Single Nucleotide Polymorphism (SNP) panels are powerful tools for assessing genetic population structure and dispersal of fishes and can enhance management practices for commercial, recreational, and subsistence mixed-stock fisheries. Arctic Char (Salvelinus alpinus), Brook Trout (Salvelinus fontinalis), and Lake Whitefish (Coregonus clupeaformis) are amongst the most harvested and consumed fish species in northern Indigenous communities in Canada, contributing significantly to food security, culture, tradition, and economy. However, genetic resources supporting Indigenous fisheries have not been widely accessible to northern communities (e.g., Inuit, Cree, and Dene). Here, we developed Genotyping-in-Thousands by sequencing (GT-seq) panels for population assignment and mixed-stock analyses of three salmonids, to support fisheries stewardship or co-management in northern Canada. Using low-coverage Whole Genome Sequencing data from 943 individuals across source populations in Cambridge Bay (Nunavut), Great Slave Lake (Northwest Territories), James Bay (Québec), and Mistassini Lake (Québec), we developed a bioinformatic SNP filtering workflow to select informative SNP markers from genotype likelihoods. These markers were then used to design GT-seq panels, thus enabling high-throughput genotyping for these species. The three GT-seq panels yielded an average of 413 autosomal loci and were validated with an average assignment accuracy of 83.03%. Thus, these GT-seq panels are powerful tools for assessing population structure and quantifying the relative contributions of populations/stocks in mixed stock fisheries across multiple regions. Interweaving these genomic-derived tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in Indigenous communities, contributing to food security programs and the economy in northern Canada.

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 (ˆ), following a brief time lag, which we hypothesize was driven by predator-prey dynamics. Diversification of prey into deepwater 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 a driver of ecological diversification and rapid speciation through cyclical glaciation.

For nearly 15 years now, environmental DNA has demonstrated its effectiveness in monitoring biodiversity. Methodological and technical improvements have significantly enhanced the field. However, the effect of factors such as sequence coverage, bioinformatic filtration and primer choice have been less explored or need to be optimized according to specific survey objectives and study site characteristics. We evaluated these factors to help optimize monitoring fish biodiversity in North American temperate lakes. We sampled water for fish community eDNA analysis in 12 lakes from southwestern Québec, Canada. The lakes were selected to encompass a wide range of surface areas and species richness. We sampled water from a total of 520 sites (25 to 50 per lake) and analyzed three mitochondrial DNA regions (12S rRNA; 16S rRNA; and cytb) using NovaSeq sequencing. Our results, based on rarefied count matrices (from a sequencing depth of 100,000 to a minimum depth of 1,000 reads per sample), showed that keeping only species in each sample if they represented at least one thousandth (species minimum read proportion threshold = 0.001) of the sample's reads was adequate to remove false positives and had a limited negative impact on true positives with low read counts. The sequencing depth was found to have a negligible impact on the accuracy of fish community assessment in a given lake. With the same sequencing depth and a complete local reference database for each primer set, a single primer set produced similar species richness medians than the combination of two or three primer sets. Overall, 12S and 16S detected more species and provided more consistent community profiles than cytb. Based on our observations, we suggest using the 12S MiFish-U primer set and applying a minimum proportion of 0.001 reads per species and site to monitor north-temperate lentic freshwater fish communities.

Beaked redfishes (Sebastes fasciatus and Sebastes mentella) of the northwest Atlantic have recently reached record abundance levels in the estuary and the 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 lower 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 these redfish species.

The role of methylation in adaptive, developmental and speciation processes has attracted considerable interest, but interpretation of results is complicated by diffuse boundaries between genetic and non-genetic variation. We studied whole genome genetic and methylation variation in the European eel, distributed from subarctic to subtropical environments, but with panmixia precluding genetically based local adaptation beyond single-generation responses. Overall methylation was 70.9%, with hypomethylation predominantly found in promoters and first exons. Redundancy analyses involving juvenile glass eels showed 0.06% and 0.03% of the variance at SNPs to be explained by localities and environmental variables, respectively, with GO terms of genes associated with outliers primarily involving neural system functioning. For CpGs 2.98% and 1.36% of variance was explained by localities and environmental variables. Differentially methylated regions particularly included genes involved in developmental processes, with hox clusters featuring prominently. Life stage (adult versus glass eels) was the most important source of inter-individual variation in methylation, likely reflecting both ageing and developmental processes. Demethylation of transposable elements relative to pure European eel was observed in European X American eel hybrids, possibly representing postzygotic barriers in this system characterized by prolonged speciation and ongoing gene flow. Whereas the genetic data are consistent with a role of single-generation selective responses, the methylation results underpin the importance of epigenetics in the life cycle of eels and suggests interactions between local environments, development and phenotypic variation mediated by methylation variation. Eels are remarkable by having retained eight hox clusters, and the results suggest important roles of methylation at hox genes for adaptive processes.

The island syndrome hypothesis (ISH) stipulates that, as a result of local selection pressures and restricted gene flow, individuals from island populations should differ from individuals within mainland populations. Specifically, island populations are predicted to contain individuals that are larger, less aggressive, more sociable, and that invest more in their offspring. To date, tests of the ISH have mainly compared oceanic islands to continental sites, and rarely smaller spatial scales such as inland watersheds. Here, using a novel set of genome-wide SNP markers in wild deer mice (Peromyscus maniculatus) we conducted a genomic assessment of predictions underlying the ISH in an inland riverine island system: analysing island-mainland population structure, and quantifying heritability of phenotypes thought to underlie the ISH. We found clear genomic differentiation between island and mainland populations and moderate to high marker-based heritability estimates fo r overall variation in traits previously found to differ in line with the ISH between mainland and island locations. FST outlier analyses highlighted 12 loci associated with differentiation between mainland and island populations. Together these results suggest that the island populations examined are on independent evolutionary trajectories, the traits considered have a genetic basis (rather than phenotypic variation being solely due to phenotypic plasticity). Coupled with the previous results showing significant phenotypic differentiation between island and mainland groups in this system, this study suggests that the ISH can hold even on a small spatial scale.

