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

Molecular Ecology, Год журнала: 2022, Номер 32(3), С. 542 - 559

Опубликована: Янв. 9, 2022

Inferring the genomic basis of local adaptation is a long-standing goal evolutionary biology. Beyond its fundamental implications, such knowledge can guide conservation decisions for populations and management concern. Here, we investigated in Coho salmon (Oncorhynchus kisutch) across entire North American range. We hypothesized that extensive spatial variation environmental conditions species' homing behaviour may promote establishment adaptation. genotyped 7829 individuals representing 217 sampling locations at more than 100,000 high-quality RADseq loci to investigate how recombination might affect detection putatively under selection took advantage precise description demographic history species from our previous work draw accurate population inferences about The results indicated genetic differentiation scans genetic-environment association analyses were both significantly affected by rate as low regions displayed an increased number outliers. By taking these confounding factors into consideration, revealed migration distance was primary selective factor driving partial parallel divergence among distant populations. Moreover, identified several candidate single nucleotide polymorphisms associated with long-distance altitude including gene known be involved other species. implications findings are discussed along applications.

Язык: Английский

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Single Nucleotide Polymorphism Markers with Applications in Conservation and Exploitation of Aquatic Natural Populations

Animals, Год журнала: 2023, Номер 13(6), С. 1089 - 1089

Опубликована: Март 18, 2023

An increasing number of aquatic species have been studied for genetic polymorphism, which extends the knowledge on their natural populations. One type high-resolution molecular marker suitable studying diversity large numbers individuals is single nucleotide polymorphism (SNP). This review an attempt to show range applications SNPs in studies populations animals. In recent years, used analysis wild and enhanced fish invertebrate habitats, exploited migratory oceans, anadromous freshwater demersal species. identification hybrids environments, study consequences restocking conservation purposes negative effects accidentally escaping from culture. are very useful identifying genomic regions correlated with phenotypic variants relevant wildlife protection, management aquaculture. Experimental size-selective catches created tanks caused evolutionary changes life cycles fishes. The research results discussed clarify whether conditions can undergo due selective harvesting targeting fastest-growing

Язык: Английский

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An updated review of the post-glacial history, ecology, and diversity of Arctic char (Salvelinus alpinus) and Dolly Varden (S. malma)

Environmental Biology of Fishes, Год журнала: 2024, Номер 107(1), С. 121 - 154

Опубликована: Янв. 1, 2024

Язык: Английский

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Genomic vulnerability of a freshwater salmonid under climate change

Evolutionary Applications, Год журнала: 2023, Номер 17(2)

Опубликована: Окт. 27, 2023

Abstract Understanding the adaptive potential of populations and species is pivotal for minimizing loss biodiversity in this era rapid climate change. Adaptive has been estimated various ways, including based on levels standing genetic variation, presence potentially beneficial alleles, and/or severity environmental Kokanee salmon, non‐migratory ecotype sockeye salmon ( Oncorhynchus nerka ), culturally economically important already impacted by effects To assess its vulnerability moving forward, we integrated analyses genotype‐environment associations, modeling sequence structural genomic variation from 224 whole genomes sampled 22 lakes British Columbia Yukon (Canada). We found that variables extreme temperatures, particularly warmer had most pervasive signature selection genome were strongest predictors putatively both structural. Genomic offset estimates, a measure vulnerability, significantly correlated with higher increases warm further highlighting risk summer heat waves are predicted to increase frequency future. Levels an metric population viability resilience, not offset. Nonetheless, our combined approach highlights importance integrating different sources information data formulate more comprehensive accurate predictions future

Язык: Английский

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Characterization of gill bacterial microbiota in wild Arctic char ( Salvelinus alpinus ) across lakes, rivers, and bays in the Canadian Arctic ecosystems

Microbiology Spectrum, Год журнала: 2024, Номер 12(3)

Опубликована: Фев. 8, 2024

ABSTRACT Teleost gill mucus has a highly diverse microbiota, which plays an essential role in the host’s fitness and is greatly influenced by environment. Arctic char ( Salvelinus alpinus ), salmonid well adapted to northern conditions, faces multiple stressors Arctic, including water chemistry modifications, that could negatively impact microbiota dynamics related health. In context of increasing environmental disturbances, we aimed characterize taxonomic distribution transcriptionally active taxa within bacterial Canadian order identify composition correlates with factors. For this purpose, total 140 adult anadromous individuals were collected from rivers, lakes, bays belonging five Inuit communities located four distinct hydrologic basins (Nunavut Nunavik) during spring (May) autumn (August). Various factors collected, latitudes, air temperatures, oxygen concentration, pH, dissolved organic carbon (DOC), salinity, chlorophyll-a concentration. The was quantified 16S rRNA gene transcripts sequencing. results showed differential activity between different geographical locations, explained latitude, and, lesser extent, temperature. Network analysis allowed detection potential dysbiosis signature (i.e., imbalance) fish Duquet Lake Hudson Strait system Five Mile Inlet connected Bay, both showing lowest alpha diversity connectivity taxa. IMPORTANCE This paper aims decipher complex relationship ) its symbiotic microbial consortium gills. widespread main protein polyunsaturated fatty acids source for people. influence parameters on wild populations remains poorly understood. However, assessing char’s community look pathogens or threaten populations. Here, concluded mainly latitude temperature, latter being correlated addition, detected potentially associated poor health status recorded these disturbed environments. With those results, hypothesized rapid climate change anthropic activities might profoundly disturb affecting their survival.

