that wheat was domesticated, suggesting a co-speciation of the host and pathogen. Similarly, another fungal pathogen Magnaporte oryzae, the causal agent of rice blast disease, underwent a host speciation due to the loss of the avirulence gene AVR-Co39 that was frequent in haplotypes from other hosts. The genetic isolation and divergence of an epidemic lineage from other populations on grasses may have resulted from rapid clonal propagation and strong selection mediated by the new domesticated host and its associated agro-ecosystem. The subsequent intensification and dissemination of this crop favored the propagation and global dispersal of clones of the rice-infecting blast pathogen (Couch, Fudal et al. 2005).
Host shift is a process in which a new pathogen emerges by adaptation to a new host that is a close relative of the former host (e.g., shifting from a wild crop to the new domesticated selection or variety of the crop). The process takes from less than 500 to 7,000 years, and the pathogen and host do not always originate in the same center of origin (Stukenbrock and McDonald 2008). An example is the shift of Rhynchosporium secalis from wild grasses to barley and rye. This was an abrupt evolutionary change that took approximately 2,500-5,000 years, much later than the domestication of barley and rye. R. secalis causes scald diseases and infects barley (Hordeum vulgare), rye (Secale cereale), and other grasses. A RFLP allelic diversity analysis of 1,366 geographical isolates indicated that the center of diversity of this pathogen did not coincide with the center of origin of barley, similar to the pattern found for the avirulence gene NIP1 (O.24). NIP1 has a dual function as both an elicitor of plant defense and as a toxin-encoding gene (O.25). NIP1 is often deleted (O.26) because its role as elicitor for plant defense drives this gene under positive diversifying selection. Further analysis of R. secalis revealed phylogenetic relationships between different host-related lineages (O.27). These analyses confirmed a later emergence of the scald pathogen, most likely between 1,200-3,600 years after the introduction of the barley agro-ecosystem into northern Europe.
Host jump describes a process through which a new pathogen emerges in a host species that is genetically distant from the original plant host (e.g., from another class or order). In this case, the geographical origin of the host does not always correspond with the geographical origin of the pathogen as observed in the host shift process. An example is the emergence of Magnaporthe oryzae, which also fits into a host-tracking co-evolutionary scenario with rice; however, the emergence of a rice-infecting lineage also involved a number of host shifts from Setaria millet to rice (Couch, Fudal et al. 2005). The close proximity