Quantifying polygenic selection in real-time adaptation to climate change

Project Information

Poly2Adapt

Grant agreement ID: 101068395

DOI

10.3030/101068395

Project closed

EC signature date 1 August 2022

Start date 1 May 2023

End date 30 April 2025

Funded under

• Marie Skłodowska-Curie Actions (MSCA)

Total cost

No data

EU contribution

€ 188 590,08

Coordinated by

UNIVERSITA POLITECNICA DELLE MARCHE
Italy

Periodic Reporting for period 1 - Poly2Adapt (Quantifying polygenic selection in real-time adaptation to climate change)

Reporting period: 2023-05-01 to 2025-04-30

Summary of the context and overall objectives of the project

Understanding how species adapt to climate change is one of the most pressing challenges in evolution and conservation biology. As climate shifts increasingly disrupt ecosystems, species that are able to evolve rapidly may be more resilient to such changes. This is particularly relevant for long-lived wild vertebrates, for which evolutionary responses are typically more challenging to study. The Poly2Adapt project, supported by the European Commission’s Marie Skłodowska-Curie Actions program, aims to transform our understanding of how adaptation operates at the genomic level in such organisms.

Focusing on the iconic King penguin (Aptenodytes patagonicus), a long-lived and iconic seabird of the Southern Ocean, this project explores the genetic basis of reproductive success and adaptation over time. The King penguin is highly suitable for such research due to its well-documented life-history traits, recent environmental pressures, and the availability of long-term ecological monitoring data. By combining genomic, transcriptomic, and epigenetic data with long-term life-history data, Poly2Adapt seeks to reveal how reproductive fitness and climate-linked adaptation manifest in the genome.

The project is producing key genomic resources and analytical frameworks that can be applied to other wildlife species. It also provides evidence relevant to EU biodiversity and climate adaptation policy, particularly in terms of developing evolutionary indicators of resilience for climate-threatened species.

Work performed from the beginning of the project to the end of the period covered by the report and main results achieved so far

The Poly2Adapt project generated a high-quality, haplotype-resolved, chromosome-level reference genome for the King penguin—substantially improving upon the previous assembly. The genome was annotated using multi-tissue transcriptomic data and shows high completeness and contiguity metrics. This new assembly is now publicly available and forms the foundation for all downstream analyses.

In parallel, the project investigated gene expression differences between the King penguin and its sister species, the Emperor penguin (A. forsteri), which breeds in the extreme Antarctic environment. This study, published in Molecular Ecology (https://doi.org/10.1111/mec.17552) revealed how shifts in tissue-specific gene networks underlie cold adaptation in the Emperor penguin, highlighting regulatory evolution as a key mechanism of adaptation.

The project’s primary ongoing analysis focuses on understanding the genomic basis of reproductive fitness in King penguins. Individuals (≥13 years old) were assigned to high or low reproductive success categories based on lifetime fledging success. Whole-genome resequencing data from these individuals (n = 64) are being used to test the role of genetic diversity, genetic load, and temporal changes in allele frequency across two decades (2001–2020), providing one of the first genome-wide tests of adaptation and fitness in a long-lived wild vertebrate.

In addition, the project is quantifying mutation and recombination rates using trio data, which will support future models of adaptive potential and genome evolution in the King penguin.

Progress beyond the state of the art and expected potential impact (including the socio-economic impact and the wider societal implications of the project so far)

Poly2Adapt delivers multiple results that go beyond the current state of the art. These include:

- The first chromosome-level reference genome for the King penguin, enabling high-resolution studies of genome architecture and evolutionary adaptation.
- A comparative transcriptomic study between the King penguin and the Emperor penguin, which identified candidate gene expression shifts associated with ecological adaptation in the two species.
- A novel framework for quantifying reproductive fitness at the genomic level in wild, long-lived vertebrates.
- Temporal genomic analyses that trace allele frequency shifts over two decades, offering insights into recent, possibly climate-driven selection.

These results lay the foundation for predictive metrics of adaptive potential in the King penguin, and potentially other species. The project also contributes publicly-available tools and pipelines for gene expression analysis, genetic load, and temporal genomics. Ensuring further uptake of these tools will require additional validation in other species and ecosystems, and integration with conservation genomic initiatives. Future steps include finalising selection analyses, validating candidate genomic regions associated with reproductive success, and expanding cross-species comparisons to derive general principles of polygenic adaptation.

Photograph of King penguins in the Crozet Archipelago. Photo credit: Timothée Poupart, IPEV