Extremely low effective population size in a captive-bred population: partial mitigation through management practices

Effective population size ( $$N_e$$ ) is a critical parameter for evaluating the evolutionary and persistence potential of endangered populations and for designing sustainable conservation strategies. Captive breeding and release programs are widely used across taxa to reduce risk of extinction when natural reproduction is insufficient or no longer possible, making it essential to assess their consequences. We used the case study of the landlocked Saimaa salmon ( Salmo salar ), one of the most critically endangered salmonid populations in Europe, with unique evolutionary significance due to its isolation from other populations since the last glaciation. Using long-term demographic data (1969-2024) from wild-caught founders of a captive breeding and release program, we estimated the effective population size under multiple scenarios of variance in reproductive success. Across scenarios, estimated $$N_e$$ ( $$\hat{N}_e$$ ) ranged from 33 to 81 individuals, representing 32%-75% of the census size. We estimated that captive breeding practices aimed at equalizing parental contributions during fertilization and early life stages increased $$\hat{N}_e$$ by 12% compared to uncontrolled reproductive conditions. However, variation in survival after early developmental stages, typically beyond direct management control, remained a key determinant of $$\hat{N}_e$$ . Estimates depended on several assumptions specific to captive breeding and should be interpreted with caution. Despite recent increases in the number of founders, $$\hat{N}_e$$ is far below recommendations of what would be needed for long-term viability and the population remains genetically vulnerable due to historical bottlenecks. Our results also highlight that while captive breeding programs can partially mitigate genetic risks, their effectiveness depends on both controlled and uncontrolled sources of variance in reproductive success. Strengthening such programs may require combining breeding management with habitat restoration and, where appropriate, genetic rescue to ensure the long-term evolutionary potential of such unique and endangered populations.