Cited by 338Evolution and Genetic DynamicsEvolution and Paleontology StudiesGenomics and Phylogenetic Studies

The DOI matches its Crossref record.

Rates of Nucleotide Substitution in Primates and Rodents and the Generation–Time Effect Hypothesis

Li, Wen-Hsiung, Ellsworth, Darrell L., Krushkal, Julia, Chang, Benny H.-J., Hewett-Emmett, David·1996·Molecular Phylogenetics and Evolution

DOI 10.1006/mpev.1996.0012

Open this paper in CoChat — free account

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.

Integrity signals

Registry

Crossref · 10.1006/mpev.1996.0012

Cites

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Sorted by citations

Items 201–300 of 338

Ligation detection reaction-TaqMan procedure for single nucleotide polymorphism detection on genomic DNA
Borodina, T. A., Lehrach, H. R., & Soldatov, A. V. (2004) · Analytical Biochemistry · doi:10.1016/j.ab.2004.05.032 · Cited by 20
Demographic Histories of ERV-K in Humans, Chimpanzees and Rhesus Monkeys
Romano, C. M., de Melo, F. L., Corsini, M. A. B., Holmes, E. C., & Zanotto, P. M. D. A. (2007) · PLoS ONE · doi:10.1371/journal.pone.0001026 · Cited by 20
“In particular, it has been established that the rate of evolution in humans suffered a slowdown relative to that of the chimpanzee [22,23], with an approximately two-fold reduction in evolutionary rate relative to Old World monkeys and chimpanzee [24].”
Genetic Structure of the French Red Squirrel Populations: Implication for Conservation
Dozières, A., Chapuis, J., Thibault, S., et al. (2012) · PLoS ONE · doi:10.1371/journal.pone.0047607 · Cited by 18
“Due to their short generation times and large effective population sizes, rodents usually show a high level of genetic diversity [39].”
Background
A Unifying Framework for Estimating Generation Time in Age-Structured Populations: Implications for Phylogenetics and Conservation Biology
Jonasson, J., Härkönen, T. J., Sundqvist, L., Edwards, S. V., & Hårding, K. C. (2022) · The American Naturalist · doi:10.1086/719667 · Cited by 20
“The effect of generation time on molecular evolutionary rates also makes it central to estimate divergence times on phylogenies (Easteal 1985; Martin and Palumbi 1993; Mooers and Harvey 1994; Li et al. 1996).”
Background
Adaptive evolution of the matrix extracellular phosphoglycoprotein in mammals
Machado, J. P., Johnson, W. E., O’Brien, S. J., Vasconcelos, V. M., & Antunes, A. (2011) · BMC Evolutionary Biology · doi:10.1186/1471-2148-11-342 · Cited by 18
“The results may also be biased by the mixing of species with long and short generation times [61], as well as the related long-branch-attraction effect in phylogenetic reconstruction.”
Background
Evolutionary dynamics of the ABCA chromosome 17q24 cluster genes in vertebrates
Li, G., Shi, P., & Wang, Y. (2006) · Genomics · doi:10.1016/j.ygeno.2006.07.015 · Cited by 18
“However, this explanation appears to be more parsimonious than the loss of ABCA8a from nonrodent lineages if we consider the accelerated mutation rate in rodents [35], which could lead to the Abca8a gene being as diverged from its progenitor (i.”
Background
Selecting sites for conservation
Balmford, A. P. (2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.006 · Cited by 17
Spatiotemporal population genetics of the endangered Perote ground squirrel (Xerospermophilus perotensis) in a fragmented landscape
Ochoa, A., Gasca‐Pineda, J., Ceballos, G., & Eguiarte, L. E. (2012) · Journal of Mammalogy · doi:10.1644/11-mamm-a-371.1 · Cited by 17
Evolution of class I alcohol dehydrogenase genes in catarrhine primates: gene conversion, substitution rates, and gene regulation
Cheung, B., Holmes, R. S., Easteal, S., & Beacham, I. R. (1999) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a026035 · Cited by 16
