Background. Genomes are highly variable in their organization, but we are far from understanding the forces driving this diversity and its evolutionary consequences. Accordingly, associating genome reorganization with evolutionary diversification remains an enduring challenge of evolutionary biology. Recent advances in molecular genetics and sequencing of diverse genomes have revealed that Transposable Elements (TEs) are playing a pivotal role in shaping genome architecture, triggering restructuring and functional changes, and producing abundant raw material for evolution. Very few empirical studies have investigated genome dynamics in naturally occurring populations and the impact of TEs on speciation and local adaptation is still elusive.

General objectives. Divergent chromosomal structure contributes to hybrid infertility and reduces the level of recombination around rearranged segments, thereby restricting gene exchange. Such reproductive isolation is predicted to facilitate the accumulation of genetic differences between lineages and to permit adaptive traits to become established. However, the importance of chromosomal speciation has been questioned, because of insufficient evidence that chromosomal rearrangements indeed restrict realized gene flow. Recent advances in the study of TEs suggest that they may be important in enhancing reproductive isolation. In this project, I propose to investigate the role of TEs in chromosomal speciation. As chromosome doubling specifically restores the fertility of hybrids between structurally divergent genomes, a promising approach is to investigate a system that has recently undergone genome doubling (i.e. a young autopolyploid complex where both diploids and polyploids still occur). In addition, autopolyploidy is unlikely to immediately induce the expression of new traits, thus offering the opportunity to assess the genomic processes supporting ecological differentiation through local adaptation. Studying genome dynamics in wild species will contribute to elucidate how genomic and evolutionary processes interact in shaping biodiversity.

Specific aims. The proposed project combines genomic and ecological methods to associate the main processes driving plant genome evolution – polyploidy, retrotransposition and genome silencing – with the evolutionary processes of speciation and ecological diversification. I suggest working with Biscutella laevigata (Brassicaceae) because it is formed of divergent diploid populations and recent autopolyploid lineages. In particular, the following questions will be addressed: Is chromosomal restructuring driving incipient speciation? Is differential TE accumulation between lineages involved in reproductive isolation? What are the mechanisms and the timing of genome reorganization during speciation? Is autopolyploidy advantageous under environmental change as it might increase the ability to both shift the distribution range and adapt to environmental heterogeneity? To what extent is genome dynamics sustaining local adaptation?

Experimental design and approaches. I suggest comparing changes in recently active TE families between genomes of diploid and polyploid populations of B. laevigata. I will thus first produce low coverage Genome Survey Sequences by 454 pyrosequencing to unravel TE families contributing to genome organization. In a first set of experiments, I will establish hybrids between naturally occurring diploids of B. laevigata as well as synthetic polyploids to assess whether intraspecific divergence in genome structure results in immediate reproductive isolation. These experimental accessions will be characterized with complementary molecular tools tracking immediate reorganization in contrasted genome fractions. I will make use of the following techniques: AFLPs marking random sequences, SSAPs marking TE insertions and their Methyl-Sensitive counterparts, as well as comparative chromosome painting. This part of the study will reveal to what extent TEs are involved in incipient speciation and the mechanisms underlying reproductive isolation. I further suggest comparing experimental and naturally occurring polyploids with a similar approach to estimate the timing of genome reorganization after polyploidization. In a complementary sub-project, a PhD student will investigate how genome reorganization is related to ecological differentiation and local adaptation. We will make use of landscape genetics approaches to infer spatial genetic structure and identify patterns of local adaptation in three pairs of marginal populations located at the trailing edge versus the leading edge of the species distribution range. The PhD student will set up a reciprocal transplant experiment among selected sites, which will allow the detection of local adaptation. Local adaptation is predicted to evolve with genome reorganization and decreasing polysomic inheritance. Accordingly, experimental crossing of polyploid accessions will further assess whether populations showing signature of adaptation to environmental heterogeneity present increased levels of disomic inheritance as compared to populations showing signature of recent expansion.

Value of the proposed project. This project tackles several important questions in our understanding of plant speciation and the role of genome dynamics in driving evolutionary diversification. In particular, this research will bridge insights offered by molecular and ecological genetics to highlight the impact of TEs on the evolutionary diversification of natural populations. The outcomes will thus be of wide interest for evolutionary and molecular biologists as well as ecologists.