Feeding ecology of redfish (Sebastes sp.) inferred from the integrated use of fatty acid profiles as complementary dietary tracers to stomach content analysis.

In the northern Gulf of St. Lawrence (nGSL), redfish (Sebastes mentella and Sebastes fasciatus combined) are at record levels of abundance following the strong recruitment of three consecutive cohorts in 2011-2013 and have become by far the most abundant demersal fish in the region. Understanding redfish trophic relationships is essential for the effective management and conservation of species in the nGSL ecosystem. To date, description and quantification of redfish diet in the region have been restricted to conventional stomach content analysis (SCA). Using analysis of fatty acid (FA) profiles as complementary dietary tracers, the authors conducted multivariate analyses on 350 livers of redfish which were collected in combination with stomach contents during a bottom-trawl scientific survey in August 2017. The predator FA profiles were compared to those of eight different redfish prey types identified as dietary important with SCA. Results suggested similitude between SCA and FA results, with zooplankton prey being more related to small (<20 cm) and medium (20-30 cm) redfish (16:1n7, 20:1n?, 22:1n9 and 20:5n3) than large (≥30 cm) ones, whereas shrimp prey seemed more related to large redfish size classes (18:2n6 and 22:6n3) relative to the small and medium ones. Although the SCA offers a glimpse in the diet only based on the most recently consumed prey, analysis of FA profiles provides a mid-term view indicating pelagic zooplankton consumption on calanoid copepod and confirming high predation pressure on shrimp. This study constitutes the first attempt of combining FA with SCA to assess the diet of redfish, highlights the benefits of FA as a qualitative tool and suggests improvements for future studies.

Genome-wide DNA methylation predicts environmentally driven life history variation in a marine fish.

Epigenetic modifications are thought to be one of the molecular mechanisms involved in plastic adaptive responses to environmental variation. However, studies reporting associations between genome-wide epigenetic changes and habitat-specific variations in life history traits (e.g., lifespan, reproduction) are still scarce, likely due to the recent application of methylome resequencing methods to non-model species. In this study, we examined associations between whole genome DNA methylation and environmentally driven life history variation in 2 lineages of a marine fish, the capelin (Mallotus villosus), from North America and Europe. In both lineages, capelin harbor 2 contrasting life history tactics (demersal vs. beach-spawning). Performing whole genome and methylome sequencing, we showed that life history tactics are associated with epigenetic changes in both lineages, though the effect was stronger in European capelin. Genetic differentiation between the capelin harboring different life history tactics was negligible, but we found genome-wide methylation changes in both lineages. We identified 9,125 European and 199 North American differentially methylated regions (DMRs) due to life history. Gene ontology (GO) enrichment analysis for both lineages revealed an excess of terms related to neural function. Our results suggest that environmental variation causes important epigenetic changes that are associated with contrasting life history tactics in lineages with divergent genetic backgrounds, with variable importance of genetic variation in driving epigenetic variation. Our study emphasizes the potential role of genome-wide epigenetic variation in adaptation to environmental variation.

Thermal adaptation rather than demographic history drives genetic structure inferred by copy number variants in a marine fish.

Increasing evidence shows that structural variants represent an overlooked aspect of genetic variation with consequential evolutionary roles. Among those, copy number variants (CNVs), including duplicated genomic regions and transposable elements (TEs), may contribute to local adaptation and/or reproductive isolation among divergent populations. Those mechanisms suppose that CNVs could be used to infer neutral and/or adaptive population genetic structure, whose study has been restricted to microsatellites, mitochondrial DNA and Amplified fragment length polymorphism markers in the past and more recently the use of single nucleotide polymorphisms (SNPs). Taking advantage of recent developments allowing CNV analysis from RAD-seq data, we investigated how variation in fitness-related traits, local environmental conditions and demographic history are associated with CNVs, and how subsequent copy number variation drives population genetic structure in a marine fish, the capelin (Mallotus villosus). We collected 1538 DNA samples from 35 sampling sites in the north Atlantic Ocean and identified 6620 putative CNVs. We found associations between CNVs and the gonadosomatic index, suggesting that six duplicated regions could affect female fitness by modulating oocyte production. We also detected 105 CNV candidates associated with water temperature, among which 20% corresponded to genomic regions located within the sequence of protein-coding genes, suggesting local adaptation to cold water by means of gene sequence amplification. We also identified 175 CNVs associated with the divergence of three previously defined parapatric glacial lineages, of which 24% were located within protein-coding genes, making those loci potential candidates for reproductive isolation. Lastly, our analyses unveiled a hierarchical, complex CNV population structure determined by temperature and local geography, which was in stark contrast to that inferred based on SNPs in a previous study. Our findings underline the complementarity of those two types of genomic variation in population genomics studies.

