Cryptogam biomass estimation using taxonomic and life form models for accurate assessment.

Accurate estimation of cryptogam biomass, encompassing bryophytes and lichens, is crucial for understanding their ecological significance. This estimation is conducted based on the strong correlations between mass and volume of cryptogams. However, mass-volume correlations vary among cryptogams because of their morphological differences. This problem can be solved using models that consider life forms that classify cryptogams based on morphological similarities. In this study, we investigated whether life form models improve cryptogam biomass estimation accuracy. The cryptogam mass-volume correlation of each life form was estimated using Bayesian linear models. The coefficients and intercepts of linear models differed between life forms, which was attributed to the morphological characteristics of each life form. Therefore, life form models can improve the accuracy of estimation models by incorporating morphological differences. However, taxonomic models that consider only the taxonomic difference (bryophytes vs lichens) demonstrated better overall estimation than the life form models, probably because of the ability of taxonomic models to capture systematic differences between bryophytes and lichens. Furthermore, these models may mitigate estimation errors related to morphological variations that cannot be adequately represented by life form types. Based on these results, we propose the appropriate use of estimation models.

Diversity of lichen mycobionts and photobionts and their relationships in the Ny-Ålesund region (Svalbard, High Arctic).

Lichens are dual organisms, with one major mycobiont and one major photobiont in each lichen symbiosis, which can survive extreme environmental conditions in the Arctic. However, the diversity and distribution of lichen photobionts in the Arctic remain poorly understood compared to their mycobiont partners. This study explored the diversity of lichen mycobionts and photobionts in 197 lichen samples collected from the Ny-Ålesund region (Svalbard, High Arctic). The nuclear ribosomal internal transcribed spacer (ITS) regions were sequenced and phylogenetic analyses were performed. The relationships between mycobionts and photobionts, as well as the association patterns, were also investigated. A total of 48 species of lichen mycobionts (16 families, nine orders) and 31 species/lineages of photobionts were identified. These 31 photobiont species belonged to one class (Trebouxiophyceae) and five genera, including 22 species of Trebouxia, five species of Asterochloris, two species of Chloroidium, one species of Symbiochloris, and one species of Coccomyxa. The results indicated that most analyzed lichen mycobionts could associate with multiple photobiont species, and the photobionts also exhibited a similar pattern. The results provided an important reference dataset for characterizing the diversity of lichen mycobionts and photobionts in the High Arctic region.

Continental scale comparison of mycobiomes in Parmelia and Peltigera lichens from Turkey and South Korea.

BACKGROUND: Lichens, traditionally considered as a simple partnership primarily between mycobiont and photobiont, are, in reality, complex holobionts comprised of a multitude of microorganisms. Lichen mycobiome represents fungal community residing within lichen thalli. While it is acknowledged that factors like the host lichen species and environmental conditions influence the structure of the lichen mycobiome, the existing research remains insufficient. To investigate which factor, host genus or location, has a greater impact on the lichen mycobiome, we conducted a comparative analysis of mycobiomes within Parmelia and Peltigera collected from both Turkey and South Korea, using high-throughput sequencing based on internal transcribed spacer region amplification. RESULTS: Overall, the lichen mycobiome was dominated by Capnodiales (Dothideomycetes), regardless of host or location. At the order level, the taxonomic composition was not significantly different according to lichen genus host or geographical distance. Hierarchical clustering of the top 100 abundant ASVs did not clearly indicate whether the lichen mycobiome was more influenced by host genus or location. Analyses of community similarity and partitioning variables revealed that the structure of the lichen mycobiome is more significantly influenced by location than by host genus. When analyzing the core mycobiome by host genus, the Peltigera mycobiome contained more ASV members than the Parmelia mycobiome. These two core mycobiomes also share common fungal strains, including basidiomycete yeast. Additionally, we used chi-squared tests to identify host genus-specialists and location-specialists. CONCLUSIONS: By comparing lichen mycobiomes of the same genera across different countries, our study advances our comprehension of these microbial communities. Our study elucidates that, although host species play a contributory role, geographic distance exerts a more pronounced impact on the structure of lichen mycobiome. We have made foundational contributions to understanding the lichen mycobiome occupying ecologically crucial niches. We anticipate that broader global-scale investigations into the fungal community structures will provide more detailed insights into fungal residents within lichens.

