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Geographic ranges of some of the chemotypes of the Ramalina americana chemotype complex (modified from C. E Culberson et al. 1990).
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The nature and significance of morphologically indistinguishable chemical races have been active areas of lichenological research for decades. This study uses a phylogenetic analysis of rDNA sequences to investigate whether the morphologically indistinguishable chemotypes of Ramalina americana are distinct species. Cladistic analysis of ITS sequenc...
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... range maps of the chemotypes were provided in the latter publication and some of the chemotypes overlap extensively. Ranges of representative chemotypes are given in Figure 2; the most obvious chemical split in the group is between the wide ranging northern, acid deficient chemotype and the multiple depside/ depsidone producing chemotypes of the Southeast. It should be noted that while the paper by C. E Culberson et al. (1990) included the related, Mesoamerican species R. sayreana and R. asahinae (the "R. ...
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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 requ...
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Citations
... In recent decades, an increasing number of studies have shown that there are a large number of unknown fungal species hiding under the names of widely distributed species (e.g.,Crespo & Lumbsch 2010, Simon et al. 2018, Moncada et al. 2021). This has been reported in various species complexes in Ramalina, such as the R. americana(LaGreca 1999) or R. siliquosa (LaGreca et al. 2020) groups (but see Stocker ...
Oceanic islands have been recognized as natural laboratories in which to study a great variety of evolutionary processes. One such process is evolutionary radiations, the diversification of a single ancestor into a number of species that inhabit different environments and differ in the traits that allow them to exploit those environments. The factors that drive evolutionary radiations have been studied for decades in charismatic organisms such as birds or lizards, but are lacking in lichen-forming fungi, despite recent reports of some lineages showing diversification patterns congruent with radiation. Here we propose the Ramalina decipiens group as a model system in which to carry out such studies. This group is currently thought to be comprised of five saxicolous species, all of them endemic to the Macaronesian region (the Azores, Madeira, Selvagens, Canary and Cape Verde islands). Three species are single-island endemics (a rare geographic distribution pattern in lichens), whereas two are widespread and show extreme morphological variation. The latter are suspected to harbor unrecognized species-level lineages. In order to use the Ramalina decipiens group as a model system it is necessary to resolve the group's phylogeny and to clarify its species boundaries. In this study we attempt to do so following an integrative taxonomy approach. We constructed a phylogenetic tree based on six molecular markers, four of which are newly developed and generated competing species hypotheses based on molecular (species discovery strategies based on both single locus and multilocus datasets) and phenotypic data (unsupervised clustering algorithms based on morphology, secondary chemistry and geographic origin). We found that taxonomic diversity in the Ramalina decipiens group has been highly underestimated in previous studies. In consequence, we describe six new species, most of them single-island endemics and provide a key to the group. Phylogenetic relationships among species have been reconstructed with almost full support which, coupled with the endemic character of the group, makes it an excellent system for the study of island radiations in lichen-forming fungi.
... The nuclear ribosomal internal transcribed spacer (ITS) has been proposed as the barcoding region for Fungi (Schoch et al. 2012) and has been successfully employed in taxonomy of the genus Ramalina (Gasparyan et al. 2017;Gumboski et al. 2018;Knudsen et al. 2018;Oh et al. 2014;Pérez-Vargas & Pérez-Ortega 2014;Stocker-Wörgötter et al. 2004). Furthermore, species circumscription and relationships within Ramalina have also been studied by reconstructing phylogenies using sequences of either monolocus or multilocus data (Hayward et al. 2014;LaGreca 1999;LaGreca et al. 2020;Sérusiaux et al. 2010). ...
... Pers. (AF112990), used as outgroup in a study on Ramalina (LaGreca 1999). ...
... or within Parmeliaceae (Wedin et al. 1999;Ohmura 2002;Articus 2004;Ohmura & Kanda 2004;Wirtz et al. 2006;Arup et al. 2007). Usnea sequences were also generated as outgroups for other taxa (LaGreca 1999;Thell et al. 2002;Schmull et al. 2011;Myllys et al. 2014). ...
