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The richness, composition, abundance, and correlation with the atmospheric oxide concentrations of the community of corticolous lichens in the urban and peri-urban areas of the city of Ibagué (Colombia) were evaluated, selecting 25 individuals of the four most abundant phorophyte species. Twenty-nine lichen taxa grouped in 13 families and 17 genera were recorded, with a higher lichen coverage and taxa richness in the urban area. A non-metric multidimensional scaling (NMDS) analysis showed the conformation of two lichen communities associated with the urban and peri-urban areas of the city, and variation in composition among the phorophyte species. Exclusive and indicator taxa were found for both zones, as well as associations between variables through the application of a general linear model. Higher concentrations of atmospheric gases CO, SO2, NO2, and O3 were found in the urban zone, and positive/negative relationships with some lichen taxa. There is high variability in the response of the lichen assemblage of urban and peri-urban ecosystems to environmental effects, with substantial or minimal changes in the variables of richness, coverage, and phorophyte association, and according to their interaction with atmospheric oxides, the patterns of potential tolerant and/or sensitive species are formed for their implementation in bioindication studies. [ABSTRACT FROM AUTHOR]

Cryptic species are common in lichen-forming fungi and have been reported from different genera in the most speciose family, Parmeliaceae. Herein, we address species delimitation in a group of mainly asexually reproducing Parmelina species. The morphologically distinct P. pastillifera was previously found nested within a morphologically circumscribed P. tiliacea based on several loci. However, these studies demonstrated a relatively high genetic diversity within P. tiliacea sensu lato. Here, we revisit the species delimitation in the group by analyzing single-nucleotide polymorphisms (SNPs) through genome-wide assessment using Restriction-Site-Associated sequencing and population genomic methods. Our data support previous studies and provide further insight into the phylogenetic relationships of the four clades found within the complex. Based on the evidence suggesting a lack of gene flow among the clades, we recognize the four clades as distinct species, P. pastillifera and P. tiliacea sensu stricto, and two new species, P. clandestina sp. nov. and P. mediterranea sp. nov. [ABSTRACT FROM AUTHOR]

The article discusses the proposal to conserve the name Lichen pullus Schreb. against L. pullus Neck. The well-established name Xanthoparmelia pulla has been used to refer to a common, brown, foliose saxicolous lichen, but the basionym had long been considered to be Parmelia pulla Ach. The article addresses the typification and status of the intended basionym to fix the application of Acharius's name. The article also discusses the typification of Schreber's name and the need for conservation of the name Xanthoparmelia pulla. The lichen is widespread and often abundant in various regions and has been extensively studied. The article concludes by acknowledging the individuals who contributed to the research. [Extracted from the article]

Recent studies have demonstrated that species boundaries among the lichen-forming fungi are in need of revision with the discovery of cryptic species in numerous clades, especially in parmelioid lichens. Here we focus on addressing the species boundaries in Canoparmelia texana, a sorediate species with a pantropical distribution that extends into temperate regions. We extracted DNA sequences of the nuclear ribosomal internal transcribed spacer region (ITS), large subunit (nuLSU) and mitochondrial small subunit (mtSSU) from samples mostly collected in Kenya, and analyzed them in a phylogenetic framework. We illustrate that our samples of the species as currently circumscribed do not form a monophyletic group but fall into two distinct clades, with the apotheciate C. nairobiensis nested within. Both of the discovered lineages have a wide distributional range and are common in Kenya, and Parmelia albaniensis C. W. Dodge is resurrected to accommodate one of the clades; consequently a new combination, Canoparmelia albaniensis (C. W. Dodge) Divakar & Kirika comb. nov., is proposed. [ABSTRACT FROM AUTHOR]

