Robert LückingBotanischer Garten und Botanisches Museum Berlin
Robert Lücking
PhD
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Introduction
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October 2011 - present
August 2001 - present
January 1995 - July 1998
Publications
Publications (665)
##Assembly-Data-START## Assembly Method :: Sequencher v. 4.7 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
##Assembly-Data-START## Assembly Method :: Sequencher v. 4.7 Sequencing Technology :: Sanger dideoxy sequencing ##Assembly-Data-END##
Two new genera, Myriochapsa M. Caceres, Lucking & Lumbsch and Nitidochapsa Parnmen, Lucking & Lumbsch, are introduced for the species Chapsa psoromica and C. leprieurii, which are not genuine Chapsa species but related to Myriotrema and Ocellularia, respectively. The following two new combinations are proposed: Myriochapsa psoromica (M. Caceres, Sa...
As part of a larger systematic and taxonomic revision of the genus Sticta in the northern Andes,
several species were discovered forming green algal and cyanobacterial photosymbiodemes, seven of which
are new to science and are described here—S. lobarioides Moncada & Coca, S. macrothallina Moncada &
Coca, S. neopulmonarioides Moncada & Coca, S. phy...
Unlabelled:
•
Premise of the study:
This study elucidates the phylogenetic position of a unique taxon of Graphidaceae occurring on rock in coastal desert areas, assessing its importance for our understanding of the evolution of the largest family of tropical lichenized fungi. •
Methods:
We used maximum likelihood and Bayesian approaches to rec...
We present a comprehensive molecular phylogeny of the lichen family Graphidaceae (subfamilies Graphidoideae and Fissurinoideae) based on partial sequences of the mtSSU, nuLSU rDNA, and RPB2 loci. The phylogeny includes all currently available sequences in Genbank plus 897 newly generated sequences, from a total of 908 ingroup OTUs representing 428...
ABSTRACT. Many of the species living on our planet remain undiscovered, among these over one million Fungi. One approach to account for undescribed species is the search in unusual habitats. Here we report on the unexpected finding of a new species of Lepidostroma (Atheliales: Lepidostromataceae) from the semi-arid Caatinga biome in northeastern Br...
The new species Sticta viviana A. Suárez & Lücking is described from Colombian paramos. It superficially resembles S. fuliginosa s. str. but differs by the small lobes with a shiny surface, the strongly branched, corymbose isidia, the dark lower tomentum, the smaller, usually sessile and urceolate cyphellae with one papilla-like outgrowth per cell...
The generic classification of Lobariaceae based on a three-gene phylogeny of mtSSU, nuLSU and ITS data, with special reference to the genus Lobariella, is reassessed. Twelve well-supported clades are recognized within Lobariaceae, which correlate with morpho-chemical and ecological features and are suggested to represent distinct generic lineages w...
Based on molecular phylogenetic studies and morphological revision, three new species of Dictyonema are described from Bolivia. Dictyonema applanatum Lücking, Dal-Forno & Wilk is characterized by an appressed filamentous thallus in which the fibrils are completely horizontally oriented and partially embedded in a gelatinous matrix formed by the thi...
In the Valle del Cauca, few studies have been devoted to the biology of lichens and the knowledge of the lichen diversity in the region is scarce. Lichens of the genera Coccocarpia and Dictyonema have been little studied and there are only very recent reports of four species (Coccocarpia etythroxyli, C. palmicola, Dictyonema glabratum, D. sericeum)...
Molecular phylogenies often reveal that taxa circumscribed by phenotypical characters are not monophyletic. While re-examination of phenotypical characters often identifies the presence of characters characterizing clades, there is a growing number of studies that fail to identify diagnostic characters, especially in organismal groups lacking compl...
Clade placement of taxa according to molecular phylogenetic analysis and phylogenetic binning according to the different classification solutions using 2, 4, or 5 clades under either ML or MP weighting.
(DOC)
In this paper, an extended molecular phylogeny was generated for the Ocellularia clade, which includes about half of the species that were previously separated in the family Thelotremataceae. Three genes (mtSSU, nuLSU, RPB2), from a total of 270 OTUs with 136 ingroup species, were sequenced to evaluate whether the core genera, Ocellularia and Myrio...