... Usnea mutabilis is sorediate. All three species were originally described from North America (Acharius 1803; Stirton 1881), but U. strigosa is considered widespread in the Americas and U. mutabilis subcosmopolitan (Clerc & Herrera-Campos 1997;LaGreca 1999;Fos & Clerc 2000;Vareschi 2001;Ohmura 2001Ohmura , 2002Calvelo & Liberatore 2002;Clerc 2007;Mercado-Díaz 2009;Randlane et al. 2009;Saag et al. 2011;Schmull et al. 2011;McDonald et al. 2013;Herrera-Campos 2016;Ohmura & Kashiwadani 2018;Funk et al. 2018;Esslinger 2019;Dorey et al. 2019;Lendemer et al. 2019;Lücking et al. 2020c). ...
We present an exhaustive analysis of the ITS barcoding marker in the genus Usnea s.lat., separated into Dolichousnea, Eumitria, and Usnea including the subgenus Neuropogon, analyzing 1,751 accessions. We found only a few low-quality accessions, whereas information on voucher specimens and accuracy and precision of identifications was of subpar quality for many accessions. We provide an updated voucher table, alignment and phylogenetic tree to facilitate DNA barcoding of Usnea, either locally or through curated databases such as UNITE. Taxonomic and geographic coverage was moderate: while Dolichousnea and subgenus Neuropogon were well-represented among ITS data, sampling for Eumitria and Usnea s.str. was sparse and biased towards certain lineages and geographic regions, such as Antarctica, Europe, and South America. North America, Africa, Asia and Oceania were undersampled. A peculiar situation arose with New Zealand, represented by a large amount of ITS accessions from across both major islands, but most of them left unidentified. The species pair Usnea antarctica vs. U. aurantiacoatra was the most sampled clade, including numerous ITS accessions from taxonomic and ecological studies. However, published analyses of highly resolved microsatellite and RADseq markers showed that ITS was not able to properly resolve the two species present in this complex. While lack of resolution appears to be an issue with ITS in recently evolving species complexes, we did not find evidence for gene duplication (paralogs) or hybridization for this marker. Comparison with other markers demonstrated that particularly IGS and RPB1 are useful to complement ITS-based phylogenies. Both IGS and RPB1 provided better backbone resolution and support than ITS; while IGS also showed better resolution and support at species level, RPB1 was less resolved and delineated for larger species complexes. The nuLSU was of limited use, providing neither resolution nor backbone support. The other three commonly employed protein-coding markers, TUB2, RPB2, and MCM7, showed variable evidence of possible gene duplication and paralog formation, particularly in the MCM7, and these markers should be used with care, especially in multimarker coalescence approaches. A substantial challenge was provided by difficult morphospecies that did not form coherent clades with ITS or other markers, suggesting various levels of cryptic speciation, the most notorious example being the U. cornuta complex. In these cases, the available data suggest that multimarker approaches using ITS, IGS and RPB1 help to assess distinct lineages. Overall, ITS was found to be a good first approximation to assess species delimitation and recognition in Usnea s.lat., as long as the data are carefully analyzed, and reference sequences are critically assessed and not taken at face value. In difficult groups, we recommend IGS as a secondary barcode marker, with the option to employ more resource-intensive approaches, such as RADseq, in species complexes involving so-called species pairs or other cases of disparate morphology not reflected in the ITS or IGS. Attempts should be made to close taxonomic and geographic gaps especially for the latter two markers, in particular in Eumitria and Usnea s.str. and in the highly diverse areas of North America and Central America, Africa, Asia, and Oceania.
... More recently, analyses of nuclear ribosomal internal transcribed spacer region (ITS) sequences suggest that two other chemotypes, C. merochlorophaea Asahina and C. novochlorophaea (Sipman) Brodo & Ahti, may also be monophyletic (Dolnik et al. 2010). In the chemically rich Ramalina americana chemotype complex, LaGreca (1999) used ITS sequences to divide the complex into two species: one, R. americana Hale, is largely acid-deficient and occurs in the northern half of the geographical range of the complex; the other, R. culbersoniorum LaGreca, encompasses five chemotypes and occupies the southern half. In another, wellstudied chemotype complex in Ramalina, the R. farinacea complex, Stocker-Wörgötter et al. (2004) found no evidence from ITS sequences for elevating any of the chemotypes to species status. ...