We used molecular data to address species delimitation in a species complex of the parmelioid genus Canoparmelia and compare the pharmacological properties of the two clades identified. We used HPLC_DAD_MS chromatography to identify and quantify the secondary substances and used a concatenated data set of three ribosomal markers to infer phylogenetic relationships. Some historical herbarium specimens were also examined. We found two groups that showed distinct pharmacological properties. The phylogenetic study supported the separation of these two groups as distinct lineages, which are here accepted as distinct species: Canoparmelia caroliniana occurring in temperate to tropical ecosystems of a variety of worldwide localities, including America, Macaronesia, south-west Europe and potentially East Africa, whereas the Kenyan populations represent the second group, for which we propose the new species C. kakamegaensis Garrido-Huéscar, Divakar & Kirika. This study highlights the importance of recognizing cryptic species using molecular data, since it can result in detecting lineages with pharmacological properties previously overlooked. [ABSTRACT FROM AUTHOR]

The widespread species Parmotrema crinitum (Ach.) M. Choisy and Parmotrema perlatum (Huds.) M. Choisy are mainly distinguished by their reproductive strategies. While P. crinitum propagates by isidia, P. perlatum produces soredia. In this study, we aim to evaluate the phylogenetic relationship between both species and to critically examine their species boundaries. To this purpose, 46 samples belonging to P. crinitum and P. perlatum were used in our analysis, including 22 for which we studied the morphology and chemistry, before extracting their DNA. We used 35 sequences of the internal transcribed spacer region of nuclear ribosomal DNA (ITS) of Parmotrema perlatum from Europe and Africa (20 of which were newly generated), and 11 of Parmotrema crinitum from Europe, North America and North Africa (two newly generated). Additionally, 28 sequences of several species from Parmotrema were included in the ITS dataset. The ITS data matrix was analyzed using different approaches, such as traditional phylogeny (maximum likelihood and Bayesian analyses), genetic distances, automatic barcode gap discovery (ABGD) and the coalescent-based method poisson tree processes (PTP), in order to test congruence among results. Our results indicate that all samples referred to P. crinitum and P. perlatum nested in a well-supported monophyletic clade, but phylogenetic relationships among them remain unresolved. Delimitations inferred from PTP, ABGD and genetic distance analyses were comparable and suggested that P. crinitum and P. perlatum belong to the same lineage. Interestingly, two samples of P. perlatum separate in a different monophyletic clade, which is supported as a different lineage by all the analyses. [ABSTRACT FROM AUTHOR]

Background: Most mammalian cells harbor molecular circadian clocks that synchronize physiological functions with the 24-h day-night cycle. Disruption of circadian rhythms, through genetic or environmental changes, promotes the development of disorders like obesity, cardiovascular diseases, and cancer. At the cellular level, circadian, mitotic, and redox cycles are functionally coupled. Evernic (EA) and usnic acid (UA), two lichen secondary metabolites, show various pharmacological activities including anti-oxidative, anti-inflammatory, and neuroprotective action. All these effects have likewise been associated with a functional circadian clock. Hypothesis/Purpose: To test, if the lichen compounds EA and UA modulate circadian clock function at the cellular level. Methods: We used three different cell lines and two circadian luminescence reporter systems for evaluating dose- and time-dependent effects of EA/UA treatment on cellular clock regulation at high temporal resolution. Output parameters studied were circadian luminescence rhythm period, amplitude, phase, and dampening rate. Results: Both compounds had marked effects on clock rhythm amplitudes and dampening independent of cell type, with UA generally showing a higher efficiency than EA. Only in fibroblast cells, significant effects on clock period were observed for UA treated cells showing shorter and EA treated cells showing longer period lengths. Transient treatment of mouse embryonic fibroblasts at different phases had only minor clock resetting effects for both compounds. Conclusion: Secondary metabolites of lichen alter cellular circadian clocks through amplitude reduction and increased rhythm dampening. [ABSTRACT FROM AUTHOR]

