To facilitate population-genetic studies, we developed simple sequence repeat (SSR) markers and a molecular species identification assay for Peltigera membranacea (Ascomycota, Peltigerales), a common ground-dwelling lichen of forest and tundra ecosystems. Additional markers were developed for its Nostoc photobiont. Twenty-one fungal markers for P. membranacea were found to be polymorphic, with the number of alleles ranging from 3–21. Nei's unbiased gene diversity ranged from 0.588 to 0.640 in four significantly structured (FST = 0.059) mycobiont populations. For the Nostoc photobiont, 14 polymorphic SSR were developed, yielding 4–14 alleles each, with gene diversity ranging from 0.062 to 0.771 in four populations showing substantial population structure (FST = 0.278). The new markers developed are suitable for population genetic studies of Peltigera membranacea and of its cyanobiont, and at the same time allowed us to distinguish 98.5% of P. membranacea specimens from morphologically similar species of Peltigera.

Bactrospora dryina is an epiphytic lichen-forming fungus specifically related to old-growth floodplain forests, which have dramatically declined in Europe over the past centuries. In order to promote conservation management of such forest remnants, we aimed to study population genetics of this rare and threatened lichen. The newly developed 16 microsatellite markers are specific for the mycobiont of B. dryina and reliably amplify either single fruiting bodies or a sterile thallus. This allows the use of these markers for the identification of sterile crusts and for quantification of recent dispersal of the species into restored habitats. We tested the markers in 264 samples collected from 10 pedunculate oak trees growing in three localities in north-eastern Switzerland. All markers were polymorphic and showed two to five alleles per locus, and unbiased gene diversity varied from 0·06 to 0·71 over three populations. The relatively low number of alleles in B. dryina is possibly the consequence of colonization of secondary habitats created by forest management. Although oaks were largely covered with a single, continuous B. dryina colony, the microsatellite markers identified single or complex multi-genotype colonizations per tree. For future population genetic studies, we recommend collection of 5–15 specimens from one tree which would enable detection of 60–80% of the multilocus genotypes present. Hierarchical AMOVA revealed high variation (70%) on host trees, and a relatively high differentiation (12%) among the three locations in NE Switzerland indicated limited gene flow between those regions. Thus, the newly developed markers showed their applicability in population genetics at different spatial scales. They will play an important role in monitoring habitat restoration for the conservation of B. dryina and associated forests and riverscapes.