Fig. 1: Retention of ancestral, co-diversifying rodent gut symbionts in laboratory mice.

a Phylogeny shows evolutionary relationships among rodent host species for which gut bacterial genomes were included in this study. b Phylogeny shows relationships among gut bacterial genomes assembled from the rodent gut microbiota. Color of outer ring denotes bacterial phyla. Inner bar surrounding phylogeny marks clades displaying significant evidence of co-diversification (nonparametric permutation test, r > 0.75, p-value < 0.01). Raw p-values and p-values corrected for multiple comparisons are presented in Supplementary Data 4. c–e Tanglegrams show concordance between gut bacterial (left) and rodent (right) phylogenetic trees. Dashed lines connect bacterial genomes with the host species from which they were recovered. Genomes derived from mice (Mus musculus) sampled in the lab or the wild are labeled. ‘W’ and ‘eW’ indicate ‘wildling’ and ‘ex-wild’ mice, respectively. Numbers left and right of tree are bootstrap support values and genome IDs, respectively. f Phylogeny shows relationships among all bacterial genomes belonging to co-diversifying clades shown in Fig. 1 that contain genomes from murids and non-murids, i.e., co-diversifying clades that could be inferred to be ancestral to murids. Circles indicate clades (colored by phylum, left) or MAGs derived from laboratory mice (grey, right). Sizes of circles indicate the number of MAGs. Identification numbers are listed to the right of each clade. Source data are provided as a Source Data file. Created in BioRender. Moeller, A. (2025) https://BioRender.com/s37r208.