BrackAdapt focused on generating and analysing large‑scale genomic resources for perch and pike from multiple brackish and freshwater sites in Sweden, Denmark and Germany, together with inland European outgroups. Key activities included:
* **Sampling and data generation:** The project consolidated existing tissue collections and, where needed, completed permits and logistics for additional sampling to balance coverage across sites. DNA extraction, library preparation and high‑throughput sequencing were organised to produce high‑coverage genomes suitable for robust population and selection analyses.
* **Data processing and quality control:** Standardised pipelines were established for read processing, alignment to high‑quality reference genomes, variant discovery and filtering. Harmonised workflows ensured that both species were treated identically to enable direct cross‑species comparisons.
* **Population structure and history:** Genotype‑likelihood and allele‑frequency based methods (e.g. PCA, admixture, demographic reconstructions) were applied to describe how populations are related, how large their effective sizes have been through time, and where gene flow among brackish and freshwater populations likely occurred.
* **Selection scans and functional exploration:** Genome‑wide scans were configured to detect regions showing unusual differentiation consistent with local adaptation to salinity. The project also set up comparative analyses to examine whether candidate regions and pathways are shared across independent brackish populations or are species‑specific.
* **Open science foundations:** Data management plans, reproducible code repositories, and analysis documentation were put in place to facilitate future publication, reuse and transparency.
Although no peer‑reviewed papers have been published within the grant period, BrackAdapt delivered substantial research assets: curated genomic datasets for two key coastal fish species; validated, reusable bioinformatics workflows; and comparative analysis frameworks that position the project’s findings for efficient dissemination.
