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A report to describe the protocols used by the FishGenome Consortium to: i) collect biological and environmental samples – Sampling Protocols ii) isolate DNA from biological and environmental samples – DNA isolation Protocols iii) perform the laboratory work required for the application of each technique iv) analyse bioinformatically the sequences derived from the laboratory procedures for the purpose of assessing fish and fish communities using Close Kin Mark Recapture (CKMR), environmental DNA (eDNA) and epigenetic age determination (DNAm). Sampling protocols detailed in this document have been designed tailoring the specific needs of the MEDITS and IBTS research surveys to allow implementation without disturbing the standard procedures carried out on board during the regular Fisheries research surveys. Application to other surveys may require small adjustments of the sampling protocols.

1. Esox lucius L. (northern pike) inhabits river, lake, and brackish water ecosystems of the temperate region in North America and Eurasia. In many areas of its native range, the species is confronted with human-induced disturbances that can affect local and regional genetic diversity. Conservation of genetic diversity constitutes an important policy objective. Therefore, we investigated how the genetic population structure and patterns suggestive of hybridisation among subpopulations from different catchments vary with the type of ecosystem (river vs. lake) and the integrity of the ecosystem assessed using ecological status assessments of the European Water Framework Directive and indices of the wetland quality (in rivers) and trophic state (in lakes). 2. In total, 1,384 pike samples from the North, Baltic, and Black Sea drainages in Germany were analysed. We differentiated between metapopulations from each hydrogeographic region using genotypes from 15 microsatellites and mitochondrial cyt b sequences. 3. Individual populations showed signs of genetic admixture ranging from almost zero to complete replacement by foreign genotypes originating from different catchments. Hierarchical general linear modelling revealed a significantly positive association of the degree of genetic hybridisation with decreasing ecological status. An eroded population substructure indicative of hybridisation was also significantly elevated in rivers relative to lakes and in heavily modified water bodies. Results were consistent when using ecological status assessments by the Water Framework Directive and an alternative environmental quality index based on the health of wetlands in rivers and trophic state in lakes. 4. We speculate that macrophyte loss through loss of wetlands or in response to eutrophication fostered genetic mixing among different subpopulations, which were brought into secondary contact either due to stocking or due to natural dispersal from foreign catchments. Our findi, German Ministry of Education and Research, Spanisch Research Council, European Maritime and Fisheries Fund http://dx.doi.org/10.13039/100014510, European Reseach Council, Ministerium für Landwirtschaft und Umwelt Mecklenburg‐Vorpommern, Peer Reviewed

Esox lucius L. (northern pike) inhabits river, lake, and brackish water ecosystems of the temperate region in North America and Eurasia. In many areas of its native range, the species is confronted with human-induced disturbances that can affect local and regional genetic diversity. Conservation of genetic diversity constitutes an important policy objective. Therefore, we investigated how the genetic population structure and patterns suggestive of hybridisation among subpopulations from different catchments vary with the type of ecosystem (river vs. lake) and the integrity of the ecosystem assessed using ecological status assessments of the European Water Framework Directive and indices of the wetland quality (in rivers) and trophic state (in lakes). In total, 1,384 pike samples from the North, Baltic, and Black Sea drainages in Germany were analysed. We differentiated between metapopulations from each hydrogeographic region using genotypes from 15 microsatellites and mitochondrial cyt b sequences. Individual populations showed signs of genetic admixture ranging from almost zero to complete replacement by foreign genotypes originating from different catchments. Hierarchical general linear modelling revealed a significantly positive association of the degree of genetic hybridisation with decreasing ecological status. An eroded population substructure indicative of hybridisation was also significantly elevated in rivers relative to lakes and in heavily modified water bodies. Results were consistent when using ecological status assessments by the Water Framework Directive and an alternative environmental quality index based on the health of wetlands in rivers and trophic state in lakes. We speculate that macrophyte loss through loss of wetlands or in response to eutrophication fostered genetic mixing among different subpopulations, which were brought into secondary contact either due to stocking or due to natural dispersal from foreign catchments. Our findings suggest

Translocation into a novel environment through common fisheries management practices, such as fish stocking, provides opportunities to study behavioural and fitness impacts of translocations at realistic ecological scales. The process of stocking, as well as the unfamiliarity with novel ecological conditions and the interactions with resident fish may affect translocated individuals, leading to alterations of behaviours and causing fitness impacts. Our objectives were to investigate how aquatic top predators behaviourally establish themselves and compete with resident individuals following introduction in a novel lake environment and to investigate the resulting fitness consequences. Using high‐resolution acoustic telemetry, we conducted whole‐lake experiments and compared the activity, activity‐space size and fate of translocated and resident individuals in two model top predators, the northern pike Esox lucius (n = 160) and European catfish Silurus glanis (n = 33). Additionally, we compared the reproductive success of translocated and resident northern pike. The experiment was conducted with large (adult) individuals of different origins, resilient to predation, but subject to agonistic interactions and competition with resident fish. Over a period of several months, the translocated catfish exhibited consistently larger activity‐space sizes than resident catfish, but did not differ from residents in activity and survival. The pike from one of the two translocated origins we tested also showed elevated space‐use, and both translocated origins revealed higher mortality rates than their resident conspecifics, indicating maladjustment to their novel environment. When non‐resident pike reproduced, they overwhelmingly produced hybrid offspring with resident fish, indicating that introductions fostered gene flow of non‐native genes. Our study indicates that fish introductions result in behavioural and fitness impacts even in large‐bodied top predators that experience lo, Leibniz Community, Besatzfisch (German Federal Ministry for Education and Research), Peer Reviewed