ArticleGenome biology and evolution2022
Mutational Signatures of Replication Timing and Epigenetic Modification Persist through the Global Divergence of Mutation Spectra across the Great Ape Phylogeny.
Article in Genome biology and evolution, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed, 32 citations in OpenAlex.
- Dynamics of mutators of arbitrary dominance in humans.bioRxiv : the preprint server for biology · 2026Article
- Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.PLoS genetics · 2026Article
- A sibling study of variation in parental mutation rates.bioRxiv : the preprint server for biology · 2026Article
- Characterization of de novo germline mutations suggests a strong male mutation bias in coppery titi monkeys (Plecturocebus cupreus).Molecular biology and evolution · 2026Article
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Methylation-associated mutagenesis underlies variation in the mutation spectrum across eukaryotes.bioRxiv : the preprint server for biology · 2025Article
- The evolution and convergence of mutation spectra across mammals.Communications biology · 2025Article
- An Expanding Universe of Mutational Signatures and Its Rapid Evolution in Single-Stranded RNA Viruses.Molecular biology and evolution · 2025Article
- The Evolutionary Interplay of Somatic and Germline Mutation Rates.Annual review of biomedical data science · 2024Review
- NeMu: a comprehensive pipeline for accurate reconstruction of neutral mutation spectra from evolutionary data.Nucleic acids research · 2024Article
- Effects of parental age and polymer composition on short tandem repeat de novo mutation rates.Genetics · 2024Article
- Epigenetic and Genetic Differentiation Between Coregonus Species Pairs.Genome biology and evolution · 2024Article
- Evolution of the Mutation Spectrum Across a Mammalian Phylogeny.Molecular biology and evolution · 2023Article
- Regularized sequence-context mutational trees capture variation in mutation rates across the human genome.PLoS genetics · 2023Article
- "Evolution of the mutation spectrum across a mammalian phylogeny".bioRxiv : the preprint server for biology · 2023Article
- Evolution of the SARS-CoV-2 Mutational Spectrum.Molecular biology and evolution · 2023Article
- The Impact of Sample Size and Population History on Observed Mutational Spectra: A Case Study in Human and Chimpanzee Populations.Genome biology and evolution · 2023Article
- Limited role of generation time changes in driving the evolution of the mutation spectrum in humans.eLife · 2023Article
- Evolution of the SARS-CoV-2 mutational spectrum.bioRxiv : the preprint server for biology · 2022Article
Corrections and comments
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2 authors at 1 institution in 1 country.
Funding
Abstract
Great ape clades exhibit variation in the relative mutation rates of different three-base-pair genomic motifs, with closely related species having more similar mutation spectra than distantly related species. This pattern cannot be explained by classical demographic or selective forces, but imply that DNA replication fidelity has been perturbed in different ways on each branch of the great ape phylogeny. Here, we use whole-genome variation from 88 great apes to investigate whether these species' mutation spectra are broadly differentiated across the entire genome, or whether mutation spectrum differences are driven by DNA compartments that have particular functional features or chromatin states. We perform principal component analysis (PCA) and mutational signature deconvolution on mutation spectra ascertained from compartments defined by features including replication timing and ancient repeat content, finding evidence for consistent species-specific mutational signatures that do not depend on which functional compartments the spectra are ascertained from. At the same time, we find that many compartments have their own characteristic mutational signatures that appear stable across the great ape phylogeny. For example, in a mutation spectrum PCA compartmentalized by replication timing, the second principal component explaining 21.2% of variation separates all species' late-replicating regions from their early-replicating regions. Our results suggest that great ape mutation spectrum evolution is not driven by epigenetic changes that modify mutation rates in specific genomic regions, but instead by trans-acting mutational modifiers that affect mutagenesis across the whole genome fairly uniformly.
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