Rates of Nucleotide Substitution in Primates and Rodents and the Generation–Time Effect Hypothesis
Abstract
DNA sequence data from introns, flanking regions, and the eta globin pseudogene region all show a significantly higher rate of nucleotide substitution in the Old World monkey lineage than in the human lineage after the separation of the two lineages, or, in other words, the data support the hominoid rate-slowdown hypothesis. Data from both protein sequences and DNA sequences show that the rate of evolution is significantly higher in the rodent lineage than in the primate lineage. Furthermore, DNA sequences from introns show that the rate of nucleotide substitution is at least two times higher in rodents than in higher primates. The male-to-female ratio of mutation rate is estimated to be between 3 and 6 in higher primates, whereas it is only 2 in mice and rats. These ratios are similar to the corresponding male-to-female ratios of germ cell divisions in higher primates and in rodents, suggesting that errors in DNA replication during germ cell division are the primary source of mutation, or, in other words, mutation is largely DNA replication-dependent. This conclusion provides further support for the generation-time effect hypothesis.
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The substitution rate in murid rodents is, on average, two to three times faster than the rate in hominid primates (apes and humans).
“For example, the substitution rate in murid rodents is, on average, two to three times faster than the rate in hominid primates (apes and humans) 32 .”
From The modern molecular clock (2003) · cites this paper as [32]
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LIFE HISTORY AND THE MALE MUTATION BIAS
Bartosch-Härlid, A., Berlin, S., Smith, N. G. C., Møller, A. P., & Ellegren, H. (2003) · Evolution · doi:10.1554/03-036 · Cited by 99 · see citing works
“Notable examples include the hominoid rateslow-down hypothesis (Li et al. 1996), which is consistent with an effect of generation time, the negative correlation between body size and rate of molecular evolution seen in a variety of taxa (Martin and Palumbi 1993a; Bromham 2002) and the slower rate…”
BackgroundResultGenomic analysis of orthologous mouse and human olfactory receptor loci
Lane, R. P., Cutforth, T., Young, J. M., Athanasiou, M., Friedman, C. L., Rowen, L., Evans, G. A., Axel, R., Hood, L., & Trask, B. J. (2001) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.131215398 · Cited by 98 · see citing works
Lercher, M. J., Williams, E. J. B., & Hurst, L. D. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003744 · Cited by 97 · see citing works
“Just this method has been applied for flies (Bauer and Aquadro 1997), rodents (Chang et al. 1994; Chang and Li 1995; Li et al. 1996; McVean and Hurst 1997; Smith and Hurst 1999a), cats (Slattery and O’Brien 1998), birds (Ellegren and Fridolfsson 1997), and primates (Shimmin, Chang, and Li 1993,…”
BackgroundMethodEvolution of genes and taxa: a primer
Doyle, J. J., & Gaut, B. S. (2000) · Plant Molecular Biology · doi:10.1023/a:1006349518932 · Cited by 95 · see citing works
“The extent to which either the time-calibrated clock or the generation-time clock holds is unclear, despite extensive empirical efforts [149, 82, 23, 83].”
BackgroundMcGowen, M. R., Grossman, L. I., & Wildman, D. E. (2012) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2012.0869 · Cited by 100 · see citing works
Heterogeneous Genomic Molecular Clocks in Primates
Kim, S., Elango, N., Warden, C., Vigoda, E., & Yi, S. V. (2006) · PLoS Genetics · doi:10.1371/journal.pgen.0020163 · Cited by 92 · see citing works
“consequence of the difference in generation times, evolutionary rates of replication-dependent substitutions are slower in hominoids than in Old World monkeys [2,4,25].”
BackgroundKAYANG, B. B., Fillon, V., Inoue‐Murayama, M., Miwa, M., Leroux, S., Fève, K., Monvoisin, J. L., Frédérique Pitel, A., Vignoles, M., Mouilhayrat, C., et al. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-101 · Cited by 93 · see citing works
“Similar times of divergence can be found between humans and New World monkeys (35 million years) or humans and Old World monkeys (30 million years) [31], for which numerous interchromosomal events have been documented [32,33].”