“Results have, however, been interpreted as showing a slower rate of substitution for the human lineage than for the Old World monkey lineage (Li, Tanimura, and Sharp 1987; Bailey et al. 1991; Seino, Bell, and Li 1992; Ellsworth, Hewett-Emmett, and Li 1993; Li et al. 1996).”
Result
Phylogenetic conservation of the androgen receptor AR45 variant form in placental mammals
Weiss, B., Faus, H., & Haendler, B. (2007) · Gene · doi:10.1016/j.gene.2007.04.037 · Cited by 17
Erratum: Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium (2001) · Nature · doi:10.1038/35079657 · Cited by 17
Adult stem cell activity in naked mole rats for long-term tissue maintenance
Montazid, S., Bandyopadhyay, S., Hart, D. W., Gao, N., Johnson, B., Thrumurthy, S. G., Penn, D. J., Wernisch, B., Bansal, M., Altrock, P. M., et al. (2023) · Nature Communications · doi:10.1038/s41467-023-44138-6 · Cited by 15
Multiple Evolutionary Rate Classes in Animal Genome Evolution
Oldmeadow, C. J., Mengersen, K. L., Mattick, J. S., & Keith, J. M. (2009) · Molecular Biology and Evolution · doi:10.1093/molbev/msp299 · Cited by 16
“The range of values for both Drosophila and mammals is quite similar, although this is probably coincidental given that the mouse lineage is believed to be evolving at a much faster rate than humans (Wu and Li 1985; Li et al. 1996).”
Background
Mitochondrial DNA Rates and Biogeography in European Newts (Genus Euproctus)
Caccone, A., Milinkovitch, M. C., Sbordoni, V., et al. (1997) · Systematic Biology · doi:10.2307/2413640 · Cited by 16
Molecular clock and recombination in primate Mhc genes
Satta, Y., Kupfermann, H., Li, Y., et al. (1999) · Immunological Reviews · doi:10.1111/j.1600-065x.1999.tb01405.x · Cited by 16
Mutational meltdown or controlled chain reaction: The dynamics of rapid plastome evolution in the hyperdiversity of Poaceae
Wang, J., Fu, G., Tembrock, L. R., et al. (2022) · Journal of Systematics and Evolution · doi:10.1111/jse.12854 · Cited by 15
“1 Rapid plastomic evolution in ancestral Poaceae Previous research has shown various factors can affect nucleotide substitution rate heterogeneity including generation time, metabolic rate, population size, stability of polymerases, speciation rate, and selection bias (Bousquet et al., 1992; Wolfe et al., 1992; Li et…”
Background
Elevated mutation rates underlie the evolution of the aquatic plant family Podostemaceae
Katayama, N., Koi, S., Sassa, A., Kurata, T., Imaichi, R., Kato, M., & Nishiyama, T. (2022) · Communications Biology · doi:10.1038/s42003-022-03003-w · Cited by 14
Transcriptional and mutational signatures of the Drosophila ageing germline
Witt, E., Langer, C. B., Svetec, N., & Zhao, L. (2023) · Nature Ecology & Evolution · doi:10.1038/s41559-022-01958-x · Cited by 16
Evolutionary Modeling of Genotype-Phenotype Associations, and Application to primate coding and Non-coding mtDNA Rate Variation
O’Connor, T. D., & Mundy, N. I. (2013) · Evolutionary Bioinformatics · doi:10.4137/ebo.s11600 · Cited by 13
Higher substitution rates and lower dN/dS for the plastid genes in Gnetales than other gymnosperms
Wáng, B., Jiang, B., Zhou, Y., Su, Y., & Wang, T. (2015) · Biochemical Systematics and Ecology · doi:10.1016/j.bse.2015.02.009 · Cited by 15
Molecular evolution of the murine tspy genes
Schubert, S., Dechend, F., Skawran, B., et al. (2000) · Cytogenetic and Genome Research · doi:10.1159/000056852 · Cited by 15
“Furthermore, our observation is also consistent with the generation-time hypothesis, which assumes that errors of DNA replication during germ cell division are the major source of mutations (Chang et al., 1994; Li et al., 1996).”
Result
Differences in Evolution Rates among Eudicotyledon Species Observed by Analysis of Protein Divergence
Cenci, A., Combes, M., & Lashermes, P. (2013) · Journal of Heredity · doi:10.1093/jhered/est025 · Cited by 14
