Wild stocks of Pacific salmonids have experienced sharp declines in abundance over the past century. Consequently, billions of fish are released each year for enhancing abundance and sustaining ...fisheries. However, the beneficial role of this widely used management practice is highly debated since fitness decrease of hatchery-origin fish in the wild has been documented. Artificial selection in hatcheries has often been invoked as the most likely explanation for reduced fitness, and most studies to date have focused on finding signatures of hatchery-induced selection at the DNA level. We tested an alternative hypothesis, that captive rearing induces epigenetic reprogramming, by comparing genome-wide patterns of methylation and variation at the DNA level in hatchery-reared coho salmon (Oncorhynchus kisutch) with those of their wild counterparts in two geographically distant rivers. We found a highly significant proportion of epigenetic variation explained by the rearing environment that was as high as the one explained by the river of origin. The differentially methylated regions show enrichment for biological functions that may affect the capacity of hatcheryborn smolts to migrate successfully in the ocean. Shared epigenetic variation between hatchery-reared salmon provides evidence for parallel epigenetic modifications induced by hatchery rearing in the absence of genetic differentiation between hatchery and natural-origin fish for each river. This study highlights epigenetic modifications induced by captive rearing as a potential explanatory mechanism for reduced fitness in hatchery-reared salmon.
Investigating how environmental features shape the genetic structure of populations is crucial for understanding how they are potentially adapted to their habitats, as well as for sound management. ...In this study, we assessed the relative importance of spatial distribution, ocean currents and sea surface temperature (SST) on patterns of putatively neutral and adaptive genetic variation among American lobster from 19 locations using population differentiation (PD) approaches combined with environmental association (EA) analyses. First, PD approaches (using bayescan, arlequin and outflank) found 28 outlier SNPs putatively under divergent selection and 9770 neutral SNPs in common. Redundancy analysis revealed that spatial distribution, ocean current‐mediated larval connectivity and SST explained 31.7% of the neutral genetic differentiation, with ocean currents driving the majority of this relationship (21.0%). After removing the influence of spatial distribution, no SST were significant for putatively neutral genetic variation whereas minimum annual SST still had a significant impact and explained 8.1% of the putatively adaptive genetic variation. Second, EA analyses (using Pearson correlation tests, bayescenv and lfmm) jointly identified seven SNPs as candidates for thermal adaptation. Covariation at these SNPs was assessed with a spatial multivariate analysis that highlighted a significant temperature association, after accounting for the influence of spatial distribution. Among the 505 candidate SNPs detected by at least one of the three approaches, we discovered three polymorphisms located in genes previously shown to play a role in thermal adaptation. Our results have implications for the management of the American lobster and provide a foundation on which to predict how this species will cope with climate change.
Investigating relationships between microbiota and their host is essential toward a full understanding of how animal adapt to their environment. Lake Whitefish offers a powerful system to investigate ...processes of adaptive divergence where the dwarf, limnetic species evolved repeatedly from the normal, benthic species. We compared the transient intestinal microbiota between both species from the wild and in controlled conditions, including their reciprocal hybrids. We sequenced the 16s rRNA gene V3‐V4 regions to (a) test for parallelism in the transient intestinal microbiota among sympatric pairs, (b) test for transient intestinal microbiota differences among dwarf, normal, and hybrids reared under identical conditions, and (c) compare intestinal microbiota between wild and captive whitefish. A significant host effect on microbiota taxonomic composition was observed when all lakes were analyzed together and in three of the five species pairs. In captive whitefish, host effect was also significant. Microbiota of both reciprocal hybrids fell outside of that observed in the parental forms. Six genera formed a bacterial core which was present in captive and wild whitefish, suggesting a horizontal microbiota transmission. Altogether, our results complex interactions among the host, the microbiota, and the environment, and we propose that these interactions define three distinct evolutionary paths of the intestinal microbiota.
Investigating the holobiont system is essential toward a full understanding of how animal adapt to their environment and, ultimately, speciation. We compared and sequenced the transient intestinal microbiota among dwarf and normal forms as well as their reciprocal hybrids of Lake Whitefish from the wild and in controlled conditions. Our results suggest complex interactions among the host, the microbiota, and the environment.
Human activities induce direct or indirect selection pressure on natural population and may ultimately affect population's integrity. While numerous conservation programs aimed to minimize ...human‐induced genomic variation, human‐induced environmental variation may generate epigenomic variation potentially affecting fitness through phenotypic modifications. Major questions remain pertaining to how much epigenomic variation arises from environmental heterogeneity, whether this variation can persist throughout life, and whether it can be transmitted across generations. We performed whole genome bisulfite sequencing (WGBS) on the sperm of genetically indistinguishable hatchery and wild‐born migrating adults of Coho salmon (Oncorhynchus kisutch) from two geographically distant rivers at different epigenome scales. Our results showed that coupling WGBS with fine‐scale analyses (local and chromosomal) allows the detection of parallel early‐life hatchery‐induced epimarks that differentiate wild from hatchery‐reared salmon. Four chromosomes and 183 differentially methylated regions (DMRs) displayed a significant signal of methylation differentiation between hatchery and wild‐born Coho salmon. Moreover, those early‐life epimarks persisted in germ line cells despite about 1.5 year spent in the ocean following release from hatchery, opening the possibility for transgenerational inheritance. Our results strengthen the hypothesis that epigenomic modifications environmentally induced during early‐life development persist in germ cells of adults until reproduction, which could potentially impact their fitness.
