Fishing has the potential to influence the life-history traits of exploited populations. However, our understanding of how fisheries can induce evolutionary genetic changes remains incomplete. The discovery of large-effect loci linked with ecologically important life-history traits, such as age at maturity in Atlantic salmon (Salmo salar), provides an opportunity to study the impacts of temporally varying fishing pressures on these traits. A 93-year archive of fish scales from wild Atlantic salmon catches from the northern Baltic Sea region allowed us to monitor variation in adaptive genetic diversity linked with age at maturity of wild Atlantic salmon populations. The dataset consisted of samples from both commercial and recreational fisheries that target salmon on their spawning migration. Using a genotyping-by-sequencing approach (GT-seq), we discovered strong within-season allele frequency changes at the vgll3 locus linked with Atlantic salmon age at maturity: fishing in the early season preferentially targeted the vgll3 variant linked with older maturation. We also found within-season temporal variation in catch proportions of different wild Atlantic salmon subpopulations. Therefore, selective pressures of harvesting may vary depending on the seasonal timing of fishing, which has the potential to cause evolutionary changes in key life-history traits and their diversity. This knowledge can be used to guide fisheries management to reduce the effects of fishing practices on salmon life-history diversity. Thus, this study provides a tangible example of using genomic approaches to infer, monitor and help mitigate human impacts on adaptively important genetic variation in nature.

Institutionen för akvatiska resurser vid Sveriges lantbruksuniversitet (SLU Aqua) presenterar årligen statusbedömningar för nationellt förvaltade fisk- och skaldjursbestånd i svenska vatten på webbportalen www.fiskbarometern.se. Fiskbarometerns statusbedömningar av fisk- och skaldjursbestånd, utgör ett viktigt underlag för hållbart nyttjande, bevarandeåtgärder och uppföljning inom fisk-, vatten- och miljöförvaltningen. I denna rapport redovisas metodiken för dessa statusbedömningar. Metodiken bidrar till en standardiserad och kvalitetssäkrad bedömningsprocess som är transparent och som vilar på vetenskaplig grund. För de flesta bestånd i Fiskbarometern baseras bedömningen på indikatorer indelade i dödlighet, biomassa/abundans och storleks-/åldersstruktur, vilka motsvarar Havsmiljödirektivets tre kriterier för bedömning av kommersiellt nyttjade bestånd (2008/56/EC). Baserat på sammanvägningen av de tre kriterierna ges respektive bestånd sedan en av fem möjliga statusbedömningar: • kan ej bedömas • mycket sannolikt inte inom biologiskt säkra gränser • sannolikt inte inom biologiskt säkra gränser • sannolikt inom biologiskt säkra gränser • mycket sannolikt inom biologiskt säkra gränser För några nationellt förvaltade bestånd finns eller pågår arbete med att utveckla analytiska beståndsmodeller. I den här rapporten presenteras riktlinjer för kvalitetssäkring och tillämpning av dem översiktligt, men den vetenskapliga granskningen av sådana modeller hanteras separat inom en process som kallas riktmärkning, vilken inte beskrivs i denna rapport. Utfall från dessa modeller översätts till samma statuskategorier som för de indikatorbaserade bedömningarna.

