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<div><span>Tree cultivation is a large contributor to the success in establishment of pathogens, as the use of a few productive clones in intensively managed plantations may encourage susceptibility to diseases. This has been observed in poplars where severe epidemics of native pathogens that were innocuous in their natural pathosystems occurred following host domestication. The North American fungus <i>Sphaerulina musiva</i> is responsible for leaf spots on the eastern cottonwood <i>Populus deltoides. </i>Following introduction of exotic poplar species 100 years ago, a canker disease caused by this pathogen emerged. This disease is severe, causing stem breakage and resulting in plantation failure. By comparing the genome of this fungus to the related poplar leaf pathogen <i>S. populicola</i> we found that the acquisition of a gene arsenal required for growth in woody tissues was at the origin of the adaptation of <i>S. musiva</i> to colonize trees. Recently, an outbreak of cankers induced by <i>S. musiva</i> was observed on <i>P. balsamifera</i> in Alberta. This suggests a host shift since this is not a known host. Analysis of individuals from this outbreak revealed an unusual pattern of diversity, with islands of diversity separated by fixed genome regions. This new population was likely the result of the hybridization of two individuals followed by limited number of recombination events. The population infecting <i>P. balsamifera</i> has strong clonality: we observed a transposon proliferation as well as fixation of the Mat1.1 allele. The shift from a sexual to a clonal population may constitute one rapid way to fix beneficial mutations. The development and expansion of poplar cultivation triggered changes in a native pathogen, resulting in a specialized population with higher fitness.</span><p> </div>