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Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae
Open accessAbstract
Although mutation rates are a key determinant of the rate of evolution they are difficult to measure precisely and global mutations rates (mutations per genome per generation) are often extrapolated from the per-base-pair mutation rate assuming that mutation rate is uniform across the genome. Using budding yeast, we describe an improved method for the accurate calculation of mutation rates based on the fluctuation assay. Our analysis suggests that the per-base-pair mutation rates at two genes differ significantly (3.80x10(-10) at URA3 and 6.44x10(-10) at CAN1) and we propose a definition for the effective target size of genes (the probability that a mutation inactivates the gene) that acknowledges that the mutation rate is nonuniform across the genome.
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“In my own simulation exploration of the mutant distribution used by Lang and Murray (2008) and by Ford et al. (2013), I also found practical nonidentifiability a stubborn problem.”
From rSalvador: An R Package for the Fluctuation Experiment (2017) · cites this paper as Lang and Murray (2008)
In the citing paper
“While other programs exist for estimating mutation rates (Lang and Murray, 2008;Zheng, 2002Zheng, , 2005Zheng, , 2007)), these require the user to implement source code into other software (i.e.Wolfram's Mathematica or The MathWorks' Matlab), whereas FALCOR is readily accessible through Java-enabled web browsers.”
From Fluctuation AnaLysis CalculatOR: a web tool for the determination of mutation rate using Luria–Delbrück fluctuation analysis (2009) · cites this paper as Lang and Murray, 2008
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Azizoğlu, A., Bijman, E. Y., & Brent, R. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.09.01.610536 · Cited by 1
Adaptive Variation in Mutagenesis Driven by Protein Self-AssemblyPreprint
Elgort, A. V., Jakobson, C. M., Byers, J. S., Futia, R. A., Chen, Y. R., Lozanoski, T. M., Harvey, Z. H., Xie, J. L., Garcia, D. M., & Jarosz, D. F. (2025) · SSRN Electronic Journal · doi:10.2139/ssrn.5177180 · Cited by 1
µ Seq: Universal mutation rate quantification via deep sequencing of a single clonal expansionPreprint
Pompei, S., Geroldi, A., Rivetti, P., Grassi, E., Vurchio, V., Tallarico, G., Corti, G., Tattini, L., Liti, G., Bertotti, A., et al. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.04.17.649315 · Cited by 1
Investigating the Rates and Drivers of Drug Resistance in Mycobacterium Tuberculosis
Gawande, R. (2015) · Digital Access to Scholarship at Harvard (DASH) (Harvard University)
Genome-destabilizing and Mutagenic Effects of Break-induced Replication in Saccharomyces cerevisiae
Deem, A. K. (2011) · Purdue e-Pubs (Purdue University System) · doi:10.7912/c2/2131
Population Genetics and Parasite Diversity
Chang, H., Daniels, R. F., & Hartl, D. L. (2012) · doi:10.1002/9781118308165.ch1
Bozorgmehr, J. H. (2013) · Computational Biology and Bioinformatics · doi:10.11648/j.cbb.20130104.11
Metadata
- Authors
- Lang, G. I., & Murray, A. W.
- Affiliations
- Harvard University (US)
- Corresponding author
- Murray, Andrew W
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2008-01-01
- Volume
- 178
- Issue
- 1
- Pages
- 67-82
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- PMC
- PMC2206112
- OpenAlex
- W2110451776
- Cited by
- 344
- References
- 26
- Citations by year
- 2026: 13 · 2025: 17 · 2024: 24 · 2023: 23 · 2022: 13 · 2021: 21 · 2020: 25 · 2019: 27 · 2018: 20 · 2017: 19 · 2016: 13 · 2015: 23 · 2014: 19 · 2013: 20 · 2012: 15
- FWCI
- 9.71
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Licence
- academic.oup.com/journals/pages/open_access/funder_policies/chorus/standard_publication_model (vor)
- Locations
- Genetics (publishedVersion)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- Funders
- National Institute of General Medical Sciences (GM 43987, P50GM068763, R01GM043987, R37GM043987)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Fungal and yeast genetics research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- Saccharomyces cerevisiae, mutation rate heterogeneity, URA3, CAN1, gene inactivation
- MeSH terms
- Amino Acid Sequence, Base Sequence, DNA Mutational Analysis, Models, Genetic, Molecular Sequence Data, Mutation, Phenotype, Saccharomyces cerevisiae, Mutagenesis, Base Pairing, Saccharomyces cerevisiae Proteins
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