School of Biology and School of Mathematics, Georgia Institute of Technology, 310 Ferst Dr, Atlanta, Georgia 30332, USA.
Evolution. 2012 Jul;66(7):2015-29. doi: 10.1111/j.1558-5646.2012.01595.x. Epub 2012 Mar 19.
The CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) system is a recently discovered type of adaptive immune defense in bacteria and archaea that functions via directed incorporation of viral and plasmid DNA into host genomes. Here, we introduce a multiscale model of dynamic coevolution between hosts and viruses in an ecological context that incorporates CRISPR immunity principles. We analyze the model to test whether and how CRISPR immunity induces host and viral diversification and the maintenance of many coexisting strains. We show that hosts and viruses coevolve to form highly diverse communities. We observe the punctuated replacement of existent strains, such that populations have very low similarity compared over the long term. However, in the short term, we observe evolutionary dynamics consistent with both incomplete selective sweeps of novel strains (as single strains and coalitions) and the recurrence of previously rare strains. Coalitions of multiple dominant host strains are predicted to arise because host strains can have nearly identical immune phenotypes mediated by CRISPR defense albeit with different genotypes. We close by discussing how our explicit eco-evolutionary model of CRISPR immunity can help guide efforts to understand the drivers of diversity seen in microbial communities where CRISPR systems are active.
CRISPR（成簇规律间隔短回文重复）系统是细菌和古菌中最近发现的一种适应性免疫防御系统，通过将病毒和质粒 DNA 定向整合到宿主基因组中发挥作用。在这里，我们在生态背景下引入了一个多尺度模型，用于研究宿主和病毒之间的动态协同进化，并纳入了 CRISPR 免疫原理。我们分析了该模型，以测试 CRISPR 免疫是否以及如何诱导宿主和病毒多样化，并维持许多共存的菌株。我们表明，宿主和病毒共同进化形成高度多样化的群落。我们观察到已存在菌株的间断替换，因此在长期来看，种群之间的相似度非常低。然而，在短期内，我们观察到与新菌株（作为单菌株和联盟）的不完全选择扫荡以及先前罕见菌株的重现一致的进化动态。多个主要宿主菌株的联盟预计会出现，因为尽管宿主菌株具有不同的基因型，但 CRISPR 防御可以介导几乎相同的免疫表型。我们最后讨论了我们关于 CRISPR 免疫的明确生态进化模型如何帮助指导理解在 CRISPR 系统活跃的微生物群落中观察到的多样性驱动因素的努力。
