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Leroux, S.

Publications and source records attributed to Leroux, S..

15 recordsLinked to original sources

Genetic determinism and inheritance of differential DNA methylation profiles across three successive generations in quail.

Environmental exposures can induce epigenetic modifications that persist across generations, potentially contributing to the transmission of environmentally-induced phenotypes. However, the extent to which such persistence of molecular changes are maintained independently of genetic mechanisms remains unclear. In this study, we investigated the evolution and genetic determinism of DNA methylation (DNAm) variation across three successive generations of Japanese quails (G0 to G2) belonging to two epilines, defined according to whether their female ancestor had received genistein supplementation (epi+) or not (epi-). Using reduced representation bisulfite sequencing (RRBS), we characterised CpG methylation patterns and identified differentially methylated cytosines (DMCs) and regions (DMRs) between control and genistein-supplemented epilines. Out of 112,745 CpG sites analysed, no DMCs or DMRs were detected between epilines in the first generation following exposure (G0), whereas 621 DMCs (36 DMRs) were identified in G1, and 1,381 DMCs (101 DMRs) in G2. Despite this progressive increase of differential methylation sites, mean differences in methylation rate between epilines were globally small. Similarly, genome-wide genetic differentiation between epilines was very limited. Overall, SNP-based heritability of DNA methylation was 0.19 indicating that genetic variation accounted for only a small part of the global variation of DNAm levels. By contrast, DNAm at differentially methylated CpG sites was extensively under genetic control, with a mean SNP-based heritability > 0.5, and meQTL analysis further identified significant associations between SNPs and methylation levels. Together, these results indicate that local DNAm differentiation in quail is under substantial genetic regulation, while the limited genetic differentiation between groups suggests that genetic variation alone can not fully explain the progressive accumulation of methylation differences following an ancestral exposure to genistein. These results support DNAm as a plausible molecular candidate mechanism in the multigenerational response to environmental exposure and highlight the complex interplay between genetic and epigenetic regulations in the inheritance of phenotypes.

genomics↗

Investigating biotic, chemical, and physical drivers of periphyton and invertebrate biomass in boreal streams supporting juvenile Atlantic salmon

1. Atlantic salmon (Salmo salar) are an anadromous fish with a broad distribution from eastern North America to western Europe, with ecological, economic, and cultural significance. Despite their expansive range, wild populations across the North Atlantic have experienced decline. Survival to reproductive age is a management concern, with a focus on identifying factors affecting the juvenile freshwater life stage. Specifically, research is needed to identify potential bottlenecks limiting freshwater productivity. 2. We addressed this research gap with a case study on the Exploits River, Newfoundland - a watershed that receives one of the largest anadromous Atlantic salmon returns in North America. We aimed to identify biotic, chemical, and physical predictors of food resources for juvenile salmon (i.e., invertebrates) and food resources for invertebrates (i.e., periphyton). To test our hypotheses, we collected data on a suite of biotic (e.g., invertebrates and periphyton), chemical (e.g., total dissolved N), and physical (e.g., wetted width) variables at 42 sites within and around this watershed. 3. We observed evidence for relationships between invertebrate biomass and biotic and temporal variables. Specifically, invertebrate biomass was higher at sites with high periphyton biomass that were sampled later in the season. In addition, we observed that periphyton biomass was related to biotic, chemical, and physical variables. Here, we present evidence for bottom-up control, with increased periphyton biomass supporting increased invertebrate biomass. 4. We expect knock-on effects where increased invertebrate biomass results in increased juvenile Atlantic salmon biomass. Our large sample size revealed some predictors of invertebrate biomass and periphyton biomass. However, we found no evidence of correlation between invertebrate biomass and chemical or physical variables. The low productivity of our maritime boreal forest system could be an outlier in expected biotic, chemical, and physical relationships in streams. 5. Our findings provide an important step forward in furthering boreal stream ecology, producing novel invertebrate and periphyton knowledge for watershed managers.

ecology↗

New chromosome-level haplotyped genome assemblies and annotation for the Japanese Quail (Coturnix Japonica)

