Use of Molecular Genetic Marker Data and Pedigree Information in Salmon Conservation Programs: A Case Study Involving Inner Bay of Fundy Atlantic Salmon

In 2000, the Department of Fisheries and Oceans, Canada, implemented a captive breeding and rearing program to prevent the imminent extirpation of endangered inner Bay of Fundy (iBoF) Atlantic Salmon.  Each year, crosses are carried out among salmon from within each of three iBoF river populations, and siblings from each cross both reared in captivity and released into native river habitat.  Offspring are then recovered from wild and captive environments, genotyped, and assigned to population-specific pedigrees.  This information is then used to select broodstock and to pair males and females for production of the next generation of salmon.  Molecular genetic data and pedigree information has been used to assess rates of loss of genetic variation in both the selection of founders (G0 salmon) and in the production of G1 offspring.  Pedigree information is also now being used to evaluate the effects of rearing environment and parental history on freshwater and marine survival and, in 2013/2014, on lifetime reproductive success in the wild. Initial analyses indicates that survival is not random, and that some females are capable of producing many more than one returning adult, a remarkable observation given the exceptionally low average rate of return of out-migrating iBoF smolt.