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Phylogenetic relationships of the Xanthoparmelia mexicana group based on a concatenated data set of ITS, mtSSU, nuLSU and MCM7. Topology based on maximum likelihood (ML) analyses. Bootstrap values above 75 and 0.95 posterior probability are indicated on each branch. The clades I, II and III are highlighted in blue, yellow and pink, respectively. Selected specimens representing clades (habit and isidia): I, X. mexicana s. lat. (A, B); II, X.pedregalensis (C, D) and III, X. mexicana s. str. (E, F), a picture of the X. mexicana type specimen from BP is included (G).
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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 incl...
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The Grosmannia penicillata complex (Ophiostomatales, Ascomycota) is one of the major species complexes in Leptographium sensu lato. Most of these are wood staining fungi associated with conifer-infesting bark beetles, and the complex encompasses the type species of the genus Grosmannia. Yet the phylogenetic relationships of species within the compl...
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... Furthermore, isidiate Xan-thoparmelia species are distributed in boreal, temperate, and tropical regions. Nevertheless, they commonly occur in semi-arid to arid regions worldwide, especially on siliceous rocks, such as granite and sandstone [74]. In Macaronesia, only six other isidiate species grow: the common and widespread Xanthoparmelia conspersa (Ehrh. ...
... Furthermore, isidiate Xanthoparmelia species are distributed in boreal, temperate, and tropical regions. Nevertheless, they commonly occur in semi-arid to arid regions worldwide, especially on siliceous rocks, such as granite and sandstone [74]. In Macaronesia, only six other isidiate species grow: the common and widespread Xanthoparmelia conspersa (Ehrh. ...
It has long been assumed that lichen-forming fungi have very large distribution ranges, and that endemic species are rare in this group of organisms. This is likely a consequence of the "everything small is everywhere" paradigm that has been traditionally applied to cryptogams. However, the description of numerous endemic species over the last decades, many of them in oceanic islands, is challenging this view. In this study, we provide another example, Xanthoparmelia ramosae, a species that is described here as new to science on the basis of morphological, chemical, and macroclimatic data, and three molecular markers (ITS rDNA, nuLSU rDNA, and mtSSU). The new species is endemic to the island of Gran Canaria but clusters into a clade composed exclusively of specimens collected in Eastern Africa, a disjunction that is here reported for the first time in lichen-forming fungi. Through the use of dating analysis, we have found that Xanthoparmelia ramosae diverged from its closely related African taxa in the Pliocene. This result, together with the reproductive strategy of the species, points to the Relict theory as a likely mechanism behind the disjunction, although the large gap in lichenological knowledge in Africa makes this possibility hard to explore any further.
... I, Lobothallia alphoplaca (Leavitt 19027). taxonomy of isidiate Xanthoparmelia needs revision (Leavitt et al. 2011, Barcenas-Peña et al. 2018). Note. ...
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 recreational 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 DNA-based 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.
RESUMEN.-El río Colorado y sus afluentes en la meseta de Colorado albergan ecosistemas fluviales desérticos úni-cos y condiciones ambientales cambiantes. Dentro de esta región, el Área Recreativa Nacional de Glen Canyon (GCNRA, por sus siglas en inglés) se compone de un terreno desértico irregular y elevado, el cual es administrado por el Servicio de Parques Nacionales de los Estados Unidos como área recreativa y de conservación. A pesar de la importan-cia ecológica y económica de GCNRA, varios componentes importantes de las comunidades ecológicas que allí se encuentran permanecen mal caracterizados, incluidos los líquenes. El caracterizar la diversidad precisa de los hongos formadores de líquenes representa un desafío debido a que se trata de grupos taxonómicos poco conocidos, regiones/hábitats escasamente explorados y diversas interpretaciones de las diferencias morfológicas, incluido el reconocimiento de formas modificadas por el medio ambiente. Para comprender mejor la diversidad de líquenes en GCNRA, utilizamos un enfoque taxonómico integrador, incorporando tanto la identificación tradicional basada en la morfología como la información del marcador de código de barras de ADN de hongos estándar (marcador ITS), para compilar un inventario completo de hongos formadores de líquenes en Fifty-Mile Canyon. En 2019 se recolectaron
... Xanthoparmelia is the most species-rich genus in lichenforming fungi (ca. 800 species; Jaklitsch et al., 2016) and is characterized by extremely high chemical diversity in terms of secondary metabolites (Elix et al., 1986;Thell et al., 2012;Divakar et al., 2013;Barcenas-Peña et al., 2018). The evolution of diverse secondary metabolites may be associated with changing habitat and substrate preferences (Boustie and Grube, 2005;Zraik et al., 2018), and has been a key diagnostic phenotypic character when identifying lichen species. ...
... We further sequenced two additional loci (mitochondrial small subunit rDNA [mtSSU] and nuclear large subunit rDNA [nuLSU]) by PCRs and Sanger sequencing or by extracting the sequence data from existing metagenomic data sets (following Barcenas-Peña et al., 2018). The primer sets for mtSSU (mrSSU1 and mrSSU3; Zoller et al., 1999) and nuLSU (LR0R and LR6; Vilgalys and Hester, 1990), were used to amplify the two additional loci. ...
