ABSTRACT. Lichen and bryophyte collections are critical for our understanding of taxonomy, physiology and morphology, phenology, ecology, and evolution. Yet, these collections, both large and small, are increasingly under threat due to lack of space or funding to maintain them. In this talk I will review the value of these collections, and their ongoing potential in scientific research. I will discuss the threats to these collections, particularly in light of recent events. Finally, I will discuss the role that we as lichenologists and bryologists play in continuing to build, maintain, and support these collections.

ABSTRACT. Here we present the computer program Mytabolites for the identification of secondary metabolites based on thin-layer chromatography plates. The program runs on Microsoft Windows and can be downloaded from the Consortium of Lichen Herbaria. It fully integrates with and can be updated through the Consortium database, which currently provides information on substances reported from 7,917 lichen species. The program is based on the most recent catalog of standardized chromatographic data by J. Elix, it also provides access to 698 images of chromatograms by F. Schumm. The initial versions of Mytabolites were inspired by Wintabolites, a 16-bit program originally developed by E. Mietzsch and H.T. Lumbsch at the University of Essen. Since 16-bit programs no longer work on modern 64-bit systems, we decided to develop Mytabolites as an alternative. In addition to the classical Wintabolites way of matching RF spot test data, Mytabolites also includes a correlation algorithm, which better accounts for the fuzziness of the data. Matching criteria for both algorithms can be fine-tuned and results returned by either matching algorithm can be switched and reviewed "on-the-fly". RF values can be combined with spot test and UV reactions of the thallus, further improving possible matches. The list of results returned when entering chromatogram data can be checked against the database of substances reported for lichen species in the Consortium. Results can be filtered for genera and/or groups of physiologically related substances. As previously in Wintabolites, it is possible to cune chromatogram data against known standards to better calibrate chromatograms, thus accounting for experimental variation. Results are automatically updated when standards are cuned or additional matching data is entered. Browsing substance data allows for side-by-side comparison of closely related metabolites with an integrated viewer for chromatogram images, where those are available. Reviewing substances from particular lichen species retrieves images from the Consortium, with a direct link to the taxon profile online.

ABSTRACT. Accurate species delimitation and understanding of evolutionary dynamics in lichenized fungi are essential for conservation, ecological studies, evolutionary research, and taxonomic clarification. In this study, we comprehensively investigate the Parmotrema perforatum group using RADseq analysis, population genomics, and phylogenetic inference with expanded sampling, including new populations of Parmotrema hypotropum from Illinois and Virginia, as well as Parmotrema hypoleucinum from Europe, California, and Mexico. Our analyses reveal distinct monophyletic clades corresponding to reproductive modes (apotheciate and sorediate taxa) and chemospecies, with the latter showing more intricate relationships than previously known. Furthermore, we observe geographic structure in species with broad geographic ranges, such as P. hypotropum and P. hypoleucinum. These findings provide valuable insights into the genetic basis of reproductive strategies, chemical diversity, geographic structuring, and evolutionary dynamics within the Parmotrema perforatum group, highlighting the power of integrated approaches in lichen taxonomy and evolution studies.

ABSTRACT. Lichens are long-lived, sessile symbiotic assemblages often exhibiting a high incidence of rarity. As an emergent trait, rarity encompasses the complexities of a species’ life-history traits and its environment. In this study, we used comparative population genomics to examine drivers and consequences of rarity in related widespread and range-restricted lichenized fungi sampled throughout the Appalachian Mountains of eastern North America. We generated robust population genomic datasets for the widespread species Punctelia rudecta, Lepraria finkii, and Usnea strigosa, and rare congeners P. appalachensis, L. lanata, and U. subfusca, totaling 924 individuals from 36 sites. Using long read sequences, we assembled high-quality reference genomes for each species. Whole-genome shotgun sequencing (WGS) short reads were aligned to reference genomes and filtered for quality before conducting downstream analyses. The pipeline we developed advances established workflows for assessing high-volume population-level WGS datasets from complex metagenomic data. Rare species populations show stronger geographic-driven genetic structure than common species, which is also reflected by reductions in signals of gene flow among those populations. Our data suggest that Lepraria lanata is highly clonal, supporting our hypothesis based on the lack of observed sexual reproductive structures throughout the genus Lepraria. Compartively, Lepraria finkii shows high levels of recombination, suggesting a cryptic recombination mechanism. All four additional species displayed evidence of recombination. Finally, we investigate the impact of habitat quality and climate on observed genetic diversity. Our findings show that rarity is associated with similar patterns of population genetic structure across taxonomically and morphologically diverse fungi.

