Search

The manna lichens, a group of vagrant species with subfruticose and subfoliose thalli in the genus Circinaria Link, have received attention for millennia. Here, a new manna lichen species, Circinaria nimisii sp. nov. (Megasporaceae), is described and illustrated. This vagrant lichen is found on Mount Olympus in Greece and is the fourth known manna lichen in Europe. The new taxon is characterized by its subfruticose, densely-branched thallus with a muddy, earthy colour, whitish pseudocyphellae on tips of branches, mature apothecia distinctly adnate to stipitate, and paraplectenchymatous cortex tissue. Molecular sequence data from the standard barcoding marker (nrITS) also corroborate the distinction of this species from closely related congeners. Finally, Agrestia zerovii , previously known only from its type locality in Ukraine, is proposed as a new synonym of Circinaria hispida. [ABSTRACT FROM AUTHOR]

DNA barcoding approaches provide powerful tools for characterizing fungal diversity. However, DNA barcoding is limited by poor representation of species-level diversity in fungal sequence databases. Can the development of custom, regionally focused DNA reference libraries improve species-level identification rates for lichen-forming fungi? To explore this question, we created a regional ITS database for lichen-forming fungi (LFF) in the Intermountain West of the United States. The custom database comprised over 4800 sequences and represented over 600 formally described and provisional species. Lichen communities were sampled at 11 sites throughout the Intermountain West, and LFF diversity was characterized using high-throughput ITS2 amplicon sequencing. We compared the species-level identification success rates from our bulk community samples using our regional ITS database and the widely used UNITE database. The custom regional database resulted in significantly higher species-level assignments (72.3%) of candidate species than the UNITE database (28.3–34.2%). Within each site, identification of candidate species ranged from 72.3–82.1% using the custom database; and 31.5–55.4% using the UNITE database. These results highlight that developing regional databases may accelerate a wide range of LFF research by improving our ability to characterize species-level diversity using DNA barcoding. [ABSTRACT FROM AUTHOR]

Thirty years after its designation as a federally endangered species, the Florida Perforate Cladonia (FPC) remains imperiled in isolated populations in the Florida scrub in the southeastern USA. For threatened and endangered species, such as FPC, reference genomes provide critical insight into genomic diversity, local adaptations, landscape-level genetics, and phylogenomics. Using high-throughput sequencing, we assemble the first draft nuclear and mitochondrial genomes for the FPC mycobiont—Cladonia perforata. We also assess genetic diversity within and among populations in southeastern Florida using genome-scale data and investigate diversity across the entire nuclear ribosomal cistron, including the standard DNA barcoding marker for fungi. The draft nuclear genome spanned 33.6 Mb, and the complete, circular mitochondrial genome was 59 Kb. We also generated the first chloroplast genome, to our knowledge, for the photobiont genus associated with FPC, an undescribed Asterochloris species. We inferred the presence of multiple, distinct mycobiont parental genotypes (genets) occurring at local scales in southeastern Florida, and strikingly, no genets were shared among even the closest sample sites. All sampled thalli shared identical mitochondrial genomes, while the nuclear ribosomal cistron showed limited variability—highlighting the genetic resolution provided by nuclear genome-scale datasets. The genomic resources generated here provide critical resources for informed conservation efforts for the FPC. [ABSTRACT FROM AUTHOR]

Lichens are well-known examples of complex symbiotic associations between organisms from different Kingdoms. Microfungi in particular, establish diverse associations with the hosting lichen thallus, as species-specific parasites or transient co-inhabitants. The whole community of lichen-associated fungi constitute the 'lichen mycobiome' comprising both ascomycetes and basidiomycetes, including filamentous and yeast taxa. Metabarcoding results and microscopy analyses show that in some thalli, basidiomycetes are frequent lichen-associated fungi but still only a few species could be axenically isolated and morphologically characterized. Within a broad project aiming at characterizing the mycobiome diversity by culture-dependent and independent approaches in two lichen species selected as reference models – Rhizoplaca melanophthalma and Tephromela atra , we succeed in isolating and culturing 76 new strains of basidiomycetous yeasts. The lichen thalli were collected in different mountain regions worldwide and at relatively high elevation. The yeast strains were isolated on different growth media and were studied for their morphological and genetic diversity. Nuclear internal transcribed spacer (ITS) and ribosomal large subunit (LSU) sequence analyses identified them to belong to ten families within the orders Agaricostilbomycetes, Cystobasidiomycetes, Microbotryomycetes, Tremellomycetes and Ustilaginomycetes. The yeasts here detected showed patterns of host-preference in a few cases and they are potentially related to the ecological conditions. [ABSTRACT FROM AUTHOR]

Lichens are major components of high altitude/latitude ecosystems. However, accurately characterizing their biodiversity is challenging because these regions and habitats are often underexplored, there are numerous poorly known taxonomic groups, and morphological variation in extreme environments can yield conflicting interpretations. Using an iterative taxonomic approach based on over 800 specimens and incorporating both traditional morphology‐based identifications and information from the standard fungal DNA barcoding marker, we compiled a voucher‐based inventory of biodiversity of lichen‐forming fungi in a geographically limited and vulnerable alpine community in an isolated sky island in the Colorado Plateau, USA—the La Sal Mountains. We used the newly proposed Assemble Species by Automatic Partitioning (ASAP) approach to empirically delimit candidate species‐level lineages from family‐level multiple sequence alignments. Specimens comprising DNA‐based candidate species were evaluated using traditional taxonomically diagnostic phenotypic characters to identify specimens to integrative species hypotheses and link these, where possible, to currently described species. Despite the limited alpine habitat (ca. 3,250 ha), we document the most diverse alpine lichen community known to date from the southern Rocky Mountains, with up to 240 candidate species/species‐level lineages of lichen‐forming fungi. 139 species were inferred using integrative taxonomy, plus an additional 52 candidate species within 29 different putative species complexes. Over 68% of sequences could not be assigned to species‐level rank with statistical confidence, corroborating the limited utility of current sequence repositories for species‐level DNA barcoding of lichen‐forming fungi. By integrating vouchered specimens, DNA sequence data, and photographic documentation, we provide an important baseline of lichen‐forming fungal diversity for the limited alpine habitat in the Colorado Plateau. These data provide an important resource for subsequent research in the ecology and evolution of lichens alpine habitats, including DNA barcodes for most putative species/species‐level lineages occurring in the La Sal Mountains, and vouchered collections representing any potentially undescribed species that can be used for future taxonomic studies. [ABSTRACT FROM AUTHOR]

Based on field collections made during the summers of 1987, 1988, and 1989, we report 159 species of lichens in 69 genera for the Jarbidge Wilderness Area (JWA) and adjacent Forest Service lands, located in the northern Great Basin, USA. Specimens were collected at 25 sites, distributed across the JWA along with two additional sites north of the wilderness boundary on Forest Service land. Collections were made from all available substrates, including rocks, bark, lignum, mosses, soil, and from the thalli of various saxicolous lichens. All basic growth forms were found, especially crustose and foliose species. Umbilicate species (Dermatocarpon spp., Rhizoplaca spp., and Umbilicaria spp.) were commonly found on rocks, while a limited number of fruticose species (Letharia spp. and Bryoria spp.) were found on bark and lignum substrates. A single, fruticose species was found on rocks (Pseudephebe minuscula). Saxicolous substrates supported the richest lichen communities, followed by corticolous and lignicolous substrates. Specifically, cottonwood spp., various conifer species, and curled leaf mountain mahogany were important bark and lignum substrates. Other taxa occurred on soil/bryophyte/detritus substrates with one species commonly collected on the thalli of various saxicolous lichens (i.e., Caloplaca epithallina). The JWA lichen flora is richer than other Nevada wilderness areas so far surveyed, with 33 putative new species records for the state of Nevada. Species richness and abundance in the JWA is likely due in part to the more mesic conditions found in the wilderness as well as its proximity to the more abundant and diverse lichen communities found in the Northern Rocky Mountains and the Pacific Northwest. Samples of two sensitive indicator species (Rhizoplaca melanophthalma and Letharia lupina) were analyzed to determine thallus concentrations of three potential air pollutants (sulfur, copper, and lead). All pollutant element concentrations were within background levels except for percent sulfur in two samples of Letharia lupina from Hummingbird Ridge (0.226%) and Emerald Lake (0.215%). Both sites are upper elevation (> 2700 m ASL) suggesting possible accumulation due to long-range transport of sulfur species from large urban areas in the Pacific Northwest. [ABSTRACT FROM AUTHOR]

