• Publications of Francois M. Lutzoni

      • Books

          • Taylor, J. W., Spatafora, J., O’Donnell, K., Lutzoni, F., James, T., Hibbett, D. S., Geiser, D., Bruns, T. D. and Blackwell, M..
          • (2004).
          • The Fungi.
          • Oxford University Press, Oxford, UK.
          • Lutzoni, F..
          • (2002).
          • Lichens.
          • Oxford University Press, Oxford, UK.
          • Pagel, M. and Lutzoni, F..
          • (2002).
          • Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation.
          • Springer Verlag, Berlin, Germany.
          • Kranner, I., and Lutzoni, F..
          • (1999).
          • Evolutionary consequences of transition to a lichen symbiotic state and physiological adaptation to oxidative damage associated with poikilohydry.
          • Marcel Dekker, New York.
      • Papers Published

          • P-L Chagnon, JM U’Ren, J Miadlikowska, F Lutzoni and A Elizabeth Arnold.
          • (2016).
          • Interaction type influences ecological network structure more than local abiotic conditions: evidence from endophytic and endolichenic fungi at a continental scale.
          • Oecologia
          • ,
          • 180
          • (1)
          • ,
          • 181-191.
          • [web]
          • R Darnajoux, F Lutzoni, J Miadlikowska and J-P Bellenger.
          • (2015).
          • Determination of elemental baseline using peltigeralean lichens from Northeastern Canada (Québec): Initial data collection for long term monitoring of the impact of global climate change on boreal and subarctic area in Canada.
          • Science of The Total Environment
          • ,
          • 533
          • ,
          • 1-7.
          • [web]
          • R Oono, E Lefèvre, A Simha and F Lutzoni.
          • (2015).
          • A comparison of the community diversity of foliar fungal endophytes between seedling and adult loblolly pines (Pinus taeda).
          • Fungal Biology
          • ,
          • 119
          • (10)
          • ,
          • 917-928.
          • [web]
          • E Gaya, S Fernández-Brime, R Vargas, RF Lachlan, C Gueidan, M Ramírez-Mejía and F Lutzoni.
          • (2015).
          • The adaptive radiation of lichen-forming Teloschistaceae is associated with sunscreening pigments and a bark-to-rock substrate shift.
          • Proceedings of the National Academy of Sciences
          • ,
          • 112
          • (37)
          • ,
          • 11600-11605.
          • [web]
          • KH Chen, J Miadlikowska, K Molnár, AE Arnold, JM U'Ren, E Gaya, C Gueidan and F Lutzoni.
          • (2015).
          • Phylogenetic analyses of eurotiomycetous endophytes reveal their close affinities to Chaetothyriales, Eurotiales, and a new order - Phaeomoniellales..
          • Molecular phylogenetics and evolution
          • ,
          • 85
          • ,
          • 117-130.
          • [web]
          Publication Description

          Symbiotic fungi living in plants as endophytes, and in lichens as endolichenic fungi, cause no apparent symptoms to their hosts. They are ubiquitous, ecologically important, hyperdiverse, and represent a rich source of secondary compounds for new pharmaceutical and biocontrol products. Due in part to the lack of visible reproductive structures and other distinctive phenotypic traits for many species, the diversity and phylogenetic affiliations of these cryptic fungi are often poorly known. The goal of this study was to determine the phylogenetic placement of representative endophytes within the Eurotiomycetes (Pezizomycotina, Ascomycota), one of the most diverse and evolutionarily dynamic fungal classes, and to use that information to infer processes of macroevolution in trophic modes. Sequences of a single locus marker spanning the nuclear ribosomal internal transcribed spacer region (nrITS) and 600 base pairs at the 5' end of the nuclear ribosomal large subunit (nrLSU) were obtained from previous studies of >6000 endophytic and endolichenic fungi from diverse biogeographic locations and hosts. We conducted phylum-wide phylogenetic searches using this marker to determine which fungal strains belonged to Eurotiomycetes and the results were used as the basis for a class-wide, seven-locus phylogenetic study focusing on endophytic and endolichenic Eurotiomycetes. Our cumulative supermatrix-based analyses revealed that representative endophytes within Eurotiomycetes are distributed in three main clades: Eurotiales, Chaetothyriales and Phaeomoniellales ord. nov., a clade that had not yet been described formally. This new order, described herein, is sister to the clade including Verrucariales and Chaetothyriales. It appears to consist mainly of endophytes and plant pathogens. Morphological characters of endophytic Phaeomoniellales resemble those of the pathogenic genus Phaeomoniella. This study highlights the capacity of endophytic and endolichenic fungi to expand our understanding of the ecological modes associated with particular clades, and provides a first estimation of their phylogenetic relationships in the Eurotiomycetes.

          • J Miadlikowska, F Kauff, F Högnabba, JC Oliver, K Molnár, E Fraker, E Gaya, J Hafellner, V Hofstetter, C Gueidan, MAG Otálora, B Hodkinson, M Kukwa, R Lücking, C Björk, HJM Sipman, AR Burgaz, A Thell, A Passo, L Myllys, T Goward, S Fernández-Brime, G Hestmark, J Lendemer, HT Lumbsch, M Schmull, CL Schoch, E Sérusiaux, DR Maddison, AE Arnold, F Lutzoni and S Stenroos.
          • (2014).
          • A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families.
          • Molecular Phylogenetics and Evolution
          • ,
          • 79
          • ,
          • 132-168.
          • [web]
          • R Oono, F Lutzoni, AE Arnold, L Kaye, JM U'Ren, G May and I Carbone.
          • (2014).
          • Genetic variation in horizontally transmitted fungal endophytes of pine needles reveals population structure in cryptic species..
          • American journal of botany
          • ,
          • 101
          • (8)
          • ,
          • 1362-1374.
          • [web]
          Publication Description

          •Fungal endophytes comprise one of the most ubiquitous groups of plant symbionts, inhabiting healthy leaves and stems of all major lineages of plants. Together, they comprise immense species richness, but little is known about the fundamental processes that generate their diversity. Exploration of their population structure is needed, especially with regard to geographic distributions and host affiliations.•We take a multilocus approach to examine genetic variation within and among populations of Lophodermium australe, an endophytic fungus commonly associated with healthy foliage of pines in the southeastern United States. Sampling focused on two pine species ranging from montane to coastal regions of North Carolina and Virginia.•Our sampling revealed two genetically distinct groups within Lophodermium australe. Our analysis detected less than one migrant per generation between them, indicating that they are distinct species. The species comprising the majority of isolates (major species) demonstrated a panmictic structure, whereas the species comprising the minority of isolates (cryptic species) demonstrated isolation by distance. Distantly related pine species hosted the same Lophodermium species, and host species did not influence genetic structure.•We present the first evidence for isolation by distance in a foliar fungal endophyte that is horizontally transmitted. Cryptic species may be common among microbial symbionts and are important to delimit when exploring their genetic structure and microevolutionary processes. The hyperdiversity of endophytic fungi may be explained in part by cryptic species without apparent ecological and morphological differences as well as genetic diversification within rare fungal species across large spatial scales.

          • J Miadlikowska, D Richardson, N Magain, B Ball, F Anderson, R Cameron, J Lendemer, C Truong and F Lutzoni.
          • (2014).
          • Phylogenetic placement, species delimitation, and cyanobiont identity of endangered aquatic Peltigera species (lichen-forming Ascomycota, Lecanoromycetes).
          • American Journal of Botany
          • ,
          • 101
          • (7)
          • ,
          • 1141-1156.
          • [web]
          • HE O'Brien, J Miadlikowska and F Lutzoni.
          • (2013).
          • Assessing population structure and host specialization in lichenized cyanobacteria..
          • New Phytol
          • ,
          • 198
          • (2)
          • ,
          • 557-566.
          • [web]
          Publication Description

          Coevolutionary theory predicts that the distribution of obligately symbiotic organisms will be determined by the dispersal ability and ecological range of both partners. We examined this prediction for lichen-forming fungi that form obligate symbioses with cyanobacteria. We compared genotypes of both partners of 250 lichens collected at multiple spatial scales in British Columbia, Canada. Multilocus sequence data collected from a subset of 128 of the specimens were used to determine the degree of recombination within the cyanobacterial populations. We found that six distinct clusters of cyanobacterial genotypes are distributed throughout the known global phylogeny of the genus Nostoc, and that each appears to be evolving clonally. Fungal specialization is high, with each species associating with either one or two of the cyanobacterial clusters, while cyanobacterial specialization varies, with clusters associating with between one and 12 different fungal species. Specialization also varies geographically, with some combinations restricted to a single site despite the availability of both partners elsewhere. Photobiont association patterns are determined by a combination of genetically based specificity, spatial population structure, and ecological factors and cannot be easily predicted by photobiont dispersal syndromes.

          • TR McDonald, E Gaya and F Lutzoni.
          • (2013).
          • Twenty-five aposymbiotic cultures of lichenizing fungi available for experimental studies on symbiotic systems.
          • Symbiosis
          • ,
          • 59
          • (3)
          • ,
          • 165-171.
          • [web]
          Publication Description

          In this study we describe the techniques used to culture 25 mycobionts spanning three classes and five orders of the leotiomyceta (Ascomycota). We find that five media, including potato-carrot, malt extract-yeast extract (MY), Bold's basal medium with nitrogen (NMBBM), oatmeal, and yeast extract with supplements (YES), are sufficient to induce ascospore germination of many lichenizing fungi and are also suitable for maintaining growth of the culture over the long term. Regular physical disruption of the cultures in liquidmedia is recommended to stimulate continued growth. Genomes of five of these lichen-forming fungal strains have been sequenced. The identity of each culture was confirmed by sequencing the nuclear ribosomal internal transcribed spacer (ITS) or the mitochondrial small subunit (mitSSU) from each strain. Additionally, the level of sequencing in terms of total number of genes sequenced for each taxon is provided. All fungal cultures have been deposited in public culture collections and, therefore, are available to the scientific community for conducting in vitro experiments. © Springer Science+Business Media Dordrecht 2013.

          • TR McDonald, FS Dietrich and F Lutzoni.
          • (2013).
          • High-throughput genome sequencing of lichenizing fungi to assess gene loss in the ammonium transporters/ammonia permeases gene family.
          • BMC Genomics
          • ,
          • 14
          • ,
          • 225.
          • S Fernández Brime, X Llimona, F Lutzoni and E Gaya.
          • (2013).
          • Phylogenetic study of Diploschistes (Graphidaceae, Ostropales, lichen-forming Ascomycota), based on morphological, chemical and molecular data.
          • Taxon
          • ,
          • 62
          • (2)
          • ,
          • 267-280.
          Publication Description

          The genus Diploschistes includes crustose lichen-forming fungi with a carbonized proper excipulum with lateral paraphyses, and a chemistry dominated by orcinol depsides. However, the taxon D. ocellatus lacks these excipular characters and has β-orcinol depsidones, raising doubts about its inclusion within this genus. Using a two-locus dataset (mtSSU, nuLSU), our phylogenetic analyses confirm the classification of D. ocellatus within Diploschistes. Three different groups have been recognized within this genus, based on ascomatal morphology: Actinostomus (perithecioid), Scruposus (urceolate), and Ocellatus (lecanoroid). These groups have been widely used in monographic studies and keys, but their taxonomic value has not been confirmed yet. Here we inferred phylogenetic relationships within Diploschistes, with a special emphasis on the D. scruposus complex, using a combined dataset consisting of morphological, chemical, nrITS, and mtSSU data in order to determine if these species groups and phenotypically based species delimitations were monophyletic. Based on our results, a new subgeneric treatment for Diploschistes is proposed, and the taxonomic value of fruiting body types is confirmed. The clade corresponding to D. ocellatus consists of two well-supported subclades, one of them grouping specimens without ascomata, having only pycnidia. It is also remarkable that the clade containing specimens of D. diacapsis subsp. neutrophilus appears distantly related to the clade containing all other accessions of D. diacapsis. Our analysis revealed that for some taxa, such as D. scruposus and D. interpediens, molecular variability did not correlate with either morphological or chemical diversity.

          • MS Green, B Ball, F Lutzoni, H Zi-Min and JM Lopez-Bautista.
          • (2012).
          • TRENTEPOHLIALES (ULVOPHYCEAE, CHLOROPHYTA) FROM COASTAL SOUTH CAROLINA.
          • JOURNAL OF PHYCOLOGY
          • ,
          • 48
          • ,
          • S15-S15.
          • [web]
          • E Gaya, F Högnabba, A Holguin, K Molnar, S Fernández-Brime, S Stenroos, U Arup, U Søchting, P Van den Boom, R Lücking, HJ Sipman and F Lutzoni.
          • (2012).
          • Implementing a cumulative supermatrix approach for a comprehensive phylogenetic study of the Teloschistales (Pezizomycotina, Ascomycota)..
          • Mol Phylogenet Evol
          • ,
          • 63
          • (2)
          • ,
          • 374-387.
          • [web]
          Publication Description

          The resolution of the phylogenetic relationships within the order Teloschistales (Ascomycota, lichen-forming-fungi), with nearly 2000 known species and outstanding phenotypic diversity, has been hindered by the limitation in the resolving power that single-locus or two-locus phylogenetic studies have provided to date. In this context, an extensive taxon sampling within the Teloschistales with more loci (especially nuclear protein-coding genes) was needed to confront the current taxonomic delimitations and to understand evolutionary trends within this order. Comprehensive maximum likelihood and bayesian analyses were performed based on seven loci using a cumulative supermatrix approach, including protein-coding genes RPB1 and RPB2 in addition to nuclear and mitochondrial ribosomal RNA-coding genes. We included 167 taxa representing 12 of the 15 genera recognized within the currently accepted Teloschistineae, 22 of the 43 genera within the Physciineae, 49 genera of the closely related orders Lecanorales, Lecideales, and Peltigerales, and the dubiously placed family Brigantiaeaceae and genus Sipmaniella. Although the progressive addition of taxa (cumulative supermatrix approach) with increasing amounts of missing data did not dramatically affect the loss of support and resolution, the monophyly of the Teloschistales in the current sense was inconsistent, depending on the loci-taxa combination analyzed. Therefore, we propose a new, but provisional, classification for the re-circumscribed orders Caliciales and Teloschistales (previously referred to as Physciineae and Teloschistineae, respectively). We report here that the family Brigantiaeaceae, previously regarded as incertae sedis within the subclass Lecanoromycetidae, and Sipmaniella, are members of the Teloschistales in a strict sense. Within this order, one lineage led to the diversification of the mostly epiphytic crustose Brigantiaeaceae and Letrouitiaceae, with a circumpacific center of diversity and found mostly in the tropics. The other main lineage led to another epiphytic crustose family, mostly tropical, and with an Australasian center of diversity--the Megalosporaceae--which is sister to the mainly rock-inhabiting, cosmopolitan, and species rich Teloschistaceae, with a diversity of growth habits ranging from crustose to fruticose. Our results confirm the use of a cumulative supermatrix approach as a viable method to generate comprehensive phylogenies summarizing relationships of taxa with multi-locus to single locus data.

          • TR McDonald, FS Dietrich and F Lutzoni.
          • (2012).
          • Multiple horizontal gene transfers of ammonium transporters/ammonia permeases from prokaryotes to eukaryotes: toward a new functional and evolutionary classification..
          • Mol Biol Evol
          • ,
          • 29
          • (1)
          • ,
          • 51-60.
          • [web]
          Publication Description

          The proteins of the ammonium transporter/methylammonium permease/Rhesus factor family (AMT/MEP/Rh family) are responsible for the movement of ammonia or ammonium ions across the cell membrane. Although it has been established that the Rh proteins are distantly related to the other members of the family, the evolutionary history of the AMT/MEP/Rh family remains unclear. Here, we use phylogenetic analysis to infer the evolutionary history of this family of proteins across 191 genomes representing all main lineages of life and to provide a new classification of the proteins in this family. Our phylogenetic analysis suggests that what has heretofore been conceived of as a protein family with two clades (AMT/MEP and Rh) is instead a protein family with three clades (AMT, MEP, and Rh). We show that the AMT/MEP/Rh family illustrates two contrasting modes of gene transmission: The AMT family as defined here exhibits vertical gene transfer (i.e., standard parent-to-offspring inheritance), whereas the MEP family as defined here is characterized by several ancient independent horizontal gene transfers (HGTs). These ancient HGT events include a gene replacement during the early evolution of the fungi, which could be a defining trait for the kingdom Fungi, a gene gain from hyperthermophilic chemoautolithotrophic prokaryotes during the early evolution of land plants (Embryophyta), and an independent gain of this same gene in the filamentous ascomycetes (Pezizomycotina) that was subsequently lost in most lineages but retained in even distantly related lichenized fungi. This recircumscription of the ammonium transporters/ammonia permeases family into MEP and AMT families informs the debate on the mechanism of transport in these proteins and on the nature of the transported molecule because published crystal structures of proteins from the MEP and Rh clades may not be representative of the AMT clade. The clades as depicted in this phylogenetic study appear to correspond to functionally different groups, with AMTs and ammonia permeases forming two distinct and possibly monophyletic groups.

          • M Prieto, I Martinez, G Aragon, C Gueidan and F Lutzoni.
          • (2012).
          • MOLECULAR PHYLOGENY OF HETEROPLACIDIUM, PLACIDIUM, AND RELATED CATAPYRENIOID GENERA (VERRUCARIACEAE, LICHEN-FORMING ASCOMYCOTA).
          • AMERICAN JOURNAL OF BOTANY
          • ,
          • 99
          • (1)
          • ,
          • 23-35.
          • [web]
          • JM U'Ren, F Lutzoni, J Miadlikowska, AD Laetsch and AE Arnold.
          • (2012).
          • Host and geographic structure of endophytic and endolichenic fungi at a continental scale.
          • American Journal of Botany
          • ,
          • 99
          • (5)
          • ,
          • 898-914.
          • [web]
          Publication Description

          Premise of the study: Endophytic and endolichenic fungi occur in healthy tissues of plants and lichens, respectively, playing potentially important roles in the ecology and evolution of their hosts. However, previous sampling has not comprehensively evaluated the biotic, biogeographic, and abiotic factors that structure their communities. Methods: Using molecular data we examined the diversity, composition, and distributions of 4154 endophytic and endolichenic Ascomycota cultured from replicate surveys of ca. 20 plant and lichen species in each of five North American sites (Madrean coniferous forest, Arizona; montane semideciduous forest, North Carolina; scrub forest, Florida; Beringian tundra and forest, western Alaska; subalpine tundra, eastern central Alaska). Key results: Endolichenic fungi were more abundant and diverse per host species than endophytes, but communities of endophytes were more diverse overall, reflecting high diversity in mosses and lycophytes. Endophytes of vascular plants were largely distinct from fungal communities that inhabit mosses and lichens. Fungi from closely related hosts from different regions were similar in higher taxonomy, but differed at shallow taxonomic levels. These differences reflected climate factors more strongly than geographic distance alone. Conclusions: Our study provides a first evaluation of endophytic and endolichenic fungal associations with their hosts at a continental scale. Both plants and lichens harbor abundant and diverse fungal communities whose incidence, diversity, and composition reflect the interplay of climatic patterns, geographic separation, host type, and host lineage. Although culture-free methods will inform future work, our study sets the stage for empirical assessments of ecological specificity, metabolic capability, and comparative genomics. © 2012 Botanical Society of America.

