ArticleMolecular biology and evolution2021
Contrast-FEL-A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches.
Article in Molecular biology and evolution, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers.
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51 citing papers in PubMed.
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- Phylogeographic epidemiology of Dabie bandavirus in East Asia: divergent transmission networks and genotype‑linked clinical severity.Infectious diseases of poverty · 2026Article
- CAPHEINE, or Everything and the Kitchen Sink: A Workflow for Automating Selection Analyses Using HyPhy.Genome biology and evolution · 2026Article
- Sensing Underwater: Diversifying Selection, Convergent Evolution and Inactivation in Sensory Receptors' Genes of Aquatic Mammals.Journal of molecular evolution · 2026Article
- Evolutionary dynamics and molecular adaptation of Rift Valley fever virus across human and non-human outbreaks in Africa.BMC genomics · 2026Article
- The Use of dN/dS Ratios to Investigate Types of Selection in Related Sexual and Asexual Lineages.Genome biology and evolution · 2026Review
- CAPHEINE, or everything and the kitchen sink: a workflow for automating selection analyses using HyPhy.bioRxiv : the preprint server for biology · 2026Article
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- Datamonkey 3: browser-native molecular evolution analysis.Frontiers in bioinformatics · 2026Article
- Shifts in bee diet breadths are associated with gene gains and losses and positive selection across olfactory receptors.G3 (Bethesda, Md.) · 2025Article
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- Genomic Alterations of the Infectious Bronchitis Virus (IBV) Strain of the GI-23 Lineage Induced by Passages in Chickens and Quails.International journal of molecular sciences · 2025Article
- Phylodynamic reconstruction of major chicken infectious anemia virus clades epidemiology, dispersal, and evolution.Frontiers in microbiology · 2025Article
- Host-driven evolution of PCV2: insights into genetic diversity and adaptation.Frontiers in immunology · 2025Article
- Untangling Zebrafish Genetic Annotation: Addressing Complexities and Nomenclature Issues in Orthologous Evaluation of TCOF1 and NOLC1.Journal of molecular evolution · 2024Article
- Molecular evolution of toothed whale genes reveals adaptations to echolocating in different environments.BMC genomics · 2024Article
- Positive selection, genetic recombination, and intra-host evolution in novel equine coronavirus genomes and other members of theMicrobiology spectrum · 2024Article
- Palaeognaths Reveal Evolutionary Ancestry of the Avian Major Histocompatibility Complex Class II.Genome biology and evolution · 2024Article
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5 authors.
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Abstract
A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K≥2 sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions.
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