Dorte Bekkevold

Introduction: Brown trout (Salmo trutta L.) is a salmonid fish considered a genetically and geographically highly structured species. The species is catalogued as vulnerable in the Spanish Red List since 1992. Based on morphological differentiation, some authors have proposed splitting Salmo trutta into many taxa and in recent years, several binomials involving morphologically differentiated Western Mediterranean brown trout morphs have regained relevance as distinct species and are now assessed in the IUCN Red List. However, Spanish legislation still considers a single species, S. trutta, inhabiting Atlantic and Mediterranean rivers. Analyses of mitochondrial DNA variation across the species’ native range have revealed numerous matrilineal lineages and helped disentangle the phylogenetic relationships and biogeographic history of brown trout. Four largely distant evolutionary lineages defined by sequencing the mitochondrial control region (Adriatic, AD, Mediterranean, ME, Atlantic, AT and Duero, DU) are native among the Iberian brown trout populations. Stocking activities have resulted in introgressive hybridization of these native populations with non-native northern Atlantic stocks throughout the Iberian rivers and compromise the evolutionary singularities of brown trout in the Iberian Peninsula. Methodology: In this study, we compare complete mitogenomes from Iberian brown trout specimens with those from other regions, using both newly sequenced samples and whole mitogenomes from the GenBank database and estimate their divergence times relative to those observed among species of other Salmoninae genera, such as Oncorhynchus and Salvelinus, to assess patterns of species-specific divergence among Iberian brown trout populations. Results: The evolutionary relationships of the specimens using their mitogenomes fitted with previous analyses using partial mitochondrial sequences and confirmed the strong differentiation among the Iberian lineages. All the branches involving distant Iberian mitogenomes are sister branches with taxa historically described under different binomials (such as Salmo macrostigma, S. multipunctatus, S. pallaryi). Conclusions: The results provide evidence supporting the existence of potentially distinct and undescribed native Salmo species in the Iberian rivers.

Managing and giving advice for mixed‐population fisheries of the same species can be challenging due to difficulties in predicting stock mixing, technical interactions, and in ensuring precautionary stock dynamics. Most fish species consist of several populations all of which need to be sustainably managed to preserve biodiversity and resilience to environmental changes, and to sustain productive fisheries. Mixing of populations of the same species with different productivity represents additional challenges for assessment and management. In such cases, there is a need to develop assessment and advice methods to consider mixed stocks and advise managers on fishing opportunities. In this study, we develop a framework including multifleet multi‐stock assessment models and forecasts where future stock dynamics depend on stock mixing, fleet‐specific fishing opportunities, and management in place. This framework is applied to the large North Sea herring stock and the overexploited western Baltic herring stock, which in part of their distribution areas are found to be mixed in both catches and surveys. The framework is used to investigate the trade‐offs between stock rebuilding and fishing opportunities in a mixed fishery. The study shows that spatial management implying transfer of quotas away from the areas where the stocks mix and towards the stock in good condition could help stock rebuilding without reducing overall fishing opportunities, however with a slower rebuilding rate compared to a more drastic fishery closure. The implementation of quota transfer should however consider the spatial relocation of fishing opportunities to avoid catch advice overshoot and inflated quotas.

In times of increased human interventions, knowledge on animal breeding-site fidelity is crucial for the conservation of important reproduction areas vital to the resilience of populations. In particular, in the marine environment, dependency of ocean-going fish on specific coastal locations are rarely implemented in spatial planning. However, when essential nursery habitats are threatened, the resilience of fish populations is jeopardized. For technical reasons, former studies on Atlantic herring could not specify if fish, returning to spawning grounds, returned to sites of their own natal origin. Combining otolith microchemistry with genetics, we show that Atlantic herring perform natal homing with rates between 56 and 73%. The implicit number of strays adopted along migration maintain the gene flow between subpopulations, supporting the hypothesized “metapopulation” concept. With respect to increasing anthropogenic impacts, this study demonstrates the need for a goal-oriented coastal zone management to ensure productive ecosystems and a sustainable fishery in the future.