          • R Gazis, J Miadlikowska, F Lutzoni, AE Arnold and P Chaverri.
          • (2012).
          • Culture-based study of endophytes associated with rubber trees in Peru reveals a new class of Pezizomycotina: Xylonomycetes.
          • Molecular Phylogenetics and Evolution
          • ,
          • 65
          • (1)
          • ,
          • 294-304.
          • [web]
          Publication Description

          Through a culture-based survey of living sapwood and leaves of rubber trees (Hevea spp.) in remote forests of Peru, we discovered a new major lineage of Ascomycota, equivalent to a class rank. Multilocus phylogenetic analyses reveal that this new lineage originated during the radiation of the 'Leotiomyceta', which resulted not only in the evolution of the Arthoniomycetes, Dothideomycetes, Eurotiomycetes, Geoglossomycetes, Lecanoromycetes, Leotiomycetes, Lichinomycetes, and Sordariomycetes, but also of the majority of hyperdiverse foliar endophytes. Because its origin is nested within this major burst of fungal diversification, we could not recover strong support for its phylogenetic relationship within the 'Leotiomyceta'. Congruent with their long phylogenetic history and distinctive preference for growing in sapwood, this new lineage displays unique morphological, physiological, and ecological traits relative to known endophytes and currently described members of the 'Leotiomyceta'. In marked contrast to many foliar endophytes, the strains we isolated fail to degrade cellulose and lignin in vitro. Discovery of the new class, herein named Xylonomycetes and originally mis-identified by ITSrDNA sequencing alone, highlights the importance of inventorying tropical endophytes from unexplored regions, using multilocus data sets to infer the phylogenetic placement of unknown strains, and the need to sample diverse plant tissues using traditional methods to enhance efforts to discover the evolutionary, taxonomic, and functional diversity of symbiotrophic fungi. © 2012 Elsevier Inc.

          • L Liwa, J Miadlikowska, BD Redelings, K Molnar and F Lutzoni.
          • (2012).
          • Are widespread morphospecies from the Lecanora dispersa group (lichen-forming Ascomycota) monophyletic?.
          • Bryologist
          • ,
          • 115
          • (2)
          • ,
          • 265-277.
          • [web]
          Publication Description

          To evaluate the current delimitation of broadly distributed morphospecies from the Lecanora dispersa group, the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S and ITS2) was analyzed phylogenetically and compared to phenotypic data variation within and among species. Phylogenetic relationships among 34 individuals representing eight species from the L. dispersa group, collected mainly from Poland and other European countries, were inferred using two types of Bayesian analyses (with and without a priori alignments), maximum likelihood and maximum parsimony approaches. The highest phylogenetic resolution and the largest number of significantly supported internodes resulted from the Bayesian analysis without a priori alignment. Inferred phylogenies confirmed a broader delimitation of the L. dispersa group, to include four additional lobate taxa: L. contractula, L. pruinosa, L. reuteri, and L. thuleana ( Arctopeltis thuleana). Lecanora crenulata, L. dispersa, L. reuterii, and the core of L. albescens and L. semipallida were all found to be monophyletic with high support (by at least one phylogenetic analysis) except the first species. Based on the ITS region, phenotypically similar individuals, thought to belong to one monophyletic group, were found to belong to multiple distantly related groups (e.g., members of L. albescens and L. hagenii), suggesting that morphological, anatomical and chemical characters may not be consistent in predicting species boundaries within the L. dispersa group. Potential undescribed species were found within phenotypically defined L. albescens and L. semipallida. Phylo-taxonomic studies of the L. dispersa group with more loci and a more extensive taxon sampling are urgently needed. © 2012 The American Bryological and Lichenological Society, Inc.

          • J Geml, F Kauff, C Brochmann, F Lutzoni, GA Laursen, SA Redhead and DL Taylor.
          • (2012).
          • Frequent circumarctic and rare transequatorial dispersals in the lichenised agaric genus Lichenomphalia (Hygrophoraceae, Basidiomycota).
          • Fungal Biology
          • ,
          • 116
          • (3)
          • ,
          • 388-400.
          • [web]
          Publication Description

          Species of the genus Lichenomphalia are mostly restricted to arctic-alpine environments with the exception of Lichenomphalia umbellifera which is also common in northern forests. Although Lichenomphalia species inhabit vast regions in several continents, no information is available on their genetic variation across geographic regions and the underlying population-phylogenetic patterns. We collected samples from arctic and subarctic regions, as well as from newly discovered subantarctic localities for the genus. Phylogenetic, nonparametric permutation methods, and coalescent analyses were used to assess phylogeny and population divergence and to estimate the extent and direction of gene flow among distinct geographic populations. All known species formed monophyletic groups, supporting their morphology-based delimitation. In addition, we found two subantarctic phylogenetic species (Lichenomphalia sp. and Lichenomphalia aff. umbellifera), of which the latter formed a well-supported sister group to L. umbellifera. We found no significant genetic differentiation among conspecific North American and Eurasian populations in Lichenomphalia. We detected high intercontinental gene flow within the northern polar region, suggesting rapid (re)colonisation of suitable habitats in response to climatic fluctuations and preventing pronounced genetic differentiation. On the other hand, our phylogenetic analyses suggest that dispersal between northern circumpolar and subantarctic areas likely happened very rarely and led to the establishment and subsequent divergence of lineages. Due to limited sampling in the Southern Hemisphere, it is currently uncertain whether the northern lineages occur in Gondwanan regions. On the other hand, our results strongly suggest that the southern lineages do not occur in the circumpolar north. Although rare transequatorial dispersal and subsequent isolation may explain the emergence of at least two subantarctic phylogenetic species lineages in Lichenomphalia, more samples from the Southern Hemisphere are needed to better understand the phylogeographic history of the genus. © 2011 The British Mycological Society.

          • BP Hodkinson, NR Gottel, CW Schadt and F Lutzoni.
          • (2012).
          • Photoautotrophic symbiont and geography are major factors affecting highly structured and diverse bacterial communities in the lichen microbiome.
          • Environmental Microbiology
          • ,
          • 14
          • (1)
          • ,
          • 147-161.
          • (Special issue entitled "Omics Driven Microbial Ecology”)
          • [web]
          Publication Description

          Although common knowledge dictates that the lichen thallus is formed solely by a fungus (mycobiont) that develops a symbiotic relationship with an alga and/or cyanobacterium (photobiont), the non-photoautotrophic bacteria found in lichen microbiomes are increasingly regarded as integral components of lichen thalli. For this study, comparative analyses were conducted on lichen-associated bacterial communities to test for effects of photobiont-types (i.e. green algal vs. cyanobacterial), mycobiont-types and large-scale spatial distances (from tropical to arctic latitudes). Amplicons of the 16S (SSU) rRNA gene were examined using both Sanger sequencing of cloned fragments and barcoded pyrosequencing. Rhizobiales is typically the most abundant and taxonomically diverse order in lichen microbiomes; however, overall bacterial diversity in lichens is shown to be much higher than previously reported. Members of Acidobacteriaceae, Acetobacteraceae, Brucellaceae and sequence group LAR1 are the most commonly found groups across the phylogenetically and geographically broad array of lichens examined here. Major bacterial community trends are significantly correlated with differences in large-scale geography, photobiont-type and mycobiont-type. The lichen as a microcosm represents a structured, unique microbial habitat with greater ecological complexity and bacterial diversity than previously appreciated and can serve as a model system for studying larger ecological and evolutionary principles. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

          • S Joneson, D Armaleo and F Lutzoni.
          • (2011).
          • Fungal and algal gene expression in early developmental stages of lichen-symbiosis..
          • Mycologia
          • ,
          • 103
          • (2)
          • ,
          • 291-306.
          • [web]
          Publication Description

          How plants and microbes recognize each other and interact to form long-lasting relationships remains one of the central questions in cellular communication. The symbiosis between the filamentous fungus Cladonia grayi and the single-celled green alga Asterochloris sp. was used to determine fungal and algal genes upregulated in vitro in early lichen development. cDNA libraries of upregulated genes were created with suppression subtractive hybridization in the first two stages of lichen development. Quantitative PCR subsequently was used to verify the expression level of 41 and 33 candidate fungal and algal genes respectively. Induced fungal genes showed significant matches to genes putatively encoding proteins involved in self and non-self recognition, lipid metabolism, and negative regulation of glucose repressible genes, as well as to a putative d-arabitol reductase and two dioxygenases. Upregulated algal genes included a chitinase-like protein, an amino acid metabolism protein, a dynein-related protein and a protein arginine methyltransferase. These results also provided the first evidence that extracellular communication without cellular contact can occur between lichen symbionts. Many genes showing slight variation in expression appear to direct the development of the lichen symbiosis. The results of this study highlight future avenues of investigation into the molecular biology of lichen symbiosis.

          • S Fernández-Brime, X Llimona, K Molnar, S Stenroos, F Högnabba, C Björk, F Lutzoni and E Gaya.
          • (2011).
          • Expansion of the stictidaceae by the addition of the saxicolous lichen-forming genus Ingvariella.
          • Mycologia
          • ,
          • 103
          • (4)
          • ,
          • 755-763.
          • [web]
          Publication Description

          The monotypic, lichen-forming genus Ingvariella originally was segregated from Diploschistes and placed within the Thelotremataceae (Ostropales) based on aspects of exciple morphology. However, the I+ hymenium and amyloid ascus wall suggest affinities to families other than the Thelotremataceae. To assess the identity of Ingvariella and to investigate its placement within the Ostropales, we inferred phylogenetic relationships of I. bispora by comparison of mtSSU rDNA and nuLSU rDNA sequences for 59 species encompassing a broad array of ostropalean fungi by means of Bayesian, maximum likelihood and weighted maximum parsimony methods. Here we report that Ingvariella is a member of the Stictidaceae, sister to the mainly saprotrophic genus Cryptodiscus. The inclusion of the first saxicolous lichenforming fungus within this family expands the broad ecological diversity of the Stictidaceae, where saprotrophic fungi, corticicolous lichen-forming fungi and lichenized and non-lichenized conspecific taxa have been described previously. We also present new insights into the relationships among other families within the Ostropales. © 2011 by The Mycological Society of America, Lawrence, KS 66044-8897.

          • M Schmull, J Miadlikowska, M Pelzer, ESW tter, V Hofstetter, E Fraker, BP Hodkinson, V Reeb, M Kukwa, HT Lumbsch, F Kauff and F Lutzoni.
          • (2011).
          • Phylogenetic affiliations of members of the heterogeneous lichen-forming fungi of the genus Lecidea sensu Zahlbruckner (Lecanoromycetes, Ascomycota).
          • Mycologia
          • ,
          • 103
          • (5)
          • ,
          • 983-1003.
          • [web]
          Publication Description

          The genus Lecidea Ach. sensu lato (sensu Zahlbruckner) includes almost 1200 species, out of which only 100 species represent Lecidea sensu stricto (sensu Hertel). The systematic position of the remaining species is mostly unsettled but anticipated to represent several unrelated lineages within Lecanoromycetes. This study attempts to elucidate the phylogenetic placement of members of this heterogeneous group of lichen-forming fungi and to improve the classification and phylogeny of Lecanoromycetes. Twenty-five taxa of Lecidea sensu lato and 22 putatively allied species were studied in a broad selection of 268 taxa, representing 48 families of Lecanoromycetes. Six loci, including four ribosomal and two protein-coding genes for 315- and 209-OTU datasets were subjected to maximum likelihood and Bayesian analyses. The resulting well supported phylogenetic relationships within Lecanoromycetes are in agreement with published phylogenies, but the addition of new taxa revealed putative rearrangements of several families (e.g. Catillariaceae, Lecanoraceae, Lecideaceae, Megalariaceae, Pilocarpaceae and Ramalinaceae). As expected, species of Lecidea sensu lato and putatively related taxa are scattered within Lecanoromycetidae and beyond, with several species nested in Lecanoraceae and Pilocarpaceae and others placed outside currently recognized families in Lecanorales and orders in Lecanoromycetidae. The phylogenetic affiliations of Schaereria and Strangospora are outside Lecanoromycetidae, probably with Ostropomycetidae. All species referred to as Lecidea sensu stricto based on morphology (including the type species, Lecidea fuscoatra [L.] Ach.) form, with Porpidia species, a monophyletic group with high posterior probability outside Lecanorales, Peltigerales and Teloschistales, in Lecanoromycetidae, supporting the recognition of order Lecideales Vain. in this subclass. The genus name Lecidea must be redefined to apply only to Lecidea sensu stricto and to include at least some members of the genus Porpidia. Based on morphological and chemical similarities, as well as the phylogenetic relationship of Lecidea pullata sister to Frutidella caesioatra, the new combination Frutidella pullata is proposed here. © 2011 by The Mycological Society of America.

          • H Thues, L Muggia, S Perez-Ortega, SE Favero-Longo, S Joneson, H O'Brien, MP Nelsen, R Duque-Thues, M Grube, T Friedl, J Brodie, CJ Andrew, R Luecking, F Lutzoni and C Gueidan.
          • (2011).
          • Revisiting photobiont diversity in the lichen family Verrucariaceae (Ascomycota).
          • EUROPEAN JOURNAL OF PHYCOLOGY
          • ,
          • 46
          • (4)
          • ,
          • 399-415.
          • [web]
          • G Hestmark, J Miadlikowska, F Kauff, E Fraker, K Molnar and F Lutzoni.
          • (2011).
          • Single origin and subsequent diversification of central Andean endemic Umbilicaria species.
          • Mycologia
          • ,
          • 103
          • (1)
          • ,
          • 45-56.
          • [web]
          Publication Description

          We studied an Andean endemic group of species of the lichen-forming fungal genus Umbilicaria from the subalpine and low-alpine zone, with their biogeographic center in Bolivia and Peru. A number of species and varieties have been described from this element, but apparent instability in several morphological traits has made it difficult to precisely delimit taxa. Based on DNA sequences of nuclear ITS, LSU and mitochondrial SSU from extensive collections from Argentina, Bolivia, Chile, Colombia, Ecuador and Peru, we present here a molecular phylogenetic analysis of this Andean endemic element within genus Umbilicaria. All analyses (MP, ML and Bayesian) support a single origin for the element and a division into two major groups characterized by different apothecium types: the Umbilicaria dichroa group and U. calvescens group. Taxa U. krempelhuberi, U. peruviana and U. subcalvescens are nested within U. calvescens and are treated as conspecific with the latter species. The endemic element shares a most recent common ancestor with the Umbilicaria vellea group, which has a worldwide distribution and contains several asexually reproducing (sorediate) species. Independent reversals to sexual reproduction might explain the evolution of two types of apothecia in this monophyletic endemic lineage. A number of cosmopolitan, mostly high-alpine, species of Umbilicaria also present in the central Andes are related only remotely to the endemic element and do not exhibit speciation into endemics. Because the Andean element dominates the Umbilicaria habitats of the low-and subalpine zones we propose that the founder colonized the Andes at a time when the mountains had not yet reached their current elevation while the high-alpine species arrived more recently. © 2011 by The Mycological Society of America.

          • E Gaya, BD Redelings, P Navarro-Rosinés, X Llimona, MD Cáceres and F Lutzoni.
          • (2011).
          • Align or not to align? Resolving species complexes within the Caloplaca saxicola group as a case study.
          • Mycologia
          • ,
          • 103
          • (2)
          • ,
          • 361-378.
          • [web]
          Publication Description

          The Caloplaca saxicola group is the main group of saxicolous, lobed-effigurate species within genus Caloplaca (Teloschistaceae, lichen-forming Ascomycota). A recent monographic revision by the first author detected a wide range of morphological variation. To confront the phenotypically based circumscription of these taxa and to resolve their relationships morphological and ITS rDNA data were obtained for 56 individuals representing eight Caloplaca species belonging to the C. saxicola group. We tested the monophyly of these eight morphospecies by performing maximum parsimony, maximum likelihood and two different types of Bayesian analyses (with and without a priori alignments). Restricting phylogenetic analyses to unambiguously aligned portions of ITS was sufficient to resolve, with high bootstrap support, five of the eight previously recognized species within the C. saxicola group. However, phylogenetic resolution of all or most of the eight species currently included as two distinct subgroups within the C. saxicola group was possible only by combining morphological characters and signal from ambiguously aligned regions with the unambiguously aligned ITS sites or when the entire ITS1 and 2 regions were not aligned a priori and included as an integral component of a Bayesian analysis (BAli-Phy). The C. arnoldii subgroup includes C. arnoldii, comprising four subspecies, and the C. saxicola subgroup encompasses seven species. Contrary to the C. saxicola subgroup, monophyly of taxa included within the C. arnoldii subgroup and their relationships could not be resolved with combined ITS and morphological data. Unequivocal morphological synapomorphies for all species except C. arnoldii and C. pusilla are recognized and presented. © 2011 by The Mycological Society of America.

          • J Miadlikowska, CL Schoch, SA Kageyama, K Molnar, F Lutzoni and B McCune.
          • (2011).
          • Hypogymnia phylogeny, including Cavernularia, reveals biogeographic structure.
          • Bryologist
          • ,
          • 114
          • (2)
          • ,
          • 392-400.
          • [web]
          Publication Description

          We inferred phylogenetic relationships using Bayesian and maximum likelihood approaches for two genera of lichenized fungi, Hypogymnia and Cavernularia (Parmeliaceae). Based on the combined ITS and GPD1 dataset from 23 species (49 specimens) of Hypogymnia and two species (8 specimens) of Cavernularia, we conclude that Hypogymnia is paraphyletic, and that it should include Cavernularia to retain its monophyly. Hypogymnia hultenii (= Cavernularia hultenii) and H. lophyrea (= C. lophyrea) are accepted here. Five species of Hypogymnia represented by more than a single individual were found to be monophyletic and significantly supported. The phylogeny reflects a statistically significant biogeographic pattern where continental-scale endemic taxa tend to occur within the same phylogenetic group. Sorediate taxa, which have worldwide or broader geographical ranges than affiliated species lacking soredia, are spread across the phylogenetic tree. Hypogymnia contains three species pairs: H. krogiae and the sorediate counterpart H. incurvoides, H. minilobata and the sorediate H. mollis, and H. lophyrea and the sorediate H. hultenii. In the case of H. minilobata, both members of the pair are restricted to a small area in southern California. In the other two cases, the fertile counterpart occurs only in North America, while the sorediate species occurs in both North America and Fennoscandia. This suggests but not proves an origin of each species pair in North America, with migration of the sorediate member to Fennoscandia following the prevailing wind direction. © 2011 The American Bryological and Lichenological Society, Inc.