Environmental DNA (eDNA) is a very promising approach to facilitate and improve the aquatic species monitoring, which is crucial for their management and conservation. In comparison with the plethora of monitoring studies in the fields, relatively few studies have focused on experimentally investigating the “ecology” of eDNA, in particular pertaining to processes influencing the detection of eDNA. The paucity of knowledge about its ecology hampers the use of eDNA analysis to its full potential. In this study, we experimentally evaluated the impact of several biotic and abiotic factors on the rate of production and degradation of eDNA. Individuals of three freshwater fish species (brown bullhead, tench, and yellow perch) with distinct ecology were placed in two types of water from the St. Lawrence River (Québec, Canada) with very distinct physicochemical characteristics and at three different temperatures. Water samples were then filtered at predetermined time intervals, and quantitative PCR was used to quantify the eDNA in each sample. We found that temperature, species, water types, and some interactions between these factors had a strong effect on the production and degradation of eDNA. The results of this study enhance our knowledge about the ecology of eDNA, thus improving eDNA data interpretation.

One of the most important steps in conservation of the subterranean life forms is to decipher their distribution and ecology, which is challenging using traditional approaches. Development of an environmental DNA (eDNA) assay provides an efficient means for discovering and monitoring subterranean life forms. In this study, the distribution of three Iranian blind cave fish species (blind Iran cave barb Garra typhlops, blind Lorestan cave barb Garra lorestanensis, and blind cave loach Eidinemacheilus smithi) was assessed using 12S rRNA gene eDNA metabarcoding performed using MiFish-U PCR primers and preliminary species distribution modelling (SDM) using bioclimatic data. The majority of sampling localities with positive detection of cave barb eDNA fall within suitable habitats in the Zagros Mountains of Iran. Our results revealed that Lorestan and Iran cave barbs have differential distribution patterns, with some extent of habitat overlap in the vicinity of the originally discovered cave barb locality. According to the observed distribution patterns, the blind Lorestan cave barb and cave loach are mostly distributed in habitats close to the Seazar River (Dez River drainage, Iran), and the blind Iran cave barb is distributed toward the west and probably in a few springs in the Karkheh River drainage. Our data support the previously proposed distribution pattern for the cave barbs, in which the species show partial niche separation and reproductive isolation, with the Lorestan cave barb being a water flow-dependent species and the Iran cave barb being a generalist species preferring variable flow rates. We showed eDNA metabarcoding to be a useful approach for ecological surveys of subterranean fish biodiversity with implications for conservation.

The boreal chorus frog (Pseudacris maculata) is at risk of extinction in parts of its range in Canada. Our objectives were to quantify the influence of local and landscape characteristics on the occurrence of the species in wetlands in southern Québec. We hypothesized that site occupancy depends on local characteristics and landscape characteristics contributing to site connectivity. We developed an environmental DNA (eDNA) method to detect the species and compared the detection probability of this method to traditional call surveys. We collected water samples at a total of 180 sites (90 in 2017, 110 in 2018), whereas we surveyed a subset of 63 sites using both eDNA and call surveys in 2018. Site occupancy varied across years, but was higher in sites where the species had been previously detected during the last 12 years by other studies. Site occupancy did not vary with other local and landscape characteristics, in part due to an apparent decrease in the number of sites occupied by the species since the last 12 years. Detection probability via eDNA (0.81; 95% CI: [0.31; 0.98]) did not differ from that of call surveys (0.62; 95% CI: [0.25; 0.89]). To identify the optimal sampling period for the boreal chorus frog, future studies should estimate the detection probability of eDNA during the breeding season and the larval development period of the species.

Humans have the ability to permanently alter aquatic ecosystems and the introduction of species is often the most serious alteration.  Non-native Smallmouth Bass (Micropterus dolomieu) were identified in Miramichi Lake c. 2008, which is a headwater tributary to the Southwest Miramichi River, a renowned Atlantic Salmon (Salmo salar) river whose salmon population is dwindling.  A containment programme managed by the Department of Fisheries and Oceans, Canada (DFO) was implemented in 2009 to confine Smallmouth Bass (SMB) to the lake.  We utilized environmental DNA (eDNA) as a detection tool to establish the potential escape of SMB into the Southwest Miramichi River.  We sampled at 26 unique sites within Miramichi Lake, the outlet of Miramichi Lake (Lake Brook), which flows into the main stem Southwest Miramichi River, and the main stem Southwest Miramichi River between August and October 2017.  We observed n=6 positive detections located in the lake, Lake Brook, and the main stem Southwest Miramichi downstream of the lake.  No detections were observed upstream of the confluence of Lake Brook and the main stem Southwest Miramichi.  The spatial pattern of positive eDNA detections downstream of the lake suggests the presence of individual fish versus lake-sourced DNA in the outlet stream discharging to the main river.  Smallmouth Bass were later confirmed by visual observation during a snorkeling campaign, and angling.  Our results, both eDNA and visual confirmation, definitively show Smallmouth Bass now occupy the main stem of the Southwest Miramichi.