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The genetic structure of natural populations of Alaskan barley yellow dwarf virus (BYDV)-PAV, BYDV-PAS, and cereal yellow dwarf virus (CYDV)- RPV from barley (Hordeum vulgare L.) and oats (Avena sativa L.) in Alaska were analyzed between 2002 and 2004. PCR products spanning the viral coat protein gene of 187 isolates were cloned and sequenced. The majority (78%) were similar to BYDV-PAS, 19% were similar to CYDV-RPV, and only about 3% resembled BYDV-PAV. The CYDVRPV isolates clustered in three groups: 44, 17, and 39% resembled RPS-like CP from Mexico, resembled RPV-like CP from New York, or formed a unique clade that was RPV=RPS recombinant CP, respectively. The patterns of genetic variation of PAS and RPV varied little over time or with respect to host plant. The difference in spatial and temporal population genetic structures of the PAS and RPV isolates suggests that these two viruses are influenced by different agroecological factors. Sequence of PCR products spanning the carboxyl terminus of the polymerase gene, the intergenic region, and most of the coat protein gene of RPV revealed two probable ancestral recombination events for some isolates.