Genome-enabled analysis of plant-pathogen migration

Trade in plant and plant products has profoundly affected the global distribution and diversity of plant pathogens. Identification of migration pathways can be used to monitor or manage pathogen movement for proactive disease management or quarantine measures. Genomics-based genetic marker discovery is allowing unprecedented collection of population genetic data for plant pathogens. These data can be used for detailed analysis of the ancestry of population samples and therefore for analysis of migration. Reconstruction of migration histories has confirmed previous hypotheses based on observational data and led to unexpected new findings on the origins of pathogens and source populations for past and recent migration. The choice of software for analysis depends on the type of migration being studied and the reproductive mode of the pathogen. Biased sampling and complex population structures are potential challenges to accurate inference of migration pathways.