          • A Crespo, F Kauff, PK Divakar, R del Prado, S Perez-Ortega, G Amo de Paz, Z Ferencova, O Blanco, B Roca-Valiente, J Nunez-Zapata, P Cubas, A Argueello, JA Elix, TL Esslinger, DL Hawksworth, A Millanes, M Carmen Molina, M Wedin, T Ahti, A Aptroot, E Barreno, F Bungartz, S Calvelo, M Candan, M Cole, D Ertz, B Goffinet, L Lindblom, R Luecking, F Lutzoni, J-E Mattsson, M Ines Messuti, J Miadlikowska, M Piercey-Normore, VJ Rico, HJM Sipman, I Schmitt, T Spribille, A Thell, G Thor, DK Upreti and HT Lumbsch.
          • (2010).
          • Phylogenetic generic classification of parmelioid lichens (Parmeliaceae, Ascomycota) based on molecular, morphological and chemical evidence.
          • TAXON
          • ,
          • 59
          • (6)
          • ,
          • 1735-1753.
          • [web]
          • MAG Otálora, G Aragón, MC Molina, I Martínez and F Lutzoni.
          • (2010).
          • Disentangling the Collema-Leptogium complex through a molecular phylogenetic study of the Collemataceae (Peltigerales, lichen-forming Ascomycota).
          • Mycologia
          • ,
          • 102
          • (2)
          • ,
          • 279-290.
          • [web]
          Publication Description

          Family Collemataceae (Peltigerales, Ascomycota) includes species of cyanolichens with foliose to fruticose or crustose thalli, with simple or septate ascospores. The current classification divides this family into two groups on the basis of ascospore types. The objective of this study was to evaluate the phylogenetic relationships within this family. Combined DNA sequence data from the nuclear large subunit and mitochondrial small subunit ribosomal RNA genes were used to evaluate monophyly of the family and the relationships between the largest genera of this family. The results revealed that this family is not monophyletic. Genera Staurolemma and Physma, currently classified within the Collemataceae, were found nested within the Pannariaceae. The second result of this study confirms that the genera Collema and Leptogium, both part of the Collemataceae s. str., are not monophyletic and that the presence of a thallus cortex is not a synapomorphy for Leptogium. The main taxonomic conclusion is that families Collemataceae and Pannariaceae were recircumscribed in light of molecular findings with the latter family now including Staurolemma and Physma. Genera Collema and Leptogium form a single mixed monophyletic group. Inferred ancestral character states within the Collema-Leptogium complex revealed that the ancestor of this family had a thallus without cortex and that a cortex evolved at least twice relatively early in the evolution of the Collemataceae s. str. These independent gains of a thallus cortex seems to be associated with a transition from colonizing bare rocks and soils in semi-arid and exposed habitats to epiphytism in shady humid forests. © 2010 by The Mycological Society of America.

          • M Prieto, I Martínez, G Aragón, MAG Otálora and F Lutzoni.
          • (2010).
          • Phylogenetic study of Catapyrenium s. str. (Verrucariaceae, lichen-forming Ascomycota) and related genus Placidiopsis.
          • Mycologia
          • ,
          • 102
          • (2)
          • ,
          • 291-304.
          • [web]
          Publication Description

          The current classification of what used to be called Catapyrenium comprises eight genera belonging to distinct lineages in the Verrucariaceae. Previous phylogenetic studies have shown that the redefined genus Catapyrenium (Catapyrenium s. str.) is monophyletic and sister of Placidiopsis within the Staurothele group, but this relationship was based on only two species from each genus. We conducted a phylogenetic study of Catapyrenium and Placidiopsis as currently delimited to evaluate the monophyly of each genus and infer infrageneric relationships. An initial family level phylogenetic analysis based on the nuLSU locus and implementing a backbone constraint tree (with both weighted maximum parsimony and bootstrap maximum likelihood approaches) was performed to infer phylogenetic placements of Catapyrenium and Placidiopsis taxa not included in previous molecular systematic studies. The results of this analysis were used to define the ingroup for a second phylogenetic analysis based on nuITS and nuLSU and centered on Catapyrenium s. str. and Placidiopsis. Placidiopsis was found to be monophyletic, whereas Catapyrenium s. str. was not. Catapyrenium dactylinum was found to be closely related to Placopyrenium caeruleopulvinum and Placopyrenium stanfordii, all of which were closely related to Placocarpus schaereri and Verrucula. In addition we found genus Placopyrenium to be polyphyletic. The resulting trees confirmed that Catapyrenium s. str. (excluding C. dactylinum) and Placidiopsis constitute two sister monophyletic entities. The data do not support Placidiopsis cinerascens and P. tenella as two distinct species because no characters can be used to distinguish them. Thus P. tenella is here reduced to synonymy with P. cinerascens. © 2010 by The Mycological Society of America.

          • MAG Otálora, I Martínez, H O'Brien, MC Molina, G Aragón and F Lutzoni.
          • (2010).
          • Multiple origins of high reciprocal symbiotic specificity at an intercontinental spatial scale among gelatinous lichens (Collemataceae, Lecanoromycetes).
          • Molecular Phylogenetics and Evolution
          • ,
          • 56
          • (3)
          • ,
          • 1089-1095.
          • [web]
          Publication Description

          Because the number of fungal species (mycobionts) exceeds the number of algae and cyanobacteria (photobionts) found in lichens by more than two orders of magnitude, reciprocal one-to-one specificity between one fungal species and one photobiont across their entire distribution is not expected in this symbiotic system, and has not previously been observed. The specificity of the cyanobacterium Nostoc found in lichens was evaluated at a broad geographical scale within one of the main families of lichen-forming fungi (Collemataceae) that associate exclusively with this photobiont. A phylogenetic study was conducted using rbcLXS sequences from Nostoc sampled from 79 thalli (representing 24 species within the Collemataceae), and 163 Nostoc sequences gathered from GenBank. Although most of the lichen-forming fungal species belonging to the Collemataceae exhibited the expected generalist pattern of association with multiple distinct lineages of Nostoc, five independent cases of one-to-one reciprocal specificity at the species level, including two that span intercontinental distributions, were discovered. Each of the five distinct monophyletic Nostoc groups, associated with these five highly specific mycobiont species, represent independent transitions from a generalist state during the evolution of both partners, which might be explained by transitions to asexual fungal reproduction, involving vertical photobiont transmission, and narrowing of ecological niches. © 2010 Elsevier Inc.

          • JM U'Ren, F Lutzoni, J Miadlikowska and AE Arnold.
          • (2010).
          • Community Analysis Reveals Close Affinities Between Endophytic and Endolichenic Fungi in Mosses and Lichens.
          • Microbial Ecology
          • ,
          • 60
          • (2)
          • ,
          • 340-353.
          • [web]
          Publication Description

          Endolichenic fungi live in close association with algal photobionts inside asymptomatic lichen thalli and resemble fungal endophytes of plants in terms of taxonomy, diversity, transmission mode, and evolutionary history. This similarity has led to uncertainty regarding the distinctiveness of endolichenic fungi compared with endophytes. Here, we evaluate whether these fungi represent distinct ecological guilds or a single guild of flexible symbiotrophs capable of colonizing plants or lichens indiscriminately. Culturable fungi were sampled exhaustively from replicate sets of phylogenetically diverse plants and lichens in three microsites in a montane forest in southeastern Arizona (USA). Intensive sampling combined with a small spatial scale permitted us to decouple spatial heterogeneity from host association and to sample communities from living leaves, dead leaves, and lichen thalli to statistical completion. Characterization using data from the nuclear ribosomal internal transcribed spacer and partial large subunit (ITS-LSU rDNA) provided a first estimation of host and substrate use for 960 isolates representing five classes and approximately 16 orders, 32 families, and 65 genera of Pezizomycotina. We found that fungal communities differ at a broad taxonomic level as a function of the phylogenetic placement of their plant or lichen hosts. Endolichenic fungal assemblages differed as a function of lichen taxonomy, rather than substrate, growth form, or photobiont. In plants, fungal communities were structured more by plant lineage than by the living vs. senescent status of the leaf. We found no evidence that endolichenic fungi are saprotrophic fungi that have been "entrapped" by lichen thalli. Instead, our study reveals the distinctiveness of endolichenic communities relative to those in living and dead plant tissues, with one notable exception: we identify, for the first time, an ecologically flexible group of symbionts that occurs both as endolichenic fungi and as endophytes of mosses. © 2010 Springer Science+Business Media, LLC.

          • HE O'Brien, J Miadlikowska and F Lutzoni.
          • (2009).
          • Assessing reproductive isolation in highly diverse communities of the lichen-forming fungal genus peltigera..
          • Evolution
          • ,
          • 63
          • (8)
          • ,
          • 2076-2086.
          • [web]
          Publication Description

          The lichen-forming fungal genus Peltigera includes a number of species that are extremely widespread, both geographically and ecologically. However, morphological variability has lead to doubts about the distinctness of some species, and it has been suggested that hybridization is common in nature. We examined species boundaries by looking for evidence of hybridization and gene flow among seven described species collected at five sites in British Columbia, Canada. We found no evidence of gene flow or hybridization between described species, with fixed differences between species for two or more of the three loci examined. Reproductive isolation did not reflect a solely clonal mode of reproduction as there was evidence of ongoing gene flow within species. In addition, we found five undescribed species that were reproductively isolated, although there was evidence of ongoing or historical gene flow between two of the new species. These results indicate that the genus Peltigera is more diverse in western North America than originally perceived, and that morphological variability is due largely to the presence of undescribed species rather than hybridization or intraspecific variation.

          • F Lutzoni and J Miadlikowska.
          • (2009).
          • Lichens..
          • Curr Biol
          • ,
          • 19
          • (13)
          • ,
          • R502-R503.
          • [web]
          • AE Arnold, J Miadlikowska, KL Higgins, SD Sarvate, P Gugger, A Way, V Hofstetter, F Kauff and F Lutzoni.
          • (2009).
          • A phylogenetic estimation of trophic transition networks for ascomycetous fungi: are lichens cradles of symbiotrophic fungal diversification?.
          • Syst Biol
          • ,
          • 58
          • (3)
          • ,
          • 283-297.
          • [web]
          Publication Description

          Fungi associated with photosynthetic organisms are major determinants of terrestrial biomass, nutrient cycling, and ecosystem productivity from the poles to the equator. Whereas most fungi are known because of their fruit bodies (e.g., saprotrophs), symptoms (e.g., pathogens), or emergent properties as symbionts (e.g., lichens), the majority of fungal diversity is thought to occur among species that rarely manifest their presence with visual cues on their substrate (e.g., the apparently hyperdiverse fungal endophytes associated with foliage of plants). Fungal endophytes are ubiquitous among all lineages of land plants and live within overtly healthy tissues without causing disease, but the evolutionary origins of these highly diverse symbionts have not been explored. Here, we show that a key to understanding both the evolution of endophytism and the diversification of the most species-rich phylum of Fungi (Ascomycota) lies in endophyte-like fungi that can be isolated from the interior of apparently healthy lichens. These "endolichenic" fungi are distinct from lichen mycobionts or any other previously recognized fungal associates of lichens, represent the same major lineages of Ascomycota as do endophytes, largely parallel the high diversity of endophytes from the arctic to the tropics, and preferentially associate with green algal photobionts in lichen thalli. Using phylogenetic analyses that incorporate these newly recovered fungi and ancestral state reconstructions that take into account phylogenetic uncertainty, we show that endolichenism is an incubator for the evolution of endophytism. In turn, endophytism is evolutionarily transient, with endophytic lineages frequently transitioning to and from pathogenicity. Although symbiotrophic lineages frequently give rise to free-living saprotrophs, reversions to symbiosis are rare. Together, these results provide the basis for estimating trophic transition networks in the Ascomycota and provide a first set of hypotheses regarding the evolution of symbiotrophy and saprotrophy in the most species-rich fungal phylum. [Ancestral state reconstruction; Ascomycota; Bayesian analysis; endolichenic fungi; fungal endophytes; lichens; pathogens; phylogeny; saprotrophy; symbiotrophy; trophic transition network.].

          • C Ruibal, C Gueidan, L Selbmann, AA Gorbushina, PW Crous, JZ Groenewald, L Muggia, M Grube, D Isola, CL Schoch, JT Staley, F Lutzoni and GSD Hoog.
          • (2009).
          • Phylogeny of rock-inhabiting fungi related to Dothideomycetes.
          • Studies in Mycology
          • ,
          • 64
          • ,
          • 123-133.
          • [web]
          Publication Description

          The class Dothideomycetes (along with Eurotiomycetes) includes numerous rock-inhabiting fungi (RIF), a group of ascomycetes that tolerates surprisingly well harsh conditions prevailing on rock surfaces. Despite their convergent morphology and physiology, RIF are phylogenetically highly diverse in Dothideomycetes. However, the positions of main groups of RIF in this class remain unclear due to the lack of a strong phylogenetic framework. Moreover, connections between rock-dwelling habit and other lifestyles found in Dothideomycetes such as plant pathogens, saprobes and lichen-forming fungi are still unexplored. Based on multigene phylogenetic analyses, we report that RIF belong to Capnodiales (particularly to the family Teratosphaeriaceae s.l.), Dothideales, Pleosporales, and Myriangiales, as well as some uncharacterised groups with affinities to Dothideomycetes. Moreover, one lineage consisting exclusively of RIF proved to be closely related to Arthoniomycetes, the sister class of Dothideomycetes. The broad phylogenetic amplitude of RIF in Dothideomycetes suggests that total species richness in this class remains underestimated. Composition of some RIF-rich lineages suggests that rock surfaces are reservoirs for plant-associated fungi or saprobes, although other data also agree with rocks as a primary substrate for ancient fungal lineages. According to the current sampling, long distance dispersal seems to be common for RIF. Dothideomycetes lineages comprising lichens also include RIF, suggesting a possible link between rock-dwelling habit and lichenisation. © 2009 CBS-KNAW Fungal Biodiversity Centre.

          • DJ McLaughlin, DS Hibbett, F Lutzoni, JW Spatafora and R Vilgalys.
          • (2009).
          • The search for the fungal tree of life.
          • Trends in Microbiology
          • ,
          • 17
          • (11)
          • ,
          • 488-497.
          • [web]
          Publication Description

          The Fungi comprise a diverse kingdom of eukaryotes that are characterized by a typically filamentous but sometimes unicellular vegetative form, and heterotrophic, absorptive nutrition. Their simple morphologies and variable ecological strategies have confounded efforts to elucidate their limits, phylogenetic relationships, and diversity. Here we review progress in developing a phylogenetic classification of Fungi since Darwin's On the Origin of Species. Knowledge of phylogenetic relationships has been driven by the available characters that have ranged from morphological and ultrastructural to biochemical and genomic. With the availability of multiple gene phylogenies a well-corroborated phylogenetic classification has now begun to emerge. In the process some fungus-like heterotrophs have been shown to belong elsewhere, and several groups of enigmatic eukaryotic microbes have been added to the Fungi. © 2009 Elsevier Ltd. All rights reserved.

          • C Gueidan, S Savić, H Thüs, C Roux, C Keller, L Tibell, M Prieto, S Heiomarsson, O Breuss, A Orange, L Fröberg, AA Wynns, P Navarro-Rosinés, B Krzewicka, J Pykälä, M Grube and F Lutzoni.
          • (2009).
          • Generic classification of the Verrucariaceae (Ascomycota) based on molecular and morphological evidence: Recent progress and remaining challenges.
          • Taxon
          • ,
          • 58
          • (1)
          • ,
          • 184-208.
          Publication Description

          Recent molecular phylogenetic analyses and morphological studies have shown that it is necessary to revise the present morphology-based generic delineation of the lichen family Verrucariaceae in order to account for evolutionary relatedness between species. Consequently, several genera were recently described or resurrected, and others were re-circumscribed. As an additional step toward this generic revision, three new genera (Hydropunctaria, Parabagliettoa, Wahlenbergiella) and eleven new combinations are proposed here. A summary of the current taxonomic and morphological circumscription of all genera investigated so far is also presented. Several monophyletic groups are identified for which further taxonomical changes will be required, but for which taxon and gene sampling is presently viewed as insufficient. Clear morphological synapomorphies were found to be rare for newly delimited genera. In some cases (reduced morphology or plesiomorphism), even the combinations of slightly homoplasious phenotypic characters do not allow a clear morphological generic circumscription. Molecular features are envisioned as characters for delimiting these taxa.

          • CL Schoch, GH Sung, F López-Giráldez, JP Townsend, J Miadlikowska, V Hofstetter, B Robbertse, PB Matheny, F Kauff, Z Wang, C Gueidan, RM Andrie, K Trippe, LM Ciufetti, A Wynns, E Fraker, BP Hodkinson, G Bonito, JZ Groenewald, M Arzanlou, GSD Hoog, PW Crous, D Hewitt, DH Pfister, K Peterson, M Gryzenhout, MJ Wingfield, A Aptroot, SO Suh, M Blackwell, DM Hillis, GW Griffith, LA Castlebury, AY Rossman, HT Lumbsch, R Lücking, B Büdel, A Rauhut, P Diederich, D Ertz, DM Geiser, K Hosaka, P Inderbitzin, J Kohlmeyer, B Volkmann-Kohlmeyer, L Mostert, K O'Donnell, H Sipman, JD Rogers, RA Shoemaker, J Sugiyama, RC Summerbell, W Untereiner, PR Johnston, S Stenroos, A Zuccaro, PS Dyer, PD Crittenden, MS Cole, K Hansen, JM Trappe, R Yahr, F Lutzoni and JW Spatafora.
          • (2009).
          • The ascomycota tree of life: A phylum-wide phylogeny clarifies the origin and evolution of fundamental reproductive and ecological traits.
          • Systematic Biology
          • ,
          • 58
          • (2)
          • ,
          • 224-239.
          • [web]
          Publication Description

          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 Fungi are resolved for the first time. Based on the 6-gene phylogeny we conducted a phylogenetic informativeness analysis of all 6 genes and a series of ancestral character state reconstructions that focused on morphology of sporocarps, ascus dehiscence, and evolution of nutritional modes and ecologies. A gene-by-gene assessment of phylogenetic informativeness yielded higher levels of informativeness for protein genes (RPB1, RPB2, and TEF1) as compared with the ribosomal genes, which have been the standard bearer in fungal systematics. Our reconstruction of sporocarp characters is consistent with 2 origins for multicellular sexual reproductive structures in Ascomycota, once in the common ancestor of Pezizomycotina and once in the common ancestor of Neolectomycetes. This first report of dual origins of ascomycete sporocarps highlights the complicated nature of assessing homology of morphological traits across Fungi. Furthermore, ancestral reconstruction supports an open sporocarp with an exposed hymenium (apothecium) as the primitive morphology for Pezizomycotina with multiple derivations of the partially (perithecia) or completely enclosed (cleistothecia) sporocarps. Ascus dehiscence is most informative at the class level within Pezizomycotina with most superclass nodes reconstructed equivocally. Character-state reconstructions support a terrestrial, saprobic ecology as ancestral. In contrast to previous studies, these analyses support multiple origins of lichenization events with the loss of lichenization as less frequent and limited to terminal, closely related species. © 2009 Society of Systematic Biologists.