ABSTRACT. Mobile Genetic Elements (MGEs) are sequence features whose movement within a genome modulates gene expression and generates novel genetic diversity. They can have both positive and negative effects on host organisms. We hypothesize that population dynamics and environmental stressors in species with small, declining populations impact defense mechanisms developed by Eukaryotes to curb the proliferation of deleterious MGEs. We used comparative genomics to contrast the MGE content in rare, threatened, and range-restricted species of lichenized fungi with species that have large, stable populations. Twenty new reference genomes were generated and six previously published long-read genomes were gathered from online data repositories. New genomes were generated with standard laboratory workflows and MGEs were annotated using RepeatModeler2. MGEs accounted for 1.53–68.85% of the genome content in the species sampled, with a total of 596–103,790 elements recovered in a given genome. Retrotransposons were the most abundant type of MGE, averaging 16.76% (±5.21) of the genome content in rare species and 12.84% (±2.86) in common species. Total MGE content followed a similar pattern, with means of 25.71% (±8.69) and 20.32% (±3.56) recovered for rare and common species, respectively. The disproportionate distribution of MGEs, particularly retrotransposons, in rare, threatened, and range-restricted species may disrupt genomic stability, yet also create novel genetic diversity in isolated populations with limited gene flow. Investigation of associations between increased extinction risks and MGE expansions is essential to understand the potential implications that these genes have for species conservation.

ABSTRACT. The interactive nature of fungi in symbioses necessitates sequencing and bioinformatically navigating complex metagenomes. In this study we aimed to determine the diversity of photosynthetic partners associated with lichenized fungal thalli, to explore the promises and challenges of long-read sequencing in investigating the genomes of less abundant symbionts, and to use the recovered genomes to test for gene family expansions and contractions that correspond with lichen-association. We used metagenomic binning and homology searches to extract photobiont reads from 22 long-read dataset generated from whole thallus DNA extractions. Photobiont organellar genomes were recovered from all samples, often at high coverage (>100x), and there were instances of recovering multiple, genetically distinct organelles from the same lichen thallus. Recovery of contigs ascribable to the photobiont nuclear genome varied from 0.03% to >90% completeness based on BUSCO scores and their taxonomic identity of the discovered photobionts correspond with reported lichen-associated algae. Validation of metagenomically derived algal contigs with long-read sequencing from thallus-derived algae in pure culture support their classification. Gene family evolution in photobionts mirrors the significant changes in genes associated with primary metabolism recovered in lichenized fungal genomes.

ABSTRACT. We will explore the level of algal diversity present in four members of the lichen family Physciacae abundant in the Chicagoland area that will vary in terms of relatedness. All lichens sampled are co-occurring thalli found on burr oak branches on the forest floor. This sampling method will allow us to assess variation across sympatric fungal species with similar ecological requirements, and explore if patterns of association are shaped by fungal evolutionary history. ITS barcode sequences will be generated from the algal component(s) of each lichen and compared with a reference database for identification. From this sample of photobionts, the clade that these individuals fall into will be identified and operational taxonomic units (OTUs) based on genetic diversity will be established. We will compare these sequences to other previously established OTUs and characterize their phylogenetic diversity. Since we will also be sampling from a group of closely related species, we will explore the amount of overlap of algal symbionts present between lichen fungi that are closely related and if there is overlap present between distantly related species. We aim to determine whether these individual lichen species tend to associate with the same OTUs of algal species. The results of this study have the potential to answer some fascinating questions and provide more insight into the drivers behind associations between photobionts and mycobionts. If the timeline and resources allow, we will possibly analyze a wider array of lichen species to achieve a greater understanding of the abundance, driving forces, and individual preferences associated with symbiont diversity.

