Summary
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.
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Abbreviations
- B:
-
cow
- H:
-
human
- M:
-
mouse
- mt:
-
mitochondrial
- MY:
-
milion years
- R:
-
rat
References
Anderson S, Bankier AT, Barrell GB, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–464
Anderson S, de Bruijn MHL, Coulson AR, Eperon IC, Sanger F, Young IG (1982) Complete sequence of bovine mitochondrial DNA. J Mol Biol 156:683–717
Bibb MJ, van Etten RA, Wright CT, Walberg MW, Clayton DA (1981) Sequence and gene organization of mouse mitochondrial DNA. Cell 26:167–180
Brown WM, George M Jr, Wilson AC (1979) Rapid evolution of animal mitochondrial DNA. Proc Natl Acad Sci USA 76: 1967–1971
Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 18:225–239
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 10:3279–3289
Chang ACY, Cochet M, Cohen SN (1980) Structural organization of human genomic DNA encoding the pro-opiomelano-cortin peptide. Proc Natl Acad Sci USA 77:4890–4894
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 1–414
Drouin J, Goodman HM (1980) Most of the coding region of rat acth-beta-lph precursor gene lacks intevening sequences. Nature 288:610–613
Grosskopf R, Feldman H (1981) Analysis of a DNA segment from rat liver mitochondria containing the genes for the cytochrome oxidase subunits I, II and III, ATPase subunit 6 and several tRNA genes. curr Genet 4:151–158
Kobayashi M, Seki T, Yaginuma K, Koike K (1981) Nucleotide sequences of small ribosomal RNA and adjacent transfer RNA genes in rat mitochondrial DNA. Gene 16:297–307
Koike K, Kobayashi M, Yaginuma K, Taira M, Yoshida E, Imai M (1982) Nucleotide sequence and evolution of the rat mitochondrial cytochrome b gene containing the ochre termination codon. Gene 20:177–185
Lanave C, Preparata G, Saccone C, Serio G (1984) A new method for calculating evolutionary substitution rates. J Mol Evol 20:86–93
Miyata T, Hayashida H, Kikuno R, Hasegawa M, Kobayashi M, Koike K (1982) Molecular clock of silent substitution: at least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes. J Mol Evol 19:28–35
Nakanishi S, Taranishi Y, Watanabe Y, Notake Y, Noda M, Kakidani H, Jingami H, Numa S (1981) Isolation and characterization of the bovine corticotropin/beta lipotropin precursor gene. Eur J Biochem 115:429–438
Notake M, Tobimatsu T, Watanabe Y, Takahashi H, Mishina M, Numa S (1983) Isolation and characterization of the mouse corticotropin-beta-lipotropin precursor gene and a related pseudogene. FEBS Lett 156:67–71
Parker RC, Watson RM (1977) Restriction endonuclease cleavage maps of rat and mouse mitochondrial DNAs. Nucleic Acids Res 4:1291–1299
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 6:553–563
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 press
Sekiya T, Kobayashi M, Seki T, Koike K (1980) Nucleotide sequence of a cloned fragment of rat mitochondrial DNA containing the replication origin. Gene 11:53–62
Wilson AC, Carlson SS, White TJ (1977) Biochemical evolution. Annu Rev Biochem 46:573–639
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Lanave, C., Preparata, G. & Saccone, C. Mammalian genes as molecular clocks?. J Mol Evol 21, 346–350 (1985). https://doi.org/10.1007/BF02115653
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DOI: https://doi.org/10.1007/BF02115653