As part of a systematic and taxonomic revision including molecular phylogenetic analysis, ten new species of the lichen genus Sticta are described from Colombia, some of them also being reported from Guatemala, Venezuela, Ecuador, Bolivia, and Chile: Sticta arachnofuliginosa Moncada & Lücking, sp. nov., S. arbuscula Moncada & Lücking, sp. nov., S....
The new genus Mangoldia Lucking, Parnmen & Lumbsch is described based on the new species M. australiana and also including M. atronitens. Mangoldia combines thallus and ascoma features of Phaeographis s.str. (e. g., P. dendritica and P. lecanographa), i.e. a white, ecorticate thallus and ascoma with exposed, brown disc and thin, partially split, th...
2012) Tres nuevas especies de Graphidaceae de Venezuela. Glalia 4(1): 1–7. — Se describen tres nuevas especies de la familia Graphidaceae halladas en el Parque Nacional Henri Pittier (Aragua-Carabobo, Venezuela): Fissurina redingerioides Lücking, J. E. Hern. & Kalb, diferenciada de Fissurina instabilis por los ascomatas arreglados en forma de poros...
Diversity of tropical lichen-forming fungi, especially crustose lichens is currently poorly known. Since lichens are important bioindicators of air pollution, forest health, and climate change, we addressed the lichen diversity in Kenya. Our study focused on the diversity of lichen-forming fungi in the Mount Kenya montane forests, where we sampled...
A fairly common species of oceanic forests in Oregon has long been filed under Graphina sp. The purpose of this paper is to resolve the disposition of this species. The Pacific Northwest taxon is here identified with Graphis pergracilis (Zahlbr.) Lücking & A. W. Archer, previously known from the Paleotropics. A similar European taxon previously kno...
The lichen-forming genus Pertusaria under its current circumscription is polyphyletic and its phylogenetic affiliations are uncertain. Here we study the species of the genera Pertusaria and Varicellaria which contain lecanoric acid as major constituent, have disciform apothecia, strongly amyloid asci, non-amyloid hymenial gel, 1-2-spored asci, and...
A numerical approach is presented to predict the number of potentially undiscovered species in groups of species that exhibit a ‘modular’ combination of character states, that is, nearly ‘free’ combination that is not random but allows for a wide range of cross-combination of character states. The method uses a character correlation index (CCI) bas...
Lichenized fungi or lichens are organisms that have been little studied in the tropics and which distribution is affected by microenvironmental factors and substrate characteristics. The present study aimed to identify phorophyte specificity and microenvironmental preferences of corticolous lichens in five phorophyte species from premontane forest...
The new combination Diorygma antillarum (Vain.) Nelsen, Lücking & Rivas Plata is proposed. This taxon lacks ascomata and produces unique isidia-like structures for vegetative dispersal. Its systematic position was clarified by incorporating molecular sequence data from the small subunit of the mitochondrial ribosomal DNA (mtSSU) and small and large...
Phorophyte specificity and microenvironmental preferences of corticolous lichens in five phorophyte species from premontane forest of Finca Zíngara, Cali, Colombia). Lichenized fungi or lichens are organisms that have been little studied in the tropics and which distribution is affected by microenvironmental factors and substrate characteristics. T...
We characterized the composition of the foliicolous lichens from the Environmental Station of Tutunendó, Choco, Colombia. A total of 113 species belonging to 31 genera, 13 families and 7 orders were found. Gomphillaceae, Pilocarpaceae, Arthoniaceae, Strigulaceae and Porinaceae were the most diverse families. Forty nine species are recorded for the...
In a continuation of our biotic inventory of lichenized fungi in Costa Rica and adjacent areas, we present a treatment of the thelotremoid Graphidaceae, that is the genera and species formerly included in Thelotremataceae. A total of 186 species in 23 genera are reported for Costa Rica, plus an additional 30 taxa for adjacent areas (El Salvador, Ni...
A survey of crustose microlichens at Los Amigos Biological Station in Amazonian Peru revealed 116 species of Graphidaceae at this site. This is the second highest number of Graphidaceae ever reported for a single site world-wide, after the Surumoni crane station in Venezuela, with 131 species, and followed by Fakahatchee Strand Park Preserve in Flo...
Three new species of Chapsa in the family Graphidaceae are described from tropical Asia. Chapsa mastersonii Rivas Plata, Lumbsch & Lücking from the Philippines is characterized by large apothecia with thickly white-pruinose discs, large, muriform, non-amyloid ascospores, and the stictic acid chemosyndrome. Chapsa wijeyaratniana Weerakon, Lumbsch &...