The worldwide, ecologically relevant lichen-forming genus Parmelia currently includes 41 accepted species, of which the Parmelia sulcata group (PSULgp) and the Parmelia saxatilis group (PSAXgp) have received considerable attention over recent decades; however, phycobiont diversity is poorly known in Parmelia s. lat. Here, we studied the diversity of Trebouxia microalgae associated with 159 thalli collected from 30 locations, including nine Parmelia spp.: P. barrenoae, P. encryptata, P. ernstiae, P. mayi, P. omphalodes, P. saxatilis, P. serrana, P. submontana , and P. sulcata. The mycobionts were studied by carrying out phylogenetic analyses of the nrITS. Microalgae genetic diversity was examined by using both nrITS and LSU rDNA markers. To evaluate putative species boundaries, three DNA species delimitation analyses were performed on Trebouxia and Parmelia. All analyses clustered the mycobionts into two main groups: PSULgp and PSAXgp. Species delimitation identified 13 fungal and 15 algal species-level lineages. To identify patterns in specificity and selectivity, the diversity and abundance of the phycobionts were identified for each Parmelia species. High specificity of each Parmelia group for a given Trebouxia clade was observed; PSULgp associated only with clade I and PSAXgp with clade S. However, the degree of specificity is different within each group, since the PSAXgp mycobionts were less specific and associated with 12 Trebouxia spp., meanwhile those of PSULgp interacted only with three Trebouxia spp. Variation-partitioning analyses were conducted to detect the relative contributions of climate, geography, and symbiotic partner to phycobiont and mycobiont distribution patterns. Both analyses explained unexpectedly high portions of variability (99 and 98%) and revealed strong correlations between the fungal and algal diversity. Network analysis discriminated seven ecological clusters. Even though climatic conditions explained the largest proportion of the variation among these clusters, they seemed to show indifference relative to climatic parameters. However, the cluster formed by P. saxatilis A/ P. saxatilis B/ Trebouxia sp. 2/ Trebouxia sp. S02/ Trebouxia sp. 3A was identified to prefer cold-temperate as well as humid summer environments. [ABSTRACT FROM AUTHOR]

Mucormycosis is caused by fungi belonging to the order Mucorales. The term "Black Fungus" has been widely applied to human pathogenic Mucorales in India. They mainly infect the sinuses and brain, lungs, stomach and intestines, and skin. While this has been considered a rare disease, thousands of cases have been reported during the second wave of COVID-19 in India, between the months of April and June 2021. Hitherto, more than 45,374 cases and over 4300 deaths have been reported among COVID-19 patients across India from April 2021 to July 21, 2021. Though the mortality rate is estimated to be 50%, it could be above 90% if left untreated. In India, Rhizopus arrhizus has been related to be the most common species to cause human mucormycosis, followed by Apophysomyces variabilis, Rhizopus microsporus, and R. homothallicus. Accurate sample identification of human pathogenic Mucorales species is challenging especially due to the frequent lack of diagnostic morphological features. Traditionally, the culture-based approach has been extensively used to isolate and characterize human pathogenic Mucorales. However, this may not be an appropriate approach to objectively isolate and characterize all species, as the germination and growth of fungal spores are highly dependent on culture media and environmental conditions. Therefore, a robust approach to the accurate and rapid identification of human pathogenic Mucorales species is a prerequisite. The metagenomic approach comprehensively sequences and analyzes all genetic material in a complex biological sample and, consequently, this could be an appropriate approach to objectively characterize human pathogenic Mucorales taxa without the need for in vitro culture. The precise identification of the species will not only be useful for the correct diagnosis of this disease, but also for the development of antifungal drugs specific for each species. Accurate and rapid species identification is desperately needed to save lives in the mucormycosis outbreak among COVID-19 patients in India and neighboring countries. [ABSTRACT FROM AUTHOR]

Abstract 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 to complement 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 among divergent 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.