ABSTRACT. Lichens represent a wealth of biodiversity. Intraspecific phenotypic plasticity in lichens continues to obscure our understanding of how ecological influences vary between species, communities, and abiotic factors. A consequence of this knowledge deficit is a lack of a clear understanding concerning functional and ecological traits that determine extinction risk for many species. A recent study found nearly 60% of the 168 lichen species researchers assessed for the International Union for Conservation of Nature (IUCN) Red List to fall under a threatened status. Lichens containing nitrogen-fixing cyanobacterial photobionts are thought to be more sensitive to environmental change than their green algal relatives, though it remains unclear which traits, if any, might make them more prone to extinction. A Few studies have started to tease out traits driving lichen rarity. Given these insights and that rare cyanolichens require more research, we propose to use a trait-based approach to determine if substrate, symbiont partner, reproductive mode, habitat type, elevation, and climate are indicative of risk in the monophyletic cyanolichen genus Peltigera. This genus is widespread in North America, making targeted field studies possible for taxa requiring additional data. Comprehensive assessments for all North American species will be synthesized and traits will be mapped phylogenetically to visualize if any might be predictors of cyanolichen risk. Use of a trait-focused methodology will elicit more quantitative ecological and evolutionary data to more efficiently address conservation-related questions. This work will add to the growing body of knowledge surrounding fungal ecology and conservation, as well as provide insight on drivers of cyanolichen risk and published IUCN Red List assessments for all North American species of Peltigera.

ABSTRACT. Fungi form close relationships with most liverwort taxa. Understanding these relationships will shed light on liverwort ecology as well as the evolution of land plants with mycorrhizal relationships. Recently, fungal structures resembling the microsclerotia of endophytic fungi have been observed in the tropical liverwort Marchantia inflexa grown in culture. Plants were collected in Trinidad, the Republic of Trinidad and Tobago from two different habitats: populations along forested streams and populations along exposed roads. These plants were then cultured on steam sterilized soil and cultivated in a common greenhouse. Interestingly, variation in the fungal colonization of cultivated M. inflexa individuals has been observed. In particular, preliminary data suggest that plants obtained from road sites have more fungal structures than plants from stream sites. There is also high variability within sites; while some plants have no fungal structures at all, other plants are highly colonized. My future research aims to further examine this variation, including examining variation in plants collected more recently from the field. Additionally, I plan to investigate the fitness consequences of this fungal colonization and determine if uncolonized individuals can become colonized if exposed to the fungus. This research presents the opportunity to develop further understanding of the ecology of M. inflexa.

ABSTRACT. In recent years, a close relationship has been shown between the increase in the diversity of the Antarctic tundra and the remote contribution of nitrogen by penguin colonies. It has also been shown that microinvertebrates and mosses can increase the values of stable nitrogen isotopes, suggesting that they absorb and accumulate nitrogen from the animal source. In this context, we wonder if the diversity of mosses is higher in the vicinity of the penguin colony, and if these mosses show high values of stable nitrogen isotopes. Moss diversity, and nutrient content measurements were made in a transect at a distance from the chinstrap penguin colony of 1200 m. We found 15 species of mosses and two species of liverworts, growing along the transect, being two species Sanionia uncinata and Polytrrichastrum alpinum, the most frequent and dominant. Furthermore, it was found that in the three sectors analyzed there are different concentrations of soil nitrogen, with the content being much higher in the area near the penguin colony within the first 250 m of distance; On the contrary, the nitrogen content of the soil is not clearly related to that of the mosses. That is to say, there is no linear increase in the Nitrogen content of the soil and mosses in direction to the penguin rockery. Furthermore, the stable N isotopes of mosses are very low (negative values), suggesting that they obtain this nutrient from other sources. Furthermore, studying the microclimate of the area, it was observed that the penguin colony is located in the most protected area from the wind, which does not allow the colony's nitrogen to travel long distances, reducing the fertilization of the mosses. Therefore, these results suggest that the mosses would not be obtaining volatile nitrogen from the penguin rookery, contrary to what has been observed in other studies. Grant FONDECYT-ANID 1181745; ANI-ANILLO ACT210021.

ABSTRACT. Bryophytes are often overlooked or summed together as one group when conducting community composition assessments, especially following disturbance events. This vacuum of knowledge concerning individual bryophyte species can cause extirpation, and the loss of functions they provide. We used herbarium specimens to study bryophyte community composition through time in the Great Smoky Mountains National Park (GSMNP), which experienced an invasive pest, the Balsam Woolly Adelgid (BWA) that drastically altered the canopy cover at high elevations, which likely altered the understory communities indirectly. We grouped bryophyte specimens collected in the park by ecologically relevant years and examined diversity changes through time, correcting for sampling bias, specifically comparing the years prior to the BWA invasion and when the canopy began recovering according to the literature. We grouped species by growth form, taxonomic order, and level of substrate specificity and performed analyses to determine if species categorized in different groups experienced different changes over time. Using herbarium specimens enhances our understanding of community responses to disturbances and the management decisions used to combat them. This is especially true for organisms, like bryophytes, which are not always examined at the species level for community change assessment studies.

