Can divergent selection save the rare Senecio hercynicus from genetic swamping by its spreading congener S. ovatus (Compositae, Senecioneae)?

• AFLP study of hybridising Senecio species along an elevational transect in Bavarian Forest National Park.
• Intensive introgressive hybridisation found all along the transect.
• Population genomic analysis of AFLP fingerprint data suggest few loci being under selection along the transect.
• Species-specific loci show neutral behaviour along the transect.
• No divergent selection regime detectable that could (re-)establish pre-zygotically isolated (biological) species.

Hybridisation leading to genetic swamping of a rare species by its more common congener is considered to become an issue of growing importance in conservation biology due to the fact that an increasing human impact on natural habitats and changes in climatic conditions will lead to higher frequencies of hybrid formation by shifting distributions and/or phenologies. In order to judge the future trajectories of hybridising plant species, which could eventually lead to the loss of taxonomic biodiversity, it is necessary to discern scenarios that lead to a complete merging of two species from those where hybridisation is an intermediary stage towards the establishment of reproductively isolated entities. We present a population-genomic approach that may allow discriminating between these two scenarios by estimating the strength of divergent selection regimes in hybrid swarms along ecological gradients. Using AFLP fingerprinting, 196 individuals from 11 populations of Senecio hercynicus and S. ovatus along an elevational transect (750–1300 m) in the Bavarian Forest National Park were genotyped for 634 anonymous loci. Based on Bayesian cluster algorithms, all populations were identified as being hybrid swarms with different admixture proportions of both parental genotypes, indicating the intense introgressive hybridisation realised in this hybrid zone. Searching for loci under selection by using either FST-based or logistic regression model-based techniques resulted in the identification of only few AFLP markers under selection, which showed a significant correlation with some climatic variables along the transect. The simultaneous finding, however, that species-specific markers were not among these selected markers support the interpretation that there is no climatically mediated divergent selection or reinforcement process going on that could (re-)establish genetically isolated (biological) species.