Parmeliaceae is the largest family of lichen-forming fungi with a worldwide distribution. We used a target enrichment data set and a qualitative selection method for 250 out of 350 genes to infer the phylogeny of the major clades in this family including 81 taxa, with both subfamilies and all seven major clades previously recognized in the subfamily Parmelioideae. The reduced genome-scale data set was analyzed using concatenated-based Bayesian inference and two different Maximum Likelihood analyses, and a coalescent-based species tree method. The resulting topology was strongly supported with the majority of nodes being fully supported in all three concatenated-based analyses. The two subfamilies and each of the seven major clades in Parmelioideae were strongly supported as monophyletic. In addition, most backbone relationships in the topology were recovered with high nodal support. The genus Parmotrema was found to be polyphyletic and consequently, it is suggested to accept the genus Crespoa to accommodate the species previously placed in Parmotrema subgen. Crespoa. This study demonstrates the power of reduced genome-scale data sets to resolve phylogenetic relationships with high support. Due to lower costs, target enrichment methods provide a promising avenue for phylogenetic studies including larger taxonomic/specimen sampling than whole genome data would allow. [ABSTRACT FROM AUTHOR]

Abstract Background The rate of nucleotide substitutions is not constant across the Tree of Life, and departures from a molecular clock have been commonly reported. Within parmelioid lichens, the largest group of macrolichens, large discrepancies in branch lengths between clades were found in previous studies. Using an extended taxon sampling, we test for presence of significant rate discrepancies within and between these clades and test our a priori hypothesis that such rate discrepancies may be explained by shifts in moisture regime or other environmental conditions. Results In this paper, the first statistical evidence for accelerated evolutionary rate in lichenized ascomycetes is presented. Our results give clear evidence for a faster rate of evolution in two Hypotrachyna clades that includes species occurring in tropical and oceanic habitats in comparison with clades consisting of species occurring in semi-arid and temperate habitats. Further we explore potential links between evolutionary rates and shifts in habitat by comparing alternative Ornstein-Uhlenbeck models. Conclusion Although there was only weak support for a shift at the base of a second tropical clade, where the observed nucleotide substitution rate is high, overall support for a shift in environmental conditions at cladogenesis is very strong. This suggests that speciation in some lichen clades has proceeded by dispersal into a novel environment, followed by radiation within that environment. We found moderate support for a shift in moisture regime at the base of one tropical clade and a clade occurring in semi-arid regions and a shift in minimum temperature at the base of a boreal-temperate clade.

Lichen-forming fungi are known to produce a large number of secondary metabolites. Some metabolites are deposited in the cortical layer of the lichen thallus where they exert important ecological functions, such as UV filtering. The fact that closely related lineages of lichen-forming fungi can differ in cortical chemistry suggests that natural product biosynthesis in lichens can evolve independent from phylogenetic constraints. Usnic acid is one of the major cortical pigments in lichens. Here we used a comparative genomic approach on 46 lichen-forming fungal species of the Lecanoromycetes to elucidate the biosynthetic gene content and evolution of the gene cluster putatively responsible for the biosynthesis of usnic acid. Whole-genome sequences were gathered from taxa belonging to different orders and families of Lecanoromycetes, where Parmeliaceae is the most well-represented taxon, and analyzed with a variety of genomic tools. The highest number of biosynthetic gene clusters was found in Evernia prunastri , Pannoparmelia angustata , and Parmotrema austrosinense , respectively, and lowest in Canoparmelia nairobiensis , Bulbothrix sensibilis , and Hypotrachyna scytodes. We found that all studied species producing usnic acid contain the putative usnic acid biosynthetic gene cluster, whereas the cluster was absent in all genomes of species lacking usnic acid. The absence of the gene cluster was supported by an additional unsuccessful search for ß-ketoacylsynthase, the most conserved domain of the gene cluster, in the genomes of species lacking usnic acid. The domain architecture of this PKS cluster—homologous to the already known usnic acid PKS cluster (MPAS) and CYT450 (MPAO)—varies within the studied species, whereas the gene arrangement is highly similar in closely related taxa. We hypothesize that the ancestor of these lichen-forming fungi contained the putative usnic acid producing PKS cluster and that the gene cluster was lost repeatedly during the evolution of these groups. Our study provides insight into the genomic adaptations to the evolutionary success of these lichen-forming fungal species and sets a baseline for further exploration of biosynthetic gene content and its evolutionary significance. [ABSTRACT FROM AUTHOR]

