ArticleProceedings of the National Academy of Sciences of the United States of America2004
Modeling the site-specific variation of selection patterns along lineages.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 71 papers.
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71 citing papers in PubMed.
- Molecular characterization and gene expression of the HSP90 gene family in Cyprinus carpio and Oreochromis niloticus under thermal stress.Fish physiology and biochemistry · 2026Article
- Infinite Mixture Models for Improved Modeling of Across-Site Evolutionary Variation.Molecular biology and evolution · 2025Article
- Next-generation development and application of codon model in evolution.Frontiers in genetics · 2023Review
- Genome-wide identification and comparative evolutionary analysis of sorbitol metabolism pathway genes in four Rosaceae species and three model plants.BMC plant biology · 2022Article
- Shifts in amino acid preferences as proteins evolve: A synthesis of experimental and theoretical work.Protein science : a publication of the Protein Society · 2021Review
- Markov-Modulated Continuous-Time Markov Chains to Identify Site- and Branch-Specific Evolutionary Variation in BEAST.Systematic biology · 2021Article
- Nonsynonymous Polymorphism Counts in Bacterial Genomes: a Comparative Examination.Applied and environmental microbiology · 2020Article
- Systems identification and characterization of β-glucuronosyltransferase genes involved in arabinogalactan-protein biosynthesis in plant genomes.Scientific reports · 2020Article
- The role of selection in the evolution of marine turtles mitogenomes.Scientific reports · 2020Article
- Detecting amino acid preference shifts with codon-level mutation-selection mixture models.BMC evolutionary biology · 2019Article
- Molecular evolution of genes encoding allergen proteins in the peanuts genus Arachis: Structural and functional implications.PloS one · 2019Article
- Positive Selection of Squalene Synthase in Cucurbitaceae Plants.International journal of genomics · 2019Article
- Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition.Molecular biology and evolution · 2018Article
- Gene Duplication Leads to Altered Membrane Topology of a Cytochrome P450 Enzyme in Seed Plants.Molecular biology and evolution · 2017Article
- Further Simulations and Analyses Demonstrate Open Problems of Phylostratigraphy.Genome biology and evolution · 2017Article
- Calculating Higher-Order Moments of Phylogenetic Stochastic Mapping Summaries in Linear Time.Journal of computational biology : a journal of computational molecular cell biology · 2017Article
- Retention of duplicated long-wavelength opsins in mosquito lineages by positive selection and differential expression.BMC evolutionary biology · 2017Article
- Positive selection and functional divergence of farnesyl pyrophosphate synthase genes in plants.BMC molecular biology · 2017Article
- Identification of positive selection in genes is greatly improved by using experimentally informed site-specific models.Biology direct · 2017Article
- Detecting Adaptation in Protein-Coding Genes Using a Bayesian Site-Heterogeneous Mutation-Selection Codon Substitution Model.Molecular biology and evolution · 2017Article
11 more citing papers are in PubMed but not listed here.
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4 authors.
Funding
Abstract
The unambiguous footprint of positive Darwinian selection in protein-coding DNA sequences is revealed by an excess of nonsynonymous substitutions over synonymous substitutions compared with the neutral expectation. Methods for analyzing the patterns of nonsynonymous and synonymous substitutions usually rely on stochastic models in which the selection regime may vary across the sequence but remains constant across lineages for any amino acid position. Despite some work that has relaxed the constraint that selection patterns remain constant over time, no model provides a strong statistical framework to deal with switches between selection processes at individual sites during the course of evolution. This paper describes an approach that allows the site-specific selection process to vary along lineages of a phylogenetic tree. The parameters of the switching model of codon substitution are estimated by using maximum likelihood. The analysis of eight HIV-1 env homologous sequence data sets shows that this model provides a significantly better fit to the data than one that does not take into account switches between selection patterns in the phylogeny at individual sites. We also provide strong evidence that the strength and the frequency of occurrence of selection might not be estimated accurately when the site-specific variation of selection regimes is ignored.
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