Lichens are classic models of symbiosis, and one of the most frequent nutritional modes among fungi. The ecologically and geographically widespread lichen-forming algal (LFA) genus Trebouxia is one of the best-studied groups of LFA and associates with over 7000 fungal species. Despite its importance, little is known about its diversification. We synthesized twenty years of publicly available data by characterizing the ecological preferences of this group and testing for time-variant shifts in climatic regimes over a distribution of trees. We found evidence for limited shifts among regimes, but that disparate lineages convergently evolved similar ecological tolerances. Early Trebouxia lineages were largely forest specialists or habitat generalists that occupied a regime whose extant members occur in moderate climates. Trebouxia then convergently diversified in non-forested habitats and expanded into regimes whose modern representatives occupy wet-warm and cool-dry climates. We rejected models in which climatic diversification slowed through time, suggesting climatic diversification is inconsistent with that expected under an adaptive radiation. In addition, we found that climatic and vegetative regime shifts broadly coincided with the evolution of biomes and associated or similar taxa. Together, our work illustrates how this keystone symbiont from an iconic symbiosis evolved to occupy diverse habitats across the globe. [ABSTRACT FROM AUTHOR]

Two new species belonging to the common and widespread lichen genus Physcia are described from western North America. One of these, P. occidentalis, is an obligately saxicolous species that reproduces by fragmentation, primarily through the production of largely terminal blastidia. Only a single very immature apothecium was observed among all collections. The species occurs from British Columbia to California, with outliers in Colorado. The other species, P. rhizinata, is a corticolous, typically fertile species lacking asexual propagules, and has often been confused with P. stellaris. It is presently known only from California. The close evolutionary relationship of these morphologically dissimilar taxa highlights the currently limited understanding of factors that lead to phenotypic divergence in lichen symbioses. [ABSTRACT FROM AUTHOR]

The La Sal Mountains in eastern Utah, USA, contain the only alpine habitat on the Colorado Plateau in Utah. These unique sky island alpine communities are vulnerable to a wide range of disturbances, including factors associated with the recent introduction of mountain goats (O. americanus). In order to monitor the potential impact of O. americanus, and other disturbances on alpine communities in the La Sals, we provide baseline estimate population densities for 'Wyoming range lichens' (Xanthoparmelia wyomingica) at two sites near Mount Laurel. Using the point-centered quarter and the quartered-neighbor methods, we estimate ca. 20 individuals/m2 at both sites. These estimates provide an important baseline for long-term monitoring of vulnerable alpine sites on the Colorado Plateau. [ABSTRACT FROM AUTHOR]

Twenty-five North American lichens are issued in this exsiccat series, numbers 151-175. In this fascicle, collections were made from nine states, including: Alaska (1), Arizona (3), California (2), Colorado (6), Idaho (1), Montana (4), Nevada (2), New Mexico (4), and Utah (2). Here, Thamnolia subuliformis (Ehrh.) W. L. Culb. (No. 173) is reported as a new species record for Utah. [ABSTRACT FROM AUTHOR]

Xanthoparmelia (Parmeliaceae, Ascomycota) is the most species-rich genus of lichen-forming fungi. Species boundaries are based on morphological and chemical features, varying reproductive strategies and, more recently, molecular sequence data. The isidiate Xanthoparmelia mexicana group is common in arid regions of North and Central America and includes a range of morphological variation and variable secondary metabolites - salazinic or stictic acids mainly. In order to better understand the evolutionary history of this group and potential taxonomic implications, a molecular phylogeny representing 58 ingroup samples was reconstructed using four loci, including ITS, mtSSU, nuLSU rDNA and MCM7. Results indicate the existence of multiple, distinct lineages phenotypically agreeing with X. mexicana. One of these isidiate, salazinic acid-containing lineages is described here as a new species, X. pedregalensis sp. nov., including populations from xerophytic scrub vegetation in Pedregal de San Angel, Mexico City. X. mexicana s. str. is less isidiate than X. pedregalensis and has salazinic and consalazinic acid, occasionally with norstictic acid; whereas X. pedregalensis contains salazinic and norstictic acids and an unknown substance. Samples from the Old World, morphologically agreeing with X. mexicana, are only distantly related to X. mexicana s. str. Our results indicate that X. mexicana is likely less common than previously assumed and ongoing taxonomic revisions are required for isidiate Xanthoparmelia species. [ABSTRACT FROM AUTHOR]

Species richness is not evenly distributed across the tree of life and a limited number of lineages comprise an extraordinarily large number of species. In lichen-forming fungi, only two genera are known to be ‘ultradiverse’ (>500 species), with the most diverse genus, Xanthoparmelia, consisting of c. 820 species. While Australia and South Africa are known as current centres of diversity for Xanthoparmelia, it is not well known when and where this massive diversity arose. To better understand the geographical and temporal context of diversification in this diverse genus, we sampled 191 Xanthoparmelia specimens representing c. 124 species/species-level lineages from populations worldwide. From these specimens, we generated a multi-locus sequence data set using Sanger and high-throughput sequencing to reconstruct evolutionary relationships in Xanthoparmelia, estimate divergence times and reconstruct biogeographical histories in a maximum likelihood and Bayesian framework. This study corroborated the phylogenetic placement of several morphologically or chemically diverse taxa within Xanthoparmelia, such as Almbornia, Chondropsis, Karoowia, Namakwa, Neofuscelia, Omphalodiella, Paraparmelia, Placoparmelia and Xanthomaculina, in addition to improved phylogenetic resolution and reconstruction of previously unsampled lineages within Xanthoparmelia. Our data indicate that Xanthoparmelia most likely originated in Africa during the early Miocene, coinciding with global aridification and development of open habitats. Reconstructed biogeographical histories of Xanthoparmelia reveal diversification restricted to continents with infrequent intercontinental exchange by long-distance dispersal. While likely mechanisms by which Xanthoparmelia obtained strikingly high levels of species richness in Australia and South Africa remain uncertain, this study provides a framework for ongoing research into diverse lineages of lichen-forming fungi. Finally, our study highlights a novel approach for generating locus-specific molecular sequence data sets from high throughput metagenomic reads. [ABSTRACT FROM AUTHOR]

Molecular data provide unprecedented insight into diversity of lichenized fungi, although morphologically cryptic species-level lineages circumscribed from sequence data often remain undescribed even in well-studies groups. Using diagnostic characters from DNA sequence data and support from the multispecies coalescent model, we formally describe a total of eleven new species and resurrect two others in the hyperdiverse lichen-forming fungal family Parmeliaceae. These include: four in the genus Melanelixia – M. ahtii sp. nov., M. epilosa comb. nov., M. hawksworthii sp. nov., and M. robertsoniorum sp. nov.; six in Melanohalea – M. austroamericana sp. nov. , M. beringiana sp. nov., M. clari sp. nov., M. columbiana sp. nov., M. davidii sp. nov., and M. tahltan sp. nov.; and three species in Montanelia – M. occultipanniformis sp. nov., M. saximontana comb. nov., and M. secwepemc sp. nov. Morphological, ecological and geographical features were revised to corroborate species descriptions. These species can consistently be distinguished by differences in nucleotide position characters in the fungal barcoding marker (ITS) and high speciation probabilities. This study helps close the “taxonomic gap” between molecular species delimitation studies and formal taxonomy by incorporating statistical evaluation of lineage independence, diagnostic differences in DNA data, and additional consideration of differences in morphology and species distributions. [ABSTRACT FROM AUTHOR]

