Microsatellite markers can provide valuable information about gene flow and population history. We developed and tested new microsatellites for the nitrophilic lichenized fungus Xanthoria parietina and studied its genetic diversity and structure within the urban area of Munich, Bavaria. We compared its local genetic pattern with that of its photobiont partner Trebouxia decolorans, for which existing microsatellites were applied. For comparison, a reference site with clean air was included in the sampling. We found support for three genetic clusters in the fungus X. parietina, which occurred intermingled in collecting sites. There was a high degree of admixture within fungal populations and individuals, and analysis of molecular variance revealed a lack of population structure in the mycobiont. The Trebouxia photobiont, in contrast, exhibited structured populations which grouped into two to five genetic clusters, and individuals showed less admixture than in the mycobiont. This indicates that the two lichen partners differ in their ability to move around in the landscape. The microsatellite markers we report are polymorphic and are suitable for population genetic studies.

Gene expression variation can be partitioned into different components (regulatory, genetic and acclimatory effects) but for lichen-forming fungi, the relative importance of each of these effects is unclear. Here, we studied gene expression in the lichen-forming fungus Lobaria pulmonaria in response to thermal stress and parasitism by the lichenicolous fungus Plectocarpon lichenum. Our experimental procedure was to acclimate lichen thalli to 4 °C over three weeks and then expose them to 15 °C and 25 °C for 2 hours each, sampling infected and visually asymptomatic thalli at each temperature. Quantitative Real-Time PCR was utilized to quantify gene expression of six candidate genes, normalizing expression values with two reference genes. We found that two genes encoding heat shock proteins (hsp88 and hsp98), two polyketide synthase genes (rPKS1, nrPKS3) and elongation factor 1-1-α (efa) were upregulated at higher temperatures. Moreover, we observed higher expression of hsp98 at 25 °C in samples infected by P. lichenum than in uninfected samples. Finally, in partial redundancy analyses, most of the explained variation in gene expression was related to temperature treatment; genetic variation and long-term acclimatization to sites contributed far less. Hence, regulatory effects (i.e. direct adjustments of gene expression in response to the temperature change) dominated over genetic and acclimatory effects in the gene expression variability of L. pulmonaria. This study suggests that L. pulmonaria could become a valuable lichen model for studying heat shock protein responses in vivo.

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.

The Hindu Kush Himalayan (HKH) region harbours some of the richest and most diverse ecosystems on the planet that are now facing substantial threats through changes in climate, land use and human population growth, with serious consequences for the biodiversity in this mountainous region. In this paper we evaluated the effects of climate change on the distribution of the tripartite epiphytic macrolichen Lobaria pindarensis, considered to be endemic to the Himalayas. To predict the current and future distribution of this species we applied the Random Forest modelling algorithm and climatic variables with a post-processing of projected distributions using a map of habitat types in the study region. We calibrated models based on 1397 species presences within an altitudinal range of 2036–4000 m and extrapolated them according to two IPCC scenarios of climate change (RCP 2·6 and RCP 8·5). Based on the results of ensemble modelling, two new localities where L. pindarensis might potentially occur were predicted. Our simulations predicted a range expansion of this epiphytic lichen to the north-east and to higher altitudes in response to climate change, although the species’ low dispersal abilities and the local availability of trees as a substratum will considerably limit latitudinal and altitudinal shifts. By contrast, assuming the species can migrate to previously unoccupied areas, and depending on different future climate scenarios, our models forecasted a habitat loss of 30–70% for L. pindarensis. The main reason for the simulated habitat loss is the expected increase in mean annual temperature (by 1·5–3·7 °C) and total annual precipitation (by 56–125 mm). Our results contribute further evidence for the high sensitivity of tripartite macrolichens, especially those from mountain areas, to climate change and particularly emphasize the vulnerability of L. pindarensis. Thus, we stress the need to develop and formulate conservation measures and strategies for the protection of this endemic species in the Hindu Kush Himalayan region.

