ArticleMolecular biology and evolution2018
Phylogeny Estimation by Integration over Isolation with Migration Models.
Article in Molecular biology and evolution, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 74 papers.
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74 citing papers in PubMed.
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- Methods to estimate marine functional connectivity: A primer.Ecological applications : a publication of the Ecological Society of America · 2026Review
- Scaling up Bayesian population phylogenomics through virtual dimension reduction.Nature communications · 2026Article
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- Demographic Models and Behavioral Assessments Uncover Distinct Species Histories in the Pseudocryptic Nudibranch GenusEcology and evolution · 2026Article
- On the robustness of Bayesian inference of gene flow to intragenic recombination and natural selection.Molecular biology and evolution · 2026Article
- More than one species of the naked mole-rat, a new biomedical model.Communications biology · 2025Article
- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- Accounting for gene flow from unsampled ghost populations while estimating evolutionary history.G3 (Bethesda, Md.) · 2025Article
- Genetic Structure ofEcology and evolution · 2025Article
- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 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
- 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
- A structured coalescent model reveals deep ancestral structure shared by all modern humans.Nature genetics · 2025Article
- Cryptic host-associated differentiation and diversity: unravelling the evolutionary dynamics of the plant pathogenIMA fungus · 2025Article
- A pangenome analysis reveals the center of origin and evolutionary history of Phytophthora infestans and 1c clade species.PloS one · 2025Article
14 more citing papers are in PubMed but not listed here.
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7 authors.
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Abstract
Phylogeny estimation is difficult for closely related populations and species, especially if they have been exchanging genes. We present a hierarchical Bayesian, Markov-chain Monte Carlo method with a state space that includes all possible phylogenies in a full Isolation-with-Migration model framework. The method is based on a new type of genealogy augmentation called a "hidden genealogy" that enables efficient updating of the phylogeny. This is the first likelihood-based method to fully incorporate directional gene flow and genetic drift for estimation of a species or population phylogeny. Application to human hunter-gatherer populations from Africa revealed a clear phylogenetic history, with strong support for gene exchange with an unsampled ghost population, and relatively ancient divergence between a ghost population and modern human populations, consistent with human/archaic divergence. In contrast, a study of five chimpanzee populations reveals a clear phylogeny with several pairs of populations having exchanged DNA, but does not support a history with an unsampled ghost population.
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