Sigisfredo Garnica

University of Tuebingen | EKU Tübingen · Institute of Evolution and Ecology

Bistorta vivipara is a widespread herbaceous perennial plant with a discontinuous pattern of distribution in arctic, alpine, subalpine and boreal habitats across the northern Hemisphere. Studies of the fungi associated with the roots of B. vivipara have mainly been conducted in arctic and alpine ecosystems. This study examined the fungal diversity...

The biogeography of neotropical fungi remains poorly understood. Here, we reconstruct the origins and diversification of neotropical lineages in one of the largest clades of ectomycorrhizal fungi in the globally widespread family Russulaceae.We inferred a supertree of 3,285 operational taxonomic units, representing worldwide internal transcribed sp...

There is increasing evidence that microbes play a key role in some plant invasions. A diverse and widespread but little understood group of plant-associated microbes are the fungal root endophytes of the order Sebacinales. They are associated with exotic populations of invasive knotweed (Reynoutria ssp.) in Europe, but their effects on the invaders...

Perennial ryegrass (Lolium perenne L.) possesses a high level of nutritional quality and is widely used as a forage species to establish permanent pastures in southern Chile. However, the productivity of most such pastures is limited by various environmental agents, such as insect pests and drought. In this context, our work stresses the need for e...

There is increasing evidence that microbes play a key role in some plant invasions. A diverse and widespread but little understood group of plant-associated microbes are the fungal root endophytes of the order Sebacinales. They are associated with exotic populations of invasive knotweed ( Reynoutria ssp.) in Europe, but their effects on the invader...

Phylogenetic analyses based on a three-locus nuclear data set (ITS1-5.8S-ITS2, the 5' end of the 28S, and the largest subunit of RNA polymerase I) supported the pagoda fungus (Podoserpula, Amylocorticiales) as a monophyletic group most closely related to species of Anomoporia, which is nonmonophyletic, and Amyloathelia. Phylogenetic relationships i...

Understanding the impacts of agricultural practices on belowground fungal communities is crucial in order to preserve biological diversity in agricultural soils and enhance their role in agroecosystem functioning. Although fungal communities are widely distributed, relatively few studies have correlated agricultural production practices. We investi...

Fungi belonging to the Entorrhizales (Entorrhizomycota) comprise biotrophic pathogens associated with roots of the Cyperaceae and Juncaceae plant species. They are nearly globally distributed but rarely studied due to a hidden lifestyle without causing visible effects on host plants. Therefore, the evolutionary origin and phylogenetic relationships...

Altitudinal gradients provide valuable information about the effects of environmental variables on changes in species richness and composition as well as the distribution of below ground fungal communities. Since most knowledge in this respect has been gathered on aboveground communities, we focused our study towards the characterization of belowgr...

Nomenclatural type definitions are one of the most important concepts in biological nomenclature. Being physical objects that can be re-studied by other researchers, types permanently link taxonomy (an artificial agreement to classify biological diversity) with nomenclature (an artificial agreement to name biological diversity). Two proposals to am...

Patterns of geographic distribution and composition of fungal communities are still poorly understood. Widespread occurrence in terrestrial ecosystems and the unique richness of interactions of Sebacinales with plants make them a target group to study evolutionary events in the light of nutritional lifestyle. We inferred diversity patterns, phyloge...

Sebacinales ITS sequences from GenBank and UNITE databases. Sequences were retrieved from GenBank using the ("Sebacina"[Organism] OR "Sebacinaceae"[Organism] OR "Sebacinales"[Organism]) AND ("internal transcribed spacer 1"[All Fields] OR "ITS"[All Fields]) AND "internal transcribed spacer 2"[All Fields] search criteria. The following criteria were...