Three names in the genus Graphis are validated: Graphis norvestitoides Sutjaritturakan, G. rongklaensis Sutjaritturakan, and Graphis arbusculaeformis (Vain.) Lücking. In addition, the new species G. pseudoaquilonia Lücking is described, differing from G. norvestitoides in the clear versus inspersed hymenium.
Three new crustose lichen species are described from Sri Lanka. Chapsa pulchella Wijeyaratne, Locking & Lumbsch is unique due to its bright red apothecial margin contrasting with the white-pruinose disc. Pyrenula ocellulata Wijeyaratne, Lucking & Lumbsch resembles Pyrenula interducta and P. mastophoroides in having an inspersed hymenium and medium-...
We studied ascospore dispersal and ontogeny in several species of Trypetheliaceae and one species of Graphidaceae with megalosporous (very large) ascospores, including Aptrootia terricola (Aptroot) Lücking, Umaña & Chaves, Architrypethelium nitens (Fée) Aptroot, A. seminudum (Mont.) Aptroot, Astrothelium diplocarpoides Müll. Arg., Laurera gigantosp...
Six new species of Graphidaceae are described from Sri Lanka, four in Graphis sensu Staiger and one each in Fissurina and Thelotrema. Fissurina srilankensis Weerakoon, Wijeyaratne & Lucking is characterized by lirellae with well-developed labia and comparatively large, muriform ascospores. Graphis allugallenensis Weerakoon, Wijeyaratne & Lucking is...
As part of an ongoing inventory of the lichenized mycota of the Caxiuanã National Forest, at Ferreira Penna Research Station in the Brazilian Amazon, two species of lichenized fungi are described as new and four new combinations are introduced: Ampliotrema megalostoma (Müll. Arg.) M. Cáceres & Lücking comb. nov., Graphis brachylirellata M. Cáceres...
The new genus Malmographina Cáceres, Rivas Plata & Lücking is introduced for Opegrapha plicosa Meissn. (syn. Graphis malmei Redinger), with the new combination Malmographina plicosa (Meiss.) Cáceres, Rivas Plata & Lücking. The taxon is characterized by prominent, striate, orange-pigmented, non-carbonized lirellae, a more or less clear hymenium, and...
The genus Graphis was revised in the framework of a study of corticolous lichens of the Caribbean part of Colombia, being one of the more representative genera in the region. We found 23 species of the genus, 19 of which are newly reported for Colombia: Graphis argentius Makhija & Adaw., G. chlorotica A. Massal., G. comma (Ach.) Spreng., G. daintre...
Here we continue to investigate the phylogenetic relationships of taxa ascribed to the primarily lichen-forming families Trypetheliaceae, Monoblastiaceae and Arthopyrenia-ceae. We demonstrate that the genera Julella and Arthopyr-enia do not form monophyletic groups with taxa from these genera instead being placed both in Pleosporales and Trypetheli...
The new foliicolous lichen Coccocarpia melloniorum Lucking from the Philippines is described and illustrated. It is morphologically similar to C. epiphylla but differs in the formation of disc-shaped isidia and dark rhizines. The species was discovered as part of a type digitization project through the Global Plant Initiative (GPI), as part of a sy...
We documented the corticolous lichen flora composition in five localities of the Colombian Caribbean region, three in the lowlands (plains) and two in the highlands (massifs). We found 348 species based on approximately 950 specimens, 215 were determined at the species level and 62 at the genus level (due to the absence of reproductive structures o...
Six species of the genus Coenogonium are reported for the first time for Colombia: Coenogonium barbatum, Coenogonium geralense, Coenogonium lisowskii, Coenogonium minimum, Coenogonium moniliforme and Coenogonium siquirrense. All originate from the Estación Ambiental de Tutunendó in the department of Chocó (Colombia).
Sixty-six species are recorded for the first time from the Fijian archipelago. Diagnostic features and distribution areas are given for each species reported here. The genera Bactrospora, Badimia, Baeomyces, Calenia, Coccotrema, Dibaeis, Gyalectidium, Gyalideopsis, Lecanora, Lepraria, Leucodecton, Megalospora, Melanotopelia, Pannaria, Peltigera, Py...
