ArticlePloS one2012
Fast and robust characterization of time-heterogeneous sequence evolutionary processes using substitution mapping.
Article in PloS one, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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31 citing papers in PubMed.
- Combining Annotation Software to Identify Orthologous Genes (CASIO) Provides a New Dataset of Orthologous Genes for Swallowtail Butterflies.Molecular ecology resources · 2026Article
- Empirical Validation of the Nearly Neutral Theory at Divergence and Population-Genomic Scales Using 144 Placental Mammal Genomes.Genome biology and evolution · 2026Article
- EMPIRICAL VALIDATION OF THE NEARLY NEUTRAL THEORY AT DIVERGENCE AND POPULATION GENOMIC SCALE USING 144 PLACENTAL MAMMALS GENOMES.bioRxiv : the preprint server for biology · 2026Article
- Stochastic Character Mapping: An Under-Exploited Approach to the Study of Molecular Evolution.Journal of molecular evolution · 2025Article
- Article
- Compensatory Evolution Following Deleterious Episodes of GC-biased Gene Conversion in Rodents.Molecular biology and evolution · 2025Article
- Genome and life-history evolution link bird diversification to the end-Cretaceous mass extinction.Science advances · 2024Article
- Base Composition, Codon Usage, and Patterns of Gene Sequence Evolution in Butterflies.Genome biology and evolution · 2023Article
- Nematode gene annotation by machine-learning-assisted proteotranscriptomics enables proteome-wide evolutionary analysis.Genome research · 2023Article
- Rates of Protein Evolution across the Marsupial Phylogeny: Heterogeneity and Link to Life-History Traits.Genome biology and evolution · 2022Article
- Divergent genes in gerbils: prevalence, relation to GC-biased substitution, and phenotypic relevance.BMC evolutionary biology · 2020Article
- Mitochondrial genomics reveals the evolutionary history of the porpoises (Phocoenidae) across the speciation continuum.Scientific reports · 2020Article
- Runaway GC Evolution in Gerbil Genomes.Molecular biology and evolution · 2020Article
- Determinants of genetic variation across eco-evolutionary scales in pinnipeds.Nature ecology & evolution · 2020Article
- Vulnerability to Fishing and Life History Traits Correlate with the Load of Deleterious Mutations in Teleosts.Molecular biology and evolution · 2020Article
- Influence of Recombination and GC-biased Gene Conversion on the Adaptive and Nonadaptive Substitution Rate in Mammals versus Birds.Molecular biology and evolution · 2019Article
- GC-biased gene conversion conceals the prediction of the nearly neutral theory in avian genomes.Genome biology · 2019Article
- In Cold Blood: Compositional Bias and Positive Selection Drive the High Evolutionary Rate of Vampire Bats Mitochondrial Genomes.Genome biology and evolution · 2018Article
- Consequences of Asexuality in Natural Populations: Insights from Stick Insects.Molecular biology and evolution · 2018Article
- Unbiased Estimate of Synonymous and Nonsynonymous Substitution Rates with Nonstationary Base Composition.Molecular biology and evolution · 2018Article
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7 authors.
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Abstract
Genes and genomes do not evolve similarly in all branches of the tree of life. Detecting and characterizing the heterogeneity in time, and between lineages, of the nucleotide (or amino acid) substitution process is an important goal of current molecular evolutionary research. This task is typically achieved through the use of non-homogeneous models of sequence evolution, which being highly parametrized and computationally-demanding are not appropriate for large-scale analyses. Here we investigate an alternative methodological option based on probabilistic substitution mapping. The idea is to first reconstruct the substitutional history of each site of an alignment under a homogeneous model of sequence evolution, then to characterize variations in the substitution process across lineages based on substitution counts. Using simulated and published datasets, we demonstrate that probabilistic substitution mapping is robust in that it typically provides accurate reconstruction of sequence ancestry even when the true process is heterogeneous, but a homogeneous model is adopted. Consequently, we show that the new approach is essentially as efficient as and extremely faster than (up to 25 000 times) existing methods, thus paving the way for a systematic survey of substitution process heterogeneity across genes and lineages.
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