Fig. 6.

Inferred clonal structure for population m6 of LTEE data is consistent with previous analysis. The clustering results from a) our method and b) previous results (Good et al. 2017) on the population m6 are almost identical. Both results indicate that m6 features long-term coexistence and competition between two clades. c) D matrix segmented into groups during the initial clustering process. The competition between two clades is reflected clearly in the D matrix as two major blocks of entries. Alleles that belong to the same clade have frequency changes that are positively correlated with one another (positive D values), while those in competing clades have anti-correlated frequency changes (negative D values).