ArticleProceedings of the National Academy of Sciences of the United States of America2023
Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- RETRACTED: Endogenous Retroviruses as Regulators of Innate Immune Signaling and InflammationViruses · 2026Review
- Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.Systematic biology · 2026Article
- Robust regression rescues poor phylogenetic decisions.BMC ecology and evolution · 2025Article
- Reconciling Gene Tree Discordance and Biogeography in European Crows.Molecular ecology · 2025Article
- A Tale of Too Many Trees: A Conundrum for Phylogenetic Regression.Molecular biology and evolution · 2025Article
- The Genomic Landscape, Causes, and Consequences of Extensive Phylogenomic Discordance in Murine Rodents.Genome biology and evolution · 2025Article
- Convergent Evolution and Predictability of Gene Copy Numbers Associated with Diets in Mammals.Genome biology and evolution · 2025Article
- Subfamily evolution analysis using nuclear and chloroplast data from the same reads.Scientific reports · 2025Article
- Insect Phylogenomics: From Experiment Planning to Post-phylogenetic Analyses.Methods in molecular biology (Clifton, N.J.) · 2025Review
- PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models.Systematic biology · 2024Article
- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
- Phylogenomic Discordance is Driven by Wide-Spread Introgression and Incomplete Lineage Sorting During Rapid Species Diversification Within Rattlesnakes (Viperidae: Crotalus and Sistrurus).Systematic biology · 2024Article
- Unifying approaches from statistical genetics and phylogenetics for mapping phenotypes in structured populations.PLoS biology · 2024Article
- Whole-genome resequencing of Chinese indigenous sheep provides insight into the genetic basis underlying climate adaptation.Genetics, selection, evolution : GSE · 2024Article
- PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models.bioRxiv : the preprint server for biology · 2023Article
- Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution.Genome biology and evolution · 2023Article
- Evaluating the Performance of Widely Used Phylogenetic Models for Gene Expression Evolution.bioRxiv : the preprint server for biology · 2023Article
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3 authors.
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No grant is acknowledged in the PubMed record.
Abstract
Phylogenetic comparative methods have long been a mainstay of evolutionary biology, allowing for the study of trait evolution across species while accounting for their common ancestry. These analyses typically assume a single, bifurcating phylogenetic tree describing the shared history among species. However, modern phylogenomic analyses have shown that genomes are often composed of mosaic histories that can disagree both with the species tree and with each other-so-called discordant gene trees. These gene trees describe shared histories that are not captured by the species tree, and therefore that are unaccounted for in classic comparative approaches. The application of standard comparative methods to species histories containing discordance leads to incorrect inferences about the timing, direction, and rate of evolution. Here, we develop two approaches for incorporating gene tree histories into comparative methods: one that constructs an updated phylogenetic variance-covariance matrix from gene trees, and another that applies Felsenstein's pruning algorithm over a set of gene trees to calculate trait histories and likelihoods. Using simulation, we demonstrate that our approaches generate much more accurate estimates of tree-wide rates of trait evolution than standard methods. We apply our methods to two clades of the wild tomato genus
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