ArticleGenome biology and evolution2020
Impact of Mutation Rate and Selection at Linked Sites on DNA Variation across the Genomes of Humans and Other Homininae.
Article in Genome biology and evolution, 2020. 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.
- CD103Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- The landscape of fitness effects of putatively functional noncoding mutations in humans.bioRxiv : the preprint server for biology · 2025Article
- Digital Image Processing to Detect Adaptive Evolution.Molecular biology and evolution · 2024Article
- Genomes of Microtus Rodents Highlight the Importance of Olfactory and Immune Systems in Their Fast Radiation.Genome biology and evolution · 2024Article
- Increased Positive Selection in Highly Recombining Genes Does not Necessarily Reflect an Evolutionary Advantage of Recombination.Molecular biology and evolution · 2024Article
- Shared evolutionary processes shape landscapes of genomic variation in the great apes.Genetics · 2024Article
- Accurate inference of population history in the presence of background selection.bioRxiv : the preprint server for biology · 2024Article
- Between but Not Within-Species Variation in the Distribution of Fitness Effects.Molecular biology and evolution · 2023Article
- Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha.Genome biology and evolution · 2023Article
- Shared evolutionary processes shape landscapes of genomic variation in the great apes.bioRxiv : the preprint server for biology · 2023Article
- Chromatin structure influences rate and spectrum of spontaneous mutations inGenome research · 2023Article
- Characterizing viral within-host diversity in fast and non-equilibrium demo-genetic dynamics.Frontiers in microbiology · 2022Article
- The Impact of Purifying and Background Selection on the Inference of Population History: Problems and Prospects.Molecular biology and evolution · 2021Article
- The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.Genome biology and evolution · 2021Article
- The impact of purifying and background selection on the inference of population history: problems and prospects.bioRxiv : the preprint server for biology · 2021Article
- Identifying branch-specific positive selection throughout the regulatory genome using an appropriate proxy neutral.BMC genomics · 2020Article
- Comparison of the Full Distribution of Fitness Effects of New Amino Acid Mutations Across Great Apes.Genetics · 2019Article
- Dissecting the Effects of Selection and Mutation on Genetic Diversity in Three Wood White (Leptidea) Butterfly Species.Genome biology and evolution · 2019Article
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3 authors.
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Abstract
DNA diversity varies across the genome of many species. Variation in diversity across a genome might arise from regional variation in the mutation rate, variation in the intensity and mode of natural selection, and regional variation in the recombination rate. We show that both noncoding and nonsynonymous diversity are positively correlated to a measure of the mutation rate and the recombination rate and negatively correlated to the density of conserved sequences in 50 kb windows across the genomes of humans and nonhuman homininae. Interestingly, we find that although noncoding diversity is equally affected by these three genomic variables, nonsynonymous diversity is mostly dominated by the density of conserved sequences. The positive correlation between diversity and our measure of the mutation rate seems to be largely a direct consequence of regions with higher mutation rates having more diversity. However, the positive correlation with recombination rate and the negative correlation with the density of conserved sequences suggest that selection at linked sites also affect levels of diversity. This is supported by the observation that the ratio of the number of nonsynonymous to noncoding polymorphisms is negatively correlated to a measure of the effective population size across the genome. We show these patterns persist even when we restrict our analysis to GC-conservative mutations, demonstrating that the patterns are not driven by GC biased gene conversion. In conclusion, our comparative analyses describe how recombination rate, gene density, and mutation rate interact to produce the patterns of DNA diversity that we observe along the hominine genomes.
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