Biology subjects

Moore, J.-S.

Publications and source records attributed to Moore, J.-S..

11 recordsLinked to original sources

bioRxiv2026

Metabolic plasticity facilitates a high-latitude life of feast and famine in Arctic char

O_LIHigh northern latitudes experience extreme winters and pronounced environmental variation. Arctic animals possess remarkable and diverse physiological mechanisms to thrive under this variation, but such mechanisms are poorly studied, particularly in the aquatic realm. C_LIO_LIWe combined Arctic field and laboratory experiments to reveal how one of Earths most northerly distributed fish species, the Arctic char, seasonally adjusts its metabolism to conserve energy over winter while not feeding and to capitalize on more optimal growth conditions in summer. C_LIO_LILaboratory reared Arctic char were fed or food deprived at common summer (8{degrees}C) and winter (2{degrees}C) temperatures for >120 days. Oxygen consumption rates were assessed as a proxy for rate of aerobic metabolic energy expenditure. Cooling from 8 to 2{degrees}C reduced resting aerobic energy expenditure by 35%, while food deprivation independently drove a reduction of 46-50%. Combined, resting energy expenditure was 197% higher under simulated summer (fed at 8{degrees}C) than winter conditions (food deprived at 2{degrees}C). C_LIO_LIReductions in resting energy expenditure with food deprivation were driven, at least in part, by marked tissue-specific decreases in organ size and protein synthesis rates in tissues with central roles in growth and digestion. C_LIO_LIWild adult anadromous Arctic char exhibited, seasonal plasticity consistent with our laboratory experiments. Resting energy expenditure at 10{degrees}C was 27% higher after summer feeding than in the spring after winter fasting, while liver and digestive organ masses were also markedly reduced overwinter. C_LIO_LIIn contrast, peak aerobic metabolic performance and relative heart mass were largely maintained during food deprivation indicating a protection of systems that support aerobic metabolic capacity. C_LIO_LIDespite recruiting strategies for substantial energy savings, wild and laboratory reared Arctic char still largely depleted their on-board fat stores with food-deprivation, underscoring that these strategies are essential when food is limited. Given that the Arctic is among the most rapidly changing regions on Earth, temperatures, productivity, and the timing of key seasonal event are all shifting with implications for the efficacy of such strategies for high-latitude animals. C_LI

zoology↗

bioRxiv2025

Conservation units for anadromous Arctic Char (Salvelinus alpinus) in the Canadian Arctic informed by genetic structure, population connectivity and adaptive genomic variation

Intraspecific genetic diversity is a crucial aspect of biodiversity conservation as it preserves evolutionary potential and enhances resilience to environmental change. Genomic-informed delineation of Conservation Units (CUs) offers ways of subdividing species into groups based on historical isolation and adaptive differentiation, to develop biologically relevant conservation and management policies. CUs have been defined in many species of harvested anadromous salmonids, but broad scale data remains lacking in the Canadian Arctic, where anadromous Arctic Char (Salvelinus alpinus) dominates catches in Indigenous-led subsistence and commercial fisheries. In this study, we use low-coverage whole-genome data from 30 Canadian populations of Arctic Char to define CUs based on population structure and connectivity, as well as adaptive genetic variation. We highlight two main genetic groups, each of which comprises three subgroups, or candidate CUs: the North (above the 67th parallel), including the North Baffin Island, Kitikmeot, and Inuvialuit Settlement Region CUs; and the South (below the 67th parallel), including the South Baffin Island, Ungava Bay, and Hudson Bay CUs. This delimitation is supported by areas of low effective migration between candidate CUs, as well as isolation-by-environment, which suggests adaptive differentiation. Finally, we discuss opportunities and caveats relating to linkage when identifying adaptive genetic variation from whole genome sequencing data through genome scans and Gene-Environment Associations.

evolutionary biology↗

bioRxiv2024

Leveraging whole genomes, mitochondrial DNA, and haploblocks to decipher complex demographic histories: an example from a broadly admixed arctic fish