Flowing down the river: Influence of hydrology on scale and accuracy of elemental composition classification in a large fluvial ecosystem.

Trace metals found in the calcified structures of fish (i.e. otolith, scales and vertebrae) serve as proxies for the ambient water composition at the time of mineralization, and these trace metals are increasingly used as a tool for assessing population structure and the migratory patterns of fish. However, the appropriate scale (e.g. resolution) for such applications can be uncertain because of a poor understanding of the spatiotemporal variations of metal-to-calcium ratios (Me:Ca) in the studied watersheds. This study aims to assess Me:Ca spatiotemporal variability within the St. Lawrence River and nine major tributaries and evaluate the ability of random-forest models to correctly identify rivers on the basis of their elemental composition. We tested the influence of daily discharge on four measured ratios (Sr:Ca, Ba:Ca, Mg:Ca and Mn:Ca) to document local and regional trace element sources and dynamics. The four element ratios displayed a low spatiotemporal variation, reflecting a marked stability over time. We observed that most element- and tributary-specific concentration-discharge relationships were either not significant or showed a weak influence, thereby confirming a stable point source dynamic. The classification performance based on a four-element model (Sr:Ca, Ba:Ca, Mg:Ca and Mn:Ca) produced a classification accuracy of 92.5%, which correspond to a small decrease of accuracy compared to the full model (25 elements, 96.6% of correct classification). A classification based on two elements (Sr:Ca and Ba:Ca) produced a lower classification accuracy (72.6%). Classification errors related mainly to tributaries in close proximity, a problem tempered by grouping these geochemically similar watersheds. Our results show that surveys of the elemental fingerprint of regional tributaries within a given region can provide critical information to determine the appropriate scale (tributary or watershed) for trace metal analysis of the hard-calcified parts of fish.

Estimating the contribution of Greenland Halibut (Reinhardtius hippoglossoides) stocks to nurseries by means of genotyping-by-sequencing: Sex and time matter.

Identification of stocks and quantification of their relative contribution to recruitment are major objectives toward improving the management and conservation of marine exploited species. Next-generation sequencing allows for thousands of genomic markers to be analyzed, which provides the resolution needed to address these questions in marine species with weakly differentiated populations. Greenland Halibut (Reinhardtius hippoglossoides) is one of the most important exploited demersal species throughout the North Atlantic, in particular in the Gulf of St. Lawrence, Canada. There, two nurseries are known, the St. Lawrence Estuary and the northern Anticosti Island, but their contribution to the renewal of stocks remains unknown. The goals of this study were (a) to document the genetic structure and (b) to estimate the contribution of the different identified breeding stocks to nurseries. We sampled 100 juveniles per nursery and 50 adults from seven sites ranging from Saguenay Fjord to offshore Newfoundland, with some sites sampled over two consecutive years in order to evaluate the temporal stability of the contribution. Our results show that after removing sex-linked markers, the Estuary/Gulf of St. Lawrence represents a single stock which is genetically distinct from the Atlantic around Newfoundland (F ST = 0.00146, p-value = .001). Population assignment showed that recruitment in both nurseries is predominantly associated with the St. Lawrence stock. However, we found that the relative contribution of both stocks to the nurseries is temporally variable with 1% contribution of the Newfoundland stock one year but up to 33% for the second year, which may be caused by year-to-year variation in larval transport into the Gulf of St. Lawrence. This study serves as a model for the identification of stocks for fisheries resources in a context where few barriers to dispersal occur, in addition to demonstrating the importance of considering sex-linked markers and temporal replicates in studies of population genomics.

Shared ancestral polymorphisms and chromosomal rearrangements as potential drivers of local adaptation in a marine fish.

