Host diversity limits the evolution of parasite local adaptation

Specificity in the interactions between hosts and their parasites can lead to local adaptation. However, the degree of local adaptation is predicted to depend upon the diversity of resistance alleles within the host population; increasing host diversity should decrease mean parasite infectivity and hence reduce local adaptation. In this study, we empirically test this prediction using the highly specific interactions between bacteria with clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR/Cas) immunity and their bacteriophage. Bacteria acquire immunity to phage by incorporating a phage-derived spacer sequence into CRISPR loci on the host genome, and phage can escape the CRISPR-mediated immunity of a specific clone by mutating the targeted sequence. We found that high levels of CRISPR allele diversity that naturally evolve in host populations exposed to phage (because each bacterial clone captures a unique phage-derived sequence) prevents phage from becoming locally adapted. By manipulating the number of CRISPR alleles in the host population, we show that phage can become locally adapted to their bacterial hosts but only when CRISPR allele diversity is low.