ArticleMolecular biology and evolution2019
A Machine Learning Method for Detecting Autocorrelation of Evolutionary Rates in Large Phylogenies.
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 33 papers.
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33 citing papers in PubMed.
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- Overexpression of the GmERF071 gene confers resistance to soybean cyst nematode in soybean.The plant genome · 2025Article
- R3F: An R package for evolutionary dates, rates, and priors using the relative rate framework.ArXiv · 2025Article
- Screening of MYB1R1 interaction withPeerJ · 2025Article
- Beyond mutations: Accounting for quantitative changes in the analysis of protein evolution.Computational and structural biotechnology journal · 2024Article
- Modeling Substitution Rate Evolution across Lineages and Relaxing the Molecular Clock.Genome biology and evolution · 2024Review
- Reliable estimation of tree branch lengths using deep neural networks.PLoS computational biology · 2024Article
- Discovering Fragile Clades and Causal Sequences in Phylogenomics by Evolutionary Sparse Learning.Molecular biology and evolution · 2024Article
- Phylogenomic insights into the first multicellular streptophyte.Current biology : CB · 2024Article
- The Genome of Plasmodium gonderi: Insights into the Evolution of Human Malaria Parasites.Genome biology and evolution · 2024Article
- Computational Reproducibility of Molecular Phylogenies.Molecular biology and evolution · 2023Article
- Modeling the Evolution of Rates of Continuous Trait Evolution.Systematic biology · 2023Article
- Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.Science advances · 2023Article
- Molecular evolutionary model based on phylogenetic and mutation analysis of SARS-CoV-2 spike protein sequences from Asian countries: A phylogenomic approach.Informatics in medicine unlocked · 2023Article
- Assessing the relative performance of fast molecular dating methods for phylogenomic data.BMC genomics · 2022Article
- Excluding Loci With Substitution Saturation Improves Inferences From Phylogenomic Data.Systematic biology · 2022Article
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4 authors.
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Abstract
New species arise from pre-existing species and inherit similar genomes and environments. This predicts greater similarity of the tempo of molecular evolution between direct ancestors and descendants, resulting in autocorrelation of evolutionary rates in the tree of life. Surprisingly, molecular sequence data have not confirmed this expectation, possibly because available methods lack the power to detect autocorrelated rates. Here, we present a machine learning method, CorrTest, to detect the presence of rate autocorrelation in large phylogenies. CorrTest is computationally efficient and performs better than the available state-of-the-art method. Application of CorrTest reveals extensive rate autocorrelation in DNA and amino acid sequence evolution of mammals, birds, insects, metazoans, plants, fungi, parasitic protozoans, and prokaryotes. Therefore, rate autocorrelation is a common phenomenon throughout the tree of life. These findings suggest concordance between molecular and nonmolecular evolutionary patterns, and they will foster unbiased and precise dating of the tree of life.
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