Язык: Английский

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Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation

Evolutionary Applications, Год журнала: 2021, Номер 14(7), С. 1880 - 1897

Опубликована: Май 8, 2021

Abstract Distinguishing neutral and adaptive genetic variation is one of the main challenges in investigating processes shaping population structure wild, landscape genomics can help identify signatures adaptation to contrasting environments. Arctic Char ( Salvelinus alpinus ) an anadromous salmonid most harvested fish species by Inuit people, including Nunavik (Québec, Canada), recently deglaciated regions world. Unlike many other salmonids, occupy coastal habitats near their natal rivers during short marine phase restricted summer ice‐free period. Our objective was document putatively genomic populations from bordering inform local fisheries management. We used genotyping sequencing (GBS) genotype 18,112 filtered single nucleotide polymorphisms (SNP) 650 individuals 23 sampling locations along >2000 km coastline. results reveal a hierarchical structure, whereby neighboring hydrographic systems harbor distinct grouped major oceanographic basins: Hudson Bay, Strait, Ungava Labrador Sea. found diversity differentiation be consistent both with expected postglacial recolonization history patterns isolation‐by‐distance reflecting contemporary gene flow. Results three gene–environment association methods supported hypothesis freshwater environments (strongest associations sea surface air temperatures salinity). support management strategy at regional scale, implications for hatchery projects climate change are discussed.

Язык: Английский

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Assessment of inter-regional dietary differences in anadromous Arctic char (Salvelinus alpinus) in Nunavik, Canada, and links with flesh quality indicators

Arctic Science, Год журнала: 2024, Номер 10(2), С. 372 - 385

Опубликована: Янв. 12, 2024

Arctic char ( Salvelinus alpinus) is a salmonid fish that the second-most consumed country food species by Nunavimmiut. Its nutritional quality determined omega-3 fatty acids and carotenoid pigments. Those molecules cannot be synthetized must acquired through diet. We sampled in 10 rivers from three marine coastal regions of Nunavik (Hudson Bay, Hudson Strait, Ungava Bay), described diet (stable isotopes δ 13 C 15 N) flesh (fatty carotenoids, measured chromatography) assessed associations between both (including also bio-impedance colorimetry). Our results suggested inter-regional differences Nunavik, where values indicated Bay was more pelagic, while it coastal. observed astaxanthin, pigment responsible for redness color, concentrations were highest char. In all sampling locations, an exceptional source confirming its importance as high-quality wild food. models suggest canthaxanthin, water content influence redness. data highlight could taken consideration to better predict impact climate change on and, ultimately, Inuit health.

Язык: Английский

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Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication

Genome Biology and Evolution, Год журнала: 2023, Номер 15(12)

Опубликована: Дек. 1, 2023

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

Язык: Английский

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Population genomics, life‐history tactics, and mixed‐stock subsistence fisheries in the northernmost American Atlantic salmon populations

Evolutionary Applications, Год журнала: 2024, Номер 17(2)

Опубликована: Фев. 1, 2024

Abstract While Atlantic salmon ( Salmo salar ) of the northernmost American populations is alimentary, economically, and culturally important for Ungava Inuit communities (Nunavik, Canada) might play a key role in persistence species global warming context, many mysteries remain about those remote atypical populations. Thus, our first aim was to document genomic structure Nunavik The second objective determine whether only migrating estuary without reaching sea, apparently unique populations, represent distinct from typical anadromous salmons subsequently explore genetic basis migratory life‐history tactics species. Finally, third goal quantify contribution each genetically population tactic mixed‐stock subsistence fishery Koksoak R. estuary. We used Genotyping‐by‐Sequencing genotype 14,061 single nucleotide polymorphisms genome 248 individuals 8 source 280 fishery. Life‐history were identified by visual assessment scales. Results show hierarchical mainly influenced isolation‐by‐distance with 7 out studied rivers. no obvious detected between marine estuarine within population, we have regions putatively associated migration tactics. all captured originated drainage mostly 2 tributaries, but inter‐annual variation these tributaries found. Our results indicate, however, that both contribute substantially fisheries there this contribution. These findings provide crucial information conservation rapidly changing ecosystem, as well management improve food security communities.

Язык: Английский

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From threats to solutions: A literature review of climate adaptation in anadromous salmon and trout

Ecosphere, Год журнала: 2025, Номер 16(1)

Опубликована: Янв. 1, 2025

Abstract Understanding the evolutionary responses of anadromous salmon and trout to climate change is critical for effective conservation planning. In this study, we conducted a comprehensive review literature published from 2010 2020 synthesize current knowledge on impacts these fish populations. Specifically, focused 199 papers that explored processes in response changing environmental conditions. Our analysis revealed several key themes, including interwoven influences human activities genetic variation, phenotypic traits, population dynamics. We found geographic patterns diversity are closely linked climatic gradients, highlighting importance strategies variation existing adaptive capacity. Additionally, temporal trends phenology, maturation age, fecundity indicate ongoing plastic change. Importantly, were identified as significant drivers maladaptation emphasize need targeted monitoring specific mitigate loss enhance study underscores identifying protecting areas high rare genes, particularly regions projected experience rapid shifts. conclusion, our findings identify strengths gaps research investigating role dynamics face By capitalizing new tools sequencing, genomic analysis, automated field data collection, can establish baselines tracking Better integration into projections future will lead more ensure long‐term resilience iconic species other wildlife.

Язык: Английский

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