Diversity and distribution of the lichen genus Umbilicaria in the Argentine Islands-Kyiv Peninsula region, the maritime Antarctic.

This paper documents the occurrence of the genus Umbilicaria in the Argentine Islands-Kyiv Peninsula region of the Graham Coast in the maritime Antarctic. The presence of seven Umbilicaria species (U. africana, U. antarctica, U. aprina, U. decussata, U. kappenii, U. nylanderiana and U. umbilicarioides) in the ice-free areas of the Argentine Islands-Kyiv Peninsula region were confirmed. The species of U. africana and U. aprina are documented from the studied region for the first time. This study moves the southern distribution limit of U. africana about 300 km to the south: to the Argentine Islands-Kyiv Peninsula region. The distribution maps of Umbilicaria species for the studied region and maritime Antarctica are prepared.

Gypsum lichens: A global data set of lichen species from gypsum ecosystems.

Lichens are significant components of the biological soil crust communities in gypsum ecosystems and are involved in several processes related to ecosystem functioning, such as water and nutrient cycles or protection against soil erosion. Although numerous studies centered on lichen taxonomy and ecology have been performed in these habitats, global information about lichen species from gypsum substrates or their distributional ranges at a global scale is lacking. Thus, we compiled a global data set of recorded lichen species growing on gypsum. This review is based on systematic searches in two bibliographic databases (Web of Science and the more specialized database Mattick's Literature Index) using various keywords related to the substrate or ecology (i.e., gypsum, gypsiferous, semiarid, saxicolous, terricolous). In addition, we revised lichen literature from countries with gypsum soils using Mattick's, Hamburg University's Worldwide checklist, and different national lichen checklists. Ultimately the review includes a total of 321 studies. This data set included 6114 specimen records belonging to 336 recorded lichen species from 26 countries throughout the world. The results showed large differences in the number of species recorded among countries, reflecting differences in the sampling effort. We provide a table with the number of studies and species in relation to gypsum surface in order to account for the bias produced by sampling effort. The number of studies carried out per country was not related to the gypsum surface but probably to other factors, such as accessibility to field sampling, economic or political factors, or the presence of a wider community of lichenologists. Thus, Spain and Germany hosted the highest number of recorded species (160 and 114 species, respectively). Outside the European continent, only a few countries had a large number of species: Morocco (46), United States (42), and Iran (37). Remarkably, countries from the southern hemisphere (i.e., Australia, Chile, Namibia, and South Africa) showed a low number of studies from gypsum lands, supporting the stated biases observed in sampling efforts among countries. Considering the most studied countries, the results show that Teloschistaceae was the most represented family in gypsum ecosystems followed by Verrucariaceae and Cladoniaceae. Regarding particular species, Psora decipiens and Squamarina lentigera were some of the most widespread and abundant species in these habitats. This data set constitutes a basic and first step toward a much more comprehensive database, to be periodically updated in future releases, which also serves to identify countries or territories where future studies should be accomplished. There are no copyright restrictions on the data; please cite this data paper if the data are used in publications and teaching events.

Lichen speciation is sparked by a substrate requirement shift and reproduction mode differentiation.

We show that obligate lignicoles in lichenized Micarea are predominately asexual whereas most facultative lignicoles reproduce sexually. Our phylogenetic analyses (ITS, mtSSU, Mcm7) together with ancestral state reconstruction show that the shift in reproduction mode has evolved independently several times within the group and that facultative and obligate lignicoles are sister species. The analyses support the assumption that the ancestor of these species was a facultative lignicole. We hypothezise that a shift in substrate requirement from bark to wood leads to differentiation in reproduction mode and becomes a driver of speciation. This is the first example of lichenized fungi where reproduction mode is connected to substrate requirement. This is also the first example where such an association is demonstrated to spark lichen speciation. Our main hypothesis is that obligate species on dead wood need to colonize new suitable substrata relatively fast and asexual reproduction is more effective a strategy for successful colonization.

Tree species identity and composition shape the epiphytic lichen community of structurally simple boreal forests over vast areas.