ABSTRACT. Communities in mountainous regions of the Pacific Northwest are vulnerable to global change, but evaluating potential risk and impacts can be challenging. Epiphytic lichens are sensitive bioindicators of global change drivers including atmospheric nitrogen deposition (Ndep) and climate. They lack a protective cuticle and active water uptake system, directly exposing them to changes in Ndep, temperature, and atmospheric moisture. Epiphytic lichen community composition is sensitive to N pollution because of species-specific responses to different N regimes. Lichen community-based airscores provide an integrated measure of deposition tolerance of lichen species within the community. Low airscores indicate a dominance by N-sensitive, oligotrophic species, while higher airscores occur with increased abundance of more N-tolerant, mesotrophic and eutrophic species. We assessed spatial variation in epiphytic lichen community composition and lichen community-based airscores to assess potential gradients in Ndep tolerance in lichen communities in North Cascades and Olympic National Parks, Pacific Northwest, USA. We hypothesized that 1) lichen communities would reflect a historic Ndep gradient across the region, with higher lichen community-based airscores closer to urban N pollution sources, and 2) current atmospheric N deposition amounts and chemistry are strong predictors of lichen community structure (α-diversity and β-diversity). We found that lichen communities in our study area were dominated by N-sensitive, oligotrophic species. Lichen community-based airscores were low and did not vary across the study area, suggesting the lack of a deposition gradient and low, background levels of Ndep that do not strongly influence lichen communities. Instead, climate variables pertaining to temperature and moisture emerged as strong drivers of lichen community structure. Changes in temperature and moisture in this region, including predicted declines in snowpack, could lead to changes in lichen community composition. Shifts in regional deposition chemistry may also play a role in impacting lichen communities and ecosystem dynamics. These results underscore the importance of considering multiple drivers of global change in assessing ecosystem health and highlights the need for comprehensive management strategies to mitigate the combined impacts of climate change and Ndep on mountainous ecosystems.

ABSTRACT. Caves are considered stable environments that serve as isolated biological ecosystems, offering markedly different conditions from the surface environment. Both bryophytes and caves are especially susceptible to anthropogenic disturbances and these impacts have impacts on the refugia capacity of caves for bryophytes. Although there is a considerable pool of knowledge for cave and bryophyte ecology, next to nothing is known about the ecology of bryophyte communities at cave entrances. We investigated the relative importance of dispersal, environmental filtering, and limiting similarity in the assembly of these communities across a gradient of anthropogenic disturbance. Our results suggest that cave entrance bryophytes are functioning as a metacommunity, and that habitat filtering is a stronger determinant of community structure than dispersal. In addition, disturbance has significant impacts on the community structure of bryophytes at these habitats. These findings have profound implications for the management of both cave entrance ecosystems and bryophytes.

ABSTRACT. Bryophytes are environmentally and ecologically significant biological indicators, as their distribution is largely determined by the climate and the land features that shape these factors. Yet it is a challenge to track the ranges of these plants and even more so to predict their future distribution patterns due to their small size and sensitivity to environmental change. This study aims to model the potential distribution of selected bryophyte species in Illinois to investigate the potential impact of global warming and determine what environmental factors affect distribution patterns. Bryophyte occurrences post 1970 of some of the most common epiphytic species and genera were investigated. Over 12,000 georeferenced occurrence records were downloaded from a public biodiversity aggregator, cleaned, and validated. The environmental variables consisted of the WorldClim Bioclim variables and National Land Cover Database land use variables, filtered to remove correlation. The occurrences and environmental variables were run through a MaxEnt model in R to generate heat maps of potential distribution. Statistical evaluation metrics and validation techniques were used to test model accuracy. Overall, current species models showed a higher level of confidence than the genera models, and all models were primarily reliant on the land use variables over the climate variables. Future models only showed minor distribution changes across climate scenarios, suggesting the use of more local indicators and further research on microclimate data. Attempting to quantify bryophyte-environment relationships and ecological niche modeling potentially provides a means of predicting how bryophytes might respond to environmental changes over time. Using such techniques enables us to test for significant differences in the characterization of niches between taxa. Successful models will not only show support for utilizing bryophytes as climate change indicators, but also for this open-source methodology in the niche modeling for other organisms. Overall, these results will possibly have important implications for species distribution patterns, conservation, land management and our understanding of ecological niche modeling using a poorly studied and overlooked group of plants.