RAD Sequencing of Chinook Salmon in Cook Inlet, Alaska: Discovering Markers Useful for Sustainable Management in a Genomic Context

Genetic tools are commonly applied to identify population structure among conservation units, estimate harvest compositions via genetic stock identification, and guide supportive breeding programs.  However, the application of genetic tools is often limited by the inability to provide information at geographic scales necessary to address conservation problems.  This mismatch of scale between genetic structure and conservation units often results from the inability of molecular markers to resolve weak genetic structure among populations of conservation interest.  Such is the case with populations of Chinook salmon from rivers in northwest Cook Inlet, Alaska.  A subsistence fishery conducted by the village of Tyonek harvests an unknown composition of Chinook salmon from genetically similar populations from multiple river systems.  We examined RAD markers in the context of a linkage-map to investigate genomic signals of adaptation among these populations and to identify adaptively important markers.  We also investigate whether adaptively important markers can be used for discrimination of weakly structured populations.