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Weak fine-scale genetic structure and considerable life-history diversity in a near-pristine subarctic Atlantic salmon (Salmo salar) river

Cádiz, María I.; Sinclair-Waters, Marion; Erkinaro, Jaakko; Orell, Panu; Lindeza, Ana S.; Frapin, Morgane; Lamarins, Amaïa; Pritchard, Victoria L.; Primmer, Craig R.
Conservation genetics : 5 (Springer Nature, 2025)

The Näätämö River, in the far north of Europe, hosts a large Atlantic salmon (Salmo salar) stock with high socio-economic value. The catchment has near-pristine environmental conditions, although there are recent signs of stock declines. It nevertheless offers a good opportunity to monitor the status of a near pristine wild salmon system. This study aimed to characterize the fine-scale genetic structure of Atlantic salmon in the Näätämö River and evaluated the possibility to assign individuals to their population of origin. We genotyped juveniles sampled from eight locations using a 60 K single nucleotide polymorphism (SNP) panel to characterize within-river genetic diversity and structure. We also tested the performance of a previously designed 180 SNP panel to assign individuals to their population of origin. The genetic structure of the Näätämö River salmon population appears weak (FST ranging from 0.001–0.035), possibly due to natural straying. The performance of the predesigned panel in assigning individuals to their population of origin was moderate to high (82–85%), but customization could further enhance its accuracy. Additionally, we described the life-history diversity of salmon within the river using a long-term scale archive of c. 22,000 individuals collected over 48 years, identifying 59 unique life-history strategies. We suggest that to protect the self-sustaining salmon population in the Näätämö River, it would be important to manage the salmon fishery and conserve the population by incorporating up-to-date knowledge of stock status, considering their genetic structure, substantial gene flow and diverse life history.

Large effect life-history genomic regions are associated with functional morphological traits in Atlantic salmon

Aykanat, Tutku; Debes, Paul V; Jansouz, Shadi; Gueguen, Lison; House, Andrew H; Ruokolainen, Annukka; Erkinaro, Jaakko; Pritchard, Victoria L; Primmer, Craig R; Bolstad, Geir H
G3: genes, genomes, genetics : 7 (Oxford University Press, 2025)

Understanding pleiotropic architectures of phenotypes is instrumental for identifying the functional basis of adaptive genetic variation in the wild. Life-history variation may have a morphological basis that mediates resource acquisition allocation pathways, but identifying the underlying genetic basis of such traits is challenging. Using Atlantic salmon (Salmo salar) juveniles reared in common garden conditions, we test if 2 life-history associated loci, six6 and vgll3, are also associated with functional morphological traits. These loci had previously shown to exhibit strong signals of adaptation and are highly correlated with sea age at maturity. We show that genetic variation at the vgll3 locus is linked to variation in morphological traits that underlie swimming performance, along a tradeoff axis between efficient cruising and maneuvering, while the genetic variation at the six6 locus was linked to variation in body-head proportions suggesting the potential functional importance of these traits for resource acquisition efficiency. However, the direction of changes in morphological traits associated with late- vs early maturing alleles was not always consistent with the expected direction of an effect to maturation timing. Our results reveal a complex morphological landscape associated with the genetic variation in these loci, possibly as a result of pleiotropy or linkage across these genomic regions.

Brain-associated alterations of Hippo pathway transcription in early maturing Atlantic salmon

Ahi, Ehsan Pashay; Verta, Jukka-Pekka; Kurko, Johanna; Ruokolainen, Annukka; Singh, Pooja; Debes, Paul Vincent; Erkinaro, Jaakko; Primmer, Craig R.
BMC ecology and evolution : 1 (BioMed Central, 2025)