Gene flow has tremendous importance for local adaptation, by influencing the fate of de novo mutations, maintaining standing genetic variation and driving adaptive introgression. Furthermore, structural variation as chromosomal rearrangements may facilitate adaptation despite high gene flow. However, our understanding of the evolutionary mechanisms impending or favouring local adaptation in the presence of gene flow is still limited to a restricted number of study systems. In this study, we examined how demographic history, shared ancestral polymorphism, and gene flow among glacial lineages contribute to local adaptation to sea conditions in a marine fish, the capelin (Mallotus villosus). We first assembled a 490-Mbp draft genome of M. villosus to map our RAD sequence reads. Then, we used a large data set of genome-wide single nucleotide polymorphisms (25,904 filtered SNPs) genotyped in 1,310 individuals collected from 31 spawning sites in the northwest Atlantic. We reconstructed the history of divergence among three glacial lineages and showed that they probably diverged from 3.8 to 1.8 million years ago and experienced secondary contacts. Within each lineage, our analyses provided evidence for large Ne and high gene flow among spawning sites. Within the Northwest Atlantic lineage, we detected a polymorphic chromosomal rearrangement leading to the occurrence of three haplogroups. Genotype-environment associations revealed molecular signatures of local adaptation to environmental conditions prevailing at spawning sites. Our study also suggests that both shared polymorphisms among lineages, resulting from standing genetic variation or introgression, and chromosomal rearrangements may contribute to local adaptation in the presence of high gene flow.

Supplementation stocking of Lake Trout (Salvelinus namaycush) in small boreal lakes: Ecotypes influence on growth and condition.

Supplementation stocking is a commonly used management tool to sustain exploited fish populations. Possible negative consequences of supplementation on local stocks are a concern for the conservation of wild fish populations. However, the direct impacts of supplementation on life history traits of local populations have rarely been investigated. In addition, intraspecific hybridization between contrasting ecotypes (planktivorous and piscivorous) has been seldom considered in supplementation plans. Here, we combined genetic (genotype-by-sequencing analysis) and life history traits to document the effects of supplementation on maximum length, growth rates, body condition and genetic admixture in stocked populations of two Lake Trout ecotypes from small boreal lakes in Quebec and Ontario, Canada. In both ecotypes, the length of stocked individuals was greater than local individuals and, in planktivorous-stocked populations, most stocked fish exhibited a planktivorous-like growth while 20% of fish exhibited piscivorous-like growth. The body condition index was positively related to the proportion of local genetic background, but this pattern was only observed in stocked planktivorous populations. We conclude that interactions and hybridization between contrasting ecotypes is a risk that could result in deleterious impacts and possible outbreeding depression. We discuss the implications of these findings for supplementation stocking.

Introgressive hybridization between wild and domestic individuals and its relationship with parasitism in brook charr Salvelinus fontinalis.

The effects of introgression on parasitism in brook charr Salvelinus fontinalis were investigated in 28 lakes with various levels of stocking in Québec, Canada. No effect of genetic background on parasitism was found at the individual level. Body length seemed to explain most of the variation observed at this level, with largest fish being more infected. However, lakes with the greater average domestic genetic background were found to display significantly lower parasite prevalence and diversity. Since our results indicate no effect of domestic genes at the individual level, the negative association with introgression found at the population level may be mainly attributed to differences in intrinsic environmental quality of lakes (e.g. fishing pressure, availability of food resources, abiotic characteristics).

Do genetic drift and accumulation of deleterious mutations preclude adaptation? Empirical investigation using RADseq in a northern lacustrine fish.

