Genetic variability and its relationship to substratum preferences within and among populations of the sorediate foliose lichen Hypogymnia physodes was investigated using sequence variation in the complete nrDNA internal transcribed spacer (ITS) region. A few samples of the putatively closely related, sorediate, H. tubulosa were also included. Samples were collected from each tree species in study sites in Estonia, Finland, and Sweden. In total, DNA sequences from 104 individuals of H. physodes and 16 of H. tubulosa were obtained. A group 1 intron situated at the end of the small subunit (SSU) of the nrDNA was detected in both species. Within-species variability was observed in both species: fifteen haplotypes were found for H. physodes and seven for H. tubulosa for the combined alignment of the intron and the ITS. Possible recombination within the total gene fragment was detected and hence the different regions (intron, ITS1, 5.8S, ITS2) were analysed separately. They show a different degree of variability both between each other and between the species. The number of haplotypes of H. physodes in the four regions are 5, 5, 1, and 5 and for H. tubulosa 5, 2, 1 and 2, respectively. A statistical parsimony estimation resulted in two unconnected networks; one containing all the samples of H. physodes and one containing all H. tubulosa samples. It was not possible to show different potentials of the different haplotypes for establishment on different substrata as the network of H. physodes indicates recombination within the ITS region which may be frequent enough to make this primarily clonally reproducing species to behave like a sexual species.

A relatively quick and simple method is presented for monitoring changes in distribution and in site and substratum preferences of epiphytic macrolichens; the method also records the natural turnover of common species. Changes in the epiphytic lichen flora in southern Sweden were recorded at 64 sites in 1986 and again in 2003. In total 1990 observations of lichens were recorded on 15 tree species, mainly on trunks but also on branches up to 2 m above the ground. Almost all species showed a high turnover with regard to substratum, including very abundant species such as Hypogymnia physodes. Many of the species had changed substratum within their sites, possibly reflecting a general change in the ecological quality of sites. Canonical Correspondence Analysis was used to extract the variation in species composition over time, using 1685 records of 55 lichen species on 8 different substrata. Some species such as Hypogymnia tubulosa had increased in abundance whilst others such as Vulpicida pinastri had decreased.

The lichens Usnea florida and U. subfloridana have since long been recognised as distinct species. They show many similarities in morphology, but have different reproductive strategies. Usnea florida is always provided with many apothecia and produces no specialised asexual propagules. Usnea subfloridana has soralia, isidiomorphs and occasionally apothecia. Phylogenetic analyses based on continuous sequences of the ITS and LSU regions of the nuclear ribosomal DNA and the gene coding for β-tubulin, show that specimens of the two species form one monophyletic group of intermixed specimens, and not two groups corresponding to morphology, which would have been expected if two species were at hand. The ‘species pair’ concept in lichenology is discussed. Other Usnea species included in the study are: U. articulata, U. barbata, U. ceratina, U. filipendula, U. hirta, U. rigida and U. wasmuthii.

The phylogenetic relationship between the Alectoriaceae and the Parmeliaceae (lichenized ascomycetes) were studied using sequences of the small subunit of the nuclear ribosomal DNA (SSU rDNA). The Alectoriaceae was represented by specimens of Alectoria ochroleuca and A. sarmentosa, and the Parmeliaceae by Bryoria capillaris, Cetraria islandica, Cornicularia normoerica, Evernia prunastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usnea florida, Vulpicida juniperina, V. pinastri and Xanthoparmelia conspersa. The results suggest that the Alectoriaceae is derived from within the Parmeliaceae, and it is suggested the families should be treated as synonyms. Morphological and anatomical characters are discussed, and it is concluded that earlier investigations might have overemphasized minor variations in ascus structure.

Three hypotheses of the phylogeny of the lichenized Parmeliaceae are constructed, using sequences of the nuclear ribosomal gene cluster (SSU, ITS, 5·8S rDNA) from Bryoria capillaris, Cetraria islandica, Evernia prunastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usnea florida, Vulpicida juniperina, V. pinastri and Xanthoparmelia conspersa. The first analysis, based on SSU sequences, shows the representatives of the Parmeliaceae to form a monophyletic group within the order Lecanorales. Usnea florida and Bryoria capillaris, sometimes classified in the families Usneaceae and Alectoriaceae, respectively, are also members of the Parmeliacceae. Cetraria and Vulpicida form a well-supported monophyletic group together with Usnea, but there is little support for any other groupings within Parmeliaceae. The second analysis is based on ITS an 5·8S sequence data of the representatives of the Parmeliaceae included in the first analysis, and supports the close relation of Cetraria and Vulpicida. Other groupings are not supported, and the topology also varies greatly with minor alignment changes. This is attributed to the included taxa being too distantly related to each other, causing alignment difficulties of the variable ITS region when a relatively small number taxa are included. It is predicted that a larger sample of phylogenetically intermediate taxa will overcome this problem. When combining the two datasets, the results are similar to the ITS results. The present study is one of the first phylogenetic studies utilizing the information in more than one gene alone in lichenized ascomycetes.

In order to identify monophyletic groups within the family Parmeliaceae, eleven taxa (Bryoria capillaris, Cetraria islandica, Evernia pruniastri, Hypogymnia physodes, Parmelia saxatilis, Platismatia glauca, Pleurosticta acetabulum, Usneaflorida, Vulpicida juniperina, V. pinastri, and Xanthoparmelia conspersa) were studied using newly produced nuclear rDNA sequence data from the ITS and 5·8S regions. The resulting evolutionary hypothesis was compared with results from previous phylogenetic analyses based on anatomy, morphology, and chemistry. The outcome of this comparison does not support the earlier proposed phylogenies but is not stable enough for identifying monophyletic groups, with one exception. The results indicate a close relationship between Cetraria and Vulpicida, which is contradictory to previous published analyses. The variation in ascus structures in the Parmeliaceae is discussed and it is questioned whether the earlier distinguished ‘ forms ’ of ascus types represent synapomorphies, if they are based on poorly supported analyses, or if they are exaggerations of relatively slight variation in shape. Further interpretations of the results are discussed and areas of future studies based on DNA-data are suggested.

High performance thin layer chromatography (HPTLC) is a method that can be used for screening lichen substances. It is as simple to use as standard TLC, but has many advantages: It is more sensitive, it is possible to run more samples in a shorter period of time, and the amount of solvent used is much smaller. The material needed and the methods used are described in detail. Horizontal chromatogram development was used. Since two of the solvents used in system B have been substituted, and since the properties of the HPTLC plates are slightly different, our results are not entirely in accordance with the standardized TLC method. A revised table for the identification of 69 lichen substances (obtained from 62 taxa) is accordingly presented.