Hydropower, utilized for centuries, is promoted globally as renewable energy. The many ecological costs associated with hydropower facilities can be mitigated, but the perceived socio-economic benefits often outweigh environmental concern. The EU Water Framework Directive (WFD), implemented in 2000, established a framework for community action in the field of water policy. It constitutes an instrument to compel hydropower facilities to align with environmental requirements. Based on the WFD and national law, a National Plan for Modern Environmental Conditions for Hydropower (NAP) was formulated in Sweden to renegotiate the environmental permits of around 2000 hydropower plants and dams. The NAP process commenced in 2022 and is estimated to last approximately 20 year. In this review, we assessed the 33 court cases completed until the end of 2024, out of which 22 resulted in permit withdrawal and dam removal, while 11 received decisions requiring remedial measures. The primary focus of remedial measures was re-establishing longitudinal connectivity; other environmental aspects received less attention, and monitoring requirements were almost non-existent. We recommend measures using adaptive design, prioritizing functionality, and monitoring over detailed technical specifications. In addition, greater attention should be given also to aquatic habitats in affected reaches: addressing e.g., flow, water levels, and temperature. In conclusion, this nation-wide process provides a unique opportunity to implement measures that could benefit entire riverine ecosystems.

Vattenkraftsutbyggnaden i Daläven har sedan tidigt under 1900-talet inneburit negativ påverkan på laxens och havsöringens reproduktion. För att kompensera fisket för förlorade fiskemöjligheter odlas och utplanteras därför dessa arter i nedre delen av älven. Sedan 1990-talet har ungefär 55 000 havsöring- och 60 000 laxungar (smolt) årligen satts ut vid Fiskeriförsöksstationen i Älvkarleby. SLU har ansvarat för driften av stationen och utsättningen sedan 2011, men på grund av utebliven finansiering kommer verksamheten avvecklas under 2025. Sammanfattningsvis bedömer SLU att avvecklingen av kompensationsodlingen sannolikt kommer att medföra negativa konsekvenser för lax- och öringbestånden i Dalälven. Om ingen annan aktör tar över utsättningen finns det en risk att det inte finns kvar någon havsvandrande laxfisk i älven efter det att fria vattenvägar till lekområden etablerats, samt att detta i sin tur riskerar att de älvspecifika bestånden av lax och havsöring i Dalälven förloras. Risken för att beståndet försvinner är störst för havsöring där SLU idag sköter all utsättning av arten (för lax genomför SLU en tredjedel av utsättningarna). Om bestånden försvinner minskar också möjligheten till framtida återetablering av vilt lekande laxfisk i Dalälven. Slutligen är lax och öring nyckelarter i ekosystemet i nedre Dalälven, och det föreligger därmed även en viss risk för påverkan på balansen i näringsväven med möjliga effekter på andra fiskarter, fåglar, däggdjur, bottendjur, plankton och vegetation om bestånden av dessa försvagas eller till och med försvinner. Vattenkraftsutbyggnaden i Daläven har sedan tidigt under 1900-talet inneburit negativ påverkan på laxens och havsöringens reproduktion. För att kompensera fisket för förlorade fiskemöjligheter odlas och utplanteras därför dessa arter i nedre delen av älven. Sedan 1990-talet har ungefär 55 000 havsöring- och 60 000 laxungar (smolt) årligen satts ut vid Fiskeriförsöksstationen i Älvkarleby. SLU har ansvarat för driften av stationen och utsättningen sedan 2011, men på grund av utebliven finansiering kommer verksamheten avvecklas under 2025. Sammanfattningsvis bedömer SLU att avvecklingen av kompensationsodlingen sannolikt kommer att medföra negativa konsekvenser för lax- och öringbestånden i Dalälven. Om ingen annan aktör tar över utsättningen finns det en risk att det inte finns kvar någon havsvandrande laxfisk i älven efter det att fria vattenvägar till lekområden etablerats, samt att detta i sin tur riskerar att de älvspecifika bestånden av lax och havsöring i Dalälven förloras. Risken för att beståndet försvinner är störst för havsöring där SLU idag sköter all utsättning av arten (för lax genomför SLU en tredjedel av utsättningarna). Om bestånden försvinner minskar också möjligheten till framtida återetablering av vilt lekande laxfisk i Dalälven. Slutligen är lax och öring nyckelarter i ekosystemet i nedre Dalälven, och det föreligger därmed även en viss risk för påverkan på balansen i näringsväven med möjliga effekter på andra fiskarter, fåglar, däggdjur, bottendjur, plankton och vegetation om bestånden av dessa försvagas eller till och med försvinner.