Western North America is the global centre of diversity for Letharia, a distinctive and cryptically diverse genus of lichenized fungi belonging to the Parmeliaceae. The genus is characterized by a shrubby, fruticose habit and presence of vulpinic acid. Previous studies using multiple fungal nuclear loci revealed the existence of two distinct species-level lineages within the traditional concept of L. vulpina and four such lineages within L. columbiana. Here we use molecular sequence data in an attempt to settle long-standing taxonomic issues in the genus. Our results confirm the widespread existence within L. vulpina s. lat. of two distinct species-level groups, each forming a mutually exclusive partnership with a separate algal clade within Trebouxia jamesii s. lat. Accordingly, we formally describe the segregate species L. lupina sp. nov. Our results also support the evolutionary independence of four candidate species previously circumscribed from L. columbiana s. lat. One of these lineages, L. ‘gracilis’, has already received species recognition as L. gracilis, while a second, L. ‘lucida’, is epitypified here against L. columbiana s. str. Based on results from species delimitation analyses under the multispecies coalescent model, the two remaining lineages, L. ‘barbata’ and L. ‘rugosa’, also warrant formal taxonomic recognition; however, we refrain from describing these species pending additional studies of diagnostic characters, ecological preference, and distributions. [ABSTRACT FROM PUBLISHER]

Identifying factors that influence species interactions is central to research in symbiotic systems. While lichens represent iconic models of symbiosis and play important roles in understanding the biology of symbiotic interactions, patterns of interactions in lichen symbionts and mechanisms governing these relationships are not well characterized. This is due, in part to the fact that current taxonomic approaches for recognizing diversity in lichen symbionts commonly fail to accurately reflect actual species diversity. In this study, we employed DNA-based approaches to circumscribed candidate species-level lineages in rock-posy lichen symbionts (mycobiont = Rhizoplaca s. lat. species; photobiont = Trebouxia species). Our results revealed a high degree of cryptic diversity in both the myco- and photobionts in these lichens. Using the candidate species circumscribed here, we investigated the specificity of the symbionts toward their partners and inferred the relative importance of various factors influencing symbiont interactions. Distinct mycobiont species complexes, ecozones, and biomes are significantly correlated with the occurrence of photobiont OTUs, indicating that complex interactions among mycobiont lineages, ecogeography, and microhabitat determine interactions between photobionts and their mycobionts in lichen symbiosis. One-to-one specificity between mycobiont and photobiont species was not found, with the exception of R. maheui that associated with a single Trebouxia OTU that was not found with other Rhizoplaca s. lat. species. We estimated the most recent common ancestor of the core Rhizoplaca group at c. 62.5 Ma, similar in age to the diverse parmelioid core group in the well-studied family Parmeliaceae. However, in contrast to Parmeliaceae, species in Rhizoplaca were found to associate with a narrow range of photobionts. Our study provides important perspectives into species diversity and interactions in iconic lichen symbiotic systems and establishes a valuable framework for continuing research into rock-posy lichens. [ABSTRACT FROM AUTHOR]

Accurate specimen identification is challenging in groups with subtle or scarce taxonomically diagnostic characters, and the use of DNA barcodes can provide an effective means for consistent identification. Here, we investigate the utility of DNA barcode identification of species in a cosmopolitan genus of lichen-forming fungi, Parmelia (Parmeliaceae). Two hundred and two internal transcribed spacer (ITS) sequences generated from specimens collected from all continents, including Antarctica, were analysed, and DNA barcodes of 14 species of Parmelia s.s. are reported. Almost all species show a barcode gap. Overall, intraspecific divergence values were lower than the threshold previously established for Parmeliaceae. However, the mean and range were elevated by deep barcode divergences in three species, indicating the likely occurrence of overlooked specieslevel lineages. Here, we provide a DNA barcode reference library with well-identified specimens sampled worldwide and sequences from most of the type material to enable easy and fast accurate sample identification and to assist in uncovering overlooked species in Parmelia s.s. Further, our results confirm the efficiency of the ITS region in the identification of species of Parmelia s.s. [ABSTRACT FROM AUTHOR]

Brown parmelioid lichens comprise a number of distinct genera in one of the most species-rich families of lichen-forming fungi, Parmeliaceae (Ascomycota). In spite of their superficial similarity, a number of studies of brown parmelioids have provided important insight into diversification in lichen-forming fungi with cosmopolitan distributions. In this study we assess species diversity, biogeography and diversification of the genus Montanelia , which includes alpine to temperate saxicolous species. We sampled each of the five known species, four of which are known from broad, intercontinental distributions. In order to identify potential biogeographical patterns, each broadly distributed species was represented by individuals collected across their intercontinental distributions. Molecular sequence data were generated for six loci, including three nuclear protein-coding markers (MCM7, RPB1, and RPB2), two nuclear ribosomal markers (ITS and nrLSU), and a fragment of the mitochondrial small subunit. We used three sequence-based species delimitations methods to validate traditional, phenotype-based species and circumscribe previously unrecognized species-level lineages in Montanelia . Relationships among putative lineages and divergence times were estimated within a coalescent-based multi-locus species tree framework. Based on the results of the species delimitation analyses, we propose that the genus Montanelia is likely comprised of six to nine species-level lineages, including previously unrecognized species-level diversity in the nominal taxa M. panniformis and M. tominii . In contrast, molecular sequence data suggest that M. predisjuncta may be conspecific with the widespread taxon M. disjuncta in spite of distinct morphological differences . The rate-based age estimation of the most recent common ancestor of Montanelia (ca. 23.1 Ma) was similar to previous estimates based on the fossil record. Furthermore, our data suggest that diversification in Montanelia occurred largely during the Neogene. At least three Montanelia species are broadly distributed throughout Asia, Europe, and North America with no evidence of phylogeographic substructure. In contrast to broadly distributed Montanelia species, our study suggests Pleistocene-dominated diversification and complex biogeographic history in the M. tominii group. Our analyses provide additional insight for understanding diversification and uncovering cryptic diversity in cosmopolitan species of lichen-forming fungi. [ABSTRACT FROM AUTHOR]

Microbial symbionts are instrumental to the ecological and long-term evolutionary success of their hosts, and the central role of symbiotic interactions is increasingly recognized across the vast majority of life. Lichens provide an iconic group for investigating patterns in species interactions; however, relationships among lichen symbionts are often masked by uncertain species boundaries or an inability to reliably identify symbionts. The species-rich lichen-forming fungal family Parmeliaceae provides a diverse group for assessing patterns of interactions of algal symbionts, and our study addresses patterns of lichen symbiont interactions at the largest geographic and taxonomic scales attempted to date. We analysed a total of 2356 algal internal transcribed spacer ( ITS) region sequences collected from lichens representing ten mycobiont genera in Parmeliaceae, two genera in Lecanoraceae and 26 cultured Trebouxia strains. Algal ITS sequences were grouped into operational taxonomic units ( OTUs); we attempted to validate the evolutionary independence of a subset of the inferred OTUs using chloroplast and mitochondrial loci. We explored the patterns of symbiont interactions in these lichens based on ecogeographic distributions and mycobiont taxonomy. We found high levels of undescribed diversity in Trebouxia, broad distributions across distinct ecoregions for many photobiont OTUs and varying levels of mycobiont selectivity and specificity towards the photobiont. Based on these results, we conclude that fungal specificity and selectivity for algal partners play a major role in determining lichen partnerships, potentially superseding ecology, at least at the ecogeographic scale investigated here. To facilitate effective communication and consistency across future studies, we propose a provisional naming system for Trebouxia photobionts and provide representative sequences for each OTU circumscribed in this study. [ABSTRACT FROM AUTHOR]

Two new species in the genus Trapelia, namely, T. calvariana Kantvilas & Lumbsch from the Tasmanian highlands and T. thieleana Kantvilas & Lumbsch from south-western Western Australia, are described. Examination of ascus types and analyses of DNA-sequence data confirmed the inclusion of these taxa in Trapelia sensu lato, but raised questions concerning the homogeneity of the genus as currently circumscribed and, in particular, the generic classification of T. lilacea Kantvilas & Elix. [ABSTRACT FROM AUTHOR]

