Supervised by:

Jean-Sébastien Moore (Regular member)

Research project description

Population genomics of arctic char (Salvelinus alpinus) in the Canadian Arctic

IntroductionThe use of genomic tools is now widespread in the delimitation of management units in fisheries, but these methods have so far seldom been applied in the Arctic. In addition to population structure, the study of adaptation processes can also inform species conservation by helping to predict their response to rapid climate change. Among the Inuit, the most heavily fished fish species is arctic char (Salvelinus alpinus), the most northerly freshwater fish in terms of its distribution, which is the result of rapid recolonization following the end of the last ice age 18,000 years ago. Despite its low genetic diversity and its young evolutionary age, this salmonid is known for its impressive morphological and ecological polymorphism, which shows an important adaptive capacity. ObjectivesMy research objectives will be (i) to reconstruct the recolonization history of arctic char in the Canadian Arctic using dense genomic data; (ii) to understand the possible impact of genome duplication and inversions on the adaptive potential of this species with low genetic diversity; and (iii) to relate my results to Inuit traditional ecological knowledge to assess their impacts on the management of the species. Study sitesThe samples were acquired from field campaigns conducted by various federal, provincial and regional partners in Nunavut and Nunavik. Further sampling will be completed to represent the main fish stocks harvested in the Canadian Arctic, with a target of about 20 communities (N = 30 per community) selected in conjunction with the regional advisory boards established under the FISHES (Fostering Indigenous Small-scale fisheries for Health, Economy and food Security) project. These boards, established in each of the study regions (Nunavik, Kitikmeot, Kivalliq and Qikiqtani), bring together Inuit wildlife managers and researchers and will help to keep Inuit research priorities at the center of the project. Material and methodsThe DNA contained in the flesh of the harvested adipose fins is extracted and then sequenced using whole genome sequencing (WGS). The presence of distinct genetic groups will be tested using principal component discriminant analysis (PCDA). We will predict whether mutations within coding genes are deleterious using the Provean software to test the hypothesis that post-glacial recolonization led to an increase in deleterious mutations in regions remote from the glacial refugium. To genotype the duplicate loci, we will particularly consider regions of the genome where residual tetrasomia is observed and we will apply a method of comparing sequenced allelic ratios [1]. To identify potential inversions, we will perform principal component analysis (PCA) on windows of 100 SNPs along the genome, using the R library "lostruct". References1. McKinney, G. J., Waples, R. K., Seeb, L. W., & Seeb, J. E. (2017). Paralogs are revealed by proportion of heterozygotes and deviations in read ratios in genotyping-by-sequencing data from natural populations. Molecular Ecology Resources, 17(4), 656–669.

Research Site Coordinates

Scientific Communications

Dallaire, X., Bouchard, R., Hénault, P., Ulmo-Diaz, G., Normandeau, E., Mérot, C., Bernatchez, L., Moore, J.-S., 2023. Widespread Deviant Patterns of Heterozygosity in Whole-Genome Sequencing Due to Autopolyploidy, Repeated Elements, and Duplication. Genome Biology and Evolution, 15(12). DOI: 10.1093/gbe/evad229.

Dallaire, X., Bouchard, R., Hénault, P., Ulmo Diaz, G., Normandeau, E., Mérot, C., Bernatchez, L., Moore, J.-S., 2023. Widespread deviant patterns of heterozygosity in whole-genome sequencing due to autopolyploidy, repeated elements, and duplication. Genome Biology and Evolution, 15(12). DOI: 10.1093/gbe/evad229.

Dallaire, X., Normandeau, É., Mainguy, J., Tremblay, J.-É., Bernatchez, L., Moore, J.-S., 2021. Genomic data support management of anadromous Arctic Char fisheries in Nunavik by highlighting neutral and putatively adaptive genetic variation. Evolutionary Applications, 14(7): 1880-1897. DOI: 10.1111/eva.13248.

Dubois, G., MacMillan, G.A., Dallaire, X., Gavin, M., Snowball, H., Kangiqsualujuuaq Youth Committee, , Lévesque, E., Amyot, M., Dedieu, J.-P., Herrmann, T.M., Franssen, J., Gérin-Lajoie, J., 2019. IMALIRIJIIT 2019. Results summary for community organizations and contributors.