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bioRxiv · 10.1101/2024.09.02.610893

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

Shang, H.·Jia, K.·Zhou, M.·Yang, H.·Ma, Y.·Zhang, R.
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Abstract

Incomplete lineage sorting (ILS) and introgression/hybridization (IH) is 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 are lacking 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 conveniently contribute to the intuitive inference of genetic relationships among lineages in future research.

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Shang, H., Jia, K., Zhou, M., Yang, H., Ma, Y., Zhang, R.. 2024-09-03. Phytop: A tool for visualizing and recognizing signals of incomplete lineage sorting and hybridization using species trees output from ASTRAL. https://doi.org/10.1101/2024.09.02.610893

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