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. 2021 May 3;12:2491. doi: 10.1038/s41467-021-22760-6

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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. 2 — a Phylogenetic network of the M. kansasii complex based on the core genome alignment of 358 isolates. b Population structure and genomic recombinations inferred by fastGEAR. Each line represents the genomic constitution (exhibited as color strips) of individual isolates according to ancestral (upper panel) or recent (lower panel) recombinations. Strip colors represent the different species as in panel (a). White strips (lower section) represent recent recombinations from unknown sources. Source data are provided as a Source Data file. c Length distribution of recombinant fragments in the four major species. Boxes show the median and interquartile range (IQR) while whiskers extend to a maximum of 1.5× IQR. d Maximum likelihood phylogeny of the four major species based on non-recombinant SNVs. Brackets indicate clusters containing isolates with an average pair-wise genomic difference of fewer than 100 SNVs. The colors of terminal nodes indicate the geographical origins of the isolates, corresponding to Fig. 1a. Filled circles indicate a human source; empty circles, an environmental source. MKMC M. kansasii main cluster.