ArticlePhilosophical transactions of the Royal Society of London. Series B, Biological sciences2019
The perils of intralocus recombination for inferences of molecular convergence.
Article in Philosophical transactions of the Royal Society of London. Series B, Biological sciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- Recombination and Incomplete Lineage Sorting Resolve the Enigma of Lysozyme Evolution.Journal of molecular evolution · 2026Article
- Practical Guide and Review of Fossil Tip-Dating in Phylogenetics.Systematic biology · 2026Review
- Selecting a Window Size for Phylogenomic Analyses of Whole Genome Alignments Using AIC.Systematic biology · 2026Article
- From Trees to Traits: A Review of Advances in PhyloG2P Methods and Future Directions.Genome biology and evolution · 2025Review
- 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
- The Meaning and Measure of Concordance Factors in Phylogenomics.Molecular biology and evolution · 2024Review
- Fast Bayesian Inference of Phylogenies from Multiple Continuous Characters.Systematic biology · 2024Article
- Detecting macroevolutionary genotype-phenotype associations using error-corrected rates of protein convergence.Nature ecology & evolution · 2023Article
- Recombination smooths the time signal disrupted by latency in within-host HIV phylogenies.Virus evolution · 2023Article
- Whole-genome analyses disentangle reticulate evolution of primroses in a biodiversity hotspot.The New phytologist · 2023Article
- Using all Gene Families Vastly Expands Data Available for Phylogenomic Inference.Molecular biology and evolution · 2022Article
- Probing the genomic limits of de-extinction in the Christmas Island rat.Current biology : CB · 2022Article
- Champagne: Automated Whole-Genome Phylogenomic Character Matrix Method Using Large Genomic Indels for Homoplasy-Free Inference.Genome biology and evolution · 2022Article
- Evolutionary Rate Variation among Lineages in Gene Trees has a Negative Impact on Species-Tree Inference.Systematic biology · 2022Article
- Investigating Morphological Complexes Using Informational Dissonance and Bayes Factors: A Case Study in Corbiculate Bees.Systematic biology · 2021Article
- Primate phylogenomics uncovers multiple rapid radiations and ancient interspecific introgression.PLoS biology · 2020Article
- Convergent evolution in the genomics era: new insights and directions.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Article
- Integrating natural history collections and comparative genomics to study the genetic architecture of convergent evolution.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2019Review
- Independent amylase gene copy number bursts correlate with dietary preferences in mammals.eLife · 2019Article
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3 authors.
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Abstract
Accurate inferences of convergence require that the appropriate tree topology be used. If there is a mismatch between the tree a trait has evolved along and the tree used for analysis, then false inferences of convergence ('hemiplasy') can occur. To avoid problems of hemiplasy when there are high levels of gene tree discordance with the species tree, researchers have begun to construct tree topologies from individual loci. However, due to intralocus recombination, even locus-specific trees may contain multiple topologies within them. This implies that the use of individual tree topologies discordant with the species tree can still lead to incorrect inferences about molecular convergence. Here, we examine the frequency with which single exons and single protein-coding genes contain multiple underlying tree topologies, in primates and Drosophila, and quantify the effects of hemiplasy when using trees inferred from individual loci. In both clades, we find that there are most often multiple diagnosable topologies within single exons and whole genes, with 91% of Drosophila protein-coding genes containing multiple topologies. Because of this underlying topological heterogeneity, even using trees inferred from individual protein-coding genes results in 25% and 38% of substitutions falsely labelled as convergent in primates and Drosophila, respectively. While constructing local trees can reduce the problem of hemiplasy, our results suggest that it will be difficult to completely avoid false inferences of convergence. We conclude by suggesting several ways forward in the analysis of convergent evolution, for both molecular and morphological characters. This article is part of the theme issue 'Convergent evolution in the genomics era: new insights and directions'.
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