... Of the six chemotypes detected on that cliff, only the acid-deficient and norstictic chemotypes appeared to interbreed with each other. There have been multiple phylogenetic studies of the genus Ramalina (Marsh 1996;LaGreca 1997;LaGreca & Lumbsch 2001;Joneson 2003;Stocker-Wörgötter et al. 2004;Sérusiaux et al. 2010;Timsina et al. 2012;Pérez-Vargas & Pérez-Ortega 2014;Gasparyan et al. 2017), and of species complexes within Ramalina (Groner & LaGreca 1997;LaGreca 1999;Ohmura et al. 2008;Hayward et al. 2014;Gumboski et al. 2018). Most of these studies utilized the ribosomal ITS region alone, although some combined ITS with another locus, such as ß-tubulin, the mitochondrial small subunit (mtSSU), or the IGS, SSU or large subunit (LSU) regions of ribosomal DNA. ...
... Clade E (98% MLBS) indicates that a broader circumscription is needed for Ramalina culbersoniorum, a chemically rich species segregated from R. americana (which, unlike R. culbersoniorum, is almost always acid-deficient) on the basis of an ITS phylogeny (LaGreca 1999). Subsequent phylogenetic studies of Ramalina (Stocker-Wörgötter et al. 2004;Timsina et al. 2012;Pérez-Vargas & Pérez-Ortega 2014;Gasparyan et al. 2017) have all indicated that R. culbersoniorum is a robustly supported, monophyletic species. ...
Lichens of the Ramalina siliquosa complex dominate seashore cliffs in Europe and South-East Asia, but their taxonomy has been vigorously debated for over a century. On many cliffs, they exhibit a bewildering zonation of chemotypes that resembles the classic zonation of organisms that occupy the littoral zone below. Do the chemotypes represent separate species, or infraspecific variation? To better understand the systematics of this group, sequences from four genetic loci (ITS, IGS, RPB1 and RPB2 ) were obtained for 59 samples from Denmark, France, Iceland, Norway, UK, Japan and Korea, including all major chemotypes. Maximum likelihood analysis of these sequences, together with sequences from 36 other Ramalina species, reveals that the complex comprises two distinct phylogenetic lineages, each including multiple chemotypes. These two putative species-level lineages correspond to the currently accepted taxa R. cuspidata and R. siliquosa . There is no evidence that these two taxa are phylogenetic sister species. Consequently, the explanation of this chemotype complex as an example of ‘sibling speciation’ is rejected. Specimens traditionally called ‘ R . siliquosa ’ from South-East Asia form a third clade, identified here as R . semicuspidata , with an additional, divaricatic acid chemotype. Other results include a robustly supported clade of Ramalina species that produce medullary depsides and depsidones; this clade includes another well-supported clade of south-eastern United States coastal plain and tropical Ramalina species. By contrast, large, strap-shaped Ramalina species that lack medullary depsides and depsidones occur in separate lineages. In addition, close relationships between the following groups of species are indicated: R. farinacea with R. subfarinacea ; R . fraxinea with R. leptocarpha , R. menziesii and R. subleptocarpha ; R. sinensis with R. unifolia . Furthermore, a new, variolaric acid-only chemotype is reported for R . farinacea , and a new, acid-deficient chemotype is reported for a more broadly circumscribed R. culbersoniorum .
... Although lichen chemicals were historically used as taxonomic markers, the delimitation of species based solely on chemistry was treated with caution. Major compounds and their biosynthetically related minor satellite compounds were however investigated as a means to classify lichens in chemosydromes to better understand the evolution of closely related taxa through their chemistry, although biomolecular data is now more commonplace [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] . Data accumulated during the 20 th century was summarized in 1996 by Huneck and Yoshimura in their compendium "Identification of Lichen Substances", comprising spectroscopic data for over 850 lichen chemicals, including TLC retardation factors, infra-red data, electron impact mass spectrometry signals, UV/visible spectra and NMR landmarks 24 . ...
... Although lichen chemicals were historically used as taxonomic markers, the delimitation of species based solely on chemistry was treated with caution. Major compounds and their biosynthetically related minor satellite compounds were however investigated as a means to classify lichens in chemosydromes to better understand the evolution of closely related taxa through their chemistry, although biomolecular data is now more commonplace [7][8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23] . Data accumulated during the 20 th century was summarized in 1996 by Huneck and Yoshimura in their compendium "Identification of Lichen Substances", comprising spectroscopic data for over 850 lichen chemicals, including TLC retardation factors, infra-red data, electron impact mass spectrometry signals, UV/visible spectra and NMR landmarks 24 . ...
