ArticleMolecular biology and evolution2020
A Bayesian Implementation of the Multispecies Coalescent Model with Introgression for Phylogenomic Analysis.
Article in Molecular biology and evolution, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 69 papers.
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69 citing papers in PubMed.
- The Impact of Incomplete Taxon Sampling on Inference of Gene Flow by Bayesian and Summary Methods Using Genomic Sequence Data.Systematic biology · 2026Article
- Gene tree patterns help answer: vicariance or dispersal?bioRxiv : the preprint server for biology · 2026Article
- Weak but Repeated Patterns of Co-Introgression of Nuclear OXPHOS Genes and Mitochondrial DNA in Iberian Wall Lizards.Genome biology and evolution · 2026Article
- Genomic Footprints of Historical Introgression Between Ancient Lineages of Wild Oryza AA-Genome Species With Widely Separated Contemporary Distributions.Genome biology and evolution · 2026Article
- From Traps to Taxa: Building a Robust DNA Barcode Reference Library for the Early Detection of Invasive Cerambycidae.Ecology and evolution · 2026Article
- Scaling up Bayesian population phylogenomics through virtual dimension reduction.Nature communications · 2026Article
- Species Diversification in the Sky Islands of Southwestern China Revealed by Genomic, Introgression, and Demographic Analyses of Asian Shrew Moles.Systematic biology · 2026Article
- Digitaria genome analyses indicate introgression may drive local adaptation and herbicide resistance.Nature communications · 2026Article
- On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection.Molecular biology and evolution · 2026Article
- Impact of Data Error on Phylogenetic Network Inference from Gene Trees Under the Multispecies Network Coalescent.Methods in molecular biology (Clifton, N.J.) · 2026Article
- What did the dove sing to Pope Gregory? Ancestral melody reconstruction in Gregorian chant using Bayesian phylogenetics.PloS one · 2026Article
- Speciation Genomics in the Tiger Whiptail Lizards (Aspidoscelis tigris Complex).Genome biology and evolution · 2025Article
- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
- Genomic identification of conservation areas amid lineage divergence and admixture in a threatened island gecko.BMC biology · 2025Article
- Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors.Molecular biology and evolution · 2025Article
- Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family.Nature communications · 2025Article
- The power of coalescent methods for inferring recent and ancient gene flow in endangered Bactrian camels.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Genomics of Neotropical biodiversity indicators: Two butterfly radiations with rampant chromosomal rearrangements and hybridization.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
9 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
4 authors.
Funding
Abstract
Recent analyses suggest that cross-species gene flow or introgression is common in nature, especially during species divergences. Genomic sequence data can be used to infer introgression events and to estimate the timing and intensity of introgression, providing an important means to advance our understanding of the role of gene flow in speciation. Here, we implement the multispecies-coalescent-with-introgression model, an extension of the multispecies-coalescent model to incorporate introgression, in our Bayesian Markov chain Monte Carlo program Bpp. The multispecies-coalescent-with-introgression model accommodates deep coalescence (or incomplete lineage sorting) and introgression and provides a natural framework for inference using genomic sequence data. Computer simulation confirms the good statistical properties of the method, although hundreds or thousands of loci are typically needed to estimate introgression probabilities reliably. Reanalysis of data sets from the purple cone spruce confirms the hypothesis of homoploid hybrid speciation. We estimated the introgression probability using the genomic sequence data from six mosquito species in the Anopheles gambiae species complex, which varies considerably across the genome, likely driven by differential selection against introgressed alleles.
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