          • D Ertz, J Miadlikowska, F Lutzoni, S Dessein, O Raspé, N Vigneron, V Hofstetter and P Diederich.
          • (2009).
          • Towards a new classification of the Arthoniales (Ascomycota) based on a three-gene phylogeny focussing on the genus Opegrapha.
          • Mycological Research
          • ,
          • 113
          • (1)
          • ,
          • 141-152.
          • [web]
          Publication Description

          A multi-locus phylogenetic study of the order Arthoniales is presented here using the nuclear ribosomal large subunit (nuLSU), the second largest subunit of RNA polymerase II (RPB2) and the mitochondrial ribosomal small subunit (mtSSU). These genes were sequenced from 43 specimens or culture isolates representing 33 species from this order, 16 of which were from the second largest genus, Opegrapha. With the inclusion of sequences from GenBank, ten genera and 35 species are included in this study, representing about 18 % of the genera and ca 3 % of the species of this order. Our study revealed the homoplastic nature of morphological characters traditionally used to circumscribe genera within the Arthoniales, such as exciple carbonization and ascomatal structure. The genus Opegrapha appears polyphyletic, species of that genus being nested in all the major clades identified within Arthoniales. The transfer of O. atra and O. calcarea to the genus Arthonia will allow this genus and family Arthoniaceae to be recognized as monophyletic. The genus Enterographa was also found to be polyphyletic. Therefore, the following new combinations are needed: Arthonia calcarea (basionym: O. calcarea), and O. anguinella (basionym: Stigmatidium anguinellum); and the use of the names A. atra and Enterographa zonata are proposed here. The simultaneous use of a mitochondrial gene and two nuclear genes led to the detection of what seems to be a case of introgression of a mitochondrion from one species to another (mitochondrion capture; cytoplasmic gene flow) resulting from hybridization. © 2008 The British Mycological Society.

          • BP Hodkinson and F Lutzoni.
          • (2009).
          • A microbiotic survey of lichen-associated bacteria reveals a new lineage from the Rhizobiales.
          • Symbiosis
          • ,
          • 49
          • (2)
          • ,
          • 163-180.
          • [web]
          Publication Description

          This study uses a set of PCR-based methods to examine the putative microbiota associated with lichen thalli. In initial experiments, generalized oligonucleotide-primers for the 16S rRNA gene resulted in amplicon pools populated almost exclusively with fragments derived from lichen photobionts (i.e., Cyanobacteria or chloroplasts of algae). This effectively masked the presence of other lichen-associated prokaryotes. In order to facilitate the study of the lichen microbiota, 16S ribosomal oligonucleotide-primers were developed to target Bacteria, but exclude sequences derived from chloroplasts and Cyanobacteria. A preliminary microbiotic survey of lichen thalli using these new primers has revealed the identity of several bacterial associates, including representatives of the extremophilic Acidobacteria, bacteria in the families Acetobacteraceae and Brucellaceae, strains belonging to the genus Methylobacterium, and members of an undescribed lineage in the Rhizobiales. This new lineage was investigated and characterized through molecular cloning, and was found to be present in all examined lichens that are associated with green algae. There is evidence to suggest that members of this lineage may both account for a large proportion of the lichen-associated bacterial community and assist in providing the lichen thallus with crucial nutrients such as fixed nitrogen. ©Springer Science+Business Media B.V. 2009.

          • S Joneson and F Lutzoni.
          • (2009).
          • Revisiting compatibility and thigmotropism in the lichen symbiosis.
          • Symbiosis
          • ,
          • 47
          • (2)
          • ,
          • 109-115.
          Publication Description

          The development of many complex stratified lichen thalli is made through stages of complex phenotypic interactions between a filamentous fungus (the mycobiont), and a trebouxioid alga (the photobiont). Typically, the second stage of this symbiotic development is marked by the envelopment of the photobiont by the mycobiont through increased lateral hyphal branching and the formation of appressoria. Previously, the mycobiont's envelopment of photobiont cells was considered thigmotropic (a growth response due to shape) as a mycobiont can envelop algal sized objects in its environment. However, after growing the mycobiont Cladonia grayi with various phototrophs and glass beads, we conclude that the mycobiont does not show this characteristic second stage morphological response when grown in non-compatible pairings. Instead, C. grayi displays a distinctive morphological growth response only in compatible symbiotic pairings, such as with its natural photobiont Asterochloris sp. © 2009 Balaban.

          • S Joneson and F Lutzoni.
          • (2009).
          • Compatibility and thigmotropism in the lichen symbiosis: A reappraisal.
          • Symbiosis
          • ,
          • 47
          • (2)
          • ,
          • 109-115.
          Publication Description

          The development of many complex stratified lichen thalli is made through stages of complex phenotypic interactions between a filamentous fungus (the mycobiont), and a trebouxioid alga (the photobiont). Typically, the second stage of this symbiotic development is marked by the envelopment of the photobiont by the mycobiont through increased lateral hyphal branching and the formation of appressoria. Previously, the mycobiont's envelopment of photobiont cells was considered thigmotropic (a growth response due to shape) as a mycobiont can envelop algal sized objects in its environment. However, after growing the mycobiont Cladonia grayi with various phototrophs and glass beads, we conclude that the mycobiont does not show this characteristic second stage morphological response when grown in non-compatible pairings. Instead, C. grayi displays a distinctive morphological growth response only in compatible symbiotic pairings, such as with its natural photobiont Asterochloris sp. © 2009 Balaban.

          • E Gaya, P Navarro-Rosinés, X Llimona, N Hladun and F Lutzoni.
          • (2008).
          • Phylogenetic reassessment of the Teloschistaceae (lichen-forming Ascomycota, Lecanoromycetes)..
          • Mycol Res
          • ,
          • 112
          • (Pt 5)
          • ,
          • 528-546.
          • [web]
          Publication Description

          The Teloschistaceae is a widespread family with considerable morphological and ecological heterogeneity across genera and species groups. In order to provide a comprehensive molecular phylogeny for this family, phylogenetic analyses were carried out on sequences from the nuclear ribosomal ITS region obtained from 114 individuals that represent virtually all main lineages of Teloschistaceae. Our study confirmed the polyphyly of Caloplaca, Fulgensia and Xanthoria, and revealed that Teloschistes is probably non-monophyletic. We also confirm here that species traditionally included in Caloplaca subgenus Gasparrinia do not form a monophyletic entity. Caloplaca aurantia, C. carphinea and C. saxicola s. str. groups were recovered as monophyletic. The subgenera Caloplaca and Pyrenodesmia were also polyphyletic. In the subgenus Caloplaca, the traditionally recognized C. cerina group was recovered as monophyletic. Because this study is based solely on ITS, to maximize taxon sampling, the inclusion of phylogenetic signal from ambiguously aligned regions in MP (recoded INAASE and arc characters) resulted in the most highly supported phylogenetic reconstruction, compared with Bayesian inference restricted to alignable sites.

          • C Gueidan, CR Villaseñor, GS de Hoog, AA Gorbushina, WA Untereiner and F Lutzoni.
          • (2008).
          • A rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages..
          • Stud Mycol
          • ,
          • 61
          • ,
          • 111-119.
          • [web]
          Publication Description

          Rock surfaces are unique terrestrial habitats in which rapid changes in the intensity of radiation, temperature, water supply and nutrient availability challenge the survival of microbes. A specialised, but diverse group of free-living, melanised fungi are amongst the persistent settlers of bare rocks. Multigene phylogenetic analyses were used to study relationships of ascomycetes from a variety of substrates, with a dataset including a broad sampling of rock dwellers from different geographical locations. Rock-inhabiting fungi appear particularly diverse in the early diverging lineages of the orders Chaetothyriales and Verrucariales. Although these orders share a most recent common ancestor, their lifestyles are strikingly different. Verrucariales are mostly lichen-forming fungi, while Chaetothyriales, by contrast, are best known as opportunistic pathogens of vertebrates (e.g. Cladophialophora bantiana and Exophiala dermatitidis, both agents of fatal brain infections) and saprophytes. The rock-dwelling habit is shown here to be key to the evolution of these two ecologically disparate orders. The most recent common ancestor of Verrucariales and Chaetothyriales is reconstructed as a non-lichenised rock-inhabitant. Ancestral state reconstructions suggest Verrucariales as one of the independent ascomycetes group where lichenisation has evolved on a hostile rock surface that might have favored this shift to a symbiotic lifestyle. Rock-inhabiting fungi are also ancestral to opportunistic pathogens, as they are found in the early diverging lineages of Chaetothyriales. In Chaetothyriales and Verrucariales, specific morphological and physiological traits (here referred to as extremotolerance) evolved in response to stresses in extreme conditions prevailing on rock surfaces. These factors facilitated colonisation of various substrates including the brains of vertebrates by opportunistic fungal pathogens, as well as helped establishment of a stable lichen symbiosis.

          • C Gueidan, C Ruibal Villasenor, S de Hoog, A Gorbushina, WA Untereiner and F Lutzoni.
          • (2008).
          • An extremotolerant rock-inhabiting ancestor for mutualistic and pathogen-rich fungal lineages.
          • Studies in Mycology
          • ,
          • 61
          • ,
          • 111-119.
          • S Savić, L Tibell, C Gueidan and F Lutzoni.
          • (2008).
          • Molecular phylogeny and systematics of Polyblastia (Verrucariaceae, Eurotiomycetes) and allied genera.
          • Mycological Research
          • ,
          • 112
          • (11)
          • ,
          • 1307-1318.
          • [web]
          Publication Description

          Phylogenetic relationships of the lichen genus Polyblastia and closely related taxa in the family Verrucariaceae (Verrucariales, Chaetothyriomycetidae) were studied. A total of 130 sets of sequences (nuLSU rDNA, nuITS rDNA and RPB1 region A-D), including 129 newly generated sequences, were analysed. Phylogenetic relationships were inferred using a Bayesian approach based on two datasets. A first analysis of a larger, two-locus dataset (nuLSU and RPB1) for 128 members of the Verrucariaceae, confirmed the polyphyly of Polyblastia, Thelidium, Staurothele, and Verrucaria, as currently construed. The second analysis focused on 56 Polyblastia and allied taxa, but using an additional locus (nuITS rDNA) and two closely related outgroup taxa. The latter analysis revealed strongly supported groups, such as Polyblastia s. str., the Thelidium group (a mixture of Polyblastia, Thelidium, Staurothele and Verrucaria species). The genus Sporodictyon, which is here accepted, also accommodates Sporodictyon terrestre comb. nov. Morphological features traditionally used for characterizing Polyblastia, Thelidium, Staurothele and Verrucaria, such as spore septation and colour, occurrence of hymenial photobiont, involucrellum structure, and substrate preference, were found to be only partially consistent within the strongly supported clades, and thus are not always reliable features for characterizing natural groups. © 2008 The British Mycological Society.

          • MAG Otálora, I Martínez, MC Molina, G Aragón and F Lutzoni.
          • (2008).
          • Phylogenetic relationships and taxonomy of the Leptogium lichenoides group (Collemataceae, Ascomycota) in Europe.
          • Taxon
          • ,
          • 57
          • (3)
          • ,
          • 907-921.
          Publication Description

          The taxonomy of the Leptogium lichenoides complex is revised here based on a morphological, ecological and molecular phylogenetic study. A phylogenetic analysis of phenotypic characters was compared to a phylogeny based on nrITS and β-tubulin data. Using these phylogenies, we concluded that what was commonly recognized as Leptogium lichenoides s.l. encompasses three distinct species. Leptogium lichenoides var. pulvinatum is now recognized as a separate species L. pulvinatum comb. nov. Leptogium aragonii sp. nov., a non-isidiate species with large thalli, is the second species part of this complex, and L. lichenoides s.str., as redefined here, is the only species of this group with isidia. We also found that Leptogium lichenoides s.l. is polyphyletic. Leptogium pulvinatum and L. lichenoides s.str. are more closely related to L. gelatinosum than to L. aragonii. The taxonomic status of L. quercicola is reduced to a variety of L. pulvinatum. Identification key, descriptions and distribution maps are presented for Leptogium aragonii, L. gelatinosum, L. intermedium, L. lichenoides s.str., L. pulvinatum, and L. pulvinatum var. quercicola.

          • A Amtoft, F Lutzoni and J Miadlikowska.
          • (2008).
          • Dermatocarpon (Verrucariaceae) in the Ozark Highlands, North America.
          • Bryologist
          • ,
          • 111
          • (1)
          • ,
          • 1-40.
          • [web]
          Publication Description

          Dermatocarpon, a saxicolous lichen, is common throughout the Ozarks Highlands of North America where exposed rock is abundant. Dermatocarpon is an understudied genus. Species delimitation is difficult because of a paucity of morphological characters and a large degree of variation within this genus. The taxonomy of Dermatocarpon in North America was recently thrown into flux because of a molecular study which limited the use of a once widely applied name, D. miniatum. The Melzer's reagent test, currently used for identifying members of the miniatum-complex in North America, is not useful for identifying Ozark specimens. A revision of Dermatocarpon for the Ozark Highlands of North America is presented based on morphological, molecular and ecological studies. The results of these studies indicate that eight taxa are present in the Ozarks. Four taxa are described new to science: D. arenosaxi, D. dolomiticum, D. luridum var. xerophilum and D. multifolium. Copyright ©2008 by The American Bryological and Lichenological Society, Inc.

          • C Gueidan, C Roux and F Lutzoni.
          • (2007).
          • Using a multigene phylogenetic analysis to assess generic delineation and character evolution in Verrucariaceae (Verrucariales, Ascomycota)..
          • Mycol Res
          • ,
          • 111
          • (Pt 10)
          • ,
          • 1145-1168.
          • [web]
          Publication Description

          Verrucariaceae are a family of mostly crustose lichenized ascomycetes colonizing various habitats ranging from marine and fresh water to arid environments. Phylogenetic relationships among members of the Verrucariaceae are mostly unknown and the current morphology-based classification has never been confronted to molecular data. A multilocus phylogeny (nuLSU, nuSSU and RPB1) was reconstructed for 83 taxa representing all main genera of this family to provide a molecular phylogenetic framework necessary to assess the current morphology-based classification. Four main well-supported monophyletic groups were recovered, one of which contains seven robust monophyletic subgroups. Most genera, as traditionally delimited, were not monophyletic. A few taxonomic changes are proposed here to reconcile the morphology-based classification with the molecular phylogeny (Endocarpon diffractellum comb. nov., Heteroplacidium fusculum comb. nov., and Bagliettoa marmorea comb. nov.). Ancestral state reconstructions show that the most recent common ancestor of the Verrucariaceae was most likely crustose with a weakly differentiated upper cortex, simple ascospores, and hymenium free of algae. As shown in this study, the use of symplesiomorphic traits to define Verrucaria, the largest and type genus for the Verrucariaceae, as well as the non monophyly of the genera Polyblastia, Staurothele and Thelidium, explain most of the discrepancies between the current classification based on morphological similarity and a classification using monophyly as a grouping criterion.

          • V Hofstetter, J Miadlikowska, F Kauff and F Lutzoni.
          • (2007).
          • Phylogenetic comparison of protein-coding versus ribosomal RNA-coding sequence data: a case study of the Lecanoromycetes (Ascomycota)..
          • Mol Phylogenet Evol
          • ,
          • 44
          • (1)
          • ,
          • 412-426.
          • [web]
          Publication Description

          The resolving power and statistical support provided by two protein-coding (RPB1 and RPB2) and three ribosomal RNA-coding (nucSSU, nucLSU, and mitSSU) genes individually and in various combinations were investigated based on maximum likelihood bootstrap analyses on lichen-forming fungi from the class Lecanoromycetes (Ascomycota). Our results indicate that the optimal loci (single and combined) to use for molecular systematics of lichen-forming Ascomycota are protein-coding genes (RPB1 and RPB2). RPB1 and RPB2 genes individually were phylogenetically more efficient than all two- and three-locus combinations of ribosomal loci. The 3rd codon position of each of these two loci provided the most characters in support of phylogenetic relationships within the Lecanoromycetes. Of the three ribosomal loci we used in this study, mitSSU contributed the most to phylogenetic analyses when combined with RPB1 and RPB2. Except for the mitSSU, ribosomal genes were the most difficult to recover because they often contain many introns, resulting in PCR bias toward numerous and intronless co-extracted contaminant fungi (mainly Dothideomycetes, Chaetothyriomycetes, and Sordariomycetes in the Ascomycota, and members of the Basidiomycota), which inhabit lichen thalli. Maximum likelihood analysis on the combined five-locus data set for 82 members of the Lecanoromycetes provided a well resolved and well supported tree compared to existing phylogenies. We confirmed the monophyly of three recognized subclasses in the Lecanoromycetes, the Acarosporomycetidae, Ostropomycetidae, and Lecanoromycetideae; the latter delimited as monophyletic for the first time, with the exclusion of the family Umbilicariaceae and Hypocenomyce scalaris. The genus Candelariella (formerly in the Candelariaceae, currently a member of the Lecanoraceae) represents the first evolutionary split within the Lecanoromycetes, before the divergence of the Acarosporomycetidae. This study provides a foundation necessary to guide the selection of loci for future multilocus phylogenetic studies on lichen-forming and allied ascomycetes.

