Ecological and genetic dynamics in six example species. (A–F) A subset of the species in Figure 2 were chosen to illustrate a range of characteristic behaviors. For each of the six species, the top panel shows the relative abundance of that species over time, whereas the bottom panel shows the frequencies of single nucleotide variants (SNVs) within that species. Colored lines indicate SNVs that underwent a significant shift in frequency over time (Methods), whereas a subset of nonsignificant SNVs are shown in light gray for comparison. The colors of temporally varying SNVs are assigned by a hierarchical clustering scheme, which is also used to determine their polarization (Methods). The shaded region denotes the antibiotic treatment period depicted in Figure 1A.
