ABSTRACT Supportive breeding programs are widely implemented to counteract demographic collapse in threatened populations. Their long‐term success, however, depends on maintaining genetic diversity while ensuring that released individuals contribute effectively to wild populations. In Atlantic salmon ( Salmo salar ), uncertainties remain regarding the capacity of captive broodstocks to preserve genetic variation and the demographic and genetic consequences of supplementation. Here, we evaluate the outcomes of a decade‐long restoration program targeting two genetically differentiated but geographically proximate Atlantic salmon populations in the Romaine watershed (Romaine and Puyjalon population, Québec, Canada). Using microsatellite data, we performed population assignment, parentage analyses, and temporal estimates of effective number of breeders and genetic diversity. We assessed broodstock performance, the contribution of stocked individuals to wild populations, and the impact of two egg incubation treatments on fry to smolt survival. Despite sustained efforts to maintain large and representative broodstocks, the failure of wild‐caught juvenile salmon to reach maturity substantially reduced the number of breeders, representing the greatest loss of genetic potential in the hatchery broodstock. Nevertheless, partial factorial mating and kinship‐based management allowed us to avoid inbreeding and preserved levels of heterozygosity and allelic richness comparable to those observed in wild populations. Stocked individuals contributed around 25% to juvenile population size in both populations, without reducing effective population size or eroding genetic differentiation. Estimates of total effective population size consistently exceeded those of wild components alone, indicating no evidence of a Ryman–Laikre effect. Finally, egg incubation in the water of the Romaine River increased survival to smolt stage for genetically Romaine individuals but not for individuals from Puyjalon, suggesting local adaptation to early rearing conditions. These results demonstrate that, when carefully designed and genetically monitored, supportive breeding can reinforce depleted salmon populations without compromising genetic diversity and integrity.

Aquatic resources are central to the global food supply and economy, particularly in the Arctic, where Inuit communities have long depended on wild resources. In the 1960s, the community of Iqaluktuuttiaq (Cambridge Bay, Nunavut, Canada) established commercial fisheries targeting Arctic charr (Salvelinus alpinus, Linnaeus, 1758), providing key employment and income. In a rapidly changing Arctic, molecular tools can enhance sustainable fisheries management. We applied a GT-seq (Genotyping-in-Thousands) panel of 377 SNP loci to distinguish five local stocks (Ekalluk, Halokvik, Jayko, Lauchlan, and Surrey) and quantify their contributions to annual harvests. A total of 1387 samples collected from four commercial sites over 8 years (2012-2020) were analyzed to assess temporal variation in stock composition. Results revealed unequal stock contributions, with Ekalluk and Halokvik comprising over 75% of catches. Spring harvests showed stable stock composition across years, while fall harvests exhibited significant interannual variation (p < 0.05). Environmental factors such as ice breakup timing (IB) and duration of 50% marine ice cover (I50) had no significant influence on stock contribution variability, likely due to limited data. Thus, GTseq offers the opportunity to explore more adaptive m anagement by capturing interannual variability in stock mixing.

Natural and anthropogenic changes have shaped the geographical distributions of freshwater fishes. During the Last Glacial Maximum (LGM), marine water retreated from the Persian Gulf, and it has been hypothesized that the Tigris River then received all tributary rivers of the present Persian Gulf and reached the Sea of Oman. In this study, we assess the extent and mechanisms of regional movements of the cyprinid freshwater fish Garra rufa and its interactions with a few surface-dwelling and subterranean congeners in the studied region. We analyzed genome-wide single nucleotide polymorphism (SNP) data and mitochondrial DNA sequences of fishes from the Tigris, Karkheh, Karun, Jarahi, Dalaki, and Mond rivers. It appears that after the LGM, colonization of G. rufa into the Mond and Dalaki drainages of the Persian Gulf, unidirectional movements of G. rufa from the Dalaki to the western drainages of the Persian Gulf and to the inland Maharlu lake basin may have occurred through river capture. Further, our results, along with published morphological data, indicate no genomic or morphologic differences between G. rufa and G. mondica as well as G. gymnothorax, questioning their status as own evolutionary units. Further, we also found signatures of introgression from G. rufa into G. tashanensis in the Jarahi drainage.

