In analyzing the silent nucleotide substitutions in some mammalian mitochondrial mRNA coding genes, we had found that the frequency of each of the four nucleotides in rat, mouse, and cow, but not in humans, is the same in the silent third codon position (Lanave C, Preparata G, Saccone C, Serio G (1984) J Mol Evol 20:86-93). Because our findings for these three species were compatible with a stationary Markov process for the evolution of nucleotide sequences, we applied such a model to calculate the effective evolutionary silent substitution rate (vs) and the divergence times among the species. In this paper we have analyzed the first and second codon positions in the same mammalian mitochondrial genes. We found that in the first and second codon positions the human mitochondrial genes satisfy the stationarity conditions. This has allowed us to use the stochastic model mentioned above to calculate the divergence times among mouse, rat, cow, and human. Furthermore, we have analyzed the silent substitution rate in one nuclear gene for these four mammals. We found that in this gene the effective silent substitution rate is about 3 times lower than in mitochondrial genes, and that humans are in this case stationary with respect to the other three mammals in the third codon position as well. Application of our Markov model to this latter gene yields divergence times consistent with our previous determinations.
Key wordsMolecular evolution Evolution of mitochondrial genes Evolution of nuclear genes Stochastic Markov chain Monte Carlo Simulation
Unable to display preview. Download preview PDF.
- Cantatore P, De Benedetto C, Gadaleta G, Gallerani R, Kroon AM, Holtrop M, Lanave C, Pepe G, Quagliariello C, Saccone C, Sbisà E (1982) The nucleotide sequences of several tRNA genes from rat mitochondria: common features and relatedness to homologous species. Nucleic Acids Res 10:3279–3289PubMedGoogle Scholar
- Chang ACY, Cochet M, Cohen SN (1980) Structural organization of human genomic DNA encoding the pro-opiomelano-cortin peptide. Proc Natl Acad Sci USA 77:4890–4894Google Scholar
- Dayhoff MO (1978) In: Dayhoff MD (ed) Atlas of protein sequence and structure. Vol. 5, Suppl 3. National Biomedical Research Foundation, Silver Spring, Maryland, pp 1–414Google Scholar
- Pepe G, Holtrop M, Gadaleta G, Kroon AM, Cantatore P, Gallerani R, De Benedetto C, Quagliariello C, Sbisà E, Saccone C (1983) Non-random patterns of nucleotide substitutions and codon strategy in the mammalian mitochondrial genes coding for identified and unidentified reading frames. Biochem Int 6:553–563PubMedGoogle Scholar
- Saccone C, De Benedetto C, Gadaleta G, Lanave C, Pepe G, Sbisà E, Cantatore P, Gallerani R, Quagliariello C, Holtrop M, Kroon AM (1983) Studies on the evolutionary history of the mammalian mitochondrial genome. In: Nagley P, Linnane AW, Peacock WJ, Pateman JA (eds) Manipulation and expression of genes in eukaryotes. Academic Press, Sydney, in pressGoogle Scholar