Recurrent selective sweeps versus trench warfare in host-parasitecoevolution: the influence of population size changes

该项目的目标是深入了解宿主-寄生虫系统的共同进化，特别是产生遗传多样性的过程。在第一个目标中，我们分析了宿主和寄生虫种群等位基因频率和大小变化耦合互变的共同进化的流行病学模型。利用这些结果，我们展示了如何根据在宿主和寄生虫的整个基因组中观察到的遗传多态性的位点频谱来量化共同进化的特征。为了做到这一点，我们从共同进化的一般模型开始，包括众所周知的等位基因匹配和基因对基因模型，经常在植物和动物文献中使用。然后我们扩展了这个确定性模型，包括每一代寄主的几代寄生虫。在第二个目标中，我们研究了随机性对宿主和寄生虫种群多态性维持的影响，以及共同进化位点上等位基因的丢失和固定。模拟了两个与生物学相关的随机过程：(i)假设在后代生产方面存在很大差异，这是许多植物和昆虫寄生虫的共同特征，因此允许在寄生虫种群中发生遗传漂变；（ii）将疾病传播的随机过程建模为影响流行病学动态的马尔可夫过程。我们特别探讨了从宿主和寄生虫的三个等位基因开始的共同进化模型产生等位基因丢失或固定的条件（从而将系统减少到双等位基因或单态种群）。我们关注的是我们观察到的共同进化的两个极端情况的条件，这两个极端情况都是我们的广义模型所描述的，也是第一个资助期工作的主题，即军备竞赛（周期性选择性扫描）和堑壕战场景。

The goal of this project is to gain insights into the coevolution of host-parasite systems, particularly processes that generate genetic diversity. In the first objective, we analyze an epidemiological model of coevolution with coupled reciprocal changes in allele frequencies and size changes of host and parasite populations. Using these results, we show how signatures of coevolution can be quantified in terms of the site frequency spectrum of genetic polymorphisms observed over the whole genome of both hosts and parasites. To do this, we start from a general model of coevolution that encompasses the well-known matching-allele and gene-for-gene models frequently used in the plant and animal literature. Then we extend this deterministic model by including several parasite generations per host generation. In the second objective, we study the influence of stochasticicity on the maintenance of polymorphism in host and parasite populations as well as the loss and fixation of alleles at coevolving loci. Two stochastic processes of biological relevance are modeled: (i) genetic drift is allowed to occur in the parasite population assuming a large variance in offspring production, which is a common feature of many plant and insect parasites; (ii) the stochastic process of disease transmission is modeled as a Markov process affecting the epidemiological dynamics. We specifically explore the conditions under which co-evolutionary models starting from three alleles in hosts and parasites generate loss or fixation of alleles (thus reducing the system to two-allele or monomorphic populations). We focus on conditions under which we observe the two extreme cases of coevolution that are both described by our generalized models and were the subject of the work of the first funding period, the arms race (recurrent selective sweeps) and trench warfare scenarios.