          • F Kauff, CJ Cox and F Lutzoni.
          • (2007).
          • WASABI: an automated sequence processing system for multigene phylogenies..
          • Syst Biol
          • ,
          • 56
          • (3)
          • ,
          • 523-531.
          • [web]
          • C Rydholm, PS Dyer and F Lutzoni.
          • (2007).
          • DNA sequence characterization and molecular evolution of MAT1 and MAT2 mating-type loci of the self-compatible ascomycete mold Neosartorya fischeri..
          • Eukaryot Cell
          • ,
          • 6
          • (5)
          • ,
          • 868-874.
          • [web]
          Publication Description

          Degenerate PCR and chromosome-walking approaches were used to identify mating-type (MAT) genes and flanking regions from the homothallic (sexually self-fertile) euascomycete fungus Neosartorya fischeri, a close relative of the opportunistic human pathogen Aspergillus fumigatus. Both putative alpha- and high-mobility-group-domain MAT genes were found within the same genome, providing a functional explanation for self-fertility. However, unlike those in many homothallic euascomycetes (Pezizomycotina), the genes were not found adjacent to each other and were termed MAT1 and MAT2 to recognize the presence of distinct loci. Complete copies of putative APN1 (DNA lyase) and SLA2 (cytoskeleton assembly control) genes were found bordering the MAT1 locus. Partial copies of APN1 and SLA2 were also found bordering the MAT2 locus, but these copies bore the genetic hallmarks of pseudogenes. Genome comparisons revealed synteny over at least 23,300 bp between the N. fischeri MAT1 region and the A. fumigatus MAT locus region, but no such long-range conservation in the N. fischeri MAT2 region was evident. The sequence upstream of MAT2 contained numerous candidate transposase genes. These results demonstrate a novel means involving the segmental translocation of a chromosomal region by which the ability to undergo self-fertilization may be acquired. The results are also discussed in relation to their significance in indicating that heterothallism may be ancestral within the Aspergillus section Fumigati.

          • V Reeb, P Haugen, D Bhattacharya and F Lutzoni.
          • (2007).
          • Evolution of Pleopsidium (lichenized Ascomycota) S943 group I introns and the phylogeography of an intron-encoded putative homing endonuclease..
          • J Mol Evol
          • ,
          • 64
          • (3)
          • ,
          • 285-298.
          • [web]
          Publication Description

          The sporadic distribution of nuclear group I introns among different fungal lineages can be explained by vertical inheritance of the introns followed by successive losses, or horizontal transfers from one lineage to another through intron homing or reverse splicing. Homing is mediated by an intron-encoded homing endonuclease (HE) and recent studies suggest that the introns and their associated HE gene (HEG) follow a recurrent cyclical model of invasion, degeneration, loss, and reinvasion. The purpose of this study was to compare this model to the evolution of HEGs found in the group I intron at position S943 of the nuclear ribosomal DNA of the lichen-forming fungus Pleopsidium. Forty-eight S943 introns were found in the 64 Pleopsidium samples from a worldwide screen, 22 of which contained a full-length HEG that encodes a putative 256-amino acid HE, and 2 contained HE pseudogenes. The HEGs are divided into two closely related types (as are the introns that encode them) that differ by 22.6% in their nucleotide sequences. The evolution of the Pleopsidium intron-HEG element shows strong evidence for a cyclical model of evolution. The intron was likely acquired twice in the genus and then transmitted via two or three interspecific horizontal transfers. Close geographical proximity plays an important role in intron-HEG horizontal transfer because most of these mobile elements were found in Europe. Once acquired in a lineage, the intron-HEG element was also vertically transmitted, and occasionally degenerated or was lost.

          • AE Arnold and F Lutzoni.
          • (2007).
          • Diversity and host range of foliar fungal endophytes: are tropical leaves biodiversity hotspots?.
          • Ecology
          • ,
          • 88
          • (3)
          • ,
          • 541-549.
          • [web]
          Publication Description

          Fungal endophytes are found in asymptomatic photosynthetic tissues of all major lineages of land plants. The ubiquity of these cryptic symbionts is clear, but the scale of their diversity, host range, and geographic distributions are unknown. To explore the putative hyperdiversity of tropical leaf endophytes, we compared endophyte communities along a broad latitudinal gradient from the Canadian arctic to the lowland tropical forest of central Panama. Here, we use molecular sequence data from 1403 endophyte strains to show that endophytes increase in incidence, diversity, and host breadth from arctic to tropical sites. Endophyte communities from higher latitudes are characterized by relatively few species from many different classes of Ascomycota, whereas tropical endophyte assemblages are dominated by a small number of classes with a very large number of endophytic species. The most easily cultivated endophytes from tropical plants have wide host ranges, but communities are dominated by a large number of rare species whose host range is unclear. Even when only the most easily cultured species are considered, leaves of tropical trees represent hotspots of fungal species diversity, containing numerous species not yet recovered from other biomes. The challenge remains to recover and identify those elusive and rarely cultured taxa with narrower host ranges, and to elucidate the ecological roles of these little-known symbionts in tropical forests.

          • AE Arnold, DA Henk, RL Eells, F Lutzoni and R Vilgalys.
          • (2007).
          • Diversity and phylogenetic affinities of foliar fungal endophytes in loblolly pine inferred by culturing and environmental PCR..
          • Mycologia
          • ,
          • 99
          • (2)
          • ,
          • 185-206.
          • [web]
          Publication Description

          We examined endophytic fungi in asymptomatic foliage of loblolly pine (Pinus taeda) in North Carolina, U.S.A., with four goals: (i) to evaluate morphotaxa, BLAST matches and groups based on sequence similarity as functional taxonomic units; (ii) to explore methods to maximize phylogenetic signal for environmental datasets, which typically contain many taxa but few characters; (iii) to compare culturing vs. culture-free methods (environmental PCR of surface sterilized foliage) for estimating endophyte diversity and species composition; and (iv) to investigate the relationships between traditional ecological indices (e.g. Shannon index) and phylogenetic diversity (PD) in estimating endophyte diversity and spatial heterogeneity. Endophytes were recovered in culture from 87 of 90 P. taeda leaves sampled, yielding 439 isolates that represented 24 morphotaxa. Sequence data from the nuclear ribosomal internal transcribed spacer (ITS) for 150 isolates revealed 59 distinct ITS genotypes that represented 24 and 37 unique groups based on 90% and 95% sequence similarity, respectively. By recoding ambiguously aligned regions to extract phylogenetic signal and implementing a conservative phylogenetic backbone constraint, we recovered well supported phylogenies based on ca. 600 bp of the nuclear ribosomal large subunit (LSUrDNA) for 72 Ascomycota and Basidiomycota, 145 cultured endophytes and 33 environmental PCR samples. Comparisons with LSUrDNA-delimited species showed that morphotaxa adequately estimated total species richness but rarely corresponded to biologically meaningful groups. ITS BLAST results were variable in their utility, but ITS genotype groups based on 90% sequence similarity were concordant with LSUrDNA-delimited species. Environmental PCR yielded more genotypes per sampling effort and recovered several distinct clades relative to culturing, but some commonly cultured clades were never found (Sordariomycetes) or were rare relative to their high frequency among cultures (Leotiomycetes). In contrast to traditional indices, PD demonstrated spatial heterogeneity in endophyte assemblages among P. taeda trees and study plots. Our results highlight the need for caution in designating taxonomic units based on gross cultural morphology or ITS BLAST matches, the utility of phylogenetic tools for extracting robust phylogenies from environmental samples, the complementarity of culturing and environmental PCR, the utility of PD relative to traditional ecological indices, and the remarkably high diversity of foliar fungal endophytes in this simplified temperate ecosystem.

          • KL Higgins, AE Arnold, J Miadlikowska, SD Sarvate and F Lutzoni.
          • (2007).
          • Phylogenetic relationships, host affinity, and geographic structure of boreal and arctic endophytes from three major plant lineages..
          • Mol Phylogenet Evol
          • ,
          • 42
          • (2)
          • ,
          • 543-555.
          • [web]
          Publication Description

          Although associated with all plants, fungal endophytes (microfungi that live within healthy plant tissues) represent an unknown proportion of fungal diversity. While there is a growing appreciation of their ecological importance and human uses, little is known about their host specificity, geographic structure, or phylogenetic relationships. We surveyed endophytic Ascomycota from healthy photosynthetic tissues of three plant species (Huperzia selago, Picea mariana, and Dryas integrifolia, representing lycophytes, conifers, and angiosperms, respectively) in northern and southern boreal forest (Québec, Canada) and arctic tundra (Nunavut, Canada). Endophytes were recovered from all plant species surveyed, and were present in

          • DS Hibbett, M Binder, JF Bischoff, M Blackwell, PF Cannon, OE Eriksson, S Huhndorf, T James, PM Kirk, R Lücking, HT Lumbsch, F Lutzoni, PB Matheny, DJ McLaughlin, MJ Powell, S Redhead, CL Schoch, JW Spatafora, JA Stalpers, R Vilgalys, MC Aime, A Aptroot, R Bauer, D Begerow, GL Benny, LA Castlebury, PW Crous, YC Dai, W Gams, DM Geiser, GW Griffith, C Gueidan, DL Hawksworth, G Hestmark, K Hosaka, RA Humber, KD Hyde, JE Ironside, U Kõljalg, CP Kurtzman, KH Larsson, R Lichtwardt, J Longcore, J Miadlikowska, A Miller, JM Moncalvo, S Mozley-Standridge, F Oberwinkler, E Parmasto, V Reeb, JD Rogers, C Roux, L Ryvarden, JP Sampaio, A Schüßler, J Sugiyama, RG Thorn, L Tibell, WA Untereiner, C Walker, Z Wang, A Weir, M Weiss, MM White, K Winka, YJ Yao and N Zhang.
          • (2007).
          • A higher-level phylogenetic classification of the Fungi.
          • Mycological Research
          • ,
          • 111
          • (5)
          • ,
          • 509-547.
          • [web]
          Publication Description

          A comprehensive phylogenetic classification of the kingdom Fungi is proposed, with reference to recent molecular phylogenetic analyses, and with input from diverse members of the fungal taxonomic community. The classification includes 195 taxa, down to the level of order, of which 16 are described or validated here: Dikarya subkingdom nov.; Chytridiomycota, Neocallimastigomycota phyla nov.; Monoblepharidomycetes, Neocallimastigomycetes class. nov.; Eurotiomycetidae, Lecanoromycetidae, Mycocaliciomycetidae subclass. nov.; Acarosporales, Corticiales, Baeomycetales, Candelariales, Gloeophyllales, Melanosporales, Trechisporales, Umbilicariales ords. nov. The clade containing Ascomycota and Basidiomycota is classified as subkingdom Dikarya, reflecting the putative synapomorphy of dikaryotic hyphae. The most dramatic shifts in the classification relative to previous works concern the groups that have traditionally been included in the Chytridiomycota and Zygomycota. The Chytridiomycota is retained in a restricted sense, with Blastocladiomycota and Neocallimastigomycota representing segregate phyla of flagellated Fungi. Taxa traditionally placed in Zygomycota are distributed among Glomeromycota and several subphyla incertae sedis, including Mucoromycotina, Entomophthoromycotina, Kickxellomycotina, and Zoopagomycotina. Microsporidia are included in the Fungi, but no further subdivision of the group is proposed. Several genera of 'basal' Fungi of uncertain position are not placed in any higher taxa, including Basidiobolus, Caulochytrium, Olpidium, and Rozella. © 2007 The British Mycological Society.

          • C Gueidan, C Roux and F Lutzoni.
          • (2007).
          • Using a multigene analysis to assess generic delineation and character evolution in the Verrucariaceae (Verrucariales, Ascomycota)..
          • Mycological Research
          • ,
          • 110
          • ,
          • 1147-1170.
          • RW Litaker, MW Vandersea, SR Kibler, KS Reece, NA Stokes, FM Lutzoni, BA Yonish, MA West, MND Black and PA Tester.
          • (2007).
          • Recognizing dinoflagellate species using its rDNA sequences.
          • Journal of Phycology
          • ,
          • 43
          • (2)
          • ,
          • 344-355.
          • [web]
          Publication Description

          Dinoflagellate taxonomy is based primarily on morphology and morphometric data that can be difficult to obtain. In contrast, molecular data can be rapidly and cost-effectively acquired, which has led to a rapid accumulation of sequence data in GenBank. Currently there are no systematic criteria for utilizing taxonomically unassigned sequence data to identify putative species that could in turn serve as a basis for testable hypotheses concerning the taxonomy, diversity, distribution, and toxicity of these organisms. The goal of this research was to evaluate whether simple, uncorrected genetic distances (p) calculated using ITS1/5.8S/ITS2 (ITS region) rDNA sequences could be used to develop criteria for recognizing putative species before formal morphological evaluation and classification. The current analysis used sequences from 81 dinoflagellate species belonging to 14 genera. For this diverse assemblage of dinoflagellate species, the within-species genetic distances between ITS region copies (p=0.000-0.021 substitutions per site) were consistently less than those observed between species (p=0.042-0.580). Our results indicate that a between-species uncorrected genetic distance of p≥0.04 could be used to delineate most free-living dinoflagellate species. Recently evolved species, however, may have ITS p values <0.04 and would require more extensive morphological and genetic analyses to resolve. For most species, the sequence of the dominant ITS region allele has the potential to serve as a unique species-specific "DNA barcode" that could be used for the rapid identification of dinoflagellates in field and laboratory studies. © 2007 No claim to original US government works.

          • J Miadlikowska, F Kauff, V Hofstetter, E Fraker, M Grube, J Hafellner, V Reeb, BP Hodkinson, M Kukwa, R Lücking, G Hestmark, MG Otalora, A Rauhut, B Büdel, C Scheidegger, E Timdal, S Stenroos, I Brodo, GB Perlmutter, D Ertz, P Diederich, JC Lendemer, P May, CL Schoch, AE Arnold, C Gueidan, E Tripp, R Yahr, C Robertson and F Lutzoni.
          • (2006).
          • New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes..
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 1088-1103.
          • [web]
          Publication Description

          The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.

          • TY James, F Kauff, CL Schoch, PB Matheny, V Hofstetter, CJ Cox, G Celio, C Gueidan, E Fraker, J Miadlikowska, HT Lumbsch, A Rauhut, V Reeb, AE Arnold, A Amtoft, JE Stajich, K Hosaka, GH Sung, D Johnson, B O'Rourke, M Crockett, M Binder, JM Curtis, JC Slot, Z Wang, AW Wilson, A Schüssler, JE Longcore, K O'Donnell, S Mozley-Standridge, D Porter, PM Letcher, MJ Powell, JW Taylor, MM White, GW Griffith, DR Davies, RA Humber, JB Morton, J Sugiyama, AY Rossman, JD Rogers, DH Pfister, D Hewitt, K Hansen, S Hambleton, RA Shoemaker, J Kohlmeyer, B Volkmann-Kohlmeyer, RA Spotts, M Serdani, PW Crous, KW Hughes, K Matsuura, E Langer, G Langer, WA Untereiner, R Lücking, B Büdel, DM Geiser, A Aptroot, P Diederich, I Schmitt, M Schultz, R Yahr, DS Hibbett, F Lutzoni, DJ McLaughlin, JW Spatafora and R Vilgalys.
          • (2006).
          • Reconstructing the early evolution of Fungi using a six-gene phylogeny..
          • Nature
          • ,
          • 443
          • (7113)
          • ,
          • 818-822.
          • [web]
          Publication Description

          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 fungi. Here we develop phylogenetic hypotheses for Fungi using data from six gene regions and nearly 200 species. Our results indicate that there may have been at least four independent losses of the flagellum in the kingdom Fungi. These losses of swimming spores coincided with the evolution of new mechanisms of spore dispersal, such as aerial dispersal in mycelial groups and polar tube eversion in the microsporidia (unicellular forms that lack mitochondria). The enigmatic microsporidia seem to be derived from an endoparasitic chytrid ancestor similar to Rozella allomycis, on the earliest diverging branch of the fungal phylogenetic tree.

          • AE Arnold and F Lutzoni.
          • (2006).
          • From the leaf to the landscape: Endophyte diversity and interactions at small and large spatial scales.
          • PHYTOPATHOLOGY
          • ,
          • 96
          • (6)
          • ,
          • S136-S137.
          • [web]
          • C Rydholm, G Szakacs and F Lutzoni.
          • (2006).
          • Low genetic variation and no detectable population structure in aspergillus fumigatus compared to closely related Neosartorya species..
          • Eukaryot Cell
          • ,
          • 5
          • (4)
          • ,
          • 650-657.
          • [web]
          Publication Description

          Aspergillus fumigatus is an anamorphic euascomycete mold with a ubiquitous presence worldwide. Despite intensive work to understand its success as a pathogen infecting immunosuppressed patients, the population dynamics and recent evolutionary history of A. fumigatus remain understudied. We examined patterns of genetic variation at three intergenic loci for 70 natural isolates from Europe, North America, South America, Asia, Africa, and Australia. The same loci were used to analyze within-population genetic variation for 33 isolates obtained from five geographic locations. Neither data set detected evidence of population differentiation or found any association between the genetic and geographic distances among these isolates. No evidence for genetic differentiation within the two A. fumigatus mating types was detected. The genetic diversity of A. fumigatus, contrasted with that of its close teleomorphic relatives, Neosartorya fischeri and Neosartorya spinosa, is remarkably low.

          • JW Spatafora, GH Sung, D Johnson, B O’Rourke, M Serdani, R Spotts, F Lutzoni, V Hofstetter, A Aptroot, C Roux, A Miller, D Geiser, J Hafellner, G Hestmark, AE Arnold, B Büdel, A Rauhut, WA Untereiner, MS Cole, C Scheidegger, M Schultz, H Sipman and C Schoch.
          • (2006).
          • A five-gene phylogeny of Pezizomycotina.
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 1020-1030.
          • [web]
          Publication Description

          Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results fromweighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-1α) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support. © 2006 by The Mycological Society of America.

          • DM Geiser, J Gueidan Miadlikowska, F Kauff, V Hofstetter, E Fraker, CL Schoch, L Tibell, WA Untereiner, A Aptroot and F Lutzoni.
          • (2006).
          • Eurotiomycetes: Eurotiomycetidae and Chaetothyriomycetidae.
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 1055-1066.
          • [web]
          Publication Description

          The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales. © 2006 by The Mycological Society of America.

          • J Miadlikowska, F Kauff, V Hofstetter, E Fraker, M Grube, J Hafellner, V Reeb, BP Hodkinson, M Kukwa, R Lücking, G Hestmark, MAG Otalora, A Rauhut, B Büdel, C Scheidegger, I Timdal, S Stenroos, I Brodo, G Perlmutter, D Ertz, P Diederich, JC Lendemer, E Tripp, R Yahr, P May, C Gueidan, AE Arnold, C Robertson and F Lutzoni.
          • (2006).
          • New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 1090-1103.
          • [web]
          Publication Description

          The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson's classification of the Lecanoromycetes (Outline of Ascomycota--2006 Myconet 12:1-82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.

