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. 2021 Nov 26;12:6929. doi: 10.1038/s41467-021-26931-3

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© The Author(s) 2021

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 4 — a Estimated theta value for each internal branch of the 14 species. b Estimated theta value for each internal branch of the 41 species. Warmer colors indicate higher theta and thus higher ILS level. Terminal branches are colored gray due to lack of data to infer theta. c–f represent the correlation analyses of topology frequency of each quartet species combination in the different dataset: the simulation without ILS by Phybase and empirical observation (c), the simulation with ILS by Phybase and empirical observation (d), the simulation with ILS by DendroPy and empirical observation (e), the simulation with ILS by Phybase and DendroPy (f). The “lm()” function in R was used to perform all the correlation analyses, and the p values were both less than 0.01. Source data are provided as a Source Data file.