Understanding genomic signatures of divergent selection underlying long-term adaptation in populations located in heterogeneous environments is a key goal in evolutionary biology. In this study, we investigated neutral, adaptive and deleterious genetic variation using 7,192 SNPs in 31 Lake Trout (Salvelinus namaycush) populations (n = 673) from Québec, Canada. Average genetic diversity was low, weakly shared among lakes, and positively correlated with lake size, indicating a major role for genetic drift subsequent to lake isolation. Putatively deleterious mutations were on average at lower frequencies than the other SNPs, and their abundance relative to the entire polymorphism in each population was positively correlated with inbreeding, suggesting that the effectiveness of purifying selection was negatively correlated with inbreeding, as predicted from theory. Despite evidence for pronounced genetic drift and inbreeding, several outlier loci were associated with temperature and found in or close to genes with biologically relevant functions notably related to heat stress and immune responses. Outcomes of gene-temperature associations were influenced by the inclusion of the most inbred populations, in which allele frequencies deviated the most from model predictions. This result illustrates challenge in identifying gene-environment associations in cases of high genetic drift and restricted gene flow and suggests limited adaptation in populations experiencing higher inbreeding. We discuss the relevance of these findings for the conservation and management, notably regarding stocking and genetic rescue, of Lake Trout populations and other species inhabiting highly fragmented habitats.

Investigating the extent of parallelism in morphological and genomic divergence among lake trout ecotypes in Lake Superior.

Understanding the emergence of species through the process of ecological speciation is a central question in evolutionary biology which also has implications for conservation and management. Lake trout (Salvelinus namaycush) is renowned for the occurrence of different ecotypes linked to resource and habitat use throughout North America. We aimed to unravel the fine genetic structure of the four lake trout ecotypes in Lake Superior. A total of 486 individuals from four sites were genotyped at 6822 filtered SNPs using RADseq technology. Our results revealed different extent of morphological and genetic differentiation within the different sites. Overall, genetic differentiation was weak but significant and was on average three times higher between sites (mean FST  = 0.016) than between ecotypes within sites (mean FST  = 0.005) indicating higher level of gene flow or a more recent shared ancestor between ecotypes within each site than between populations of the same ecotype. Evidence of divergent selection was also found between ecotypes and/or in association with morphological variation. Outlier loci found in genes related to lipid metabolism and visual acuity were of particular interest in this context of ecotypic divergence. However, we did not find clear indication of parallelism at the genomic level, despite the presence of phenotypic parallelism among some ecotypes from different sampling sites. Overall, the occurrence of different levels of both genomic and phenotypic differentiation between ecotypes within each site with several differentiated loci linked to relevant biological functions supports the presence of a continuum of divergence in lake trout.

Impact of forest harvesting on trophic structure of eastern Canadian Boreal Shield lakes: insights from stable isotope analyses.

Perturbations on ecosystems can have profound immediate effects and can, accordingly, greatly alter the natural community. Land-use such as forestry activities in the Canadian Boreal region have increased in the last decades, raising concerns about their potential impact on aquatic ecosystems. The objective of this study was to evaluate the impact of forest harvesting on trophic structure in eastern Canadian Boreal Shield lakes. We measured carbon and nitrogen stable isotopes values for aquatic primary producers, terrestrial detritus, benthic macroinvertebrates, zooplankton and brook trout (Salvelinus fontinalis) over a three-year period in eight eastern Boreal Shield lakes. Four lakes were studied before, one and two years after forest harvesting (perturbed lakes) and compared with four undisturbed reference lakes (unperturbed lakes) sampled at the same time. Stable isotope mixing models showed leaf-litter to be the main food source for benthic primary consumers in both perturbed and unperturbed lakes, suggesting no logging impact on allochthonous subsidies to the littoral food web. Brook trout derived their food mainly from benthic predatory macroinvertebrates in unperturbed lakes. However, in perturbed lakes one year after harvesting, zooplankton appeared to be the main contributor to brook trout diet. This change in brook trout diet was mitigated two years after harvesting. Size-related diet shift were also observed for brook trout, indicating a diet shift related to size. Our study suggests that carbon from terrestrial habitat may be a significant contribution to the food web of oligotrophic Canadian Boreal Shield lakes. Forest harvesting did not have an impact on the diet of benthic primary consumers. On the other hand, brook trout diet composition was affected by logging with greater zooplankton contribution in perturbed lakes, possibly induced by darker-colored environment in these lakes one year after logging.

Nurses' perceptions and attitudes towards new ADU technology and use.

