Research Document - 2014/069
Within- and among-population genetic variation in Outer Bay of Fundy Atlantic Salmon (Salmo salar L.), with special emphasis on the Saint John River system in the context of recent human impacts
By P. O'Reilly, R. Jones, and S. Rafferty
Abstract
Recent declines in the number of adult Atlantic Salmon (Salmo salar) returns to rivers of the Outer Bay of Fundy (OBoF), and low probability of population rescue by conspecifics from neighbouring Designatable Units (DUs), have precipitated the recent designation of OBoF Atlantic Salmon as endangered by the Committee on the Status of Endangered Wildlife in Canada. Although a number of factors are likely involved in historic and the more recent reductions in anadromous runs in the OBoF, there has been considerable focus on the direct role of hydroelectric facilities on the Saint John River (SJR) system, and possible associated effects of large-scale mitigation stocking that commenced in the early 1970s, including loss of within-population genetic variation and the homogenization of putative tributary stocks above Mactaquac Dam and the resulting loss of local adaptation.
This research document will report on results of analyses of two molecular genetic datasets (originally collected for other purposes), one involving eight small sample collections obtained from the OBoF analyzed at a limited set of seven microsatellite loci, and another involving only two OBoF locations, but analyzed at a larger set of 17 microsatellite loci. Both datasets include at least one tributary of the SJR above and one below Mactaquac Dam, and multiple reference populations from other DUs.
Overall, little evidence of marked reductions in genetic diversity in tributaries above Mactaquac Dam (potentially impacted by reductions in census and effective population sizes) relative to those below Mactaquac Dam was found. Indeed, levels of variation within OBoF sample collections overall are comparable to those obtained from large populations in the Gaspé-Southern Gulf of St. Lawrence DU and elsewhere, and considerably greater than many sample collections obtained from the Inner Bay of Fundy and the Southern Upland DUs.
Additionally, statistically significant differences in allele frequency distributions were observed between two sets of sample collections obtained from locations above Mactaquac Dam, suggesting that potentially heightened stocking-mediated gene flow may not have completely homogenized populations above Mactaquac Dam. On the other hand, levels of genetic structuring across tributaries above Mactaquac Dam were lower (approximately half) compared to sample collections obtained from tributaries below Mactaquac Dam. Although these results may reflect the effects of stocking-related increases in gene flow among upper SJR tributaries, similar patterns (greater differentiation among lower river tributaries compared to upper river tributaries) have also been observed in other large (and less impacted) river systems, indicating that it is also possible that patterns in the SJR system may reflect natural biological processes.
Results presented here, and similar findings on the impacts of stocking on homogenization and loss of local adaptation in other endangered populations of Atlantic Salmon (discussed in this document), indicate that although the potential risks of hatchery stocking on wild populations are substantial, findings of even large-scale, long-term stocking, involving local and/or non-local salmon, cannot alone be taken as evidence that complete homogenization of wild populations has taken place, that extensive loss of local adaptation and fitness has occurred, and that conservation measures aimed at protecting remaining populations are not warranted.
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