ArticleGenome biology2008
Human-macaque comparisons illuminate variation in neutral substitution rates.
Article in Genome biology, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 38 papers.
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Who cites it
38 citing papers in PubMed, 58 citations in OpenAlex.
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- Mutational Signatures of Replication Timing and Epigenetic Modification Persist through the Global Divergence of Mutation Spectra across the Great Ape Phylogeny.Genome biology and evolution · 2022Article
- The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.Genome biology and evolution · 2021Article
- Non-B DNA: a major contributor to small- and large-scale variation in nucleotide substitution frequencies across the genome.Nucleic acids research · 2021Article
- What can be learned by scanning the genome for molecular convergence in wild populations?Annals of the New York Academy of Sciences · 2020Review
- Extreme differences between human germline and tumor mutation densities are driven by ancestral human-specific deviations.Nature communications · 2020Article
- Sex-specific changes in the aphid DNA methylation landscape.Molecular ecology · 2019Article
- NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans.Genome biology · 2019Article
- Large scale variation in the rate of germ-line de novo mutation, base composition, divergence and diversity in humans.PLoS genetics · 2018Article
- Evolution of Local Mutation Rate and Its Determinants.Molecular biology and evolution · 2017Article
- The Impact of Linked Selection in Chimpanzees: A Comparative Study.Genome biology and evolution · 2016Article
- Nucleotide diversity analysis highlights functionally important genomic regions.Scientific reports · 2016Article
- Determining the Effect of Natural Selection on Linked Neutral Divergence across Species.PLoS genetics · 2016Article
- Are Synonymous Sites in Primates and Rodents Functionally Constrained?Journal of molecular evolution · 2016Article
- Inferring Very Recent Population Growth Rate from Population-Scale Sequencing Data: Using a Large-Sample Coalescent Estimator.Molecular biology and evolution · 2015Article
- Breaking bad: The mutagenic effect of DNA repair.DNA repair · 2015Review
- The effects of chromatin organization on variation in mutation rates in the genome.Nature reviews. Genetics · 2015Review
- Article
- The role of mutation rate variation and genetic diversity in the architecture of human disease.PloS one · 2014Article
Corrections and comments
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundThe evolutionary distance between human and macaque is particularly attractive for investigating local variation in neutral substitution rates, because substitutions can be inferred more reliably than in comparisons with rodents and are less influenced by the effects of current and ancient diversity than in comparisons with closer primates. Here we investigate the human-macaque neutral substitution rate as a function of a number of genomic parameters.
resultsUsing regression analyses we find that male mutation bias, male (but not female) recombination rate, distance to telomeres and substitution rates computed from orthologous regions in mouse-rat and dog-cow comparisons are prominent predictors of the neutral rate. Additionally, we demonstrate that the previously observed biphasic relationship between neutral rate and GC content can be accounted for by properly combining rates at CpG and non-CpG sites. Finally, we find the neutral rate to be negatively correlated with the densities of several classes of computationally predicted functional elements, and less so with the densities of certain classes of experimentally verified functional elements.
conclusionOur results suggest that while female recombination may be mainly responsible for driving evolution in GC content, male recombination may be mutagenic, and that other mutagenic mechanisms acting near telomeres, and mechanisms whose effects are shared across mammalian genomes, play significant roles. We also have evidence that the nonlinear increase in rates at high GC levels may be largely due to hyper-mutability of CpG dinucleotides. Finally, our results suggest that the performance of conservation-based prediction methods can be improved by accounting for neutral rates.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.