Long-distance seed dispersal may blur ecotypic divergence in a terrestrial orchid

Gene flow and adaptive divergence are key aspects in ecological speciation. Long-distance gene flow is hard to detect and few studies estimate gene flow in combination with adaptive divergence. The aim of this study was to investigate long-distance dispersal and adaptive divergence in fen orchid (Liparis loeselii (L.) Rich.). We used amplified fragment length polymorphism (AFLP)-based assignment tests to quantify long-distance dispersal at two different regions in Northwest Europe. In addition, genomic divergence between fen orchid populations occupying two distinguishable habitats, wet dune slacks and alkaline fens, was investigated by a genome scan approach at different spatial scales (continental, landscape and regional) and based on 451 AFLP loci. We expected that different habitats would contribute to strong divergence and restricted gene flow resulting in isolation-by-adaptation. Instead, we found remarkably high levels of gene flow and low levels of adaptive divergence. At least 15% of the assigned individuals originated from among-population dispersal events with dispersal distances up to 220 km. Six (1.3%) ‘outlier’ loci, potentially reflecting local adaptation to habitat-type, were identified with high statistical support. Of these, only one was an outlier in multiple independent dune-fen population comparisons and thus possibly reflecting truly parallel divergence. Signals of adaptation in response to habitat type were most evident at the scale of individual populations. These findings suggest that the homogenizing effect of gene flow may overwhelm divergent selection associated to habitat type in fen orchids in Northwest Europe.