          • FA Fernández, AN Miller, SM Huhndorf, FM Lutzoni and S Zoller.
          • (2006).
          • Systematics of the genus Chaetosphaeria and its allied genera: Morphological and phylogenetic diversity in north temperate and neotropical taxa.
          • Mycologia
          • ,
          • 98
          • (1)
          • ,
          • 121-130.
          • [web]
          Publication Description

          Chaetosphaeria is a common saprobic pyrenomycete genus with simple, homogeneous teleomorphs and complex, diverse anamorphs. As currently circumscribed in the literature, the genus encompasses 30 species distributed in four 'natural groups', and includes morphological entities in 11 anamorphic genera. Species frequently have been defined primarily based on characters of the anamorphs resulting in species with almost indistinguishable teleomorphs. This study aimed to assess the value and significance of morphological characters in resolving phylogenetic relationships in Chaetosphaeria and its allied genera. Phylogenetic relationships of 42 taxa, representing 29 species distributed in Chaetosphaeria and five related genera, were estimated with partial sequences of the nuclear LSU rDNA and β-tubulin genes. Sequences were analyzed with maximum parsimony, maximum likelihood and Bayesian methods. Phylogenetic analyses of these two genes combined revealed two major lineages. The Chaetosphaeria lineage includes 21 species possessing both typical and new sexual and asexual morphologies. The lineage contains a strongly supported monophyletic clade of 13 species and eight paraphyletic taxa; the latter includes C. innumera, the type species of the genus. The second major lineage includes groupings concordant with the morphological circumscriptions of the genera Melanochaeta, Melanopsammella, Striatosphaeria, Zignoëlla and the new genus Tainosphaeria. © 2006 by The Mycological Society of America.

          • JW Spatafora, GH Sung, D Johnson, C Hesse, B O'Rourke, M Serdani, R Spotts, F Lutzoni, V Hofstetter, J Miadlikowska, V Reeb, C Gueidan, E Fraker, T Lumbsch, R Lücking, I Schmitt, K Hosaka, A Aptroot, C Roux, AN Miller, DM Geiser, J Hafellner, G Hestmark, AE Arnold, B Büdel, A Rauhut, D Hewitt, WA Untereiner, MS Cole, C Scheidegger, M Schultz, H Sipman and CL Schoch.
          • (2006).
          • A five-gene phylogeny of Pezizomycotina.
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 1018-1028.
          • [web]
          Publication Description

          Pezizomycotina is the largest subphylum of Ascomycota and includes the vast majority of filamentous, ascoma-producing species. Here we report the results fromweighted parsimony, maximum likelihood and Bayesian phylogenetic analyses of five nuclear loci (SSU rDNA, LSU rDNA, RPB1, RPB2 and EF-1α) from 191 taxa. Nine of the 10 Pezizomycotina classes currently recognized were represented in the sampling. These data strongly supported the monophyly of Pezizomycotina, Arthoniomycetes, Eurotiomycetes, Orbiliomycetes and Sordariomycetes. Pezizomycetes and Dothideomycetes also were resolved as monophyletic but not strongly supported by the data. Lecanoromycetes was resolved as paraphyletic in parsimony analyses but monophyletic in maximum likelihood and Bayesian analyses. Leotiomycetes was polyphyletic due to exclusion of Geoglossaceae. The two most basal classes of Pezizomycotina were Orbiliomycetes and Pezizomycetes, both of which comprise species that produce apothecial ascomata. The seven remaining classes formed a monophyletic group that corresponds to Leotiomyceta. Within Leotiomyceta, the supraclass clades of Leotiomycetes s.s. plus Sordariomycetes and Arthoniomycetes plus Dothideomycetes were resolved with moderate support. © 2006 by The Mycological Society of America.

          • DM Geiser, C Gueidan, J Miadlikowska, F Lutzoni, F Kauff, V Hofstetter, E Fraker, CL Schoch, L Tibell, WA Untereiner and A Aptroot.
          • (2006).
          • Eurotiomycetes: Eurotiomycetidae and chaetothyriomycetidae.
          • Mycologia
          • ,
          • 98
          • (6)
          • ,
          • 1053-1064.
          • [web]
          Publication Description

          The class Eurotiomycetes (Ascomycota, Pezizomycotina) is a monophyletic group comprising two major clades of very different ascomycetous fungi: (i) the subclass Eurotiomycetidae, a clade that contains most of the fungi previously recognized as Plectomycetes because of their mostly enclosed ascomata and prototunicate asci; and (ii) the subclass Chaetothyriomycetidae, a group of fungi that produce ascomata with an opening reminiscent of those produced by Dothideomycetes or Sordariomycetes. In this paper we use phylogenetic analyses based on data available from the Assembling the Fungal Tree of Life project (AFTOL), in addition to sequences in GenBank, to outline this important group of fungi. The Eurotiomycetidae include producers of toxic and useful secondary metabolites, fermentation agents used to make food products and enzymes, xerophiles and psychrophiles, and the important genetics model Aspergillus nidulans. The Chaetothyriomycetidae include the common black yeast fungi, some of which are pathogens of humans and animals, as well as some primarily lichenized groups newly found to be phylogenetically associated with this group. The recently proposed order Mycocaliciales shows a sister relationship with Eurotiomycetes. The great majority of human pathogenic Pezizomycotina are Eurotiomycetes, particularly in Eurotiales, Onygenales and Chaetothyriales. Due to their broad importance in basic research, industry and public health, several genome projects have focused on species in Onygenales and Eurotiales. © 2006 by The Mycological Society of America.

          • Lutzoni.
          • (2005).
          • Erratum: (American Journal of Botany (October 2004) 91:10 (1450)).
          • American Journal of Botany
          • ,
          • 92
          • (1)
          • ,
          • i.
          • HE O'Brien, J Miadlikowska and F Lutzoni.
          • (2005).
          • Assessing host specialization in symbiotic cyanobacteria associated with four closely related species of the lichen fungus Peltigera.
          • European Journal of Phycology
          • ,
          • 40
          • (4)
          • ,
          • 363-378.
          • [web]
          Publication Description

          Heterocystous cyanobacteria form symbiotic associations with a wide range of plant and fungal hosts. We used a molecular phylogenetic approach to investigate the degree of host specialization of cyanobacteria associated with four closely related species of the lichenized fungus Peltigera, and to compare these strains with other symbiotic cyanobacteria. We conducted phylogenetic analyses on 16S, rbcLX, and trnL sequences from cyanobacteria associated with multiple specimens of each lichen species and from symbionts of other fungi and plants, as well as from free-living strains of Nostoc and related genera of cyanobacteria. The genus Nostoc comprises two divergent lineages, but symbiotic strains occur primarily within a single monophyletic lineage that also includes free-living representatives. Cyanobacteria from the same lichen species were often more closely related to strains from other species or to plant symbionts or free-living strains than to each other. These results indicate that host specialization is low for the genus Nostoc, and suggest that opportunities for coevolution with its partners may be rare. © 2005 British Phycological Society.

          • M Paoletti, C Rydholm, EU Schwier, MJ Anderson, G Szakacs, F Lutzoni, JP Debeaupuis, JP Latgé, DW Denning and PS Dyer.
          • (2005).
          • Evidence for sexuality in the opportunistic fungal pathogen Aspergillus fumigatus.
          • Current Biology
          • ,
          • 15
          • (13)
          • ,
          • 1242-1248.
          • [web]
          Publication Description

          Aspergillus fumigatus is a medically important opportunistic pathogen and a major cause of respiratory allergy [1]. The species has long been considered an asexual organism. However, genome analysis has revealed the presence of genes associated with sexual reproduction, including a MAT-2 high-mobility group mating-type gene and genes for pheromone production and detection (Galagan et al., personal communication; Nierman et al., personal communication; [2, 3]). We now demonstrate that A. fumigatus has other key characteristics of a sexual species. We reveal the existence of isolates containing a complementary MAT-1 α box mating-type gene and show that the MAT locus has an idiomorph structure characteristic of heterothallic (obligate sexual outbreeding) fungi [4, 5]. Analysis of 290 worldwide clinical and environmental isolates with a multiplex-PCR assay revealed the presence of MAT1-1 and MAT1-2 genotypes in similar proportions (43% and 57%, respectively). Further population genetic analyses provided evidence of recombination across a global sampling and within North American and European subpopulations. We also show that mating-type, pheromone-precursor, and pheromone-receptor genes are expressed during mycelial growth. These results indicate that A. fumigatus has a recent evolutionary history of sexual recombination and might have the potential for sexual reproduction. The possible presence of a sexual cycle is highly significant for the population biology and disease management of the species. ©2005 Elsevier Ltd All rights reserved.

          • D Bhattacharya, V Reeb, DM Simon and F Lutzoni.
          • (2005).
          • Phylogenetic analyses suggest reverse splicing spread of group I introns in fungal ribosomal DNA.
          • BMC Evolutionary Biology
          • ,
          • 5
          • (68)
          • .
          • [web]
          Publication Description

          Background: Group I introns have spread into over 90 different sites in nuclear ribosomal DNA (rDNA) with greater than 1700 introns reported in these genes. These ribozymes generally spread through endonuclease-mediated intron homing. Another putative pathway is reverse splicing whereby a free group I intron inserts into a homologous or heterologous RNA through complementary base-pairing between the intron and exon RNA. Reverse-transcription of the RNA followed by general recombination results in intron spread. Here we used phylogenetics to test for reverse splicing spread in a taxonomically broadly sampled data set of fungal group I introns including 9 putatively ancient group I introns in the rDNA of the yeast-like symbiont Symbiotaphrina buchneri. Results: Our analyses reveal a complex evolutionary history of the fungal introns with many cases of vertical inheritance (putatively for the 9 introns in S. buchneri) and intron lateral transfer. There are several examples in which introns, many of which are still present in S. buchneri, may have spread through reverse splicing into heterologous rDNA sites. If the S. buchneri introns are ancient as we postulate, then group I intron loss was widespread in fungal rDNA evolution. Conclusion: On the basis of these results, we suggest that the extensive distribution of fungal group I introns is at least partially explained by the reverse splicing movement of existing introns into ectopic rDNA sites. © 2005 Bhattacharya et al; licensee BioMed Central Ltd.

          • F Lutzoni, F Kauff, CJ Cox, D McLaughlin, G Celio, B Dentinger, M Padamsee, D Hibbett, TY James, E Baloch, M Grube, V Reeb, V Hofstetter, C Schoch, AE Arnold, J Miadlikowska, J Spatafora, D Johnson, S Hambleton, M Crockett, R Shoemaker, GH Sung, R Lücking, T Lumbsch, K O'Donnell, M Binder, P Diederich, D Ertz, C Gueidan, K Hansen, RC Harris, K Hosaka, YW Lim, B Matheny, H Nishida, D Pfister, J Rogers, A Rossman, I Schmitt, H Sipman, J Stone, J Sugiyama, R Yahr and R Vilgalys.
          • (2004).
          • Assembling the fungal tree of life: progress, classification, and evolution of subcellular traits..
          • Am J Bot
          • ,
          • 91
          • (10)
          • ,
          • 1446-1480.
          • [web]
          Publication Description

          Based on an overview of progress in molecular systematics of the true fungi (Fungi/Eumycota) since 1990, little overlap was found among single-locus data matrices, which explains why no large-scale multilocus phylogenetic analysis had been undertaken to reveal deep relationships among fungi. As part of the project "Assembling the Fungal Tree of Life" (AFTOL), results of four Bayesian analyses are reported with complementary bootstrap assessment of phylogenetic confidence based on (1) a combined two-locus data set (nucSSU and nucLSU rDNA) with 558 species representing all traditionally recognized fungal phyla (Ascomycota, Basidiomycota, Chytridiomycota, Zygomycota) and the Glomeromycota, (2) a combined three-locus data set (nucSSU, nucLSU, and mitSSU rDNA) with 236 species, (3) a combined three-locus data set (nucSSU, nucLSU rDNA, and RPB2) with 157 species, and (4) a combined four-locus data set (nucSSU, nucLSU, mitSSU rDNA, and RPB2) with 103 species. Because of the lack of complementarity among single-locus data sets, the last three analyses included only members of the Ascomycota and Basidiomycota. The four-locus analysis resolved multiple deep relationships within the Ascomycota and Basidiomycota that were not revealed previously or that received only weak support in previous studies. The impact of this newly discovered phylogenetic structure on supraordinal classifications is discussed. Based on these results and reanalysis of subcellular data, current knowledge of the evolution of septal features of fungal hyphae is synthesized, and a preliminary reassessment of ascomal evolution is presented. Based on previously unpublished data and sequences from GenBank, this study provides a phylogenetic synthesis for the Fungi and a framework for future phylogenetic studies on fungi.

          • V Reeb, F Lutzoni and C Roux.
          • (2004).
          • Contribution of RPB2 to multilocus phylogenetic studies of the euascomycetes (Pezizomycotina, Fungi) with special emphasis on the lichen-forming Acarosporaceae and evolution of polyspory..
          • Mol Phylogenet Evol
          • ,
          • 32
          • (3)
          • ,
          • 1036-1060.
          • [web]
          Publication Description

          Despite the recent progress in molecular phylogenetics, many of the deepest relationships among the main lineages of the largest fungal phylum, Ascomycota, remain unresolved. To increase both resolution and support on a large-scale phylogeny of lichenized and non-lichenized ascomycetes, we combined the protein coding-gene RPB2 with the traditionally used nuclear ribosomal genes SSU and LSU. Our analyses resulted in the naming of the new subclasses Acarosporomycetidae and Ostropomycetidae, and the new class Lichinomycetes, as well as the establishment of the phylogenetic placement and novel circumscription of the lichen-forming fungi family Acarosporaceae. The delimitation of this family has been problematic over the past century, because its main diagnostic feature, true polyspory (numerous spores issued from multiple post-meiosis mitoses) with over 100 spores per ascus, is probably not restricted to the Acarosporaceae. This observation was confirmed by our reconstruction of the origin and evolution of this form of true polyspory using maximum likelihood as the optimality criterion. The various phylogenetic analyses carried out on our data sets allowed us to conclude that: (1) the inclusion of phylogenetic signal from ambiguously aligned regions into the maximum parsimony analyses proved advantageous in reconstructing phylogeny; however, when more data become available, Bayesian analysis using different models of evolution is likely to be more efficient; (2) neighbor-joining bootstrap proportions seem to be more appropriate in detecting topological conflict between data partitions of large-scale phylogenies than posterior probabilities; and (3) Bayesian bootstrap proportion provides a compromise between posterior probability outcomes (i.e., higher accuracy, but with a higher number of significantly supported wrong internodes) vs. maximum likelihood bootstrap proportion outcomes (i.e., lower accuracy, with a lower number of significantly supported wrong internodes).

          • J Miadlikowska and F Lutzoni.
          • (2004).
          • Phylogenetic classification of peltigeralean fungi (Peltigerales, Ascomycota) based on ribosomal RNA small and large subunits..
          • Am J Bot
          • ,
          • 91
          • (3)
          • ,
          • 449-464.
          • [web]
          Publication Description

          To provide a comprehensive molecular phylogeny for peltigeralean fungi and to establish a classification based on monophyly, phylogenetic analyses were carried out on sequences from the nuclear ribosomal large (LSU) and small (SSU) subunits obtained from 113 individuals that represent virtually all main lineages of ascomycetes. Analyses were also conducted on a subset of 77 individuals in which the ingroup consisted of 59 individuals representing six families, 12 genera, and 54 species potentially part of the Peltigerineae/Peltigerales. Our study revealed that all six families together formed a strongly supported monophyletic group within the Lecanoromycetidae. We propose here a new classification for these lichens consisting of the order Peltigerales and two suborders-Collematineae subordo nov. (Collemataceae, Placynthiaceae, and Pannariaceae) and Peltigerineae (Lobariaceae, Nephromataceae, and Peltigeraceae). To accommodate these new monophyletic groups, we redefined the Lecanorineae, Pertusariales, and Lecanorales sensu Eriksson et al. (Outline of Ascomycota-2003, Myconet 9: 1-103, 2003). Our study confirms the monophyly of the Collemataceae, Lobariaceae, Nephromataceae, and Peltigeraceae, and the genera Nephroma, Sticta, and Peltigera. However, Leptogium, Lobaria, Pseudocyphellaria, and Solorina were found to be nonmonophyletic genera. Reconstruction of ancestral symbiotic states within the Peltigerales, using maximum likelihood (ML) and a Bayesian approach to account for phylogenetic uncertainty, revealed an evolutionary scenario in which bimembered associations with cyanobacteria were ancestral, followed by multiple independent acquisitions of green algae to form tripartite symbioses and rare subsequent losses of the cyanobiont to form bimembered symbioses with green algae.

          • P Haugen, V Reeb, F Lutzoni and D Bhattacharya.
          • (2004).
          • The evolution of homing endonuclease genes and group I introns in nuclear rDNA..
          • Molecular Biology and Evolution
          • ,
          • 21
          • (1)
          • ,
          • 105-116.
          • [web]
          Publication Description

          Group I introns are autonomous genetic elements that can catalyze their own excision from pre-RNA. Understanding how group I introns move in nuclear ribosomal (r)DNA remains an important question in evolutionary biology. Two models are invoked to explain group I intron movement. The first is termed homing and results from the action of an intron-encoded homing endonuclease that recognizes and cleaves an intronless allele at or near the intron insertion site. Alternatively, introns can be inserted into RNA through reverse splicing. Here, we present the sequences of two large group I introns from fungal nuclear rDNA, which both encode putative full-length homing endonuclease genes (HEGs). Five remnant HEGs in different fungal species are also reported. This brings the total number of known nuclear HEGs from 15 to 22. We determined the phylogeny of all known nuclear HEGs and their associated introns. We found evidence for intron-independent HEG invasion into both homologous and heterologous introns in often distantly related lineages, as well as the "switching" of HEGs between different intron peripheral loops and between sense and antisense strands of intron DNA. These results suggest that nuclear HEGs are frequently mobilized. HEG invasion appears, however, to be limited to existing introns in the same or neighboring sites. To study the intron-HEG relationship in more detail, the S943 group I intron in fungal small-subunit rDNA was used as a model system. The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns.

          • P Haugen, V Reeb, F Lutzoni and D Bhattacharya.
          • (2004).
          • The Evolution of Homing Endonuclease Genes and Group I Introns in Nuclear rDNA.
          • Molecular Biology and Evolution
          • ,
          • 21
          • (1)
          • ,
          • 129-140.
          • [web]
          Publication Description

          Group I introns are autonomous genetic elements that can catalyze their own excision from pre-RNA. Understanding how group I introns move in nuclear ribosomal (r)DNA remains an important question in evolutionary biology. Two models are invoked to explain group I intron movement. The first is termed homing and results from the action of an intron-encoded homing endonuclease that recognizes and cleaves an intronless allele at or near the intron insertion site. Alternatively, introns can be inserted into RNA through reverse splicing. Here, we present the sequences of two large group I introns from fungal nuclear rDNA, which both encode putative full-length homing endonuclease genes (HEGs). Five remnant HEGs in different fungal species are also reported. This brings the total number of known nuclear HEGs from 15 to 22. We determined the phylogeny of all known nuclear HEGs and their associated introns. We found evidence for intron-independent HEG invasion into both homologous and heterologous introns in often distantly related lineages, as well as the "switching" of HEGs between different intron peripheral loops and between sense and antisense strands of intron DNA. These results suggest that nuclear HEGs are frequently mobilized. HEG invasion appears, however, to be limited to existing introns in the same or neighboring sites. To study the intron-HEG relationship in more detail, the S943 group I intron in fungal small-subunit rDNA was used as a model system. The S943 HEG is shown to be widely distributed as functional, inactivated, or remnant ORFs in S943 introns.

