Periodic Reporting for period 1 - BrackAdapt (Using genomics to understand how freshwater fishes turned a lethal environment into an ideal habitat)
Período documentado: 2023-09-01 hasta 2025-08-31
Coastal and estuarine zones are changing rapidly as sea levels rise and rainfall patterns shift. These changes alter the salt content (salinity) of waters where rivers meet the sea, reshaping habitats that many fish depend on. Most fish are adapted either to fresh water or to the open sea; only a few can cope with the constantly changing salinities in estuaries. Yet these brackish areas are highly productive and support important fisheries and local biodiversity.
The Baltic Sea—the world’s largest brackish water body—offers a natural laboratory to study how fish adapt to these demanding conditions. Two freshwater species, European perch (Perca fluviatilis) and pike (Esox lucius), have each evolved brackish-water ecotypes in parts of the Baltic that can thrive at salt levels lethal to non‑adapted freshwater individuals. Understanding *how* these ecotypes arose, *which* genomic changes enable their tolerance to salinity, and *whether* similar solutions evolved repeatedly is vital for predicting how fish will respond to ongoing environmental change.
The BrackAdapt project set out to:
* Generate high‑coverage whole‑genome data from freshwater and brackish populations of perch and pike across the western Baltic region and inland reference sites.
* Reconstruct population structure, demographic history, and connectivity among populations to understand past responses to environmental change.
* Identify genomic regions and biological pathways linked to salinity tolerance and trace when and where adaptive changes emerged and spread.
* Test the repeatability of evolution by assessing whether adaptation to brackish habitats followed parallel routes within and between species.
By providing a genomic basis for salinity tolerance and mapping population connectivity, the project aims to inform conservation and fisheries management, support climate adaptation strategies for coastal ecosystems, and protect locally adapted biodiversity.
The Baltic Sea—the world’s largest brackish water body—offers a natural laboratory to study how fish adapt to these demanding conditions. Two freshwater species, European perch (Perca fluviatilis) and pike (Esox lucius), have each evolved brackish-water ecotypes in parts of the Baltic that can thrive at salt levels lethal to non‑adapted freshwater individuals. Understanding *how* these ecotypes arose, *which* genomic changes enable their tolerance to salinity, and *whether* similar solutions evolved repeatedly is vital for predicting how fish will respond to ongoing environmental change.
The BrackAdapt project set out to:
* Generate high‑coverage whole‑genome data from freshwater and brackish populations of perch and pike across the western Baltic region and inland reference sites.
* Reconstruct population structure, demographic history, and connectivity among populations to understand past responses to environmental change.
* Identify genomic regions and biological pathways linked to salinity tolerance and trace when and where adaptive changes emerged and spread.
* Test the repeatability of evolution by assessing whether adaptation to brackish habitats followed parallel routes within and between species.
By providing a genomic basis for salinity tolerance and mapping population connectivity, the project aims to inform conservation and fisheries management, support climate adaptation strategies for coastal ecosystems, and protect locally adapted biodiversity.
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.
* **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.
BrackAdapt advances estuarine adaptation research in three ways:
1. Freshwater-to‑brackish adaptation: Most prior genomic work has examined marine species moving into brackish habitats. By centring on *freshwater* species that evolved brackish ecotypes, BrackAdapt addresses a contrasting evolutionary route where genetic drift and smaller population sizes may shape adaptation differently.
2. Replicated, cross‑species design: Using matched sampling designs and identical analytical pipelines for perch and pike enables powerful tests of parallel evolution—within species (across multiple brackish populations) and between species. This design supports general conclusions about how frequently nature “reuses” similar genomic solutions for the same environmental challenge.
3. From genomic signals to mechanisms: By linking outlier genomic regions to candidate genes and pathways involved in osmoregulation, the project builds the bridge from statistical signals to plausible biological mechanisms relevant to salinity tolerance.
Potential next steps to ensure uptake and impact** include: targeted functional validation of top candidate genes (e.g. expression studies under controlled salinity changes), integration with physiological and telemetry data to connect genotype to performance, and coordinated data releases with user‑friendly summaries for managers.
The expected impacts are:
* Scientific:** New insight into the tempo and mode of rapid adaptation to environmental stress in vertebrates; reusable datasets and pipelines for the community.
* Societal and economic:** Knowledge to support resilient coastal fisheries and recreational angling by recognising and protecting locally adapted stocks.
* Environmental:** Evidence to guide habitat restoration and connectivity measures that maintain adaptive potential under changing salinity regimes.
1. Freshwater-to‑brackish adaptation: Most prior genomic work has examined marine species moving into brackish habitats. By centring on *freshwater* species that evolved brackish ecotypes, BrackAdapt addresses a contrasting evolutionary route where genetic drift and smaller population sizes may shape adaptation differently.
2. Replicated, cross‑species design: Using matched sampling designs and identical analytical pipelines for perch and pike enables powerful tests of parallel evolution—within species (across multiple brackish populations) and between species. This design supports general conclusions about how frequently nature “reuses” similar genomic solutions for the same environmental challenge.
3. From genomic signals to mechanisms: By linking outlier genomic regions to candidate genes and pathways involved in osmoregulation, the project builds the bridge from statistical signals to plausible biological mechanisms relevant to salinity tolerance.
Potential next steps to ensure uptake and impact** include: targeted functional validation of top candidate genes (e.g. expression studies under controlled salinity changes), integration with physiological and telemetry data to connect genotype to performance, and coordinated data releases with user‑friendly summaries for managers.
The expected impacts are:
* Scientific:** New insight into the tempo and mode of rapid adaptation to environmental stress in vertebrates; reusable datasets and pipelines for the community.
* Societal and economic:** Knowledge to support resilient coastal fisheries and recreational angling by recognising and protecting locally adapted stocks.
* Environmental:** Evidence to guide habitat restoration and connectivity measures that maintain adaptive potential under changing salinity regimes.