Single nucleotide polymorphism (SNP) panels are powerful tools for assessing the 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 among 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, 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 418 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 using 525 individuals with an average assignment accuracy of 83%. 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 genomic data derived from these tools with Traditional Ecological Knowledge will ensure the sustainable harvest of three culturally important salmonids in Indigenous communities, contributing to food security programmes and the economy in Northern Canada.

Most population genomic tools rely on accurate single nucleotide polymorphism (SNP) calling and filtering to meet their underlying assumptions. However, genomic complexity, resulting from structural variants, paralogous sequences, and repetitive elements, presents significant challenges in assembling contiguous reference genomes. Consequently, short-read resequencing studies can encounter mismapping issues, leading to SNPs that deviate from Mendelian expected patterns of heterozygosity and allelic ratio. In this study, we employed the ngsParalog software to identify such deviant SNPs in whole-genome sequencing (WGS) data with low (1.5×) to intermediate (4.8×) coverage for four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata). The analyses revealed that deviant SNPs accounted for 22% to 62% of all SNPs in salmonid datasets and approximately 11% in the American Eel dataset. These deviant SNPs were particularly concentrated within repetitive elements and genomic regions that had recently undergone rediploidization in salmonids. Additionally, narrow peaks of elevated coverage were ubiquitous along all four reference genomes, encompassed most deviant SNPs, and could be partially associated with transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, underestimated pairwise FST values, and overestimated nucleotide diversity. Considering the widespread occurrence of deviant SNPs arising from a variety of sources, their important impact in estimating population parameters, and the availability of effective tools to identify them, we propose that excluding deviant SNPs from WGS datasets is required to improve genomic inferences for a wide range of taxa and sequencing depths.

Captive rearing in salmon hatcheries can have considerable impacts on both fish phenotype and fitness within a single generation, even in the absence of genetic change. Evidence for hatchery-induced changes in DNA methylation is becoming abundant, though questions remain on the sex-specificity of these effects, their persistence until spawning and potential for transmission to future generations. Here we performed whole genome methylation sequencing of fin tissue for 16 hatchery and 16 wild Atlantic salmon (Salmo salar) returning to spawn in the Rimouski River, Québec, Canada. We identified two cohorts of hatchery-reared salmon through methylation analysis, one of which was epigenetically similar to wild fish, suggesting that supplementation efforts may be able to minimize the epigenetic effects of hatchery rearing. We found considerable sex-specific effects of hatchery rearing, with few genomic regions being affected in both males and females. We also analysed the methylome of 32 F1 offspring from four groups (pure wild, pure hatchery origin and reciprocal hybrids). We found that few epigenetic changes due to parental hatchery rearing persisted in the F1 offspring though the patterns of inheritance appear to be complex, involving nonadditive effects. Our results suggest that the epigenetic effects of hatchery rearing can be minimal in F0. There may also be minimal epigenetic inheritance and rapid loss of epigenetic changes associated with hatchery rearing. However, due to sex-specificity and nonadditive patterns of inheritance, methylation changes due to captive rearing are rather complex and the field would benefit from further research on minimizing the epigenetic effects of captive rearing in conservation efforts.

Catch- and-release fishing is a common conservation practice in recreational fisheries for Atlantic Salmon, although the effects on the reproductive success of caught- and-released fish are poorly understood. Herein, we compared the relative reproductive success of caught- and-released to non-caught salmon and tested the effect of temperature at release on reproductive success in the Rimouski River, Québec, Canada. At least 83% of caught- and-released salmon that moved upstream of a dam successfully reproduced, including fish that have been released in water above 20°C. However, the reproductive success of caught- and-released female salmon was only 73% of the reproductive success of non-caught salmon. Moreover, the increasing temperature did not affect the reproductive success of released fish that entered a trap, but fish caught at warmer temperatures were less likely to enter the trap. Our findings should be useful for evaluating the risks and benefits of catch- and-release, and for optimising conservation practices used for the preservation of Atlantic salmon populations.

