Fig. 2: The H. bakeri and H. polygyrus genomes are highly divergent.

a Gene tree of the ribosomal internal transcribed spacer 2 (ITS2) in laboratory isolates of H. bakeri, wild isolates of H. polygyrus, and outgroup taxa. The sequences are from Cable et al. ³⁷ or the nuclear genomes of individuals sequenced as part of this work (highlighted in bold). The location of the laboratory or wild mouse colony from which each individual was collected is indicated. Bootstrap support values are shown for the branches subtending the H. bakeri and H. polygyrus clades. Branch lengths represent the number of substitutions per site; scale is shown. b The relative position of 2667 BUSCO genes in the H. bakeri and H. polygyrus genomes. Points are coloured by Nigon element. c Whole-genome alignment between H. bakeri and H. polygyrus from minimap2. The position of each alignment in the H. bakeri reference and the nucleotide identity is shown. Only alignments that are ≥5 kb are shown. d Synonymous site divergence in 2670 BUSCO genes in the H. bakeri and H. polygyrus genomes. Solid represent LOESS smoothing functions fitted to the data; standard error is shown using grey shading. Dotted line indicates mean synonymous site divergence (6.6%). Source data this figure can be found in the Source Data file and the GitHub repository.