The project ”Management of mixed cod stocks in the transition zone between the North Sea and the Baltic Sea: How can this be achieved most efficiently?” focused on one of the key challenges for assessment and management of fish stocks: Movement of individuals and stocks mixing. The project focused on resolving issues of stock mixing in cod stocks between the North Sea (Subarea 4), Skagerrak (SD 20), Kattegat (SD 20), the western Baltic (Belt Sea (SD 22), and Sound (SD 23)), and the eastern Baltic Sea (SDs 24 – 32). The project was funded by European Maritime and Fisheries Fund and the Danish Fisheries Agency. The activities in the project involved providing new biological knowledge on genetic and ecological connectivity, advancing methods, and providing a tool to evaluate the impact of stock mixing on stock assessment.Genetic identification of populationsFull genome resequencing data revealed marked genetic differences between samples of fish at spawning time collected in the North Sea, eastern Baltic Sea and the transition zone between the two areas (i.e. SD 21-SD 24). In contrast, we found limited divergence between spawning fish collected in the southern Kattegat, Belt Sea, Sound and Arkona Sea (SD 24, spring), suggesting that these fish belong to the same biological population, identifying a total of three major biological units for management in this system. Weaker gradient signals within the transition zone may be related to introgression in the hybrid zone from parental populations in the North Sea and eastern Baltic Sea, and they are much weaker than any difference observed between the three populations. Future sampling may refine these analyses, in particular regarding the relationship between spawning fish in the transition zone. However, they are not expected to change the overall relationship and magnitude of differentiation between the three populations presented in the currentreport.Genetic identification of population mixingThrough the use of a panel of genetic markers specifically designed to identify population of origin in a scenario with three baselines (North Sea, transition zone, eastern Baltic Sea, as supported by the genomic analyses above) we analyzed samples collected across the full transition zone to estimate proportions from the three baseline populations. The results confirmed previous findings of substantial mixing in the Kattegat and Arkona Sea, with North Sea fish and transition zone fish mixing in Kattegat and eastern Baltic Sea fish and transition zone fish mixing in the Arkona Sea. We also confirmed the gradient of mixing in the Kattegat, with higher proportions of North Sea fish in the northern parts of the area. In contrast, we found limited mixing in the Belt Sea and the Sound where fish appeared to be primarily of transition zone origin. While data for older age classes were limited, we also found evidence for higher proportions of North Sea fish among younger age classes, as also reported in previous studies.Natal origin and movements of adultsThis project investigated the natal origin and adult movements of cod in the transition zone, focusing on spatial differences in the chemical composition (the chemical “fingerprint”) recorded in the cod’s otoliths. Examining the elements analyzed in this study, it becomes apparent that they reflect gradients in environmental conditions and physiological processes, aligning with known mechanisms of otolith biomineralization. Therefore, otolith chemistry proves to be a suitable method for assessing the movement patterns of fish in the transition zone.The analyses of the otolith cores, representing the natal origin of cod, revealed spatial variations in their chemical fingerprint, indicating at least three different clusters (= spawning areas). Without baseline samples from cod larvae, it is not possible to identify where these spawning areas are, but combined with knowledge of known spawning areas, the results suggested that the cod originated primarily from the North Sea (concentrated in the Skagerrak and northern Kattegat), the Southern Kattegat (spread throughout Kattegat and partly in the Sound and Belt Sea), and the Belt Sea (predominantly found in the Belt Sea and the Sound). The contribution of the spawning area clusters varies significantly among different year classes of cod, indicating fluctuations in the relative contribution of cod originating from each spawning area.Cod inhabiting the Skagerrak and northern Kattegat regions either exhibit a similar chemical fingerprint throughout their lives or exhibit extensive mixing. Generally, these cod populations do not migrate south into the western Baltic Sea. However, some cod in the southernmost Kattegat display a Belt Sea/Sound signal throughout their lives, which is likely not due to movements but rather due to the incomplete alignment of environmental gradients with the boundaries of management areas. In contrast, the Belt Sea region predominantly hosts cod that remain resident throughout their lives, with minimal movements observed. In contrast, cod in the Sound region show a connection with the Belt Sea. The majority of cod immigrate from the Belt Sea to the Sound before the age of 3 and tend to remain resident there. However, occasional Belt Sea signals detected at irregular intervals suggest some movement in and out of the Sound.The combined analysis of natal origin and adult movements provided valuable insights into the dynamics of the cod population in the transition zone. While cod in this zone may originate from different