DOUBLE-TROUBLE: Replaying the ‘genome duplication’ tape of life: the adaptive potential of polyploidy in a stressful or changing environment
Description of the PI
Yves Van de Peer (YVdP) obtained his PhD in 1996 at the University of Antwerp, Belgium. After a postdoctoral fellowship at the University of Konstanz, Germany, he was hired at Ghent University (BE) as Group Leader of VIB (Department of Plant Systems Biology) in 2000 and as an Associate Professor at Ghent University in 2001, and promoted to Full Professor in 2008. YVdP’s research group is considered a genome analysis powerhouse specialized in the study of the structure and evolution of (plant) genomes. Because of their unique expertise and experience in gene prediction, genome annotation, and genome analysis, his research group has been, and still is, involved in many international genome projects. YVdP is particularly interested in the study of gene and genome duplications as well as in the evolution of novel gene functions after duplication. YVdP published more than 450 papers, many of which in high-profile journals such as Nature, Nature Genetics, Nature Reviews Genetics, Science, PNAS, Genome Research, and The Plant Cell. YVdP has an H-index > 100 and his work has been cited more than 60,000 times. For many consecutive years, YVdP has been a Highly Cited Researcher (Web of Science; https://hcr.clarivate.com). In 2013, YVdP received a highly prestigious ERC Advanced Grant entitled “DOUBLE-UP: The evolutionary significance of genome duplications for natural and artificial organism populations”, and in 2018 another one entitled “DOUBLE-TROUBLE: Replaying the ‘genome duplication’ tape of life: the adaptive potential of polyploidy in a stressful or changing environment”. YVdP is Organizer and Chair of the bi-annual international Current Opinion Conference on Plant Genome Evolution. This meeting was held in 2011, 2013, 2015, 2017, and 2019. YVdP is a member of the Royal Flemish Academy of Belgium for Science and the Arts (KVAB; since 2012) and serves on the Editorial Boards of five international journals (The Plant Journal, PeerJ, Genome Biology and Evolution, Current Plant Biology, Frontiers in Genetics). YVdP is also part-time professor at the University of Pretoria, South Africa. A full list of publications can be found here.
Description of the project
Thousands of species are polyploid. However, the long-term establishment of organisms that have undergone ancient whole genome duplications (WGDs) has been exceedingly rare and when we analyse the genomes of plants and animals, we can, at most, find evidence for a very limited number of WGDs that survived on the longer term. The paucity of (established) ancient genome duplications and the existence of so many species that are currently polyploid provides a fascinating paradox. There is growing evidence that the majority of ancient WGDs were established at specific times in evolution, for instance during periods of environmental change and periods of mass-extinction. The reason for this ‘stress’-polyploidy relationship has been the subject of considerable speculation and several hypotheses have been put forward to explain this observation: (a) stressful conditions promote polyploid formation; (b) polyploidisation causes a niche shift allowing polyploids to grow in conditions that are unsuitable for their non-polyploid ancestors; and (c) polyploids have an increased evolvability and consequently adapt faster to a changing environment. Here, we want to unravel the mechanistic underpinnings of why and how polyploids can outcompete non-polyploids. We will address these questions by replaying the ‘genome duplication tape of life’ in two different model systems, namely Chlamydomonas and Spirodela (duckweed). We will run long-term evolutionary (and resequencing) experiments. We will complement these experiments with in-silico experiments based on so-called digital organisms running on artificial genomes. Complementary modelling approaches will also be employed to study the effects of polyploidy from an eco-evolutionary dynamics perspective. By integrating the results obtained from these in vivo and in silico experiments, we will obtain important novel insights in the adaptive potential of polyploids under stressful conditions or during times of environmental and/or climate change.
