Figure 2. Gene-wide dn/ds analysis of the core genomes of the two radiating lineages.

dn/ds analysis for lineage 3 (A) and for lineage 4 (B). The mean values plotted on the y-axis were obtained from the dn/ds values of pairs of orthologs. Genes are ordered according to their position in the genome of Bc (A) and Bq (B). Genes with elevated dn/ds values homologous to known colonization factors of Bartonella (based on previously published results [16], [43]–[45]), are depicted by colors. at, putative autotransporter, bep, Bartonella effector protein, hbp, hemin-binding protein, iba, inducible Bartonella autotransporter, virB, VirB T4SS protein, trw, Trw T4SS protein. Genes encoding hypothetical proteins known to be important for colonization are depicted by open black squares (one in lineage 3, four in lineage 4). In lineage 3, three genes exhibit average dn/ds values ≫1 (marked by crosses). This is explained by the fact that between Br and B1-1C, only non-synonymous mutations but no synonymous mutations have been detected in these three genes. As all three genes revealed ω<1 in the other pair-wise comparisons, they were treated as outliers and excluded from further analysis.