The HOTSPOT project addresses a fundamental problem in biology: whether evolution is repeatable in complex organisms. Understanding this is important because it will give us information about the fundamental rules of evolutionary change that apply to all living things. Knowing these rules is of fundamental interest for our understanding of ‘how life works’ and also has practical implications for society: these rules will help us to eventually evolve organisms to meet our designs, for example, better crops or other products.
We test a straightforward hypothesis: If different species independently adapt to the same change by the same mechanisms (signaled by the same novel genetic changes in the independently adapted lineages, or common ‘HOTSPOTs’ of change in the genomes), then this suggests that evolution is at least somewhat constrained and predictable. If, however, this hypothesis is false and on the other hand, evolution works with different changes each time (different genetic changes with no common HOTSPOTs), then we learn something important as well: this would tell us that evolution is flexible and can take several paths in response to the challenge.
As a model we take advantage of the fact that many species have independently adapted to a particular stringent challenge, whole genome duplication (WGD, giving rise to polyploidy). Thus, the first objective (field collections, meiotic characterization, and reference genome sequencing) is to find populations of the four species we have identified as appropriate for study in the wild, collect samples, to test that their genomes are stable at meiosis (when cells divide to make gametes and we can judge if the genome is indeed stable—and thus whether evolutionary adaptation has indeed occurred to the WGD state—and to create the high-quality reference genomes to be used in the next objective. That next objective (Genome scans) then focuses on finding the evolutionary signature of adaptation to WGD by sequencing the genomes of many individuals that have overcome this challenge vs of those that have not. By looking at the changes specifically in the WGD individuals, we inferred mechanisms underlying their success and indeed whether there might be common change HOTSPOTs. In the last objective (functional follow-up) we test the functions of the candidate changes we discovered.
