Genetic differentiation and diversity do not explain variation in heterosis or inbreeding depression

Assisted gene flow can restore genetic diversity when genetic drift has driven deleterious alleles to high frequencies in small, isolated populations. Previous crosses among 20 populations of Gymnadenia conopsea documented the strongest heterosis and the weakest inbreeding depression in sparse and small populations, consistent with fixation of mildly deleterious alleles by genetic drift. We genotyped the populations used for crosses for 1,728 SNPs and tested the following predictions: 1) heterosis increases with genetic differentiation (FST) to donor populations and decreases with genetic diversity in the recipient population, 2) inbreeding depression increases with genetic diversity, and 3) genetic diversity increases, and mean FST to other populations decreases, with population size and density. Pairwise FST ranged from very low to moderate (0.005-0.20) and genetic diversity varied moderately among populations (proportion of polymorphic loci=0.52-0.75). However, neither FST between populations, nor genetic diversity in the recipient population, was related to the strength of heterosis. There was also no association between genetic diversity and the strength of inbreeding depression. Genetic diversity increased and mean FST decreased with population size, consistent with reduced diversity and increased differentiation of small populations by genetic drift. The results indicate that the loci conferring heterosis are not mirrored by overall population differentiation, and limited additional information on potential source populations for genetic rescue is gained by the genetic data. Instead, controlled crosses can directly reveal positive effects of introducing new genetic material, and is a simple method with high potential in conservation.