ArticleSystematic biology2022
Maximum Parsimony Inference of Phylogenetic Networks in the Presence of Polyploid Complexes.
Article in Systematic biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Unravelling Complex Hybrid and Polyploid Evolutionary Relationships Using Phylogenetic Placement of Homologous Gene Copies from Target Enrichment Data.Systematic biology · 2026Article
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- Phylogenetic networks empower biodiversity research.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Variance ofFrontiers in genetics · 2025Article
- Accurate Inference of the Polyploid Continuum Using Forward-Time Simulations.Molecular biology and evolution · 2024Article
- Complex but Clear Allopolyploid Pattern of Subtribe Tussilagininae (Asteraceae: Senecioneae) Revealed by Robust Phylogenomic Evidence, with Development of a Novel Homeolog-Sorting Pipeline.Systematic biology · 2024Article
- Polyphest: fast polyploid phylogeny estimation.Bioinformatics (Oxford, England) · 2024Article
- Complex Polyploids: Origins, Genomic Composition, and Role of Introgressed Alleles.Systematic biology · 2024Article
- Detecting genetic gain and loss events in terms of protein domain: Method and implementation.Heliyon · 2024Article
- Subgenome-aware analyses reveal the genomic consequences of ancient allopolyploid hybridizations throughout the cotton family.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Phylogenetic Analysis of Allotetraploid Species Using Polarized Genomic Sequences.Systematic biology · 2023Article
- Evolution of hygrophytic plant species in the Anatolia-Caucasus region: insights from phylogenomic analyses of Cardamine perennials.Annals of botany · 2023Article
- Phylotranscriptomics supports numerous polyploidization events and phylogenetic relationships inFrontiers in plant science · 2023Article
- Reticulate Evolution in the Western Mediterranean Mountain Ranges: The Case of theFrontiers in plant science · 2022Article
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Authors and funding
5 authors.
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Abstract
Phylogenetic networks provide a powerful framework for modeling and analyzing reticulate evolutionary histories. While polyploidy has been shown to be prevalent not only in plants but also in other groups of eukaryotic species, most work done thus far on phylogenetic network inference assumes diploid hybridization. These inference methods have been applied, with varying degrees of success, to data sets with polyploid species, even though polyploidy violates the mathematical assumptions underlying these methods. Statistical methods were developed recently for handling specific types of polyploids and so were parsimony methods that could handle polyploidy more generally yet while excluding processes such as incomplete lineage sorting. In this article, we introduce a new method for inferring most parsimonious phylogenetic networks on data that include polyploid species. Taking gene tree topologies as input, the method seeks a phylogenetic network that minimizes deep coalescences while accounting for polyploidy. We demonstrate the performance of the method on both simulated and biological data. The inference method as well as a method for evaluating evolutionary hypotheses in the form of phylogenetic networks are implemented and publicly available in the PhyloNet software package. [Incomplete lineage sorting; minimizing deep coalescences; multilabeled trees; multispecies network coalescent; phylogenetic networks; polyploidy.].
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