ArticleMolecular biology and evolution2023
PhyloAcc-GT: A Bayesian Method for Inferring Patterns of Substitution Rate Shifts on Targeted Lineages Accounting for Gene Tree Discordance.
Article in Molecular biology and evolution, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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18 citing papers in PubMed, 23 citations in OpenAlex.
- Disruption of mitonuclear coadaptation and compensatory evolution after an extreme dietary shift in carnivorous butterflies.Molecular biology and evolution · 2026Article
- Adaptive molecular convergence is pervasive across deep time and largely decoupled from phenotypic convergence.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Mitochondrial Genome Evolution: The Influence of Partitioning, Calibration, and Gene Heterogeneity on Pleurodontan Substitution Rates.Journal of molecular evolution · 2026Article
- Phylogenomic Approaches to Study Adaptive Evolution in Mammals: From Aging to Aquatic Lifestyles.Annual review of genetics · 2025Review
- Gene-Specific Substitution Rates for the Vespertilionidae (Chiroptera: Mammalia) Mitochondrial Genome, with the Description of Three new Mitogenomes.Journal of molecular evolution · 2025Article
- Linking phenotype to genotype using comprehensive genomic comparisons.Current opinion in genetics & development · 2025Review
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- Convergent Molecular Evolution Associated With Repeated Transitions to Gregarious Larval Behavior in Heliconiini.Molecular biology and evolution · 2025Article
- ERCnet: Phylogenomic Prediction of Interaction Networks in the Presence of Gene Duplication.Molecular biology and evolution · 2025Article
- Article
- 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
- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
- Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations.PLoS biology · 2024Article
- RERconverge Expansion: Using Relative Evolutionary Rates to Study Complex Categorical Trait Evolution.bioRxiv : the preprint server for biology · 2023Article
- Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies.Nature communications · 2023Article
- Repeated evolution of similar phenotypes: Integrating comparative methods with developmental pathways.Genetics and molecular biology · 2023Article
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6 authors at 2 institutions in 1 country.
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Abstract
An important goal of evolutionary genomics is to identify genomic regions whose substitution rates differ among lineages. For example, genomic regions experiencing accelerated molecular evolution in some lineages may provide insight into links between genotype and phenotype. Several comparative genomics methods have been developed to identify genomic accelerations between species, including a Bayesian method called PhyloAcc, which models shifts in substitution rate in multiple target lineages on a phylogeny. However, few methods consider the possibility of discordance between the trees of individual loci and the species tree due to incomplete lineage sorting, which might cause false positives. Here, we present PhyloAcc-GT, which extends PhyloAcc by modeling gene tree heterogeneity. Given a species tree, we adopt the multispecies coalescent model as the prior distribution of gene trees, use Markov chain Monte Carlo (MCMC) for inference, and design novel MCMC moves to sample gene trees efficiently. Through extensive simulations, we show that PhyloAcc-GT outperforms PhyloAcc and other methods in identifying target lineage-specific accelerations and detecting complex patterns of rate shifts, and is robust to specification of population size parameters. PhyloAcc-GT is usually more conservative than PhyloAcc in calling convergent rate shifts because it identifies more accelerations on ancestral than on terminal branches. We apply PhyloAcc-GT to two examples of convergent evolution: flightlessness in ratites and marine mammal adaptations, and show that PhyloAcc-GT is a robust tool to identify shifts in substitution rate associated with specific target lineages while accounting for incomplete lineage sorting.
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