The study of phylogeography has transitioned from mitochondrial haplotypes to genome-wide analyses, blurring the line between this field and population genomics. Whole-genome sequencing offers the opportunity to join use both and provides the density of markers necessary to investigate genetic linkage and recombination along the genome. This facilitates the unraveling of complex demographic histories of admixture between divergent lineages, as is often the case in species evolving in recently deglaciated habitats. In this study, we sequenced 1120 Arctic Char genomes from 33 populations across Canada and Western Greenland to characterize patterns of genetic variation and diversity, and how they are shaped by hybridization between the Arctic and Atlantic glacial lineages. Several lines of evidence supported mito-nuclear discordance in lineage distribution, with all Canadian populations under the 66th parallel being characterized by introgression from the Atlantic lineage, leading to higher nuclear genetic diversity. By scanning the genome using local PCAs, we identified putative low-recombining haploblocks as local ancestry tracts from either lineage and described the impacts of recombination on the introgression landscape in admixed populations. Finally, we inferred conflicting origins of recolonization using whole genomes vs. ancestry tracts for the Arctic lineage, suggesting that haplotypes sheltered from introgression by low recombination could enlighten complex post-glacial histories. Overall, we argue that Whole-Genome Sequencing, even at low depths of coverage, provides a versatile approach to the study of phylogeographic dynamics.

evolutionary biology↗

bioRxiv2024

Estimating survival of an anadromous salmonid using Bayesian hierarchical models applied to acoustic telemetry, biological, and environmental data

Hierarchical modelling is frequently used to model ecological processes because of its ability to handle complex ecological phenomena by decomposing them into naturally explainable sub-models. Hierarchical Bayesian approaches have gained widespread use in health, social, and environmental sciences, including in the estimation of demo-graphic parameters such as survival. In this study, we combine Bayesian hierarchical models with acoustic telemetry data to estimate survival probabilities for high-latitude populations of an anadromous salmonid, the Arctic char (Salvelinus alpinus), while in-corporating environmental and biological covariates to assess their impact on survival. The model we present here can also account for temporally varying detection probabilities due to changes to the acoustic receiver array design and seasonal variation in the detection probabilities related to environmental conditions (e.g., ice vs. no ice). As previously documented in this species, survival was high (> 0.87) and we found that the covariates pertaining to sea ice coverage and Fultons condition factor impacted the survival probabilities. Contrary to our expectations, high-condition fish had lower survival rates. Survival was also considerably lower during the summer (open-water) compared to winter (ice-covered) seasons. While the biological explanations and implications of these findings require further exploration, they nonetheless demonstrate the utility of this approach. Specifically, we present a hierarchical Bayesian model that can consider environmental and biological covariates while accounting for varying detection probabilities, a major concern of acoustic telemetry studies. The model can be easily adapted for other taxa with similar life histories where mark recapture data are available and can be extended to include additional environmental (e.g., salinity) and biological parameters (e.g., sex).

ecology↗

bioRxiv2024

Home range spillover in habitats with impassable boundaries: Causes, biases, and corrections using autocorrelated kernel density estimation

O_LIAn animals home range plays a fundamental role in determining its resource use and overlap with conspecifics, competitors and predators, and is therefore a common focus of movement ecology studies. Autocorrelated kernel density estimation addresses many of the shortcomings of traditional home range estimators when animal tracking data is autocorrelated, but other challenges in home range estimation remain. C_LIO_LIOne such issue is known as spillover bias, in which home range estimates do not respect impassable movement boundaries (e.g., shorelines, fences), and occurs in all forms of kernel density estimation. While several approaches to addressing spillover bias are used when estimating home ranges, these approaches introduce bias throughout the remaining home range area, depending on the amount of spillover removed, or are otherwise inaccessible to most ecologists. Here, we introduce local corrections to home range kernels to mitigate spillover bias in (autocorrelated) kernel density estimation in the continuous time movement model (ctmm) package, and demonstrate their performance using simulations with known home range extents and distributions, and a real world case study. C_LIO_LISimulation results showed that local corrections minimised bias in bounded home range area estimates, and resulted in more accurate distributions when compared to commonly used post-hoc corrections, particularly at small-intermediate sample sizes. C_LIO_LIComparison of the impacts of local vs post-hoc corrections to bounded home ranges estimated from lake trout (Salvelinus namaycush) demonstrated that local corrections constrained bias within the remaining home range area, resulting in proportionally smaller home range areas compared to when post-hoc corrections are used. C_LI

ecology↗

bioRxiv2023

Widespread deviant patterns of heterozygosity in whole-genome sequencing due to autopolyploidy, repeated elements and duplication