“…reach sexual maturity) was shown to influence the rates of nucleotide substitutions in animals as the reduced number of replication of germline cells per generation is assumed to reduce the number of mutations during DNA duplication between successive generations (Li et al. 1996; Wu and Li 1985).”
Background
Predicting the occurrence of host‐associated differentiation in parasitic arthropods: a quantitative literature review
Harrison, K., Tarone, A. M., DeWitt, T. J., & Medina, R. F. (2021) · Entomologia Experimentalis et Applicata · doi:10.1111/eea.13123 · Cited by 14
“In addition, asexually reproducing arthropods possess short generation times, decreasing the geological time required for host-speciﬁc adaptations to become apparent to researchers (Martin & Palumbi, 1993; Li et al., 1996).”
Background
Evolution of genes and taxa: a primer
Doyle, J. J., & Gaut, B. S. (2000) · Springer eBooks · doi:10.1007/978-94-011-4221-2_1 · Cited by 14
Estimates of the Mutation Rate per Year Can Explain Why the Molecular Clock Depends on Generation Time
Lewin, L. E., & Eyre‐Walker, A. (2025) · Molecular Biology and Evolution · doi:10.1093/molbev/msaf069 · Cited by 21
Correlated evolutionary rates across genomic compartments in Annonaceae
Hoekstra, P. H., Wieringa, J. J., SMETS, E. F., Brandão, R. D., Lopes, J. D. C., Erkens, R. H. J., & Chatrou, L. W. (2017) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2017.05.026 · Cited by 13
“The literature indicating that substitution rates vary among evolutionary lineages (Britten, 1986; Li et al., 1996), genomes (Drouin et al., 2008; Wolfe et al., 1987), genes (Dickerson, 1971; Zhu et al., 2014), and individual sites (e.g. codon positions, Bofkin and Goldman, 2007; Simmons et al.,…”
Background
Distribution and space use of seed‐dispersing rodents in central Pyrenees: implications for genetic diversity, conservation and plant recruitment
Urgoiti, J., Muñóz, A., Espelta, J. M., et al. (2018) · Integrative Zoology · doi:10.1111/1749-4877.12301 · Cited by 13
Sequences and Evolution of Human and Squirrel Monkey Blue Opsin Genes
Shimmin, L. C., Mai, P., & Li, W. (1997) · Journal of Molecular Evolution · doi:10.1007/pl00006157 · Cited by 13
“The average K of 0.096 for the introns is significantly lower than the general substitution frequency (0.139) between humans and members of the New World monkeys (Li et al. 1996).”
BackgroundInfluentialSelf-citation
Predicting the impact of environmental change
Norris, K. J., & Stillman, R. A. (2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.010 · Cited by 13
The origin and loss of interferon regulatory factor 10 (IRF10) in different lineages of vertebrates
Li, W., Wang, Z., Liang, Y., Huang, W., & Huang, B. (2022) · Gene · doi:10.1016/j.gene.2022.147083 · Cited by 12
Self-citation
CALIBRATION AGE AND QUARTET DIVERGENCE DATE ESTIMATION
Brochu, C. A. (2004) · Evolution · doi:10.1554/03-509 · Cited by 12
“…relatives, which is often interpreted as a reflection of higher metabolic rates or faster generation times (e.g., Martin and Palumbi 1993; Li et al. 1996), might in some cases reflect the younger calibration points used for smaller mammal divergences (Slowinski and Arbogast 1999; but see…”
The Dynamics, Causes, and Impacts of Mammalian Evolutionary Rates Revealed by the Analyses of Capybara Draft Genome Sequences
Babarinde, I. A., & Saitou, N. (2020) · Genome Biology and Evolution · doi:10.1093/gbe/evaa157 · Cited by 11
Social insect colony size is correlated with rates of molecular evolution
Rubin, B. E. R. (2022) · Insectes Sociaux · doi:10.1007/s00040-022-00859-3 · Cited by 12
Orthologous microsatellites, transposable elements, and DNA deletions correlate with generation time and body mass in neoavian birds
Ji, Y., Feng, S., Wu, L., Fang, Q., Brüniche–Olsen, A., DeWoody, J. A., Cheng, Y., Zhang, D., Hao, Y., Song, G., et al. (2022) · Science Advances · doi:10.1126/sciadv.abo0099 · Cited by 16