Interactions between environmental factors and complex life‐history characteristics of marine organisms produce the genetic diversity and structure observed within species. Our main goal was to test ...for genetic differentiation among eastern oyster populations from the coastal region of Canadian Maritimes against expected genetic homogeneity caused by historical events, taking into account spatial and environmental (temperature, salinity, turbidity) variation. This was achieved by genotyping 486 individuals originating from 13 locations using RADSeq. A total of 11,321 filtered SNPs were used in a combination of population genomics and environmental association analyses. We revealed significant neutral genetic differentiation (mean FST = 0.009) between sampling locations, and the occurrence of six major genetic clusters within the studied system. Redundancy analyses (RDAs) revealed that spatial and environmental variables explained 3.1% and 4.9% of the neutral genetic variation and 38.6% and 12.2% of the putatively adaptive genetic variation, respectively. These results indicate that these environmental factors play a role in the distribution of both neutral and putatively adaptive genetic diversity in the system. Moreover, polygenic selection was suggested by genotype–environment association analysis and significant correlations between additive polygenic scores and temperature and salinity. We discuss our results in the context of their conservation and management implications for the eastern oyster.
Large rivers and their estuaries are structurally complex and comprise a diversity of habitats supporting a rich biodiversity. As a result, identifying and monitoring fish communities using ...traditional methods in such systems may often be logistically challenging. Using the mitochondrial DNA 12S MiFish primers, we performed an eDNA metabarcoding analysis to assess the effect of spatial and environmental factors on the variation of the fish community structure along most of the St. Lawrence River/Estuary/Gulf (Québec Canada), a transect spanning 1300 km across a diversity of habitats from a fluviatile non‐tidal section to a marine environment. A total of 129 species were identified including freshwater and marine species. For the freshwater sectors, eDNA identified 80 species compared with the 85 species previously reported based on conventional sampling. eDNA also revealed similar species diversity and communities in the fluviatile section of the St. Lawrence River. Furthermore, our study improved current knowledge about the brackish and marine sections by describing community transition between freshwater and marine fish communities in association with a drastic shift in environmental conditions observed between the end of the fluvial estuary and the beginning of the middle (brackish) estuary. Altogether, this study exemplifies how eDNA metabarcoding is a powerful tool to document fish community shifts in large temperate lotic ecosystems.
eDNA metabarcoding efficiently identified the vast majority of fish species of the St. Lawrence River /Estuary/Gulf (Quebec Canada). eDNA metabarcoding identified a pattern of fish communities differentiation strongly associated with a series of longitudinal hydro‐morphological structures and to the upstream–downstream effect of a gradient of salinity, temperature, and tide height variations.
Accurate data characterizing species distribution and abundance are critical for conservation and management of aquatic resources. Inventory methods, such as gillnet surveys, are widely used to ...estimate distribution and abundance of fish. However, gillnet surveys can be costly in terms of material and human resources, may cause unwanted mortality in the fish communities being studied, and is subject to size and species selection bias. Detecting allochthonous DNA released by species in their environment (i.e., environmental DNA, hereafter eDNA) could be used as a noninvasive and less costly alternative. In this study, we directly compare eDNA metabarcoding and gillnets for monitoring freshwater fish communities in terms of species richness and relative species abundance. Metabarcoding was performed with the 12S Mifish primers. We also used species‐specific quantitative PCR (qPCR) for the most abundant species, the walleye (Sander vitreus), to compare estimated relative abundance with metabarcoding and gillnet captures. Water sample collection, prior to gillnet assessment, was performed on 17 sites in the hydroelectric impoundment of the Rupert River (James Bay, Canada), comparing two water filtration methods. After controlling for amplification biases and repeatability, we show that fish communities’ complexity is better represented using eDNA metabarcoding than previously recorded gillnet data and that metabarcoding read count correlates with qPCR (r = 0.78, p < .001) in reflecting walleye abundance. Finally, based on partial redundancy analysis, we identified alpha chlorophyll, pH, and dissolved oxygen as environmental variable candidates that may influence differences in fish relative abundance between metabarcoding and gillnets. Altogether, our study demonstrates that the proposed eDNA metabarcoding method can be used as an efficient alternative or complementary technique adapted to the biomonitoring of the fish communities in boreal aquatic ecosystems.
We showed that eDNA metacording outperform gillnets survey to detect freshwater fish communities. Our results also suggest that eDNA metabarcoding can be used to infer fish abundance and biomass. Together, it suggest that eDNA is a usable tool for fish conservation and management.
