ArticleMolecular biology and evolution2011
A random effects branch-site model for detecting episodic diversifying selection.
Article in Molecular biology and evolution, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 246 papers.
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Who cites it
246 citing papers in PubMed.
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- Organization of neuropeptide systems in the human brain.Nature neuroscience · 2026Article
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- Ecological interactions and genomic innovation fueled the evolution of ray-finned fish endothermy.Science advances · 2025Article
- Functionality of highly diverged Imd like genes identified in stinkbugs and bedbugs.Scientific reports · 2025Article
- Mutations in the signal peptide of effector gene Pi04314 contribute to the adaptive evolution of the Phytophthora infestans.BMC ecology and evolution · 2025Article
- Bioluminescence and environmental light drive the visual evolution of deep-sea shrimp (Oplophoroidea).Communications biology · 2025Article
- Characterization of Complete Mitochondrial Genome of Badri Breed of Bos indicus (Bovidae: Bovinae): Selection Pressure and Comparative Analysis.Biochemical genetics · 2025Article
- Positive selection analyses identify a single WWE domain residue that shapes ZAP into a more potent restriction factor against alphaviruses.PLoS pathogens · 2024Article
- Diversity and Evolution of Frog Visual Opsins: Spectral Tuning and Adaptation to Distinct Light Environments.Molecular biology and evolution · 2024Article
- Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants.bioRxiv : the preprint server for biology · 2024Article
- Molecular Footprints ofAdvances in virology · 2024Article
- Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies.The Journal of experimental biology · 2023Article
- Positive selection analyses identify a single WWE domain residue that shapes ZAP into a super restriction factor.bioRxiv : the preprint server for biology · 2023Article
- Opsin Gene Duplication in Lepidoptera: Retrotransposition, Sex Linkage, and Gene Expression.Molecular biology and evolution · 2023Article
186 more citing papers are in PubMed but not listed here.
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6 authors.
Funding
Abstract
Adaptive evolution frequently occurs in episodic bursts, localized to a few sites in a gene, and to a small number of lineages in a phylogenetic tree. A popular class of "branch-site" evolutionary models provides a statistical framework to search for evidence of such episodic selection. For computational tractability, current branch-site models unrealistically assume that all branches in the tree can be partitioned a priori into two rigid classes--"foreground" branches that are allowed to undergo diversifying selective bursts and "background" branches that are negatively selected or neutral. We demonstrate that this assumption leads to unacceptably high rates of false positives or false negatives when the evolutionary process along background branches strongly deviates from modeling assumptions. To address this problem, we extend Felsenstein's pruning algorithm to allow efficient likelihood computations for models in which variation over branches (and not just sites) is described in the random effects likelihood framework. This enables us to model the process at every branch-site combination as a mixture of three Markov substitution models--our model treats the selective class of every branch at a particular site as an unobserved state that is chosen independently of that at any other branch. When benchmarked on a previously published set of simulated sequences, our method consistently matched or outperformed existing branch-site tests in terms of power and error rates. Using three empirical data sets, previously analyzed for episodic selection, we discuss how modeling assumptions can influence inference in practical situations.
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