ITS alignment of Sebacinales used for age estimation and assessment of phylogenetic structure. (FASTA)

This file contains information about the priors and parameters used in BEAST to obtain Basidiomycota age estimates. (TXT)

List of primers with nucleotide sequences used in this study. Primers marked with asterisks were only used for DNA sequencing. (XLS)

A maximum likelihood (ML) tree of Basidiomycota with calibration points. Bootstrap values ≥ 70% are given. (PDF)

This file contains information about the fossil calibration approach used for Basidiomycota. Including a table of all Basidiomycota fossils with species name (if available), times, epochs, citations and calibration usages. (DOC)

This file contains information about the priors and parameters used in BEAST to obtain Sebacinales age estimates. (XML)

Basidiomycota specimens used in this study. The species names, collection numbers, herbarium vouchers or strain identifiers and the GenBank accession numbers are given. Sequences newly generated for this study are indicated in bold. (XLS)

Table containing MOTU designations, nutrition strategies, geographic distributions, and GenBank accession numbers of sequences used for analysis in R. (XLS)

A concatenated sequence alignment of the Basidiomycota dataset (i). The alignment comprises 18S, 28S, rpb1 and atp6 sequences with a length of 4,438bp. (NEX)

A maximum likelihood (ML) tree of Sebacinales with bootstrap values. (PDF)

[This corrects the article DOI: 10.1371/journal.pone.0147107.].

Different distance-based threshold selection approaches were used to assess and compare use of the internal transcribed spacer (ITS) region to distinguish among 901 Cortinarius species represented by >3000 collections. Sources of error associated with genetic markers and selection approaches were explored and evaluated using MOTUs from genus and li...

The evolutionary history, divergence times and phylogenetic relationships of Uleiella chilensis (Ustilaginomycotina, smut fungi) associated with Araucaria araucana were analysed. DNA sequences from multiple gene regions and morphology were analysed and compared to other members of the Basidiomycota to determine the phylogenetic placement of smut fu...

Entorrhiza is a small fungal genus comprising 14 species that all cause galls on roots of Cyperaceae and Juncaceae. Although this genus was established 130 years ago, crucial questions on the phylogenetic relationships and biology of this enigmatic taxon are still unanswered. In order to infer a robust hypothesis about the phylogenetic position of...

Morphological and molecular discrepancies in the biodiversity of monophyletic groups are challenging. The intention of this study was to find out whether the high molecular diversity in Sebacinales can be verified by micromorphological characteristics. Therefore, we carried out molecular and morphological studies on all generic type species of Seba...

Endophytic fungi are known to be commonly associated with herbaceous plants, however, there are few studies focusing on their occurrence and distribution in plant roots from ecosystems with different land uses. To explore the phylogenetic diversity and community structure of Sebacinales endophytes from agricultural and grassland habitats under diff...

A taxonomic re-evaluation of the Ceratobasidium-Rhizoctonia group suggests that Ceratobasidium contains only the type species C. calosporum, which deviates in micromorphological and ultrastructural characters from all other species so far included in that genus. Rhizoctonia species are compared with the type species of Ceratobasidium, Cejpomyces, O...

Background Phylogenetic studies, particularly those based on rDNA sequences from plant roots and basidiomata, have revealed a strikingly high genetic diversity in the Sebacinales. However, the factors determining this genetic diversity at higher and lower taxonomic levels within this order are still unknown. In this study, we analysed patterns of g...

To study the diversity and phylogenetic structure of Sebacinales communities from eight vegetation communities along an altitudinal gradient in the Bavarian Alps (Germany), we analysed 456 thalli or roots of plants. We detected 264 sebacinoid sequences, spanning the intergenic transcribed spacer region, 5.8S and D1/D2 regions of the nuclear rRNA ge...

A total of 35 population samples of the liverwort genera Aneura (A. pinguis) and Riccardia (R. latifrons, R. multifida, and R. palmata) were sampled from diverse habitats and geographical provenances in Germany, Austria, and Switzerland. Light and transmission electron microscopy were used to characterise the morphological features of the associati...

Fungi are believed to be diverse in the tropics, but because many groups are only known from their DNA sequences this hampers comparative diversity studies. We investigated mycorrhizal Sebacinales (Basidiomycota) of 67 individuals of Ericaceae and Orchidaceae in a tropical mountain ecosystem in Southern Ecuador to provide a first estimate of whethe...

