ArticleMolecular ecology2022
A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model.
Article in Molecular ecology, 2022. 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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17 citing papers in PubMed.
- The Complex Interplay between Evolutionary Flexibility and Diversification in a Family of Spiders.Systematic biology · 2026Article
- Scaling up Bayesian population phylogenomics through virtual dimension reduction.Nature communications · 2026Article
- Estimating Waiting Distances between Genealogy Changes under a Multi-Species Extension of the Sequentially Markov Coalescent.Systematic biology · 2026Article
- On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection.Molecular biology and evolution · 2026Article
- The Impact of Sequencing and Genotyping Errors on Bayesian Analysis of Genomic Data under the Multispecies Coalescent Model.Molecular biology and evolution · 2025Article
- Inference of Gene Flow between Species from Genomic Data When the Mode, Direction, and Lineages are Misspecified.Molecular biology and evolution · 2025Article
- Recombination and phylogenetic inference.Evolutionary journal of the Linnean Society · 2025Article
- Uncovering ghost introgression through genomic analysis of a distinct eastern Asian hickory species.The Plant journal : for cell and molecular biology · 2024Article
- Major patterns in the introgression history ofeLife · 2023Article
- Efficient Bayesian inference under the multispecies coalescent with migration.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Estimation of species divergence times in presence of cross-species gene flow.Systematic biology · 2023Article
- Inferring the Direction of Introgression Using Genomic Sequence Data.Molecular biology and evolution · 2023Article
- Power of Bayesian and Heuristic Tests to Detect Cross-Species Introgression with Reference to Gene Flow in the Tamias quadrivittatus Group of North American Chipmunks.Systematic biology · 2023Article
- Highly differentiated loci resolve phylogenetic relationships in the Bean Goose complex.BMC ecology and evolution · 2023Article
- Article
- A simulation study to examine the impact of recombination on phylogenomic inferences under the multispecies coalescent model.Molecular ecology · 2022Article
- Detecting introgression from phylogenetic invariant site patterns using machine learning.Applications in plant sciencesArticle
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3 authors.
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Abstract
Phylogenomic analyses under the multispecies coalescent model assume no recombination within locus and free recombination among loci. Yet, in real data sets intralocus recombination causes different sites of the same locus to have different genealogical histories so that the model is misspecified. The impact of recombination on various coalescent-based phylogenomic analyses has not been systematically examined. Here, we conduct a computer simulation to examine the impact of recombination on several Bayesian analyses of multilocus sequence data, including species tree estimation, species delimitation (by Bayesian selection of delimitation models) and estimation of evolutionary parameters such as species divergence and introgression times, population sizes for modern and extinct species, and cross-species introgression probabilities. We found that recombination, at rates comparable to estimates from the human being, has little impact on coalescent-based species tree estimation, species delimitation and estimation of population parameters. At rates 10 times higher than the human rate, recombination may affect parameter estimation, causing positive biases in introgression times and ancestral population sizes, although species divergence times and cross-species introgression probabilities are estimated with little bias. Overall, the simulation suggests that phylogenomic inferences under the multispecies coalescent model are robust to realistic amounts of intralocus recombination.
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