The species of the Parmelia saxatilis complex occurring in the Iberian Peninsula were revised. Eight species are accepted, including a new species found in southern Spain, described as P. rojoi A. Crespo, V. J. Rico & Divakar. The new species, which forms a sister-group relationship with P. saxatilis s. str., is rare in the Iberian Peninsula and is restricted to higher altitudes of northern and central Spain. Parmelia rojoi differs from P. saxatilis by generally narrower isidia and a more fragile thallus. The segregation of the new species is also supported by ITS (rDNA) and Mcm7 (MS456) phylogeny and multispecies coalescent-based approaches, including StarBEAST and BP&P. Furthermore, the divergence of P. rojoi is dated back to the Pleistocene, c. 2.13 Ma. A key to the identification of species from the P. saxatilis complex with their diagnostic features is provided. All species of the complex known from Europe are also found in the Iberian Peninsula. We hypothesize that P. rojoi is a relict species that survived the Pleistocene glaciations in refugia in Spain and has been unable to extend its distributional range in postglacial periods. [ABSTRACT FROM AUTHOR]

Taxonomic identifications in some groups of lichen-forming fungi have been challenge largely due to the scarcity of taxonomically relevant features and limitations of morphological and chemical characters traditionally used to distinguish closely related taxa. Delineating species boundaries in closely related species or species complexes often requires a range of multisource data sets and comprehensive analytical methods. Here we aim to examine species boundaries in a group of saxicolous lichen forming fungi, the Aspiciliella intermutans complex (Megasporaceae), widespread mainly in the Mediterranean. We gathered DNA sequences of the nuclear ribosomal internal transcribed spacer (nuITS), the nuclear large subunit (nuLSU), the mitochondrial small subunit (mtSSU) ribosomal DNA, and the DNA replication licensing factor MCM7 from 80 samples mostly from Iran, Caucasia, Greece and eastern Europe. We used a combination of phylogenetic strategies and a variety of empirical, sequence-based species delimitation approaches to infer species boundaries in this group. The latter included: the automatic barcode gap discovery (ABGD), the multispecies coalescent approach *BEAST and Bayesian Phylogenetics and Phylogeography (BPP) program. Different species delimitation scenarios were compared using Bayes factors species delimitation analysis. Furthermore, morphological, chemical, ecological and geographical features of the sampled specimens were examined. Our study uncovered cryptic species diversity in A. intermutans and showed that morphology-based taxonomy may be unreliable, underestimating species diversity in this group of lichens. We identified a total of six species-level lineages in the A. intermutans complex using inferences from multiple empirical operational criteria. We found little corroboration between morphological and ecological features with our proposed candidate species, while secondary metabolite data do not corroborate tree topology. The present study on the A. intermutans species-complex indicates that the genus Aspiciliella, as currently circumscribed, is more diverse in Eurasia than previously expected. [ABSTRACT FROM AUTHOR]

