ArticleGenetics2023
Demographic history inference and the polyploid continuum.
Article in Genetics, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Genomic basis of adaptation to serpentine soil in two Alyssum species shows convergence with Arabidopsis across 20 million years of divergence.Annals of botany · 2026Article
- Genomic perspectives on the inference of evolutionary changes in ecological life-history traits.Quantitative plant biology · 2026Review
- The polyploid continuum and the landscape of polyploid genomic variation.American journal of botany · 2025Review
- Bistable Mutation-Selection Equilibria and Violations of Fisher's Theorem in Tetraploids: Insights from Nonlinear Dynamics.bioRxiv : the preprint server for biology · 2025Article
- Repeated polyploidization shapes divergence in floral morphology inProceedings of the National Academy of Sciences of the United States of America · 2025Article
- Multiple Autopolyploid Arabidopsis lyrata Populations Stabilized by Long-Range Adaptive Introgression Across Eurasia.Molecular biology and evolution · 2025Article
- Parameter Scaling in Population Genetics Simulations may Introduce Unintended Background Selection: Considerations for Scaled Simulation Design.Genome biology and evolution · 2025Article
- Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations.Molecular biology and evolution · 2024Article
- Article
- Complex evolutionary processes maintain an ancient chromosomal inversion.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- dadi-cli: Automated and distributed population genetic model inference from allele frequency spectra.bioRxiv : the preprint server for biology · 2023Article
- Population structure and hybridization under contemporary and future climates in a heteroploid foundational shrub species (Frontiers in plant science · 2023Article
- Variant calling in polyploids for population and quantitative genetics.Applications in plant sciencesArticle
- Hijacking a rapid and scalable metagenomic method reveals subgenome dynamics and evolution in polyploid plants.Applications in plant sciencesArticle
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Authors and funding
4 authors.
Funding
Abstract
Polyploidy is an important generator of evolutionary novelty across diverse groups in the Tree of Life, including many crops. However, the impact of whole-genome duplication depends on the mode of formation: doubling within a single lineage (autopolyploidy) versus doubling after hybridization between two different lineages (allopolyploidy). Researchers have historically treated these two scenarios as completely separate cases based on patterns of chromosome pairing, but these cases represent ideals on a continuum of chromosomal interactions among duplicated genomes. Understanding the history of polyploid species thus demands quantitative inferences of demographic history and rates of exchange between subgenomes. To meet this need, we developed diffusion models for genetic variation in polyploids with subgenomes that cannot be bioinformatically separated and with potentially variable inheritance patterns, implementing them in the dadi software. We validated our models using forward SLiM simulations and found that our inference approach is able to accurately infer evolutionary parameters (timing, bottleneck size) involved with the formation of auto- and allotetraploids, as well as exchange rates in segmental allotetraploids. We then applied our models to empirical data for allotetraploid shepherd's purse (Capsella bursa-pastoris), finding evidence for allelic exchange between the subgenomes. Taken together, our model provides a foundation for demographic modeling in polyploids using diffusion equations, which will help increase our understanding of the impact of demography and selection in polyploid lineages.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.