Seven foliicolous species growing in tropical regions of Vietnam are reported as new to the country. Described are Arthonia accolens, Calenia aspidota, Calopadia subcoerulescens, Coenogonium minimum, Fellhanera rhapidophylli, F. semecarpi, and Porina subnitidula. Among them, Coenogonium minimum and Porina subnitidula are reported for the first time...
A brief discussion of the Encyclopedia of Life and the LifeDesks websites as a means to assemble and publish species pages and taxonomic information on the internet, for both the scientific community and the public, is provided. The lichen family Parmeliaceae is the first large group of lichenized fungi for which a concerted effort is currently bei...
The Verrucariaceae (Ascomycota) is a family of mostly lichenized fungi with a unique diversity of algal symbionts, including some algae that are rarely or never associated with other lichens. The phylogenetic position of most of these algae has not yet been studied and, because morphology-based identifications can often be misleading, molecular dat...
Despite their potential shortcomings for phylogenetic inference, sometimes only morphological data are available for systematic classification. Computational methods are used to determine morphological site patterns congruent with the molecular tree in order to improve the accuracy of the classification of taxa for which only morphological data exi...
The new genus Halegrapha is introduced, with six species (five new species and one new combination) from Australia, the Philippines, Malaysia, Kenya, Mexico, and the United States: H. chimaera Rivas Plata & Lücking (type species; Philippines), H. floridana Common & Lücking (United States: Florida), H. intergrapha Hale ex Lücking (Malaysia), H. keny...
Nearly one-fourth of the lichen-forming fungi associate with trentepohlialean algae, yet their genetic diversity remains unknown. Recent work focusing on free-living trentepohlialean algae has provided a phylogenetic context within which questions regarding the lichenization of these algae can be asked. Here, we concentrated our sampling on trentep...
UNIVERSITY OF FLORIDA GAINESVILLE The FLORIDA MUSEUM OF NATURAL HISTORY is Florida's state museum of natural history, dedicated to understanding, preserving, and interpreting biological diversity and cultural heritage. The BULLETIN OF THE FLORIDA MUSEUM OF NATURAL HISTORY is a peer-reviewed journal that publishes results of original research in zoo...
The number of undescribed species of lichenized fungi has been estimated at roughly 10,000. Describing and cataloging these would take the existing number of taxonomists several decades; however, the support for taxonomy is in decline worldwide. In this paper we emphasize the dire need for taxonomic expertise in lichenology. We bring together 103 c...
The number of undescribed species of lichenized fungi has been estimated at roughly 10,000. Describing and cataloging these would take the existing number of taxonomists several decades; however, the support for taxonomy is in decline worldwide. In this paper we emphasize the dire need for taxonomic expertise in lichenology. We bring together 103 c...
Molecular phylogenetic analysis of the mitochondrial small subunit and nuclear large subunit ribosomal DNA revealed that the lichen genus Graphis sensu Staiger represents two separate lineages. Graphis s.str. comprises the species of the G. scripta and G. subserpentina groups ('Eugraphis'), as well as the G. striatula group sensu Lücking. For the s...
We present a novel method to encode ambiguously aligned regions in fixed multiple sequence alignments by 'Pairwise Identity and Cost Scores Ordination' (PICS-Ord). The method works via ordination of sequence identity or cost scores matrices by means of Principal Coordinates Analysis (PCoA). After identification of ambiguous regions, the method comp...
As part of an ongoing comprehensive inventory of Galapagos lichens, a first assessment of the morphology and anatomy of basidiolichens from the archipelago is presented here. It is the basis for further studies of the taxonomy, ecology and biogeography of this poorly known group of lichens. Four genera, all in Hygrophoraceae, can be distinguished:...
A revised classification for the emended family Graphidaceae is proposed, based on recent phylogenetic studies, including the finding that three previously separated families (Asterothyriaceae, Gomphillaceae, Thelotremataceae) are nested within Graphidaceae and in part polyphyletic. The family comprises three major clades which are here delimited a...
The genus Trinathotrema Lücking, Rivas Plata & Mangold is introduced to accommodate the common and widely distributed lichens Ocellularia stictidea and Conotrema lumbricoides, as Trina-thotrema lumbricoides (Sipman) Sipman & Aptroot comb. nova and T. stictideum (Nyl.) Lücking, Miranda & Kalb comb. nova. Molecular analysis shows that the genus forms...
