Phytop: a tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL

文献类型： 外文期刊

第一作者： Shang, Hong-Yun

作者： Shang, Hong-Yun;Zhou, Min-Jie;Yang, Hao;Ma, Yong-Peng;Zhang, Ren-Gang;Shang, Hong-Yun;Zhou, Min-Jie;Yang, Hao;Ma, Yong-Peng;Zhang, Ren-Gang;Shang, Hong-Yun;Zhou, Min-Jie;Yang, Hao;Zhang, Ren-Gang;Jia, Kai-Hua;Li, Nai-Wei;Tian, Xiao-Ling

作者机构：

期刊名称：HORTICULTURE RESEARCH （ 影响因子：8.5； 五年影响因子：9.1 ）

ISSN： 2662-6810

年卷期： 2025 年 12 卷 3 期

页码：

收录情况： SCI

摘要： 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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