ArticleHorticulture research2025
Phytop: a tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL.
Article in Horticulture research, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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21 citing papers in PubMed.
- Phylogenomic evidence provides insights into the phylogeny and speciation patterns in the subgenus Caloscordum (Allium, Amaryllidaceae).Cladistics : the international journal of the Willi Hennig Society · 2026Article
- Phylotranscriptomics Allows Distinguishing Major Gene Flow Events from Incomplete Lineage Sorting in Rapidly Diversifying Mimetic Orchids (Genus Ophrys).Genome biology and evolution · 2026Article
- Contrasting Dispersal Histories Shape Distinct Evolutionary Trajectories Between Malesian and PantropicalEcology and evolution · 2026Article
- Phylogenomics and species delimitation of an annual gentian complex on the Qinghai-Tibet Plateau.BMC plant biology · 2026Article
- Phylogenomic conflict in Moraceae: Evidence for pervasive introgression and incomplete lineage sorting.Plant diversity · 2026Article
- Nuclear phylogenomic analysis of Allium (Amaryllidaceae) species from Kazakhstan reveals incomplete lineage sorting and gene flow.BMC plant biology · 2026Article
- Disentangling complex language contact and admixture in the broad Gansu-Qinghai region.Fundamental research · 2026Article
- Accurate Identification ofPlants (Basel, Switzerland) · 2026Article
- Phylogenetic discordance arises from incomplete lineage sorting and pre-speciation introgression during erosion-mediated radiation of Asian warty newts.Zoological research · 2026Article
- Phylogenomics unravels the early divergence and diversification in Bignoniaceae.Plant diversity · 2026Article
- Phylogeny of waterfowl (Anseriformes) constructed using genome sequences provides insights into topological incongruences.Molecular biology and evolution · 2026Article
- The complete mitochondrial genome ofFrontiers in plant science · 2026Article
- Analysis of a near telomere-to-telomere genome of Phellodendron amurense reveals insights into berberine biosynthesis.Nature communications · 2025Article
- When islands collide: Divergence predicts outcomes of secondary contact during the fusion of Sulawesi's paleo-archipelago.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Do syngameons exist in tropical trees? Challenges to determine their existence and estimate their frequency.Biology letters · 2025Review
- Mitonuclear Discordance of Beetles Shaped by Incomplete Lineage Sorting and Introgression Under Loose Interaction Mechanism.Molecular biology and evolution · 2025Article
- Reticulate allopolyploidy and subsequent dysploidy drive evolution and diversification in the cotton family.Nature communications · 2025Article
- Phylogenomics of East Asian lineage within subgenus Anguinum (Allium, Amaryllidaceae): insights into its taxonomic puzzles and phylogenetic conflicts.BMC plant biology · 2025Article
- Phylogenomic Analyses Reveal Species Relationships and Phylogenetic Incongruence with New Member Detected inPlants (Basel, Switzerland) · 2025Article
- SOI: robust identification of orthologous synteny with the Orthology Index and broad applications in evolutionary genomics.Nucleic acids research · 2025Article
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8 authors.
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Abstract
Incomplete lineage sorting (ILS) and introgression/hybridization (IH) are prevalent in nature and thus frequently result in discrepancies within phylogenetic tree topologies, leading to misinterpretation of phylogenomic data. Despite the availability of numerous tools for detecting ILS and IH among species, many of these tools lack effective visualization, or are time-consuming, or require prior predetermination. Here, we addressed these shortcomings by developing a fast-running, user-friendly tool called Phytop. By defining ILS and IH indices to quantify ILS and IH, this tool can detect the extent of ILS and IH among lineages with high reliability, and can visualize them based on the gene tree topology patterns constructed using ASTRAL. We tested Phytop extensively using both simulated and real data, and found that it enables users to quickly and conveniently estimate the extent of ILS and IH, thus clarifying the phylogenetic uncertainty. Phytop is available at https://github.com/zhangrengang/phytop and is expected to contribute to the intuitive and convenient inference of genetic relationships among lineages in future research.
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