Heiomasia is a new genus that includes two sterile species producing unique isidia-like structures for vegetative dispersal. Their systematic position was clarified using molecular analysis of the small subunit of the mitochondrial ribosomal DNA (mtSSU). The two species form a strongly supported clade occupying a somewhat isolated position within G...
Epizoic foliicolous liverworts and lichens are reported for the first time from insects, two species of the Shield Mantis Choeradodis, C. rhombicollis and C. rhomboidea (Mantodea: Mantidae: Choeradodineae) in Costa Rica. Five species of liverworts, 23 species of lichens, and several unidentified fungi were found growing mainly on the pronotum, but...
Parmelioid lichens are a diverse and ubiquitous group of foliose lichens. Generic delimitation in parmelioid lichens has been in a state of flux since the late 1960s with the segregation of the large, heterogeneous genus Parmelia into numerous smaller genera. Recent molecular phylogenetic studies have demonstrated that some of these new genera were...
Six new records of foliicolous lichens for Vietnam are described and illustrated. These are: Aderkomyces albostrigosus f. albostrigosus, A. albsostrigosus f. aggregatus, Asterotherium rotuliforme, Byssoloma vanderystii, Fellhanera emarginata and Trichothelium minutum. The species were collected at Thác Dray Sap region (commonly called Dray Sac Wate...
The fungal order Ostropales is unique in Ascomycota for including both lichen-forming and non-lichenized species and species with optional nutritional strategies depending on substrate. To address the phylogenetic relationships within the order, we assembled a dataset of 78 ostropalean species, including all major clades and 23 taxa that are only o...
The fungal order Ostropales is unique in Ascomycota for including both lichen‐forming and non‐lichenized species and species with optional nutritional strategies depending on substrate. To address the phylogenetic relationships within the order, we assembled a dataset of 78 ostropalean species, including all major clades and 23 taxa that are only o...
The new species Graphis collinsiae Lücking & Lumbsch is described from the Fiji Islands. The species belongs to the G. insulana aggregate and is intermediate between G. insulana (Müll. Arg.) Lücking & Sipman and G. subhiascens (Müll. Arg.) Lücking. All three species have a similar thallus and lirellae morphology and anatomy and ascospore-type, but...
Graphis flavopalmicola is described as a new lichenized fungus from Jeju Island (South Korea). It is characterized by smooth, whitish-gray, UV+ pale yellow thallus (lichexanthone), unbranched to irregularly branched lirellae; completely carbonized exciple, and transversely 5-9-septate ascospores. It differs from the closely related G. palmicola chi...
Thelotremoid lichens (Ostropales, Ascomycota) with a trentepohlioid photobiont in Tierra del Fuego, the Falkland Islands, the South Island of New Zealand, and subpolar islands of the southern Hemisphere are studied. Twenty-five species are accepted, with three species described as new to science: Melanotopelia blepharostoma Lumbsch & Divakar, Topel...
Chapsa rubropruinosa Messuti & Codesal collected in Argentina is described as new to science. The species is characterized by a thin thallus, apothecia with a pigmented disc, and transversely septate, hyaline, non-amyloid to faintly amyloid ascospores with thin cell walls. Chapsa minor is recorded for the first time from South America. The new comb...
In the course of an ongoing systematic and taxonomic revision of the lichen family Graphidaceae (including Thelotremataceae), we present world-wide keys to the currently accepted thelotremoid genera and species, excluding the columellate taxa and their relatives of the Ocellularia-Myriotrema-Stegobolus clade (Melanotrema, Myriotrema, Ocellularia, O...
Thelotremoid lichens (Ostropales, Ascomycota) with a trentepohlioid photobiont in Tierra del Fuego, the Falkland Islands, the South Island of New Zealand, and subpolar islands of the southern Hemisphere are studied. Twenty-five species are accepted, with three species described as new to science: Melanotopelia blepharostoma Lumbsch & Divakar, Topel...
As part of an ongoing comprehensive inventory of the Galapagos lichen flora, all species in the Graphidaceae from the archipelago have been revised using both historic and recent collections. A total of forty-two species is reported here, of which thirty-four were previously unknown from the archipelago and two are described as new to science: Grap...
We present a comprehensive phylogeny derived from 5 genes, nucSSU, nucLSU rDNA, TEF1, RPB1 and RPB2, for 356 isolates and 41 families (six newly described in this volume) in Dothideomycetes. All currently accepted orders in the class are represented for the first time in addition to numerous previously unplaced lineages. Subclass Pleosporomycetidae...
