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Report

Teaser, summary, work performed and final results

Periodic Reporting for period 2 - HOTSPOT (Genomic hotspots of adaptation to whole genome duplication)

Teaser

Summary

This project addresses a fundamental problem in biology: whether evolutionary change is repeatable in complex organisms. Understanding this is important for society because it will give us information about the fundamental rules of evolutionary change that apply to all living things. Knowing these rules is of very high interest for our understanding about how life works and also has practical implications: knowing these rules will help us to eventually evolve organisms to meet our designs, for example better crops or other products.

This project tests a straightforward hypothesis: If independent species adapt to the same change with the same mechanism (signalled, for example, by the same genetic alterations in all the adapted populations), then this suggests that evolution is constrained and predictable. If, however, this hypothesis is false and if on the other hand evolution works with different changes each time (different genetic changes), then we learn something important also: this would suggest that evolution is flexible and can take several paths in response to the challenge. This will help us understand evolutionary change broadly and it will also teach us how we might eventually engineer changes into organisms in ways that are stable and have fewer side effect than otherwise.

The project takes advantage of the fact that many species have independently adapted to a particular challenge, the duplication of their entire genome. Thus, the first objective (Collections, meiotic characterisation and reference genome sequencing) is to find populations of the several species we have identified as appropriate for study in the wild, to collect the samples, to test that their genomes are stable at meiosis (the time when cells divide to make gametes and we can judge if the genome is indeed stable), and to create from scratch the reference genomes to be used in the next objective. This next objective (Genome scans for selection at WGD in other Brassicaceae and in autotetraploid Mimulus guttatus) then focusses on finding the evolutionary signature of adaptation to whole genome duplication (WGD) by sequencing the genomes of individuals that have encountered this challenge (WGD) and of those that have not. By looking at the changes that occur specifically in the individuals that have doubled genomes, we can infer the mechanistic changes underlying their evolutionary success. In the last objective (Functional follow-up on select candidates) we test the biological functions of the candidate changes we detect to understand the functional outcome of the genetic changes we detected.

Work performed

Thus far in the project we have been able to make strong progress on our aims designated for the first half of the five year project, having completed almost all of the field, laboratory and analysis work for the first two of our three objectives. We have identified populations and collected samples, sequenced their genomes (hundreds so far), and started to localise and characterise the genetic changes that stand as the strongest candidates responsible for the species\' remarkable adaptations to living with doubled genomes. Thus far, our early results suggest that different species show very different adaptations to genome doubling, even though the fundamental challenge to living with a doubled genome is similar in all species. This suggests strongly that evolution may have many options to deal with the challenges associated with genome doubling and that there may be able to find many ways to make healthy changes to processes that are even as fundamentally conserved as chromosome segregation, which is a major barrier to evolutionary fitness for species immediately following genome duplication.

Final results

The state of the art at the outset of this project is that we had high resolution results for a single species regarding the way it adapted to genome duplication. Now we have good indications of the mechanisms employed by several additional species and thus can make initial assessment regarding how constrained and conserved each speciesâ€™ evolutionary response is across the diversity of life. In short, we have indication that these evolutionary responses are not very conserved or constrained and that evolution is quite free than had been previously anticipated in â€˜choosing a pathâ€™ down which it may go in regard to the genomic and functional changes it employs to deal with a particular challenge. We expect that results until the end of the project will show in a high resolution that in response to an identical challenge, different species will almost always show individual responses. This will indicate that there is latitude in the functional response that evolution may make in response to conserved challenges, and that the genome is flexible and can be modified in diverse ways to deal with challenges.