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Molecular clock of silent substitution: At least six-fold preponderance of silent changes in mitochondrial genes over those in nuclear genes

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Summary

For each of eleven different types of nuclear genes, comparisons of the protein coding sequences were made between human, mouse and rat pairwisely, and the evolutionary rate of silent substitution, v nucl.S , was estimated. It is shown that the v nucl.S is not only very high (=5.37×10−9/site/yr), but also approximately uniform for different genes regardless of the types, which confirms our previous results (Miyata et al. 1980b). This is in sharp contrast to the rate of protein evolution which differes greatly from protein to protein. Furthermore the v nucl.S is shown to be approximately constant with respect to different divergence times, at least within a short time period (≤75 Myr). Based on these observations, we propose a new molecular clock which has several advantages over a protein clock. Using this clock, we show that the rate of amino acid replacement in the immunoglobulin Ck gene of b4 rabbit is unexpectedly high, almost comparable to the rate of silent changes. This rate may be the highest one for protein evolution that we know so far. We further examine the rate of silent substitutions in mitochondrial genes comparing mouse and rat. Surprisingly the rate is extremely high (≥35×10−9/site/yr), at least 6-times as high as the corresponding rate of nuclear genes. Based on the estimate, we discuss a possible origin of the rapid rate found in mitochondrial DNA.

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Abbreviations

URF:

Unidentified reading frame

yr:

Year

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Authors and Affiliations

  1. Department of Biology, Faculty of Science, Kyushu University, 812, Fukuoka, Japan

    Takashi Miyata, Hidenori Hayashida & Reiko Kikuno

  2. The Institute of Statistical Mathematics, 4-6-7 Minami-Azabu, Minato-ku, 106, Tokyo, Japan

    Masami Hasegawa

  3. Cancer Institute, Japanese Foundation for Cancer Research, Toshima-ku, 170, Tokyo, Japan

    Midori Kobayashi & Katsuro Koike

Authors
  1. Takashi Miyata
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  2. Hidenori Hayashida
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  3. Reiko Kikuno
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  4. Masami Hasegawa
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  5. Midori Kobayashi
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  6. Katsuro Koike
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Miyata, T., Hayashida, H., Kikuno, R. et al. 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 (1982). https://doi.org/10.1007/BF02100221

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