The inclusion of molecular data is increasingly an integral part of studies assessing species boundaries. Analyses based on predefined groups may obscure patterns of differentiation, and population assignment tests provide an alternative for identifying population structure and barriers to gene flow. In this study, we apply population assignment tests implemented in the programs STRUCTURE and BAPS to single nucleotide polymorphisms from DNA sequence data generated for three previous studies of the lichenized fungal genus Letharia. Previous molecular work employing a gene genealogical approach circumscribed six species-level lineages within the genus, four putative lineages within the nominal taxon L. columbiana (Nutt.) J.W. Thomson and two sorediate lineages. We show that Bayesian clustering implemented in the program STRUCTURE was generally able to recover the same six putative Letharia lineages. Population assignments were largely consistent across a range of scenarios, including: extensive amounts of missing data, the exclusion of SNPs from variable markers, and inferences based on SNPs from as few as three gene regions. While our study provided additional evidence corroborating the six candidate Letharia species, the equivalence of these genetic clusters with species-level lineages is uncertain due, in part, to limited phylogenetic signal. Furthermore, both the BAPS analysis and the ad hoc ΔK statistic from results of the STRUCTURE analysis suggest that population structure can possibly be captured with fewer genetic groups. Our findings also suggest that uneven sampling across taxa may be responsible for the contrasting inferences of population substructure. Our results consistently supported two distinct sorediate groups, ‘L. lupina’ and L. vulpina, and subtle morphological differences support this distinction. Similarly, the putative apotheciate species ‘L. lucida’ was also consistently supported as a distinct genetic cluster. However, additional studies will be required to elucidate the relationships of other L. columbiana s.l. populations with the two sorediate genetic clusters. [ABSTRACT FROM AUTHOR]

While the distribution and ranges of arctic plants were greatly affected by the advance and retreat of ice sheets, the impact of glacial and interglacial cycles on lichenized fungi remains largely unexplored. Inn this study we examine the impact of Pleistocene climatic changes on two closely related Xanthomendoza (Teloschistaceae, Ascomycota) species with distinct distribution patterns and reproductive strategies. We selected X. borealis, which occurs in polar regions of both hemispheres, and the corticolous X. montana, which is restricted to montane shrublands in western North America. We analyzed the complete nuclear ribosomal internal transcribed spacer region (ITS) to confirm the monophyly and relative ages of X. borealis and X. montana. We estimated molecular diversity and population demographics statistics, mismatch distributions, and Bayesian skyline plots for both species. Our data indicate that X. montana experienced a Late Pleistocene population expansion. We suggest that major shifts in vegetation types as a result of Pleistocene climate change had a substantial impact on distribution patterns and the demographic history of X. montana. In contrast, results from this study indicate that the demographic history of X. borealis is consistent with long-term stability, although low genetic variability in the ITS marker for X. borealis limits overall confidence in this inference. We propose that X. borealis has been able to maintain a stable population size across climatic shifts, likely through effective dispersal to suitable habitats and suggests that climatic conditions during Pleistocene glacial cycles were not inherently unfavorable or restrictive for some high altitude/latitude lichen-forming fungal species. Investigating mating systems for these two Xanthomendoza species may provide important insights about the factors affecting population demographics and reproduction in lichen-forming fungi in general. [ABSTRACT FROM AUTHOR]

Aim The relative importance of long-distance dispersal versus vicariance in determining the distribution of lichen-forming fungi remains unresolved. Here, we examined diversity and distributions in a cosmopolitan lichen-forming fungal species complex, Rhizoplaca melanophthalma sensu lato (Ascomycota), across a broad, intercontinental geographical distribution. We sought to determine the temporal context of diversification and the impacts of past climatic fluctuations on demographic dynamics within this group. Location Antarctica, Asia, Europe, North America and South America. Methods We obtained molecular sequence data from a total of 240 specimens of R. melanophthalma s.l. collected across five continents. We assessed the monophyly of candidate species using individual gene trees and a tree from a seven-locus concatenated data set. Divergence times and relationships among candidate species were evaluated using a multilocus coalescent-based species tree approach. Speciation probabilities were estimated using the coalescent-based species delimitation program bpp. We also calculated statistics on molecular diversity and population demographics for independent lineages. Main conclusions Our analyses of R. melanophthalma s.l. collected from five continents supported the presence of six species-level lineages within this complex. Based on current sampling, two of these lineages were found to have broad intercontinental distributions, while the other four were limited to western North America. Of the six lineages, five were found on a single mountain in the western USA and the sixth occurred no more than 200 km away from this mountain. Our estimates of divergence times suggest that Pleistocene glacial cycles played an important role in species diversification within this group. At least three lineages show evidence of recent or ongoing population expansion. [ABSTRACT FROM AUTHOR]

The new species Oropogon evernicus Essl. & S. Leavitt and O. protocetraricus S. Leavitt & Essl. are described from montane regions of Central America, further increasing the diversity of this genus in the New World. Oropogon evernicus is separated from O. americanus by the presence of medullary tissue directly beneath the pseudocyphellae, while O. protocetraricus is separated from O. caespitosus by the presence of protocetraric acid. The segregation of both species is confirmed by molecular sequence data (nuclear ITS, nuLSU, and β-tubulin). Both species appear to have split from their most recent common ancestor during the Miocene, supporting Miocene-dominated diversification of neotropical Oropogon species found in Central America. [ABSTRACT FROM PUBLISHER]

Fungal selectivity (range of potential partners) for algal symbionts has been found to vary in lichen associations. Although a large number of studies have focused on the taxonomy and evolution of fungi in the speciose parmelioid clade (Parmeliaceae, Ascomycota), fungal-algal interactions in this ecologically and evolutionarily diverse group remain largely unexplored. In this study we investigated the algal symbionts of Xanthoparmelia fungi in western North America. We generated sequence data from a total of 58 rock shield lichens (Xanthoparmelia fungi + Trebouxia algae) collected across three sites in a subalpine community in southern Utah, USA. We explored the role of substrates, secondary metabolite variation, phenotype-based Xanthoparmelia species, mycobiont genetic population clusters, and sitespecific differences in structuring assemblages of algae. Our results indicate that Xanthoparmelia fungi associate with a broad range of Trebouxia lineages in a local, subalpine habitat. Most algae sampled form part of the diverse Trebouxia 'arboricola/gigantea' clade, while a small number of algae from outside of this clade were also found to associate with the Xanthoparmelia species investigated here. Our results also revealed multiple Trebouxia lineages within the T. 'arboricola/gigantea' clade that have not been previously recognized. Furthermore, accumulation curves suggested that additional algal diversity in rock shield lichen communities in the sampled subalpine habitat may be recovered with increased sampling. Overall, we found no clear association of algal clades with traditional phenotype-based Xanthoparmelia species, mycobiont genetic population clusters, distinct extrolites, or substrates. However, our data revealed significant genetic structuring of Trebouxia communities in separate subalpine meadow areas in a relatively homogeneous subalpine community. Significant site-specific differences in Trebouxia diversity in rock shield lichen communities and low selectivity suggest that photobiont flexibility may play an important role in overall successful colonization of rock shield lichens across a wide array of habitats in western North America. [ABSTRACT FROM AUTHOR]

The relationship of Aspicilia uxoris within Megasporaceae is assessed within a phylogenetic context. ‘Aspicilia’ uxoris and other related species are recovered as sister to the genus Lobothallia s. str. and described here as a new genus. Teuvoa (Ascomycota, Megasporaceae) is erected based on nuclear ITS and LSU sequence data and morphological characters. In addition to Teuvoa uxoris, a second species, T. junipericola, is added to the new genus based on material collected from North America. Teuvoa junipericola, T. uxoris and T. tibetica form a group with 8-spored asci, absence of extrolites, rather short-sized conidia and ascospores, lack of a subhypothecial algal layer, and different substratum preferences (on organic substratum) with a sister relationship to genus Lobothallia s. lat. (Aspicilia subgenus Pachyothallia Clauzade & C. Roux). Based on spore measurements of the holotypes, Lecanora ferganensis Tomin from central Asia (Kyrgyzstan, Tajikistan and Uzbekistan), Lecanora atrodiscata Gintovt, from Tajikistan and Lecanora takyroides Dzhur. from Turkmenistan are new synonyms to T. uxoris. A lectotype for Lecanora ferganensis is designated, expanding the known distribution of T. uxoris from Algeria, Morocco and Spain, into Central Asia. [ABSTRACT FROM AUTHOR]