The Japanese quail (Coturnix japonica) is a widely used model organism in developmental biology, genetics, and agriculture. Here, we present new, haplotyped, high-quality genome assemblies of the Japanese quail, generated using a combination of state-of-the-art sequencing technologies, including PacBio HiFi long reads, Oxford Nanopore sequencing, and Hi-C scaffolding. This assembly has a total length of 1.19 Gb, 80% of which is included in chromosomes, and is highly complete (BUSCO score aves_odb10: 97.3). Assembly metrics show a marked improvement in contiguity, with a significantly higher scaffold N50 and a lower number of contigs compared to the reference genome assembly. Remarkably, the assembly extends previously truncated chromosome ends, with 31 telomeres detected. In addition, we merged the existing Ensembl and Refseq annotations and obtained a combined set of 26,102 genes, of which 25,038 genes were successfully mapped on the improved assembly haplotype 1 (Cjap1.hap1). Together, these new genome assemblies and their enriched annotation provide a robust genomic framework for future research. They enhance our ability to investigate developmental processes, genetic and epigenetic inheritance, and host-pathogen interactions. Furthermore, they offer valuable insights for conservation genetics and sustainable breeding programs. This resource represents a critical step forward in leveraging the full potential of the Japanese quail as a model species in both basic and applied research.

genomics↗

Shifting forage selection subsidizes seasonal resource scarcity

O_LINitrogen (N) is limiting for terrestrial herbivores, particularly over winter. Caribou (Rangifer tarandus) have adapted to seasonal scarcity of N by accruing muscle mass during the growing season when N is more abundant. C_LIO_LINitrogen stored in muscle tissue is then relied upon during winter to compensate for dietary deficits. Once their diet shifts from N-rich vascular plants to N-poor lichen over winter, caribou can lose [~]30% of their muscle mass. As catabolized N is shed in urine on wintering grounds, caribou could act as elemental transport across seasons and landscapes. Furthermore, if deposited N is taken up by lichen or other winter forage, it might enrich the nitrogen-poor winter diet of caribou in the future. C_LIO_LIWe tested this potential transport via three steps. We analysed Cladonia spp. lichen and vascular plants upon which caribou forage across Fogo Island, Newfoundland, using %N content as our metric of forage quality. We then compared seasonal habitat selection responses to forage quality by caribou using integrated step selection analyses. In summer, caribou selected areas with higher vascular plant %N but did not select nor avoid Cladonia quality. In contrast, caribou selected sites with higher quality Cladonia in winter but responded neutrally to vascular plant quality. C_LIO_LIWe compared seasonal distributions of caribou to determine whether nitrogen consumed in summer and deposited in winter would occur in spatially discrete locations. Population-level kernel density estimates for summer and winter in this island herd were mostly non-overlapping, lending credence to the potential landscape effects of N transport. C_LIO_LIWhen viewed together with established seasonal changes in woodland caribou physiology, sociality, and forage preferences, the shifts in habitat selection and seasonal ranges we observe here could serve as an adaptive strategy for caribou to recycle N and mitigate winter nutrient scarcity. C_LI

ecology↗

Transgenerational transmission of an environmental modification in quails: changes in phenotypic variance components across three generations

BackgroundWhile epigenetic variations can contribute to shaping phenotypic diversity, it can be challenging to isolate and quantify the portion of trait variability under non-genetic influence. In this study we compared the phenotypic responses for different traits of two epilines of Japanese quails (Coturnix japonica) across three generations, using a large sample size. These epilines were built in parallel following (epi +), or not (epi -), an initial genistein ingestion in the ancestors diet and were maintained to harbour a similar genetic structure. ResultsLinear models were fitted to extract the fraction of variance allocated to multiple factors such as family, sex and epiline. The latter was found to be significantly associated with body weight. The contribution of the epiline to phenotypic variability progressively increased from the first generation (G0) to the last (G2), leading - for example in body weight at slaughter - to an average difference for adult males and females in G2 of 9 grams and 14 grams respectively, between epi + offspring and controls (epi-). ConclusionsAlthough these findings suggest genetic drift, they could also reveal a possible transgenerational effect of the initial diet disruption. The analysis of other phenotypes displayed rare significant effects of the epiline. This innovative experimental design offered a unique opportunity to better understand the evolution of phenotypic variability and the parameters constituting it across three generations following or not an environmental change.