För att kompensera för kraftigt minskad naturlig reproduktion orsakad av vattenkraftsutbyggnad sker odling och utsättning av betydande mängder lax och havsöring i ett flertal av våra större vattendrag. Varje år tas nya avelsfiskar in för kramning (sea ranching). I Sverige ska all kompensationsodlad utsatt fisk vara fettfeneklippt. Tidigare märktes även en andel av lax- och havsöringsungarna (smolten) med yttre så kallade Carlinmärken, där inrapporterade återfynd har använts för olika studier och uppföljningar. Av flera olika anledningar har dock dessa märkningar i princip upphört. Som ett alternativ till yttre märkning har molekylärgenetiska analyser av återvändande avelsfisk börjat användas för att samla in information om de kompensationsodlade lax- och havsöringsstammarna. Genom att dra nytta av det faktum att samtliga individer bär på en unik genuppsättning, går det att baserat på data från återkommande DNA-analyser av avelsfisk göra diverse uppföljningar av odlingsverksamheten. De första DNA-analyserna genomfördes 2014. Därefter har antalet stammar som omfattas av analyserna gradvis ökat. Resultat från DNA-analyser av lax och havsöring erhållna till och med aveln 2018 har presenterats tidigare (Söderberg m.fl. 2019). I denna rapport ges en uppdaterad sammanställning av slutsatser och erfarenheter baserad på fortsatta analyser (t.o.m. aveln 2022) av totalt sju lax- och sex havsöringsstammar. Samtliga de undersökta lax- och havsöringsstammarna uppvisade jämförelsevis hög genetisk variationsgrad, vilket kan förklaras av att det genom åren ingått inslag av älvsfrämmande individer bland de kramade avelsfiskarna. För lax i Skellefteälven observerades dock en signifikant minskad variationsgrad (färre anlagsvarianter) från 2014 till 2022 vilken kan återspegla en relativt hög förekomst av sterila hanar i kombination med att man relativt nyligen övergått till att para en hona med endast en hane. Under samma tidsperiod uppvisade laxen i Ljusnan tecken på ökad genetisk variationsgrad, vilket sammanfaller med en kraftigt ökad andel identifierad älvsfrämmande avelsfisk (från 3-4 % 2014-2015 till drygt 50 % 2022, en extremt hög nivå). Med undantag för Ljusnan varierade den genomsnittliga andelen älvsfrämmande lax mellan 0,3 och 3,3 %. Även för havsöring var andelen älvsfrämmande avelsfisk identifierad via DNA låg och utan något exempel på en större förändring över tid. Hos båda arterna härstammade de flesta älvsfrämmande avelsfiskarna från geografiskt mer närliggande älvar. Hittills (t.o.m. 2022) har ca 25 % av de DNA-analyserade avelslaxarna identifierade föräldrar från tidigare år, där Skellefteälven och Lagan dominerar tack vare längst tidsserier. Inom några år förväntas föräldrar till samtliga odlade individer från de sju laxstammar som ingår i projektet att kunna identifieras. För havsöring, som analyserats under kortare tid, är andelen med identifierade föräldrar hittills endast 8 %. Även för denna art förväntas en snabbt ökande andel avelsfisk med identifierade föräldrar under de kommande åren. Andelen identifierade helsyskon som råkat bli parade med varandra varierade mellan noll och några få procent per år och stam, med tendens till något högre andelar hos havsöring jämfört med lax. Avslutningsvis ges några exempel där DNA-baserade föräldraskapsbestämningar (för lax) använts som utgångspunkt för storleksjämförelser av hanar och honor med olika antal år i havet, ursprungsidentifieringar av kustfångade odlade individer, konstruktion av stamträd (pedigree) samt beräkningar av genetiskt effektiv populationsstorlek (Ne). Baserat på antal återvändande avkommor per kramad förälder beräknades Ne för lax i Skellefteälven och Lagan till omkring 200 respektive 320 (per generation), vilket understiger det långsiktiga mål om Ne ≥ 500 som ofta refereras till i genetiska bevarandesammanhang. För att erhålla ökade effektiva populationsstorlekar krävs sannolikt fler avelslaxar i kombination med åtgärder som syftar till att ge en minskad variation i antalet avkommor per förälder.