Dating of fungal divergences with molecular clocks thus far has yielded highly inconsistent results. The origin of fungi was estimated at between 660 million and up to 2.15 billion y ago, and the divergence of the two major lineages of higher fungi, Ascomycota and Basidiomycota, at between 390 million y and up to 1.5 billion y ago. Assuming that th...
The ancestors of fungi are believed to be simple aquatic forms with flagellated spores, similar to members of the extant phylum Chytridiomycota (chytrids). Current classifications assume that chytrids form an early-diverging clade within the kingdom Fungi and imply a single loss of the spore flagellum, leading to the diversification of terrestrial...
The Agaricales is the largest and most diverse order of mushroom-forming Basidiomycota, with over 100 natural groups recognized in recent Fungal Tree of Life studies. Most agarics are either saprotrophic or ectomycorrhizal fungi, but the family Hygrophoraceae is in part characterized by a unique and remarkable diversity of lichenized forms. The mos...
Phylogenetic diversity of lichen photobionts is low compared to that of fungal counterparts. Most lichen fungi are thought to be associated with just four photobiont genera, among them the cyanobacteria Nostoc and Scytonema, two of the most important nitrogen fixers in humid ecosystems. Although many Nostoc photobionts have been identified using is...
A world-wide key to the genus Graphis is presented, based on extensive type studies and revision of several thousand historical and recent collections. A total of 330 species are accepted and included in the key, and a further 205 epithets are listed as synonyms. The structured key includes taxonomic information on type specimens of epithets consid...
The species-level taxonomy of the genus Graphis sensu Staiger was revised using numerical taxonomy and cladistic techniques. In its current circumscription, Graphis includes more than 300 species and is characterized by lirellae with well-developed, carbonized labia usually concealing the disc and usually hyaline, I+ blue-violet, transversely septa...
Microstelium hyalinum Pat. and Acrospermum puiggarii Speg., established as non-lichenized fungi in 1899 and 1919, respectively, are conspecific with Gomphillus ophiosporus Kalb & Vězda, a muscicolous lichen described in 1988, widespread and common throughout the Neotropics. This is another example where crustose lichens with reduced thallus morphol...
A corticolous Graphis discovered in the southern part of Venezuela is described as new to science. The new species, Graphis breussii sp. nov., is characterized by rather large, prominent lirellae with striate labia and apically thin complete thalline cover, a completely carbonized exciple, four submuriform ascospores per ascus, and norstictic acid;...
We present a 6-gene, 420-species maximum-likelihood phylogeny of Ascomycota, the largest phylum of Fungi. This analysis is the most taxonomically complete to date with species sampled from all 15 currently circumscribed classes. A number of superclass-level nodes that have previously evaded resolution and were unnamed in classifications of the Fung...
We present a revised phylogeny of lichenised Dothideomyceta (Arthoniomycetes and Dothideomycetes) based on a combined data set of nuclear large subunit (nuLSU) and mitochondrial small subunit (mtSSU) rDNA data. Dothideomyceta is supported as monophyletic with monophyletic classes Arthoniomycetes and Dothideomycetes; the latter, however, lacking sup...
Four new taxa of the lichenized, foliicolous ascomycete genus Chroodiscus are described from Southeast Asia: Chroodiscus defectus Papong & Lücking, Ch. homchantarae Papong & Lücking, Ch. khaolungensis Papong & Lücking and Ch. khaosokensis Papong & Lücking. Chroodiscus argillaceus (Müll. Arg.) Lücking & Papong ( = Chroodiscus parvisporus Kalb & Lück...
We revised the original material of the invalidly published names Pyrenotrichum ‘atrocyaneum’, P. ‘mirum’, and P. ‘podosphaera’ R. Sant. Pyrenotrichum ‘atrocyaneum’ represents the campylidia of the recently described Kantvilasia hians, while P. ‘mirum’ corresponds to the campylidia of ‘Lopadium’ tayabasense, a species that externally resembles Calo...
As part of an ongoing lichen biodiversity inventory in Costa Rica, we present a survey on the taxonomy of the basidiolichen genus Dictyonema. Two species are described as new: D. melvinii Chaves, Lücking, & Umaña (also known from Colombia and Bolivia), and D. minor Lücking, Navarro, & Sipman (also known from Colombia and Venezuela). A total of 11 t...
