Phylogenetic relationships of the 13 completely sequenced S. suis strains. (A) Maximum likelihood tree based on 522 concatenated core genes with nearly identical lengths in the 13 S. suis genomes. Branch lengths indicate the number of SNPs, scale as indicated. (B) UPGMA (unweighted pair-group method with arithmetic means) tree based on the presence or absence of 2374 orthologous genes generated from clustering of all CDSs. All strain specific genes were removed to reduce the number of genes acquired occasionally during horizontal gene transfer. Branch lengths represent genetic differences occurring since the previous bifurcation node.