genetics↗

An extensive and unbiased genome-wide scan for parent-of-origin expressed genes in the pig clarifies the conservation landscape of genomic imprinting

Genomic imprinting, a mechanism resulting in parent-of-origin expression of genes through epigenetic regulation, intersects with a broad range of biological fields including evolution, molecular genetics and epigenetics and determinism of complex traits. Although next generation sequencing technologies enable nowadays to detect imprinted genes in a genome-wide manner, a wide spectrum of this phenomena is evaluated only in humans and mice. Here, we propose to map genes showing a parental expression bias in hypothalamus, muscle and placenta in piglets around birth using an extensive and unbiased strategy that relied on reciprocal crosses, genetics reconstruction of parental phases after imputation and statistical analyses discriminating parent-of-origin from allele-specific expression. We detected 440 unique genes with a weak to exclusive parental expression bias including 114 unique genes with an imbalance ratio above 25:75. About thirty imprinted genes are common to human and/or mice and an equivalent number is shared between tissues, suggesting an overall weak conservation landscape of genomic imprinting. Interestingly, we identified novel parent-of-origin expressed genes involved in neurodevelopmental (PITRM1, Pitrilysin Metallopeptidase 1) and fetal growth (FAM20B, Glycosaminoglycan Xylosylkinase and POU6F2, POU Class 6 Homeobox 2) functions. In addition, deeper analyses of specific loci likely highlighted lineage-specific imprinted genes such as a Zinc Finger Protein 300-like gene as well as specific imprinted isoforms of COPG2 (COPI Coat Complex Subunit Gamma 2), a gene showing conflicting data in the literature. Altogether, our results bring pig as the most comprehensively and exhaustively documented species for genomic imprinting after human and mice organisms. A weak conservation of this mechanism across species and tissues suggested a distinction between a small number of core imprinted genes and others parent-of-origin expressed genes that seemed subjected to evolutionary forces for acquiring their imprinting status either in a lineage-specific or tissue-specific manner.

genomics↗

Molecular responses of chicken embryos to maternal heat stress through DNA methylation and gene expression

Climate change, with its repercussions on agriculture, is one of the most important adaptation challenges for livestock production. Poultry production is a major source of proteins for human consumption all over the world. With a growing human population, improving poultrys adaptation to environmental constraints becomes critical. Extensive evidence highlights the influence of environmental variations on epigenetic modifications. The aim of this paper is therefore to explore chickens molecular response to maternal heat stress. We employed Reduced Representation Bisulfite Sequencing (RRBS) to generate genome-wide single-base resolution DNA methylation profiling and RNA sequencing (RNA-seq) to profile the transcriptome of the brains of embryos hatched from dams reared under either heat stress (32 {degrees}C) or thermoneutrality (22{degrees}C). We detected 289 significant differentially methylated CpG sites (DMCs) and one differentially methylated region (DMR) between heat stressed and control groups. These DMCs were associated with 357 genes involved in processes such as cellular response to stimulus, developmental processes and immune function. In addition, we identified 11 genes differentially expressed between the two groups of embryos, and identified ATP9A as a target gene of maternal heat stress on offspring. This study provides a body of fundamental knowledge on adaptive mechanisms concerning heat tolerance in chickens.

genomics↗

Integrating ecosystem and contaminant models to predict the effects of ecosystem fluxes on contaminant dynamics

