Mammalian genes as molecular clocks?

SummaryIn 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.

[1]  K. Turksen,et al.  Isolation and characterization , 2006 .

[2]  F. Sanger,et al.  Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. , 1982, Journal of molecular biology.

[3]  Koike Katsuro,et al.  Nucleotide sequence and evolution of the rat mitochondrial cytochrome b gene containing the ochre termination codon , 1982 .

[4]  K. Koike,et al.  Nucleotide sequences of small ribosomal RNA and adjacent transfer RNA genes in rat mitochondrial DNA. , 1981, Gene.

[5]  K. Koike,et al.  Nucleotide sequence of a cloned fragment of rat mitochondrial DNA containing the replication origin. , 1980, Gene.

[6]  H. Feldmann,et al.  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 , 1981, Current Genetics.

[7]  W. Brown,et al.  Rapid evolution of animal mitochondrial DNA. , 1979, Proceedings of the National Academy of Sciences of the United States of America.

[8]  S. Nakanishi,et al.  Isolation and Characterization of the Bovine Corticotropin/β-Lipotropin Precursor Gene , 2005 .

[9]  R. Watson,et al.  Restriction endonuclease cleavage maps of rat and mouse mitochondrial DNAs. , 1977, Nucleic acids research.

[10]  A. C. Chang,et al.  Structural organization of human genomic DNA encoding the pro-opiomelanocortin peptide. , 1980, Proceedings of the National Academy of Sciences of the United States of America.

[11]  M. Taira,et al.  Nucleotide sequence and evolution of the rat mitochondrial cytochrome b gene containing the ochre termination codon. , 1982, Gene.

[12]  C. Saccone,et al.  The nucleotide sequences of several tRNA genes from rat mitochondria: common features and relatedness to homologous species. , 1982, Nucleic acids research.

[13]  G. Serio,et al.  A new method for calculating evolutionary substitution rates , 2005, Journal of Molecular Evolution.

[14]  H. Goodman,et al.  Most of the coding region of rat ACTHβ–LPH precursor gene lacks intervening sequences , 1980, Nature.

[15]  T. Miyata,et al.  Molecular clock of silent substitution: At least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes , 1982, Journal of Molecular Evolution.

[16]  F. Sanger,et al.  Sequence and organization of the human mitochondrial genome , 1981, Nature.

[17]  Koike Katsuro,et al.  Nucleotide sequences of small ribosomal RNA and adjacent transfer RNA genes in rat mitochondrial DNA. , 1981 .

[18]  M. Mishina,et al.  Isolation and characterization of the mouse corticotropin‐β‐lipotropin precursor gene and a related pseudogene , 1983, FEBS letters.

[19]  Koike Katsuro,et al.  Nucleotide sequence of a cloned fragment of rat mitochondrial DNA containing the replication origin. , 1980 .

[20]  Allan C. Wilson,et al.  Mitochondrial DNA sequences of primates: Tempo and mode of evolution , 2005, Journal of Molecular Evolution.

[21]  C. Saccone,et al.  Non-random patterns of nucleotide substitutions and codon strategy in the mammalian mitochondrial genes coding for identified and unidentified reading frames. , 1983, Biochemistry international.

[22]  D. A. Clayton,et al.  Sequence and gene organization of mouse mitochondrial DNA , 1981, Cell.