Various anthropogenic disturbances affect the succession of aquatic habitats along dendritic river networks. Bioindicator taxa, such as fish, can be used to assess the effects of these disturbances on habitat quality. Environmental DNA (eDNA) metabarcoding offers a novel approach to complement traditional sampling and analysis of bioindicator taxa. Here, we apply a trait-based biomonitoring framework, focusing on fish tolerance to pollution, to assess habitat quality and fragmentation within two watersheds in southern Québec (Canada). We sampled 193 sites within the dendritic networks of the Châteauguay and St. François watersheds and estimated fish community tolerance indices on the basis of 12S metabarcoding. We found a significant correlation between the fish community tolerance index and environmental factors such as subwatershed land use, precipitation and elevation. We also found that river fragmentation caused by dams affected fish assemblages and native fish movement but also prevented the spread of the non-native common carp. Finally, we applied random-forest modelling to predict the tolerance of fish communities to disturbances in unsampled areas, providing a broader understanding of habitat quality within catchments. Our research highlights how eDNA metabarcoding for large-scale biomonitoring and river fragmentation studies provides a cost-effective and non-invasive method for assessing fish biodiversity and riverine ecosystem health.

The conservation of stream salamanders relies on effective monitoring of these cryptic species in freshwater habitats increasingly affected by human activities. Environmental DNA (eDNA) and environmental RNA (eRNA) offer non-invasive alternatives to conventional active search methods. However, knowledge gaps remain regarding how eDNA and eRNA (collectively environmental nucleic acids; eNA) signals vary across space and time under natural field conditions, limiting their integration into monitoring programs. We evaluated eNA signals in small headwater streams in Quebec (Canada), focusing on the northern two-lined salamander (Eurycea bislineata) and the spring salamander (Gyrinophilus porphyriticus). We collected water samples over three consecutive days during fall and winter, and we assessed eNA detection and concentration using species-specific qPCR assays targeting mitochondrial markers. Detection rates of eDNA were consistently high across seasons, highlighting its suitability for rapid presence-absence surveys. In contrast, eRNA detection rates were lower in the fall, but increased with repeated sampling. In winter, eRNA detection rates were near zero, consistent with salamanders’ markedly reduced metabolic rate during overwintering, suggesting that mitochondrial eRNA primarily represents metabolically active individuals rather than species presence alone. The concentrations of eNA were positively associated with salamander abundance in fall. Our results demonstrate the value of eNA-based approaches for the monitoring of stream salamanders under natural field conditions.

Advances in genomics have facilitated the delineation of fisheries management units, which can be challenging in systems such as large lakes, in which high gene flow tends to limit genetic structure. In Great Slave Lake, Lake Whitefish populations have supported an important commercial fishery since the mid-1940s. The genetic structure of Lake Whitefish, however, has never been assessed, preventing the implementation of population-specific monitoring. Using low-coverage whole-genome resequencing of 305 samples from 10 sampling locations, we identified eight genetically differentiated populations of Lake Whitefish in Great Slave Lake and its main tributary, the Slave River. In the lake, we observed elevated levels of genetic differentiation among putative spawning locations in environmentally heterogeneous sections of the Main Basin despite small geographic distances among sites. In contrast, we observed weak genetic structure between populations in the comparatively homogeneous East Arm despite large geographic distances. Our observations suggest that mechanisms such as spawning site fidelity, adfluvial migratory behaviour, or local adaptation might shape population structure in this system. Using genome-wide scans, we found multiple genomic regions of elevated differentiation, with some displaying patterns coherent with chromosomal inversions. These results highlight the potential role of chromosomal rearrangements in maintaining local adaptation in the face of gene flow in environmentally heterogeneous lakes. Overall, our study provides novel insights into the genetic structure of fish populations in vast, recently deglaciated lakes. Furthermore, our results highlight the power of genomic data for population delineation in systems with high gene flow. Lastly, our precise assessment of genetic structure will provide a baseline for the genetic monitoring of culturally and socio-economically important Lake Whitefish commercial fisheries in this subarctic Great Lake.