... It has been hypothesized that it may require specific phenotypic adaptation to help with attaching to different substrate types; furthermore, different fungal lineages often have very different chemistry preferences (e.g., pH value) of their substrate (Brodo, 1973). Xanthoparmelia species generally associated with siliceous rock or sandstone worldwide (Hale, 1985(Hale, , 1988(Hale, , 1990Elix et al., 1986;Barcenas-Peña et al., 2018;Leavitt et al., 2018). We found samples from different substrate types having overlapped distribution of secondary metabolite compositions (Figure 4), which supports the hypothesis that rock and soil substrate types may exhibit similar chemical profiles. ...
Arid soil habitats are challenging for sedentary and slow-growing lichens because the integrity of the substrate can easily be disturbed by natural forces, e.g., wind and flood. Yet, adaptation into such habitat types occurred multiple times in lichens that may be associated with specific morphological and ecological adaptations. We studied the genetic and chemical diversity of the lichen-forming fungal genus Xanthoparmelia in Western Australia, where it is abundant in both arid and temperate ecoregions occurring on both soil and rock substrates. We found frequent evolutionary transitions among substrate types and between arid and temperate habitats. However, specific chemical phenotypes were not associated with different habitat and substrate types, and the level of phenotypic (the composition of secondary metabolites) divergence was not correlated with the level of genetic divergence among taxa. The study closes by discussing the importance of arid soil habitats for evolutionary diversification in the hyperdiverse genus Xanthoparmelia.
Lichens are symbiotic associations resulting from interactions among fungi (primary and secondary mycobionts), algae and/or cyanobacteria (primary and secondary photobionts), and specific elements of the bacterial microbiome associated with the lichen thallus. The question of what is a species, both concerning the lichen as a whole and its main fungal component, the primary mycobiont, has faced many challenges throughout history and has reached new dimensions with the advent of molecular phylogenetics and phylogenomics. In this paper, we briefly revise the definition of lichens and the scientific and vernacular naming conventions, concluding that the scientific, Latinized name usually associated with lichens invariably refers to the primary mycobiont, whereas the vernacular name encompasses the entire lichen. Although the same lichen mycobiont may produce different phenotypes when associating with different photobionts or growing in axenic culture, this discrete variation does not warrant the application of different scientific names, but must follow the principle "one fungus = one name". Instead, broadly agreed informal designations should be used for such discrete morphologies, such as chloromorph and cyanomorph for lichens formed by the same mycobiont but with either green algae or cyanobacteria. The taxonomic recognition of species in lichen-forming fungi is not different from other fungi and conceptual and nomenclatural approaches follow the same principles. We identify a number of current challenges and provide recommendations to address these. Species delimitation in lichen-forming fungi should not be tailored to particular species concepts but instead be derived from empirical evidence, applying one or several of the following principles in what we call the LPR approach: lineage (L) coherence vs. divergence (phylogenetic component), phenotype (P) coherence vs. divergence (morphological component), and/or reproductive (R) compatibility vs. isolation (biological component). Species hypotheses can be established based on either L or P, then using either P or L (plus R) to corroborate them. The reliability of species hypotheses depends not only on the nature and number of characters but also on the context: the closer the relationship and/or similarity between species, the higher the number of characters and/or specimens that should be analyzed to provide reliable delimitations. Alpha taxonomy should follow scientific evidence and an evolutionary framework but should also offer alternative practical solutions, as long as these are scientifically defendable. Taxa that are delimited phylogenetically but not readily identifiable in the field, or are genuinely cryptic, should not be rejected due to the inaccessibility of proper tools. Instead, they can be provisionally treated as undifferentiated complexes for purposes that do not require precise determinations. The application of infraspecific (gamma) taxonomy should be restricted to cases where there is a biological rationale, i.e., lineages of a species complex that show limited phylogenetic divergence but no evidence of reproductive isolation. Gamma taxonomy should not be used to denote discrete phenotypical variation or ecotypes not warranting the distinction at species level. We revise the species pair concept in lichen-forming fungi, which recognizes sexually and asexually reproducing morphs with the same underlying phenotype as different species. We conclude that in most cases this concept does not hold, but the actual situation is complex and not necessarily correlated with reproductive strategy. In cases where no molecular data are available or where single or multi-marker approaches do not provide resolution, we recommend maintaining species pairs until molecular or phylogenomic data are available. This recommendation is based on the example of the species pair Usnea aurantiacoatra vs. U. antarctica, which can only be resolved with phylogenomic approaches, such as microsatellites or RADseq. Overall, we consider that species delimitation in lichen-forming fungi has advanced dramatically over the past three decades, resulting in a solid framework, but that empirical evidence is still missing for many taxa. Therefore, while phylogenomic approaches focusing on particular examples will be increasingly employed to resolve difficult species complexes, broad screening using single barcoding markers will aid in placing as many taxa as possible into a molecular matrix. We provide a practical protocol how to assess and formally treat taxonomic novelties. While this paper focuses on lichen fungi, many of the aspects discussed herein apply generally to fungal taxonomy. The new combination Arthonia minor (Lücking) Lücking comb. et stat. nov. (Bas.: Arthonia cyanea f. minor Lücking) is proposed.
