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. 2024 Jan 31;15:936. doi: 10.1038/s41467-024-45024-5

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© The Author(s) 2024

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. 6 — a Proportionally scaled, color-coded semi-circles correspond to copy number estimates, calculated by Compare²² with the red color representing contaminated and blue color standing for cleaned data. Additionally, the copy numbers for seven prominent internal nodes are provided within the species tree as text node labels. b Bar plots show the bias of individual contaminated genomes introduced to copy number prediction at six selected internal nodes (N37: LUCA, N42: LECA, N46: TSAR+Archaeplastida, N51: Archaeplastida, N58:Amorphea, N61:Opisthokonta), where 100% corresponds to the copy number inferred from clean data. Abbreviations used on bar plot legends: Filt: decontaminated, Cont: contaminated. Species name abbreviation key is provided as part of the species tree leaf node labels in panel a. Bar plot are colored according to taxon lineages of the genomes with blue color representing animals, purple corresponding to fungi, green standing for plants and orange for other eukaryotes. Bars corresponding to clean data are colored in light grey, while those ones that stand for unfiltered data are charted in dark grey.