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

Dallaire, Xavier; Normandeau, Éric; Mainguy, Julien; Tremblay, Jean‐Éric; Bernatchez, Louis; Moore, Jean‐Sébastien

doi:10.1111/eva.13248

Cited by 19 publications

(20 citation statements)

References 164 publications

(227 reference statements)

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“…A smaller yet non-negligible role of precipitation (10% of all outliers) and temperature (7%) was also observed, while geology appears to play a relatively minor role, in contrast with other studies in salmonids (Quéméré et al, 2016). The role of precipitation and temperature as selective forces have also been demonstrated in other salmonids (Bourret et al, 2013;Dallaire et al, 2021;Eliason et al, 2011; as well as in other taxa, including in plants (Leroy et al, 2020) and Drosophila (Kapun, Fabian, Goudet, & Flatt, 2016). In salmonids, Michelleti et al (2018) suggested that extremely high precipitation is likely to impose an additional energetic cost during migration to spawning grounds.…”

Section: Multiple Environmental Variables Potentially Driving Local Adaptationmentioning

confidence: 64%

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

Rougemont

Xuereb

Dallaire

et al. 2021

Preprint

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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.

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Section: Multiple Environmental Variables Potentially Driving Local Adaptationmentioning

confidence: 64%

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

Rougemont

Xuereb

Dallaire

et al. 2021

Preprint

Self Cite

View full text Add to dashboard Cite

show abstract

“…A smaller yet non‐negligible role of precipitation (10% of all outliers) and temperature (7%) was also observed, while geology appears to play a relatively minor role, in contrast to other studies in salmonids (Quéméré et al, 2016). The roles of precipitation and temperature as selective forces have also been demonstrated in other salmonids (Bourret et al, 2013; Dallaire et al, 2021; Eliason et al, 2011; Micheletti et al, 2018) as well as in other taxa, including in plants (Leroy et al, 2020) and Drosophila (Kapun et al, 2016). In salmonids, Micheletti et al (2018) suggested that extremely high precipitation is likely to impose an additional energetic cost during migration to spawning grounds.…”

Section: Discussionmentioning

confidence: 85%

“…In recent years, landscape genomic methods (Narum & Hess, 2011) and genotype-environment association analyses (GEAs) (e.g., Bernatchez, 2016;Forester et al, 2018;Villemereuil et al, 2014) have been developed to identify signals of adaptation. Many riverscape genomic studies have investigated the effect of temperature, precipitation regime, geology, various distance variables (elevation, migration distance) or barriers to migration (e.g., dams) on local adaptation (e.g., Moore et al, 2017;Micheletti et al, 2018, Dallaire et al, 2021. A major challenge in thoroughly interpreting genome scans and GEAs is to accurately take into account the effect of demographic history.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2022

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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 behaviour may promote the establishment of local adaptation. We genotyped 7829 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. The 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 candidate single nucleotide polymorphisms associated with longdistance 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.

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“…Indeed, migration distance was the most important variable identified in the recent range‐wide analysis of local adaptation in Coho (Rougemont et al, 2022 ) and its importance as a selective factor has been reported for other salmonid species that undergo spawning migrations (Hecht et al, 2015 ; Micheletti et al, 2018 ; Moore et al, 2017 ). Both temperature and precipitation have been identified as important environmental predictors of genetic variation for Arctic char ( Salvelinus alpinus ) in marine and freshwater habitats (Dallaire et al, 2021 ) and are likely to amplify stressors associated with long‐distance migrations for anadromous salmonid species (Flanagan et al, 2018 ; Gilbert & Tierney, 2018 ; Micheletti et al, 2018 ). While their specific impact is uncertain, the detection of strong correlations between candidate loci and environmental variables suggests that local adaptation is occurring at the geographic scale studied, and thus conservation planning should target the protection of adaptive genetic diversity in this region (Flanagan et al, 2018 ).…”

Section: Discussionmentioning

confidence: 99%

“…It is now possible to sequence genome‐wide genetic variation across thousands of markers for most organisms, making it feasible to generate large‐scale genomic data sets for applied conservation and management (Allendorf et al, 2010 ; Waples & Lindley, 2018 ). These larger data sets increase precision and accuracy of inferences regarding population structure and connectivity (Benestan et al, 2015 ; Rougemont et al, 2019 ; Vendrami et al, 2017 ), and allow for screening of genome‐wide markers to identify variants potentially underlying adaptation based on associations with environmental conditions or phenotypes (Dallaire et al, 2021 ; Moore et al, 2017 ; Rellstab et al, 2015 ; Thompson et al, 2020 ; Waples et al, 2022 ). Different patterns of genetic structure may be detected by either neutral or putatively adaptive genetic markers, thereby warranting consideration of different approaches for spatial management (Hanson et al, 2020 ; Xuereb et al, 2021 ).…”

Section: Introductionmentioning

confidence: 99%

Re‐evaluating Coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data

Xuereb

Rougemont

Dallaire

et al. 2022

Evolutionary Applications

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Conservation units (CUs) are important tools for supporting the implementation of standardized management practices for exploited species. Following the adoption of the Wild Salmon Policy in Canada, CUs were defined for Pacific salmon based on characteristics related to ecotype, life history and genetic variation using microsatellite markers as indirect measures of local adaptation. Genomic data sets have the potential to improve the definition of CUs by reducing variance around estimates of population genetic parameters, thereby increasing the power to detect more subtle patterns of population genetic structure and by providing an opportunity to incorporate adaptive information more directly with the identification of variants putatively under selection. We used one of the largest genomic data sets recently published for a nonmodel species, comprising 5662 individual Coho salmon (Oncorhynchus kisutch) from 149 sampling locations and a total of 24,542 high‐quality SNPs obtained using genotyping‐by‐sequencing and mapped to the Coho salmon reference genome to (1) evaluate the current delineation of CUs for Coho in Canada and (2) compare patterns of population structure observed using neutral and outlier loci from genotype–environment association analyses to determine whether separate CUs that capture adaptive diversity are needed. Our results reflected CU boundaries on the whole, with the majority of sampling locations managed in the same CU clustering together within genetic groups. However, additional groups that are not currently represented by CUs were also uncovered. We observed considerable overlap in the genetic clusters identified using neutral or candidate loci, indicating a general congruence in patterns of genetic variation driven by local adaptation and gene flow in this species. Consequently, we suggest that the current CU boundaries for Coho salmon are largely well‐suited for meeting the Canadian Wild Salmon Policy's objective of defining biologically distinct groups, but we highlight specific areas where CU boundaries may be refined.

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

Abstract: This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

Cited by 19 publications

References 164 publications

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

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

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

Re‐evaluating Coho salmon (Oncorhynchus kisutch) conservation units in Canada using genomic data

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