Data from: The impact of bottlenecks on microbial survival, adaptation and phenotypic switching in host-pathogen interactions

Microbial pathogens and viruses can often maintain sufficient population diversity to evade a wide range of host immune responses. However, when populations experience bottlenecks, as occurs frequently during initiation of new infections, pathogens require specialized mechanisms to regenerate diversity. We address the evolution of such mechanisms, known as stochastic phenotype switches, which are prevalent in pathogenic bacteria. We analyze a model of pathogen diversification in a changing host environment that accounts for selective bottlenecks, wherein different phenotypes have distinct transmission probabilities between hosts. We show that under stringent bottlenecks, such that only one phenotype can initiate new infections, there exists a threshold stochastic switching rate below which all pathogen lineages go extinct, and above which survival is a near certainty. We determine how quickly stochastic switching rates can evolve by computing a fitness landscape for the evolutionary dynamics of switching rates, and analyzing its dependence on both the stringency of bottlenecks and the duration of within-host growth periods. We show that increasing the stringency of bottlenecks or decreasing the period of growth results in faster adaptation of switching rates. Our model provides strong theoretical evidence that bottlenecks play a critical role in accelerating the evolutionary dynamics of pathogens.

微生物病原体与病毒通常可维持充足的种群多样性，以逃逸宿主多样的免疫应答。然而，当种群遭遇瓶颈效应时——这一现象在新感染启动阶段频繁发生——病原体需要特化机制以重建种群多样性。我们针对这类被称为随机表型转换（stochastic phenotype switches）的特化机制的演化展开研究，该类机制在病原菌中广泛存在。我们分析了一个宿主环境动态变化下的病原体多样化模型，该模型纳入了选择性瓶颈效应：不同表型在宿主间的传播概率存在显著差异。研究结果显示，在严格瓶颈条件下（即仅单一表型可启动新感染），存在一个临界随机转换速率：当转换速率低于该临界值时，所有病原体谱系均会灭绝；而高于该临界值时，病原体种群存活几乎成为必然。我们通过计算随机转换速率演化动力学的适应度景观（fitness landscape），并分析其对瓶颈严格程度与宿主内增殖周期时长的依赖关系，明确了随机转换速率的演化速度。研究表明，提升瓶颈的严格程度或缩短宿主内增殖周期，均可加快转换速率的适应进程。本模型提供了强有力的理论证据，证明瓶颈效应在加速病原体进化动力学过程中发挥着关键作用。