Disentangling the genetic origins of a plant pathogen during disease spread using an original molecular epidemiology approach

The advent of molecular epidemiology has greatly improved our ability to identify population sources and track pathogen movement. Yet the wide spatial and temporal scales usually considered are useful only to infer historical migration pathways. In this study, Bayesian genetic assignments and a landscape epidemiology approach were combined to unravel genetic origin and annual spread during a single epidemic of a plant pathogen: the poplar rust fungus Melampsora larici-populina. The study focused on a particular area—the Durance River valley—which enabled inoculum sources to be identified and channeled spread of the epidemic along a one-dimensional corridor. Spatio-temporal monitoring of disease showed that the epidemic began in the upstream part of the valley and spread out downstream. Using genetic assignment tests, individuals collected at the end of the epidemic were sorted into two genetic groups; very few hybrids were detected, although individuals from both groups coexisted locall...

分子流行病学（molecular epidemiology）的兴起，极大提升了我们识别病原种群来源、追踪病原传播动态的能力。然而，常规研究中采用的大范围时空尺度，仅能用于推断病原的历史迁移路径。本研究结合贝叶斯遗传归属分析与景观流行病学（landscape epidemiology）方法，解析了一种植物病原——杨树叶锈病菌（Melampsora larici-populina）单次流行事件中的遗传起源与年度传播规律。本研究聚焦于迪朗斯河谷（Durance River valley）这一特定区域，该区域的地理格局便于明确病原接种体来源，并使病害流行沿一维廊道定向传播。病害的时空监测结果显示，此次流行始于河谷上游区域，并沿河道向下游扩散。通过遗传归属检测，流行末期采集的病原菌株被划分为两个遗传类群；尽管两类群的菌株在局部区域共存，但仅检测到极少量杂交个体……