Data from: Effective population size in a partially clonal plant is not predicted by the number of genetic individuals

Estimating effective population size (Ne) is important for theoretical and
practical applications in evolutionary biology and conservation.
Nevertheless, estimates of Ne 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 Ne.
In this study, we analysed two populations of the orchid Cypripedium
calceolus to understand how the rate of clonal vs. sexual reproduction
affected Ne. We genotyped >1,000 ramets at microsatellite
and SNP loci, and estimated contemporary Ne 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 Ne. We considered factors potentially affecting our
estimates, including different marker types and sampling strategies, and
the influence of pseudoreplication in genomic datasets
on Ne confidence intervals. The magnitude
of Ne/Nramets and Ne/Ngenets ratios we provide may be
used as reference points for other species with similar life-history
traits. Our findings demonstrate that Ne 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 Ne. This is especially relevant in species of
conservation concern, in which population declines may not be detected by
only ascertaining the number of genets.