  Meloidogyne root knot nematodes (RKN) can infect most of the world's
agricultural crop species and are among the most important of all plant
pathogens. As yet however we have little understanding of their origins or the
genomic basis of their extreme polyphagy. The most damaging pathogens reproduce
by mitotic parthenogenesis and are suggested to originate by interspecific
hybridizations between unknown parental taxa. We sequenced the genome of the
diploid meiotic parthenogen Meloidogyne floridensis, and use a comparative
genomic approach to test the hypothesis that it was involved in the hybrid
origin of the tropical mitotic parthenogen M. incognita. Phylogenomic analysis
of 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 hybrid
origins of M. incognita. Analysis of the M. floridensis genome revealed many
gene loci present in divergent copies, as they are in M. incognita, indicating
that it too had a hybrid origin. The triploid M. incognita is shown to be a
complex double-hybrid between M. floridensis and a third, unidentified parent.
The agriculturally important RKN have very complex origins involving the mixing
of several parental genomes by hybridization and their extreme polyphagy and
agricultural success may be related to this hybridization, producing
transgressive variation on which natural selection acts. Studying RKN variation
via individual marker loci may fail due to the species' convoluted origins, and
multi-species population genomics is essential to understand the hybrid
diversity and adaptive variation of this important species complex. This
comparative genomic analysis provides a compelling example of the importance
and complexity of hybridization in generating animal species diversity more
generally.