Evolution and Circulation of Type-2 Vaccine-Derived Polioviruses in Nad Ali District of Southern Afghanistan during June 2009-February 2011
Sharif, S., Abbasi, B. H., Khurshid, A., Alam, M. M., Shaukat, S., Angez, M., Rana, M. S., & Zaidi, S. S. Z. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088442 · Cited by 12
“net) was used to calculate the genetic distances and phylogenetic tree was constructed by the neighbor-joining algorithm [23] with Kimura 2-parameter model using 1000 bootstrap replicate values to correct multiple substitutions rate at a site [24].”
Method
Genetic structure across the GBR: evidence from short-lived gobies
Farnsworth, C. A., Bellwood, D. R., & van Herwerden, L. (2009) · Marine Biology · doi:10.1007/s00227-009-1375-y · Cited by 11
Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals
Link, V., Aguilar‐Gómez, D., Ramírez-Suástegui, C., Hurst, L. D., & Cortez, D. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx155 · Cited by 10
Application of comparative genomics in fish endocrinology
Power, D. M., INGLETON, P. M., & Clark, M. S. (2002) · International review of cytology · doi:10.1016/s0074-7696(02)21012-8 · Cited by 11
Germ Line Mutation Rates in Old World Monkeys
Tran, L. A., & Pfeifer, S. P. (2018) · Wiley eBooks · doi:10.1002/9780470015902.a0028242 · Cited by 9
TraitRateProp: a web server for the detection of trait-dependent evolutionary rate shifts in sequence sites
Karin, E. L., Ashkenazy, H., Wicke, S., Pupko, T., & Mayrose, I. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkx288 · Cited by 10
Male Mutation Bias and Possible Long‐Term Effects of Human Activities
Cotton, S., & Wedekind, C. (2010) · Conservation Biology · doi:10.1111/j.1523-1739.2010.01524.x · Cited by 10
“…support for the influence of age at reproduction on αm comes from the observation that generation times decrease from primates to dogs to mice and rats, taxa that have αm-values of 4–6, 3, and 2, respectively (Li et al. 1996; Makova et al. 2004; Lindblad-Toh et al. 2005; Taylor et al. 2006).”
Background
From teeth to pad: tooth loss and development of keratinous structures in sirenians
Hautier, L., Rodrigues, H. G., Ferreira‐Cardoso, S., Emerling, C. A., Porcher, M.-L., Asher, R. J., Miguez, R. P., & Delsuc, F. (2023) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2023.1932 · Cited by 9
“Being large-bodied mammals with long generation times, elevated longevity, and small population sizes, sirenians have a low rate of evolution, which leads to a decreased nucleotide substitution rate [45 – 48].”
Background
Variation in DNA Substitution Rates among Lineages Erroneously Inferred from Simulated Clock-Like Data
Schwartz, R. S., & Mueller, R. L. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009649 · Cited by 9
“For example, species with shorter generation times may have higher substitution rates because more rounds of DNA replication in germs cells produce more mutations per unit time [13,14,15].”
Background
LIFE HISTORY AND THE MALE MUTATION BIAS
Bartosch-Härlid, A., Berlin, S., Smith, N. G. C., Mosller, A. P., & Ellegren, H. (2003) · Evolution · doi:10.1111/j.0014-3820.2003.tb00251.x · Cited by 9
Conservation policies and programmes affecting birds
Boere, G. C., & Rubec, C. D. A. (2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.013 · Cited by 9
erratum: Homologues of Twisted gastrulation are extracellular cofactors in antagonism of BMP signalling
Scott, I., Blitz, I. L., Pappano, W., Maas, S. A., Cho, K. W. Y., & Greenspan, D. (2001) · Nature · doi:10.1038/35079659 · Cited by 2
The pace of mitochondrial molecular evolution varies with seasonal migration distance
Pegan, T. M., Berv, J. S., Gulson‐Castillo, E. R., Kimmitt, A. A., & Winger, B. M. (2023) · Evolution · doi:10.1093/evolut/qpad200 · Cited by 10
Mitochondrial D-loop diversity of grasscutter (Thryonomys swinderianus Rodentia: Hystricomorpha) in Ghana
