Genomics of eco-evolutionary dynamics in coevolving predator-prey systems

相互作用物种的互惠进化变化是物种多样化和形成的主要驱动力，主要研究宿主-寄生虫系统和互惠相互作用。尽管捕食者-猎物相互作用是常见的，并以双方的强烈选择为特征，但捕食者-猎物共同进化及其对多样化的影响很少被研究，而且从未在序列水平上进行过研究。在这里，我们建议将长期的实验进化研究与微生物种群的全基因组测序相结合。我们让7种细菌在没有和存在纤毛虫四膜虫（捕食者）的情况下在重复培养中进化34个月。我们已经收集了种群规模随时间变化的数据，并开始从保存的样本中分析猎物和捕食者在猎物（生长和防御纤毛虫）和捕食者（生长和攻击）表型水平上的进化变化。在拟议的项目中，我们计划从多个时间点对捕食者和猎物种群进行排序。在前人研究的基础上，我们的目标是确定适应性等位基因的变化，跟踪等位基因随时间的变化轨迹，比较猎物物种内部和物种之间的变化，将猎物和捕食者种群的变化联系起来，并最终将这些动态与表型和种群大小的变化联系起来。这些将是在基因组水平上追踪捕食者-猎物共同进化的第一批数据，包括整个基因组和整个种群随时间的信息。实验设计使我们能够进一步比较同一物种的重复内以及跨物种的进化变化，为我们提供了独特的机会来评估进化变化的可重复性，包括突变产生及其轨迹，以及进化变化的模式，如选择性扫描、克隆干扰或频率依赖选择的发生。

Reciprocal evolutionary changes of interacting species are major drivers for diversification and speciation and have mainly been studied in host-parasite systems and for mutualistic interactions. Although predator-prey interactions are commonplace and characterized by strong selection from both sides, predator-prey coevolution and its consequences on diversification have rarely been studied and never on the sequence level. Here we propose to combine a long-term experimental evolution study with whole genome sequencing of microbial populations over time. We allowed 7 bacterial species to evolve in replicate cultures in the absence and in the presence of the ciliate Tetrahymena thermophila (predator) for 34 months. We have already collected data on the population sizes over time and started to assay evolutionary changes in the prey and predator on the phenotype level of prey (growth and defense against ciliate) and predator (growth and offence) from preserved samples. Within the proposed project, we plan to sequence predator and prey populations from multiple time points. Based on previous work, we aim to identify adaptive allele changes, follow allele trajectories over time, compare within and between species changes in the prey, correlate changes in the prey and predator population and finally link these dynamics to the phenotypic and population size changes. These will be the first data following predator-prey coevolution on the genome level including information on the whole genome and for whole populations over time. The experimental design allows us further to compare evolutionary changes within replicates of the same species as well as across species, giving us the unique opportunity to assess the repeatability of evolutionary change in terms of mutations arsing and their trajectory as well as in terms of patterns of evolutionary change, such as the occurrence of selective sweeps, clonal interference or frequency dependent selection.