Greatly simplified ecosystems are often neglected for biodiversity studies. However, these simplified systems dominate in many regions of the world, and a lack of understanding of what shapes species occurrence in these systems can have consequences for biodiversity and ecosystem services at a massive scale. In Fennoscandia, ~90% of the boreal forest (~21Mha) is structurally simplified with little knowledge of how forest structural elements shape the occurrence and diversity of for example epiphytic lichens in these managed forests. One form of structural simplification is the reduction of the number and frequency of different tree species. As many lichen species have host tree preferences, it is particularly likely that this simplification has a huge effect on the lichen community in managed forests. In a 40-70 years old boreal forest in Sweden, we therefore related the occurrence and richness of all observed epiphytic lichens to the host tree species and beta and gamma lichen diversity at the forest stand level to the stand's tree species composition and stem diameter. Picea abies hosted the highest lichen richness followed by Pinus sylvestris, Quercus robur, Alnus glutinosa, Betula spp., and Populus tremula. However, P. tremula hosted twice as many uncommon species as any of the other tree species. Stand level beta and gamma diversity was twice as high on stands with four compared to one tree species, and was highest when either coniferous or deciduous trees made up 40-50% of the trees. The stem diameter was positively related to lichen richness at the tree and stand level, but negatively to beta diversity. For biodiversity, these findings imply that leaving a few trees of a different species during forest thinning is unlikely as effective as combining life-boat trees for endangered species with an even tree species mixture.

Cytogenetic and oxidative effects of three lichen extracts on human peripheral lymphocytes.

In the present study, we investigated cytogenetic and oxidative [total antioxidant capacity (TAC), total oxidant status (TOS)] effects of methanol and water extracts of Cladonia chlorophaea (Flörke ex Sommerf.) Sprengel, Dermatocarpon miniatum (L.) W.Mann and Parmelia saxatilis (L.) Ach. on cultured human lymphocytes. In addition, different phenolic compounds in the extracts were quantified by high performance liquid chromatography (HPLC) analysis. As a result of HPLC analysis, methanol extracts of all lichen species tested had higher phenolic compounds. Likewise, methanol extracts of each lichen increased TAC levels in lymphocytes more than water extracts. The TOS levels of the cells treated with different concentrations (1-100 mg/L) of the extracts decreased due to the increasing concentration of the extracts. Genotoxicity experiments revealed that the tested lichen extracts did not significantly increase (p > 0.05) the level of genotoxicity on human peripheral lymphocyte culture compared to the negative control group. The results showed that C. chlorophaea, D. miniatum and P. saxatilis lichens, which were found to be a rich source of phenolic compounds, might be of interest in the pharmaceutical and food industries.

Linking a Gene Cluster to Atranorin, a Major Cortical Substance of Lichens, through Genetic Dereplication and Heterologous Expression.

The depside and depsidone series compounds of polyketide origin accumulate in the cortical or medullary layers of lichen thalli. Despite the taxonomic and ecological significance of lichen chemistry and its pharmaceutical potentials, there has been no single piece of genetic evidence linking biosynthetic genes to lichen substances. Thus, we systematically analyzed lichen polyketide synthases (PKSs) for categorization and identification of the biosynthetic gene cluster (BGC) involved in depside/depsidone production. Our in-depth analysis of the interspecies PKS diversity in the genus Cladonia and a related Antarctic lichen, Stereocaulon alpinum, identified 45 BGC families, linking lichen PKSs to 15 previously characterized PKSs in nonlichenized fungi. Among these, we identified highly syntenic BGCs found exclusively in lichens producing atranorin (a depside). Heterologous expression of the putative atranorin PKS gene (coined atr1) yielded 4-O-demethylbarbatic acid, found in many lichens as a precursor compound, indicating an intermolecular cross-linking activity of Atr1 for depside formation. Subsequent introductions of tailoring enzymes into the heterologous host yielded atranorin, one of the most common cortical substances of macrolichens. Phylogenetic analysis of fungal PKS revealed that the Atr1 is in a novel PKS clade that included two conserved lichen-specific PKS families likely involved in biosynthesis of depsides and depsidones. Here, we provide a comprehensive catalog of PKS families of the genus Cladonia and functionally characterize a biosynthetic gene cluster from lichens, establishing a cornerstone for studying the genetics and chemical evolution of diverse lichen substances. IMPORTANCE Lichens play significant roles in ecosystem function and comprise about 20% of all known fungi. Polyketide-derived natural products accumulate in the cortical and medullary layers of lichen thalli, some of which play key roles in protection from biotic and abiotic stresses (e.g., herbivore attacks and UV irradiation). To date, however, no single lichen product has been linked to respective biosynthetic genes with genetic evidence. Here, we identified a gene cluster family responsible for biosynthesis of atranorin, a cortical substance found in diverse lichen species, by categorizing lichen polyketide synthase and reconstructing the atranorin biosynthetic pathway in a heterologous host. This study will help elucidate lichen secondary metabolism, harnessing the lichen's chemical diversity, hitherto obscured due to limited genetic information on lichens.

