Fig. 8

Consensus tree of Staphylococcus aureus flocks mapped to the USA300TCH1516 genome. a The neighbor joining the bootstrap consensus tree for 100 simulations is shown. The majority of the genome occupies the largest branch consisting of a virtual polytomy (red). Four other branches of note are highlighted, the largest of which describes the flock consisting of genes from the recombined region (green). b We constructed HMMs from the orthologous groups (genes) in each of the four dominant flocks and queried them against a USA300TCH1516 reference. Their genomic locations are shown in the four tracks displayed here. The outermost track is composed of genes from the largest flock. The second track localizes genes from the second largest flock to the known recombined region