Atlantic Salmon (Salmo salar) are typically anadromous; however, some individuals complete their life cycle in freshwater. A widely documented scenario suggests that this resident tactic arose independently in each river via isolation from anadromous Atlantic Salmon populations after the last ice age. Yet, origin of residency remains poorly studied in the North Shore region of the Gulf of St. Lawrence (Canada). To address this, we genotyped 189 resident and 196 anadromous individuals from five watersheds at 43 microsatellite markers. We found marked genetic differences between tactics within rivers, likely resulting from different levels of gene flow associated with geographic isolation, suggesting that residents may not have always been isolated as expected. Moreover, exploratory demographic inference analyses suggest that residents may have a common ancestral source, which does not support the strict independent development model typically expected. This pattern is rather more consistent with a two-wave colonization events and/or ancestral intracontinental gene flow. These findings bring nuances and complexity to views on the origin of residency in Atlantic Salmon, and are valuable for guiding conservation practices.

In the Northwest Atlantic, demersal spawning of capelin generally occurs when sea surface temperatures reach > 12˚C and become too warm for beach spawning. Demersal spawning has rarely been reported in northern Labrador, where beach spawning events occur less frequently since the past decades. We surveyed Makkovik Bay in August 2018 to document the spawning behaviour of capelin in northern Labrador (55˚N). No beach spawning was reported in the bay in 2018, but using a hull-mounted echosounder and environmental DNA analyses, we detected 30 demersal schools over 8 days (1–8 August) in bottom depths ranging from 10 to 29 m. Capelin eggs were sampled at one of the schooling sites, on a large flat rock, confirming that at least some of these schools were capelin spawning aggregations. Sea surface temperatures where demersal schools were detected were very close to or above the 12˚C threshold (11.1˚C to 14.2˚C), and bottom temperatures ranged from -0.7˚C to 4.9˚C. Fish density within the confirmed spawning school was 43 ind. m−3. The absence of beach spawning in Makkovik Bay in 2018 and the occurrence of demersal spawning suggest that only documenting beach spawning events might result in false negatives when monitoring coastal capelin occurrence and spawning in subarctic and arctic regions.

Effective monitoring strategies are key for aquatic species conservation, but traditional methods often require significant resources, especially in large aquatic systems. The emergence of quantitative environmental DNA (eDNA) is a promising alternative. Yet, few studies have evaluated the possibility of quantifying Atlantic salmon abundance with eDNA when individuals are at low abundance and occur in large river systems. In this study, we tested the efficacy of eDNA to monitor and quantify daily variation in smolt counts during their downstream migration in a large river system with low abundance of smolts. During the 2021 and 2022 downstream migrations, trap nets were used to conduct a daily census of smolts in the Romaine and Puyjalon rivers (Qu & eacute;bec, Canada) while eDNA samples were collected daily over a transect perpendicular to the riverbank. Using quantitative real-time qPCR, we showed that discharge-corrected eDNA concentrations were positively correlated with daily smolt counts for both years. In addition, we found that controlling for temperature and precipitation improved model transferability between years, showing the importance of considering environmental correlates when using eDNA for abundance quantification. Finally, smolt counts were correlated with eDNA concentrations on the same day, but not with eDNA concentrations 1 or 2 days prior, highlighting the capacity of the model to track daily fluctuations in smolt abundance. Our results underscore the potential of using eDNA to monitor Atlantic salmon in large river systems with low smolt abundance when the river hydrology and environmental conditions are documented.

The panmictic American eel (Anguilla rostrata) displays a wide range of intraspecific phenotypic variation as well as geographical sex bias and differential recruitment. By definition, panmictic species lack genetic structure, thus local adaptation through genetic variation cannot explain the presence of intraspecific variation. As a result, the contrasting phenotypes observed in the American eel could be attributed to either spatially varying selection, phenotypic plasticity (often mediated through epigenetic changes), or the interaction of both processes. Here we explore, for the first time, the role of DNA methylation in acclimatization in a panmictic species, the American eel, as well as its association with salinity and geography in Northeastern Canada. Using whole genome bisulfite sequencing in 72 individuals, we found that DNA methylation patterns were associated with geography and to a lesser degree with salinity. We identified a genomic region with differential methylation associated with salinity that falls inside the SOCS2 gene, which has been previously linked to salinity differences in other fish species, as well as to metabolism and somatic growth regulation. This study advances our understanding of how panmictic species or populations with high gene flow acclimatize to variable environments in the absence of heritable genetic local adaptation.

