ArticleGenome biology and evolution2011
Substitution patterns are GC-biased in divergent sequences across the metazoans.
Article in Genome biology and evolution, 2011. 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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23 citing papers in PubMed, 42 citations in OpenAlex.
- Effect of Different Types of Sequence Data on Palaeognath Phylogeny.Genome biology and evolution · 2023Article
- Selection for Cheaper Amino Acids Drives Nucleotide Usage at the Start of Translation in Eukaryotic Genes.Genomics, proteomics & bioinformatics · 2021Article
- Sequencing refractory regions in bird genomes are hotspots for accelerated protein evolution.BMC ecology and evolution · 2021Article
- The Laboratory Domestication of Zebrafish: From Diverse Populations to Inbred Substrains.Molecular biology and evolution · 2020Article
- GC content of vertebrate exome landscapes reveal areas of accelerated protein evolution.BMC evolutionary biology · 2019Article
- GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.Genome biology · 2019Article
- The consequences of sequence erosion in the evolution of recombination hotspots.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2017Review
- Article
- The mutation spectrum in genomic late replication domains shapes mammalian GC content.Nucleic acids research · 2016Article
- Recombination Rate Variation Modulates Gene Sequence Evolution Mainly via GC-Biased Gene Conversion, Not Hill-Robertson Interference, in an Avian System.Molecular biology and evolution · 2016Article
- Crossovers are associated with mutation and biased gene conversion at recombination hotspots.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- GC-Content evolution in bacterial genomes: the biased gene conversion hypothesis expands.PLoS genetics · 2015Article
- Germline methylation patterns determine the distribution of recombination events in the dog genome.Genome biology and evolution · 2014Article
- A fine-scale recombination map of the human-chimpanzee ancestor reveals faster change in humans than in chimpanzees and a strong impact of GC-biased gene conversion.Genome research · 2014Article
- Article
- Kr/Kc but not dN/dS correlates positively with body mass in birds, raising implications for inferring lineage-specific selection.Genome biology · 2014Article
- Twisted signatures of GC-biased gene conversion embedded in an evolutionary stable karyotype.Molecular biology and evolution · 2013Article
- GC-biased gene conversion in yeast is specifically associated with crossovers: molecular mechanisms and evolutionary significance.Molecular biology and evolution · 2013Article
- A model-based analysis of GC-biased gene conversion in the human and chimpanzee genomes.PLoS genetics · 2013Article
- The role of GC-biased gene conversion in shaping the fastest evolving regions of the human genome.Molecular biology and evolution · 2012Article
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2 authors at 2 institutions in 1 country.
Funding
Abstract
The fastest-evolving regions in the human and chimpanzee genomes show a remarkable excess of weak (A,T) to strong (G,C) nucleotide substitutions since divergence from their common ancestor. We investigated the phylogenetic extent and possible causes of this weak to strong (W → S) bias in divergent sequences (BDS) using recently sequenced genomes and recombination maps from eight trios of eukaryotic species. To quantify evidence for BDS, we inferred substitution histories using an efficient maximum likelihood approach with a context-dependent evolutionary model. We then annotated all lineage-specific substitutions in terms of W → S bias and density on the chromosomes. Finally, we used the inferred substitutions to calculate a BDS score-a log odds ratio between substitution type and density-and assessed its statistical significance with Fisher's exact test. Applying this approach, we found significant BDS in the coding and noncoding sequence of human, mouse, dog, stickleback, fruit fly, and worm. We also observed a significant lack of W → S BDS in chicken and yeast. The BDS score varies between species and across the chromosomes within each species. It is most strongly correlated with different genomic features in different species, but a strong correlation with recombination rates is found in several species. Our results demonstrate that a W → S substitution bias in fast-evolving sequences is a widespread phenomenon. The patterns of BDS observed suggest that a recombination-associated process, such as GC-biased gene conversion, is involved in the production of the bias in many species, but the strength of the BDS likely depends on many factors, including genome stability, variability in recombination rate over time and across the genome, the frequency of meiosis, and the amount of outcrossing in each species.
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