Insights into the genetic basis of local adaptation and drivers of population differentiation improve our understanding of evolution and the maintenance of biological diversity. Characterising adaptively important genetic variation also allows more efficient planning of conservation and management actions. We used a genome-wide SNP array to analyse the genetic population structure of a large Atlantic salmon ( Salmo salar ) population in the interconnected Tornio/Torne and Kalix River system of the Baltic Sea basin, and to identify genomic signatures of fine-scale selection within it. We identified signals of selection and genotype-environment associations (GEA) especially on chromosome (Chr) 9, including on a haploblock containing the six6 gene and other loci that have been earlier suggested to be adaptively important in salmonids. We also detected signals of selection in genome regions including other genes of ecological relevance, such as two known appetite-controlling genes in the melanocortin system ( pomca on Chr 9 and mc4r on Chr 14), and the maturation-associated gene taar13c-like (on Chr 21). Variation in these and other identified candidate genes may potentially reflect differential selective pressures experienced by salmon from different parts of the large river system, regarding traits related to e.g. vision, feeding and growth, age at maturity and/or migratory timing. This indicates a need for management strategies to consider ecologically important genomic regions such as these, in order to protect adaptive genetic diversity in wild salmon populations.

AbstractJuvenile salmonids often experience high mortality rates during migration and bird predation is a common source of mortality. Research suggests that hatchery‐reared salmonids are more prone to predation than wild salmonids, and that Atlantic salmon (Salmo salar) experience lower predation than Sea trout (Salmo trutta), yet telemetry studies have displayed equivocal results. Here, using a large data set on passive integrated transponder (PIT) tagged hatchery‐reared and wild juveniles of Atlantic salmon and Sea trout (25,769 individuals) we investigate predation probability by piscivorous birds (mainly Great Cormorants Phalarocorax carbo) on salmonids originating from River Dalälven in Sweden. Bird colonies and roosting sites were scanned annually (2019–2021), and the temporal dynamics of bird predation on salmonids released in 2017–2021 was assessed. Hatchery‐reared trout was clearly most susceptible to cormorant predation (0.31, 90% credibility interval [CRI] = 0.14–0.53), followed by wild trout (0.19, 90% CRI = 0.08–0.37), hatchery‐reared salmon (0.13, 90% CRI = 0.07–0.23), and wild salmon (0.08, 90% CRI = 0.04–0.14), in subsequent order. This order in predation probability was consistent across all studied tag‐ and release‐years, suggesting that the opportunistic foraging of cormorants affects the overall survival of juvenile salmonids, but that the inherent predation risk between different salmonid types differs systematically.

Climate change, biological invasions, and anthropogenic disturbance pose a threat to the biodiversity and function of Arctic freshwater ecosystems. Understanding potential changes in fish species distribution and richness is necessary, given the great importance of fish to the function of freshwater ecosystems and as a resource to humans. However, information gaps limit large-scale studies and our ability to determine patterns and trends in space and time. This study takes the first step in determining circumpolar patterns of fish species richness and composition, which provides a baseline to improve both monitoring and conservation of Arctic freshwater biodiversity. Information on species presence/absence was gathered from the Circumpolar Biodiversity Monitoring Program's Freshwater Database and used to examine patterns of freshwater fish gamma-, alpha-, and beta-diversity across 234 degrees of longitude in the Arctic. The metrics of diversity provided information on species richness and composition across hydrobasins, ecoregions, and Arctic zones. Circumpolar patterns of fish species biodiversity varied with latitude, isolation, and coarse ecoregion characteristics; patterns were consistent with historic and contemporary barriers to colonisation and environmental characteristics. Gamma-diversity was lower in the high Arctic compared to lower latitude zones, but alpha-diversity did not decrease with increasing latitude below 71 degrees N, reflecting glacial history. Alpha-diversity was reduced to a single species, Arctic charr Salvelinus alpinus, in ecoregions above 71 degrees N, where gamma-diversity was the lowest. Beta-diversity indicated little variation in the composition and richness of species across the High Arctic; at lower latitudes, ecoregions contained more species, although species composition turned over across large spatial extents. In an analysis of five ecoregions in the circumpolar Arctic, physical isolation, and ecoregion area and topography were identified as strong drivers of gamma-, alpha-, and beta-diversity. Physical isolation reduced the gamma- and alpha-diversity, and changes in beta-diversity between adjacent locations were due mainly to losses in species richness, rather than due to differences in species composition. Heterogeneity of habitats, environmental gradients, and geographic distance probably contributed to patterns of fish dissimilarity within and across ecoregions. This study presents the first analysis of large-scale patterns of freshwater fish biodiversity in the circumpolar Arctic. However, information gaps in space, time, and among taxonomic groups remain. Future inclusion of extensive archive and new data will allow future studies to test for changes and drivers of the observed patterns of biodiversity. This is important given the potential impacts of ongoing and accelerating climate change, land use, and biotic exchange on Arctic fish biodiversity.

