Silke Werth

Myricaria Desv. (Tamaricaceae) is a genus of shrubs that play a keystone role in montane riparian ecosystems across Eurasia, shaping riverine habitats and supporting ecological function. The genus has a centre of origin in the Qinghai–Tibetan Plateau and exhibits a broad distribution, but many species boundaries are unresolved. Here, we present the first phylogenomic analysis of Myricaria using the Angiosperms353 target enrichment bait set, with sampling across its full geographic range. Off-target plastid loci were extracted from next-generation sequencing data using the CAPTUS bioinformatics pipeline. We infer species relationships using ASTRAL-IV and network analysis with SplitsTree, in conjunction with morphology. We also provide a taxonomic treatment of the genus, integrating our morphological observations and phylogenomic analyses for species delimitations. Based on our analyses, recognise two infrageneric sections: sect. Parallelantherae (containing only M. elegans ) and sect. Myricaria (the remainder of the genus, with type species M. germanica ). We also propose synonymising M. davurica , M. bracteata and M. squamosa with M. germanica . Although species boundaries in the Asian highlands remain unresolved, we conclude that the species M. elegans , M. germanica , M. laxiflora , M. longifolia , M. platyphylla , and M. pulcherrima are well-supported both phylogenomically and morphologically.

Fungi engage in associations with other organisms across a continuum from pathogenic to mutualistic lifestyles. Hence, they require a compendium of molecular capacities, including partner recognition, extracellular signaling, nutrient exchange, immune modulation, and control of microbial competitors. In filamentous pathogens such traits are frequently associated with compartmentalized genomes, including rapidly evolving secreted proteins known as effectors and expanded receptor families, but it remains unclear whether similar genomic principles shape mutualistic fungal symbioses. Here, we generated a chromosome-scale super-pangenome for the lichen-forming genus Peltigera, comprising 41 mycobiont assemblies representing eleven species, together with genomes of associated Nostoc and, in tripartite species, Coccomyxa photobionts. The mycobiont genomes revealed extensive variation in genome size, transposable element content, biosynthetic gene clusters, and lineage-specific gene content, with pronounced expansions in tripartite species. Across Peltigera, secreted protein encoding genes were preferentially located in TE-rich regions. We further identified Starship-like transposon elements, expanded antimicrobial protein repertoires, and a large, previously underestimated repertoire of fungal GPCRs dominated by Pth11-like receptors. Layer-specific transcriptomics of a P. rufescens thallus showed differential expression of several interaction-associated gene families, e.g. lectins, antimicrobial proteins and Pth11-like GPCRs. These data indicate that pathogenic and mutualistic fungi might exhibit shared genomic principles, including genome compartmentalization, mobile-element-associated diversification, and the expansion of molecular repertoires involved in recognition, extracellular control and signaling.

River network connectivity and postglacial history jointly shape patterns of pollen-and seed-mediated gene flow in riparian plants, yet their relative contributions across spatial and temporal scales remain incompletely understood. Myricaria germanica Desv., a pioneer riparian shrub formerly widespread along European rivers but now restricted to fragmented headwaters, provides an ideal model to investigate how river systems structure genetic connectivity. We analysed genetic diversity, population structure, and migration across 2,212 individuals from 67 populations spanning 12 Central European river catchments using 20 nuclear and six chloroplast microsatellite loci. By integrating biparentally inherited nuclear markers with maternally inherited chloroplast markers, we disentangled pollen- and seed-mediated gene flow across historical and contemporary timescales. Both marker systems revealed low genetic diversity, high inbreeding, and strong population differentiation. Nuclear microsatellites showed significant isolation by distance and extensive historical connectivity, with coalescent analyses indicating high pollen-mediated gene flow among catchments and identifying the Rhine and Danube as major long-term sources of migrants. In contrast, chloroplast microsatellites exhibited stronger spatial structure, limited admixture, and highly directional historical seed dispersal, consistent with constrained hydrochorous dispersal routes. Contemporary migration analyses further showed that present-day seed-mediated gene flow is largely confined within catchments, despite widespread historical pollen connectivity. Together, these results support a two-phase postglacial history in M. germanica , involving rare, directional seed dispersal during recolonization followed by prolonged pollen-mediated gene flow. Our findings highlight catchments as biologically meaningful management units and underscore the importance of conserving river network connectivity to preserve both the evolutionary legacy and long-term adaptive potential of riparian populations.

Sticta canariensis is a lichen which is rare in all parts of its range in Atlantic Europe and Macaronesia, where it occurs in laurisilva forests, a habitat highly threatened by global change. Thus, this species is of high priority for inclusion in conservation programmes where genetic diversity should be considered. We have established new microsatellite loci and generated a dataset that demonstrates the genetic diversity of the lichen-forming fungus S. canariensis from eight locations across its disjunct range, in Macaronesia, Norway and England. We genotyped 25 microsatellite loci for 65 specimens and detected five genetic clusters which resemble major geographical divisions, specifically among the Macaronesian archipelagos. The total number of observed alleles ranged from 2 to 22. These are the first microsatellite markers developed for S. canariensis and they will be useful for population genetic studies and for conservation assessments.

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.