Adenyo, C., Hayano, A., KAYANG, B. B., Owusu, E. H., & Inoue‐Murayama, M. (2013) · Open Journal of Animal Sciences · doi:10.4236/ojas.2013.33022 · Cited by 8
“This is usually the case for mtDNA D-loop and most especially for rodents because they have short generation intervals [29,30].”
Background
Polymorphisms and functional differences in aryl hydrocarbon receptors (AhR) in Japanese field mice, Apodemus speciosus
Ishiniwa, H., Sogawa, K., Yasumoto, K., & Sekijima, T. (2010) · Environmental Toxicology and Pharmacology · doi:10.1016/j.etap.2010.03.006 · Cited by 8
Understanding Neutral Genomic Molecular Clocks
Yi, S. V. (2007) · Evolutionary Biology · doi:10.1007/s11692-007-9010-7 · Cited by 10
“Interestingly, the degree of male-driven evolution is weaker in rodents, in which the difference of generation times between males and females is smaller than that in primates (Chang et al. 1994; Li et al. 1996).”
Background
Characterization of expressed class II MHC sequences in the banner-tailed kangaroo rat (Dipodomys spectabilis) reveals multiple DRB loci
Busch, J. D., Waser, P. M., & DeWoody, J. A. (2008) · Immunogenetics · doi:10.1007/s00251-008-0323-1 · Cited by 8
“2007) and have rapid rates of molecular evolution (Li et al. 1996; Triant and DeWoody 2006), it remains to be determined if MHC organization will be conserved across families.”
Background
Phylogenomic analyses reveal a molecular signature linked to subterranean adaptation in rodents
Du, K., Yang, L., & He, S. (2015) · BMC Evolutionary Biology · doi:10.1186/s12862-015-0564-1 · Cited by 10
The curious case of Bradypus variegatus sloths: populations in threatened habitats are biodiversity components needing protection
Silva, S. M., Dávila, J. A., Voirin, B., Lopes, S., Ferrand, N., & Moraes‐Barros, N. (2017) · Biodiversity and Conservation · doi:10.1007/s10531-017-1493-7 · Cited by 8
Rapid Nonsynonymous Evolution of the Iron-Sulfur Protein in Anthropoid Primates
Doan, J. W., Schmidt, T. R., Wildman, D. E., Goodman, M., Weiss, M. L., & Grossman, L. I. (2005) · Journal of Bioenergetics and Biomembranes · doi:10.1007/s10863-005-4121-2 · Cited by 8
Energy and spatial order in niche and community
Wright, S. D., & Rohde, K. (2013) · Biological Journal of the Linnean Society · doi:10.1111/bij.12141 · Cited by 8
“Where there are higher total rates of germ cell division in lineages with shorter generation times, heritable mutations have also been found to occur more frequently (Li et al., 1996).”
Background
Efficiency of Nuclear and Mitochondrial Markers Recovering and Supporting Known Amniote Groups
Lambret-Frotté, J., Perini, F. A., & Russo, C. (2012) · Evolutionary Bioinformatics · doi:10.4137/ebo.s9656 · Cited by 7
Biodiversity – evolution, species, genes
Bruford, M. W. (2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.002 · Cited by 7
Why conserve bird diversity?
Bibby, C. J. (2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.003 · Cited by 7
Evolutionary rates of nuclear and organellar genomes are linked in land plantsPreprint
Asar, Y., Sauquet, H., & Ho, S. Y. W. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.08.05.606707 · Cited by 7
“This may be because taller plants have slower growth in their apical meristem and so undergo fewer cycles of mitosis (Li et al. 1996; Lanfear et al. 2013).”
Background
Accelerated growth increases the somatic epimutation rate in trees
Zhou, M., Schmied, G., Vo, B. T., Bradatsch, M., Resente, G., Hazarika, R. R., Kakoulidou, I., Costa, M. C. D., Serra, M., Peters, R. L., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-65404-9 · Cited by 13
Morphological, chromosomal, and molecular evolution are uncoupled in pocket mice
Modi, W. S. (2003) · Cytogenetic and Genome Research · doi:10.1159/000076303 · Cited by 6