          • S Zoller and F Lutzoni.
          • (2003).
          • Slow algae, fast fungi: exceptionally high nucleotide substitution rate differences between lichenized fungi Omphalina and their symbiotic green algae Coccomyxa..
          • Mol Phylogenet Evol
          • ,
          • 29
          • (3)
          • ,
          • 629-640.
          • [web]
          Publication Description

          Omphalina basidiolichens are obligate mutualistic associations of a fungus of the genus Omphalina (the exhabitant) and a unicellular green alga of the genus Coccomyxa (the inhabitant). It has been suggested that symbiotic inhabitants have a lower rate of genetic change compared to exhabitants because the latter are more exposed to abiotic environmental variation and competition from other organisms. In order to test this hypothesis we compared substitution rates in the nuclear ribosomal internal transcribed spacer region (ITS1, 5.8S, ITS2) among fungal species with rates among their respective algal symbionts. To ensure valid comparisons, only taxon pairs (12) with a common evolutionary history were used. On average, substitution rates in the ITS1 portion of Omphalina pairs were 27.5 times higher than rates in the corresponding pairs of Coccomyxa since divergence from their respective ancestor at the base of the Omphalina/Coccomyxa lineage. Substitution rates in the 5.8S and the ITS2 portions were 2.4 and 18.0 times higher, respectively. The highest rate difference (43.0) was found in the ITS1 region. These are, to our knowledge, the highest differences of substitution rates reported for symbiotic organisms. We conclude that the Omphalina model system conforms to the proposed hypothesis of lower substitution rates in the inhabitant, but that the mode of transmission of the inhabitant (vertical versus horizontal) could be a prevailing factor in the regulation of unequal rates of nucleotide substitution between co-evolving symbionts. Our phylogenetic study of Coccomyxa revealed three main lineages within this genus, corresponding to free-living Coccomyxa, individuals isolated from basidiolichens Omphalina and Coccomyxa isolated from ascolichens belonging to the Peltigerales.

          • J Miadlikowska, F Lutzoni, T Goward, S Zoller and D Posada.
          • (2003).
          • New approach to an old problem: Incorporating signal from gap-rich regions of ITS and rDNA large subunit into phylogenetic analyses to resolve the Peltigera canina species complex..
          • Mycologia
          • ,
          • 95
          • (6)
          • ,
          • 1181-1203.
          • [web]
          Publication Description

          The Peltigera canina species complex consists of foliose lichenized bitunicate ascohymenial discomycetes forming section Peltigera within the genus Peltigera (Lecanoromycetes, lichen-forming Ascomycetes). To test the circumscription of highly polymorphic species and to resolve relationships among putative members of the P. canina complex, part of the nuclear ribosomal DNA large subunit (LSU rDNA) and the entire internal-transcribed spacer (ITS rDNA) were sequenced for 84 individuals representing 33 putative Peltigera taxa. Seventeen of the 25 taxa from the P. canina complex are well established and widely accepted. The remaining eight taxa have been proposed recently but are undescribed. A hypervariable region in ITS1 (ITS1-HR, sites 111-237 in our alignment) showed remarkable variation in length, especially in the P. canina complex, ranging from 8 to 126 bp, and contained several microsatellites. We describe here an alignment-free method to code such large gap-rich hypervariable regions for phylogenetic analyses. Variation among ITS1-HR sequences greatly contributed to species delimitation and species identification and can be a major asset to future population studies for specific species within section Peltigera. Sequences of ITS1-HR alone were sufficient to identify all existing species of Peltigera from the P. canina species complex and related sections Retifoveatae and Horizontales included in this study. However, only when INAASE (for short ambiguously aligned regions) and ITS1-HR coded characters were added to the combined analysis of nonambiguous LSU and ITS sites was it possible to reach the level of phylogenetic resolution and support necessary to disentangle the P. canina complex. We report here complete concordance between phylogenetically based and morphologically based species delimitation for 15 of the 17 species from the P. canina complex (P. canina, P. cinnamomea, P. degenii, P. evansiana, P. frigida, P. kristinssonii, P. laciniata, P. lambinonii, P. lepidophora, P. membranacea, P. monticola, P. ponojensis, P. praetextata, P. rufescens and P. ulcerata). Four of the eight newly proposed but undescribed taxa most likely represent new species (P. "fuscopraetextata", P. "neocanina", P. "neorufescens" and P. "scotteri") within the P. canina complex. We found that morphologically and chemically distinct P. didactyla s. str. and P. didactyla var. extenuata form two non-sister monophyletic entities, therefore the latter taxon should be recognized at the species level (P. extenuata). The North American and European populations of the morphologically uniform P. degenii might represent two sibling species because they were found to be genetically distinct and monophyletic. Two major monophyletic groups within the P. canina complex (CICADE = CInnamomea + CAnina + DEgenii group and PORUDI = POnojensis + RUfescens + DIdactyla group) seem to be correlated with different humidity preferences. Although some authors previously have suggested interspecies recombination within the P. canina complex, we did not find statistically significant evidence for this phenomenon based on LSU and ITS sequences.

          • U Søchting and F Lutzoni.
          • (2003).
          • Molecular phylogenetic study at the generic boundary between the lichen-forming fungi Caloplaca and Xanthoria (Ascomycota, Teloschistaceae).
          • Mycological Research
          • ,
          • 107
          • (11)
          • ,
          • 1266-1276.
          • [web]
          Publication Description

          A molecular phylogenetic analysis of rDNA was performed for seven Caloplaca, seven Xanthoria, one Fulgensia and five outgroup species. Phylogenetic hypotheses are constructed based on nuclear small and large subunit rDNA, separately and in combination. Three strongly supported major monophyletic groups were revealed within the Teloschistaceae. One group represents the Xanthoria fallax-group. The second group includes three subgroups: (1) X. parietina and X. elegans; (2) basal placodioid Caloplaca species followed by speciations leading to X. polycarpa and X. candelaria; and (3) a mixture of placodioid and endolithic Caloplaca species. The third main monophyletic group represents a heterogeneous assemblage of Caloplaca and Fulgensia species with a drastically different metabolite content. We report here that the two genera Caloplaca and Xanthoria, as well as the subgenus Gasparrinia, are all polyphyletic. The taxonomic significance of thallus morphology in Teloschistaceae and the current delimitation of the genus Xanthoria is discussed in light of these results.

          • E Gaya, F Lutzoni, S Zoller and P Navarro-Rosinés.
          • (2003).
          • Phylogenetic study of Fulgensia and allied Caloplaca and Xanthoria species (Teloschistaceae, lichen-forming ascomycota).
          • American Journal of Botany
          • ,
          • 90
          • (7)
          • ,
          • 1095-1103.
          • [web]
          Publication Description

          Fulgensia Massal. & De Not. is a widespread genus with considerable morphological and ecological heterogeneity across species. For this reason, the taxonomic delimitation of this genus has been controversial. Relationships among species of Fulgensia, Caloplaca Th. Fr., and Xanthoria (Fr.) Th. Fr. (Lecanorales) were investigated based on a comprehensive phylogenetic analysis of 62 DNA sequences from the nuclear ribosomal internal transcribed spacer (ITS) region using maximum parsimony (MP) and likelihood (ML). Ambiguously aligned (INAASE coded characters) and unambiguous regions were analyzed separately and combined when using MP as the optimization criterion. All our analyses confirm the polyphyly of this genus as three distinct lineages: Fulgensia sensu stricto, F. australis, and F. schistidii. We report here that Caloplaca, Fulgensia, and Xanthoria together form two main sister lineages. One lineage includes Fulgensia schistidii (part of the C. saxicola group), Xanthoria, and most of the lobed Caloplaca species belonging to the Gasparrinia group. A second main lineage comprises the remaining Caloplaca species, Fulgensia sensu stricto, and F. australis. Therefore, the traditional generic level classification schemes for the family Teloschistaceae appear to be highly artificial. All three genera were found to be nonmonophyletic. We demonstrate here that the ITS is appropriate to resolve relationships across the Telos-chistaceae. However, a combination of an MP analysis, in which ambiguously aligned regions are accommodated using INAASE, with an ML analysis, in which phylogenetic confidence is estimated using a Bayesian approach, is needed.

          • T McDonald, J Miadlikowska and F Lutzoni.
          • (2003).
          • The lichen genus Sticta in the Great Smoky Mountains: A phylogenetic study of morphological, chemical, and molecular data.
          • Bryologist
          • ,
          • 106
          • (1)
          • ,
          • 61-79.
          Publication Description

          In this paper we segregate specimens from the genus Sticta in the Great Smoky Mountains National Park into phenotypic groups corresponding to putative species using traditional taxonomic methods, paying particular attention to specimens from the S. weigelii s. 1. group, then employ phylogenetic analyses and rigorous statistics to test the robustness of these species groups. In order to circumscribe putative species and to resolve the S. weigelii complex, morphological, chemical, and molecular characters from the nuclear ribosomal DNA sequences of the entire Internal Transcribed Spacer region are analyzed separately and simultaneously using maximum parsimony or maximum likelihood. In addition to the bootstrap method, Bayesian statistics with the Markov Chain Monte Carlo algorithm are used to estimate branch robustness on the resulting reconstructed trees. Five out of six analyses recover the same five monophyletic putative species from the genus Sticta, indicating the concordance of DNA-based and morphology-based species delimitation. The phylogenies show that lichens identified as S. weigelii represented S. beauvoisii and the two new species described here - S. carolinensis and S. fragilinata. Sticta weigelii s. s. does not occur in the park. Specimens from Oregon identified as S. weigelii belong to another unnamed Sticta taxon. The remaining two monophyletic groups represent two species well known from the park-S. fuliginosa and S. limbata. Characteristics of secondary compounds detected by Thin Layer Chromatography (TLC) and High Performance Liquid Chromatography (HPLC) in S. fragilinata thalli are provided. Detailed descriptions, including morphology and chemistry, are provided for four Sticta species found in the Smoky Mountains: S. beauvoisii, S. carolinensis, S. fragilinata and S. fuliginosa.

          • ME Alfaro, S Zoller and F Lutzoni.
          • (2003).
          • Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence.
          • Molecular Biology and Evolution
          • ,
          • 20
          • (2)
          • ,
          • 255-266.
          • [web]
          Publication Description

          Bayesian Markov chain Monte Carlo sampling has become increasingly popular in phylogenetics as a method for both estimating the maximum likelihood topology and for assessing nodal confidence. Despite the growing use of posterior probabilities, the relationship between the Bayesian measure of confidence and the most commonly used confidence measure in phylogenetics, the nonparametric bootstrap proportion, is poorly understood. We used computer simulation to investigate the behavior of three phylogenetic confidence methods: Bayesian posterior probabilities calculated via Markov chain Monte Carlo sampling (BMCMC-PP), maximum likelihood bootstrap proportion (ML-BP), and maximum parsimony bootstrap proportion (MP-BP). We simulated the evolution of DNA sequence on 17-taxon topologies under 18 evolutionary scenarios and examined the performance of these methods in assigning confidence to correct monophyletic and incorrect monophyletic groups, and we examined the effects of increasing character number on support value. BMCMC-PP and ML-BP were often strongly correlated with one another but could provide substantially different estimates of support on short internodes. In contrast, BMCMC-PP correlated poorly with MP-BP across most of the simulation conditions that we examined. For a given threshold value, more correct monophyletic groups were supported by BMCMC-PP than by either ML-BP or MP-BP. When threshold values were chosen that fixed the rate of accepting incorrect monophyletic relationship as true at 5%, all three methods recovered most of the correct relationships on the simulated topologies, although BMCMC-PP and ML-BP performed better than MP-BP. BMCMC-PP was usually a less biased predictor of phylogenetic accuracy than either bootstrapping method. BMCMC-PP provided high support values for correct topological bipartitions with fewer characters than was needed for nonparametric bootstrap.

          • K O'Donnell, FM Lutzoni, TJ Ward and GL Benny.
          • (2002).
          • Erratum: Evolutionary relationships among mucoralean fungi (zygomycota): Evidence for family polyphyly on a large scale (Mycologia (2001) 93:2).
          • Mycologia
          • ,
          • 93
          • (4)
          • ,
          • 814-.
          • F Kauff and F Lutzoni.
          • (2002).
          • Phylogeny of the Gyalectales and Ostropales (Ascomycota, Fungi): Among and within order relationships based on nuclear ribosomal RNA small and large subunits.
          • Molecular Phylogenetics and Evolution
          • ,
          • 25
          • (1)
          • ,
          • 138-156.
          • [web]
          Publication Description

          Despite various morphological and anatomical similarities, the two orders Gyalectales (lichenized ascomycetes) and Ostropales (lichenized and non-lichenized ascomycetes) have been considered to be distantly related to each other and their position within the Ascomycota was unsettled. To estimate relationships within these groups and their respective phylogenenetic placement within the Ascomycota, we analyzed DNA sequences from the nuclear small and large subunit ribosomal RNA genes using Maximum Parsimony, Maximum Likelihood, and Bayesian statistics with Markov chain Monte Carlo algorithms. Support for internal branches estimated with bootstrap was compared to Bayesian posterior probabilities. We report here that the Ostropales, in their current circumscription, are paraphyletic, and that the Ostropales s.l. include the Gyalectales and Trapeliaceae. The Unitunicate Ascohymenials are redelineated to include the Ostropales s.l., as defined here, and the Baeomycetaceae. Dimerella and Coenogonium are congeneric, and Petractis thelotremella and P. hypoleuca are reunited with members of the genus Gyalecta. In addition to requiring less computational time, Bayesian inference of phylogeny recovered the same topology as a conventional heuristic search using Maximum Likelihood as the optimization criterion and seems superior to bootstrapping in estimating support for short internal branches. © 2002 Elsevier Science (USA). All rights reserved.

          • FK Barker and FM Lutzoni.
          • (2002).
          • The utility of the incongruence length difference test.
          • Systematic Biology
          • ,
          • 51
          • (4)
          • ,
          • 625-637.
          • [web]
          • SA Redhead, JM Moncalvo, R Vilgalys and F Lutzoni.
          • (2002).
          • Phylogeny of agarics: Partial systematics solutions for bryophilous omphalinoid agarics outside of the Agaricales (euagarics).
          • MYCOTAXON
          • ,
          • 82
          • ,
          • 151-168.
          • [web]
          • J Miadlikowska, B McCune and F Lutzoni.
          • (2002).
          • Pseudocyphellaria perpetua, a new lichen from western North America.
          • Bryologist
          • ,
          • 105
          • (1)
          • ,
          • 1-10.
          Publication Description

          Pseudocyphellaria perpetua McCune & Miadlikowska is described as a new species of lichenized fungus from Oregon, U.S.A. Morphologically similar to some forms of P. crocata, P. perpetua is separated from that species by a yellow medulla and predominantly marginal soralia. Comparison of ITS and LSU nrDNA sequences support taxonomic distinctness of these two species. Phylogenetic analyses were conducted on LSU and ITS nrDNA data sets separately and simultaneously using maximum parsimony and maximum likelihood as optimization criteria. All analyses except one (maximum parsimony on LSU nrDNA data alone) confirmed the monophyly of P. perpetua. There are two distinct groups within the P. perpetua clade represented by specimens sampled from near the type locality in Oregon, and specimens outside of Oregon (eastern Canada, eastern Russia and eastern U.S.A.). The genus Pseudocyphellaria is very likely polyphyletic, consisting of at least two highly divergent groups.

          • SA Redhead, F Lutzoni, JM Moncalvo and R Vilgalys.
          • (2002).
          • Phylogeny of agarics: Partial systematics solutions for core Omphalinoid genera in the Agaricales (Euagarics).
          • Mycotaxon
          • ,
          • 83
          • ,
          • 19-57.
          Publication Description

          The taxonomy of species previously assigned to Omphalina sensu lato or Clitocybe is reevaluated in light of recent molecularly-based phylogenetic hypotheses. Nomenclatural complications involving generic and specific names, lectotypifications and changes to the Code are analysed. Lichenomphalia gen. nov. (type Hygrophorus hudsonianus, syn. Omphalina hudsoniana) is proposed for lichenized former omphalinas. Ampulloclitocybe gen. nov. (type Agaricus clavipes, syn. Clitocybe clavipes) is erected for its type species. Arrhenia is emended to include greyish species formerly included in Omphalina, but excluding reddish brown species related to Omphalina pyxidata, the conserved lectotype for Omphalina. The genera Cantharellula, Chrysomphalina, Gerronema, Glabrocyphella, Gliophorus, Haasiella, Hygrophorus, Hygrocybe, Pseudoarmillariella, and Rickenella, and the generic names Botrydina, Coriscium, Leptoglossum, Phaeotellus, Phytoconis, and Semiomphalina are discussed.

          • ME Alfaro, S Zoller and F Lutzoni.
          • (2001).
          • Comparative performance of the bootstrap and Bayesian MCMC sampling in assessing phylogenetic confidence: a simulation study.
          • AMERICAN ZOOLOGIST
          • ,
          • 41
          • (6)
          • ,
          • 1379-1379.
          • [web]
          • F Lutzoni, M Pagel and V Reeb.
          • (2001).
          • Major fungal lineages are derived from lichen symbiotic ancestors.
          • Nature
          • ,
          • 411
          • (6840)
          • ,
          • 937-940.
          • [web]
          Publication Description

          About one-fifth of all known extant fungal species form obligate symbiotic associations with green algae, cyanobacteria or with both photobionts. These symbioses, known as lichens, are one way for fungi to meet their requirement for carbohydrates. Lichens are widely believed to have arisen independently on several occasions, accounting for the high diversity and mixed occurrence of lichenized and non-lichenized (42 and 58%, respectively) fungal species within the Ascomycota. Depending on the taxonomic classification chosen, 15-18 orders of the Ascomycota include lichen-forming taxa, and 8-11 of these orders (representing about 60% of the Ascomycota species) contain both lichenized and non-lichenized species. Here we report a phylogenetic comparative analysis of the Ascomycota, a phylum that includes greater than 98% of known lichenized fungal species. Using a Bayesian phylogenetic tree sampling methodology combined with a statistical model of trait evolution, we take into account uncertainty about the phylogenetic tree and ancestral state reconstructions. Our results show that lichens evolved earlier than believed, and that gains of lichenization have been infrequent during Ascomycota evolution, but have been followed by multiple independent losses of the lichen symbiosis. As a consequence, major Ascomycota lineages of exclusively non-lichen-forming species are derived from lichen-forming ancestors. These species include taxa with important benefits and detriments to humans, such as Penicillium and Aspergillus.

