Thesis (M.S., Bioinformatics & Computational Biology)--University of Idaho, June 2014 | Potato virus Y (PVY) exists as a complex of strains, including a growing number of recombinants. Evolution of PVY proceeds rapidly through recombination, leading to adaptation of the virus to multiple potato cultivars and a wider range of environmental conditions. The origins of PVY recombinants were studied through whole genome sequencing of PVY genomes and subsequent phylogenetic and recombination analyses. A collection of 119 newly sequenced PVY isolates and 166 PVY whole genomes from the GenBank database was subjected to phylogenetic analysis focusing on genome sections commonly involved in recombination. Evolutionary relationships of these sections were thusly determined and a substantial diversity was revealed within both non-recombinant and recombinant strain types, with several lineages identified. Recombination analysis was then conducted to find novel recombinants, and 12 were identified. There are now 28 known recombinant patterns. It is now hypothesized that all known recombinant types of PVY originated more than once.