ArticleGenome research2015
Quantification of GC-biased gene conversion in the human genome.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 89 papers.
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Who cites it
89 citing papers in PubMed, 153 citations in OpenAlex.
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.PLoS genetics · 2026Article
- Interpreting GC content differences across populations at polymorphic sites.bioRxiv : the preprint server for biology · 2026Article
- Sequence context and methylation interact to shape germline mutation rate variation at CpG sites.bioRxiv : the preprint server for biology · 2026Article
- Polarising SNPs Without Outgroup.Molecular ecology resources · 2026Article
- The performance of genetic-constraint metrics varies significantly across the human noncoding genome.bioRxiv : the preprint server for biology · 2026Article
- Multispecies pangenomes reveal a pervasive influence of population size on structural variation.Science (New York, N.Y.) · 2025Article
- Direct detection of meiotic recombination events in the highly heterozygous amphioxus genome.Advanced biotechnology · 2025Article
- Evolution of GC-biased gene conversion by natural selection.Genetics · 2025Article
- Compensatory Evolution Following Deleterious Episodes of GC-biased Gene Conversion in Rodents.Molecular biology and evolution · 2025Article
- Dinucleotide preferences underlie apparent codon preference reversals in theProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Sparse haplotype-based fine-scale local ancestry inference at scale reveals recent selection on immune responses.Nature communications · 2025Article
- Incorporating genetic load contributes to predicting Arabidopsis thaliana's response to climate change.Nature communications · 2025Article
- Comparative population pangenomes reveal unexpected complexity and fitness effects of structural variants.bioRxiv : the preprint server for biology · 2025Article
- Fast and accurate deep learning scans for signatures of natural selection in genomes using FASTER-NN.Communications biology · 2025Article
- High prevalence of PRDM9-independent recombination hotspots in placental mammals.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Increased Positive Selection in Highly Recombining Genes Does not Necessarily Reflect an Evolutionary Advantage of Recombination.Molecular biology and evolution · 2024Article
- The Patterns of Codon Usage between Chordates and Arthropods are Different but Co-evolving with Mutational Biases.Molecular biology and evolution · 2024Article
- Shared evolutionary processes shape landscapes of genomic variation in the great apes.Genetics · 2024Article
- Shared evolutionary processes shape landscapes of genomic variation in the great apes.bioRxiv : the preprint server for biology · 2023Article
- GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes.Genome research · 2023Article
29 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors at 6 institutions in 4 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Much evidence indicates that GC-biased gene conversion (gBGC) has a major impact on the evolution of mammalian genomes. However, a detailed quantification of the process is still lacking. The strength of gBGC can be measured from the analysis of derived allele frequency spectra (DAF), but this approach is sensitive to a number of confounding factors. In particular, we show by simulations that the inference is pervasively affected by polymorphism polarization errors and by spatial heterogeneity in gBGC strength. We propose a new general method to quantify gBGC from DAF spectra, incorporating polarization errors, taking spatial heterogeneity into account, and jointly estimating mutation bias. Applying it to human polymorphism data from the 1000 Genomes Project, we show that the strength of gBGC does not differ between hypermutable CpG sites and non-CpG sites, suggesting that in humans gBGC is not caused by the base-excision repair machinery. Genome-wide, the intensity of gBGC is in the nearly neutral area. However, given that recombination occurs primarily within recombination hotspots, 1%-2% of the human genome is subject to strong gBGC. On average, gBGC is stronger in African than in non-African populations, reflecting differences in effective population sizes. However, due to more heterogeneous recombination landscapes, the fraction of the genome affected by strong gBGC is larger in non-African than in African populations. Given that the location of recombination hotspots evolves very rapidly, our analysis predicts that, in the long term, a large fraction of the genome is affected by short episodes of strong gBGC.
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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.