Testing the Effect of Metabolic Rate on DNA Variability at the Intra-Specific Level
McGaughran, A., & Holland, B. R. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009686 · Cited by 6
“Despite this, several researchers have reported observing correlations between rate of evolution and other factors [5,45,46].”
Background
Limited effects of among-lineage rate variation on the phylogenetic performance of molecular markers
Schwartz, R. S., & Mueller, R. L. (2010) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2009.12.025 · Cited by 6
Selective mutation accumulation: a computational model of the paternal age effect
Whelan, E. C., Nwala, A. C., Osgood, C. J., & Olariu, S. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw528 · Cited by 6
Analysis of Intron Sequences at the Class II HLA-DRB1 Locus: Implications for the Age of Allelic Diversity
Bergström, T. F., Josefsson, A., Erlich, H. A., et al. (2004) · Hereditas · doi:10.1111/j.1601-5223.1997.t01-1-00001.x · Cited by 6
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., et al. (2004) · Evolution · doi:10.1554/03-638 · Cited by 6
The genetic origin of mouse annexin VIII
Fernández, M. P., Copeland, N. G., Gilbert, D. J., Jenkins, N. A., & Morgan, R. O. (1998) · Mammalian Genome · doi:10.1007/s003359900671 · Cited by 6
The role of APOBEC3-induced mutations in the differential evolution of monkeypox virus
Li, X., Habibipour, S., Chou, T., & Yang, O. O. (2023) · Virus Evolution · doi:10.1093/ve/vead058 · Cited by 6
Molecular Evidence on Primate Origins and Evolution
Raaum, R. L. (2014) · Springer eBooks · doi:10.1007/978-3-642-39979-4_85 · Cited by 7
Derivedness Index for Estimating Degree of Phenotypic Evolution of Embryos: A Study of Comparative Transcriptomic Analyses of Chordates and Echinoderms
Leong, J. C. K., Li, Y., Uesaka, M., Uchida, Y., Omori, A., Hao, M., Wan, W., Dong, Y., Ren, Y., Zhang, S., et al. (2021) · Frontiers in Cell and Developmental Biology · doi:10.3389/fcell.2021.749963 · Cited by 6
“However, various factors, such as different generation turnover times (Martin and Palumbi, 1993; Li et al., 1996) and population sizes (Woolfit, 2009; Lynch et al.”
Background
Generation Time in Stage-Structured Populations under Fluctuating Environments
Giaimo, S., & Traulsen, A. (2022) · The American Naturalist · doi:10.1086/722608 · Cited by 5
“The generation time may play a role in the diversity of mutation rates (Martin and Palumbi 1993; Ohta 1993; Li et al. 1996; Thomas et al. 2010; Sayres et al. 2011; Weller andWu 2015; Amster and Sella 2016; Gao et al. 2016).”
Background
Analysis of DNA of higher primates using inter-SINE PCR
Ryabinina, N. L., Bannikova, A. A., Шереметьева, В. А., et al. (2008) · Russian Journal of Genetics · doi:10.1134/s1022795408030046 · Cited by 5
“This finding can probably be explained by lower mutation rate in higher primates, which is caused by longer generation time in higher primates compared to small mammals [ 21 ].”
Result
Outside the reserve: pandemic threats to bird biodiversity
Pain, D. J., & Donald, P. F. (2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.009 · Cited by 5
Five Hundred Sixty-Five Triples of Chicken, Human, and Mouse Candidate Orthologs
Ouyang, M., Case, J., Tirunagaru, V. G., & Burnside, J. (2003) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2475-9 · Cited by 5
“Gu and Li (1992; see also Li et al. 1996) studied 54 protein-encoding genes of human, rodent (rat or mouse), and chicken.”
Background
Multimeric Hemoglobin of the Australian Brine Shrimp Parartemia
Coleman, M., Matthews, C. M., & Trotman, C. N. A. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003837 · Cited by 5
Measuring spontaneous deleterious mutation process
Kondrashov, A. S. (1998) · Contemporary issues in genetics and evolution · doi:10.1007/978-94-011-5210-5_16 · Cited by 5
Rates of Molecular Evolution of Primates