Most population genomic tools rely on accurate SNP calling and filtering to meet their underlying assumptions. However, genomic complexity, due to 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 data from four species: Arctic Char (Salvelinus alpinus), Lake Whitefish (Coregonus clupeaformis), Atlantic Salmon (Salmo salar), and the American Eel (Anguilla rostrata), with low (2X) to intermediate (6X) coverage. The analyses revealed that deviant SNPs accounted for up to 62% of all SNPs in salmonid datasets and approximately 10% 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 attributed to transposons and tandem repeats. Including these deviant SNPs in genomic analyses led to highly distorted site frequency spectra, apparent homogenization of populations and underestimating pairwise FST values. Considering the widespread occurrence of deviant SNPs arising from a variety of source, 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. Significance: Genomes can be very repetitive and hard to assemble into a reference, which can lead to biases when genotyping genetic markers in complex genomic regions. Here, we draw attention to this issue in various whole-genome datasets and validate a method to identify problematic SNPs at low coverage. We also explore processes creating such SNPs and their consequences on common population genomics analyses.

genomics↗

bioRxiv2021

Long distance migration is a major factor driving local adaptation at continental scale in Coho Salmon

Inferring the genomic basis of local adaptation is a long-standing goal of evolutionary biology. Beyond its fundamental evolutionary implications, such knowledge can guide conservation decisions for populations of conservation and management concern. Here, we investigated the genomic basis of local adaptation in the Coho salmon (Oncorhynchus kisutch) across its entire North American range. We hypothesized that extensive spatial variation in environmental conditions and the species homing behavior may promote the establishment of local adaptation. We genotyped 7,829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect the detection of loci putatively under selection and took advantage of the precise description of the demographic history of the species from our previous work to draw accurate population genomic inferences about local adaptation. Results indicated that genetic differentiation scans and genetic-environment association analyses were both significantly affected by variation in recombination rate as low recombination regions displayed an increased number of outliers. By taking these confounding factors into consideration, we revealed that migration distance was the primary selective factor driving local adaptation and partial parallel divergence among distant populations. Moreover, we identified several candidates SNP associated with long distance migration and altitude including a gene known to be involved in adaptation to altitude in other species. The evolutionary implications of our findings are discussed along with conservation applications.

evolutionary biology↗

bioRxiv2020

Population structure and genomic evidence for local adaptation to freshwater and marine environments in anadromous Arctic Char (Salvelinus alpinus) throughout Nunavik, Canada

Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure in the wild, and landscape genomics can help identify signatures of adaptation to contrasting environments. Arctic Char (Salvelinus alpinus) is an anadromous salmonid and the most harvested fish species by Inuit people, particularly so in Nunavik (Canada), one of the most recently deglaciated region in the world. Unlike most other anadromous salmonids, Arctic Char occupy coastal habitats near their overwintering rivers during their marine phase. The main objective of this study was to document the putative neutral and adaptive genomic variation of anadromous Arctic Char populations in Nunavik (Quebec, Canada) and bordering regions. A second objective was to interpret our results in the context of fisheries management in Nunavik. We used genotyping-by-sequencing (GBS) to genotype 18,112 filtered single nucleotide polymorphisms (SNPs) for 650 individuals sampled in 23 locations (average sample size per location = 28) along >2,000 km of coastline. Our results reveal a hierarchical genetic structure, whereby neighboring hydrographic systems harbour distinct populations grouping within major oceanographic basins, namely the Hudson Bay, Hudson Strait, Ungava Bay and Labrador Sea. We found genetic diversity and differentiation to be consistent with both the expected post-glacial recolonization history and patterns of isolation-by-distance reflecting contemporary gene flow. Furthermore, using three gene-environment association (GEA) methods we found genomic evidence for local adaptation to freshwater and marine environmental components, especially in relation to sea-surface and air temperatures during summer, as well as salinity. Our results support fisheries management at a regional level, and other implications on hatchery projects and adaptation to climate change are discussed.

genomics↗

bioRxiv2019

Demographic history, linked selection, and recombination shape the genomic landscape of a broadly distributed Pacific salmon.

