Fig. 1

Phylogenetic relationships and population structure of 437 S. aureus isolates from animal and human hosts. a Maximum likelihood tree showing the phylogenetic relationships of 437 S. aureus genomes. The tree was built using the SNPs extracted from 1,586 core genes. The tree was rooted using the BAPS Cluster 2, which was closest to the outgroup (Staphylococcus argenteus MSHR1132 (NCBI accession number: GCA_000236925.1; Supplementary Fig. 1). Colored branches represent the 12 sequence clusters inferred by the program BAPS. Within each cluster, the hosts from which isolates in the cluster were derived from are shown in the shaded branches. The three outer rings represent the host, sequence type (ST), and the presence of the SCCmec in each genome. Branch scale represents the number of nucleotide substitutions per site. b Proportion and distribution of S. aureus isolates by host within each sequence cluster. c Proportion and distribution of S. aureus isolates by host within each major ST. For panels b and c, the total number of genomes in each category are shown on top of the bars and the colors of the bars correspond to the color legend of hosts in panel a