Field studies and conceptual work on hybridization-mediated extinction risk in climate relicts are extremely rare. Nuphar pumila (Nymphaeaceae) is one of the most emblematic climate relicts in Europe with few isolated populations in the Alpine arc. The extent of introgression with related lowland and generalist species Nuphar lutea has never been studied using molecular methods. All biogeographical regions where N. pumila naturally occurs in the neighbourhood of the Alpine arc were sampled and studied using nuclear microsatellite markers. Furthermore, we used forward-in-time simulations and Approximate Bayesian Computation to check whether an introgression scenario fits with the observed admixture patterns and estimated the demographic parameters associated with this process. Our study confirms ongoing hybridization between N. pumila and N. lutea and validates it by the use of population models. More than 40 % of investigated N. pumila individuals were admixed and hybrids were found in over 60 % of studied populations. The introgression is bidirectional and is most likely a result of very recent gene flow. Our work provides strong evidence for rapid extinction risk and demographic swamping between specialized climatic relicts and closely related generalists. The remaining pure populations of N. pumila are rare in the Alpine arc and deserve high conservation priority.

The Alps played an important role in the biogeography of European plants and acted as a refugium for numerous species during the interglacial cycles. We investigated Nuphar pumila, one of the most emblematic glacial relicts of the Alps, by carrying out exhaustive literature and field surveys to collect relevant data on its distribution and threats. We further evaluated the level of introgression with the closely related N. lutea based on microsatellite data from natural populations across the Alps as well as from all ex situ collections and reintroductions in Switzerland. According to our results, more than 60% of the known N. pumila populations went extinct, and the species currently presents 37 natural populations in the investigated area. A large number of populations were affected by eutrophication (69%) and hybridization with N. lutea (53%). Priority should be given to the in situ conservation of genetically pure populations, while ex situ cultures should be applied to nearly extinct populations and the genetically pure individuals still present in hybrid populations. N. pumila is an excellent representative of the wetland/aquatic glacial relicts that are particularly affected by the combination of climate change and habitat degradation. International integration of research and conservation programs is needed to limit the decline of such rare species in the Alps.