Understanding the processes shaping the dynamics of anadromous fish populations is essential for their management and conservation. Yet, little is known about how variation in performance at sea affects their population dynamics. Here we show that variation in body growth at sea contributes to explaining variation in the reproductive potential for 2 Atlantic salmon Salmo salar populations, but to a varying extent. To this end, we assembled data collected during 50 yr for 2 Baltic salmon populations of hatchery origin, including annually released smolts, survival at sea estimates, size-specific growth at sea, annual length distributions of returning adult females and their reproductive potential. The regression models fitted to explain the reproductive potential of our 2 study populations improved when growth at sea was included as an explanatory variable, in addition to smolt year class abundance and estimates of their survival at sea. This link between body growth at sea and population-level reproductive potential suggests that growth at sea can be important to consider when resolving variation in recovery and dynamics among salmon populations sharing the same sea.

Intra-species genetic homogenization arising from anthropogenic impacts is a major threat to biodiversity. However, few taxa have sufficient historical material to systematically quantify long-term genetic changes. Using archival DNA collected over approximately 100 years, we assessed spatio-temporal genetic change in Atlantic salmon populations across the Baltic Sea, an area heavily impacted by hydropower exploitation and associated with large-scale mitigation stocking. Analysis was carried out by screening 82 SNPs in 1680 individuals from 13 Swedish rivers. We found an overall decrease in genetic divergence and diminished isolation by distance among populations, strongly indicating genetic homogenization over the past century. We further observed an increase in genetic diversity within populations consistent with increased gene flow. The temporal genetic change was lower in larger wild populations than in smaller wild and hatchery-reared ones, indicating that larger populations have been able to support a high number of native spawners in relation to immigrants. Our results demonstrate that stocking practices of salmon in the Baltic Sea have led to the homogenization of populations over the last century, potentially compromising their ability to adapt to environmental change. Stocking of reared fish is common worldwide, and our study is a cautionary example of the potentially long-term negative effects of such activities.

Determining the origin of individuals in mixed population samples is key in many ecological, conservation and management contexts. Genetic data can be analyzed using genetic stock identification (GSI), where the origin of single individuals is determined using Individual Assignment (IA) and population proportions are estimated with Mixed Stock Analysis (MSA). In such analyses, allele frequencies in a reference baseline are required. Unknown individuals or mixture proportions are assigned to source populations based on the likelihood that their multilocus genotypes occur in a particular baseline sample. Representative sampling of populations included in a baseline is important when designing and performing GSI. Here, we investigate the effects of family sampling on GSI, using both simulated and empirical genotypes for Atlantic salmon (Salmo salar). We show that nonrepresentative sampling leading to inclusion of close relatives in a reference baseline may introduce bias in estimated proportions of contributing populations in a mixed sample, and increases the amount of incorrectly assigned individual fish. Simulated data further show that the induced bias increases with increasing family structure, but that it can be partly mitigated by increased baseline population sample sizes. Results from standard accuracy tests of GSI (using only a reference baseline and/or self-assignment) gave a false and elevated indication of the baseline power and accuracy to identify stock proportions and individuals. These findings suggest that family structure in baseline population samples should be quantified and its consequences evaluated, before carrying out GSI.

Anadromous salmonid fishes frequently exhibit strong geographic population structuring. However, population genetic differentiation of Atlantic salmon (Salmo salar) at fine geographic scales differs across equivalent spatial extents in different regions. So far, fine-scale genetic differentiation has not been assessed in rivers of the Baltic Sea, a region that contains an evolutionarily distinct Atlantic salmon lineage. Thus, Baltic salmon are currently managed on the river level, without focus on potential genetic structure and diversity within rivers. Here, we used microsatellites to characterize the genetic structure of wild juvenile salmon sampled throughout the interconnected, northern Baltic Tornio and Kalix Rivers. We found genetic differentiation within the two rivers, but not between them: salmon in the upper reaches differed from individuals in the lower reaches, regardless of river system. Further, examining smolts migrating from the river to the sea and adults returning from the sea to spawn, we found an association between the genetic structure and seasonal migration timing. Out-migrating smolts genetically assigned to upper river reaches were older and tended to reach the sea later in the season than smolts from the lower reaches. In contrast, mature adults originating from the upper reaches returned to the river early in the season. Our observation of genetic population structuring between downstream and upstream reaches of the large Tornio and Kalix rivers, and its association with migration timing, implies that careful temporal management of the northern Baltic fisheries would help to preserve the diversity and sustainability of the wild salmon stocks of these rivers.

