We have analyzed the genotypic diversity of Sugarcane yellow leaf virus (SCYLV) collected from North, South, and Central America by fingerprinting assays and selective cDNA cloning and sequencing. One group of isolates from Colombia, designated the C-population, has been identified as residing at the root node between a separable superpopulation structure of SCYLV and other members of the family Luteoviridae, indicating that the progenitor viruses of the North, South, and Central American isolates of the SCYLV superpopulation most likely arose from a C-population structure. From a model of intrafamilial evolution (F. Moonan et al., Virology 269:156-171, 2000), a prediction could be made that within the SCYLV species, the capacity of genomic sequence divergence would range from lowest in the capsid protein open reading frame 3 (ORF 3) to highest in a region spanning across the carboxy-terminal end of the RNA-dependent RNA polymerase ORF. We have demonstrated the validity and applicability of this intrafamilial model for the prediction of intraspecies SCYLV diversity. Analysis of spatial phylogenetic variation (SPV) within the SCYLV isolates could not be assessed by application of a "partial likelihoods assessed through optimization" (PLATO)-derived intraspecies model alone. However, application of a PLATO-derived intrafamilial model with the intraspecies-derived model allowed distinction of three forms of SPV. Two of the SPV forms identified correspond to the extremes in a continuum of sequence evolution displayed in a SCYLV superpopulation structure, and the third form was diagnostic of a C-population structure. The application of these types of models has value in terms of predicting the types of SCYLV intraspecies diversity that may exist worldwide, and in general, may be useful in application for more informed design of transgenes for use in the elicitation of homology-dependent virus resistance mechanisms in transgenic plants.In the Americas, Sugarcane yellow leaf virus (SCYLV) is associated with a disease referred to as yellow leaf syndrome (YLS [3,5,6,47,55]), although a similar disease via phytoplasma infection may produce otherwise identical symptomology and is also currently referred to as YLS disease in certain areas of the world (6, 45). In sugarcane, losses of as high as 50% have been estimated to have occurred in field sites as the result of virus-induced YLS (55).The complete SCYLV genome has been sequenced and characterized and most closely resembles viruses of the family Luteoviridae in the genus Polerovirus (36, 48). The results of these studies indicate that SCYLV, like Polerovirus members of the family Luteoviridae, encode at least six definable open reading frames (ORFs) typically listed as ORFs 0 to 5 (4,7,31,32,35,36,43,48). ORFs 0 and 1 are thought to produce peptides via alternate translational start sites from the monopartite genomic RNA of SCYLV, and ORFs 3 and 4 are thought to produce peptides via alternate translation from a subgenomic RNA. These studies also indicate that a fusion pe...