Scope and method of study. The objective of this study was to enhance our understanding of the ecology of plant viruses from native plants and their phylogenetic relationship with related viruses from cultivated crops. To achieve this objective I performed three studies in which: (1) I reviewed evolution of virulence (EOV) in native and cultivated plants from wide groups of viruses from the literature; (2) I tested the effect of site, plant host and year on the composition of viruses isolated from six native plant hosts; and (3) I constructed a phylogeny of a previously unreported plant virus infecting native plants from subfamily Comovirinae with related members infecting cultivated crops. The second and third studies were based on viruses isolated from plant samples collected from the Tallgrass Prairie Preserve (TGPP) in Osage County, Oklahoma over four years (2004–2008).;Findings and conclusions. I found that the evolution of virulence (EOV) not only results from the genetic compatibility between plant viruses and hosts but is also influenced by many ecological factors. In nature, rich host diversity may influence high genetic drift on viruses and limits adaptation of virulent variants. While in cultivated conditions, factors such as high density of susceptible hosts, low host diversity and spread of efficient vectors provide adaptive advantage to virulent variants. Partial canonical correspondence analysis on plant virus data from TGPP shows that plant virus composition has a significant relationship with host identity but not a clear relationship with site and year. Variation partitioning indicates host identity explains about 5% variation in virus composition. Virus and host relationships could not be interpreted from host taxonomy and ecology. A phylogenetic relation of a previously unreported virus, TGP Comovirin-1 from this study with related members of Secoviridae from cultivated plants reveals monophyletic origin. However, TGP Comovirin-1 appears as a separate sister branch in Comovirinae clade with no significant bootstrap support with existing genera. Divergent relationship of TGP Comovirin-1 likely represents ancient characters within the subfamily and may relate to its evolution in natural conditions as reported in other groups. The study of plant viruses from nature may have implications in understanding evolution and epidemiology of viruses in crops.
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