New lineages of photobionts in Bolivian lichens expand our knowledge on habitat preferences and distribution of Asterochloris algae.

We studied the biodiversity of Asterochloris photobionts found in Bolivian lichens to better understand their global spatial distribution and adaptation strategies in the context of a worldwide phylogeny of the genus. Based on nuclear ITS rDNA, the chloroplast rbcL gene and the actin type I gene we reconstructed a phylogenetic tree that recovered nine new Asterochloris lineages, while 32 Bolivian photobiont samples were assigned to 12 previously recognized Asterochloris lineages. We also show that some previously discovered Asterochloris photobiont species and lineages may occur in a broader spectrum of climatic conditions, and mycobiont species and photobionts may show different preferences along an altitude gradient. To reveal general patterns of of mycobiont specificity towards the photobiont in Asterochloris, we tested the influence of climate, altitude, geographical distance and effects of symbiotic partner (mycobiont) at the species level of three genera of lichen forming fungi: Stereocaulon, Cladonia and Lepraria. Further, we compared the specificity of mycobionts towards Asterochloris photobionts in cosmopolitan, Neotropical, and Pantropical lichen forming fungi. Interestingly, cosmopolitan species showed the lowest specificity to their photobionts, but also the lowest haplotype diversity. Neotropical and Paleotropical mycobionts, however, were more specific.

Deep divergence between island populations in lichenized fungi.

Macaronesia is characterized by a high degree of endemism and represents a noteworthy system to study the evolutionary history of populations and species. Here, we compare the population-genetic structure in three lichen-forming fungi, the widespread Lobaria pulmonaria and two Macaronesian endemics, L. immixta and L. macaronesica, based on microsatellites. We utilize population genetic approaches to explore population subdivision and evolutionary history of these taxa on the Canary Islands, Madeira, Azores, and the western Iberian Peninsula. A common feature in all species was the deep divergence between populations on the Azores, a pattern expected by the large geographic distance among islands. For both endemic species, there was a major split between archipelagos. In contrast, in the widespread L. pulmonaria, divergent individuals were distributed across multiple archipelagos, suggesting a complex evolutionary history involving repeated migration between islands and mainland.

Phylogenetic revision of South American Teloschistaceae (lichenized Ascomycota, Teloschistales) reveals three new genera and species.

Members of the poorly investigated family Teloschistaceae in South America, mostly from Bolivia and Peru, were examined using molecular and morphological data here for the first time. In recent phylogenetic reclassifications of Teloschistaceae, South American representatives were poorly represented but shown to belong to subfamilies Teloschistoideae and Xanthorioideae. In this study, we expanded the sampling of South American taxa and investigated mainly the lobate, sublobate, and squamulose members of Caloplaca s.l., using morphological characters and a molecular phylogeny based on a combined three-locus data set (one mitochondrial and two nuclear loci). Building upon new phylogenies at the family and subfamily levels (Teloschistoideae), we propose here three new genera: Andina, Aridoplaca, and Cinnabaria, with the type species Andina citrinoides, Aridoplaca peltata, and Cinnabaria boliviana. We also propose to reduce Tarasginia to synonymy with Sirenophila and Tayloriellina to synonymy with Villophora and introduce three new combinations: Dufourea ottolangei, D. volkmarwirthii, and Villophora erythrosticta. Scutaria andina is reported as new to Bolivia. A critical revision of the subfamily Brownlielloideae confirmed recent findings that it is an artifactual taxon based on a "chimeric" data set, with the type genus being part of Teloschistoideae.