Tëtushkin, E. Y. (2003) · Russian Journal of Genetics · doi:10.1023/a:1024707801415 · Cited by 4
“In the same year, evidence contradicting this conclusion was published [55].”
BackgroundResultInfluential
WDR75: An essential protein for ribosome assembly undergoing purifying selection
Lee, L., & Whittall, J. B. (2025) · PLoS ONE · doi:10.1371/journal.pone.0318395 · Cited by 4
Evolutionary analysis of the anti-viral STAT2 gene of primates and rodents: Signature of different stages of an arms race
Landau, L. J. B., Fam, B. S. D. O., Yépez, Y., Caldas-Garcia, G. B., Pissinatti, A., Falótico, T., Reales, G., Schüler‐Faccini, L., Sortica, V. A., & Bortolini, M. C. (2021) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2021.105030 · Cited by 4
Comparing Rates of Linage Diversification with Rates of Size and Shape Evolution in Catarrhine Crania
Simons, E. A., Frost, S. R., Harvati, K., McNulty, K. P., & Singleton, M. (2020) · Evolutionary Biology · doi:10.1007/s11692-020-09500-2 · Cited by 5
Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics
Li, T., Chamberlin, S. G., Caraco, M. D., Liberles, D. A., Gaucher, E. A., & Benner, S. A. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-25 · Cited by 4
“Synonymous substitution can be used draw inferences about functional change in protein, explore the influence of generation time on the rate of sequence divergence[7,8], measure the underlying rate of mutation in natural lineages [9-12], detect different rates of mutation in different lineages [13,14], understand the…”
Background
Búsqueda de la mutación delta F508 y análisis de dos polimorfismos de nucleótido único en el gen CFTR, en una muestra de población general de Valparaíso, Chile
Alejandra Vera, L., Henríquez-Roldán, C. F., R, F. J. G., et al. (2005) · Revista médica de Chile · doi:10.4067/s0034-98872005000700003 · Cited by 4
POPULATION-GENETIC CHARACTERISTICS OF DOMESTIC REINDEER OF YAKUTIA BASED ON WHOLE-GENOME SNP ANALYSIS
Kharzinova, V. R., Dotsev, A. V., Solovieva, A. D., Fedorov, V. I., Okhlopkov, I. M., Wimmers, K., Reyer, H., Brem, G., & Zinovieva, N. A. (2017) · Sel skokhozyaistvennaya Biologiya · doi:10.15389/agrobiology.2017.4.669eng · Cited by 4
“In addition to high-density, SNPs are characterized by a very low mutation rate per generation ( 10-8), which makes them excellent markers for studying molecular evolution [22, 23].”
Background
Molecular Evidence of Primate Origins and Evolution
Raaum, R. L. (2013) · Springer eBooks · doi:10.1007/978-3-642-27800-6_85-1 · Cited by 4
“Their method takes advantage of the observation that the neutral rate of molecular evolution is correlated with generation time (Wu and Li 1985; Li et al. 1996; Yi et al. 2002; Tsantes and Steiper 2009).”
Background
The Pattern of Nucleotide Difference at Individual Codons Among Mouse, Rat, and Human
Friedman, R. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi113 · Cited by 4
“…in rodents, particularly murid rodents, in comparison to other placental mammals (Wu and Li 1985; Gu and Li 1992; Easteal, Collet, and Betty 1995; Li et al. 1996), but so far little attention has been paid to the possibility of evolutionary rate differences among the murid rodents themselves.”
Background
Germline mutation rate is elevated in young and old parents in Caenorhabditis remanei
Chen, H., Krieg, T., Mautz, B. S., Jolly, C., Scofield, D. G., Maklakov, A. A., & Immler, S. (2023) · Evolution Letters · doi:10.1093/evlett/qrad052 · Cited by 5
“Although the relative importance of the two sources is currently unclear, replication-driven mutations are generally assumed to be the primary source of germline mutations (Crow, 2000; Drost & Lee, 1995; Li et al., 1996b).”
Background
Hepatitis B virus genome asymmetry in hepatocellular carcinoma.
Shokrgozar, Z., Tayebi, S., Minucheher, Z., et al. (2012) · PubMed · Cited by 3