· Bedömningen baseras på litteratur om laxens biologi och om påverkansfaktorer från havsbaserad vindkraft. Det finns i dagsläget inga vindparker där det förekommer lax i svenska hav så att man kan studera faktiska effekter, och inte heller några undersökningar från vindparker i andra länder. · Enligt nuvarande kunskapsläge bedöms risken som låg att vandrande lax påverkas negativt, om vindparker anläggs med bottenfasta fundament med ett långt avstånd mellan tornen och lokaliseras i utsjön på ett inte alltför grunt vattendjup (mer än cirka 30 meter). · Risken för negativ påverkan på vandrande lax bedöms som låg även vid användning av flytande fundament, men osäkerheten är något högre. De kablar som transporterar el från flytande fundament kommer att ligga i vattenmassan och skulle komma närmare laxen än vid användning av bottenfasta fundament. Det magnetiska fältet från kablarna har dock en mycket begränsad spridning, i storleksordningen högst enstaka meter. · Även om risken bedöms som låg så är det viktigt med uppföljande studier i och omkring de vindparker som anläggs, med fokus på att klarlägga laxens beteende vid anläggningarna. Om flera vindparker byggs är en samordnad övervakning viktig för att kunna följa eventuella kumulativa effekter. Syftet med undersökningarna skulle vara att klarlägga kunskapsläget och ge möjlighet att identifiera behov av anpassningar för att lindra eventuella oförutsedda negativa effekter på större rumslig skala, till exempel vandringsmönster.

Öringen har en komplex livscykel och bestånd kan innehålla varierande grad av stationära och vandrande individer. Öringen finns i många miljöer, från havet till fjällsjöar, och har bland annat krav på goda strömvattenmiljöer, fria vandringsvägar och en god miljö i kustområdet. Många bestånd av öring är generellt sett små och därför känsliga för negativ miljöpåverkan och fiske. Risken för genetisk utarmning är stor i små och reproduktivt isolerade populationer. Där möjlighet finns har dock öringen i regel ett genutbyte med andra närliggande populationer, vilket minskar riskerna för förlust av genetisk variation och inavel samt medför ökad återhämtningsförmåga. Dagens bestånd av havsöring är generellt svagare än historiskt, då stora arealer i rinnande vatten inte längre kan nås på grund av vandringshinder. Fisket efter öring domineras av fritidsfiske vars fångstmängder och omfattning är dåligt kända. För att skatta öringens beståndsstatus behöver specifika uppföljningsbara förvaltningsmål för öring tas fram. Förekomsten av många små bestånd medför svårigheter (och höga kostnader) för övervakning och bedömning av beståndsstatus för enskilda lokala bestånd. Förvaltningen av öring bör därför vara områdesbaserad, där varje område har liknande miljö- och påverkansfaktorer. Förvaltningen bör även vara ekosystembaserad och adaptiv, för att snabbt kunna anpassas till rådande förhållanden (torka och andra påverkansfaktorer). Adaptiv förvaltning kräver flexibla regelverk och en i övrigt transparent förvaltning, samt datainsamling/övervakning i typiska öringvattendrag spridda över hela landet inklusive ett antal representativa (för enskilda förvaltningsområden) ”indexvattendrag” med utökad datainsamling.

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.

The noble crayfish (Astacus astacus) is an endangered freshwater species in Europe. The main threat is from lethal crayfish plague, caused by the oomycete Aphanomyces astaci that has been spread over Europe by introduced North American crayfish species, acting as chronic carriers of the disease. Most of the remaining noble crayfish populations are found in the Baltic Sea area, and there is an urgent need to implement conservation actions to slow down or halt the extinction rate in this region. However, limited knowledge about the genetic structure of populations in this area has so far precluded the development of conservation strategies that take genetic aspects into consideration. Key objectives of this large-scale genetic study, covering 77 locations mainly from northern Europe, were to describe the contemporary population genetic structure of the noble crayfish in the Fennoscandian peninsula (Sweden, Norway, and Finland), taking postglacial colonization history into account, and to evaluate how human activities such as stocking have affected the genetic structure of the populations. Analyses of 15 microsatellite markers revealed three main genetic clusters corresponding to populations in northern, middle, and southern Fennoscandia, with measures of genetic diversity being markedly higher within populations in the southern cluster. The observed genetic structure probably mirrors two main colonizations of the Baltic Sea basin after the last glaciation period. At the same time, several deviations from this pattern were observed, reflecting past human translocations of noble crayfish. The results are discussed in relation to the conservation and management of this critically endangered species. In particular, we recommend increased efforts to protect the few remaining noble crayfish populations in southern Fennoscandia and the use of genetic information when planning stocking activities, such as reintroductions following local extinctions.