Recent studies using sequence data from multiple loci and coalescent-based species delimitation have revealed several species-level lineages within the phenotypically circumscribed taxon Rhizoplaca melanophthalma sensu lato. Here, we formally describe five new species within this group, R. occulta, R. parilis, R. polymorpha, R. porterii, and R. shushanii, using support from the coalescent-based species delimitation method implemented in the program Bayesian Phylogenetics and Phylogeography (BPP) as the diagnostic feature distinguishing new species. We provide a reference DNA sequence database using the ITS marker as a DNA barcode for identifying species within this complex. We also assessed intraspecific genetic distances within the six R. melanophthalma sensu lato species. While intraspecific genetic distances within the phenotypically cryptic lineages within this broadly distributed lineage. Overall, our results demonstrate the potential for accurately identifying species within the R. melanophthalma group by using molecularbased identification methods.five new species were less than or equal to the lowest interspecific pairwise comparison values, an overlap in genetic distances within the R. melanophthalma sensu stricto clade suggests the potential for additional phenotypically cryptic lineages within this broadly distributed lineage. Overall, our results demonstrate the potential for accurately identifying species within the R. melanophthalma group by using molecular-based identiication methods. [ABSTRACT FROM AUTHOR]

Recent studies using sequence data from multiple loci and coalescent-based species delimitation have revealed several species-level lineages within the phenotypically circumscribed taxon Rhizoplaca melanophthalma sensu lato. Here, we formally describe five new species within this group, R. occulta, R. parilis, R. polymorpha, R. porterii, and R. shushanii, using support from the coalescent-based species delimitation method implemented in the program Bayesian Phylogenetics and Phylogeography (BPP) as the diagnostic feature distinguishing new species. We provide a reference DNA sequence database using the ITS marker as a DNA barcode for identifying species within this complex. We also assessed intraspecific genetic distances within the six R. melanophthalma sensu lato species. While intraspecific genetic distances within the five new species were less than or equal to the lowest interspecific pairwise comparison values, an overlap in genetic distances within the R. melanophthalma sensu stricto clade suggests the potential for additional phenotypically cryptic lineages within this broadly distributed lineage. Overall, our results demonstrate the potential for accurately identifying species within the R. melanophthalma group by using molecularbased identification methods. [ABSTRACT FROM AUTHOR]

Abstract: Accurate species circumscriptions are central for many biological disciplines and have critical implications for ecological and conservation studies. An increasing body of evidence suggests that in some cases traditional morphology-based taxonomy have underestimated diversity in lichen-forming fungi. Therefore, genetic data play an increasing role for recognizing distinct lineages of lichenized fungi that it would otherwise be improbable to recognize using classical phenotypic characters. Melanohalea (Parmeliaceae, Ascomycota) is one of the most widespread and common lichen-forming genera in the northern Hemisphere. In this study, we assess traditional phenotype-based species boundaries, identify previously unrecognized species-level lineages and discuss biogeographic patterns in Melanohalea. We sampled 487 individuals worldwide, representing 18 of the 22 described Melanohalea species, and generated DNA sequence data from mitochondrial, nuclear ribosomal, and protein-coding markers. Diversity previously hidden within traditional species was identified using a genealogical concordance approach. We inferred relationships among sampled species-level lineages within Melanohalea using both concatenated phylogenetic methods and a coalescent-based multilocus species tree approach. Although lineages identified from genetic data are largely congruent with traditional taxonomy, we found strong evidence supporting the presence of previously unrecognized species in six of the 18 sampled taxa. Strong nodal support and overall congruence among independent loci suggest long-term reproductive isolation among most species-level lineages. While some Melanohalea taxa are truly widespread, a limited number of clades appear to have much more restricted distributional ranges. In most instances the concatenated gene tree and multilocus species tree approaches provided similar estimates of relationships. However, nodal support was generally higher in the phylogeny estimated from concatenated data, and relationships among taxa within one major clade were largely unresolved in the species tree. This study contributes to our understanding of diversity and evolution in common lichen-forming fungi by incorporating multiple locus sequence data to circumscribe morphologicallly cryptic lineages and infer relationships within a coalescent-based species tree approach. [Copyright &y& Elsevier]

Despite the recent advancements in recognizing diversity in lichen-forming fungi, assessing the timing of diversification remains largely unexplored in these important fungal symbionts. To better understand the evolutionary processes driving diversification in common lichen-forming fungi, we investigated the phylogeny and biogeography of the broadly distributed Melanelixia fuliginosa/ M. glabratula group, using molecular data from six nuclear markers. Phylogenetic analyses of individual gene alignments and combined data provide strong evidence for five species-level lineages within this species complex. Three of these lineages correspond to the previously described species M. fuliginosa, M. glabratula, and M. subaurifera. The remaining two lineages, ' M. sp. 1' and ' M. sp. 2', merit species recognition based on genealogical concordance. Both M. glabratula and M. subaurifera had broad intercontinental distributions, sharing identical haplotypes among intercontinental populations. Based on the current sampling, M. fuliginosa s.s. was represented exclusively by European material and was not collected in North America. ' M. sp. 1' was represented by collections from Scotland and Spain; and ' M. sp. 2' was represented by collections in California, USA. Environmental factors driving the contrasting distribution patterns in this group remain unknown. Divergence times estimated using a coalescence-based multilocus species-tree approach suggest that diversification within the M. fuliginosa/ M. glabratula group occurred exclusively during the Miocene. The results of the present study indicate that phenotypically cryptic lichen-forming fungal species-level lineages may be relatively ancient and do not necessarily reflect recent divergence events. Furthermore, diagnosable phenotypic differences may be absent even millions of years after the initial divergence. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, ●●, ●●-●●. [ABSTRACT FROM AUTHOR]

The article discusses the challenge of identifying lichenized fungal species which are difficult to discern while chemical characters lack chemical characters. It says that a reference DNA sequence database, which was generated from identified specimens can provide an alternative to determine the species by DNA barcoding. It mentions that the most sequenced fungal genetic marker was the internal transcribed spacer region (ITS) of the nuclear ribosomal RNA cistron.

Premise of the study: Diversification in neotropical regions has been attributed to both Tertiary geological events and Pleistocene climatic fl uctuations. However, the timing and processes driving speciation in these regions remain unexplored in many important groups. Here, we address the timing of diversification in the neotropical lichenized fungal genus Oropogon (Ascomycota) and assess traditional species boundaries. Methods: We analyzed sequence data from three loci to assess phenotypically circumscribed Oropogon species from the Oaxacan Highlands, Mexico. We provide a comparison of dated divergence estimates between concatenated gene trees and a calibrated multilocus species-tree using substitution rates for two DNA regions. We also compare estimates from a data set excluding ambiguously aligned regions and a data set including the hyper-variable regions in two ribosomal markers. Key results: Phylogenetic reconstructions were characterized by well-supported monophyletic clades corresponding to traditionally circumscribed species, with the exception of a single taxon. Divergence estimates indicate that most diversification of the sampled Oropogon species occurred throughout the Oligocene and Miocene, although diversification of a single closely related clade appears to have occurred during the late Pliocene and into the Pleistocene. Divergence estimates calculated from a data set with ambiguously aligned regions removed were much more recent than those from the full data set. Conclusions: Overall, our analyses place the majority of divergence events of Oropogon species from the Oaxacan Highlands within the Neogene and provide strong evidence that climatic changes during the Pleistocene were not a major factor driving speciation in the lichenized genus Oropogon in neotropical highlands. [ABSTRACT FROM AUTHOR]