A thorough reconstruction of historical processes is essential for a comprehensive understanding the mechanisms shaping patterns of genetic diversity. Indeed, past and current conditions influencing effective population size have important evolutionary implications for the efficacy of selection, increased accumulation of deleterious mutations, and loss of adaptive potential. Here, we gather extensive genome-wide data that represent the extant diversity of the Coho salmon (Oncorhynchus kisutch) to address two objectives. We demonstrate that a single glacial refugium is the source of most of the present-day genetic diversity, with detectable inputs from a putative secondary micro-refugium. We found statistical support for a scenario whereby ancestral populations located south of the ice sheets expanded in postglacial time, swamping out most of the diversity from other putative micro-refugia. Demographic inferences revealed that genetic diversity was also affected by linked selection in large parts of the genome. Moreover, we demonstrate that the recent demographic history of this species generated regional differences in the load of deleterious mutations among populations, a finding that mirrors recent results from human populations and provides increased support for models of expansion load. We propose that insights from these historical inferences should be better integrated in conservation planning of wild organisms, which currently focuses largely on neutral genetic diversity and local adaptation, with the role of potentially maladaptive variation being generally ignored.

evolutionary biology↗

bioRxiv2017

Migration Harshness Drives Habitat Choice And Local Adaptation In Anadromous Arctic Char: Evidence From Integrating Population Genomics And Acoustic Telemetry

Migration is a ubiquitous life history trait with profound evolutionary and ecological consequences. Recent developments in telemetry and genomics, when combined, can bring significant insights on the migratory ecology of non-model organisms in the wild. Here, we used this integrative approach to document dispersal, gene flow and potential for local adaptation in anadromous Arctic Char from six rivers in the Canadian Arctic. Acoustic telemetry data from 124 tracked individuals indicated asymmetric dispersal, with a large proportion of fish (72%) tagged in three different rivers migrating up the same short river in the fall. Population genomics data from 6,136 SNP markers revealed weak, albeit significant, population differentiation (average pairwise FST = 0.011) and asymmetric dispersal was also revealed by population assignments. Approximate Bayesian Computation simulations suggested the presence of asymmetric gene flow, although in the opposite direction to that observed from the telemetry data, suggesting that dispersal does not necessarily lead to gene flow. These observations suggested that Arctic Char home to their natal river to spawn, but may overwinter in rivers with the shortest migratory route to minimize the costs of migration in non-breeding years. Genome scans and genetic-environment associations identified 90 outlier markers putatively under selection, 23 of which were in or near a gene. Of these, at least four were involved in muscle and cardiac function, consistent with the hypothesis that migratory harshness could drive local adaptation. Our study illustrates the power of integrating genomics and telemetry to study migrations in non-model organisms in logistically challenging environments such as the Arctic.

evolutionary biology↗

bioRxiv2016

Sex matters in Massive Parallel Sequencing: Evidence for biases in genetic parameter estimation and investigation of sex determination systems

Using massively parallel sequencing data from two species with different life history traits -- American lobster (Homarus americanus) and Arctic Char (Salvelinus alpinus) -- we highlighted how an unbalanced sex ratio in the samples combined with a few sex-linked markers may lead to false interpretations of population structure and thus to potentially erroneous management recommendations. Multivariate analyses revealed two genetic clusters that separated males and females instead of showing the expected pattern of genetic differentiation among ecologically divergent (inshore vs. offshore in lobster) or geographically distant (east vs. west in Arctic Char) sampling locations. We created several subsamples artificially varying the sex ratio in the inshore/offshore and east/west groups, and then demonstrated that significant genetic differentiation could be observed despite panmixia for lobster, and that Fst values were overestimated for Arctic Char. This pattern was due to 12 and 94 sex-linked markers driving differentiation for lobster and Arctic Char, respectively. Removing sex-linked markers led to nonsignificant genetic structure (lobster) and a more accurate estimation of Fst (Arctic Char). We further characterized the putative functions of sex-linked markers. Given that only 9.6% of all marine/diadromous population genomic studies to date reported sex information, we urge researchers to collect and consider individual sex information. In summary, we argue that sex information is useful to (i) control sex ratio in sampling, (ii) overcome \"sex-ratio bias\" that can lead to spurious genetic differentiation signals and (iii) fill knowledge gaps regarding sex determining systems.

genomics↗