Genome Duplication & Polyploidy

Nature Reviews Genetics 2009

Detailed analyses of the genomes of several model organisms revealed that gene duplications have played a prominent role in the evolutionary history of many eukaryotes. In addition, ancient whole-genome duplications (WGDs), also referred to as paleopolyploidizations, have been reported in most evolutionary lineages. Their evolutionary importance, however, remains a major topic of discussion, ranging from an evolutionary dead end to a road toward evolutionary success, with evidence supporting both fates.

Both angiosperm (flowering plants) and vertebrate ancestors have undergone at least two separate WGDs. In the vertebrate lineage, a third WGD occurred in the ancestor of teleost fish. In the angiosperm lineage, subsequent and sometimes repeated WGDs have been reported in all major clades. All flowering plants and vertebrates have thus descended from an ancestor who doubled its genome. Ancient WGDs have also been documented in other kingdoms. Nevertheless, paleopolyploidy events seem to be extremely rare, and the number of established ancient WGDs very small. The evolutionary success of land vertebrates, fishes, and flowering plants however, would suggest that, although descendants of WGD events do not survive often, when they do survive their evolutionary lineage can be very successful. The observation that WGDs often seem to give rise to very species-rich groups of organisms suggest that polyploid species have outcompeted their diploid progenitors or diploid sister lineages, or alternatively, that polyploidy can facilitate diversification and speciation of organisms. Another question is whether these ancient WGDs have survived by coincidence or whether they could survive only because they did occur, or were selected for, at very specific times, for instance during major ecological upheavals and periods of extinction. To adress these questions we study the patterns and effects of WGDs at different levels.

Using state-of-the-art phylogenetic dating methods we recently analyzed 41 plant genomes and found a strongly nonrandom pattern of genome duplications over time with many WGDs clustering around the Cretaceous–Paleogene (K–Pg) extinction event about 66 million years ago. This suggests that the environmental and ecological conditions during the time of polyploidization may be of crucial importance, and that the establishment of WGDs is potentially promoted during times of environmental stress.

We are also developing computational models of artificial gene regulatory networks and use population-based evolutionary simulations and evolutionary robotics to study the effects and evolutionary fate and significance of small- and large-scale genome duplications. For example, we are investigating their consequences on genome and network evolution, and are examining whether gene and genome duplications could potentially be benefical for adaptation and/or survival and under which specific conditions and scenarios. Finally, we hope that results from our studies on WGDs using simulated evolutionary robots could in turn benefit the field of evolutionary robotics and lead to the development of better evolutionary robots.

Van de Peer, Y., Mizrachi, E., & Marchal, K. (2017). The evolutionary significance of polyploidy. NATURE REVIEWS GENETICS, 18(7), 411–424

Vanneste, Kevin, Baele, G., Maere, S., & Van de Peer, Y. (2014). Analysis of 41 plant genomes supports a wave of successful genome duplications in association with the Cretaceous-Paleogene boundary. GENOME RESEARCH, 24(8), 1334–1347

Vanneste, Kevin, Maere, S., & Van de Peer, Y. (2014). Tangled up in two: a burst of genome duplications at the end of the Cretaceous and the consequences for plant evolution. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 369(1648)

Lohaus, R., & Van de Peer, Y. (2016). Of dups and dinos: evolution at the K/Pg boundary. (Y. Van de Peer & J. C. Pires, Eds.)CURRENT OPINION IN PLANT BIOLOGY, 30, 62–69