ArticleGenetics1999
The causes of synonymous rate variation in the rodent genome. Can substitution rates be used to estimate the sex bias in mutation rate?
Article in Genetics, 1999. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- KitBase Expanded: An Integrated Genomic and Phenotypic Resource for 3,268 Fast-Neutron-Irradiated Rice Mutants.Database : the journal of biological databases and curation · 2026Article
- Chronic Hepatitis B Treatment Strategies Using Polymerase Inhibitor-Based Combination Therapy.Viruses · 2021Review
- Extra base hits: Widespread empirical support for instantaneous multiple-nucleotide changes.PloS one · 2021Article
- Male Mutation Bias Is the Main Force Shaping Chromosomal Substitution Rates in Monotreme Mammals.Genome biology and evolution · 2017Article
- Faster-X adaptive protein evolution in house mice.Genetics · 2014Article
- The site-wise log-likelihood score is a good predictor of genes under positive selection.Journal of molecular evolution · 2013Article
- Divergence of imprinted genes during mammalian evolution.BMC evolutionary biology · 2010Article
- Evolution and survival on eutherian sex chromosomes.PLoS genetics · 2009Article
- Evidence that replication-associated mutation alone does not explain between-chromosome differences in substitution rates.Genome biology and evolution · 2009Article
- Characteristics, causes and evolutionary consequences of male-biased mutation.Proceedings. Biological sciences · 2007Review
- Preliminary assessment of the impact of microRNA-mediated regulation on coding sequence evolution in mammals.Journal of molecular evolution · 2006Article
- Analysis of transitions at two-fold redundant sites in mammalian genomes. Transition redundant approach-to-equilibrium (TREx) distance metrics.BMC evolutionary biology · 2006Article
- Male-driven evolution in closely related species of the mouse genus Mus.Journal of molecular evolution · 2005Article
- Insertions and deletions are male biased too: a whole-genome analysis in rodents.Genome research · 2004Article
- Functional bias and spatial organization of genes in mutational hot and cold regions in the human genome.PLoS biology · 2004Review
- Functional constraints and frequency of deleterious mutations in noncoding DNA of rodents.Proceedings of the National Academy of Sciences of the United States of America · 2003Article
- Estimate of the mutation rate per nucleotide in humans.Genetics · 2000Article
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Authors and funding
2 authors.
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Abstract
Miyata et al. have suggested that the male-to-female mutation rate ratio (alpha) can be estimated by comparing the neutral substitution rates of X-linked (X), Y-linked (Y), and autosomal (A) genes. Rodent silent site X/A comparisons provide very different estimates from X/Y comparisons. We examine three explanations for this discrepancy: (1) statistical biases and artifacts, (2) nonneutral evolution, and (3) differences in mutation rate per germline replication. By estimating errors and using a variety of methodologies, we tentatively reject explanation 1. Our analyses of patterns of codon usage, synonymous rates, and nonsynonymous rates suggest that silent sites in rodents are evolving neutrally, and we can therefore reject explanation 2. We find both base composition and methylation differences between the different sets of chromosomes, a result consistent with explanation 3, but these differences do not appear to explain the observed discrepancies in estimates of alpha. Our finding of significantly low synonymous substitution rates in genomically imprinted genes suggests a link between hemizygous expression and an adaptive reduction in the mutation rate, which is consistent with explanation 3. Therefore our results provide circumstantial evidence in favor of the hypothesis that the discrepancies in estimates of alpha are due to differences in the mutation rate per germline replication between different parts of the genome. This explanation violates a critical assumption of the method of Miyata et al., and hence we suggest that estimates of alpha, obtained using this method, need to be treated with caution.
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