Background: Factors promoting diversification in lichen symbioses remain largely unexplored. While Pleistocene events have been important for driving diversification and affecting distributions in many groups, recent estimates suggest that major radiations within some genera in the largest clade of macrolichens (Parmeliaceae, Ascomycota) vastly predate the Pleistocene. To better understand the temporal placement and sequence of diversification events in lichens, we estimated divergence times in a common lichen-forming fungal genus, Melanohalea, in the Northern Hemisphere. Divergence times were estimated using both concatenated gene tree and coalescent-based multilocus species tree approaches to assess the temporal context of major radiation events within Melanohalea. In order tocomplement our understanding of processes impacting genetic differentiation, we also evaluated the effects of Pleistocene glacial cycles on population demographics of distinct Melanohalea lineages, differing in reproductive strategies. Results: We found that divergence estimates, from both concatenated gene tree and coalescent-based multilocus species tree approaches, suggest that diversification within Melanohalea occurred predominantly during the Miocene and Pliocene, although estimated of divergence times differed by up to 8.3 million years between the two methods. These results indicate that, in some cases, taxonomically diagnostic characters may be maintained amongdivergent lineages for millions of years. In other cases, similar phenotypic characters among non-sister taxa, including reproductive strategies, suggest the potential for convergent evolution due to similar selective pressures among distinct lineages. Our analyses provide evidence of population expansions predating the last glacial maximum in the sampled lineages. These results suggest that Pleistocene glaciations were not inherently unfavorable or restrictive for some Melanohalea species, albeit with apparently different demographic histories between sexually and vegetatively reproducing lineages. Conclusions: Our results contribute to the understanding of how major changes during the Miocene and Pliocene have been important in promoting diversification within common lichen-forming fungi in the northern Hemisphere. Additionally, we provide evidence that glacial oscillations have influenced current population structure of broadly distributed lichenized fungal species throughout the Holarctic. [ABSTRACT FROM AUTHOR]

Abstract: Mounting evidence suggests many morphology-based species circumscriptions in lichenized ascomycetes misrepresent fungal diversity. The lichenized ascomycete genus Xanthoparmelia includes over 800 described species displaying a considerable range of morphological and chemical variation. Species circumscriptions in this genus have traditionally been based on thallus morphology, medullary chemistry, and the presence or absence of sexual or asexual reproductive structures. Notwithstanding concerted effort on the part of taxonomists to arrive at a natural classification, modern taxonomic concepts for the most part remain unclear. Here we assess the evolution of characters traditionally regarded as taxonomically important by reconstructing a phylogenetic hypothesis based on sequence data from four nuclear ribosomal markers as well as fragments from two protein-coding nuclear loci. A total of 414 individuals were tested, representing 19 currently accepted species. Most sampled species, as currently circumscribed, were recovered as polyphyletic, suggesting that major diagnostic characters have evolved in a homoplasious manner. The vagrant growth form, distinct medullary chemistries, and production of vegetative diaspores appear to have evolved independently multiple times. Application of a population assignment test resulted in the recognition of 21 species-level genetic clusters, each of which was supported by a comparison of genetic distances as well as a Bayesian species delimitation method calculating probabilities associated with speciation events. Inferred clusters are largely incongruent with traditionally circumscribed species due to the prevalence of cryptic diversity and, in some cases, high levels of intraspecific morphological and chemical variation. These results call for a major taxonomic revision of Xanthoparmelia species in western North America. [Copyright &y& Elsevier]

Abstract: A growing body of evidence indicates that in some cases morphology-based species circumscription of lichenized fungi misrepresents the number of existing species. The cosmopolitan “rock posy” lichen (Rhizoplaca melanophthalma) species-complex includes a number of morphologically distinct species that are both geographically and ecologically widespread, providing a model system to evaluate speciation in lichen-forming ascomycetes. In this study, we assembled multiple lines of evidence from nuclear DNA sequence data, morphology, and biochemistry for species delimitation in the R. melanophthalma species-complex. We identify a total of ten candidate species in this study, four of which were previously recognized as distinct taxa and six previously unrecognized lineages found within what has been thus far considered a single species. Candidate species are supported using inferences from multiple empirical operational criteria. Multiple instances of sympatry support the view that these lineages merit recognition as distinct taxa. Generally, we found little corroboration between morphological and chemical characters, and previously unidentified lineages were morphologically polymorphic. However, secondary metabolite data supported one cryptic saxicolous lineage, characterized by orsellinic-derived gyrophoric and lecanoric acids, which we consider to be taxonomically significant. Our study of the R. melanophthalma species-complex indicates that the genus Rhizoplaca, as presently circumscribed, is more diverse in western North American than originally perceived, and we present our analyses as a working example of species delimitation in morphologically cryptic and recently diverged lichenized fungi. [Copyright &y& Elsevier]

In the United States, research natural areas (RNAs) are permanently established to maintain areas of natural ecosystem significance. The Upper Sand Creek Research Natural Area (USCRNA) in the Escalante River watershed in southern Utah was established nearly a quarter century ago. However, the botanical diversity has remained largely unknown. To provide data to aid in preserving and maintaining biological and genetic diversity in USCRNA, we surveyed vascular plant, bryophyte, and lichen diversity within the RNA in 2021. We document high vascular plant (187 species) and lichen (152 species / candidate species) diversity, in addition to 15 bryophyte species. These preliminary inventories will be critical for investigating ecosystem function and integrity, providing a baseline for future research. [ABSTRACT FROM AUTHOR]

Simple Summary: This paper reports on two new species and two new records of the lichen-forming fungal genus Peltula Nyl., highlighting progress in our investigation of Chinese Peltula spp. The external morphology, anatomy, and molecular systematics were comprehensively analyzed to support the species delimitation. The results contribute to the knowledge of species diversity and geographical distributions of Peltula species in China. In this study, two new species, Peltula confusa Q.X. Yang & X.L. Wei, sp. nov., growing in a dry microenvironment within a semi-humid area, and Peltula subpatellata Q.X. Yang & X.L. Wei, sp. nov., occurring in arid and semi-arid regions, are described. In addition, two species, P. polyspora (Tuck.) Wetmore and P. obscuratula (Nyl.) Poelt ex Egea, are recorded for the first time in China. All four species are described based on morphological, anatomical and molecular data. Peltula confusa is characterized by a lighter, brighter, and more yellowish upper surface than other species of this genus, with discs concentrated in the central part of squamules, and a thick lower cortex. Peltula subpatellata can be distinguished from P. patellata (Bagl.) Swinscow & Krog by its non-thickened and sometimes darkened margins and sometimes the presence of peltate squamules. Phylogenetic analysis based on DNA sequences of four loci (ITS, nrSSU, nrLSU, and RPB2) demonstrates the placement of these species within Peltula, and supports current species delimitations. We suggest that the growth substrate should be considered as an additional characteristic for species delimitation. [ABSTRACT FROM AUTHOR]

Recent work has suggested exceptional species-level diversity in the lichen-forming Lecanora polytropa complex (Lecanoraceae, Ascomycota). However, biogeographic patterns and the spatial structuring of this diversity remains poorly known. To investigate diversity across multiple spatial scales, we sampled members of this species complex from two distinct regions—the Pacific Coast Ranges in southern Alaska, USA, and montane habitats in Spain. We also included sequence data from several species within this complex that were recently described from populations in France. Using the standard DNA barcoding marker and a sequence-based species delimitation approach (ASAP), we inferred a total of 123 candidate species (SHs) within the Lecanora polytropa complex, 32 of which were sampled for the first time here. Of 123 SHs, 21 had documented intercontinental distributions, while the vast majority were found at much smaller spatial scales. From our samples collected from Alaska, USA, and Spain, representing 36 SHs, we found high genetic diversity occurring within each sampled site, but limited overlap among all sites. Mountain ranges in both regions had high proportions of endemic lineages, with the highest diversity and endemism occurring in mountain ranges in Spain. Our sequence data generally support the recent taxonomic proposals, and an integrative taxonomy may help partly resolve the taxonomic conundrums within this hyper-diverse lineage. [ABSTRACT FROM AUTHOR]

