Identification of discrete and unique assemblages of individuals or populations is central to the management of exploited species. Advances in population genomics provide new opportunities for re-evaluating existing conservation units but comparisons among approaches remain rare. We compare the utility of RAD-seq, a single nucleotide polymorphism (SNP) array and a microsatellite panel to resolve spatial structuring under a scenario of possible trans-Atlantic secondary contact in a threatened Atlantic Salmon, Salmo salar, population in southern Newfoundland. Bayesian clustering indentified two large groups subdividing the existing conservation unit and multivariate analyses indicated significant similarity in spatial structuring among the three data sets. mtDNA alleles diagnostic for European ancestry displayed increased frequency in southeastern Newfoundland and were correlated with spatial structure in all marker types. Evidence consistent with introgression among these two groups was present in both SNP data sets but not the microsatellite data. Asymmetry in the degree of introgression was also apparent in SNP data sets with evidence of gene flow towards the east or European type. This work highlights the utility of RAD-seq based approaches for the resolution of complex spatial patterns, resolves a region of trans-Atlantic secondary contact in Atlantic Salmon in Newfoundland and demonstrates the utility of multiple marker comparisons in identifying dynamics of introgression.

Individual assignment and genetic mixture analysis are commonly utilized in contemporary wildlife and fisheries management. Although microsatellite loci provide unparalleled numbers of alleles per locus, their use in assignment applications is increasingly limited. However, next‐generation sequencing, in conjunction with novel bioinformatic tools, allows large numbers of microsatellite loci to be simultaneously genotyped, presenting new opportunities for individual assignment and genetic mixture analysis. Here, we scanned the published Atlantic salmon genome to identify 706 microsatellite loci, from which we developed a final panel of 101 microsatellites distributed across the genome (average 3.4 loci per chromosome). Using samples from 35 Atlantic salmon populations (n = 1,485 individuals) from coastal Labrador, Canada, a region characterized by low levels of differentiation in this species, this panel identified 844 alleles (average of 8.4 alleles per locus). Simulation‐based evaluations of assignment and mixture identification accuracy revealed unprecedented resolution, clearly identifying 26 rivers or groups of rivers spanning 500 km of coastline. This baseline was used to examine the stock composition of 696 individuals harvested in the Labrador Atlantic salmon fishery and revealed that coastal fisheries largely targeted regional groups (<300 km). This work suggests that the development and application of large sequenced microsatellite panels presents great potential for stock resolution in Atlantic salmon and more broadly in other exploited anadromous and marine species.

Variable hydropower production leads to hydropeaking, which causes discharge fluctuations that are potentially harmful to aquatic organisms. In this study, an experimental approach was used to investigate hydropeaking effects and associated hydraulic and habitat conditions on the home range and movement of juvenile Atlantic salmon Salmo salar. Prior studies examined the responses of Atlantic salmon and brook trout Salvelinus fontinalis to experimental hydropeaking during summer and autumn. The present study focused on Atlantic salmon, involved more rapid and extreme discharge manipulation, and included winter experiments to reflect influences of reduced temperature, ice conditions, and seasonal differences in behavior and habitat selection. Experiments were conducted over a range in discharge (0.5-5.0 m 3 /s) that resulted in dramatic habitat changes in the wide, shallow, boulder-strewn study reach. Experiments were repeated in summer and winter; however, the winter range in discharge was narrower due to constraints on water release. Fish response was monitored using manual telemetry in both seasons, and fixed telemetry was used to monitor fine-scale diel winter movements. Atlantic salmon had larger home ranges and were more mobile during all flow conditions and over diel cycles in summer than in winter, and there was anecdotal evidence of stranding in isolated pools in summer. Stream morphology, in addition to the magnitude of discharge change, was an important determinant of the propensity to move. In our study, there were considerable refugia from increased velocity and dewatering, which may have reduced the need to move. In winter, fish remained relatively sedentary in comparison with the summer foraging period, and this behavior may increase the likelihood for dewatering, stranding, and freezing. A secondary concern with hydropeaking regimes is the energetic cost to fish of moving to find suitable habitats, and during summer this cost could affect stored energy reserves, which could, in turn, affect overwinter survival.

Fisheries targeting mixtures of populations risk the overutilization of minor stock constituents unless harvests are monitored and managed. We evaluated stock composition and exploitation of Atlantic salmon (Salmo salar) in a subsistence fishery in coastal Labrador, Canada, using genetic mixture analysis and individual assignment with a microsatellite baseline (15 loci, 11 829 individuals, 12 regional groups) encompassing the species’ western Atlantic range. Bayesian and maximum likelihood mixture analyses of fishery samples over 6 years (2006–2011; 1772 individuals) indicate contributions of adjacent stocks of 96%–97%. Estimates of fishery-associated exploitation were highest for Labrador salmon (4.2%–10.6% per year) and generally <1% for other regions. Individual assignment of fishery samples indicated nonlocal contributions to the fishery (e.g., Quebec, Newfoundland) were rare and primarily in southern Labrador, consistent with migration pathways utilizing the Strait of Belle Isle. This work illustrates how genetic analysis of mixed stock Atlantic salmon fisheries in the Northwest Atlantic using this new baseline can disentangle exploitation and reveal complex migratory behaviours.

In insular Newfoundland, Canada, studies were conducted from 1999 to 2003 on the effects of 'simulated' hydropeaking power generation on juvenile Atlantic salmon (Salmo salar). In 1999, Atlantic salmon parr were released into an experimental reach below a hydroelectric facility and flow was manipulated over a range of discharge (1.0-4.2 m 3 s -1 ) during a series of 'experiments' simulating hydropeaking in both summer and fall. Fish were implanted with radio transmitters, manually tracked, precisely located (±1 m), habitat selection evaluated, and movement response determined. Experiments were continued in 2002 and 2003 to contrast response of salmon between summer and winter, the magnitude of flow changes were greater (0.7-5.2 m 3 s -1 ) and changes were made more rapidly (instantly). As discharge was increased, velocity and depth use by parr increased, and fish adapted behaviourally by increased contact with the substrate. Salmon parr also exhibited two distinct movement patterns in the summer and fall of 1999 studies; high site fidelity or considerable movement during trials. Salmon were more mobile during both static and dynamic flow conditions and throughout the diel cycle in the summer of 2002 experiment, and 2 fish were stranded and died, the only time this happened in the four series of experiments. Within each experiment generally there were no differences between movements at static high and low flows for day and night movements, with one exception, and night time movements were always greatest, again with one exception. During dynamic flow changes, within each experiment, distances moved during down ramping and up ramping were not significantly different except in the summer of 1999. Overall, comparing between experiments for up and down ramping events, distances moved in the summer of 2002 were statistically higher than for all other experiments. Not surprisingly, the home ranges of fish in the summer of 2002 were also the greatest while the smallest home ranges were in the winter of 2003. Results suggest hydropeaking regimes may be energetically costly potentially affecting over-winter survival which is related to energy reserves obtained during summer. Collectively these studies provide comprehensive information on the response of juvenile Atlantic salmon parr to hydropeaking, on both diel and seasonal scales, and will assist hydro producers and regulators design and operate hydropeaking regimes to minimize ecological impact.