Aim: Contemporary species' distributions are shaped by both geography and historical events, such as extinction, diversification in specific areas and long‐distance dispersals. In the most diverse family of lichen‐forming fungi, Parmeliaceae, the Hypogymnioid clade, is an example of an evolutionary lineage comprised of species occurring in temperate to subpolar regions in both hemispheres. Here, we elucidate the timing of diversification events and the impact of historical events on the species distribution in this lineage. Location: Worldwide. Taxon: Genera Arctoparmelia, Brodoa, Hypogymnia and Pseudevernia (Parmeliaceae). Methods: Our sampling focused on the most diverse genus of the clade, Hypogymnia, including c. 70% of the described species. We reconstructed phylogenetic relationships using a multi‐locus data set, estimated divergence times, and inferred ancestral distributions. Results: Our analyses suggest that the ancestor of the Hypogymnioid clade occurred in the Holarctic. In each of the four genera, all recovered as monophyletic here, diversification have occurred largely during the Miocene and Pliocene. A number of currently accepted species did not form monophyletic groups, especially in cases where specimens were collected from distinct geographic areas, with multiple, distinct clades corresponding to the geographic region of origin. Our results suggest that only a very few species in the Hypogymnioid clade have cosmopolitan distributions, all of which reproduces using vegetative propagules including both symbiotic partners. Main conclusions: While the diversification occurred predominantly in the Northern Hemisphere during the Miocene, a long‐distance dispersal event from the Northern to the Southern Hemisphere, resulted in diversification of a clade of species largely restricted to the Southern Hemisphere. Similar to other groups in this diverse family, our study highlights the need for re‐evaluation of species boundaries among members of the Hypogymnioid clade. [ABSTRACT FROM AUTHOR]

Multilocus phylogenetic studies revealed a high level of cryptic diversity within the lichen-forming fungal genus Maronina (Protoparmelioideae, Parmeliaceae). Coalescent-based species delimitation suggested that most of the cryptic molecular lineages warranted recognition as separate species. Here we study the morphology and chemistry of these taxa and formally describe eight new species based on phenotypical and molecular characters. Further, we evaluate the use of ITS rDNA as a DNA barcode for identifying species in this genus. For the first time, we obtained an ITS sequence of Maronina australiensis, the type species of the genus and showed that it is phylogenetically not closely related to species currently placed in Maronina or Protoparmelia. We assembled a dataset of 66 ITS sequences to assess the interspecies genetic distances amongst the twelve Maronina species using ITS as DNA barcode. We found that Maronina and Protoparmelia form a supported monophyletic group whereas M. australiensis is sister to both. We therefore propose a new genus Neoprotoparmelia to accommodate the tropical-subtropical species within Protoparmelioideae, with Neoprotoparmelia corallifera as the type, N. amerisidiata, N. australisidiata, N. brasilisidiata, N. capensis, N. crassa, N. pauli, N. plurisporibadia and N. siamisidiata as new species and N. capitata, N. isidiata, N. multifera, N. orientalis and N. pulchra as new proposed combinations. We provide a key to Neoprotoparmelia and confirm the use of ITS for accurately identifying species in this group. [ABSTRACT FROM AUTHOR]

An account of thelotremoid species of Graphidaceae in India is provided, which includes 124 species in 24 genera. Ocellularia and Thelotrema are the most diverse genera represented by 34 and 18 species, respectively. Type specimens were re-examined and additional samples studied morphologically and chemically. One new species, Ocellularia upretii S. Joshi, Divakar, Lumbsch & Lücking, is described; it is characterized by a greyish green thallus, porinoid ascomata, brown proper exciple, simple, carbonized columella, clear hymenium, transversely septate, amyloid ascospores of 110–125×15–20 µm and an absence of secondary metabolites. Asteristion australianum , Astrochapsa mirabilis , Cruentotrema cruentatum , C. kurandense , Ocellularia violacea and Thelotrema adjectum are reported as new to the country, and Astrochapsa mirabilis , Melanotrema submicrosporoides , Ocellularia annuloelevata , O. subkeralensis and Rhabdodiscus verrucoisidiatus are proposed as new combinations. Diploschistes awasthii , Ocellularia gupeti , O. leucina, O. mahabalei , Thelotrema confertum and T. verrucorugosum are synonymized under D. scruposus , O. neomasonhalei , O. urceolaris , O. thelotremoides , Chapsa leprocarpoides and T. rugatulum , respectively, with Ocellularia canariana and O. verrucomarginata reduced to synonymy with O. allosporoides. [ABSTRACT FROM AUTHOR]