Genome scans are a powerful tool to detect natural selection in natural populations among a larger sample of marker loci. We used replicated habitat comparisons to search for consistent signals of selection among contrasting populations of the seagrass Zostera marina, a marine flowering plant with important ecological functions. We compared two different habitat types in the North Frisian Wadden Sea, either permanently submerged (subtidal) or subjected to aerial exposure (intertidal). In three independent population pairs, each consisting of one tidal creek and one tidal flat population each, we carried out a genome scan with 14 expressed sequence tag (EST)-derived microsatellites situated in 5'- or 3'-untranslated regions of putative genes, in addition to 11 anonymous genomic microsatellites. By using two approaches for outlier identification, one anonymous and two EST-derived microsatellites showed population differentiation patterns not consistent with neutrality. These microsatellites were detected in several parallel population comparisons, suggesting that they are under diverging selection. One of these loci is linked to a putative nodulin gene, which is responsible for water channelling across cellular membranes, suggesting a functional link of the observed genetic divergence with habitat characteristics.

Eelgrass Zostera marina is an ecosystem-engineering species of outstanding importance for coastal soft sediment habitats that lives in widely diverging habitats. Our Wrst goal was to detect divergent selection and habitat adaptation at the molecular genetic level; hence, we compared three pairs of permanently submerged versus intertidal populations using genome scans, a genetic markerbased approach. Three diVerent statistical approaches for outlier identiWcation revealed divergent selection at 6 loci among 46 markers (6 SNPs, 29 EST microsatellites and 11 anonymous microsatellites). These outlier loci were repeatedly detected in parallel habitat comparisons, suggesting the inXuence of habitat-speciWc selection. A second goal was to test the consistency of the general genome scan approach by doubling the number of gene-linked microsatellites and adding single nucleotide polymorphism (SNP) loci, a novel marker type for seagrasses, compared to a previous study. Reassuringly, results with respect to selection were consistent among most marker loci. Functionally interesting marker loci were linked to genes involved in osmoregulation and water balance, suggesting diVerent osmotic stress, and reproductive processes (seed maturation), pointing to diVerent life history strategies. The identiWed outlier loci are valuable candidates for further investigation into the genetic basis of natural selection.

Zostera marina, the dominant seagrass on the Northern Hemisphere, forms the basis of important but threatened marine ecosystems. Here, we report 14 microsatellite DNA markers derived from an expressed sequence tag library corresponding to a wide range of genes. All loci were moderately to highly polymorphic, with allele numbers ranging from three to eight in a single Wadden Sea population of 48 individuals. Observed heterozygosities ranged from 0.082 to 0.837. Reaction conditions for five pooled polymerase chain reactions are given. The markers will advance the population genetics of seagrasses because they allow indirect tests of selection on closely linked genes