Periodic Reporting for period 1 - EXPLOAD (EXamining how Past demography affects genetic LOad using Ancient DNA)
Reporting period: 2022-06-01 to 2024-11-30
DNA can survive millennia post-mortem, spanning ecological and evolutionary transitions and providing a unique window into the processes underlying biodiversity. As such sequencing ancient DNA from temporally spaced samples can allow the testing of hypotheses related to evolutionary responses to ecological change and novel selection pressures through direct quantification of ecological and genetic parameters collected before, during and after genetic changes in selection pressures. This ERC project will do just this, taking advantage of a natural experiment of an emblematic study system in evolutionary biology: parallel independent adaptation to freshwater by marine-adapted threespine sticklebacks through the rise in frequency of freshwater-associated alleles. Utilising palaeogenomics to sample genomes along this evolutionary continuum and the project will address a key and long-standing question: is there a mutational cost to natural selection? This is a timely question, as ongoing rapid global climatic change is a major source of novel selection pressures, therefore, understanding the dynamics of natural selection will provide key insights into potential outcomes for biodiversity. The methods developed in this project will not only benefit the growing field of paleogenomics but also other fields where data is collected in a temporal manner, such as experimental evolution and epidemiology. Ultimately, achievement of these goals requires the formation of a dedicated, closely knit team, focusing on both the methodological challenges as well as their bigger picture application to high-risk high- gain ventures. Thanks to ERC funding this can become a reality, enabling the interface of palaeogenomics and evolutionary biology to be pushed to the new limits of the modern sequencing era.
A primary research and technological achievement of the first half of the ERC COG project EXPLOAD has been to generate genome-wide genotypes of the target species, threespine sticklebacks, from DNA extracted from sediments dated to the Late Pleistocene (13,000 years ago). This was achieved by processing approximately two orders of magnitude more sediment (approximately 25g) than previous sedimentary ancient DNA studies (sedaDNA), which typically use <0.5 grams. To be able to extract DNA and then build it into genomic ‘libraries’ and amplify these by polymerase chain reaction (PCR) is extremely challenging due to the inhibitors, such as organic material, within the sediment which can alter pH, thereby inhibiting downstream enzymatic reactions (such as PCR and library build steps). This required developing a manual laboratory DNA extraction protocol, and trouble-shooting as the extraction progressed. The results enabled the tracking of evolutionary changes in the genomes of threespine sticklebacks from different sediment layers, and therefore through time, a key objective of the ERC Project (see WP1-4, Objective 3, Deliverable 3). The results of this work were published in Current Biology: Laine et al. DOI:https://doi.org/10.1016/j.cub.2024.01.056. In 2021, sequencing DNA from soil was nominated as one of the scientific breakthroughs of the year:
https://www.science.org/content/article/breakthrough-2021(opens in new window). This project has taken the field of sedaDNA a significant step forward, providing genomic data of unprecedented resolution from ancient sediments. I anticipate this being highly influential on the field of ancient DNA in the coming years. The PhD student associated with the project is currently processing multiple cores from different lakes of different ages to test evolutionary hypotheses central to the project (Objective 3).
https://www.science.org/content/article/breakthrough-2021(opens in new window). This project has taken the field of sedaDNA a significant step forward, providing genomic data of unprecedented resolution from ancient sediments. I anticipate this being highly influential on the field of ancient DNA in the coming years. The PhD student associated with the project is currently processing multiple cores from different lakes of different ages to test evolutionary hypotheses central to the project (Objective 3).
The challenges and advances in our approach to obtaining genome-wide genotype data can be seen as a ‘game-changer’, in terms of the resolution afforded to study genomic changes through time, concurrent with metagenomic data and geological data, which provide an understanding of the ecological changes that such genomic adaptation are associated with.