Abstract
Summary Virus–host interactions are a key factor shaping population dynamics of microbial species. The CRISPR ‐ Cas adaptive immune system confers sequence‐specific immunity to viral infection and has the potential to dramatically shape coevolutionary interactions between viruses and their microbial hosts. To assess evolutionary dynamics of CRISPR loci, we have sampled a population of closely related S ulfolobus islandicus strains from K amchatka, R ussia at two time points, 10 years apart. Sequence analysis of the conserved trailer sequences reveals that alleles are reassorted among three CRISPR spacer loci into combinatorial genotypes. Reassortment provides the evolutionary independence of CRISPR loci from one another as demonstrated by the differential change in allele frequencies between two time points. Genome sequences of 12 strains from this population also reveal very recent horizontal gene transfer of novel, divergent cas gene cassettes. The evolutionary independence of CRISPR loci from each other and of the cas genes that control their function are consistent with the evolutionary expectation that reassortment increases the efficiency of adaptation at these loci that are likely under strong selection by lytic viruses.