Predicting the long‐term impact of releases and introgression from non‐native strains into wild populations remains an important conservation issue, particularly in fishes where stocking and aquaculture escapes have led to widespread genetic admixture between wild and cultured conspecifics. Here, we investigated the genetic response of two wild sea trout, Salmo trutta L., populations following long‐term stocking programmes with non‐native conspecifics. This included temporal sampling spanning 23 years and genome‐wide SNP data from two neighbouring Danish rivers that from the 1970's to 1990's were heavily stocked with partially domesticated, non‐local hatchery strains. To estimate wild‐hatchery admixture we analysed 3656 SNPs in 195 wild‐caught fish, 74 hatchery strain fish, and expanded collections temporally by analysing a subset 288 SNPs in 489 additional fish. Admixture estimates decreased from 46% to 62% input from the stocked strains to 25% seven generations after the last stocking. Introgression varied across the genome, indicative of selection for and against specific hatchery gene variants under wild conditions. For the first time in trout, strong temporal allele frequency changes were observed in a gene region harbouring the maturation gene six6 likely associated with divergent selection on age‐at‐maturity under hatchery versus wild conditions. The two populations showed low overlap between SNPs identified as under negative (or purifying) selection. Results point to selection against hatchery fish and partial recovery of both populations but also emphasise the role of local dynamics in shaping genetic responses to anthropogenic pressure and support the notion that introgression is likely to incur long‐lasting changes to the genetic make‐up of wild populations.

Ostrea edulis, the European flat oyster, was once a widespread economically and ecologically important marine species, but has suffered dramatic declines over the past two centuries. Consequently, there has been a surge in European restoration efforts, many of which focus on restocking as a conservation measure. In this study, we used whole‐genome sequencing (WGS) data to investigate the population structure, demographic history, and patterns of local adaptation of O. edulis across its natural distribution with increased sampling densities at Scandinavian localities. Results revealed seven distinct genetic clusters, including previously undescribed complex population structure in Norway, and evidence for introgression between genetic clusters in Scandinavia. We detected large structural variants (SVs) on three pseudo‐chromosomes. These megabase long regions were characterised by strong linkage disequilibrium and clear geographical differentiation, suggestive of chromosomal inversions potentially associated with local adaptation. The results indicated that genomic traces of past translocations of non‐native O. edulis were still present in some individuals, but overall, we found limited evidence of major impacts of translocations on the scale of contemporary population structure. Our findings highlight the importance of considering population structure and signatures of selection in the design of effective conservation strategies to preserve and restore wild native European flat oyster populations, and we provide direct knowledge safeguarding sustainable mitigation actions in this important species.

Sea trout, the anadromous ecotype of the species Salmo trutta, are subject to multiple threats, including exploitation and aquaculture impacts in the marine environment, habitat fragmentation and pollution in freshwaters, loss of genetic resilience due to interbreeding with hatchery strains and environmental change. Small streams contribute relatively little biomass to European sea trout stocks but are thought to be important in maintaining genetic diversity and therefore wider population resilience. The current study combined data from acoustic telemetry, stable isotopes, genetics and scalimetry to assess the current status of sea trout in the rivers Stiffkey and Glaven, two locally important chalkstreams in East Anglia, UK, to provide an evidence base for future management. The incidence of anadromy was low, and most sea trout were near migrants, residing in the lower reaches of rivers and close to the tidal outfalls. A small number migrated to the North Sea where they were vulnerable to exploitation in the coastal fishery, which comprises a mixed stock. Straying between the two rivers was recorded among 10% of sea trout, leading to apparent high gene flow. Nonetheless, genetic data also demonstrated structuring of River Glaven trout into two distinct groups. Quantification of patterns of freshwater and estuarine habitat use, and of passage at cross-channel obstructions, was used to identify where remedial measures such as habitat restoration would be most effectively targeted. Findings are discussed in the context of local supplementary stocking and the potential impact of the nearshore fishery on limited and vulnerable small stream anadromous trout populations.

