Multiple rounds of whole genome duplication (WGD) followed by re-diploidization have occurred throughout the evolutionary history of angiosperms. To understand why these cycles occur, much work has been done to model the genomic consequences and evolutionary significance of WGD. Since the machinations of diploidization are strongly influenced by the mode of speciation (whether a lineage was derived from ancient allo or autopolyploid), methods which can classify ancient whole genome duplication events as allo or auto are of great importance. Here we present a forward-time polyploid genome evolution simulator called SpecKS. Using extensive simulations, we demonstrate that allo and autopolyploid-derived species exhibit differently shaped Ks histograms. We also demonstrate sensitivity of the Ks histogram to the effective population size (Ne) of the ancestral species. Our findings indicate that error in the common method of estimating WGD time from the Ks histogram peak scales with the degree of allopolyploidy, and we present an alternative, accurate estimation method that is independent of the degree of allopolyploidy. Lastly, we use SpecKS results to derive tests that reveal whether a genome is descended from allo or autopolyploidy, and whether the ancestral species had a high or low Ne. We apply this test to transcriptomic data for over 200 species across the plant kingdom, validating the theory that the majority of angiosperm lineages are derived from allopolyploidization events.