Biodiversity assessment is an important part of conservation management that ideally can be accomplished with noninvasive methods without influencing the structure and functioning of ecosystems. ...Environmental DNA (eDNA) metabarcoding has provided a promising tool to enable fast and comprehensive monitoring of entire ecosystems, but widespread adoption of this technique requires performance evaluations that compare it with conventional surveys. We compared eDNA metabarcoding and trawling data to evaluate their efficiency to characterize demersal fish communities in the Estuary and Gulf of Saint‐Lawrence, Canada. Seawater and bottom trawling samples were collected in parallel at 84 stations. For a subset of 30 of these stations, water was also collected at three different depths (15, 50, and 250 m) across the water column. An eDNA metabarcoding assay based on the 12S mitochondrial gene using the MiFish‐U primers was applied to detect fish eDNA. We detected a total of 88 fish species with both methods combined, with 72 species being detected by eDNA, 64 species detected by trawl, and 47 species (53%) overlapped between both methods. eDNA was more efficient for quantifying species richness, mainly because it detected species known to be less vulnerable to trawling gear. Our results indicated that the relative abundance estimated by eDNA and trawl is significantly correlated for species detected by both methods, while the relationship was also influenced by environmental variables (temperature, depth, salinity, and oxygen). Integrating eDNA metabarcoding to bottom trawling surveys could provide additional information on vertical fish distribution in the water column. Environmental DNA metabarcoding thus appears to be a reliable and complementary approach to trawling surveys for documenting fish biodiversity, including for obtaining relative quantitative estimates in the marine environment.
Map of the 84 sampling sites. Detailed map of the 84 sampling sites in Estuary and Gulf of St. Lawrence (EGSL). Red circles represent stations where trawling and eDNA sampling were done simultaneously only at bottom (n = 54). Green circles represent stations where trawling and eDNA sampling were done simultaneously at bottom and where eDNA sampling was additionally performed at different depths in the water column (n = 30). The insert shows the location of the sampling area within North America (red rectangle).
The analysis of environmental DNA (eDNA) is a powerful tool to increase the efficiency of species detection and monitoring in aquatic ecosystems. Yet, several points remain to be clarified in order ...to estimate with better precision the distribution and abundance of targeted species, such as the dispersion and dilution of eDNA in large lotic systems. This study aimed to document the dispersion patterns of eDNA in the St. Lawrence River, the largest fluvial system in eastern North America. Caged Brown trout (Salmo trutta) were placed in two different water masses present in this part of the river, the Ottawa River, and water from the outlet of the Laurentian Great Lakes. eDNA detection of the caged fish was performed for two days following cage removal at 53 sampling stations located at 500 upstream, and 10, 100, 500, 1,000, and 5,000 m downstream from the cages. Quantitative PCR analysis using a Brown trout specific assay revealed a positive detection only at downstream stations and up to 5,000 m. To further investigate patterns of dispersion, the relative concentrations of eDNA were predicted using a bidimensional hydrodynamic model, calibrated for downstream advection and lateral mixing of particles (i.e., quantification of 2D dispersion). The detection and the quantities of eDNA obtained by qPCR analyses were compared with the model predictions. Our model which predicts a low lateral mixing and a downstream flow in direct line from the eDNA source best fits the results. We discuss how such studies can improve our capacity to produce more precise estimates of species abundance and distribution in order to better interpret eDNA signals in large lotic systems.
We showed how eDNA disperses in fluvial environment using a hydrodynamic bidimensional model. Our results reveal little transverse dispersion, implying a laminar dispersion of eDNA.
Abstract
Dense single nucleotide polymorphism (SNP) arrays are essential tools for rapid high-throughput genotyping for many genetic analyses, including genomic selection and high-resolution ...population genomic assessments. We present a high-density (200 K) SNP array developed for the Eastern oyster (Crassostrea virginica), which is a species of significant aquaculture production and restoration efforts throughout its native range. SNP discovery was performed using low-coverage whole-genome sequencing of 435 F1 oysters from families from 11 founder populations in New Brunswick, Canada. An Affymetrix Axiom Custom array was created with 219,447 SNPs meeting stringent selection criteria and validated by genotyping more than 4,000 oysters across 2 generations. In total, 144,570 SNPs had a call rate >90%, most of which (96%) were polymorphic and were distributed across the Eastern oyster reference genome, with similar levels of genetic diversity observed in both generations. Linkage disequilibrium was low (maximum r2 ∼0.32) and decayed moderately with increasing distance between SNP pairs. Taking advantage of our intergenerational data set, we quantified Mendelian inheritance errors to validate SNP selection. Although most of SNPs exhibited low Mendelian inheritance error rates overall, with 72% of called SNPs having an error rate of <1%, many loci had elevated Mendelian inheritance error rates, potentially indicating the presence of null alleles. This SNP panel provides a necessary tool to enable routine application of genomic approaches, including genomic selection, in C. virginica selective breeding programs. As demand for production increases, this resource will be essential for accelerating production and sustaining the Canadian oyster aquaculture industry.
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