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Emerging plant pathogens have largely been a consequence of the movement of pathogens to new geographic regions. Another documented mechanism for the emergence of plant pathogens is hybridization between individuals of different species or subspecies, which may allow rapid evolution and adaptation to new hosts or environments. Hybrid plant pathogens have traditionally been difficult to detect or confirm, but the increasing ease of cloning and sequencing PCR products now makes the identification of species that consistently have genes or alleles with phylogenetically divergent origins relatively straightforward. We investigated the genetic origin of  Phytophthora andina , an increasingly common pathogen of Andean crops  Solanum betaceum ,  S. muricatum ,  S. quitoense , and several wild  Solanum  spp. It has been hypothesized that  P. andina  is a hybrid between the potato late blight pathogen  P. infestans  and another  Phytophthora  species. We tested this hypothesis by cloning four nuclear loci to obtain haplotypes and using these loci to infer the phylogenetic relationships of  P. andina  to  P. infestans  and other related species. Sequencing of cloned PCR products in every case revealed two distinct haplotypes for each locus in  P. andina , such that each isolate had one allele derived from a  P. infestans  parent and a second divergent allele derived from an unknown species that is closely related but distinct from  P. infestans ,  P. mirabilis , and  P. ipomoeae . To the best of our knowledge, the unknown parent has not yet been collected. We also observed sequence polymorphism among  P. andina  isolates at three of the four loci, many of which segregate between previously described  P. andina  clonal lineages. These results provide strong support that  P. andina  emerged via hybridization between  P. infestans  and another unknown  Phytophthora  species also belonging to  Phytophthora  clade 1c.

The Plant Pathogen Phytophthora andina Emerged via Hybridization of an Unknown Phytophthora Species and the Irish Potato Famine Pathogen, P. infestans