Bayesian skyline plot showing the population size through time for human-associated S. suis, which is constructed based on a subsample of HAC isolates (n=174). The Y-axis represents the effective population size, and the X-axis is calendar years. The line shows the median estimate of the population size. Blue shading shows 95% highest posterior density. Timed phylogeny of the subsample of HAC isolates (n=174). Maximum clade credibility tree is produced using strict-clock model in BEAST2. Major sub-lineages in Asia are indicated (I, II, III). Acquisition of the 89-kb pathogenicity island is indicated by a red pentagon. Acquisition of the 78-kb pathogenicity island, and the 127-kb MGE are indicated by black and green pentagon, respectively. The blue and red block of heatmaps represent the presence of MGEs and ARGs, respectively. Gray represents absence. 