Pollution is one of the major drivers of ecosystem change in the Anthropocene. Toxic chemicals are not constrained to their source of origin as they cross ecosystem boundaries via biotic (e.g., animal migration) and abiotic (e.g., water flow) vectors. Meta-ecology has led to important insights on how spatial flows or subsidies of matter across ecosystem boundaries can have broad impacts on local and regional ecosystem dynamics but has not yet addressed the dynamics of pollutants. Understanding how these meta-ecosystem processes on contaminant dynamics may reverberate up a food chain is important even if they might be difficult to predict. Here we derive a modelling framework to predict how spatial ecosystem fluxes can influence contaminant dynamics and how the severity of this impact is dependent on the type of ecosystem flux leading to the spatial coupling (e.g., herbivore movement vs abiotic chemical flows). We mix an analytical and numerical approach to analyze our integrative model which couples two distinct sub-components - an ecosystem model and a contaminant model. We observe an array of dynamics for how chemical concentrations change with increasing nutrient input and loss rate across trophic levels. When we tailor our range of chemical parameter values to specific organic chemicals our results demonstrate that increasing nutrient input rates can lead to trophic dilution in pollutants such as polychlorinated biphenyls across trophic levels. Yet, increasing nutrient loss rate causes an increase in concentrations of chemicals across all trophic levels. A sensitivity analysis demonstrates that nutrient recycling is an important ecosystem process impacting contaminant concentrations, generating predictions to be addressed by future empirical studies. Importantly, our model demonstrates the utility of our framework for identifying drivers of contaminant dynamics in connected ecosystems including the importance that a) ecosystem processes, and b) movement, especially movement of lower trophic levels, have on contaminant concentrations. For example, how increasing nutrient loss rate leads to increasing contaminant concentrations, or how movement of lower trophic levels contributes to elevated herbivore contaminant concentrations. This dynamic is particularly relevant given that the flow of matter between ecosystems also serves as a vector for the transport of contaminants.

ecology↗

A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities: a rabbit model

Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high density Affymetrix(R) AxiomOrcun SNP Array and phenotyped into 6 different groups ordered from the lighter to the darker. Genome-wide association analyses pinpointed an oligogenic determinism, under recessive and additive inheritance, involving genes already known in melanogenesis (ASIP, KIT, MC1R, TYR), and likely processed pseudogenes linked to ribosomal function, RPS20 and RPS14. We also identified (i) gene-gene interactions through ASIP:MC1R affecting light cream/beige phenotypes while KIT:RPS responsible of dark chocolate/brown colors and (ii) a genome-wide epistatic network involving several others coloration genes such as POT1 or HPS5. Finally, we determined the recessive inheritance of the English spotting phenotype likely involving a copy number variation affecting at least the end of the coding sequence of the KIT gene. Our analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype. Moreover, the characterization of a network including genes that contribute to melanogenesis and pigmentation, two processes affected in various human disorders, shows the potential interest of our rabbit model for transversal studies.

genetics↗

Integrating plant stoichiometry and feeding experiments: state-dependent forage choice and its implications on body mass

Intraspecific feeding choices account for a large portion of herbivore foraging in many ecosystems. Plant resource quality is heterogeneously distributed, affected by nutrient availability and growing conditions. Herbivores navigate landscapes, making feeding decisions according to food qualities, but also energetic and nutritional demands. We test three non-exclusive foraging hypotheses using the snowshoe hare (Lepus americanus): 1) herbivores feeding choices and body conditions respond to intraspecific plant quality variation, 2) feeding responses are mitigated when energetic demands are high, and 3) feeding responses are inflated when nutritional demands are high. We measured black spruce (Picea mariana) nitrogen, phosphorus, and terpene compositions, as indicators of quality, within a snowshoe hare trapping grid and found plant growing conditions to explain spruce quality variation (R2 < 0.36). We then offered two qualities of spruce (H1) from the trapping grid to hares in cafeteria-style experiments and measured their feeding and body condition responses (n = 75). We proxied energetic demands (H2) with ambient temperature and coat insulation (% white coat) and nutritional demands (H3) with the spruce quality (nitrogen and phosphorus content) in home ranges. Hares that preferred higher-quality spruce lost less weight during experiments (p = 0.018). The results supported our energetic predictions: hares in colder temperatures and with less-insulative coats (lower % white) consumed more spruce and were less selective towards high-quality spruce. Collectively, we found variation in plant growing conditions within herbivore home ranges substantial enough to affect herbivore body conditions, but any plant-herbivore interactions are also mediated by animal energetic states.

ecology↗

Comparing global and regional maps of intactness in the boreal region of North America: Implications for conservation planning in one of the world's remaining wilderness areas

