ArticleMolecular biology and evolution2019
Bayesian Detection of Convergent Rate Changes of Conserved Noncoding Elements on Phylogenetic Trees.
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 42 papers.
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Who cites it
42 citing papers in PubMed.
- Functional convergence of regulatory regions provides vital insights into mammalian gliding adaptation.Science China. Life sciences · 2026Article
- CNEwrap: a scalable toolkit with a novel algorithm for large-scale genome-wide accelerated conserved non-coding elements detection.Nucleic acids research · 2026Article
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- MoleRate: comparing molecular relative evolutionary rates to detect convergent evolution.Evolution; international journal of organic evolution · 2026Article
- Remodeling ofScience advances · 2026Article
- Phylogenomic Approaches to Study Adaptive Evolution in Mammals: From Aging to Aquatic Lifestyles.Annual review of genetics · 2025Review
- Detecting Convergence of Amino Acid Physicochemical Properties Underlying the Organismal Adaptive Convergent Evolution.Molecular ecology resources · 2025Article
- Language models reveal a complex sequence basis for adaptive convergent evolution of protein functions.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- Evolution of cetacean-specific conserved non-coding elements suggests their role in the limb changes during secondary aquatic adaptation.BMC biology · 2025Article
- Prediction of local convergent shifts in evolutionary rates with phyloConverge.Bioinformatics (Oxford, England) · 2025Article
- A phylogenetic approach to comparative genomics.Nature reviews. Genetics · 2025Review
- ERCnet: Phylogenomic Prediction of Interaction Networks in the Presence of Gene Duplication.Molecular biology and evolution · 2025Article
- Convergent evolution of noncoding elements associated with short tarsus length in birds.BMC biology · 2025Article
- The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.Genome biology and evolution · 2025Article
- Diversity ofFrontiers in cell and developmental biology · 2025Article
- The macroevolutionary dynamics of pharyngognathy in fishes fail to support the key innovation hypothesis.Nature communications · 2024Article
- Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc.Integrative and comparative biology · 2024Article
- RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution.Molecular biology and evolution · 2024Article
- Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations.PLoS biology · 2024Article
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4 authors.
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Abstract
Conservation of DNA sequence over evolutionary time is a strong indicator of function, and gain or loss of sequence conservation can be used to infer changes in function across a phylogeny. Changes in evolutionary rates on particular lineages in a phylogeny can indicate shared functional shifts, and thus can be used to detect genomic correlates of phenotypic convergence. However, existing methods do not allow easy detection of patterns of rate variation, which causes challenges for detecting convergent rate shifts or other complex evolutionary scenarios. Here we introduce PhyloAcc, a new Bayesian method to model substitution rate changes in conserved elements across a phylogeny. The method assumes several categories of substitution rate for each branch on the phylogenetic tree, estimates substitution rates per category, and detects changes of substitution rate as the posterior probability of a category switch. Simulations show that PhyloAcc can detect genomic regions with rate shifts in multiple target species better than previous methods and has a higher accuracy of reconstructing complex patterns of substitution rate changes than prevalent Bayesian relaxed clock models. We demonstrate the utility of PhyloAcc in two classic examples of convergent phenotypes: loss of flight in birds and the transition to marine life in mammals. In each case, our approach reveals numerous examples of conserved nonexonic elements with accelerations specific to the phenotypically convergent lineages. Our method is widely applicable to any set of conserved elements where multiple rate changes are expected on a phylogeny.
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