Figure 3. Model captures the emergence of trailer-end clonality in CRISPR loci.

Computational reconstructions show the loss of trailer-end diversity from CRISPR loci. Reconstructions show the 45 most frequent host strains at the 100^th, 500^th and 7000^th iterations of a representative simulation without spacer deletion. In each panel, the rows show distinct host strains, with their spacers allayed across the columns from right to left as in Figures 1, 2 and S1. Circles indicate spacers perfectly matching any of the 300 most frequent viral strains in that iteration. To preserve space, 128 clonal columns are removed in iteration 7000 prior to the divergence of sub-populations from a common ancestor (arrow). Notably one ancestral population still at low frequency (∼0.007 as shown in Figure S4) in the 100^th iteration is the common ancestor of all surviving strains.