In vitro evaluation of lysozyme activity and antimicrobial effect of extracts from four Tunisian lichens: Diploschistes ocellatus, Flavoparmelia caperata, Squamarina cartilaginea and Xanthoria parietina.

Since lichens have been recognised as a potential natural source of bioactive substances, the aim of this study was to investigate the antimicrobial, lysozyme and antifungal effects of methanol, acetone and quencher extracts from four lichens: Diploschistes ocellatus, Flavoparmelia caperata, Squamarina cartilaginea and Xanthoria parietina. The results showed that the tested extracts had antimicrobial activity against Gram-positive and Gram-negative bacteria and anti-candida, and inhibit the spore germination of tested fungi. The different extracts varied in their effect as determined by the diameter of the inhibition zone, the highest values being observed with the methanol and acetone extracts (29.5 and 27.5 mm, respectively) for S. cartilaginea against Enterococcus faecalis. For powdered material (quencher), F. caperata showed the highest inhibition diameter (25.5 mm) against Staphylococcus aureus. The Minimum Inhibitory Concentration (MIC) values varied from 125 to 2000 µg mL-1. Methanol extracts of S. cartilaginea were more active against Enterobacter cloacae (MIC 125 µg mL-1) and Staphylococcus aureus (MIC 125 µg mL-1), and also affected lysozyme activity against Staphylococcus aureus, as well as the morphology of fungal hyphae. This study demonstrated that the investigated species are a potential source of bioactive compounds which are potentially important antimicrobial agents.

The Under-explored Extracellular Proteome of Aero-Terrestrial Microalgae Provides Clues on Different Mechanisms of Desiccation Tolerance in Non-Model Organisms.

Trebouxia sp. (TR9) and Coccomyxa simplex (Csol) are desiccation-tolerant lichen microalgae with different adaptive strategies in accordance with the prevailing conditions of their habitats. The remodelling of cell wall and extracellular polysaccharides depending on water availability are key elements in the tolerance to desiccation of both microalgae. Currently, there is no information about the extracellular proteins of these algae and other aero-terrestrial microalgae in response to limited water availability. To our knowledge, this is the first report on the proteins associated with the extracellular polymeric substances (EPS) of aero-terrestrial microalgae subjected to cyclic desiccation/rehydration. LC-MS/MS and bioinformatic analyses of the EPS-associated proteins in the two lichen microalgae submitted to four desiccation/rehydration cycles allowed the compilation of 111 and 121 identified proteins for TR9 and Csol, respectively. Both sets of EPS-associated proteins shared a variety of predicted biological functions but showed a constitutive expression in Csol and partially inducible in TR9. In both algae, the EPS-associated proteins included a number of proteins of unknown functions, some of which could be considered as small intrinsically disordered proteins related with desiccation-tolerant organisms. Differences in the composition and the expression pattern between the studied EPS-associated proteins would be oriented to preserve the biochemical and biophysical properties of the extracellular structures under the different conditions of water availability in which each alga thrives.

Neogene speciation and Pleistocene expansion of the genus Pseudephebe (Parmeliaceae, lichenized fungi) involving multiple colonizations of Antarctica.