Dispersal is a highly variable trait influenced by life history and ecological factors, affecting gene flow when dispersers successfully reproduce. Anadromous salmonids, with their diverse migratory strategies and ecological traits, serve as an ideal model for studying dispersal evolution, showcasing significant inter- and intraspecific variation. Although environmental factors like temperature likely influence dispersal propensity, their effects remain poorly documented. This study compares dispersal patterns and population structure in lake whitefish (Coregonus clupeaformis) and brook charr (Salvelinus fontinalis) along the subarctic coastline of James Bay, covering four degrees of latitude. These species differ in life history and population size, representing contrasting ends of a continuum influencing dispersal and gene flow. We hypothesised that lake whitefish, with shorter freshwater residency and potentially reduced olfactory imprinting, would disperse more frequently than brook charr. Using low-coverage whole-genome sequencing, we found that lake whitefish exhibited broader-scale population structure and greater long-distance dispersal capacity than brook charr. Surprisingly, both species showed similar dispersal rates and population differentiation levels. However, lake whitefish had effective population sizes approximately 10 times larger than brook charr, indicating that while their dispersal is common, it results in lower effective gene flow. Moreover, dispersal rates in both species were lower in the northern study area, likely due to colder temperatures, delayed ice break and shorter growing seasons. These findings yield insights into how life history and environmental variation shape dispersal evolution in migratory species.

Understanding the genetic architecture of economically important traits is essential for the design and implementation of efficient breeding programs. Here, we analysed 3,653 Eastern oysters (Crassostrea virginica) from 62 crossing groups and 307 full-sib families, all genotyped with a 200 K SNP array, to (i) estimate heritability and genetic correlations for six growth-related traits, (ii) detect quantitative trait loci (QTL) and candidate genes, and (iii) compare the accuracy of pedigree- (PBLUP) versus genomic-based (GBLUP) predictions across marker densities, selection strategies (physical distance (PD) versus linkage disequilibrium (LD) and phenotype-based genotyping strategies. SNP-based Heritabilities ranged from 0.33 to 0.56, and genetic correlations among traits exceeded 0.61, indicating strong pleiotropy. GWAS revealed a polygenic architecture with a shared QTL on chromosome 2; the top SNP explained ≤ 1.1

IntroductionEnvironmental DNA (eDNA) metabarcoding of water is increasingly being used to monitor coastal biodiversity shifts. However, we have limited knowledge of whether samples collected during discreet temporal periods depict holistic ecosystem changes over longer time spans.MethodsHere, we show how eDNA community structure varies across repeated sampling events at different temporal scales ranging from years to months to days at an Arctic coastal site, Churchill (Canada), using metabarcoding analyses of water eDNA samples with four universal primer pairs (two primers in COI and two in the 18S rRNA).ResultsDaily variations were highly dynamic and less structured, likely due to the stochastic nature of estuarine ecosystems, but there was a clear annual consistency in eDNA communities with a high proportion of shared taxa between years. However, monthly sampling was the most efficient for capturing holistic biodiversity.DiscussionWe provide recommendations for optimal eDNA metabarcoding sampling design based on our observations. The study underscores the importance of understanding biological and physical factors altering eDNA detection to improve the efficiency of detecting and interpreting long-term eDNA changes.

