Widhelm, T. 2019: [Thesis:] Phylogenomic Systematics of Lichenized Fungi at Multiple Taxonomic Levels. - University of Illinois at Chicago, Chicago. 245 pp. [RLL List # 258 / Rec.# 41552] Abstract: The past few decades has seen a surge in molecular data used to understand the evolution of lichenized fungi. Studies have been conducted to understand the taxonomic placement of lichenized fungi in the fungal kingdom, the diversification of higherlevel taxonomic groups, the delimitation of species, and the genetic structure of populations. As in many other groups, the taxonomic value of morphological and chemical phenotypic characters for lichenized fungi are difficult to assess without other independent sources of data. Therefore, molecular data have provided a new line of evidence to critically evaluate the usefulness of phenotypic characters. Today lichenologists are using molecular data to test traditional hypotheses of homology based on phenotypic data. Generally, the findings are that many traditional systematic concepts are incongruent with molecular concepts, but a deeper understanding of the evolutionary history is gained. The first chapter in this dissertation introduces the evolution, taxonomy, and biogeography of lichenized fungi. The remaining chapters all use molecular data to understand the evolutionary relationships of lichenized fungi at different levels of taxonomy. Two chapters focus on the diversification of taxonomic groups above the species level, the next chapter focuses on population genetics, and the final chapter focuses on the delimitation of species boundaries. Three chapters in this dissertation focus on the lobarioid clade in the family Peltigeraceae which until the past 10 years was not well studied. The lobarioid clade was once the family Lobariaceae, but it was recently synonymized with Peltigeraceae using a temporal banding approach. Temporalbanding is becoming a trend in higherlevel classification of lichenized fungi and uses timecalibrated phylogenies to identify and define temporal bands for comparable ranks above the species level and aims for a more consistent taxonomic ranking system. Chapter two, “Multiple historical processes obscure phylogenetic relationships in a taxonomically difficult group” is the first study in lichenized fungi to use targetcapturing. Nearly 400 singlecopy nuclear loci were sequenced to reconstruct the first timecalibrated phylogeny of the lobarioid clade of Peltigeraceae. The first molecular phylogeny reconstructed for this clade used three genetic loci, but could not resolve the nodes along the backbone, leaving the relationships of genera unresolved. Using two orders of magnitude more loci, this study aimed to resolve these relationships. The stem age of the lobariod clade was like other families found in previous research and the generic relationships became clearer, but the backbone was still resistant to resolution. Further investigation found evidence that this was can be explained by historic processes, including ancient hybridizations and rapid diversification that occurred near the CretaceousPaleogene boundary. Hundreds of individual gene trees had massive genetree discordance and evidence for ancient reticulate evolution. Due to these evolutionary processes, even with 400 loci, the generic relationships remain somewhat unresolved, but a clearer understanding of the processes influencing the evolution of the group was gained. Chapter three, “Oligocene origin and drivers of diversification in the genus Sticta” used a fivelocus timecalibrated phylogeny to understand the timing of diversification of the genus. This study was the first to reconstruct a timecalibrated, multilocus phylogeny for the genus Sticta. Other genuslevel studies in lichenized fungi that estimated divergence times among species at worldwide to regional scales found that most lichenized genera diversified within the last 40 Mya and in Sticta, the timing of diversification was similar. This dissertation chapter also used ancestral state reconstructions to understand the how photobiont association and Andean uplift influenced the diversification of the genus. An ancestral range reconstruction was also conducted to estimate where Sticta could have originated. Chapter four is the final chapter on lobarioid species, “Using RADseq to understand the circumAntarctic distribution of the lichenized fungus Pseudocyphellaria glabra” uses restrictionsiteassociated DNA sequencing (RADseq) to understand the biogeography and population genetics of a single species with a disjunct range, separated by oceans and seas, occurring in Australia, Chile, and New Zealand. The use of RADseq is challenging in lichenized fungi because isolation of DNA from a lichen thallus results in a metagenome composed mostly of the mycobiont DNA, but it also contains DNA of the photobiont and the microbiome. In this chapter, a reference genome was generated so P. glabra mycobiont RAD loci could be used to estimate patterns of genetic differentiation among populations collected in Australia, Chile, and New Zealand and to infer how major physical barriers such as the Pacific Ocean limit genetic exchange among populations. Chapter five, “Picking holes in traditional species delimitations: an integrative taxonomic reassessment of the Parmotrema perforatum group” focuses on a species complex in another family, Parmeliaceae. This species delimitation study required the collection of population samples from eastern Texas and western Louisiana, where all six species live in sympatry. The aim was to use a sevenlocus dataset and the integration of a variety of analytical methods determine if the genetic lineages inferred correlated with the traditional species circumscriptions based on secondary chemistry and mode of reproduction. Integrative taxonomy is increasingly used in lichenized fungi to assess species boundaries that were established using phenotypic characters and most studies find that traditional phenotypebased species delimitation vastly underestimated the number of species observed with the “general lineage concept“ (GLC) of species. The GLC encourages the use of multiple sources of data to serve as independent lines of evidence in order to generate a robust hypothesis of species boundaries. In this final dissertation chapter, multiple lines of evidence were used including concatenated maximum likelihood phylogeny reconstruction, Bayesian STRUCTURE analysis, multispecies coalescent species tree estimations, and the morphology conidia to determine species boundaries. The main result was that genetic lineages did not correspond directly with the traditional sixspecies delimitation based solely on secondary chemistry and reproductive mode. The genetic data discovered three lineages with a more complicated evolutionary history than traditionally assumed. This dissertation outlines the work that was a training program on the latest research techniques in the field of lichenology. The research conducted encompassed most aspects that a professional systematist will encounter in a career. This includes planning field collection trips in the USA and foreign countries, which required obtaining grants and collection permits, preparation of logistical aspects, such as rental cars and accommodations, finding appropriate habitats, collecting and identifying specimens in the field, and finally, getting the specimens back safely so the research could be conducted. Once back in Chicago, the specimens were processed for deposition in the herbarium of the Field Museum, prepared for DNA isolation and sequencing, and analyzed on high performance servers. But the most challenging aspect was interpreting the results of the analyses, finding what was learned, and then framing the ideas in the context of what is already known, not just in the field of lichenology, but in the broader disciplines of systematics and evolutionary biology. The Biological Sciences PhD program at UIC and the collections and laboratories at the Field Museum provided excellent training for me to transform myself from an amateur lichen enthusiast, to a scientist that understands lichens in a much broader perspective.