The green algal photobionts of 12 Xanthoria, seven Xanthomendoza, two Teloschistes species and Josefpoeltia parva (all Teloschistaceae) were analyzed. Xanthoria parietina was sampled on four continents. More than 300 photobiont isolates were brought into sterile culture. The nuclear ribosomal internal transcribed spacer region (nrITS; 101 sequences) and the large subunit of the RuBiSco gene (rbcL; 54 sequences) of either whole lichen DNA or photobiont isolates were phylogenetically analyzed. ITS and rbcL phylogenies were congruent, although some subclades had low bootstrap support. Trebouxia arboricola,T. decolorans and closely related, unnamed Trebouxia species, all belonging to clade A, were found as photobionts of Xanthoria species. Xanthomendoza species associated with either T. decolorans (clade A), T. impressa, T. gelatinosa (clade I) or with an unnamed Trebouxia species. Trebouxia gelatinosa genotypes (clade I) were the photobionts of Teloschistes chrysophthalmus,T. hosseusianus and Josefpoeltia parva. Only weak correlations between distribution patterns of algal genotypes and environmental conditions or geographical location were observed.

Photobiont diversity within populations of Xanthoria parietina was studied at the species level by means of ITS analyses and at the subspecific level with fingerprinting techniques (RAPD-PCR) applied to sterile cultured algal isolates. Populations from coastal, rural and urban sites from NW, SW and central France and from NE Switzerland were investigated. Between 8 and 63 samples per population, altogether 150 isolates, were subjected to phenetic and ordination analyses. Epiphytic samples of X. parietina associated with different genotypes of Trebouxia decolorans but saxicolous samples contained T. arboricola. For comparison the T. gelatinosa photobiont of a small population of Teloschistes chrysophthalmus (4 samples) was investigated. ITS sequences of T. decolorans isolates from different geographic locations were largely similar. In all populations a surprisingly high diversity of genotypes was observed in Trebouxia isolated from lichen thalli growing side by side. As Trebouxia spp. are assumed to be asexually reproducing haplonts, the genetic background of this diversity is discussed. Fingerprinting techniques are a powerful tool for obtaining valuable insights into the genetic diversity within the algal partner of lichen-forming fungi at the population level, provided that sterile cultured isolates are available.

Lichens are a fascinating example of a symbiotic mutualism. It is still uncertain which processes guide fungal-photobiont interactions, and whether they are random or of a more complex nature. Here, the fungal-algal interactions in Ramalina menziesii and co-occurring taxa are analyzed by using DNA sequences of the algal Internal Transcribed Spacer region (ITS), to investigate fungal-algal associations in juvenile R. menziesii and allied species. Algal species were identified by a combination of BLAST searches, median-joining network analysis, and Bayesian phylogenetics. Fungal-algal networks were analyzed for nestedness, both at the species and haplotype level (fungal species vs. algal haplotypes), and the networks were inspected for evidence of compartmentalization. Bayesian phylogenetic trees indicated that the widespread green alga Trebouxia decolorans associated with R. menziesii, as well as six other fungal species. Four additional fungal species interacted with four different species of Trebouxia. Only in one out of ten samples were algal haplotypes shared with the nearest neighbours of juvenile R. menziesii. Fungal-algal species interactions were compartmentalized, while at the level of algal haplotypes, nestedness was found. This pattern is similar to the compartmentalization found in other intimately interacting mutualists.

Population genetic studies of lichen-forming fungi and their algae require appropriate sampling schemes that ensure representative sampling of the genetic variability. One question is whether mycobiont and photobiont populations require different sampling strategies. Here, I applied rarefaction methods to a dataset containing three microsatellite loci of Lobaria pulmonaria and three microsatellite loci of its green-algal photobiont, Dictyochloropsis reticulata. I analysed the sample sizes required for 1) the number of individuals per population, 2) the number of individuals required across a landscape and 3) the number of populations. The analyses were performed separately for the mycobiont and photobiont loci to detect any differences in the accumulation of genetic diversity among the symbionts that would require different sampling schemes. About 20 individuals were sufficient at the population level; within landscapes, 300–400 samples and about 25–30 populations covered most of the allelic diversity. The results indicated that a slightly higher sampling effort was required for the photobiont than for the mycobiont. The optimal sampling strategy strongly depends on the research question, the spatial scale of investigation, and the type of analysis to be performed with the data.

Population genetics investigates the distribution of genetic variation in natural populations and the genetic differentiation among populations. Lichen-forming fungi are exciting subjects for population genetic studies due to their obligate symbiosis with a green-algal and/or cyanobacterial photobiont, and because their different reproductive strategies could influence fungal genetic structures in various ways. In this review, first, I briefly summarize the results from studies of chemotype variation in populations of lichen-forming fungi. Second, I compare and evaluate the DNA-based molecular tools available for population genetics of lichen-forming fungi. Third, I review the literature available on the genetic structure of lichen fungi to show general trends. I discuss some fascinating examples, and point out directions for future research.