Highlights • DNA metabarcoding captured more diversity in lichen inventories than voucher-based approaches. • High overlap in OTU diversity between technicians and a professional's metacommunity samples. • DNA barcoding cannot discriminate presence of established thalli from unestablished propagules. • DNA metabarcoding offers a complementary approach for assessing lichen biodiversity. Abstract Comprehensive lichen inventories at biomonitoring reference sites provide valuable ecological information but are notoriously difficult to obtain. Due to the limited number of specialists and challenges with generating objective species inventories, investigating alternative or complementary strategies for compiling lichen inventories is paramount to improve biomonitoring strategies. The aim of this study was to determine if targeted community DNA metabarcoding provides an efficient, objective and reliable approach for characterizing lichen-forming fungal diversity in biomonitoring research. To evaluate if reliable biodiversity data could be obtained efficiently and objectively, metacommunity samples were collected by trained field technicians and a professional lichenologist at a previously established biomonitoring reference site in east-central Nevada, USA. Using amplicon-based high-throughput sequencing of a portion of the fungal DNA barcoding marker, the internal transcribed spacer region, molecular operational taxonomic units (OTUs) were inferred and used as a proxy for species diversity. OTUs from individual sampling efforts and two DNA extraction methods were compared to data from the original, voucher-based inventory at the same site. Treating OTUs as a proxy for species diversity, a 1.6-fold increase in diversity of lichen-forming fungi was observed when comparing the targeted community DNA metabarcoding to the initial, voucher-based inventories – 72 OTUs vs. 43 species. Strikingly, substantial overlap in captured OTU diversity was observed between minimally trained technicians and a professional lichenologist metacommunity samples. Based on these results, targeted community DNA metabarcoding is a promising strategy for creating objective lichen inventories. However, metabarcoding cannot discriminate the presence of established thalli from that of spores or propagules (in absence of established thalli) present in the sample/area. Therefore, targeted community DNA metabarcoding for assessing lichen biodiversity offers a complementary, rather than a substitutive sampling strategy. [ABSTRACT FROM AUTHOR]

Species of lichen-forming fungi (LFF) display an array of geographical distribution patterns. Among the broadly distributed lichen-forming fungal species, the degree of reproductive isolation and genetic substructure among populations varies widely, in some cases masking unrecognized diversity or meaningful biogeographical patterns. Lecidea atrobrunnea (Raymond ex Lam. & DC.) Schaer. s. lat. (Lecideaceae) is a widespread species complex that has been studied for over two centuries since its initial description. The diversity of the L. atrobrunnea group is highest in western North America, where a dizzying array of morphologies and chemistry can occur at local scales. Here we investigate whether the assumed cosmopolitan distribution of L. atrobrunnea s. lat. is an artifact of taxonomic limitations and masks biogeographical patterns in this species complex. To address these questions, we compiled sequence data from the standard fungal barcoding marker (ITS) for over 100 specimens within this complex, in addition to genome-scale data from a subset of these representing over 1600 single-copy nuclear genes spanning over 3 Mb of the genome. Our study corroborates the perspective that the morphologically and chemically variable Lecidea atrobrunnea group reflects a complex of distinct species-level lineages, with 42–83 candidate species inferred from the ITS region and high levels of diversity inferred from a subset of specimens using genome-scale data. However, both phenotype- and molecular-based species boundaries remained unsettled, with the most common nominal taxa recovered as highly polyphyletic and with conflict among different molecular species delimitation approaches. Our study also highlights the potential for geographically restricted species, with fascinating biogeographical patterns, challenging, in part, the assumed cosmopolitan distribution of L. atrobrunnea s. lat. This study provides valuable direction for future research that will be crucial in understanding diversification and establishing a robust taxonomy for this well-known species complex. [ABSTRACT FROM AUTHOR]

Pleistocene climatic fluctuations influenced patterns of genetic variation and promoted speciation across a wide range of species groups. Lichens are commonly found in habitats that were directly impacted by glacial cycles; however, the role of Pleistocene climate in driving speciation in most lichen symbionts remains unclear. This uncertainty is due in part to limitations in our ability to accurately recognize independently evolving lichen-forming fungal lineages and a lack of relevant fossil calibrations. Using a coalescent-based species tree approach, we estimated divergence times for two sister clades in the genus Xanthoparmelia (Parmeliaceae) restricted to western North America. We assessed the influence of two different species circumscription scenarios and various locus-specific rates of molecular evolution on divergence estimates. Species circumscriptions were validated using the program BP&P. although speciation was generally supported in both scenarios, divergence times differed between traditional species circumscriptions and those based on genetic data, with more recent estimates resulting from the former. Similarly, rates of evolution for different loci resulted in variable divergence time estimates. However, our results unambiguously indicate that diversification in the sampled Xanthoparmelia clades occurred during the Pleistocene. Our study highlights the potential impact of ambiguous species circumscriptions and uncertain rates of molecular evolution on estimating divergence times within a multilocus species tree framework. [ABSTRACT FROM AUTHOR]

Macro-morphological features traditionally used to segregate genera in Parmeliaceae have been shown to be highly plastic, placing limits on their taxonomic value. Here we aim to elucidate the evolutionary relationships of the genera Relicina and Relicinopsis and reassess the phenotypic features traditionally used to separate these genera. To this end, we gathered ribosomal DNA sequences of ITS, nuLSU and mtSSU and analyzed them in a phylogenetic framework. Relicina was recovered as paraphyletic, with Relicinopsis nested within, and three different clades were identified within Relicina. Alternative hypothesis tests significantly rejected the monophyly of Relicina. Our results indicate that the presence or absence of bulbate cilia is of limited taxonomic value in this clade. Based on differences in conidia, however, we propose to accept Relicinopsis as a subgenus within Relicina as Relicina subgen. Relicinopsis (Elix & Verdon) Kirika, Divakar & Lumbsch. It is proposed that five new combinations of species previously classified in Relicinopsis be placed in Relicina. [ABSTRACT FROM AUTHOR]

Subalpine habitats in sky islands in the Southwestern USA are currently facing large-scale transformations. Lichens have widely been used as bioindicators of environmental change. On the Colorado Plateau, fruticose lichens occur in patchy, disconnected populations, including unique lichen-draped conifer sites in subalpine forests in the La Sal Mountains in southeastern Utah. Here, we document the distribution and fungal diversity within these lichen communities. We find that lichen-draped conifer sites in the La Sal Mountains are restricted to only three known, small areas in Picea englemannii forests above 3000 m above sea level, two of which have recently been impacted by wildfire. We document 30 different species of lichen-forming fungi in these communities, several which represent the first reports from the Colorado Plateau. We also characterize mycobiont haplotype diversity for the fruticose lichens Evernia divaricata, Ramalina sinensis, and multiple Usnea species. We also report a range of diverse fungi associated with these lichens, including genetic clusters representing 22 orders spanning seven classes of Ascomycetes and fewer clusters representing Basidiomycetes. Our results provide a baseline for ongoing monitoring and help to raise awareness of unique lichen communities and other biodiversity in the region. [ABSTRACT FROM AUTHOR]

Two new species belonging to the lichen genus Anaptychia are described from western North America. Anaptychia nevadensis is superficially similar to the Eurasian A. desertorum but is distinguished by having longer ascospores, in producing scant pruina only near the lobe tips, and in regularly producing variolaric acid. Anaptychia roemerioides is described to accommodate North American material which has previously been called A. ulotrichoides. It is macro-morphologically identical to the Asian species A. roemeri but differs in having longer ascospores and conidia. Both new species are strongly supported by phylogenetic analysis of ITS sequences. We also call attention to the existence of a further undescribed but possibly cryptic species within A. elbursiana. Variolaric acid is newly reported to occur occasionally in A. desertorum and A. elbursiana. A global key to the desert species of Anaptychia is provided. [ABSTRACT FROM AUTHOR]

Biodiversity inventories are important for informing land management strategies, conservation efforts, and for biomonitoring studies. For many organismal groups, including lichens, comprehensive, accurate inventories are challenging due to the necessity of taxonomic expertise, limitations in sampling protocols, and the commonplace occurrence of morphologically cryptic species and other undescribed species. Lichen communities in arid regions are often dominated by crustose lichens, which have been particularly difficult to incorporate into biodiversity inventories. Here, we explore the utility of DNA metabarcoding for characterizing the diversity of lichen-forming fungi at a typical crustose lichen-dominated site on the Colorado Plateau in the southwestern USA. We assessed the consistency of independent sampling efforts to comprehensively document lichen diversity, evaluated the capability of minimally trained technicians to effectively sample the lichen communities, and provide a metagenomic-based inventory of lichen diversity, including representative sequence data, for a diverse, crustose-dominate lichen community on the Colorado Plateau. Our results revealed that crustose lichen communities in the southwestern USA are more diverse than traditionally thought, and community metabarcoding is a promising strategy for characterizing the lichen-forming fungal diversity more thoroughly than other methods. However, consistently sampling the diversity of crustose lichen communities, even at small spatial scales, remains difficult. Interpreting these results within a traditional taxonomic context remains challenging without the use of vouchers. [ABSTRACT FROM AUTHOR]