BackgroundTomasco, I. H., & Lessa, E. P. (2011) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2011.06.014 · Cited by 93 · see citing works
“…allow us to reject alternative, non-selectionist explanations of rate variation, such as a relaxation of purifying selection, variation in metabolic rate, body mass, population size, and generation time among lineages (Bromham et al., 1996; Li et al., 1996; Martin, 1995; Martin and Palumbi, 1993).”
BackgroundLartillot, N., & Delsuc, F. (2011) · Evolution · doi:10.1111/j.1558-5646.2011.01558.x · Cited by 92 · see citing works
PHYLOGEOGRAPHY OF THE PLANKTONIC CHAETOGNATH SAGITTA SETOSA REVEALS ISOLATION IN EUROPEAN SEAS
Peijnenburg, K. T. C. A., Breeuwer, J. A. J., Pierrot-Bults, A. C., & Menken, S. B. J. (2004) · Evolution · doi:10.1111/j.0014-3820.2004.tb01728.x · Cited by 91 · see citing works
Insights from human/mouse genome comparisons
Pennacchio, L. A. (2003) · Mammalian Genome · doi:10.1007/s00335-002-4001-1 · Cited by 86 · see citing works
“While it remains unclear why this has occurred, one possible explanation is the shorter generation time and consequent increased amount of selection in mice relative to humans (Li et al. 1996).”
BackgroundComparative analysis of protein coding sequences from human, mouse and the domesticated pig
Jørgensen, F. G., Hobolth, A., Hornshøj, H., Bendixen, C., Fredholm, M., & Schierup, M. H. (2005) · BMC Biology · doi:10.1186/1741-7007-3-2 · Cited by 84 · see citing works
“For a more thorough discussion of the generation time hypothesis in mammals see [43].”
Genetic structure of fragmented populations of red squirrel (Sciurus vulgaris) in the UK
Barratt, E. M., Gurnell, J., Malarky, G., Deaville, R. C., & Bruford, M. W. (1999) · Molecular Ecology · doi:10.1046/j.1365-294x.1999.00771.x · Cited by 85 · see citing works
The Mouse Lemur, a Genetic Model Organism for Primate Biology, Behavior, and Health
Ezran, C., Karanewsky, C. J., Pendleton, J. L., Sholtz, A., Biermann, M. R., Willick, J., Razafindrakoto, A., Zohdy, S., Albertelli, M. A., & Krasnow, M. A. (2017) · Genetics · doi:10.1534/genetics.116.199448 · Cited by 81 · see citing works
Why does dosage compensation differ between XY and ZW taxa?
Naurin, S., Hansson, B., Bensch, S., & Hasselquist, D. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.11.006 · Cited by 79 · see citing works
- Authors
- Li, W.-H., Ellsworth, D. L., Krushkal, J., Chang, B. H.-J., & Hewett-Emmett, D.
- Affiliations
- The University of Texas Health Science Center at Houston (US)
- Venue
- Molecular Phylogenetics and Evolution
- Publisher
- Elsevier BV
- Published
- 1996-02
- Volume
- 5
- Issue
- 1
- Pages
- 182-187
- ISSN
- 1055-7903 (ISSN-L)
- OpenAlex
- W2068919087
- Cited by
- 335
- References
- 0
- Citations by year
- 2026: 3 · 2025: 5 · 2024: 3 · 2023: 8 · 2022: 10 · 2021: 6 · 2020: 4 · 2019: 5 · 2018: 11 · 2017: 11 · 2016: 9 · 2015: 6 · 2014: 9 · 2013: 17 · 2012: 9
- FWCI
- 10.99
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Molecular Phylogenetics and Evolution (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Physical Sciences › Earth and Planetary Sciences › Paleontology › Evolution and Paleontology Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Keywords
- nucleotide substitution rates, Old World monkeys, hominoid evolution, rodent evolution, primate evolution, introns, DNA replication errors, mutation rate
- MeSH terms
- Animals, DNA, Female, Globins, Humans, Introns, Male, Models, Genetic, Mutation, Primates, Pseudogenes, Rodentia, Sex Chromosomes, Time Factors, Hominidae, Evolution, Molecular, Mice, Rats
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