourfold degenerate site composition show how mutational biases at the DNA level translate to amino acid biases in mitochondrial proteins