Conservation genomics of Atlantic salmon: variation in gene expression between and within regions of the Bay of Fundy

Due to difficulties in identifying important within-species biodiversity for effective species management and conservation, the use of multiple complementary sources of information is required to identify and assess the designation of conservation units based on the degree of variation among populations within a species. In this study, we combined estimates of microsatellite and transcriptomic variation to assess the population structure and potential for adaptive variation of threatened Atlantic salmon, Salmo salar, among rivers in the Bay of Fundy. In general, population structure identified by genetic differentiation was consistent with the patterns of variation in gene expression, although there was not a strong correlation between neutral genetic variation and variation in gene expression. Both data sets provided clear indication of strong regional differentiation between rivers located within the inner Bay of Fundy relative to rivers located within the outer Bay of Fundy or the Southern Upland region, and there was also support for more refined population structure. Both data sets indicated that Atlantic salmon populations from the inner and outer Bay of Fundy reflect unique genetic lineages, with some evidence of population differentiation between regions of the inner Bay of Fundy, and between individual rivers within a region. Consistency of the microarray data across 2 years helped to validate the use of this technique as a useful tool in assessment of variation among wild populations for species conservation.