Sexual dimorphism can evolve through sex-specific regulation of the same gene set. However, sex chromosomes can also facilitate this by directly linking gene expression to sex. Moreover, differences in gene content between heteromorphic sex chromosomes contribute to sexual dimorphism. Understanding patterns of sex-biased gene expression across organisms is important for gaining insight into the evolution of sexual dimorphism and sex chromosomes. Moreover, studying gene expression in species with recently established sex chromosomes can help understand the evolutionary dynamics of gene loss and dosage compensation. The three-spined stickleback is known for its strong sexual dimorphism, especially during the reproductive period. Sex is determined by a young XY sex chromosome pair with a non-recombining region divided into three strata, which have started to degenerate. Using the high multiplexing capability of 3′ QuantSeq to sequence the sex-biased transcriptome of the liver, gills, and brain, we provide the first characterization of sex-specific transcriptomes from ~80 sticklebacks (40 males and 40 females) collected from a natural population during the reproductive period. We find that the liver is extremely differentiated between sexes (36% of autosomal genes) and reflects ongoing reproduction, while the brain shows very low levels of differentiation (0.78%) with no functional enrichment. Finally, the gills exhibit high levels of differentiation (5%), suggesting that sex should be considered in physiological and ecotoxicological studies of gill responses in fishes. We also find that sex-biased gene expression in hemizygous genes is mainly driven by a lack of dosage compensation. However, sex-biased expression of genes that have conserved copies on both sex chromosomes is likely driven by the degeneration of Y allele expression and a down-regulation of male-beneficial mutations on the X chromosome.

Understanding how environmental gradients shape population genetic structure is critical for elucidating evolutionary dynamics in heterogeneous landscapes. The St. Lawrence Estuary, spanning fluvial, middle, and marine zones, presents a steep salinity gradient that serves as an ideal setting to study such a question. Three-spined sticklebacks (Gasterosteus aculeatus) thrive across these zones, offering an ideal model system to investigate the interplay of gene flow and natural selection in shaping population structure. Using whole-genome resequencing of sticklebacks from 12 sites, this study aimed to resolve fine-scale population structure and investigate how genetic diversity and differentiation are influenced by selection and gene flow. By integrating single nucleotide polymorphisms (SNPs) and structural variants (SVs), we assessed differentiation patterns, examined clinal variation, and evaluated the relative roles of gene flow and selection in shaping population dynamics. Our findings reveal clear genetic differentiation between fluvial and saltwater populations, with Baie-Saint-Paul forming a potential third group. Salinity emerged as a key driver of genetic structure, with clinal variation in allele frequencies suggesting ongoing adaptation along the gradient. Demographic modeling indicated a history of secondary contact with recent and weak gene flow. Structural variants, particularly indels, complemented SNP-based analyses, underscoring their importance in detecting fine-scale population structure. These results highlight the complex interplay of evolutionary forces shaping biodiversity in transitional environments, providing a basis for exploring local adaptation in connected populations and contributing to broader efforts in conservation genomics.

ABSTRACTBeaked redfishes (Sebastes fasciatus and Sebastes mentella) of the northwest Atlantic have recently reached record abundance levels in the estuary and northern Gulf of St. Lawrence, dominated by Sebastes mentella. Knowledge of their diet composition is essential to understand the trophic role that these groundfish play in the ecosystem. The objective of the present study was to compare the performance of visual examination and DNA metabarcoding of stomach contents of the same individual redfish caught in the estuary and northern Gulf of St. Lawrence. Using a universal metazoan mitochondrial cytochrome c oxidase subunit I (COI) marker, we identified a total of 24 taxonomic groups, composed of 22 species and two genera in the content of 185 stomachs with DNA metabarcoding. We compared these results to the 25 prey types, eight identified at the genus and nine at the species level, obtained with visual stomach content analysis (SCA). While both techniques revealed a similar diet composition, our results showed that the SCA and DNA metabarcoding perform differently for particular prey categories, both in terms of detectability and taxonomic resolution, as well as in the estimated relative importance of weight and occurrence in the diet. The use of DNA metabarcoding along with SCA validates and improves the taxonomic resolution of visually determined prey, which supports the concept that both techniques provide useful complementary information on the diet of redfish and likely other fish species.