Sustainable fisheries management is important for the continued harvest of the world's marine resources, especially as they are increasingly challenged by a range of climatic and anthropogenic factors. One of the pillars of sustainable fisheries management is the accurate identification of the biological units, i.e., populations. Here, we developed and implemented a genetic baseline for Atlantic herring harvested in the Norwegian offshore fisheries to investigate the validity of the current management boundaries. This was achieved by genotyping > 15,000 herring from the northern European seas, including samples of all the known populations in the region, with a panel of population‐informative SNPs mined from existing genomic resources. The final genetic baseline consisted of ~1000 herring from 12 genetically distinct populations. We thereafter used the baseline to investigate mixed catches from the North and Norwegian Seas, revealing that each management area consisted of multiple populations, as previously suspected. However, substantial numbers (up to 50% or more within a sample) of herring were found outside of their expected management areas, e.g., North Sea autumn‐spawning herring north of 62° N (average = 19.2%), Norwegian spring‐spawning herring south of 62° N (average = 13.5%), and western Baltic spring‐spawning herring outside their assumed distribution area in the North Sea (average = 20.0%). Based upon these extensive observations, we conclude that the assessment and management areas currently in place for herring in this region need adjustments to reflect the populations present. Furthermore, we suggest that for migratory species, such as herring, a paradigm shift from using static geographic stock boundaries towards spatial dynamic boundaries is needed to meet the requirements of future sustainable management regimes.

Genetic data have greatly increased means to understand fish marine migration behaviours at large spatial scale within a quantitative framework. The anadromous sea trout is a prized target of recreational fishery and an important ecosystem component in freshwater and marine coastal habitats in large parts of temperate northern Europe. Nonetheless, little is known about population distributions while feeding at sea. To reconcile notions about feeding migrations being predominantly locally restricted or not, we used SNP data for 3465 trout representing >100 rivers to identify population origins of 903 coastally feeding fish captured throughout the North Sea-Baltic Sea transition area. Across areas, coastal collections generally showed marked stock-mixing and overall 70:30% native:non-native fish with seasonal variation corresponding with spawning run timing. Data revealed strong spatial feeding segregation between trout from the Scandinavian Peninsula and the European continent. This is surprising given the short distances between areas, but is in alignment with strong genetic differentiation between populations in these areas. Estimation of stock complexity of coastal feeding aggregations showed no spatial trend through the North Sea-Baltic Sea transition area otherwise characterized by strong environmental clines. Analyses of scale samples collected in the 1950s indicate that stock-mixing was consistent over almost 70 years.

Fish stocks composed of several populations are considered to have more stable productivity than stocks containing only one or few populations. This stability is attributed to complementary or independent dynamics among the populations within the stock—the so-called portfolio effect. Declines of populations within stocks that have delayed recovery potentially increase risk to productivity and local extinctions. Portfolio effects may be relevant in the Baltic Sea, where autumn-spawning herring was the dominant herring ecotype until the early/mid-20th century. The current fishery assessment and management in the area assumes that the abundance of autumn spawning herring has been negligible since the 1970s; the share of spring spawning herring has become dominant and is considered to be the only ecotype. Data from a multi-annual ichthyoplankton survey in the southern Baltic Sea (Bornholm Basin) during autumn 2002–2019 show that abundance and spatial distribution of the smallest larval stages have increased significantly. This pattern could be due to an increase in autumn spawners in the area. Genetic studies confirm that these larval herring are offspring from true autumn spawners. Preserving intraspecific diversity is critical for a species’ future abilities to adapt to and survive in changing environmental conditions. Thus, our results not only provide new insights to the temporal dynamics of herring ecotypes and challenge the current understanding of central Baltic herring stock processes in general, but are also important in the context of monitoring, assessment, and spatial management of herring in the Baltic Sea.

Populations of anadromous brown trout, also known as sea trout, have suffered recent marked declines in abundance due to multiple factors, including climate change and human activities. While much is known about their freshwater phase, less is known about the species' marine feeding migrations. This situation is hindering the effective management and conservation of anadromous trout in the marine environment. Using a panel of 95 single nucleotide polymorphism markers we developed a genetic baseline, which demonstrated strong regional structuring of genetic diversity in trout populations around the English Channel and adjacent waters. Extensive baseline testing showed this structuring allowed high‐confidence assignment of known‐origin individuals to region of origin. This study presents new data on the movements of anadromous trout in the English Channel and southern North Sea. Assignment of anadromous trout sampled from 12 marine and estuarine localities highlighted contrasting results for these areas. The majority of these fisheries are composed predominately of stocks local to the sampling location. However, there were multiple cases of long‐distance movements of anadromous trout, with several individuals originating from rivers in northeast England being caught in the English Channel and southern North Sea, in some cases more than 1000 km from their natal region. These results have implications for the management of sea trout in inshore waters around the English Channel and southern North Sea.