Background: Pubertal timing is a key life history trait, shaped by ecological pressures to balance reproductive success and survival. Emerging evidence suggests a link between adiposity and early maturation, potentially through hormonal signaling pathways governing puberty timing. The timing of sexual maturation in Atlantic salmon has a strong genetic basis in addition to being linked with environmental shifts and lipid reserves. A gene encoding a co-factor of the Hippo pathway, vgll3, is a major determinant of maturation timing in salmon. The Hippo pathway is known for its evolutionary conserved molecular signal role in both sexual maturation and adipogenesis. Results: In this study, we tested the expression of Hippo pathway genes in the brain of immature and mature male Atlantic salmon carrying either the early or the late maturation genotype of vgll3. We found increased brain expression of a major Hippo pathway kinase (lats1b) in individuals with early maturation genotypes of vgll3 before maturation development of testes was evident. Moreover, we found components and regulating partners of the Hippo pathway showing differential expression in brain of individuals with early and late vgll3 genotypes prior to maturation. This may suggest a role for the Hippo pathway in central nervous system processes that regulate the preparation for maturation. Conclusions: This study characterizes transcriptional changes in components of the Hippo pathway in the brain in relation to vgll3-mediated early maturation in Atlantic salmon, highlighting the potential involvement of this pathway in the central regulation of maturation prior to gonadal development.

Mesohabitat Evaluation Reveals Variable Abundances and Habitat Choice in Juvenile Atlantic Salmon Across Diverse Habitats in the Main Stem of a Large Sub‐Arctic River

Metsäniemi, Tuomas; Orell, Panu; Foldvik, Anders; Kuusela, Jorma; Kurkilahti, Mika; Erkinaro, Jaakko
Ecology of freshwater fish : 3 (Wiley-Blackwell, 2025)

Large main stem rivers typically provide a variety of mesohabitat types, but their abundance, distribution and role in providing habitat for juvenile salmonids have rarely been analysed. The quantity of meso-scale habitats and their juvenile Atlantic salmon abundance was surveyed in the large sub-arctic River Teno in northernmost Fennoscandia. Different habitat types were mapped using the Norwegian Mesohabitat Classification Method (NMCM). Juvenile salmon abundance in different mesohabitats, on various substrates, depths and lateral positions across the channel was estimated by electrofishing boat surveys. Most of the Teno main stem (67%) was dominated by fine substrate and > 50 cm s−1 flow velocity. Typical juvenile salmon-rearing habitats, such as rapids, riffles and glides, comprised 32% of the riverbed. Data from NMCM and electrofishing surveys were used in generalised linear models to describe the relationship between habitat variables and juvenile salmon (YOY and parr) abundance. Juvenile abundance varied a lot across and within mesohabitats; in general, abundance was higher in areas with depth ≤ 70 cm than in deeper areas, and in middle sections of the river compared to those near shorelines. Juvenile salmon were documented also in sandy areas, although in low abundances, and in relatively high abundances in areas deeper than typically considered important for juvenile salmon. These areas should be considered in assessing habitat potential for juvenile salmon production. NMCM proved to be a fast, cost-effective method for surveying large areas for habitat assessment.

Invading and range-expanding pink salmon inform management actions for marine species on the move

Dunmall, Karen M; Bean, Colin W; Berntsen, Henrik H; Ensing, Dennis; Erkinaro, Jaakko; Irvine, James R; Kendall, Neala W; Kitching, Tor; Langan, Joseph A; Millane, Michael; Oxman, Dion S; Radchenko, Vladimir I; Thorstad, Eva B; Utne, Kjell Rong
Ices journal of marine science : 1 (Oxford University Press, 2025)

Species redistributions, whether resulting from invasions or range expansions, pose similar challenges for conservation and management. Redistribution impacts on host ecosystems and species combine with those from climate change, which are already acute at northern latitudes. Using pink salmon Oncorhynchus gorbuscha, which are native to the Pacific Ocean, we employ knowledge Exchange to inform decision-making in non-native marine areas: they are expanding their range to the Arctic Ocean and are invasive in the Atlantic Ocean. The predicted future marine distribution of pink salmon focuses effort on where and when pink salmon are present and informs on potential interactions with native species. Management actions taken in the Atlantic Ocean to reduce invasive pink salmon are resource-intensive, but removed salmon could be a food resource. Addressing identified gaps regarding the invasion potential of pink salmon, interactions among pink salmon and other species, and current mitigation efforts would support forward-thinking management decisions given predictions of continued environmental change. We also highlight steps that can be taken immediately to coordinate actions and better inform responses. Managed for production in the Pacific and as an invasion in the Atlantic, pink salmon provide a tangible approach to informed decision-making through collaboration for marine species on the move.