Genomic approaches to guide the conservation and management of wild Atlantic salmon

• Main Author: Miettinen, Antti
• Other Authors: Elmer, Kathryn, University of Helsinki, Faculty of Biological and Environmental Sciences, Doctoral Programme in Wildlife Biology, University of Helsinki, Institute of Biotechnology, Helsingin yliopisto, bio- ja ympäristötieteellinen tiedekunta, Luonnonvaraisten eliöiden tutkimuksen tohtoriohjelma, Helsingfors universitet, bio- och miljövetenskapliga fakulteten, Doktorandprogrammet i forskning om vilda organismer, Pritchard, Victoria, Primmer, Craig
• Format: Doctoral or Postdoctoral Thesis
• Language: English
• Published: Helsingin yliopisto 2023
• Subjects: ecology; evolutionary biology; conservation genetics; luonnonsuojelugenetiikka; Tornio; Kalix; Atlantic salmon; Salmo salar
• Online Access: http://hdl.handle.net/10138/567105

Genetic variation is the foundation of all biological diversity. Documenting and understanding this variation and factors affecting it is paramount in the era of global biodiversity loss. This can be achieved through genomic approaches that provide insights into adaptively important genetic diversity. Such information can be used for efficient planning of conservation and management actions for natural populations. In particular, the discovery of large-effect loci linked to important life-history diversity allows studying the impacts of different selection pressures on ecologically relevant genetic variation. In this thesis, I characterised fine-scale genetic structuring and putatively adaptive genetic variation in the largest Atlantic salmon (Salmo salar) stock in the Baltic Sea region, spawning in the Tornio and Kalix Rivers. Furthermore, I used an archive of tissue samples spanning 93 years (from 1928 to 2020) to examine how temporally varying fishing mortality may affect adaptively important genetic and life-history diversity in this actively exploited stock. First, using 18 microsatellite markers, we found that upstream and downstream reaches of the large Tornio-Kalix River complex were genetically differentiated. This genetic structure was linked to life-history variation: migration timing at different life stages varied between salmon from upper and lower parts of the river system. Second, we used a genome-wide SNP array of 60,252 markers to further explore the fine-scale population structure and to detect potentially adaptive genetic variation in the Tornio-Kalix. We identified further population genetic substructuring and strong candidates for genomic regions putatively under locally divergent selection. These regions contained genes previously associated with major life-history variation, such as migration and maturation timing of Atlantic salmon. Third, we developed a genotyping-by-sequencing SNP panel to monitor spatiotemporal variation in harvesting pressures imposed by commercial and recreational ...