Estimating effective population size (N_e) is important for theoretical and practical applications in evolutionary biology and conservation. Nevertheless, estimates of N_e in organisms with complex life-history traits remain scarce because of the challenges associated with estimation methods. Partially clonal plants capable of both vegetative (clonal) growth and sexual reproduction are a common group of organisms for which the discrepancy between the apparent number of individuals (ramets) and the number of genetic individuals (genets) can be striking, and it is unclear how this discrepancy relates to N_e.

In this study, we analysed two populations of the orchid Cypripedium calceolus to understand how the rate of clonal vs. sexual reproduction affected N_e. We genotyped >1,000 ramets at microsatellite and SNP loci, and estimated contemporary N_e with the linkage disequilibrium method, starting from the theoretical expectation that variance in reproductive success among individuals caused by clonal reproduction and by constraints on sexual reproduction would lower N_e. We considered factors potentially affecting our estimates, including different marker types and sampling strategies, and the influence of pseudoreplication in genomic datasets on N_e confidence intervals. The magnitude of N_e/N_ramets and N_e/N_genets ratios we provide may be used as reference points for other species with similar life-history traits. Our findings demonstrate that N_e in partially clonal plants cannot be predicted based on the number of genets generated by sexual reproduction, because demographic changes over time can strongly influence N_e. This is especially relevant in species of conservation concern, in which population declines may not be detected by only ascertaining the number of genets.

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