Restoring and maintaining viable, productive, and diverse natural lake trout (Salvelinus nameschus) stocks requires detailed information on the genetic basis of reproductive success and survival across Great Lakes environments. Recently, the emergence of natural lake trout recruitment in most management units in Lake Huron has been detected. Strain type and hybridization between strains appeared to be important for emergence of wild stocks. The goals of this study are to: (1) develop genomics tools and data from lake trout, with emphasis on understanding the genetic basis of emergence of wild recruitment in Lake Huron; (2) quantify the relative importance of inter-strain hybridization and potential for domestication selection in hatchery strains, 3) quantify evidence of selection and, 4) quantify associations between lake physical features with genetic variation at adaptive and neutral loci genome-wide. Our primary hypothesis is that increased natural recruitment in Lake Huron is associated with alleles or combinations of alleles at adaptive loci that are associated with increased survival of individuals from one or more hatchery strains or emergence of novel adaptive hybrid genotypes or increased diversity (i.e., hybrid vigor) in wild relative to hatchery fish. To identify thousands of genetic markers (SNPs) genome-wide and in functional genes and gene regions, we will use RAD-seq (restriction site associated DNA sequencing). Understanding the genetic basis of differential strain success will lead to more effective Great Lakes restoration strategies.
IDENTIFICATION OF ADAPTIVE GENES ASSOCIATED WITH LAKE TROUT SURVIVAL AND RECRUITMENT IN DIFFERENT AND CHANGING GREAT LAKE ENVIRONMENTS