ArticleMolecular biology and evolution2019
Robust Method for Detecting Convergent Shifts in Evolutionary Rates.
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 35 papers.
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35 citing papers in PubMed, 56 citations in OpenAlex.
- Comparative Genomics Reveals Convergent Evolution Between Avivorous Bats (Ia io and Nyctalus aviator).Integrative zoology · 2026Article
- Evolutionary Rate Covariation Across Malaria Parasite Species Enables Inference of Protein Interactions.Genome biology and evolution · 2026Article
- Genomic signature of repeated transitions to diurnality in spiders.Molecular biology and evolution · 2026Article
- The genetic foundations of convergent traits.Nature reviews. Genetics · 2026Review
- Evolutionary rate covariation across malaria parasite species enables inference of protein interactions.bioRxiv : the preprint server for biology · 2026Article
- Parallel Selection for Longevity in Mammals and Birds.bioRxiv : the preprint server for biology · 2025Article
- Evolutionary Dynamics of Oncosuppression Under Selection Pressure.Life (Basel, Switzerland) · 2025Article
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- ERC2.0 evolutionary rate covariation update improves inference of functional interactions across large phylogenies.Genome research · 2025Article
- Evolutionary sparse learning reveals the shared genetic basis of convergent traits.Nature communications · 2025Article
- ERC 2.0 - evolutionary rate covariation update improves inference of functional interactions across large phylogenies.bioRxiv : the preprint server for biology · 2025Article
- The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.Genome biology and evolution · 2025Article
- Practical Guidance and Workflows for Identifying Fast Evolving Non-Coding Genomic Elements Using PhyloAcc.Integrative and comparative biology · 2024Article
- Distinct Genes with Similar Functions Underlie Convergent Evolution in Myotis Bat Ecomorphs.Molecular biology and evolution · 2024Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
- Diverse signatures of convergent evolution in cactus-associated yeasts.PLoS biology · 2024Article
- A phylogenetic method linking nucleotide substitution rates to rates of continuous trait evolution.PLoS computational biology · 2024Article
- Convergent rates of protein evolution identify novel targets of sexual selection in primates.Evolution; international journal of organic evolution · 2024Article
- Molecular Footprints on Osmoregulation-Related Genes Associated with Freshwater Colonization by Cetaceans and Sirenians.Journal of molecular evolution · 2023Article
- Diverse signatures of convergent evolution in cacti-associated yeasts.bioRxiv : the preprint server for biology · 2023Article
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4 authors at 1 institution in 1 country.
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Abstract
Identifying genomic elements underlying phenotypic adaptations is an important problem in evolutionary biology. Comparative analyses learning from convergent evolution of traits are gaining momentum in accurately detecting such elements. We previously developed a method for predicting phenotypic associations of genetic elements by contrasting patterns of sequence evolution in species showing a phenotype with those that do not. Using this method, we successfully demonstrated convergent evolutionary rate shifts in genetic elements associated with two phenotypic adaptations, namely the independent subterranean and marine transitions of terrestrial mammalian lineages. Our original method calculates gene-specific rates of evolution on branches of phylogenetic trees using linear regression. These rates represent the extent of sequence divergence on a branch after removing the expected divergence on the branch due to background factors. The rates calculated using this regression analysis exhibit an important statistical limitation, namely heteroscedasticity. We observe that the rates on branches that are longer on average show higher variance, and describe how this problem adversely affects the confidence with which we can make inferences about rate shifts. Using a combination of data transformation and weighted regression, we have developed an updated method that corrects this heteroscedasticity in the rates. We additionally illustrate the improved performance offered by the updated method at robust detection of convergent rate shifts in phylogenetic trees of protein-coding genes across mammals, as well as using simulated tree data sets. Overall, we present an important extension to our evolutionary-rates-based method that performs more robustly and consistently at detecting convergent shifts in evolutionary rates.
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