Research Document - 2012/077

Within- and among-population genetic variation in the Southern Upland Designatable Unit of Maritime Atlantic Salmon (Salmo salar L.)

By P. O’Reilly, S. Rafferty, and J. Gibson

Abstract

Genetic variation was surveyed at 17 microsatellite loci from 1,039 individuals from 11 rivers of the Southern Upland of Nova Scotia, and several small and large reference populations from elsewhere in Atlantic Canada. Levels of within-population genetic variation were lower in sample collections obtained from rivers of the Southern Upland compared to those obtained from New Brunswick, but generally speaking, similar to or slightly greater than those from endangered populations of the inner Bay of Fundy. Within the Southern Upland, south and southwest sample collections, including Salmon River Digby, Tusket, and Round Hill, were more genetically depauperate, with the latter exhibiting nearly half the level of allele richness observed in the more variable northeast Southern Upland collections. Based on several indicators, contemporaneous sample collections from Medway, St. Mary’s East Branch, and Salmon River Guysborough are the most genetically variable of those analyzed here from this Designatable Unit.

Levels of genetic structuring among sample collections from different river populations (excluding within-river sample collections) of the Southern Upland varied from F_ST = 0.014 to 0.168, and averaged F_ST = 0.054. However, after removal of comparisons involving the highly divergent Round Hill sample collection, average F_ST estimates were 0.039, comparable to that reported in other studies over similar geographic ranges. Generally speaking, salmon from the 11 Southern Upland populations clustered into two major sub-groupings, reflecting Salmon Fishing Area (SFA) 21 (Salmon River Digby, Tusket, Medway, LaHave and Gold rivers) and SFA 20 (Musquodoboit, Moser, St. Mary’s, Salmon River Digby, and Country Harbour rivers). In the first sub-group, the clustering of sample collections in both phylogenetic and factorial correspondence analyses generally appears to mirror coastal distance, and likely reflects the effects of decreasing effective migration and gene flow with small increases in geographic distance. In the second sub-group, patterns are more complex, with sample collections from neighbouring rivers sometimes exhibiting high levels of differentiation. Sample collections from Musquodoboit and Moser rivers, in particular, are relatively divergent from other sample collections from this sub-group, including each other. Based on levels and patterns of within- and among-population genetic variation only, Medway and either St. Mary’s East Branch or Salmon River Guysborough may be important populations for prioritization of conservation efforts, followed by Moser and Musquodoboit river populations.

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