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. 2024 Oct 16;635(8037):178–185. doi: 10.1038/s41586-024-07991-z

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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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 8 — dN/dS vs dS (A,B) dN/dS vs dS between the different populations (hpAfrica2 excluded) and hpAfrica2 for the undifferentiated (A) and differentiated (B) genes. Thus, all comparisons involve hpAfrica2 strains and the dots are coloured based on the non-hpAfrica2 population. In addition, the shape represents the ecospecies of the non-hpAfrica2 strain, the dots represent Hardy strains while the crosses represent the Ubiquitous strains; the primates and H. acinonychis strains are indicated with squares and circles, respectively. (C,D) dN/dS vs dS between the Ubiquitous and Hardy strains for the undifferentiated (C) and differentiated (D) genes (subplots based on whether the Hardy strains were H. acinonychis or non-H. acinonychis). For the C and D subplots, all comparisons involve one Hardy (H. acinonychis or non-H. acinonychis) and one Ubiquitous strain, and the dots are coloured based on the Ubiquitous strain population. In all cases, each dot represents the value for a non-outgroup strain, averaged over their values when compared against the different outgroup strains (the outgroups are hpAfrica2 for subplots A and B and H. acinonychis or Hardy H. pylori for subplots C and D). (E) Relationship between dS and Average Nucleotide Identity (ANI) for the same comparisons as shown in panel D.