BACKGROUND: The introduction of a new technology in hospitals - Automated Dispensing Units (ADUs) - aims to contribute to more secure, safe, efficient and cost effective health services. Several studies highlight the beneficial effects of similar technologies as well as their cost-savings potential but there is little literature exploring nurses' perceptions and attitudes towards technology acceptance and the impact on technology use in a healthcare unit. OBJECTIVE: This research aimed to explore nurses' perceptions and attitudes towards current technology use on their units and towards the introduction of ADU technology and use with nursing staff in two different hospitals in South-East New-Brunswick, Canada. METHODS: Semi-structured interviews were realized with the collaboration of nursing staff from two hospitals which were in urban and rural settings, prior to the introduction of ADUs in hospital wards. RESULTS: Findings in this study highlight the fact that missing medications (i.e., doses not available in cart) are inherently related to the completion of nursing staff's medication distribution routine. Missing doses cause delays in medication delivery which may increase the occurrence of medication errors. Participants described current technology use as an intricate part of their routine. The latter is mainly utilized for patient monitoring and information retrieval. Overall, interview data indicated that ADU technology introduction is positively perceived by nursing staff particularly if the technology reduces missing doses events. CONCLUSIONS: Findings in this study underscore important concerns expressed by nursing staff regarding ADU technology integration into the current medication process and its impact on time management. Pre-implementation training and technical support were identified as important factors in facilitating technology acceptance and proper technology use.

Antioxidant and anti-inflammatory activities of quercetin 7-O-ß-D-glucopyranoside from the leaves of Brasenia schreberi.

Brasenia schreberi Gmel. (Cabombaceae) is an aquatic plant that grows in eastern Asia, Australia, Africa, and North and Central America. B. schreberi leaf extracts were obtained by sequential solvent extraction with dichloromethane, methanol, and water. The antioxidant potential of each extract was assessed by using the oxygen radical absorbance capacity (ORAC) assay. With this method, methanol and water extracts were found to be active with mean ± standard deviation values of 7 ± 2 and 5.1 ± 0.5 µmol Trolox® equivalents (TE)/mg, respectively. Two major phenolic compounds, quercetin-7-O-ß-D-glucopyranoside and gallic acid, were respectively isolated from the methanolic and water extracts. Both compounds exhibited antioxidant activities, in particular quercetin-7-O-ß-D-glucopyranoside (ORAC value, 18 ± 4 µmol TE/µmol). In contrast to its well-known antioxidant homologue quercetin, quercetin-7-O-ß-D-glucopyranoside does not inhibit growth of human fibroblasts (WS-1) or murine macrophages (RAW 264.7). Some flavonoids have been reported to possess beneficial effects in cardiovascular and chronic inflammatory diseases associated with overproduction of nitric oxide. Quercetin-7-O-ß-D-glucopyranoside possesses anti-inflammatory activity, inhibiting expression of inducible nitric oxide synthase and release of nitric oxide by lipopolysaccharide-stimulated RAW 264.7 macrophages in a dose-dependent manner. Quercetin-7-O-ß-D-glucopyranoside also inhibited overexpression of cyclooxygenase-2 and granulocyte macrophage-colony-stimulating factor.

Historical introgression and the role of selective vs. neutral processes in structuring nuclear genetic variation (AFLP) in a circumpolar marine fish, the capelin (Mallotus villosus).

The capelin (Mallotus villosus) is a widespread marine fish species for which previous work has identified geographically distinct mtDNA clades, the frontiers of which are well within adult and larval dispersal capabilities. Here, we use AFLPs to test for the presence of nuclear gene flow among clades. In addition, we evaluate genetic structuring within one clade, the Northwest Atlantic (NWA). We found that each of the mtDNA clades corresponds with a unique nuclear DNA genetic cluster. Within the NWA clade, we detected individuals with small but significant amounts of genetic ancestry from other clades, likely due to historical introgression. Further support for historical introgression comes from analyses of variance in locus-specific differentiation, which support introgression between some clades and divergence without gene flow between others. Within the NWA, we identified two genetic clusters that correspond to sites in geographically adjacent areas. However, these clusters differ primarily at 'outlier' loci, and a genetic subdivision (K=2) was not supported by genetic clustering programs using neutral loci. Significant neutral F(ST) differentiation was found only between sites that otherwise differed at outlier loci. Thus, these populations may be in the initial stages of 'isolation by adaptation'. These results suggest strong between-clade reproductive isolation despite opportunities for gene flow and support the hypothesis that selection can contribute to divergence in otherwise 'open' systems.