Widespread geographic distributions in lichens have been usually explained by the high dispersal capacity of their tiny diaspores. However, recent phylogenetic surveys have challenged this assumption and provided compelling evidence for cryptic speciation and more restricted distribution ranges in diverse lineages of lichen-forming fungi. To evaluate these scenarios, we focus on the fungal genus Pseudephebe (Parmeliaceae) which includes amphitropical species, a distribution pattern whose origin has been a matter of debate since first recognized in the nineteenth century. In our study, a six-locus dataset and a broad specimen sampling covering almost all Earth's continents is used to investigate species delimitation in Pseudephebe. Population structure, gene flow and dating analyses, as well as genealogical reconstruction methods, are employed to disentangle the most plausible transcontinental migration routes, and estimate the timing of the origin of the amphitropical distribution and the Antarctic populations. Our results demonstrate the existence of three partly admixed phylogenetic species that diverged between the Miocene and Pliocene, and whose Quaternary distribution has been strongly driven by glacial cycles. Pseudephebe minuscula is the only species showing an amphitropical distribution, with populations in Antarctica, whereas the restricted distribution of P. pubescens and an undescribed Alaskan species might reflect the survival of these species in European and North American refugia. Our microevolutionary analyses suggest a Northern Hemisphere origin for P. minuscula, which could have dispersed into the Southern Hemisphere directly and/or through "mountain-hopping" during the Pleistocene. The Antarctic populations of this species are sorted into two genetic clusters: populations of the Antarctic Peninsula were grouped together with South American ones, and the Antarctic Continental populations formed a second cluster with Bolivian and Svalbard populations. Therefore, our data strongly suggest that the current distribution of P. minuscula in Antarctica is the outcome of multiple, recent colonizations. In conclusion, our results stress the need for integrating species delimitation and population analyses to properly approach historical biogeography in lichen-forming fungi.

Ontology and values anchor indigenous and grey nomenclatures: a case study in lichen naming practices among the Samí, Sherpa, Scots, and Okanagan.

Ethnobotanical research provides ample justification for comparing diverse biological nomenclatures and exploring ways that retain alternative naming practices. However, how (and whether) comparison of nomenclatures is possible remains a subject of discussion. The comparison of diverse nomenclatural practices introduces a suite of epistemic and ontological difficulties and considerations. Different nomenclatures may depend on whether the communities using them rely on formalized naming conventions; cultural or spiritual valuations; or worldviews. Because of this, some argue that the different naming practices may not be comparable if the ontological commitments employed differ. Comparisons between different nomenclatures cannot assume that either the naming practices or the object to which these names are intended to apply identifies some universally agreed upon object of interest. Investigating this suite of philosophical problems, I explore the role grey nomenclatures play in classification. 'Grey nomenclatures' are defined as those that employ names that are either intentionally or accidently non-Linnaean. The classification of the lichen thallus (a symbiont) has been classified outside the Linnaean system by botanists relying on the International Code of Nomenclature for algae, fungi, and plants (ICN). But, I argue, the use of grey names is not isolated and does not occur exclusively within institutionalized naming practices. I suggest, 'grey names' also aptly describe nomenclatures employed by indigenous communities such as the Samí of Northern Finmark, the Sherpa of Nepal, and the Okanagan First Nations. I pay particular attention to how naming practices are employed in these communities; what ontological commitments they hold; for what purposes are these names used; and what anchors the community's nomenclatural practices. Exploring the history of lichen naming and early ethnolichenological research, I then investigate the stakes that must be considered for any attempt to preserve, retain, integrate, or compare the knowledge contained in both academically formalized grey names and indigenous nomenclatures in a way that preserves their source-specific informational content.

Ethnobotany of dye plants in Southern Italy, Mediterranean Basin: floristic catalog and two centuries of analysis of traditional botanical knowledge heritage.

BACKGROUND: Since ancient times, man has learned to use plants to obtain natural dyes, but this traditional botanical knowledge (TBK) is eroding. In the late, during, and the early 1800s, there was an increase in research related to dye species, and this allowed the development of industry and economy in rural contexts of Southern Italy. Today, dyes are mainly obtained from synthetic products, and this leads to risks for human health related to pollution. METHODS: Starting from the literature, three catalogs of the dyeing species (plants, algae, fungi, and lichens) used in the Mediterranean Basin and mainly in Southern Italy have been created. Percentages of parts used and colors extracted from species have been recorded and analyzed. The plant species present in the catalogs have been verified in the territories of Southern Italy, and the data have been registered. An ethnobotanical survey was conducted, in the region of Southern Italy, to verify the erosion level of traditional botanical knowledge, linked to the ethnobotanical dyeing, over time. RESULTS: A total of 524 species were recorded among plants, algae, fungi, and lichens, and related parts used and extracted pigments. Most uses concern the stems and leaves, and the most frequent color is yellow. From the on-field survey operations, 283 plant species have been verified. These represent 64.31% of the species reported in the flora of the dye plants produced. The results, from the ethnobotanical survey, show that only 8.6% of TBK remained in the collective memory. CONCLUSIONS: This catalog is among the largest in this sector and is the basis for studies related to the restoration of an eco-sustainable economy which would allow the development of marginal areas present throughout Southern Italy.