RAxML ML phylogram from an alignment of 576 calochroid sequences of ITS-5.8S. Support values are derived from 1000 bootstrap replicates. GenBank accession numbers: DQ08XXXX are from [16]; DQ32XXXX, DQ3508242 and DQ66XXXX are from [1]; AY17XXXX are from [13], AY66XXXX from [15], EFO1XXXX from [25]; AF50XXXX are from [26]; AF3XXXXX and AY03XXXX are f...

Population mutation rate, effective sample size (ESS), time of divergence and direction of migration estimates within C. arcuatorum, C. aureofulvus and C. elegantior population samples. The parameters are as follows: θ1, θ2 and θA, are the mean population rates for the Old World, the New World and the ancestral population, respectively; t is the me...

Population samples used in this study and their respective voucher numbers, GenBank numbers, collection date, collection site, host tree(s), collector and determinator. Holotype specimens are marked in bold. Herbarium abbreviations: IB = Herbarium Innsbruck, Austria; JFA = J. F. Ammirati material deposited at the Burke Museum, Herbarium, University...

Specimens used in this study and their respective collection sites, host tree(s), herbarium numbers and GenBank accession numbers. Herbarium abbreviations: Arangu-Cort = Herbarium Sociedad Micológica Aranguren, Spain; IB = Herbarium Innsbruck, Austria; JFA = J. F. Ammirati, MES = Matthew Smith; MTS = Michelle Seidl, ST = Steve Trudell, BW = Ben Woo...

Cortinarius species in section Calochroi display local, clinal and circumboreal patterns of distribution across the Northern Hemisphere where these ectomycorrhizal fungi occur with host trees throughout their geographical range within a continent, or have disjunct intercontinental distributions, the origins of which are not understood. We inferred...

Ten new species of Cortinarius are described from Costa Rican neotropical montane forests based on morphological and molecular phylogenetic data. Morphological features of the basidiomes and nuclear rDNA sequence analyses place these species in the following clades: Anomali (Cortinarius sericeolazulinus), Cotoneus (Cortinarius aureopigmentatus), Li...

Phylogenetic relationships in the genus Cortinarius with emphasis on European species were studied by integrating a molecular phylogenetic analysis of nuclear rDNA sequences with morphological, chemical, and ecological data. Internal transcribed spacers (ITS1 and ITS2, including 5.8S) and the D1–D2 regions of nuclear rDNA of 262 Cortinarius species...

Phylogenetic relationships of Sebacinales based on maximum likelihood analysis of partial nuclear-encoded ribosomal large subunit sequences. Color boxes indicate type of symbiosis. Sequences from fruitbodies or cultures that can be assigned to morphospecies are in bold. Circled numbers highlight sequences or clades that are mentioned in the article...

Analytical sample-based rarefaction curve of endophytic Sebacinales, derived from partial nuclear-encoded ribosomal large subunit sequences. Sequences are treated as samples, sequences of ≥99% similarity were assigned to the same sequence type. Confidence intervals are based on 1000 replicates. As the curve is still far from its saturation level, m...

Host plants from which endophytic Sebacinales were sequenced for this study and assignment to plant families. Sequences marked with an asterisk are from herbarium specimens collected in the 1830/40s by G.W. Schimper and T. Kotschy. (XLS)

Map of primers used for PCR and sequencing in the present study. The map is based on GenBank sequences AY505557 and DQ520096, primer lengths are not drawn to scale. The ruler gives number of base pairs, starting from the 5′ end of primer NS13. (PDF)

Inconspicuous basidiomycetes from the order Sebacinales are known to be involved in a puzzling variety of mutualistic plant-fungal symbioses (mycorrhizae), which presumably involve transport of mineral nutrients. Recently a few members of this fungal order not fitting this definition and commonly referred to as 'endophytes' have raised considerable...

