Data from: Multi-scale model of CRISPR-induced coevolutionary dynamics: diversification at the interface of Lamarck and Darwin

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 multi-scale 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 extant strains, so 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 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系统（Clustered Regularly Interspaced Short Palindromic Repeats，成簇的规律间隔的短回文重复序列）是近年来在细菌与古菌中发现的一类适应性免疫防御机制，其通过将病毒与质粒DNA定向整合至宿主基因组中发挥功能。本研究提出了一种多尺度的宿主-病毒动态共演化模型，该模型在生态背景下融入了CRISPR免疫的作用原理。我们对该模型进行分析，以验证CRISPR免疫是否以及如何介导宿主与病毒的多样化演化，并维持多种共存菌株的稳定存在。研究结果显示，宿主与病毒通过共演化可形成具有高度多样性的群落。我们观测到现存菌株会发生间断性替代，使得种群在长期尺度下的整体相似性极低。但在短期尺度下，观测到的演化动态同时符合两种模式：新型菌株的不完全选择性清扫，以及此前稀有菌株的重现。研究预测将出现多株优势宿主菌株的协同类群，原因在于不同基因型的宿主菌株，其通过CRISPR防御介导的免疫表型却几乎完全一致。最后，本文讨论了本研究构建的显式CRISPR免疫生态-演化模型，将如何助力解析CRISPR系统活跃的微生物群落中多样性维持的驱动因素。