Multidisciplinary Evaluation of a 10‐Year Restoration Program for Two Endangered Atlantic Salmon ( Salmo salar ) Populations

ABSTRACT

Supportive breeding programs are widely implemented to counteract demographic collapse in threatened populations. Their long‐term success, however, depends on maintaining genetic diversity while ensuring that released individuals contribute effectively to wild populations. In Atlantic salmon ( Salmo salar ), uncertainties remain regarding the capacity of captive broodstocks to preserve genetic variation and the demographic and genetic consequences of supplementation. Here, we evaluate the outcomes of a decade‐long restoration program targeting two genetically differentiated but geographically proximate Atlantic salmon populations in the Romaine watershed (Romaine and Puyjalon population, Québec, Canada). Using microsatellite data, we performed population assignment, parentage analyses, and temporal estimates of effective number of breeders and genetic diversity. We assessed broodstock performance, the contribution of stocked individuals to wild populations, and the impact of two egg incubation treatments on fry to smolt survival. Despite sustained efforts to maintain large and representative broodstocks, the failure of wild‐caught juvenile salmon to reach maturity substantially reduced the number of breeders, representing the greatest loss of genetic potential in the hatchery broodstock. Nevertheless, partial factorial mating and kinship‐based management allowed us to avoid inbreeding and preserved levels of heterozygosity and allelic richness comparable to those observed in wild populations. Stocked individuals contributed around 25% to juvenile population size in both populations, without reducing effective population size or eroding genetic differentiation. Estimates of total effective population size consistently exceeded those of wild components alone, indicating no evidence of a Ryman–Laikre effect. Finally, egg incubation in the water of the Romaine River increased survival to smolt stage for genetically Romaine individuals but not for individuals from Puyjalon, suggesting local adaptation to early rearing conditions. These results demonstrate that, when carefully designed and genetically monitored, supportive breeding can reinforce depleted salmon populations without compromising genetic diversity and integrity.