ArticlePLoS genetics2021
Phylogenomic assessment of the role of hybridization and introgression in trait evolution.
Article in PLoS genetics, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed.
- Unravelling Complex Hybrid and Polyploid Evolutionary Relationships Using Phylogenetic Placement of Homologous Gene Copies from Target Enrichment Data.Systematic biology · 2026Article
- Loss, persistence and reversal of phenotypic traits.Biological reviews of the Cambridge Philosophical Society · 2026Review
- When Complex Models Fit the Wrong Mechanistic Complexity in Phylogenomic Analysis.Journal of molecular evolution · 2026Article
- Phylogenomic comparative methods: Accurate evolutionary inferences in the presence of gene tree discordance.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Deep Ancestral Introgression Shapes Evolutionary History of Dragonflies and Damselflies.Systematic biology · 2022Article
- Whole-Genome Resequencing of Worldwide Wild and Domestic Sheep Elucidates Genetic Diversity, Introgression, and Agronomically Important Loci.Molecular biology and evolution · 2022Article
- The effects of introgression across thousands of quantitative traits revealed by gene expression in wild tomatoes.PLoS genetics · 2021Article
- Determining the probability of hemiplasy in the presence of incomplete lineage sorting and introgression.eLife · 2020Article
- Detecting introgression from phylogenetic invariant site patterns using machine learning.Applications in plant sciencesArticle
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4 authors.
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Abstract
Trait evolution among a set of species-a central theme in evolutionary biology-has long been understood and analyzed with respect to a species tree. However, the field of phylogenomics, which has been propelled by advances in sequencing technologies, has ushered in the era of species/gene tree incongruence and, consequently, a more nuanced understanding of trait evolution. For a trait whose states are incongruent with the branching patterns in the species tree, the same state could have arisen independently in different species (homoplasy) or followed the branching patterns of gene trees, incongruent with the species tree (hemiplasy). Another evolutionary process whose extent and significance are better revealed by phylogenomic studies is gene flow between different species. In this work, we present a phylogenomic method for assessing the role of hybridization and introgression in the evolution of polymorphic or monomorphic binary traits. We apply the method to simulated evolutionary scenarios to demonstrate the interplay between the parameters of the evolutionary history and the role of introgression in a binary trait's evolution (which we call xenoplasy). Very importantly, we demonstrate, including on a biological data set, that inferring a species tree and using it for trait evolution analysis in the presence of gene flow could lead to misleading hypotheses about trait evolution.
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