Abstract Captive‐breeding programs are among the most adopted conservation practices to mitigate the loss of biodiversity, including genetic diversity. However, both genetic and nongenetic changes occurring in captivity can reduce the fitness of supplemented individuals, which complicate rehabilitation efforts. In the case of Atlantic salmon, the intensity of changes that occur in captivity and their impact on fitness will vary with the stocking practice adopted. In this study, we test whether salmon stocked at the parr stage have reduced reproductive success compared with their wild conspecifics and whether they contribute to increase genetic diversity in the targeted population. To do so, we use high‐throughput microsatellite sequencing of 38 loci to accurately assign 2381 offspring to a comprehensive set of possible parents from a supplemented Atlantic salmon population in Québec, Canada. Captive‐bred salmon stocked at the parr stage had fewer mates than their wild conspecifics, as well as a reduced relative reproductive success (RSS) compared with their wild counterparts. Nonetheless, in comparison with previous studies, stocking at the parr stage significantly improved RSS compared with salmon stocked as smolts and they displayed a reduction in reproductive success similar to salmon stocked as fry, which spend less time in captivity than parr. Moreover, supplementation of captive‐bred salmon significantly contributed to increasing genetic diversity. These results should contribute to informing resource managers in determining the best stocking practice to enhance Atlantic salmon populations.

Captive-breeding programs as well as and catch-and-release are among the most commonly adopted conservation practices in recreational fisheries. However, risks and benefits associated with their implementation are rarely evaluated. In the case of Atlantic Salmon, while previous studies revealed that captive-bred fish show reduced fitness compared to their wild counterparts in nature. Yet, few examined the extent and causes of their reduced reproductive success or directly compared their contribution to enhance genetic diversity to that of wild fish, including mature male parr. Furthermore, only one study specifically measured the reproductive success of caught and released Atlantic salmon in natural settings, and no study to date evaluated if released salmon are able to reproduce when released at temperature above 20°C which is known to increase post-release mortality. Here, we use high-throughput microsatellite sequencing of 38 loci to accurately assign 2500 offspring to a comprehensive set of possible parents from a supplemented Atlantic salmon population in Québec, Canada. The resolved molecular pedigree provided informative insight on the reproductive pattern of both captive-bred salmon and caught-and-released salmon. Captive-bred salmon had fewer partners than their wild conspecifics which lead to a significant reduction of reproductive success relative to that of their wild counterparts. Supplementation of captive-bred salmon significantly contributed to increase genetic diversity but mature male parr did so to an even greater extent and significantly inflated the number of alleles found among offspring. Moreover, our results showed that that at least 83% of caught-and-released salmon did successfully reproduced although caught-and-released female salmon have a significantly reduced reproductive success, averaging 73% of the reproductive output of non-caught salmon. Reproductive success of released salmon was not influenced by water temperature over 20°C which suggests either that the studied population is locally adapted to warm waters or that they behaviorally regulated body temperature by accessing nearby thermal refugia. Our results should help refining managers’ ability to analyze the risks and benefits associated with captive-breeding and catch-and-release, and thus, optimize conservation practices used for the preservation of Atlantic salmon populations.

Symbioses between plants and nitrogen-fixing cyanobacteria are benchmark biological systems to understand mutualism and patterns of coevolution. The diversity of cyanobacteria associated to non-vascular land plants is still being unraveled, with a huge gap in knowledge from tropical areas, especially in hornworts. We focus on the Neotropical hornwort Leiosporoceros dussii, which has a semi-permanent association with cyanobacteria. Unlike other hornworts, the peculiar Nostoc canals suggest cyanobiont specificity and selectivity. Here, we characterize the first hornwort bacteriome and focus on the endophytic cyanobacteria by describing its morphology, metagenomic diversity and phylogeny between two sampling sites in Panama. First, we use a metagenomic analyses (16S) from gametophytes from Río El Guayabo and Río Indio in Panama to identify the endophytic bacteria community of L. dussii. To provide more information on the cyanobacterial endophytes, we have extracted cyanobacterial endophytes to measure cell size variation and use the markers trnL and rbcLX to determine their phylogenetic relationships. Finally, we use stable isotope δ 15N to assess nitrogen flow in the plants. We find little diversity in Leiosporoceros bacteriome but observe significant community variations between sites. Results indicate a lack of cyanobacterial specificity of cyanobacteria associated to Leiosporoceros, with six unrelated clades of Nostoc forming a polyphyletic assemblage. Four clades are nested within bacteria collected as free-living taxa suggesting that typically non-symbiotic cyanobacteria can be associated with this hornwort. Finally, the little nitrogen fractioning of the plant suggests the role of the cyanobacterial symbionts in nitrogen fixation. This study provides the first hornwort bacteriome and is an important step in the characterization of tropical bryophyte symbioses.