Two Decades of the Immersiporthe knoxdaviesiana (Cryphonectriaceae) Canker Outbreak Driven by Clonal Pathogen Lineages

Immersiporthe knoxdaviesiana (Cryphonectriaceae) causes an aggressive canker disease on native Myrsine melanophloeos in South Africa. The disease was first reported in the early 2000s in a Western Cape botanical garden, and is characterised by stem cankers that girdle branches, causing dieback and tree death. Nothing is known regarding the origin of the pathogen or the drivers of this serious disease. We developed 15 polymorphic microsatellite markers using genome sequences for two I. knoxdaviesiana isolates to consider these questions. The genotypes of 90 isolates, originating from historical and recent outbreaks of the disease, newly discovered populations, and asymptomatic host tissues, were determined. Population genetic analyses revealed remarkably low genetic diversity, with only three genotypes detected across all isolates. A single genotype dominated both the original outbreak population and collections made from the same locality almost two decades later, suggesting long‐term persistence of a clonal population. Additional genotypes were detected outside the primary outbreak area, including one recovered exclusively from asymptomatic host tissues. A previously unknown sexual state of I. knoxdaviesiana was discovered, although microsatellite data provided no evidence of random mating. Pathogenicity tests showed that isolates representing all identified genotypes could cause lesions on M. melanophloeos . The clonal structure and low diversity in the epidemic population are typical of an invasive species undergoing a population bottleneck through a founder event. However, evidence from this study showing that I. knoxdaviesiana exists as an endophyte in healthy trees suggests that it could be a native pathogen exhibiting increased aggressiveness under changing environmental conditions.