ABSTRACTLong‐term biological monitoring and management depend on efficient protocols and methodology to characterize and precisely describe species distributions and diversity. In recent years, environmental DNA has progressively become a tool of choice in survey programs. However, the effect of variables such as sampling effort and sampling design still requires consideration. Simple random, grid, and transect‐based sampling methods are widely used in ecological surveys to obtain an unbiased estimation of species richness and community structure. However, under certain conditions where spatial information is available, sampling design and sequencing depth can be optimized to reduce effort and cost. Here, we evaluate different subsampling approaches to identify sampling strategies that are both easily implemented in the field and provide optimal recovery of species diversity for a given sampling effort. With a homogeneous grid‐based sampling (25–50 samples by lake) of 12 freshwater lakes in southeastern Québec, and using the 12S MiFish metabarcoding primer set, we demonstrate that random and stratified designs perform similarly to detect 90% and 95% of species. However, we found that, under certain circumstances, stratified sampling outperformed random sampling, requiring lower numbers of samples to detect the same species diversity. We also demonstrate that for the minimum sequence threshold and sample replication used in our study, a sequencing depth of 50K reads per sample is adequate to obtain a reliable portrayal of species richness. In this study, we contribute to the effort of eDNA sampling standardization by providing data for selecting the best sampling design, sequence depth, and sample size to detect 90%–95% of fish species found in temperate lakes.

Abstract The evolutionary histories of adaptive radiations can be marked by dramatic demographic fluctuations. However, the demographic histories of ecologically-linked co-diversifying lineages remain understudied. The Laurentian Great Lakes provide a unique system of two such radiations that are dispersed across depth gradients with a predator-prey relationship. We show that the North American Coregonus species complex (“ciscoes”) radiated rapidly prior to the Last Glacial Maximum (80–90 kya), a globally warm period, followed by rapid expansion in population size. Similar patterns of demographic expansion were observed in the predator species, Lake Charr (Salvelinus namaycush), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deep water created ecological opportunities for the predators, facilitating their demographic expansion, which is consistent with an upward adaptive radiation cascade. This study provides a new timeline and environmental context for the origin of the Laurentian Great Lakes fish fauna, and firmly establishes this system as drivers of ecological diversification and rapid speciation through cyclical glaciation.

AbstractConservation of the Atlantic salmon Salmo salar requires to monitor the spatial distribution and abundance of juveniles at a local scale in tributaries. However, tributaries are rarely accounted for in monitoring programs despite their importance for juvenile life stages. This is mainly because inventories of young salmon populations in tributaries can be technically challenging with traditional methods, as the number of tributaries in a watershed can be important and their access limited compared to the main stem. In this study, we tested the use of environmental DNA (eDNA) to quantify the abundance of juvenile Atlantic salmon in tributaries. We successfully detected eDNA of juvenile Atlantic salmon in 19 tributaries of three main rivers of the Gaspé Peninsula (Québec, Canada) using quantitative real‐time PCR analyses. By comparing the eDNA approach with electrofishing surveys conducted in parallel to water sampling, we found that eDNA concentrations positively correlated with juvenile abundance, total biomass, and body surface area. The use of the allometrically scaled mass (ASM) instead of abundance improved the correlation. Furthermore, we demonstrated that the levels of eDNA molecules detected for juvenile Atlantic salmon were also correlated with water temperature and canopy cover measured in each tributary. Finally, we tested if eDNA concentrations measured in a tributary could be used as a reliable indicator of juvenile abundance or biomass in that tributary. We found that our models slightly better predicted juvenile biomass than juvenile abundance. The use of ASM did not improve model prediction, suggesting that further refinement would be required in the future. Our method will facilitate the implementation of conservation practices appropriate to the ecology of juvenile Atlantic salmon in tributaries.

In the context of climate change, it is crucial to understand whether animals that have been domesticated and (or) selected maintain their abilities to adapt to changes in their thermal environment. Here, we tested how selection for absence of early sexual maturation combined with better growth performance may have impacted thermal resistance and gene expression response in the presence of thermal stress in brook charr Salvelinus fontinalis (Mitchill, 1814). We performed temperature challenge tests on brook charr 0+ juveniles and studied the expression of genes involved in the response to oxidative stress, in synthesis of heat shock proteins, or involved in regulation of apoptosis, in heart and liver tissues. Juveniles from the selected lineage had a higher thermal resistance than controls and a loss of equilibrium occurred on average 1 °C above what was observed for the controls. The relative expressions of catalase and HSP70 were significantly higher in juveniles from the selection program. Overall, thermally sensitive fish were characterized by low mass and length and lower relative expressions of genes associated with stress response. Our results indicate that selection for traits of interests may be indirectly related to the significant lineage effect on growth in early stages of development.