Research Document - 2013/076

Within- and among-population genetic variation in Eastern Cape Breton Atlantic Salmon and the prioritization of populations for conservation (Salmo salar L.)

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

Abstract

Genetic variation was surveyed at 15 microsatellite loci from 798 Atlantic salmon (Salmo salar L.) juveniles collected from seven rivers of the Eastern Cape Breton Designatable Unit, and several reference rivers from elsewhere in Atlantic Canada, including two from the west coast of Cape Breton. In general, levels of within-population genetic variation (allele richness and expected heterozygosity) were slightly lower in East Cape Breton salmon relative to salmon from the large reference populations analyzed, but differences were not significant. Within East Cape Breton, population genetic variation was slightly reduced in salmon from the far east coast of Cape Breton Island (Grand and Inhabitants rivers) compared to salmon from North Central Cape Breton (North Aspy, North (Victoria), Baddeck and Middle rivers), but again these differences were modest and not statistically significant. The Indian Brook sample collection (the only one obtained from the Bras d’Or Lake) exhibited the lowest level of allele richness of any originating from East Cape Breton, approaching levels observed in the sample collection obtained from the small (Stewiacke River) reference population included here. Although overall, reductions in levels of genetic variation were modest in East Cape Breton sample collections compared to reference collections, many also exhibited multiple pairs of loci that appear to be in linkage disequilibrium; a subset of these same sample collections also exhibited multiple loci that deviate from Hardy-Weinberg expectations. Taken together, these data indicate that several East Cape Breton river populations (North Aspy, Indian Brook, Grand and Inhabitants) may have experienced recent population bottlenecks.

Levels of genetic structuring (F_ST) between sample collections obtained from different East Cape Breton rivers varied from 0.0035-0.0363 (=0.0193), and all pairwise comparisons were significant following adjustments for multiple tests. Sample collections from North Central Cape Breton, with the exception of that obtained from the North (Victoria) River, exhibited very little genetic differentiation (F_ST=0.0035-0.0.0083, F_ST =0.0.00653), and cluster closely together in phylogenetic and factorial correspondence analyses.  These same three sample collections also exhibited very little differentiation from that obtained from the nearby Margaree River of the Gaspé-Southern Gulf of St. Lawrence Designatable Unit (F_ST =0.0086), and this similarity was again reflected in both phylogenetic and factorial correspondence analyses.  The Indian Brook sample collection was well differentiated from all others analyzed, and represents a second major grouping of East Cape Breton salmon surveyed here. Inhabitants and Grand sample collections were relatively differentiated from each other, and from all others from East Cape Breton in multiple analyses, though the former showed some similarity to the sample collection obtained from the Mabou River of the Gaspé-Southern Gulf of St. Lawrence Designatable Unit, and the latter similarity to the sample collection obtained from the St. Mary’s River of the Southern Upland Designatable Unit.  These two sample collections (Grand and Inhabitants) may represent two additional groupings of East Cape Breton Atlantic salmon. Possible indications of within-population structuring was observed in North (Victoria) sample collection, suggesting the presence of a fifth group of East Cape Breton Atlantic salmon, though additional analyses of further samples from this location are required to substantiate these latter findings. Patterns of within- and among-population genetic variation observed here may help inform efforts to prioritize Atlantic salmon populations from the East Cape Breton Designatable Unit for conservation.

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