AbstractIdentifying factors determining the performance of individuals is an essential part of resolving what drives population dynamics. For species undergoing ontogenetic shifts in resource and habitat use, this entails assessing individual performance in all habitats used. Whereas survival and growth of anadromous Atlantic salmon, Salmo salar L., in its juvenile, river habitat are known to depend on size‐dependent foraging and food availability, individual performance of salmon in the growth habitat out at sea is commonly explained only by abiotic factors. Still, individuals undergo this habitat shift to grow large, suggesting performance should be food‐dependent also in the growth habitat. Because fish communities are highly size‐structured, the link between predators and their prey may depend on their respective body sizes. Here, we study whether the performance of Baltic Sea salmon in its growth habitat is food‐ and size‐dependent, by combining extensive diet and body size data of Baltic salmon with spatially resolved monitoring data on abundance and size distribution of their main prey, herring, Clupea harengus L., and sprat, Sprattus sprattus L. We found that both the species and size composition of prey in the diet varied with salmon body size. By accounting for this size‐dependent predation and the spatially varying size distribution of prey species, we could explain the variation in salmon diet composition among salmon individuals in different Baltic Sea basins and of different length. The proportion of sprat in diet of salmon was better explained by size‐specific prey availability (SSP) than total prey biomass, especially for small salmon. Further, salmon body condition increased with SSP, whereas total prey biomass could not explain variation in the condition of salmon. These findings demonstrate that food‐ and size‐dependent processes indeed can influence the performance of anadromous fish also in large marine systems. Thus, we argue that consideration of these processes, stretching across habitats, is important for understanding performance and dynamics of predatory fish in open aquatic systems, as well as for successful management of species such as Atlantic salmon.

1. Inferring the dynamics of populations in time and space is a central challenge in ecology. Intra-specific structure (for example genetically distinct sub-populations or meta-populations) may require methods that can jointly infer the dynamics of multiple populations. This is of particular importance for harvested species, for which management must balance utilization of productive populations with protection of weak ones. 2. Here we present a novel method for simultaneous learning about the spatio-temporal dynamics of multiple populations that combines genetic data with prior information about abundance and movement, akin to an integrated population modelling approach. We apply the Bayesian genetic mixed stock analysis to 17 wild and 10 hatchery-reared Baltic salmon (S. salar) stocks, quantifying uncertainty in stock composition in time and space, and in population dynamics parameters such as migration timing and speed. 3. The genetic data were informative about stock-specific movement patterns, updating priors for migration path, timing and speed. Use of a population dynamics model allowed robust interpolation of expected catch composition at areas and times with no genetic observations. Our results indicate that the commonly used "equal prior probabilities" assumption may not be appropriate for all mixed stock analyses: incorporation of prior information about stock abundance and movement resulted in more plausible and precise estimates of mixture compositions in time and space. 4. The model we present here forms the basis for optimizing the spatial and temporal allocation of harvest to support the management of mixed populations of migratory species.

The genetic structure of nine wild, seven hatchery-reared, and one presumably mixed, sea trout (Salmo trutta L.) populations sampled from watersheds along the Swedish Baltic Sea coast was analysed using ten microsatellite loci. DNA-information was evaluated as a baseline for mixed stock analysis (MSA) and individual assignment (IA). A clear genetic structure with distinct populations was identified (global F (ST) = 0.066), with significant regional differentiation. Average gene diversity (H (e)) was similar among samples of wild and reared trout, whereas levels of heterozygote deficiency differed significantly (wild: H (e) = 0.70, F (IS) = 0.075; reared: H (e) = 0.69, F (IS) = 0.022). The high F (IS) found in wild samples indicates presence of within-river sub-structuring. Evaluation with realistic-fishery simulations indicated that the baseline resolution was sufficient for MSA, at least at a regional level. Hierarchical MSA and IA analyses of real catches from two coastal fisheries showed that populations from the northern region contributed about 90 % to the catch. Analysed individually, the two fisheries differed in catch compositions despite a short geographic distance among sites. One fishery mainly caught sea trout from a small wild population whereas the other fishery was dominated by reared sea trout. Stock composition analysis is a valuable tool for refining exploitation rate estimates for individual sea trout populations in mixed coastal fisheries, as well as for investigating migration patterns in the Baltic Sea.