The evolutionary significance of ancient whole genome duplications
Friday seminar by Yves Van de Peer (Note the time!)
Recent analyses of eukaryotic genome sequences have revealed that gene duplication, by which identical copies of genes are created within a single genome by unequal crossing over, reverse transcription, or the duplication of entire genomes, has been rampant. The creation of extra genes by such duplication events has now been generally accepted as crucial for evolution and of major importance for adaptive radiations of species and the general increase of genetic and biological complexity. We have developed software to identify remnants of large-scale gene duplication events and more recently, we have also developed mathematical models that simulate the birth and death of genes based on observed age distributions of duplicated genes, considering both small and large scale duplication events. Applying our model to the model plant Arabidopsis shows that much of the genetic material in extant plants, i.e., about 60 % has been created by several genome duplication events. More importantly, it seems that a major fraction of that material could have been retained only because it was created through large-scale gene duplication events. In particular transcription factors, signal transducers, and regulatory genes in general seem to have been retained subsequent to large-scale gene duplication events. Since the divergence of (duplicated) regulatory genes is being considered necessary to bring about phenotypic variation and increase in biological complexity, it is indeed tempting to conclude that such large scale gene duplication events have indeed been of major importance for evolution. In a second part of my talk, I will focus on the more recent genome duplication events that have occurred in plants. Many different plant lineages seem to have experienced relatively recent genome duplications. Starting from paralogous genes lying in duplicated segments or identified in large EST collections, we dated these youngest duplication events through penalized likelihood phylogenetic tree inference and show that a majority of these independent genome duplications are clustered in time, and seem to coincide with the Cretaceous-Tertiary (KT) boundary. The KT extinction event is the most recent large-scale mass extinction caused by one or more catastrophic events such as a massive asteroid impact and increased volcanic activity. These events are believed to have generated global wildfires and dust clouds that cut off sunlight during long periods of time resulting in approximately 60% of plant species going extinct, as well as a majority of animals, including dinosaurs. From recent studies suggesting that polyploid species can have higher adaptability and increased tolerance to different environmental conditions, we propose that polyploidization may have contributed to the survival and propagation of several plant lineages during or following the KT extinction event. Due to advantages such as altered gene expression leading to hybrid vigor and an increased set of genes and alleles available for selection, polyploid plants might have been better able to adapt to the drastically changed environment, 65 million years ago.
Yves Van de Peer
Professor in Bioinformatics and Genome Biology
Associate Department Director, VIB Department of Plant Systems Biology
Group Leader Bioinformatics and Systems Biology