Population structure of E. coli at different iterative-PopPUNK levels. (A) Comparison of PopPUNK clusters and a phylogenetic tree. The outer solid ring represents 9 PopPUNK clusters at 50% of the MACD, corresponding to nine E. coli phylogroups. The middle ring contains 42 clusters at 20% of the MACD, corresponding to 42 clusters from phylogenetic tree at 20% SNP distance. The inner solid ring shows 94 PopPUNK clusters at 7.9% of the MACD, corresponding to 92 E. coli ST groups. Colors in the tree leaves and branches are used to present these 92 STs and nine phylogroups, respectively. The parameters used for estimating PopPUNK clusters were all set to default with BGMM model (two components). (B) The distribution of matching rate and the number of clusters being estimated at multiple levels for this set of E. coli genomes. The tree was plotted using iTOL (https://itol.embl.de/). The comparison of PopPUNK clusters and an iterative-PopPUNK tree is available as Supplemental Figure S2. The original figure with high resolution is available as Supplemental Figure S3.
