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. 2024 Mar 20;628(8007):424–432. doi: 10.1038/s41586-024-07182-w

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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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Fig. 2 — a, A kSNP⁴⁵ maximum-likelihood whole-genome phylogenetic tree. For each Fn genome (n = 135), the tree end points indicate the niche origin (CRC (orange); oral (blue)) and the bar colour indicates the Fn subspecies (Fna (red); Fnn (gold); Fnp (purple); Fnv (brown)). Within Fna, the background colour indicates the Fna clade (Fna C1 (green); Fna C2 (lavender)). b, A clustered dendrogram of the ANI matrix. The bar colour indicates the Fn subspecies (Fna (red); Fnn (gold); Fnp (purple); Fnv (brown)). The Fna clades are highlighted with green and lavender boxes. ANI values are reported in Supplementary Tables 4 and 5. c, A GiG-map visualization of the protein-coding gene content across Fn genomes. The top bar colour indicates the Fn subspecies (Fna (red); Fnn (gold); Fnp (purple); Fnv (brown)) and the box colour indicates the Fna clade (Fna C1 (green); Fna C2 (lavender)). The inset on the right highlights groups of protein-coding genes that are distinct between Fna C1 and Fna C2. An interactive GiG-map dataset is available at https://fredhutch.github.io/fusopangea/. d, PCA of Anvi’o gene clusters by presence and absence in each genome. The colours indicate the Fn subspecies and Fna clades (Fnn (gold); Fnp (purple); Fnv (brown); Fna C1 (green); Fna C2 (lavender)). The ellipses are drawn to 95% confidence. e, Left: PCA of Fna genome-wide methyl-modified nucleotide sequences. The ellipses are drawn to 95% confidence. The overlay of the PCA biplot shows the top five nucleotide motifs that are driving the Fna clade bifurcation. Right: a table indicating the distribution of each motif across the Fna clades. The colour indicates the Fna clade (Fna C1 (green); Fna C2 (lavender)). f, A column graph depicting the proportion of Fna CRC-associated and Fna oral-associated genomes, subset by Fna clade (Fna C1 (green); Fna C2 (lavender)). The statistical analysis was carried out using a two-sample z-test, two-tailed. NS, not significant. The graphics in f were created using BioRender.com.