EXamining how Past demography affects genetic LOad using Ancient DNA

Projektinformationen

EXPLOAD

ID Finanzhilfevereinbarung: 101045346

DOI

10.3030/101045346

Projekt abgeschlossen

EK-Unterschriftsdatum 2 Mai 2022

Startdatum 1 Juni 2022

Enddatum 31 Mai 2026

Finanziert unter

• European Research Council (ERC)

Gesamtkosten

€ 625 229,00

EU-Beitrag

€ 625 229,00

Koordiniert durch

UNIVERSITETET I OSLO
Norway

Periodic Reporting for period 1 - EXPLOAD (EXamining how Past demography affects genetic LOad using Ancient DNA)

Berichtszeitraum: 2022-06-01 bis 2024-11-30

Zusammenfassung vom Kontext und den Gesamtzielen des Projekts

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.

Arbeit, die ab Beginn des Projekts bis zum Ende des durch den Bericht erfassten Berichtszeitraums geleistet wurde, und die wichtigsten bis dahin erzielten Ergebnisse

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. 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).

Fortschritte, die über den aktuellen Stand der Technik hinausgehen und voraussichtliche potenzielle Auswirkungen (einschließlich der bis dato erzielten sozioökonomischen Auswirkungen und weiter gefassten gesellschaftlichen Auswirkungen des Projekts)

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.

Changes in freshwater and marine ancestry in three-spined sticklebacks during the formation of a pos

Stratigraphy of Jossavannet core, showing the ecological and geological co- ntext of the sediment la

Patterns of stickleback marine and freshwater ancestry in sediment layers