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 the author's own simulation exploration of the mutant distribution used by Lang and Murray (2008) and by Ford et al. (2013), practical nonidentifiability was a stubborn problem.
“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)
Other programs for estimating mutation rates require the user to implement source code into other software, whereas FALCOR is readily accessible through Java-enabled web browsers.
“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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- 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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