Abstract Habitat loss and degradation due to human-induced landscape alterations are considered to be a major threat to biodiversity. The decline of biodiversity may occur with a time delay leading to a so called extinction debt. Therefore, determining extinction risks and conservation status is not always straightforward. Several life history traits might play a role for the accumulation of an extinction debt. Thus, perennial plant species capable of vegetative propagation might be able to persist temporarily in degraded habitats even though sexual and evolutionary processes are effectively halted. We studied Cnidium dubium , which occurs in scattered patches along river corridors in Central Europe and is critically endangered in Germany. It is a perennial species which is able to propagate clonally. Our aims were to reconstruct demographic processes regarding clonal propagation and gene flow along 400 km of river stretch and with respect to the position in the flooplain, i.e. before or behind dykes. We also wanted to determine whether there is evidence for an extinction debt in C. dubium and to use our insights for conservation recommendations. For this, we used nuclear microsatellites and maternally inherited chloroplast DNA markers and applied a systematic grid based sampling strategy for small scale geographic structures. We observed a high level of clonal propagation. In 935 analysed plants we observed only 121 different genotypes and of 50 studied patches of C. dubium the majority (31 patches) consisted of one single genotype each. Patch size and position were correlated with clonal diversity. Large patches and patches behind dykes exhibited higher clonal diversity. There was no evidence for a large scale genetic substructuring of the study area and no differences in overall genetic diversity between upstream and downstream patches as well as between patches before and behind the dykes. High levels of heterozygosity and a high number of 18 chloroplast DNA haplotypes togetherwith a slightly elevated inbreeding coefficient (Fis) point toward a high level of ancestral polymorphism in an out of equilibrium population due to high levels of clonal propagation and low levels of gene flow and recombination. Therefore, we assume that an extinction debt is present in C. dubium. As a management strategy, we propose to transplant ramets between multiple patches to increase the number of mating partners and therefore restore sexual reproduction.

Predominance of clonal propagationconceals extinction risks of the highly endangered floodplain herbCnidium dubium