A genome-wide investigation of microsatellite mismatches and the association with body mass among bird species
Fan, H., & Guo, W. (2018) · PeerJ · doi:10.7717/peerj.4495 · Cited by 3
Codon Signature Extremes In Eukaryote genomes
Karlin, S., & Carmelli, D. (2006) · Israel Journal of Ecology and Evolution · doi:10.1560/ijee_52_3-4_281 · Cited by 3
Identity by descent genome segmentation based on single nucleotide polymorphism distributions.
Blackwell, T. W., Rouchka, E. C., & States, D. J. (1999) · PubMed · Cited by 3
The interface between research, education and training
Bennun, L. (2002) · Cambridge University Press eBooks · doi:10.1017/cbo9780511606304.012 · Cited by 2
Evolution of HLA-DRB loci, DRB1 lineages, and alleles: analyses of intron-1 and -2 sequences
Bergström, T. F., Mack, S. J., Gyllensten, U. B., et al. (2000) · Major Histocompatibility Complex · doi:10.1007/978-4-431-65868-9_25 · Cited by 2
HLA Sequence Polymorphism and the Origin of Humans
Erlich, H. A., Bergström, T. F., Stoneking, M., et al. (1996) · Science · doi:10.1126/science.274.5292.1552-b · Cited by 2
Culture as a Life History Character
Grove, M. L. (2023) · Oxford University Press eBooks · doi:10.1093/oso/9780190096168.003.0007 · Cited by 2
Implementation of SNPs in pig genetics: LD and QTL analysis
Jungerius, B. (2004) · doi:10.18174/121601 · Cited by 3
Genetics of equine insect bite hypersensitivity and genetic diversity in horses
Shrestha, M. (2017) · doi:10.18174/396810 · Cited by 2
“The mutation rate is estimated at 10 changes per nucleotide per generation (Li et al., 1996).”
Background
Repeat associated mechanisms of genome evolution and function revealed by the Mus caroli and Mus pahari genomesPreprint
Thybert, D., Roller, M., Navarro, F. C. P., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/158659 · Cited by 2
The SHR/Akr Y chromosome reveals repeated turnover of the rat pseudoautosomal regionPreprint
Bellott, D. W., Skaletsky, H., Hughes, J. F., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.28.656580 · Cited by 2
“This is likely a result of the rapid evolution of NPY sequence (Hughes et al. 2010), compounded by the accelerated rate of evolution in the rodent lineage (Li et al. 1996; Li and Wu 1987).”
Research proceedings on primate comparative genomics
Liao, C., & Bing, S. U. (2013) · Zoological Research · doi:10.3724/sp.j.1141.2012.01108 · Cited by 1
“…X 染色体上 10 kb 区域, 黑猩猩种内 DNA 序列的差异是人类的 3 倍 (Kaessmann et al, 2001)。如果把人类、倭黑猩猩和黑猩猩(非洲东部、西部和中部)更大区域的 DNA 进行比较, 发现黑猩猩序列的种内差异是人类的 1.5 倍之多(Yu et al, 2003)。在中性位点上(即该位点发生改变并不影响生物体的适合度), 可以利用观察到的物种间替换率来估计突变率。大猿的每年突变率在进化过程中比较稳定, 旧大陆猴的突变率比大猿的高 30%, 狐猴的突变率是大猿的 2 倍(Liu et al, 2003), 小鼠的突变率是大猿的 5…”
Influential
Mutation Rate Variation and Other Challenges in 2-LTR Dating of Primate Endogenous Retrovirus Integrations
van der Kuyl, A. C. (2024) · Journal of Molecular Evolution · doi:10.1007/s00239-024-10225-5 · Cited by 1
“The effect has been largely attributed to differences in generation time, more specifically, the number of germ line DNA replications, especially when comparing humans with monkeys (Li et al. 1996) but also with apes (Besenbacher et al. 2019).”

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)
ORCID: Li, Wen-Hsiung
Ellsworth, Darrell L.
Krushkal, Julia
Chang, Benny H.-J.
Venue: Molecular Phylogenetics and Evolution
Publisher: Elsevier BV
Published: 1996-02
Volume: 5
Issue: 1
Pages: 182-187
ISSN: 1055-7903 (ISSN-L)
DOI: 10.1006/mpev.1996.0012
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
Licence: www.elsevier.com/tdm/userlicense/1.0/ (tdm)
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

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review

Rates of Nucleotide Substitution in Primates and Rodents and the Generation–Time Effect Hypothesis

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cited by

Related

Metadata

Record

About these checks