Lichens are widespread symbioses and play important roles in many terrestrial ecosystems. The genetic structure of lichens is the result of the association between fungal and algal populations constituting the lichen thallus. Using eight fungus- and seven alga-specific highly variable microsatellite markers on within-population spatial genetic data from 62 replicate populations across Europe, North America, Asia and Africa, we investigated the contributions of vertical and horizontal transmission of the photobiont to the genetic structure of the epiphytic lichen Lobaria pulmonaria. Based on pairwise comparisons of multilocus genotypes defined separately for the mycobiont and for the photobiont, we inferred the transmission mode of the photobiont and the relative contribution of somatic mutation and recombination. After constraining the analysis of one symbiont to pairs of individuals with genetically identical symbiotic partners, we found that 77% of fungal and 70% of algal pairs were represented by clones. Thus, the predominant dispersal mode was by means of symbiotic vegetative propagules (vertical transmission), which dispersed fungal and algal clones co-dependently over a short distance, thus shaping the spatial genetic structure up to distances of 20m. Evidence for somatic mutation generating genetic diversity was found in both symbionts, accounting for 30% of pairwise comparisons in the alga and 15% in the fungus. While the alga did not show statistically significant evidence of recombination, recombination accounted for 7.7% of fungal pairs with identical algae. This implies that, even in a mostly vegetatively reproducing species, horizontal transmission plays a role in shaping the symbiotic association, as shown in many coral and other symbioses in nature.

In lichen symbiosis, fungal and algal partners form close associations, often codispersed by vegetative propagules. Due to the particular interdependence, processes such as colonization, dispersal or genetic drift are expected to result in congruent patterns of genetic structure in the symbionts. To study the population structure of an obligate symbiotic system in Europe, we genotyped the fungal and algal symbionts of the epiphytic lichen Lobaria pulmonaria at eight and seven microsatellite loci, respectively, and analysed about 4300 L. pulmonaria thalli from 142 populations from the species' European distribution range. Based on a centroid approach, which localizes centres of genetic differentiation with a high frequency of geographically restricted alleles, we identified the South Italy-Balkan region as the primary glacial refugial area of the lichen symbiosis. Procrustean rotation analysis and a distance congruence test between the fungal and algal population graphs indicated general concordance between the phylogeographies of the symbionts. The incongruent patterns found in areas of postglacial recolonization may show the presence of an additional refugial area for the fungal symbiont, and the impact that horizontal photobiont transmission and different mutation rates of the symbionts have on their genotypic associations at a continental scale.

Availability of suitable trees is a primary determinant of range contractions and expansions of epiphytic species. However, switches between carrier tree species may blur co-phylogeographic patterns. We identified glacial refugia in southeastern Europe for the tree-colonizing lichen Lobaria pulmonaria, studied the importance of primeval forest reserves for the conservation of genetically diverse populations and analyzed differences in spatial genetic structure between primeval and managed forests with fungus-specific microsatellite markers. Populations belonged to either of two genepools or were admixed. Gene diversity was higher in primeval than in managed forests. At small distances up to 170 m, genotype diversity was lower in managed compared with primeval forests. We found significant associations between groups of tree species and two L. pulmonaria genepools, which may indicate “hitchhiking” of L. pulmonaria on forest communities during postglacial migration. Genepool B of L. pulmonaria was associated with European Beech (Fagus sylvatica) and we can hypothesize that genepool B survived the last glaciation associated within the refuge of European Beech on the Coastal and Central Dinarides. The allelic richness of genepool A was highest in the Alps, which is the evidence for a northern refuge of L. pulmonaria. Vicariant altitudinal distributions of the two genepools suggest intraspecific ecological differentiation.