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In many aquatic plant taxa, classification based on morphology has always been difficult. Molecular markers revealed that the complexity in several of these aquatic taxa could be addressed to recurrent hybridization events and cryptic species diversity. The submerged macrophyte genus  Ruppia  is one of these aquatic genera with a complex taxonomy due to the absence of clear distinguishable traits and several hybridization events. Two species co-exist throughout Europe,  R. maritima  and  R. spiralis  (previously known as  R. cirrhosa ), but recent molecular studies also found several indications of hybridization, introgression and chloroplast capture between these species. However, the full extent and frequency of hybridization and introgression in this genus has not been studied so far, nor is it clear how these hybrid lineages can co-exist locally with their parental species. In this paper, we wanted to detect whether a single coastal wetland where both species co-exist can act as a  Ruppia  hybrid zone. As a case study, we chose the Camargue, a Mediterranean coastal wetland that harbors a wide diversity in aquatic habitats, especially in terms of salinity and hydro-regime. We sampled several  Ruppia  populations within this wetland. To identify each sample and reconstruct the local genetic structure of the two parental species and their hybrids, we used both chloroplast and nuclear microsatellite markers. Afterward, we tested whether different species had different habitat preferences. Our results confirmed that  R. maritima  and  R. spiralis  are two strongly divergent species with different reproductive ecologies and different habitat preferences. This prevents frequent hybridization and consequently we could not detect any trace of a recent hybridization event. However, we found several populations of later-generation hybrids, including a population of  R. maritima x hybrid  backcrosses. The hybrid populations occupy a different habitat and are genetically distinct from their parental species, although they tend to be morphological similar to parental  R. maritima . Although local hybridization and introgression in  Ruppia  is less frequent than we expected, the taxonomy of  Ruppia  is complicated due to ancient hybridizations and several back-crossings.

Hidden Hybridization and Habitat Differentiation in a Mediterranean Macrophyte, the Euryhaline Genus Ruppia