ArticleSystematic biology2018
HyDe: A Python Package for Genome-Scale Hybridization Detection.
Article in Systematic biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 104 papers.
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104 citing papers in PubMed.
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- Introgression and parental conflict shape repeated occurrences of postzygotic isolation in Mimulus.Current biology : CB · 2026Article
- Phylogenetic discordance arises from incomplete lineage sorting and pre-speciation introgression during erosion-mediated radiation of Asian warty newts.Zoological research · 2026Article
- Genomics of Sable (Martes zibellina) × Pine Marten (Martes martes) Hybridization.Genome biology and evolution · 2026Article
- Resolving the Taxonomic Enigma ofEcology and evolution · 2026Article
- Phylogenetic systematics of Juncaceae.American journal of botany · 2026Article
- Genomic consequences of residual recombination in a hybrid apomictic hickory complex.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
- Inference of Cross-Species Gene Flow Using Genomic Data Depends on the Methods: Case Study of Gene Flow in Drosophila.Systematic biology · 2025Article
- Towards a Research Programme Aiming at Causes and Consequences of Reticulate Evolution.Biology · 2025Review
- Phylogenomic discordance is driven mainly by pervasive ancient hybridization and incomplete lineage sorting during the early divergence of major angiosperm lineages.Plant communications · 2025Article
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
- Detecting Introgression in Shallow Phylogenies: How Minor Molecular Clock Deviations Lead to Major Inference Errors.Molecular biology and evolution · 2025Article
- Introgression and Parental Conflict Shape Repeated Occurrences of Postzygotic Isolation.bioRxiv : the preprint server for biology · 2025Article
44 more citing papers are in PubMed but not listed here.
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4 authors.
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Abstract
The analysis of hybridization and gene flow among closely related taxa is a common goal for researchers studying speciation and phylogeography. Many methods for hybridization detection use simple site pattern frequencies from observed genomic data and compare them to null models that predict an absence of gene flow. The theory underlying the detection of hybridization using these site pattern probabilities exploits the relationship between the coalescent process for gene trees within population trees and the process of mutation along the branches of the gene trees. For certain models, site patterns are predicted to occur in equal frequency (i.e., their difference is 0), producing a set of functions called phylogenetic invariants. In this article, we introduce HyDe, a software package for detecting hybridization using phylogenetic invariants arising under the coalescent model with hybridization. HyDe is written in Python and can be used interactively or through the command line using pre-packaged scripts. We demonstrate the use of HyDe on simulated data, as well as on two empirical data sets from the literature. We focus in particular on identifying individual hybrids within population samples and on distinguishing between hybrid speciation and gene flow. HyDe is freely available as an open source Python package under the GNU GPL v3 on both GitHub (https://github.com/pblischak/HyDe) and the Python Package Index (PyPI: https://pypi.python.org/pypi/phyde).
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