While analytical techniques in natural products research massively shifted to liquid chromatography-mass spectrometry, lichen chemistry remains reliant on limited analytical methods, Thin Layer Chromatography being the gold standard. To meet the modern standards of metabolomics within lichenochemistry, we announce the publication of an open access MS/MS library with 250 metabolites, coined LDB for Lichen DataBase, providing a comprehensive coverage of lichen chemodiversity. These were donated by the Berlin Garden and Botanical Museum from the collection of Siegfried Huneck to be analyzed by LC-MS/MS. Spectra at individual collision energies were submitted to MetaboLights (https://www.ebi.ac.uk/metabolights/MTBLS999) while merged spectra were uploaded to the GNPS platform (CCMSLIB00004751209 to CCMSLIB00004751517). Technical validation was achieved by dereplicating three lichen extracts using a Molecular Networking approach, revealing the detection of eleven unique molecules that would have been missed without LDB implementation to the GNPS. From a chemist’s viewpoint, this database should help streamlining the isolation of formerly unreported metabolites. From a taxonomist perspective, the LDB offers a versatile tool for the chemical profiling of newly reported species.
... A.L. Sm. are likely affected by an evapotranspiration gradient [18]. Additionally, another pair of morphologically indistinguishable but chemically distinct Ramalina species is subdivided in their geographical distributional range [19]. Variability of secondary metabolites within the chemospecies of Cladonia chlorophaea-group is also attributed to physiography [20]. ...
Diversity of secondary lichen metabolites and their relationship to substrate and environmental parameters were studied in saxicolous lichens in the Middle and South Urals of Russia. Atranorin, usnic acid, gyrophoric acid, zeorin, norstictic acid, antraquinones and stictic acid were found in 73, 42, 41, 37, 36, 35 and 32 species, respectively, of 543 taxa collected. One hundred and ninety six species (i.e., 36% of total species documented) contained no secondary metabolites. Spectra of secondary metabolites of crustose lichens varied on different rock types, while in fruticose and foliose groups only those species without lichen acids were dependent on the substrate type. In Canonical Correspondence Analysis, secondary lichen metabolites were subdivided into groups depending on the concentration of Ca and metals in the substrate. Gyrophoric, lobaric, psoromic, rhizocarpic and stictic acids were common in crustose lichens in metal-poor habitats; species with antraquinones and lichens without any secondary metabolites were most abundant on limestone (alkalic and metal-poor), while other common lichen metabolites had no to minimal dependence on the chemistry of the substrate. The two additional abiotic factors affecting the composition of secondary metabolites were the maximum temperature of the warmest month and elevation. Our results suggest a range of possible relationships exist among lichen acids, rocks and climatic parameters. Furthermore, the same metabolite may affect both accumulation of metals and stress tolerance under unfavorable conditions.
... Four of the suspected adventives (Evernia prunastri, Ramalina americana, R. farinacea, and Xanthoria parietina) were almost certainly transplanted from further north along the Atlantic Coast in New England where they are presumed to be native , Hinds & Hinds 2007. Based on its documented range, the fifth species, Ramalina culbersoniorum, was likely transplanted from the southern Appalachian Mountains or southeastern Coastal Plain , LaGreca 1999. The role of nurseries in expanding or altering the distribution of lichen species in North America has not been studied in detail. ...
A checklist of the lichens and allied fungi from Mercer County, New Jersey, is presented. It was derived from inventories of 14 tracts of preserved and undeveloped land, which yielded 905 collections and 174 taxa. These include 37 new records for New Jersey, two of which, Catinaria neuschildii and Strangospora pinicola, have been rarely reported from North America. It also includes Agonimia flabelliformis, which is newly reported for North America from localities throughout the Appalachian and Ozark Mountains. Catillaria patteeana is described as new to science as well. These inventories demonstrate that substantial lichen diversity remains undiscovered even in densely populated regions of the Mid-Atlantic characterized by highly fragmented and disturbed natural landscapes with relatively small areas of unaltered, contiguous core-natural habitat.
... Lichenology has a long history of discussion about whether different chemotypes are part of intraspecific variation (e.g., Hawksworth 1976;Lumbsch, 1998). Molecular studies are essential to answer such questions LaGreca, 1999;Stocker-Wörgötter et al., 2004;Truong et al., 2013a) and to test whether chemistry is a good predictor in species delimitation analyses (Alors et al., 2016;Lendemer, 2012;Resl et al., 2016;Schmitt and Lumbsch, 2004). ...
