Fig. 1.

Cattle specialist C. jejuni emerged from a background of host generalists. (A) C. jejuni isolates (1,198) from chicken (yellow), ruminants (blue), and other sources (white) are shown on a phylogenetic tree reconstructed using an approximation of the ML algorithm implemented in RAxML, with the major MLST clonal complexes indicated next to the associated genome sequence cluster. The cattle specialist ST-61 clonal complex can be seen emerging from the generalist ST-21 complex (dashed box). The scale bar indicates the estimated number of substitutions per site. (B) ML tree of the branch differentiating ST-61 complex (blue) from ST-21 complex (yellow) isolates highlighting the existence of intermediate isolates (different shades of blue) indicative of step-wise cattle specialization. (C) Average nucleotide identity for pairwise comparisons of 1,208 core and 290 soft core genes for 46 genomes of ST-21 complex (yellow), 49 genomes of ST-61 complex (blue), and 4 intermediate isolates from ST-38 and ST-5161 (black line, black dotted, and black dotted, respectively).