LTREB: Genetic analysis of metapopulation processes in the Silene-microbotryum host-pathogen system

在自然界中，生物种群通常聚集在不同的斑块中，随着时间的推移，它们交换移民，可能会灭绝，后来又重新定居。这种动态种群碎片化的遗传后果已经在理论上进行了研究，但由于需要大量的长期数据，实验研究滞后。拟议中的研究将利用近30年来从一种植物（白色campion）和一种相关疾病（花药黑穗病）的数百个种群中收集的数据来弥补这一差距。有了这些数据，我们将能够跟踪当地人口的遗传，因为他们出生，交换移民，以及可能灭绝。这些观察结果对于理解遗传如何影响灭绝和殖民成功非常重要。更广泛地说，了解相互联系的种群的动态对于预测疾病如何从局部斑块发生，入侵物种如何传播，或者当物种稀少或发生在碎片化栖息地时物种的遗传如何改变是至关重要的。该研究的主要目的是跟踪相互联系的种群中灭绝和殖民化的过程，并研究这些过程如何创造和破坏遗传多样性。这一建议是建立在一项28年的研究基础上的，该研究是对白色玉米花（Silene latifolia）及其病原菌Microbotryum violaceum（花药黑穗病）的数值动力学研究。这个项目使用长期的种群遗传方法来描述大量的殖民和灭绝事件，并随着时间的推移跟踪种群。所使用的方法将包括长期监测（最终对800多个种群进行30年的监测）和持续的基因取样（最终进行15年的监测）。沉默种群的高通量基因组研究将为遗传分化、新建立种群的亲代、种群扩张或收缩期间的基因流动、种子库的遗传后果以及近亲繁殖和遗传拯救对种群持久性的重要性提供前所未有的解决方案。此外，在本研究过程中发生了广泛的人口统计学变化，这为探索寄主植物和病害的非平衡系统的群体遗传学开辟了潜力。Silene/Microbotryum系统已成为许多实验室的模型，该研究将提供公开可用的人口统计和基因组数据、活体收集和DNA样本的长期数据集。这项研究将在生态学、基因组学、生物信息学和计算生物学等重要领域提供及时的科学训练。

In nature, populations of organisms are generally clustered into distinct patches that, over time, exchange migrants and perhaps suffer extinction and later recolonization. The genetic consequences of this dynamic population fragmentation has been studied in theory, but experimental studies have lagged behind because of the large quantity of long-term data that are required. The proposed research will close this gap using nearly three decades of data collected from hundreds of populations of a plant (white campion) and an associated disease (anther smut). With these data, we will be able to follow the genetics of local populations as they are born, exchange migrants, and possibly go extinct. These observations are important for understanding how genetics affects extinction and colonization success. More broadly, understanding the dynamics of interconnected populations is fundamental to predicting how disease outbreaks can occur from local patches, how invasive species spread, or how the genetics of species can be altered when they are rare or occur in fragmented habitats. The major objective of the proposed research is to follow the process of extinction and colonization in interconnected populations and study how these processes create and destroy genetic diversity. This proposal builds on a now 28-year study of the numerical dynamics of Silene latifolia (white campion) and its pathogen Microbotryum violaceum (anther smut). This project uses a long-term population genetic approach to characterize numerous colonization and extinction events and to follow populations through time. Methods used will include long-term monitoring (eventually more than over 800 populations for 30 yrs) and continued genetic sampling (eventually 15yrs). High throughput genomic studies of Silene populations will provide unprecedented resolution of changes in genetic divergence, the parentage of newly established populations, gene flow during population expansion or contraction, the genetic consequences of seed banks and the importance of inbreeding and genetic rescue for population persistence. Also, broad demographic shifts have occurred during the course of this study, opening up the potential to explore the population genetics of non-equilibrium systems of both the host plant and the disease. The Silene/Microbotryum system has become a model for numerous labs, and this research will provide a publicly available long-term data set of demographic and genomic data, living collections, and DNA samples. This study will provide scientific training in timely important fields of ecology, genomics, bioinformatics, and computational biology.