Biological processes such as hybridization, incomplete lineage sorting and gene flow can obscure the recognition of distinct evolutionary lineages, particularly in groups of organisms that have recently diverged. Therefore, compiling pieces of evidence from diverse data sources is critical to accurately assess species boundaries in such groups. The increasing availability of DNA sequence data allows for a much deeper understanding of diversification and speciation processes and their consequences on biodiversity. In this study, we applied an integrative approach based on DNA sequence, chemical, geographic and morphological data to attempt to define species boundaries in the lichen-forming genus Usnea (Parmeliaceae), particularly the U. cornuta aggregate, a cosmopolitan species group. We provide the first species delimitation for this group in the neotropics based on the multispecies coalescent (MSC) model. Using ITS rDNA and two protein-coding genes, Mcm7 and RPB1, we estimated the species tree under the MSC model in a Bayesian framework using STACEY. Our results indicate that at least nine strongly supported distinct lineages coexist in the U. cornuta aggregate, which are well chemically characterized. Additionally, we found evidence for the polyphyly of three morphospecies, Usnea brasiliensis, U. cornuta and U. dasaea.
... Discussion.-Ramalina americana and R. culbersoniorum form a pair of closely related species that differ only in chemistry (Brodo et al. 2001, LaGreca 1999. Some chemotypes of R. culbersoniorum can be separated from R. americana using spot tests, but TLC is the best and most accurate method. ...
... Discussion.-This species is morphologically identical to Ramalina americana and differs only chemically in the presence of various substances in addition to usnic acid (LaGreca 1999). Specimens that cannot be studied with TLC should be identified as R. americana s.l. ...
***AVAILABLE ONLINE VIA JSTOR: https://www.jstor.org/stable/e26976761
Delmarva (also known as the Delmarva Peninsula), the name itself at once invites questions and invokes history. Just as the name is an aggregation (of Delaware, Maryland and Virginia), so is the land an aggregation of floras and faunas, of political units and cultures, of times and places. Situated between the Chesapeake Bay, America’s beleaguered estuarine jewel, the Delaware Bay, an area of critical global importance to migrating shorebirds, and the inexorably rising waters of the Atlantic Ocean, Delmarva is a vast peninsula defined by coexistence and contrasts, a meeting place of north and south, of urban and rural, of past and future. Like Delmarva, lichens are also defined by coexistence and contrast. They are among the most remarkable products of evolution: fungi that have entered into obligate symbioses with algae and cyanobacteria. Together the two form complex and striking structures unlike any other in nature. While this specialized lifestyle has allowed lichens to survive, and even thrive, in nearly every ecosystem on land, it also means these fungi cannot survive on their own. In fact, lichens are extremely sensitive to habitat loss, degradation and disturbance. Lichens have long been an integral component of the Delmarva landscape. They serve important functions in the environment, supplying food and shelter for animals, and providing ecosystem services that ultimately benefit human welfare and society. As we show in this book, while the link between lichens and Delmarva in the past is clear, how exactly they fit into the narrative for the future of Delmarva is an open question. We wrote this book with the goal of providing a resource that would open the world of these neglected species to anyone who wanted to learn about them. Our work draws on more than four years of detailed study in the region, trudging through swamps and reveling in beaches. There are many resources to learn about, identify and appreciate other groups of Delmarva biodiversity, such as birds and wildflowers. Yet to date there has never been such a resource for lichens. In this volume we treat the 299 species of lichens that have been documented from Delmarva to date, all of which are presumed to be native. This includes not just the macrolichens, some of which have been treated elsewhere, but also the microlichens that have long been neglected in North American floras. For each species, we provide a description, a discussion of its distribution and ecology, a proposed conservation rank, and a comparison with similar species. We have also assembled a discussion of Delmarva natural history, checklists that are arranged alphabetically and evolutionarily, and a complete set of identification keys. A distribution map for each species is also included that shows the range of the species in the context of the broader Washington D.C. metro region, and contrasts the historical occurrences with those from modern times. Nearly all of the species are illustrated with color photographs. Our hope is that publication of this work will prove to be a turning point for the lichens in the Mid-Atlantic Region, serving as inspiration to explore and appreciate a long-neglected component of biodiversity. While the book focuses on Delmarva, it covers the majority of species that occur along the Atlantic Coast from Norfolk, Virginia, to Cape Cod, Massachusetts. Thus the area covered by this book includes the metropolitan areas of Washington, D.C., Philadelphia and New York.
