ArticleMolecular biology and evolution2019
Large-Scale Comparative Analysis of Codon Models Accounting for Protein and Nucleotide Selection.
Article in Molecular biology and evolution, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
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- Adaptive evolution of odorant receptors is associated with elaborations of social organization in ants.Molecular biology and evolution · 2026Article
- Predicting the antigenic evolution of seasonal influenza viruses using phylogenetic convergence.bioRxiv : the preprint server for biology · 2026Article
- Multiple transitions to high l-DOPA 4,5-dioxygenase activity reveal molecular pathways to convergent betalain pigmentation in Caryophyllales.The New phytologist · 2025Article
- Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians.Journal of molecular evolution · 2023Article
- Evolutionary Shortcuts via Multinucleotide Substitutions and Their Impact on Natural Selection Analyses.Molecular biology and evolution · 2023Article
- Evolution is not Uniform Along Coding Sequences.Molecular biology and evolution · 2023Article
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- X chromosomes show relaxed selection and complete somatic dosage compensation across Timema stick insect species.Journal of evolutionary biology · 2022Article
- An ancient truncated duplication of the anti-Müllerian hormone receptor type 2 gene is a potential conserved master sex determinant in the Pangasiidae catfish family.Molecular ecology resources · 2022Article
- Dynamics of sex-biased gene expression during development in the stick insect Timema californicum.Heredity · 2022Article
- Convergent consequences of parthenogenesis on stick insect genomes.Science advances · 2022Article
- The Evolutionary History of Vertebrate Adhesion GPCRs and Its Implication on Their Classification.International journal of molecular sciences · 2021Article
- BASE: A novel workflow to integrate nonubiquitous genes in comparative genomics analyses for selection.Ecology and evolution · 2021Article
- Inferring the number and position of changes in selective regime in a non-equilibrium mutation-selection framework.BMC ecology and evolution · 2021Article
- The evolutionary history of manatees told by their mitogenomes.Scientific reports · 2021Article
- Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination.Applied and environmental microbiology · 2020Article
- Divergent genes in gerbils: prevalence, relation to GC-biased substitution, and phenotypic relevance.BMC evolutionary biology · 2020Article
- Synonymous Site-to-Site Substitution Rate Variation Dramatically Inflates False Positive Rates of Selection Analyses: Ignore at Your Own Peril.Molecular biology and evolution · 2020Article
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3 authors.
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Abstract
There are numerous sources of variation in the rate of synonymous substitutions inside genes, such as direct selection on the nucleotide sequence, or mutation rate variation. Yet scans for positive selection rely on codon models which incorporate an assumption of effectively neutral synonymous substitution rate, constant between sites of each gene. Here we perform a large-scale comparison of approaches which incorporate codon substitution rate variation and propose our own simple yet effective modification of existing models. We find strong effects of substitution rate variation on positive selection inference. More than 70% of the genes detected by the classical branch-site model are presumably false positives caused by the incorrect assumption of uniform synonymous substitution rate. We propose a new model which is strongly favored by the data while remaining computationally tractable. With the new model we can capture signatures of nucleotide level selection acting on translation initiation and on splicing sites within the coding region. Finally, we show that rate variation is highest in the highly recombining regions, and we propose that recombination and mutation rate variation, such as high CpG mutation rate, are the two main sources of nucleotide rate variation. Although we detect fewer genes under positive selection in Drosophila than without rate variation, the genes which we detect contain a stronger signal of adaptation of dynein, which could be associated with Wolbachia infection. We provide software to perform positive selection analysis using the new model.
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