In Europe 21 cpDNA haplotypes of Ruppia were reported earlier. Only one haplotype appeared to be common in Ruppia maritima L. whereas two rare variants were observed in the Baltic Sea indicating a potential diversity hotspot. Because nuclear ITS sequences were similar for 22 populations across the continent, we used 12 nuclear microsatellites to investigate their genetic structure and to check for isolation-by-distance resulting from multiple bird-mediated dispersal events. Hybrid populations contributed to 30% more alleles in SW Europe. Fifteen diploid ‘pure’ R. maritima populations showed very low allelic diversity, except for the Baltic, very low gene diversity and significant inbreeding (overall FIS = 0.231). Many cases of monomorphic loci or total fixation for only two alleles per locus appeared consistent with selfing behavior. All populations were significantly bottlenecked. R. maritima showed very high levels of differentiation between sites (overall FST = 0.585). Baltic populations were most divergent from other gene pools across Europe. Isolation-by-distance only was found for allelic divergence. We concluded that bird-mediated dispersal of R. maritima seeds did not homogenize the genetic structure but promoted scattered, isolated and unique multilocus genotypes. For R. maritima, gene pools are clustering a series of populations within relevant biogeographic regions. Together with the historical and current loss of small saline ponds and wetlands, this diploid R. maritima albeit, should be considered as rare and threatened in most European countries, in particular for Mediterranean, SW Atlantic and far inland sites.
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