Distinctive groups of fungi are involved in the diverse mycorrhizal associations of land plants. All previously known mycorrhiza-forming Basidiomycota associated with trees, ericads, liverworts or orchids are hosted in Agaricomycetes, Agaricomycotina. Here we demonstrate for the first time that Atractiellomycetes, members of the 'rust' lineage (Puc...

Section Calochroi is one of the most species-rich lineages in the genus Cortinarius (Agaricales, Basidiomycota) and is widely distributed across boreo-nemoral areas, with some extensions into meridional zones. Previous phylogenetic studies of Calochroi (incl. section Fulvi) have been geographically restricted; therefore, phylogenetic and biogeograp...

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Traditional classifications of agaric fungi involve gross morphology of their fruit bodies and meiospore print-colour. However, the phylogeny of these fungi and the evolution of their morphological and ecological traits are poorly understood. Phylogenetic analyses have already demonstrated that characters used in traditional classifications of basi...

Although coevolution is acknowledged to occur in nature, coevolutionary patterns in symbioses not involving species-to-species relationships are poorly understood. Mycorrhizal plants are thought to be too generalist to coevolve with their symbiotic fungi; yet some plants, including some orchids, exhibit strikingly narrow mycorrhizal specificity. He...

The mycorrhizal state of epiphytic orchids has been controversially discussed, and the state and mycobionts of the pleurothallid orchids, occurring abundantly and with a high number of species on stems of trees in the Andean cloud forest, were unknown. Root samples of 77 adult individuals of the epiphytic orchids Stelis hallii, S. superbiens, S. co...

We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that c...

We reassessed the circumscription of the cantharelloid clade and identified monophyletic groups by using nLSU, nSSU, mtSSU and RPB2 sequence data. Results agreed with earlier studies that placed the genera Cantharellus, Craterellus, Hydnum, Clavulina, Membranomyces, Multiclavula, Sistotrema, Botryobasidium and the family Ceratobasidiaceae in that c...

Dikaryotic and haploid mycelia of more than 150 gilled species of euagarics were studied morphologically and by molecular phylogenetic methods. The morphological investigations revealed anamorphs in more than 90 species that were often specific at the genus or family level. Thallic conidiogenesis dominated and varied from fragmentation of normally...

Phylogenetic relationships of 54 European Phlegmacium species, including members of most of the sections of classical systematics, were studied, integrating macro-, micromorphological and chemical characters of the basidiomes, as well as molecular phylogenetic analysis of nuclear rDNA sequences. Microscopical structures of the basidiomes were studi...

Phylogenetic relationships of 54 European Phlegmacium species, including members of most of the sections of classical systematics, were studied, integrating macro-, micromorphological and chemical characters of the basidiomes, as well as molecular phylogenetic analysis of nuclear rDNA sequences. Microscopical structures of the basidiomes were studi...

Thirty South American species of Cortinarius belonging to the subgenera Telamonia, Dermocybe, Myxacium, Phlegmacium, and Cystogenes were studied using an integrated approach that included morphological, anatomical, and ultrastructural data, and also molecular phylogenetic analysis of nuclear rDNA sequences. The micromorphology of the basidiomes was...

Four new Cortinarius species are described from Nothofagus forests in South Chile. Cortinarius aurantiorufus and C. punctatisporus, subgenus Phlegmacium, stirps Inflatipes, are mainly characterized by a viscid to glutinous pileus and a bulbous whitish stipe. They differ in the color of the pileus, and shape, ornamentation, and size of the basidiosp...

Four new Cortinarius species are described from Nothofagus forests in South Chile. Cortinarius aurantiorufus and C. punctatisporus, subgenus Phlegmacium, stirps Inflatipes, are mainly characterized by a viscid to glutinous pileus and a bulbous whitish stipe. They differ in the color of the pileus, and shape, ornamentation, and size of the basidiosp...

Pseudohelicomyces albus gen. et sp. nov. is described. It is characterised by the presence of hyaline, cylindrical arthroconidia originating from either spiral vegetative hyphae or from spiral, branched conidiophores. The hyphae and conidiophorés may or may not possess clamp connections. The characteristics of the basidiocarps formed in culture wer...