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.

Detta biologiska underlag sammanfattar situationen for Bottniska vikens bestand av lax och havsoring. Underlaget har skrivits efter att Havs- och vattenmyndigheten bestallt biologisk radgivning fran SLU Aqua avseende andrade foreskrifter for fiske i svaga alvar (FIFS 2004:37) samt for svenskt nyttjande och fordelning av laxkvoten (FIFS 2004:25 och 2004:36) med sarskilt fokus pa skydd av Vindelalvens laxbestand. Inledningsvis ges en generell beskrivning av laxbestandens utveckling och halsostatus dar aven svaga bestand som ar i behov av akuta forvaltningsatgarder identifieras. Darefter utvarderas tankbara forvaltningsatgarder varav vissa tidigare diskuterats vid ett arbetsmote mellan Havs- och vattenmyndigheten, Lansstyrelserna i Vasterbotten och Norrbotten samt SLU Aqua i Lulea 2018-11-21. I underlaget utvarderas aven forslag fran Lansstyrelsen i Vasternorrland avseende forandrade fiskeregler i och utanfor Ljungan. Avslutningsvis ges en kort sammanfattning av havsoringens bestandsstatus samt forslag pa atgarder i vattendragen i syfte att minska negativa effekter av fiske.

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 spatial structure of species is important for their dynamics and evolution, but also for management and conservation. There are numerous ways of inferring spatial structures, and information from multiple methods is becoming more common to examine how different processes shape the spatial structures of species to improve fish management. Here, we investigate the spatial structure of a suite of Baltic Sea fish species based on the following: (i) spatial (presumably neutral) genetic differentiation, reviewed from the literature, and (ii) spatial synchrony in abundance changes from time series of fishery-independent surveys, which we currently find to be underused given the amount of data available. For each of these two methods, species were classified as having a distinct, continuous or no/weak spatial structure. In addition, based on each source of information, we estimated the spatial scale of management units for species. The results show that only among species confined to the coastal zone the two sources of information yielded a congruence of the spatial structure (displaying a continuous spatial structure). In contrast, offshore species show weak spatial genetic structure but stronger spatial structure of synchrony in abundance. Based on this, we suggest that population genetic structure and synchrony in abundance should be used as complementary information as they reflect different spatial processes and suggest that management actions should differ with respect to scale depending on the management targets applied. We propose similar analysis should be applied to areas outside the Baltic Sea, and other stock identification methods, to improve management of fish resources.

The survival of Baltic salmon Salmo salar during the first year at sea (post-smolt stage) has declined since the beginning of the 1990s. In this analysis, we complement previous studies on possible causes of this decline by considering a suite of environmental parameters, potential change in predation pressure, and post-smolt growth. Marine survival estimates were found to be negatively correlated with temperature, indicating that warming conditions have not favoured survival. Survival was also found to be positively correlated with dissolved oxygen levels and regionally related to shifts in salinity. These relationships were further studied in context to the potential predation on post-smolts by one of the main piscivores in the Baltic, Eastern Baltic cod (Gadus morhua callarias). Concomitant with changes in environmental conditions, Baltic cod has changed its latitudinal range, moving northward in the Baltic, possibly in response to warming conditions. These changes lead us to hypothesize that predation pressure on salmon may have increased in recent years as cod has now occupied habitats used by salmon post-smolts during their southward feeding migrations. This predation may have been intensified as a result of anoxic conditions in the central basin by concentrating predation interactions in coastal waters and/or the upper water column typically occupied by salmon post-smolts. Indicators of post-smolt growth were applied to test the alternate hypothesis that mortality is growth-mediated; these indicators lacked a time series trend, which supports the contention that shifting predation pressure rather than feeding opportunities is responsible for the decline in post-smolt survival in Baltic salmon.

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.