Molecular Clock of Viral Evolution, and the Neutral Theory

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 1990 Dec 1

PMID 2263602

Citations 80

Authors

T Gojobori

E N Moriyama

M Kimura

Affiliations

Soon will be listed here.

Abstract

Evolution of viral genes is characterized by enormously high speed compared with that of nuclear genes of eukaryotic organisms. In this paper, the evolutionary rates and patterns of base substitutions are examined for retroviral oncogenes, human immunodeficiency viruses (HIV), hepatitis B viruses (HBV), and influenza A viruses. Our results show that the evolutionary process of these viral genes can readily be explained by the neutral theory of molecular evolution. In particular, the neutral theory is supported by our observation that synonymous substitutions always much predominate over nonsynonymous substitutions, even though the substitution rate varies considerably among the viruses. Furthermore, the exact correspondence between the high rates of evolutionary base substitutions and the high rates of production of mutants in RNA viruses fits very nicely to the prediction of the theory. The linear relationship between substitution numbers and time was examined to evaluate the clock-like property of viral evolution. The clock appears to be quite accurate in the influenza A viruses in man.

Citing Articles

Examining the molecular clock hypothesis for the contemporary evolution of the rabies virus.

Durrant R, Cobbold C, Brunker K, Campbell K, Dushoff J, Ferguson E PLoS Pathog. 2024; 20(11):e1012740.

PMID: 39585914 PMC: 11627394. DOI: 10.1371/journal.ppat.1012740.

A sequence-based evolutionary distance method for Phylogenetic analysis of highly divergent proteins.

Cao W, Wu L, Xia X, Chen X, Wang Z, Pan X Sci Rep. 2023; 13(1):20304.

PMID: 37985846 PMC: 10662474. DOI: 10.1038/s41598-023-47496-9.

Neutral theory and beyond: A systematic review of molecular evolution education.

Forsythe D, Hsu J Ecol Evol. 2023; 13(8):e10365.

PMID: 37529584 PMC: 10375367. DOI: 10.1002/ece3.10365.

A variant-dependent molecular clock with anomalous diffusion models SARS-CoV-2 evolution in humans.

Goiriz L, Ruiz R, Garibo-I-Orts O, Conejero J, Rodrigo G Proc Natl Acad Sci U S A. 2023; 120(30):e2303578120.

PMID: 37459528 PMC: 10372551. DOI: 10.1073/pnas.2303578120.

L-shaped distribution of the relative substitution rate (c/μ) observed for SARS-COV-2's genome, inconsistent with the selectionist theory, the neutral theory and the nearly neutral theory but a near-neutral balanced selection theory: Implication on....

Wu C, Paradis N, Lakernick P, Hryb M Comput Biol Med. 2023; 153:106522.

PMID: 36638615 PMC: 9814386. DOI: 10.1016/j.compbiomed.2022.106522.

References

Kimura M . Evolutionary rate at the molecular level. Nature. 1968; 217(5129):624-6. DOI: 10.1038/217624a0. View

Gojobori T, Moriyama E, Ina Y, Ikeo K, Miura T, Tsujimoto H . Evolutionary origin of human and simian immunodeficiency viruses. Proc Natl Acad Sci U S A. 1990; 87(11):4108-11. PMC: 54056. DOI: 10.1073/pnas.87.11.4108. View

Miyata T, Yasunaga T, Obata M, Honjo T . Nucleotide sequence divergence of mouse immunoglobulin gamma 1 and gamma 2b chain genes and the hypothesis of intervening sequence-mediated domain transfer. Proc Natl Acad Sci U S A. 1980; 77(4):2143-7. PMC: 348668. DOI: 10.1073/pnas.77.4.2143. View

Li W, Gojobori T, Nei M . Pseudogenes as a paradigm of neutral evolution. Nature. 1981; 292(5820):237-9. DOI: 10.1038/292237a0. View

Holland J, Spindler K, Horodyski F, Grabau E, Nichol S, VandePol S . Rapid evolution of RNA genomes. Science. 1982; 215(4540):1577-85. DOI: 10.1126/science.7041255. View

Gojobori T, Yokoyama S . Rates of evolution of the retroviral oncogene of Moloney murine sarcoma virus and of its cellular homologues. Proc Natl Acad Sci U S A. 1985; 82(12):4198-201. PMC: 397963. DOI: 10.1073/pnas.82.12.4198. View

Gojobori T, Yokoyama S . Molecular evolutionary rates of oncogenes. J Mol Evol. 1987; 26(1-2):148-56. DOI: 10.1007/BF02111288. View

Kimura M . Molecular evolutionary clock and the neutral theory. J Mol Evol. 1987; 26(1-2):24-33. DOI: 10.1007/BF02111279. View

Saitou N, Nei M . Polymorphism and evolution of influenza A virus genes. Mol Biol Evol. 1986; 3(1):57-74. DOI: 10.1093/oxfordjournals.molbev.a040381. View

10.

Nei M, Gojobori T . Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol. 1986; 3(5):418-26. DOI: 10.1093/oxfordjournals.molbev.a040410. View

11.

Hayashida H, Toh H, Kikuno R, Miyata T . Evolution of influenza virus genes. Mol Biol Evol. 1985; 2(4):289-303. DOI: 10.1093/oxfordjournals.molbev.a040352. View

12.

Li W, Tanimura M, Sharp P . Rates and dates of divergence between AIDS virus nucleotide sequences. Mol Biol Evol. 1988; 5(4):313-30. DOI: 10.1093/oxfordjournals.molbev.a040503. View

13.

Yokoyama S . Molecular evolution of the human and simian immunodeficiency viruses. Mol Biol Evol. 1988; 5(6):645-59. DOI: 10.1093/oxfordjournals.molbev.a040520. View

14.

Orito E, Mizokami M, Ina Y, Moriyama E, Kameshima N, Yamamoto M . Host-independent evolution and a genetic classification of the hepadnavirus family based on nucleotide sequences. Proc Natl Acad Sci U S A. 1989; 86(18):7059-62. PMC: 297993. DOI: 10.1073/pnas.86.18.7059. View

15.

Temin H . Retrovirus variation and evolution. Genome. 1989; 31(1):17-22. DOI: 10.1139/g89-007. View

16.

Kimura M . Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature. 1977; 267(5608):275-6. DOI: 10.1038/267275a0. View