Weeds, trees or tomatoes; no matter the plant genome of interest, Yves Van de Peer and associate Bioinformaticians at the VIB-Ugent research institute repeatedly observe that the last genome duplication to have occurred in all extant plants happened at the same time—65 million years ago.  This is a rather peculiar date considering it coincides with earth's last mass extinction event.  With this factoid in mind, an inference can be made; duplicated chromosome mutants (polyploids) have a strong advantage during times of environmental hardship.

Although we're all aware of the Permian extinction and that virtually every organism on earth was impacted by it, the fact that Van de Peer's bioinformatic sampling of various genomes yielded a uniform date across several phyla of plants is quite impressive.

At first, Van de Peer group's sampling methods estimated that this genome duplication occurred between 40 and 80 million years ago.  With room for improvement, the VIB-Ugent bioinformaticians worked to refine this highly complex dating method.  Equipped with their expertise in comparative genome analysis and an extensive database, they developed a very precise method for dating gene duplication events.

The dating method is based on evolutionary relationship charts called, "phylogenetic trees."  Phylogenetic trees statistically deduce the order of mutational genetic events that have taken place throughout evolutionary history.  Approximate dates can also be incorporated into phylogenetic analysis.   These time lines are calibrated by the fossil record—by knowing when species of plants anatomically diverged, corresponding molecular events can be dated.

Simple in principle, but in truth, highly sophisticated tree construction methods were used and researchers repeated this process for numerous duplication sites.  Finally, they made a distribution of gene duplication dates and discovered that for most plants, the peak of this distribution was about 65 million years ago.

From these results, the VIB researchers concluded that plants with a duplicated genome were apparently the most "well adapted" for survival in the dramatically changed environment.

As the story goes, planet earth was struck by a large space rock 65 million years ago, which incidentally, ended the era of overgrown terrestrials and opened a new door for mammalian opportunists.  Our eukaryotic cousins, the plants, also have their own story of regime change; polyploid mutants that were typically disadvantageous were now favored.

During meiosis and mitosis, chromosomes separate.  However, sometimes this separation fails which leads to diploid gametes (instead of haploid) or tetraploid somatic cells (instead of diploid).  In plants, diploid gametes can self-fertilize which create tetraploid zygotes.  The final result are offspring with a duplicate set of chromosomes—typically a genetic disaster.

"Many organisms are diploid and we can assume that these have been well adapted to the environment through natural selection.  Polyploid organisms usually have reduced fertility and have problems competing with their diploid progenitors.  However, when the environment suddenly changes, the more extreme phenotypes suddenly become the better adapted ones," explains Bioinformatics and Genome Biology Professor, Yves Van de Peer.

In previous research, Van de Peer had discovered very old genome duplications in early ancestors of vertebrates and fish.  These duplications were probably crucial for the development of more complex vertebrates and thus of human beings as well. 

Gene duplication is a mechanism that creates diversity—precisely what populations desperately need to survive during times of sudden environmental change.  What's interesting is that although most duplicates are disadvantageous, natural selection favors retention of regulatory gene mutations which account for a good majority of duplicate genes we find in various genomes.

Regulatory genes encode proteins that regulate the expression of other genes and are primarily responsible for major morphological changes across phyla.  In general, DNA sequences across organisms are highly conserved, so observed morphological diversity is explained by regulatory genes expressing themselves at different times during development.  As opposed to other genes, a mutation in a regulatory genetic region will have a faster and more profound impact on phenotype.

 "We can see which genes have been retained following these duplication events, and we have shown that in particular regulatory genes—the genes that drive evolution, have been retained.  Therefore, we can speculate that these duplication events have been crucial for the survival and evolution of complex vertebrates such as humans," Van de Peer said.

Overall, genome duplication is probably a universal mechanism that has ensured that the role of our planet's vertebrates and flowering plants has become much greater over time.  With extreme conditions present, these genetic mutants were survivors and Van de Peer's research illustrates that DNA duplication is indeed a mechanism for "survival of the fittest."

Watson, J. D., Baker, T. A., Bell, S. P., Gann, A., Levine, M., Losick, R. (2004).  Molecular Biology of the Gene (5th ed). San Francisco, CA: Pearson Education Inc.