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Meloidogyne root knot nematodes (RKN) can infect most of the world'sagricultural crop species and are among the most important of all plantpathogens. As yet however we have little understanding of their origins or thegenomic basis of their extreme polyphagy. The most damaging pathogens reproduceby mitotic parthenogenesis and are suggested to originate by interspecifichybridizations between unknown parental taxa. We sequenced the genome of thediploid meiotic parthenogen Meloidogyne floridensis, and use a comparativegenomic approach to test the hypothesis that it was involved in the hybridorigin of the tropical mitotic parthenogen M. incognita. Phylogenomic analysisof gene families from M. floridensis, M. incognita and an outgroup species M.hapla was used to trace the evolutionary history of these species' genomes,demonstrating that M. floridensis was one of the parental species in the hybridorigins of M. incognita. Analysis of the M. floridensis genome revealed manygene loci present in divergent copies, as they are in M. incognita, indicatingthat it too had a hybrid origin. The triploid M. incognita is shown to be acomplex double-hybrid between M. floridensis and a third, unidentified parent.The agriculturally important RKN have very complex origins involving the mixingof several parental genomes by hybridization and their extreme polyphagy andagricultural success may be related to this hybridization, producingtransgressive variation on which natural selection acts. Studying RKN variationvia individual marker loci may fail due to the species' convoluted origins, andmulti-species population genomics is essential to understand the hybriddiversity and adaptive variation of this important species complex. Thiscomparative genomic analysis provides a compelling example of the importanceand complexity of hybridization in generating animal species diversity moregenerally.

The complex hybrid origins of the root knot nematodes revealed through comparative genomics