Evolutionary drivers of reproductive fitness in two endangered forest trees

Summary Population genetics theory predicts a relationship between fitness, genetic diversity (H0) and effective population size (Ne), which is often tested through heterozygosity‐fitness correlations (HFCs). We tested whether population and individual fertility and heterozygosity are correlated in two endangered Mexican spruces (Picea martinezii and Picea mexicana) by combining genomic, demographic and reproductive data (seed development and germination traits). For both species, there was a positive correlation between population size and seed development traits, but not germination rate. Individual genome‐wide heterozygosity and seed traits were only correlated in P. martinezii (general‐effects HFC), and none of the candidate single nucleotide polymorphisms (SNPs) associated with individual fertility showed heterozygote advantage in any species (no local‐effects HFC). We observed a single and recent (c. 30 thousand years ago (ka)) population decline for P. martinezii; the collapse of P. mexicana occurred in two phases separated by a long period of stability (c. 800 ka). Recruitment always contributed more to total population census than adult trees in P. mexicana, while this was only the case in the largest populations of P. martinezii. Equating fitness to either H0 or Ne, as traditionally proposed in conservation biology, might not always be adequate, as species‐specific evolutionary factors can decouple the expected correlation between these parameters.