Though North Americas boreal forest contains some of the largest remaining intact and wild ecosystems in the world, human activities are systematically reducing its extent. Consequently, forest intactness and human influence maps are increasingly used for monitoring and conservation planning in the boreal region. We compare eight forest intactness and human impact maps to provide a multi-model assessment of intactness in the boreal region. All maps are global in extent except for Global Forest Watch Canadas Human Access (2000) and Intact Forest Landscapes (2000, 2013) maps, although some global maps are restricted to areas that were at least 20% treed. As a function of each maps spatial coverage in North America, the area identified as intact ranged from 55% to 79% in Canada and from 32% to 96% in Alaska. Likewise, the similarity between pairs of datasets in the Canadian boreal ranged from 0.58 to 0.86 on a scale of 0-1. In total, 45% of the region was identified as intact by the seven most recent datasets. There was also variation in the ability of the datasets to account for anthropogenic disturbances that are increasingly common in the boreal region, such as those associated with resource extraction. In comparison to a recently developed high resolution regional disturbance dataset, the four human influence datasets (Human Footprint, Global Human Modification, Large Intact Areas, and Anthropogenic Biomes), in particular, omitted 59-85% of all linear disturbances and 54-89% of all polygonal disturbances. In contrast, the global IFL, Canadian IFL, and Human Access maps omitted 2-7% of linear disturbances and 0.1-5% of polygonal disturbances. Several differences in map characteristics, including input datasets and methods used to develop the maps may help explain these differences. Ultimately, the decision on which dataset to use will depend on the objectives of each specific conservation planning project, but we recommend using datasets that 1) incorporate regional anthropogenic activities, 2) are updated regularly, 3) provide detailed information of the methods and input data used, and 4) can be replicated and adapted for local use. This is especially important in landscapes that are undergoing rapid change due to development, such as the boreal forest of North America.

ecology↗

Forage stoichiometry predicts the home range size of a small terrestrial herbivore

Consumers make space use decisions based on resource quality. Most studies that investigate the influence of resource quality on the spatial ecology of consumers use diverse proxies for quality including measures based on habitat classification, forage species diversity and abundance, and nutritional indicators, e.g., protein. Ecological stoichiometry measures resource quality in terms of elemental ratios, e.g., carbon (C):nitrogen (N) ratio, but rarely have these currencies been used to study consumer space use decisions. Yet, elemental ratios provide a uniquely quantitative way to assess resource quality. Consequently, ecological stoichiometry allows for investigation of how consumers respond to spatial heterogeneity in resource quality by changing their space use, e.g. their home range size, and how this may influence ecosystem dynamics and trophic interactions. Here, we test whether the home range size of a keystone boreal herbivore, the snowshoe hare (Lepus americanus), varies with differences in the C:N, C:phosphorus (P), and N:P ratios of two preferred forage species, lowland blueberry (Vaccinium angustifolium) and red maple (Acer rubrum). We consider forage resources with higher C content relative to N and P to be lower quality than resources with lower relative C content. We use a novel approach, combining elemental distribution models with herbivore home range size estimates to test our hypothesis that hare home range size will be smaller in areas with access to high, homogeneous resource quality compared to areas with access to low, heterogeneous resource quality during summer months. Our results support our prediction for lowland blueberry, but not for red maple. Herbivore home range size decreased with increasing blueberry foliage quality, but also with decreasing spatial heterogeneity in blueberry foliage quality, i.e. N or P content. Herbivores in the boreal forest face strong nutritional constraints due to the paucity of N and P. Access to areas of high, homogeneous resource quality is paramount to meeting their dietary requirements with low effort. In turn, this may influence community (e.g., trophic interactions) and ecosystem (e.g., nutrient cycling) processes. Paradoxically, our study shows that taking a reductionist approach of viewing resources through a biochemical lens can lead to holistic insights of consumer spatial ecology.

ecology↗

Modelling the spatial-temporal distributions and associated determining factors of a keystone pelagic fish