spawning areas, they are largely resident within the respective management areas as adults. Consequently, the project results suggested the presence of an ecological stock separation into two distinct stocks: The Skagerrak/Kattegat and the Belt Sea/Sound.Stock mixing: Combining genetics and otolith chemistryCollectively, the compilation of knowledge gained from historical data and new samples, from genome sequencing and otolith chemistry, indicate that there is considerable genetic and ecological structuring of cod between the North Sea and the Baltic Sea, with three genetically distinct populations: 1. North Sea, 2. eastern Baltic Sea and 3. transition zone (Kattegat, Belt Sea, Sound and Arkona Sea). The geographic distribution of these populations overlap in the Kattegat and Arkona Sea, respectively. While it was not possible to detect genetic differentiation in the transition zone, otolith chemistry revealed considerable ecological stock structuring. This scenario is consistent with considerable exchange of individuals between areas, presumably as a result of drift of early life stages. While cod in the transition zone may originate from different spawning areas (two apparently distinct areas were identified), they are largely resident within the geographical areas they settle into as adults. This leads to stock structuring in the transition zone with an ecological separation into two distinct components: 1. the (eastern) Skagerrak and the Kattegat, 2. the Belt Sea and the Sound.For cod in Belt Sea, the Sound and the spring-spawners in the Arkona Sea, the combined genetic and otolith chemistry results thus indicate that the current management area for western Baltic is appropriate. In the Kattegat, the spatially and temporally variable mixing dynamics with the North Sea need to be considered for a sustainable management of the stock, similarly to the mixing scenario with the eastern Baltic cod in the Arkona Sea. Recommendations as to what type of stock assessment approach is most suitable for this complex system of genetic and ecological stock structuring is not within the scope of this project.Impact of fish movements and stock mixing on stock assessmentThis project implemented the prototype of a simulation tool to evaluate migration impacts on stock assessment and propose mitigation strategies. While functional, the tool can be improved with documentation, user-friendly implementations, and inclusion of additional factors. Simulations highlighted challenges in specifying complex scenarios and limited data availability. Migration patterns affected assessment data. Closing parts of the norther Kattegat, for example, showed potential for stock recovery. A cost-benefit analysis compared genetic samples and otolith shape analysis for stock composition estimation. Precision and cost influenced the choice between methods. Note that the analysis did not consider sample collection or baseline costs. Given the new biological knowledge on genetic and ecological stock structure, movement patterns in the transition zone from the North Sea to the eastern Baltic, this will be the next focus area for the application of this tool.Potential management scenariosBased on the collective genetics, otolith chemistry and modelling simulation results from this project, we have identified three different scenarios for how stock mixing could be implemented in stock assessment and management for cod stocks in the transition zone:• Area-based assessment and management – current scenario. This is a status quo scenario, where current practices are continued with two distinct stocks in the transition zone: Kattegat and the western Baltic Sea (Belt Sea, Sound and Arkona Sea), with separate stock assessments and TACs, irrespective of genetic population. Stock mixing of eastern/wester Baltic cod in the Arkona Sea is already implemented in stock assessment. By not addressing stock mixing of North Sea/Kattegat populations, the severely declined Kattegat population is at risk of local depletion.• Area-based assessment and management – updated scenario. This scenario implies continuing with current practices of separate stock assessments for the current management areas Kattegat and western Baltic Sea (Belt Sea, Sound and Arkona Sea). In addition to the stock mixing of eastern/wester Baltic cod in the Arkona Sea the mixing of North Sea and Kattegat cod in the Kattegat should be addressed in a similar approach. This scenario disregards the fact that cod in the transition zone are genetically the same population, but would on the other hand reflect the ecological stock structuring, and thereby minimize the risk of local depletion of population components.• Population-based stock assessment and management. A population-based approach to stock assessment would require cod from the Kattegat, Belt Sea, Sound and Arkona Sea to be combined into a single stock representing the genetic “transitions zone population”. Stock mixing proportions in the transition zone population would need to be estimated for these areas, based on a genetic split of commercial and survey data. Subsequently, TACs can be allocated to exiting management areas, but should be informed by genetic estimates of mixing proportions in the different management areas to link estimated harvest rates in geographical areas to the stock assessments/advice for the underlying biological populations. components not accounted for with genetic split data, ii) how to allocate area-specific TACs, and iii) how to deal with social and political considerations
