Determinants of Mutation Rate Variation in the Human Germline
Open accessAbstract
Because germline mutations are the source of all evolutionary adaptations and heritable diseases, characterizing their properties and the rate at which they arise across individuals is of fundamental importance for human genetics. After decades during which estimates were based on indirect approaches, notably on inferences from evolutionary patterns, it is now feasible to count de novo mutations in transmissions from parents to offspring. Surprisingly, this direct approach yields a mutation rate that is twofold lower than previous estimates, calling into question our understanding of the chronology of human evolution and raising the possibility that mutation rates have evolved relatively rapidly. Here, we bring together insights from studies of human genetics and molecular evolution, focusing on where they conflict and what the discrepancies tell us about important open questions. We begin by outlining various methods for studying the properties of mutations in humans. We review what we have learned from their applications about genomic factors that influence mutation rates and the effects of sex, age, and other sources of interindividual variation. We then consider the mutation rate as a product of evolution and discuss how and why it may have changed over time in primates.
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Given that mutation rates per base pair per generation are thought to be similar across vertebrates and Drosophila, organisms with larger genome sizes are expected to carry more recessive lethals.
“Given that the mutation rates per base pair per generation are thought to be similar across vertebrates and Drosophila (Ségurel et al. 2014), organisms with larger genome sizes are expected to carry more recessive lethals.”
From An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans (2015) · cites this paper as Ségurel et al. 2014
Figure 3 in ‘The Effect of Generation Time on the Mutation Rate Per Year’ places human and Drosophila per-base-pair, per-generation estimates on the same scale, and its caption identifies the estimates used for each. The copy does not establish that rates are similar across vertebrates generally; the prediction about recessive lethals is the citing authors’ inference, not the part attached to this citation. No page number is available in the indexed passages. (LLM, conf=0.78)
Experimental — accuracy not yet measuredThe older assumption that the human lineage's mutation rate changed little since the human-chimpanzee common ancestor is losing credibility because direct mutation rate estimates conflict with molecular-clock-based estimates.
“It was once assumed that the human lineage's mutation rate had changed little since we shared a common ancestor with chimpanzees, but this assumption is losing credibility owing to the conflict between direct mutation rate estimates and molecular-clock-based estimates (8,9).”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [8]
CpG transitions accumulate in a more clocklike manner than other mutations.
“Given such a general challenge to the molecular clock assumption, it may be wise to infer demographic history from mutations such as CpG transitions that accumulate in a more clocklike way than other mutations (8,20).”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [8]
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The Simons Genome Diversity Project: 300 genomes from 142 diverse populations
Mallick, S., Li, H., Lipson, M., Mathieson, I., Gymrek, M., Racimo, F., Zhao, M., Chennagiri, N., Nordenfelt, S., Tandon, A., et al. (2016) · Nature · doi:10.1038/nature18964 · Cited by 1,584 · see citing works
Evidence for archaic adaptive introgression in humans
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Overlooked roles of DNA damage and maternal age in generating human germline mutations
Gao, Z., Moorjani, P., Sasani, T. A., Pedersen, B. S., Quinlan, A. R., Jorde, L. B., Amster, G., & Przeworski, M. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1901259116 · Cited by 229 · see citing works
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Evidence for recent, population-specific evolution of the human mutation rate
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Janecka, M., Mill, J., Basson, M. A., Goriely, A., Spiers, H., Reichenberg, A., Schalkwyk, L., & Fernandes, C. (2017) · Translational Psychiatry · doi:10.1038/tp.2016.294 · Cited by 140 · see citing works
An Estimate of the Average Number of Recessive Lethal Mutations Carried by Humans
Gao, Z., Waggoner, D., Stephens, M., Ober, C., & Przeworski, M. (2015) · Genetics · doi:10.1534/genetics.114.173351 · Cited by 109 · see citing works
Self-citationA natural mutator allele shapes mutation spectrum variation in mice
Sasani, T. A., Ashbrook, D. G., Beichman, A. C., Lu, L., Palmer, A. A., Williams, R. W., Pritchard, J. K., & Harris, K. (2022) · Nature · doi:10.1038/s41586-022-04701-5 · Cited by 64 · see citing works
- Authors
- Ségurel, L., Wyman, M. J., & Przeworski, M.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Columbia University (US)
- Howard Hughes Medical Institute (US)
- Venue
- Annual Review of Genomics and Human Genetics
- Publisher
- Annual Reviews
- Published
- 2014-08-31
- Volume
- 15
- Issue
- 1
- Pages
- 47-70
- ISSN
- 1527-8204 (ISSN-L)
- 1545-293X
- OpenAlex
- W2166880412
- Cited by
- 289
- References
- 188
- Citations by year
- 2026: 18 · 2025: 12 · 2024: 19 · 2023: 24 · 2022: 24 · 2021: 25 · 2020: 21 · 2019: 30 · 2018: 21 · 2017: 36 · 2016: 32 · 2015: 25 · 2014: 2
- FWCI
- 4.20
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Annual Review of Genomics and Human Genetics (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Funders
- Howard Hughes Medical Institute
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Keywords
- germline mutation rate, de novo mutations, human evolution, molecular evolution, genetic disorders
- MeSH terms
- Animals, DNA, Humans, Genome, Human, Germ-Line Mutation, Evolution, Molecular, Genomics, Mutation Rate
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