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

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.

Acknowledgements

We thank the two anonymous reviewers for their insightful comments and constructive suggestions, which have significantly improved the quality of manuscript and enhance the utility of Phytop. This study was financial support by the strategic priority research program of Kunming Institute of Botany, Chinese Academy of Sciences (KIBXD202401), Natural Science Foundation of China (32471734 and 32360336), CAS ‘Light of West China’ Program, Yunnan Provincial Science and Technology Mission (202404BI090014).

Author Contributions

R. Z. and Y. M. conceived and designed the study. R. Z. performed software development. H. S. and R. Z. wrote the manuscript. R. Z. and H. S completed the data analysis and prepared the figures. R. Z., Y. M., N. L., and K. J. revised the manuscript. M. Z., X. T., and H. Y. tested the software and helped with data analysis.

Data availability

The code for Phytop is freely available on GitHub (https://github.com/zhangrengang/phytop).

Conflict of interest statement

The authors declare no conflicts of interest.

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