Yesterday's polyploids and the mystery of diploidization

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Abstract
The 2R hypothesis, which states that two rounds of genome duplication occurred during the early evolution of vertebrates, is difficult to test because its predictions are not clear. Map-based studies have tended to support the 2R hypothesis, whereas tree-based (phylogenetic) studies have not. Inaccurate phylogenetic trees, gene conversion and ancient tandem duplications can all interfere with tree-based approaches to testing the 2R hypothesis. We know little about the molecular basis of diploidization, the evolutionary process by which a tetraploid species 'decays' to become a diploid. Different loci can appear to have different duplication dates due to either segmental allotetraploidy or independent diploidization of each locus. The draft sequence of the human genome does not provide strong support for the 2R hypothesis. Extensive gene deletion and genomic rearrangement could potentially obliterate any evidence of paleopolyploidy, even if it had occurred.