ArticleGenetics2019
Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models.
Article in Genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed, 36 citations in OpenAlex.
- Phylogenetic Methods Meet Deep Learning.Genome biology and evolution · 2025Article
- Polymorphism-Aware Models in RevBayes: Species Trees, Disentangling Balancing Selection, and GC-Biased Gene Conversion.Molecular biology and evolution · 2024Article
- Half a Century of Controversy: The Neutralist/Selectionist Debate in Molecular Evolution.Genome biology and evolution · 2024Article
- Rapid Targeted Assembly of the Proteome Reveals Evolutionary Variation of GC Content in Avian Lice.Bioinformatics and biology insights · 2024Article
- GC-biased gene conversion drives accelerated evolution of ultraconserved elements in mammalian and avian genomes.Genome research · 2023Article
- Purifying selection against spurious splicing signals contributes to the base composition evolution of the polypyrimidine tract.Journal of evolutionary biology · 2023Article
- Evolutionary dynamics of pseudoautosomal region 1 in humans and great apes.Genome biology · 2022Article
- Nucleotide Usage Biases Distort Inferences of the Species Tree.Genome biology and evolution · 2022Article
- GC-biased gene conversion in X-chromosome palindromes conserved in human, chimpanzee, and rhesus macaque.G3 (Bethesda, Md.) · 2021Article
- Evidence for a force favoring GC over AT at short intronic sites in Drosophila simulans and Drosophila melanogaster.G3 (Bethesda, Md.) · 2021Article
- Article
- The Effects of GC-Biased Gene Conversion on Patterns of Genetic Diversity among and across Butterfly Genomes.Genome biology and evolution · 2021Article
- Runaway GC Evolution in Gerbil Genomes.Molecular biology and evolution · 2020Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
As multi-individual population-scale data become available, more complex modeling strategies are needed to quantify genome-wide patterns of nucleotide usage and associated mechanisms of evolution. Recently, the multivariate neutral Moran model was proposed. However, it was shown insufficient to explain the distribution of alleles in great apes. Here, we propose a new model that includes allelic selection. Our theoretical results constitute the basis of a new Bayesian framework to estimate mutation rates and selection coefficients from population data. We apply the new framework to a great ape dataset, where we found patterns of allelic selection that match those of genome-wide GC-biased gene conversion (gBGC). In particular, we show that great apes have patterns of allelic selection that vary in intensity-a feature that we correlated with great apes' distinct demographies. We also demonstrate that the AT/GC toggling effect decreases the probability of a substitution, promoting more polymorphisms in the base composition of great ape genomes. We further assess the impact of GC-bias in molecular analysis, and find that mutation rates and genetic distances are estimated under bias when gBGC is not properly accounted for. Our results contribute to the discussion on the tempo and mode of gBGC evolution, while stressing the need for gBGC-aware models in population genetics and phylogenetics.
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