Revision of two collections of Gomphillus from Papua New Guinea and Chile, previously identified as Gomphillus ophiosporus and G. calycioides, respectively, revealed that these represent an undescribed species, G. morchelloides Lücking & Sérus. The new species is characterized by short-stipitate, apically much broadened, cerebriform to morchelloid...
Based on a study of 22 sites in northeastern Brazil, including the three main vegetation types, coastal Mata Atlântica (Zona da Mata), Caatinga and Brejos de Altitude (rain forest enclaves in Caatinga areas), we studied the distribution and habitat preferences of 456 crustose and microfoliose lichen species. Alpha-diversity ranged between three and...
A synopsis of the lichen family Gomphillaceae in eastern North America is presented, based mainly on collections made by the second author during the past 30 years. A total of 57 taxa is reported for the area, including 11 species and one variety new to science: Arthotheliopsis floridensis Lücking & W. R. Buck, sp. nov., Echinoplaca areolata Lückin...
A revision of the lichen genus Gomphillus Nyl. in the Americas reveals that G. caribaeus W. R. Buck does not belong in that genus, but is a member of the Pilocarpaceae in the Lecanorales. Because of its distinctive features, the species cannot be accommodated in any of the known genera of that family, and the new genus Bryogomphus Lücking, W. R. Bu...
Questions
Questions (6)
I need to run GMYC but seem to be hitting a wall. The GMYC web server is not responding for hours, although the tree is quite small. I have previously also done this in R and wanted to do this now, but apparently the "splits" package which contains the GMYC algorithm does not exist anymore? There only is a package "split" which has nothing to do with "splits". Any advice would be highly appreciated.
Robert
I generally use GTR+I+G for phylogenetic analysis, as this is the universal substitution model, with other models being simplifications by equalizing rates. Model testing generally uses the argument that GTR may be overfitting, but I have not yet seen a study where that would really cause substantial effects. Usually, when I do model testing, GTR+I+G is always close to the top and the differences in likelihood and AICc or BIC are usually minor. Also, commonly I get e.g. TVM+I+G as best fitting model, which differs from GTR+I+G in that AG and GC are equal (sometimes TPM, with three equal rates). Given that model testing depends on alignment details (e.g. removal of ambiguously aligned regions changes original base frequencies), among other factors, and there are parameters other than base and substitution frequencies that may influence particular substitutions (e.g. secondary structure), I wonder whether it is actually justified to chose an only slightly deviating model over GTR, when the latter is close to the best model in AICc or BIC and actual topologies or support, when using e.g. TVM or GTR, do not really differ, except maybe for non-supported branches. Isn't it OK to use GTR per default, making no assumptions about the data, compared to fitting a marginally better model such as TVM that depends on certain details and in the end makes no or very little difference?
I would like to start a small discussion on the problem of the taxonomic paradoxon, in popular saying also known as the chicken and egg problem. This recent paper claims to solve the paradoxon, but I believe this is not the case. While one can certainly argue that even the "species" is an artificial construct, as long as we do taxonomy and we use taxonomy as a tool to address evolutionary processes, we should be able to resolve the taxonomic paradoxon of species delimitation through time. Horizontally it can be done by using parameters such as phylogeny (topology, support, branch length) and reproductive biology. However, these measures collapse entirely if we look at a lineage backwards in time. By default, we postulate that any generation stems from a prior generation belonging to the same species. Even if mutations occur and are inherited, this does per se not "generate" new species, as speciation is a lengthy process of genetic variation sorted out by environmental factors. The only instance one could imagine spontaneous speciation is where partner recognition is highly specific based on narrow chemical stimuli (key-lock principle), but that would apply to particular organisms only. So the paradoxon lies in the notion that if you compare individuals along the same lineage using a given distance, they would resolve as distinct species, but you could freely shift that intervall along the time axis and hence there would be no fixed moment of speciation, which means you would be essentially unable to assign individuals to distinct taxa along that lineage. By extension, if you had access to all living individuals ever existing on this planet, you could not classify them naturally, since even at a branching point, two subsequent generations could not be distinguished. So how to we solve this? Or are we just happy that our taxonomic classifications rely on the fact that all past individuals that could mess with them are extinct? One of the practical applications of this important question is paraphyly, and the many different opinions in this respect seem to indicate that this question can indeed not be resolved?