The Colorado River and its tributaries on the Colorado Plateau are home to unique desert river ecosystems and changing environmental conditions. Within this region, the Glen Canyon National Recreation Area (GCNRA) is composed of rugged, high desert terrain and is managed by the United States National Park Service as both a recrea - tional and conservation area. Despite the ecological and economic importance of GCNRA, significant components of the ecological communities therein remain poorly characterized, including lichens. Accurately characterizing lichen-forming fungal diversity is challenging due to poorly known taxonomic groups, underexplored regions/habitats, and varying interpretations of morphological differences, including the recognition of environmentally modified forms. To better understand lichen diversity in GCNRA, we used an integrative taxonomic approach, incorporating both traditional morphology-based identification and information from the standard fungal DNA barcoding marker, the ITS, to compile a thorough inventory of lichen-forming fungi in Fifty-Mile Canyon. Vouchered lichen specimens were collected in 2019, and from these the ITS marker was sequenced. Candidate species-level lineages were delimited from family-level multiple sequence alignments using the Assemble Species by Automatic Partitioning web server. Specimens comprising DNAbased candidate species were then evaluated using traditional taxonomically diagnostic characters to link these, where possible, to currently described species. For Fifty-Mile Canyon, we document 100 putative species in 15 families, each represented by vouchered specimens, ITS sequence data, and photographic documentation. For comparison, a survey of historic records from GCNRA revealed a total of 124 documented lichen-forming fungal species throughout the NRA and adjacent land. Approximately 50% of the species documented in Fifty-Mile Canyon had not previously been found in GCNRA, and similar proportions of species diversity have been documented in GCNRA but not observed in our survey. We report 3 species new to North America--Calogaya ferrugineoides (H. Magn.) Arup, Frödén & Søchting, Endocarpon deserticola T. Zhang, X.L. Wei & J.C. Wei, and Xanthocarpia ferrarii (Bagl.) Frödén, Arup & Søchting--verified using ITS sequencing data. In addition, Circinaria squamulosa sp. nov. is formally described here, currently known only from sandstone slabs in Fifty-Mile Canyon. However, the taxonomic identity of many of the candidate species from Fifty-Mile Canyon remained ambiguous at the species level, and some collections likely represent undescribed species-level lineages. Our results revealed unexpected, high species-level diversity of lichen-forming fungi at local scales and that overall lichen diversity across the entire GCNRA is likely vastly undercounted. These data--including DNA barcodes for the vast majority of lichen-forming fungi occurring in this canyon--provide an important resource that can be integrated into subsequent lichen biodiversity research in the southwestern United States and other semiarid climates. [ABSTRACT FROM AUTHOR]

Twenty-five North American lichens are issued in Fascicle VIII of the "Anderson and Shushan: Lichens of Western North America" series, numbers 176–200. This fascicle is comprised of material representing specimens from the Rhizoplaca melanophthalma aggregate, including the vagrant taxa R. arbuscula, R. haydenii, and R. idahoensis; two collections representing unattached forms in the R. porteri group – R. melanophthalma ssp. crispa and an erratic form of R. porteri; and two umbilicate saxicolous taxa, R. robusta and R. shushanii, the former described as new to science here. We also provide the first morphological description for R. shushanii, a species that was initially described based on diagnostic DNA sequence characters. [ABSTRACT FROM AUTHOR]

Context: The emergence of antibiotic resistant pathogens is a serious global health threat. Hence, the search for new antibiotic drugs from various natural sources should be given high priority. Lichens produce a variety of low molecular weight metabolic compounds and many cultures have utilized these compounds in traditional medicine for centuries. Objective: Report the antibiotic properties of extracts from 34 North American lichens screened against four pathogenic bacteria. Materials and methods: The micro-well dilution method was used to determine the minimum inhibitory concentration (MIC) of acetone and methanol extracts of 34 lichen species against four bacterial strains. Major chemical compounds in each species were identified using thin layer chromatography (TLC). Results: Most of the lichen extracts demonstrated inhibitory effects against Staphylococcus aureus, Pseudomonas aeruginosa, and methicillin-resistant S. aureus (MRSA) with MIC values ranging from 3.9 to 500 µg/ml. In addition, extracts from three species, Letharia columbiana (Nutt.) J. W. Thomson (Parmeliaceae), Letharia vulpina (L.) Hue (Parmeliaceae), and Vulpicida canadensis (Räsänen) J.-E. Mattsson & M. J. Lai (Parmeliaceae) (MIC = 125-500 µg/ml) were also effective against Escherichia coli. Generally, acetone extractions were found to be more effective than methanol extractions. Discussion and conclusion: Results of this study show that lichen extracts provide significant antimicrobial activity against both Gram-positive and Gram-negative bacteria. These results suggest that lichens may be an important potential source of antibacterial drugs. [ABSTRACT FROM AUTHOR]

[Display omitted] • Wanderlust lichens occur in isolated populations in steppe habitats in North America. • A 19 Mb alignment revealed high, spatially structured genetic diversity. • R. robusta , a sexually reproducing taxon, is nested within this asexual lineage. • Wanderlust lichens don't fully occupy the areas of highest distribution probability. The northern North American Cordillera is a globally significant center of endemism. In western North America, imperiled arid steppe habitats support a number of unique species, including several endemic lichens. However, processes driving diversification and endemism in this region remain unclear. In this study, we investigate diversity and phylogeography of the threatened wanderlust lichens (mycobiont = Rhizoplaca species) which occur unattached on calcareous soils in steppe habitats. Wanderlust lichens comprise three species of lichen-forming fungi (LFF) – Rhizoplaca arbuscula , R. haydenii , and R. idahoensis (endangered, IUCN Red List) – which occur in fragmented populations in Idaho and Wyoming, with more limited populations in southern Montana and northern Utah. These lichens reproduce almost exclusively via large, asexual vegetative propagules. Here, our aims were to (i) assess the evolutionary origin of this group and identify phylogeographic structure, (ii) infer ancestral geographic distributions for lineages within this clade, and (iii) use species distribution modeling to better understand the distribution of contemporary populations. Using a genome-skimming approach, we generated a 19.1Mb alignment, spanning ca. half of the complete LFF genome, from specimens collected throughout the entire range of wanderlust lichens. Based on this phylogeny, we investigated phylogeographic patterns using RASP. Finally, we used MaxEnt to estimate species distribution models for R. arbuscula and R. haydenii. We inferred a highly structured topology, with clades corresponding to distinct geographic regions and morphologies collected throughout the group's distribution. We found that R. robusta , a sexually reproducing taxon, is clearly nested within the vagrant Rhizoplaca clade. Phylogeographic analyses suggest that both dispersal and vicariance played significant roles throughout the evolutionary history of the vagrant Rhizoplaca clade, with most of the dispersal events originating from the Salmon Basin in eastern Idaho – the center of diversity for this group. Despite the fact that wanderlust lichens are dispersal limited due to large, unspecialized vegetative propagules, we inferred multiple dispersal events crossing the Continental Divide. Comparing herbarium records with species distribution models suggests that wanderlust lichens don't fully occupy the areas of highest distribution probability. In fact, documented records often occur in areas predicted to be only marginally suitable. These data suggest a potential mismatch between contemporary habitats outside of the center of diversity in eastern Idaho with the most suitable habitat, adding to the vulnerability of this imperiled complex of endemic lichens. [ABSTRACT FROM AUTHOR]

Sixteen species of brown parmelioids are reported from Greenland, including one species of Cetrariella, three species of Melanelia, two species of Melanelixia, six species of Melanohalea, and four species of Montanelia. Descriptions and a key are provided. [ABSTRACT FROM AUTHOR]