Multiple origins of the same polyploid species pose the question: Does evolution repeat itself in these independently formed lineages? Tragopogon is a unique evolutionary model for the study of recent and recurrent allopolyploidy. The allotetraploids T. mirus (T. dubius x T. porrifolius) and T. miscellus (T. dubius x T. pratensis) formed repeatedly following the introduction of three diploids to the United States. Concerted evolution has consistently occurred in the same direction (resulting in loss of T. dubius rDNA copies). Both allotetraploids exhibit homeolog loss, with the same genes consistently showing loss, and homeologs of T. dubius preferentially lost in both allotetraploids. We have also documented repeated patterns of tissue-specific silencing in multiple populations of T. miscellus. Hence, some aspects of genome evolution may be "hardwired," although the general pattern of loss is stochastic within any given population. On the basis of the study of F(1) hybrids and synthetics, duplicate gene loss and silencing do not occur immediately following hybridization or polyploidization, but gradually and haphazardly. Genomic approaches permit analysis of hundreds of loci to assess the frequency of homeolog loss and changes in gene expression. This methodology is particularly promising for groups such as Tragopogon for which limited genetic and genomic resources are available.