Cited by 344Evolution and Genetic DynamicsFungal and yeast genetics researchDNA Repair Mechanisms

Estimating the Per-Base-Pair Mutation Rate in the Yeast Saccharomyces cerevisiae

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Lang, Gregory I, Murray, Andrew W·2008·Genetics

Abstract

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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Crossref · 10.1534/genetics.107.071506

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25 of 25 references verified0 citation errors · 0 not checkable

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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.”

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Authors
Lang, G. I., & Murray, A. W.
Affiliations
Harvard University (US)
Corresponding author
Murray, Andrew W
Venue
Genetics
Published
2008-01-01
Volume
178
Issue
1
Pages
67-82
ISSN
  • 0016-6731 (ISSN-L)
  • 1943-2631
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
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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