Data from: 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 locally downstream in the valley. The epidemic originated from two genetically distinct inoculum sources. Individuals of each group then dispersed southwards along the Durance River and became mixed in poplar riparian stands. These two genetic groups were found previously at a wider spatial scale and proved to result from distinct evolutionary histories on either wild or cultivated poplars. This study showed that the two groups can mix during an epidemic but do not hybridize because they then reproduce asexually. In general, the methods employed here could be useful for elucidating the genetic origin and retracing the colonization history and migration pathways of recent epidemics.

分子流行病学（molecular epidemiology）的问世，极大增强了我们识别病原种群来源、追踪病原传播路径的能力。然而，常规研究所采用的广时空尺度分析，仅能用于推断历史迁移路径。本研究结合贝叶斯遗传归属分析（Bayesian genetic assignments）与景观流行病学（landscape epidemiology）方法，解析了植物病原落叶松杨栅锈菌（Melampsora larici-populina）单次流行期间的遗传起源与年度传播动态。研究聚焦于迪朗斯河谷（Durance River valley）这一特定区域，该区域可明确界定接种源（inoculum sources），且病害流行沿一维廊道定向推进。时空监测结果显示，本次流行始于河谷上游，并沿河道向下游扩散。通过遗传归属分析，流行末期采集的菌株被划分为两个遗传类群；尽管两类群菌株在河谷下游局部区域共存，但仅检测到极少量杂交体。本次流行起源于两个遗传特征迥异的接种源，随后各类群菌株沿迪朗斯河向南扩散，并在河岸生境的杨树种群中发生混合。此前在更大空间尺度的研究中已发现这两个遗传类群，且证实它们分别源自野生或栽培杨树的不同演化历史。本研究表明，两类群可在流行过程中发生混合，但由于其以无性繁殖方式繁衍，并未产生杂交后代。总体而言，本研究采用的方法可为阐明近期流行事件的遗传起源、追溯其定殖历史与迁移路径提供有效手段。