The photosynthetic apparatus of lichen photobionts has been well‐characterized by chlorophyll fluorescence analysis (e.g., by pulse amplitude modulation [PAM]), which provides a proxy of the activity of photosystem II (PSII) and its antenna. However, such kinetics are unable to directly characterize photosystem I (PSI) activity and the associated alternative electron pathways that may be involved in photoprotection. Instead, PSI can be probed in vivo by near‐infrared absorption, measured at the same time as standard chlorophyll fluorescence (e.g., using the WALZ Dual PAM). Here, we used the Dual PAM to investigate cyclic electron flow and photoprotection in a range of mostly temperate lichens sampled from shaded to more open microhabitats. Sun species displayed lower acceptor side limitation of PSI (Y[NA]) early in illumination when compared to shade species, indicative of higher flavodiiron‐mediated pseudocyclic electron flow. In response to high irradiance, some lichens accumulate melanin, and Y[NA] was lower and NAD(P)H dehydrogenase (NDH‐2)‐type cyclic flow was higher in melanised than pale forms. Furthermore, non‐photochemical quenching (NPQ) was higher and faster relaxing in shade than sun species, while all lichens displayed high rates of photosynthetic cyclic electron flow. In conclusion, our data suggest that (1) low acceptor side limitation of PSI is important for sun‐exposed lichens; (2) NPQ helps shade species tolerate brief exposure to high irradiance; and (3) cyclic electron flow is a prominent feature of lichens regardless of habitat, although NDH‐2‐type flow is associated with high light acclimation.

Photosymbiodemes are a special case of lichen symbiosis where one lichenized fungus engages in symbiosis with two different photosynthetic partners, a cyanobacterium and a green alga, to develop two distinctly looking photomorphs. We compared gene expression of thallus sectors of the photosymbiodeme‐forming lichen Peltigera britannica containing cyanobacterial photobionts with thallus sectors with both green algal and cyanobacterial photobionts and investigated differential gene expression at different temperatures representing mild and putatively stressful conditions. First, we quantified photobiont‐mediated differences in fungal gene expression. Second, because of known ecological differences between photomorphs, we investigated symbiont‐specific responses in gene expression to temperature increases. Photobiont‐mediated differences in fungal gene expression could be identified, with upregulation of distinct biological processes in the different morphs, showing that interaction with specific symbiosis partners profoundly impacts fungal gene expression. Furthermore, high temperatures expectedly led to an upregulation of genes involved in heat shock responses in all organisms in whole transcriptome data and to an increased expression of genes involved in photosynthesis in both photobiont types at 15 and 25°C. The fungus and the cyanobacteria exhibited thermal stress responses already at 15°C, the green algae mainly at 25°C, demonstrating symbiont‐specific responses to environmental cues and symbiont‐specific ecological optima.

Lobaria pindarensis is an endemic species of the Himalayas and the Hengduan Mountains. Little information is available on the phylogeography genetics and colonization history of this species or how its distribution patterns changed in response to the orographic history of the Himalayas and Hengduan Mountains. Based on samples covering a major part of the species' distribution range, we used 443 newly generated sequences of nine loci for molecular coalescent analyses in order to reconstruct the evolutionary history of L. pindarensis, and to reconstruct the species' ancestral phylogeographic distributions using Bayesian binary MCMC analyses. The results suggest that current populations originated from the Yunnan region of the Hengduan Mountains in the middle Pliocene, and that the Himalayas of Bhutan were colonized by a lineage that diverged from Yunnan ca. 2.72 Ma. The analysis additionally indicates that the Nepal and Xizang areas of the Himalayas were colonized from Yunnan as well, and that there was later a second dispersal event from Yunnan to Bhutan. We conclude that the change in climate and habitat related to the continuous uplift of the Himalayas and the Hengduan Mountains in the late Pliocene and middle Pleistocene influenced the geographic distribution pattern of L. pindarensis.

Antibiotics are primarily found in the environment due to human activity, which has been reported to influence the structure of biotic communities and the ecological functions of soil and water ecosystems. Nonetheless, their effects in other terrestrial ecosystems have not been well studied. As a result of oxidative stress in organisms exposed to high levels of antibiotics, genotoxicity can lead to DNA damage and, potentially, cell death. In addition, in symbiotic organisms, removal of the associated microbiome by antibiotic treatment has been observed to have a big impact on the host, e.g., corals. The lung lichen Lobaria pulmonaria has more than 800 associated bacterial species, a microbiome which has been hypothesized to increase the lichen’s fitness. We artificially exposed samples of L. pulmonaria to antibiotics and a stepwise temperature increase to determine the relative effects of antibiotic treatments vs. temperature on the mycobiont and photobiont gene expression and the viability and on the community structure of the lichen-associated bacteria. We found that the mycobiont and photobiont highly reacted to different antibiotics, independently of temperature exposure. We did not find major differences in bacterial community composition or alpha diversity between antibiotic treatments and controls. For these reasons, the upregulation of stress-related genes in antibiotic-treated samples could be caused by genotoxicity in L. pulmonaria and its photobiont caused by exposure to antibiotics, and the observed stress responses are reactions of the symbiotic partners to reduce damage to their cells. Our study is of great interest for the community of researchers studying symbiotic organisms as it represents one of the first steps to understanding gene expression in an endangered lichen in response to exposure to toxic environments, along with dynamics in its associated bacterial communities.