Formally described species woefully underrepresent phylogenetic diversity in the common lichen photobiont genus Trebouxia (Trebouxiophyceae, Chlorophyta): An impetus for developing an integrated taxonomy.

Lichens provide valuable systems for studying symbiotic interactions. In lichens, these interactions are frequently described in terms of availability, selectivity and specificity of the mycobionts and photobionts towards one another. The lichen-forming, green algal genus Trebouxia Puymaly is among the most widespread photobiont, associating with a broad range of lichen-forming fungi. To date, 29 species have been described, but studies consistently indicate that the vast majority of species-level lineages still lack formal description, and new, previously unrecognized lineages are frequently reported. To reappraise the diversity and the evolutionary relationships of species-level lineages in Trebouxia, we assembled DNA sequence data from over 1600 specimens, compiled from a range of sequences from previously published studies, axenic algal cultures, and lichens collected from poorly sampled regions. From these samples, we selected representatives of the currently known genetic diversity in the lichenized Trebouxia and inferred a phylogeny from multi-locus sequence data (ITS, rbcL, cox2). We demonstrate that the current formally described species woefully underrepresent overall species-level diversity in this important lichen-forming algal genus. We anticipate that an integrative taxonomic approach, incorporating morphological and physiological data from axenic cultures with genetic data, will be required to establish a robust, comprehensive taxonomy for Trebouxia. The data presented here provide an important impetus and reference dataset for more reliably characterizing diversity in lichenized algae and in using lichens to investigate the evolution of symbioses and holobionts.

Evolutionary conservation of within-family biodiversity patterns.

The tendency for species to retain their ancestral biological properties has been widely demonstrated, but the effect of phylogenetic constraints when progressing from species to ensemble-level properties requires further assessment. Here we test whether community-level patterns (environmental shifts in local species richness and turnover) are phylogenetically conserved, assessing whether their similarity across different families of lichens, insects, and birds is dictated by the relatedness of these families. We show a significant phylogenetic signal in the shape of the species richness-elevation curve and the decay of community similarity with elevation: closely related families share community patterns within the three major taxa. Phylogenetic influences are partly explained by similarities among families in conserved traits defining body plan and interactions, implying a scaling of phylogenetic effects from the organismal to the community level. Consequently, the phylogenetic signal in community-level patterns informs about how the historical legacy of a taxon and shared responses among related taxa to similar environments contribute to community assembly and diversity patterns.

Genome-scale data reveal the role of hybridization in lichen-forming fungi.

Advancements in molecular genetics have revealed that hybridization may be common among plants, animals, and fungi, playing a role in evolutionary dynamics and speciation. While hybridization has been well-documented in pathogenic fungi, the effects of these processes on speciation in fungal lineages with different life histories and ecological niches are largely unexplored. Here we investigated the potential influence of hybridization on the emergence of morphologically and reproductively distinct asexual lichens. We focused on vagrant forms (growing obligately unattached to substrates) within a clade of rock-dwelling, sexually reproducing species in the Rhizoplaca melanophthalma (Lecanoraceae, Ascomycota) species complex. We used phylogenomic data from both mitochondrial and nuclear genomes to infer evolutionary relationships and potential patterns of introgression. We observed multiple instances of discordance between the mitochondrial and nuclear trees, including the clade comprising the asexual vagrant species R. arbuscula, R. haydenii, R. idahoensis, and a closely related rock-dwelling lineage. Despite well-supported phylogenies, we recovered strong evidence of a reticulated evolutionary history using a network approach that incorporates both incomplete lineage sorting and hybridization. These data suggest that the rock-dwelling western North American subalpine endemic R. shushanii is potentially the result of a hybrid speciation event, and introgression may have also played a role in other taxa, including vagrant species R. arbuscula, R. haydenii and R. idahoensis. We discuss the potential roles of hybridization in terms of generating asexuality and novel morphological traits in lichens. Furthermore, our results highlight the need for additional study of reticulate phylogenies when investigating species boundaries and evolutionary history, even in cases with well-supported topologies inferred from genome-scale data.