Mobile pelagic species habitat is structured around dynamic oceanographic and ecological processes which operate and interact horizontally and vertically throughout the water column and change over time. However, pelagic species movements and distributions are often poorly understood. We use the Maxent species distribution model to assess how changes in the relative importance of modelled oceanographic (e.g., temperature) and climatic variables (e.g., the North Atlantic Oscillation) over 17-years affect the monthly average horizontal and vertical distribution of a keystone pelagic forage species, Atlantic Canadian capelin (Mallotus villosus). We show the range and distribution of capelin occurrence probabilities vary across horizontal and vertical axes over time, with binary presence/absence predictions indicating capelin occupy between 0.72% (April) and 3.45% (November) of the total modelled space. Furthermore, our analysis reveals that the importance of modelled oceanographic variables, such as temperature, vary between months (44% permutation importance in August to 2% in May). By capturing the spatial dynamics of capelin over horizontal, vertical, and temporal axes, our analysis builds on work that improves our understanding and predictive modelling ability of pelagic species distributions under current and future conditions for pro-active ecosystem-based management.

ecology↗

RH mapping by sequencing: chromosome-scale assembly of the duck genome

Like many other species, the duck genome has been sequenced thanks to the technological breakthrough provided by the emergence of Next Generation Sequencing (NGS). The resulting de novo assemblies are however made of thousands of scattered scaffolds. To achieve chromosome-scale contiguity, long-range intermediate genome maps remain indispensable. Radiation Hybrid (RH) maps have been used to assist the generation of chromosome-scale genome assemblies by taking advantage of the high density SNP chips that provide a large number of markers that can be efficiently genotyped on the panel. In the absence of such a resource in duck, we sequenced 100 hybrid clones of a duck RH panel enabling direct genotyping of the assembly scaffolds on the panel. The rationale is to use scaffolds as markers and to genotype the scaffolds by sequencing the clones: the presence/absence of a scaffold in a particular sequenced hybrid is attested by the presence/absence of reads mapping specifically to this scaffold. The detection of scaffolds exhibiting a chromosomal breakage resulting from the irradiation process revealed itself to be a critical issue of this genotyping by sequencing process. This process resulted in the construction of RH vectors for 2,027 scaffolds, representing a total of about 1 Gb of sequences (95% of the current Duck genome assembly). The subsequent linkage analysis enabled the construction of RH maps and therefore to organize, i.e. order and orient, the scaffolds into pseudomolecules associated to the corresponding duck chromosomes. We describe here the whole mapping process, from sequence-based genotyping to the construction of comparative maps, as well as few examples of intra-chromosomal rearrangements that have been identified by the comparison with the chicken, turkey and zebra finch genomes and subsequently confirmed by FISH. We describe a method to order and orient sequence scaffolds into super-scaffolds spanning entire chromosomes. The method, which requires a pre-existing RH panel and sequence scaffolds from an NGS assembly, relies on a shallow sequencing of the RH clones. This approach was applied to the duck genome and produced chromosome-scale scaffolds for 29 out of the 41 duck chromosomes.

genomics↗

On the prevalence of uninformative parameters in statistical models applying model selection in applied ecology

Research in applied ecology provides scientific evidence to guide conservation policy and management. Applied ecology is becoming increasingly quantitative and model selection via information criteria has become a common statistical modeling approach. Unfortunately, parameters that contain little to no useful information are commonly presented and interpreted as important in applied ecology. I review the concept of an uninformative parameter in model selection using information criteria and perform a literature review to measure the prevalence of uninformative parameters in model selection studies applying Akaikes Information Criterion (AIC) in 2014 in four of the top journals in applied ecology (Biological Conservation, Conservation Biology, Ecological Applications, Journal of Applied Ecology). Twenty-one percent of studies I reviewed applied AIC metrics. Many (31.5 %) of the studies applying AIC metrics in the four applied ecology journals I reviewed had or were very likely to have uninformative parameters in a model set. In addition, more than 40 % of studies reviewed had insufficient information to assess the presence or absence of uninformative parameters in a model set. Given the prevalence of studies likely to have uninformative parameters or with insufficient information to assess parameter status (71.5 %), I surmise that much of the policy recommendations based on applied ecology research may not be supported by the data analysis. I provide warning signals and a decision tree to help reduce the prevalence of uninformative parameters in studies applying model selection with information criteria. The four warning signals and decision tree should assist authors, reviewers, and editors to screen for uninformative parameters in studies applying model selection with information criteria. In the end, careful thinking at every step of the scientific process and greater reporting standards are required to detect uninformative parameters in studies adopting an information criteria approach.

ecology↗