RESEARCH ARTICLE Effective number of breeders in relation to census size as management tools for Atlantic salmon conservation in a context of stocked populations Charles Perrier 1 • Julien April 2 • Guillaume Cote 1 • Louis Bernatchez 1 • Me ´lanie Dionne 2 Received: 11 February 2015 / Accepted: 15 July 2015 / Published online: 21 July 2015 Ó Springer Science+Business Media Dordrecht 2015 Abstract Monitoring short-term fluctuations in effective population sizes (N e ) and effective number of breeders (N b ), as well as their ratio to adult census population size (N e /N c and N b /N c ), provide insight into population demography and inform conservation programs towards limiting long-term loss of evolutionary potential in wild populations. In this study, we monitored short-term varia- tions of N b and N b /N c over three consecutive years for nine Atlantic salmon populations from Quebec, Canada. We documented how these population genetic parameters were influenced by anadromous population size as well as yearly and long-term stocking intensity. Towards this end, 15 microsatellites were used to genotype about 100 one-year- old parrs for each of three consecutive years for nine genetically distinct populations (total n = 2506) from Que ´bec, Canada. Yearly stocking intensity had a negative effect on N b /N c , possibly as a consequence of a reduced reproductive contribution of stocked relative to wild fish. However, the impact of long-term stocking intensity on N b / N c was not significant, which may indicate relatively weak carry-over effects of stocking on future generations. Also, N b /N c was negatively correlated with N C , suggesting compensatory mechanisms, as previously reported in other salmonids. Overall, this study provides evidence of rela- tively weak and short-term effect of stocking on N b /N c ratio in Atlantic salmon populations and suggests potential biological mechanisms leading to the significant negative relationship between N b /N c and N c . Keywords Effective population size  Effective number of breeders  Census size  Atlantic salmon  Linkage disequilibrium  Single sample estimator Introduction Effective population size over a generation (N e ) (Wright 1931) and effective number of breeders over a reproductive cycle (N b ), are among the most important parameters in conservation biology and are widely used for genetic monitoring. N e influences the rate of loss of genetic vari- ation due to evolutionary drift, the extent of inbreeding and inbreeding depression, the adaptive potential and the extinction risks of populations (Charlesworth 2009). N b refers to the effective number of breeders during a single breeding event (Waples 2005). This parameter is generally more easily quantifiable than N e since it can be inferred from a single cohort, and might thus be a more accessible parameter for managers dealing with yearly conservation decisions (Waples 2005; Luikart et al. 2010; Tallmon et al. 2010). Along with improved genotyping methods, many methods have been developed in order to infer N e or N b from individual multilocus genotypes (Luikart et al. 2010; Waples and Do 2010). N e or N b estimates can therefore be more readily used to formulate recommendations for the conservation of wild populations for mitigating loss of Electronic supplementary material The online version of this article (doi:10.1007/s10592-015-0758-5) contains supplementary material, which is available to authorized users. & Charles Perrier charles5perrier@gmail.com 1 De ´partement de Biologie, Institut de Biologie Inte ´grative et des Syste `mes (IBIS), Universite ´ Laval, Quebec G1V 0A6, Canada 2 Direction de la faune aquatique, Ministe `re des Fore ˆts, de la Faune et des Parcs du Que ´bec, 880 chemin Ste-Foy, Quebec G1S 4X4, Canada 123 Conserv Genet (2016) 17:31–44 DOI 10.1007/s10592-015-0758-5