On both recent and ancient time scales, polyploidy (genome doubling) has been a significant evolutionary force in plants. Here, we examined multiple individuals from reciprocally formed populations of Tragopogon miscellus, an allotetraploid that formed repeatedly within the last 80 years from the diploids T. dubius and T. pratensis. Using cDNA-AFLPs followed by genomic and cDNA cleaved amplified polymorphic sequence (CAPS) analyses, we found differences in the evolution and expression of homeologous loci in T. miscellus. Fragment variation within T. miscellus, possibly attributable to reciprocal formation, comprised 0.6% of the cDNA-AFLP bands. Genomic and cDNA CAPS analyses of 10 candidate genes revealed that only one ''transcript-derived fragment'' (TDF44) showed differential expression of parental homeologs in T. miscellus; the T. pratensis homeolog was preferentially expressed by most polyploids in both populations. Most of the cDNA-AFLP polymorphisms apparently resulted from loss of parental fragments in the polyploids. Importantly, changes at the genomic level have occurred stochastically among individuals within the independently formed populations. Synthetic F 1 hybrids between putative diploid progenitors are additive of their parental genomes, suggesting that polyploidization rather than hybridization induces genomic changes in Tragopogon. P OLYPLOIDY, or genome doubling, has been an important process in many eukaryotic lineages, particularly in flowering plants. Recent genome-level studies have revealed that even the model ''diploid'' plant Arabidopsis thaliana has undergone several rounds of whole-genome duplication (Vision et al. 2000;Blanc et al. 2003;Bowers et al. 2003;Blanc and Wolfe 2004b). Many polyploid plants are allopolyploids, having arisen through hybridization between genetically distinct entities (usually species) and chromosome doubling. This combination of divergent but compatible genomes in allopolyploids may provide a novel substrate for evolutionary processes (Stebbins 1950;Levin 1983;Grant 2002;Osborn et al. 2003). As all genes in allopolyploids are duplicated, a number of possibilities exist for the evolutionary fate of the homeologs (genes duplicated by polyploidy). Theory predicts three potential outcomes for these duplicated genes: (1) both copies are retained and remain functional, (2) one copy retains the original function while the other copy is lost or silenced, or (3) the two copies diverge such that each copy assumes only a part of the original gene function (subfunctionalization) or one copy acquires a new function (neofunctionalization) (Ohno 1970;Lynch and Conery 2000;Prince and Pickett 2002).In recent years, studies of genome evolution and gene expression have been in the foreground of polyploidy research (Leitch and Bennett 1997;Soltis and Soltis 1999;Wendel 2000;Liu and Wendel 2003). Much of this work has been conducted on Arabidopsis (Comai et al. 2000;Lee and Chen 2001), Brassica (Lukens et al. 2004Pires et al. 2004b), and crop plants, such as wheat (Feld...