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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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“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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Braverman, J. M., Hamilton, M. B., & Johnson, B. A. (2016) · Journal of Molecular Evolution · doi:10.1007/s00239-016-9752-x · Cited by 1
“…effects on synonymous substitution rates have been widely observed at multiple loci for mammalian species (Kimura 1983; Wu and Li 1985; Li et al. 1987; Ohta 1993, 1995; Li et al. 1996; Pesole et al. 1999; Gissi et al. 2000; Kumar and Subramanian 2002; Kim et al. 2006; Tsantes and Steiper 2009).”
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Wang, C. Y., & Leung, F. C.-C. (2007) · Poultry Science · doi:10.1093/ps/86.3.453 · Cited by 1
“, 1999), probably because of generation time (Laird et al., 1969; Li et al., 1996) or body size (Martin and Palumbi, 1993; Bromham, 2002).”
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Thornlow, B. P., Armstrong, J. C., Holmes, A., Corbett-Detig, R. B., & Lowe, T. M. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/661942 · Cited by 1
Mutation and Diversity in Avian Sex Chromosomes
Sundström, H. (2003) · Uppsala University Publications (Uppsala University) · Cited by 1
Bergeault, K. (2010) · theses.fr (ABES) · doi:10.70675/ad0a0bc4z037ez4d39zaefbz66c7e48b1b2d · Cited by 1
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Hucks, D. (2008) · UTA ResearchCommons (University of Texas Arlington)
(2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.014
Romano, C. M. (2009) · Digital Library of Theses and Dissertations (Universidade de São Paulo) · doi:10.11606/t.42.2009.tde-29012010-105745
Krieger, J., & Fuerst, P. A. (2008) · Springer eBooks · doi:10.1007/978-1-4020-8437-9_4
“Characteristics of sturgeons and paddlefish that have been proposed previously to account for slow rates of molecular evolution in other taxa include long generation time (Kohne, 1970; Li et al., 1987; Ohta, 1993; Mooers and Harvey, 1994; Li et al., 1996) and low metabolic rate (Martin and Palumbi, 1993; Martin, 1999).”
BackgroundBromham, L. D. (2013) · Encyclopedia of Life Sciences · doi:10.1002/9780470015902.a0001802.pub3
Sterner, K. N., & Wildman, D. E. (2011) · Journal of Human Evolution · doi:10.1016/j.jhevol.2011.02.003
Norris, K. J., & Pain, D. J. (2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.001
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Cooper, N. (2013) · Figshare · doi:10.6084/m9.figshare.650217.v1
“2008), the most famous examples being “slow” primates (especially hominoids) and “fast” rodents (Li et al. 1996).”
BackgroundMachado, J. P. (2014) · Portuguese National Funding Agency for Science, Research and Technology (RCAAP Project by FCT) · doi:10.34626/mt58-1180
Vuillaumier, S., Lapouméroulie, C., Lehn, P., et al. (1997) · médecine/sciences · doi:10.4267/10608/436
“concernant l’accélération des taux d’évolution des régions flanquantes et des introns de nombreux gènes chez les rongeurs par rapport aux primates [8].”
BackgroundTesting Patterns of Nucleotide Substitution Rates at Multiple Genes
Tao, W. X. (2002) · NCSU Libraries Repository (North Carolina State University Libraries)
LEGUMINOSAE) BASED ON NDHF AND RPLJ6 CHLOROPLAST GENE SEQUENCES1
Schnabel, A., & Wendel, J. F. (1998)
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Gao, Z., Wyman, M. J., Sella, G., & Przeworski, M. (2015) · arXiv (Cornell University) · doi:10.48550/arxiv.1507.06890
“Therefore, the general observation that substitution rate in mammals tends to decrease with increasing generation times [7,10,16] is not necessarily expected; in fact, its existence requires very specific conditions on ontogenesis to hold (shown in Fig 3B).”
BackgroundInfluentialTranscriptional and mutational signatures of the aging germlinePreprint
Witt, E., Langer, C. B., Svetec, N., & Zhao, L. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.11.22.469565
“Some studies have attributed excess paternal mutations to the increased number of cell divisions that cycling spermatogonial stem cells undergo throughout the life of the male (Drost and Lee, 1995; Gao et al., 2011; Li et al., 1996).”
Background(2012) · Wiley eBooks · doi:10.1002/9781119968535.refs
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Hoekstra, P. H. (2022) · doi:10.18174/565105
(2004) · Wiley eBooks · doi:10.1002/0471647527.refs
Suprovych, T. M., Suprovych, M. P., Бандура, В. В., et al. (2023) · Podilian Bulletin Agriculture Engineering Economics · doi:10.37406/2706-9052-2023-1.29
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Lo, B.-W., Lin, H.-F., Kong, S., Wu, W., Wang, S. C.-L., Lu, X., & Wang, H. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.10.22.619299
“Each round of male syconia is typically synchronized in a way such We observed a significantly higher substitution rate in W. sp. 2 than that of W. sp. 3 (Table 3), which is expected given the differences in generation time (Li et al. 1996).”
BackgroundModeling the Evolution of Ultraconserved Elements by Indels
Biller, P. D. N. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf299 · Cited by 1
Webb, A. E. (2015) · Dublin City University Open Access Institutional Repository (Dublin City University)
Xie, Z., Liu, J., Zhang, Y., Ma, X., Fan, B., Wang, S., Du, Z., & Wang, L. (2026) · International Journal of Biological Macromolecules · doi:10.1016/j.ijbiomac.2026.151114
Flight style and metabolism shape the tempo of genome evolution in birds
Ji, Y., Wu, L., Li, D., Feng, S., Fang, Q. F. Q., Xiong, Y., Chang, Y., Cooper, J. C., Yu, X., Zhang, K., et al. (2026) · PLoS Biology · doi:10.1371/journal.pbio.3003884
“For instance, animals with shorter generation times undergo more rounds of germline DNA replication and thus will accumulate more mutations [7,8].”
Inheritance of somatic mutations and epigenetic variations in plants
Rogo, U., Fambrini, M., & Pugliesi, C. (2026) · Plant Biology · doi:10.1111/plb.70270
“This pattern suggests that species with long lifespans, both plants and animals, have evolved adaptive mechanisms to mitigate the accumulation of deleterious somatic variants (Li et al .”
Always read the introduction : integrating regulatory and coding sequence evolution in yeast
Evangelisti, A. M. (2010) · UNM’s Digital Repository (University of New Mexico)
Carlson, A. (2007) · KU ScholarWorks (University of Kansas)
Latent variable models in statistical genetics
Oldmeadow, C. J. (2009)
Metadata
- 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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