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. 2021 Jul 7;12:4059. doi: 10.1038/s41467-021-24128-2

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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. 1 — Top panel: from the phylogenetic simulations. a Comparisons between 3000 taxa simulated using a phylogenetic tree with 3000 tips and a constant rate of diversification. b Comparisons in the same dataset except that 30 of 3000 taxa each have two very closely related genomes sequenced. Bottom panel: from genomes subsampled from the 90K genome dataset. c Two genomes were randomly selected from each of the 397 named species with ≥10 genomes. d Two phylogenetic representative genomes were selected for each of the 397 named species with ≥10 genomes.