          • K O'Donnell, FM Lutzoni, TJ Ward and GL Benny.
          • (2001).
          • Evolutionary relationships among mucoralean fungi (Zygomycota): Evidence for family polyphyly on a large scale.
          • Mycologia
          • ,
          • 93
          • (2)
          • ,
          • 286-296.
          Publication Description

          Mucorales (Zygomycota) are ubiquitous, morphologically simple terrestrial fungi that are united taxonomically by possession of a coenocytic mycelium upon which nonmotile mitotic spores are produced asexually in uni- to multispored sporangia, and zygospores, where known, are produced following fusion of sexually compatible hyphae. Here we report the first comprehensive phylogenetic analysis of essentially all genera of Mucorales (63 species, 54 genera and 13 families) based on partial nucleotide sequence data of nuclear small subunit (18S) ribosomal RNA and nuclear large subunit (28S) ribosomal RNA genes, translation elongation factor-1α gene exons, and a morphological data set consisting of 1826, 389, 1092 and 11 characters, respectively. Individual and combined data sets were analyzed by unequally weighted maximum parsimony (MP) to investigate evolutionary relationships among and within mucoralean families. A Micromucor-Umbelopsis clade, traditionally included in the Mortierellaceae, was identified as the basal sister-group to all other Mucorales. A major discovery of this study is that traditional family-level classification schemes for this order appear to be highly artificial as evidenced by polyphyly of four of the seven families containing two or more genera. As presently circumscribed, these four families include 83% of the Mucorales. In addition, the largest and best known genera, Mucor and Absidia, were resolved as polyphyletic. The results provide a robust phylogenetic framework for additional evolutionary studies of the Mucorales.

          • K O'Donnell, FM Lutzoni, TJ Ward and GL Benny.
          • (2001).
          • Evolutionary relationships among mucuralean fungi (Zygomycota): Evidence for family polyphyly on a large scale (vol 93, pg 286, 2001).
          • MYCOLOGIA
          • ,
          • 93
          • (4)
          • ,
          • 814-814.
          • [web]
          • JM Moncalvo, FM Lutzoni, SA Rehner, J Johnson and R Vilgalys.
          • (2000).
          • Phylogenetic relationships of agaric fungi based on nuclear large subunit ribosomal DNA sequences..
          • Syst Biol
          • ,
          • 49
          • (2)
          • ,
          • 278-305.
          • [web]
          Publication Description

          Phylogenetic relationships of mushrooms and their relatives within the order Agaricales were addressed by using nuclear large subunit ribosomal DNA sequences. Approximately 900 bases of the 5' end of the nucleus-encoded large subunit RNA gene were sequenced for 154 selected taxa representing most families within the Agaricales. Several phylogenetic methods were used, including weighted and equally weighted parsimony (MP), maximum likelihood (ML), and distance methods (NJ). The starting tree for branch swapping in the ML analyses was the tree with the highest ML score among previously produced MP and NJ trees. A high degree of consensus was observed between phylogenetic estimates obtained through MP and ML. NJ trees differed according to the distance model that was used; however, all NJ trees still supported most of the same terminal groupings as the MP and ML trees did. NJ trees were always significantly suboptimal when evaluated against the best MP and ML trees, by both parsimony and likelihood tests. Our analyses suggest that weighted MP and ML provide the best estimates of Agaricales phylogeny. Similar support was observed between bootstrapping and jackknifing methods for evaluation of tree robustness. Phylogenetic analyses revealed many groups of agaricoid fungi that are supported by moderate to high bootstrap or jackknife values or are consistent with morphology-based classification schemes. Analyses also support separate placement of the boletes and russules, which are basal to the main core group of gilled mushrooms (the Agaricineae of Singer). Examples of monophyletic groups include the families Amanitaceae, Coprinaceae (excluding Coprinus comatus and subfamily Panaeolideae), Agaricaceae (excluding the Cystodermateae), and Strophariaceae pro parte (Stropharia, Pholiota, and Hypholoma); the mycorrhizal species of Tricholoma (including Leucopaxillus, also mycorrhizal); Mycena and Resinomycena; Termitomyces, Podabrella, and Lyophyllum; and Pleurotus with Hohenbuehelia. Several groups revealed by these data to be nonmonophyletic include the families Tricholomataceae, Cortinariaceae, and Hygrophoraceae and the genera Clitocybe, Omphalina, and Marasmius. This study provides a framework for future systematics studies in the Agaricales and suggestions for analyzing large molecular data sets.

          • D Bhattacharya, F Lutzoni, V Reeb, D Simon, J Nason and F Fernandez.
          • (2000).
          • Widespread occurrence of spliceosomal introns in the rDNA genes of ascomycetes.
          • Molecular Biology and Evolution
          • ,
          • 17
          • (12)
          • ,
          • 1971-1984.
          Publication Description

          Spliceosomal (pre-mRNA) introns have previously been found in eukaryotic protein-coding genes, in the small nuclear RNAs of some fungi, and in the small- and large-subunit ribosomal DNA genes of a limited number of ascomycetes. How the majority of these introns originate remains an open question because few proven cases of recent and pervasive intron origin have been documented. We report here the widespread occurrence of spliceosomal introns (69 introns at 27 different sites) in the small- and large-subunit nuclear-encoded rDNA of lichen-forming and free-living members of the Ascomycota. Our analyses suggest that these spliceosomal introns are of relatively recent origin, i.e., within the Euascomycetes, and have arisen through aberrant reverse-splicing (in trans) of free pre-mRNA introns into rRNAs. The spliceosome itself, and not an external agent (e.g., transposable elements, group II introns), may have given rise to these introns. A nonrandom sequence pattern was found at sites flanking the rRNA spliceosomal introns. This pattern (AG-intron-G) closely resembles the proto-splice site (MAG-intron-R) postulated for intron insertions in pre-mRNA genes. The clustered positions of spliceosomal introns on secondary structures suggest that particular rRNA regions are preferred sites for insertion through reverse-splicing.

          • F Lutzoni, P Wagner, V Reeb and S Zoller.
          • (2000).
          • Integrating ambiguously aligned regions of DNA sequences in phylogenetic analyses without violating positional homology.
          • Systematic Biology
          • ,
          • 49
          • (4)
          • ,
          • 628-651.
          Publication Description

          Phylogenetic analyses of non-protein-coding nucleotide sequences such as ribosomal RNA genes, internal transcribed spacers, and introns are often impeded by regions of the alignments that are ambiguously aligned. These regions are characterized by the presence of gaps and their uncertain positions, no matter which optimization criteria are used. This problem is particularly acute in large-scale phylogenetic studies and when aligning highly diverged sequences. Accommodating these regions, where positional homology is likely to be violated, in phylogenetic analyses has been dealt with very differently by molecular systematists and evolutionists, ranging from the total exclusion of these regions to the inclusion of every position regardless of ambiguity in the alignment. We present a new method that allows the inclusion of ambiguously aligned regions without violating homology. In this three-step procedure, first homologous regions of the alignment containing ambiguously aligned sequences are delimited. Second, each ambiguously aligned region is unequivocally coded as a new character, replacing its respective ambiguous region. Third, each of the coded characters is subjected to a specific step matrix to account for the differential number of changes (summing substitutions and indels) needed to transform one sequence to another. The optimal number of steps included in the step matrix is the one derived from the pairwise alignment with the greatest similarity and the least number of steps. In addition to potentially enhancing phylogenetic resolution and support, by integrating previously nonaccessible characters without violating positional homology, this new approach can improve branch length estimations when using parsimony.

          • J Miadlikowska and F Lutzoni.
          • (2000).
          • Phylogenetic revision of the genus Peltigera (lichen-forming Ascomycota) based on morphological, chemical, and large subunit nuclear ribosomal DNA data.
          • International Journal of Plant Sciences
          • ,
          • 161
          • (6)
          • ,
          • 925-958.
          • [web]
          Publication Description

          Peltigera (Peltigerineae, lichenized Ascomycota) is one of the most widespread lichen genera incorporating bi- and trimembered associations involving fungi, green algae (cf. Coccomyxa), and cyanobacteria (cf. Nostoc). A wide range of morphological and chemical (secondary compounds) variation at both the intra- and inter-specific levels is present in this genus. Compared to many other genera of macrolichens: its taxonomy, including chemotaxonomy, still remains poorly understood. Existing infrageneric classifications of Peltigera are almost exclusively based on photobiont composition of the thallus. These classifications assumed that bi- and trimembered taxa were distinct monophyletic entities. The genus Peltigera has never been the focus of a comprehensive phylogenetic study. The most recent and widely accepted subdivision of the genus into seven groups is based mainly on morphological and chemical characters. Relationships among species of Peltigera are investigated here using chemical, morphological, and large subunit nuclear ribosomal DNA (LSU nrDNA) data. We test the monophyly of these seven morpho-chemical Peltigera groups and propose a classification based on a phylogenetic approach. Data sets of 42 chemical characters (terpenoids), 31 morphological characters, and 1135 LSU nrDNA characters for 96 samples representing 38 Peltigera species, eight undescribed putative Peltigera species, and nine species from seven potentially closely related genera from Peltigerineae were subjected to maximum parsimony analyses. Morphological, chemical, and molecular analyses were carried out independently and on a combined data set. Monophyly of Peltigera, including Hydrothyria, was confirmed. The genus Hydrothyria is transferred to Peltigera and a new combination Peltigera hydrothyria Miadlikowska and Lutzoni is proposed. Eight monophyletic sections within the genus Peltigera, with high bootstrap support, are circumscribed: sections Peltigera, Polydactylon Miadlikowska and Lutzoni, Chloropeltigera Gyeln., Peltidea (Ach.) Vain., Horizontales Miadlikowska and Lutzoni, Retifoveatae Miadlikowska and Lutzoni, Phlebia Wallr., and Hydrothyriae Miadlikowska and Lutzoni. Unequivocal morphological and chemical synapomorphies for all sections except section Peltidea are recognized and presented. A key for identification of the sections is provided. In addition, a key based on four main terpenoids for determination of the chemotypes and species within section Polydactylon is included. Five terpenoids (50-54) identified on thin-layer chromatography plates for P. elisabethae and P. horizontalis chemotype I are added to the list of substances found in Peltigera. Five chemotypes, mainly from Poland and Norway, are reported from Peltigera thalli for the first time: P. malacea chemotype V, P. leucophlebia chemotype II, P. hymenina chemotypes II and III, and P. collina chemotype IV. Three main types of vein structure in Peltigera were recognized based on SEM studies.

          • QX Wu, GM Mueller, FM Lutzoni, YQ Huang and SY Guo.
          • (2000).
          • Phylogenetic and biogeographic relationships of Eastern Asian and Eastern North American disjunct Suillus species (fungi) as inferred from nuclear ribosomal RNA its sequences.
          • Molecular Phylogenetics and Evolution
          • ,
          • 17
          • (1)
          • ,
          • 37-47.
          • [web]
          Publication Description

          Species of Suillus produce fleshy, pored mushrooms. They are important symbiotic (ectomycorrhizal) partners of many coniferous trees. The genus includes several putative eastern Asian and eastern North American disjunct species, i.e., the S. americanus-S. sibiricus and S. decipiens-S. spraguei complexes. Phylogenetic relationships among the groups were determined to further understand the biogeographic pattern. Analyses were based on 40 sequences of the ITS region of the nuclear ribosomal RNA tandem repeats, representing 18 distinct species/populations. Our phylogenetic analyses suggested that: (1) Chinese and United States' (U.S.) S. spraguei plus S. decipiens form a strongly supported monophyletic group, with North American S. decipiens and Chinese S. spraguei being sister taxa; (2) S. americanus, Asian and U.S. S. sibiricus, plus S. umbonatus form a clade supported by a high bootstrap value; and (3) little ITS sequence divergence exists within the latter group compared to the S. decipiens-S. spraguei clade. Phylogenetic patterns revealed by this Study imply a close phylogenetic relationship between eastern Asian and eastern North American disjunct population/species of Suillus. These fungi display relatively high host fidelity (at least to the host subgenus level), suggesting potential coevolutionary/comigratory trends. (C) 2000 Academic Press.

          • S Zoller, F Lutzoni and C Scheidegger.
          • (1999).
          • Genetic variation within and among populations of the threatened lichen Lobaria pulmonaria in Switzerland and implications for its conservation.
          • Molecular Ecology
          • ,
          • 8
          • (12)
          • ,
          • 2049-2059.
          • [web]
          Publication Description

          The foliose epiphytic lichen Lobaria pulmonaria has suffered a significant decline in European lowlands during the last decades and therefore is considered as endangered throughout Europe. An assessment of the genetic variability is necessary to formulate biologically sound conservation recommendations for this species. We investigated the genetic diversity of the fungal symbiont of L. pulmonaria using 143 specimens sampled from six populations (two small, one medium, three large) in the lowland, the Jura Mountains, the pre-Alps and the Alps of Switzerland. Among all nuclear and mitochondrial regions sequenced for this study, variability was found only in the internal transcribed spacer (ITS I), with three polymorphic sites, and in the nuclear ribosomal large subunit (nrLSU), with four polymorphic sites. The variable sites in the nrLSU are all located within a putative spliceosomal intron. We sequenced these two regions for 81 specimens and detected six genotypes. Two genotypes were common, two were found only in the more diverse populations and two were found only in one population each. There was no correlation between population size and genetic diversity. The highest genetic diversity was found in populations where the fungal symbiont is reproducing sexually. Populations with low genetic diversity included only the two same common genotypes. Our study provides evidence suggesting that L. pulmonaria is self-incompatible and heterothallic. Based on our results we give populations with sexually reproducing individuals a higher rank in terms of conservation priority than strictly asexual populations. The remaining lowland populations are so small, that one single catastrophic event such as a windthrow might destroy the entire population. Hence we suggest augmenting such populations in size and genetic diversity using small thallus fragments or vegetative diaspores collected in other populations. As we did not detect any locally adapted genotypes, these transplants can be taken from any other genetically diverse population in Switzerland.

          • FA Fernández, FM Lutzoni and SM Huhndorf.
          • (1999).
          • Teleomorph-anamorph connections: The new pyrenomycetous genus Carpoligna and its Pleurothecium anamorph.
          • Mycologia
          • ,
          • 91
          • (2)
          • ,
          • 251-262.
          Publication Description

          Several collections of a pyrenomycete identified as Chaetosphaeria were made from decorticated wood of twigs and branches in Costa Rica, Panama, Puerto Rico and continental USA. Discrete and continuous characters of the ascomata, asci and ascospores in these collections show that they are very similar morphologically and represent populations of the same species. However, culturing of single ascospore isolates from these collections yielded an anamorph unlike the typical phialidic anamorphs of Chaetosphaeria. This anamorph fits the description of Pleurothecium recurvatum, for which a teleomorph connection has not been yet established. Sequences of the ITS region of the nuclear ribosomal DNA of three collections from Costa Rica, Puerto Rico and USA were compared and found to be 98% similar. Parsimony and maximum likelihood analyses of sequences of the large subunit nuclear-encoded ribosomal DNA from representative taxa of eight ascomycetous orders show this ascomycete as a monophyletic group distinct from Chaetosphaeria. Statistical analyses of hypothetical trees based on the most parsimonious and the most likely trees rule out phylogenetic affinities of this pyrenomycete to Chaetosphaeria. These analyses suggest possible affinities to the Hypocreales and/or the Microascales. Based on morphology of the anamorph and analyses of ribosomal DNA sequence data, Carpoligna pleurothecii gen. et sp. nov. are described. The implications of the phylogenetic relationships of Carpoligna in the practical identification of morphologically similar pyrenomycetes are discussed.

          • F Lutzoni and FK Barker.
          • (1999).
          • Sampling confidence envelopes of phylogenetic trees for combinability testing: A reply to Rodrigo.
          • Systematic Biology
          • ,
          • 48
          • (3)
          • ,
          • 596-603.
          • S Zoller, F Lutzoni and C Scheidegger.
          • (1999).
          • Genetic variability within and among populations of the threatened foliose lichen Lobaria pulmonaria (L.).
          • Molecular Ecology
          • ,
          • 8
          • ,
          • 2049-2060.
          • Hoffm. in Switzerland..
          • F Lutzoni and M Pagel.
          • (1997).
          • Accelerated evolution as a consequence of transitions to mutualism..
          • Proc Natl Acad Sci U S A
          • ,
          • 94
          • (21)
          • ,
          • 11422-11427.
          • [web]
          Publication Description

          Differential rates of nucleotide substitutions among taxa are a common observation in molecular phylogenetic studies, yet links between rates of DNA evolution and traits or behaviors of organisms have proved elusive. Likelihood ratio testing is used here for the first time to evaluate specific hypotheses that account for the induction of shifts in rates of DNA evolution. A molecular phylogenetic investigation of mutualist (lichen-forming fungi and fungi associated with liverworts) and nonmutualist fungi revealed four independent transitions to mutualism. We demonstrate a highly significant association between mutualism and increased rates of nucleotide substitutions in nuclear ribosomal DNA, and we demonstrate that a transition to mutualism preceded the rate acceleration of nuclear ribosomal DNA in these lineages. Our results suggest that the increased rate of evolution after the adoption of a mutualist lifestyle is generalized across the genome of these mutualist fungi.

          • FM Lutzoni.
          • (1997).
          • Phylogeny of lichen- and non-lichen-forming omphalinoid mushrooms and the utility of testing for combinability among multiple data sets..
          • Syst Biol
          • ,
          • 46
          • (3)
          • ,
          • 373-406.
          • (journal cover)
          • [web]
          Publication Description

          As an initial step toward developing a model system to study requirements for and consequences of transitions to mutualism, the phylogeny of a group of closely related lichenized and nonlichenized basidiomycetes (Omphalina) was reconstructed. The phylogenetic analyses are based on four data sets representing different regions of the nuclear ribosomal repeat unit (ITS1, 5.8S, ITS2, and 25S) obtained from 30 species of Omphalina and related genera. The resulting phylogenetic trees from each of these four data sets, when analyzed separately, were not identical. Testing for the combinability of these four data sets suggested that they could not be combined in their entirety. The removal of ambiguous alignments and saturated sites was sufficient, after reapplying the combinability test on the pruned data sets, to explain the topological discrepancies. In this process, the first of two complementary tests developed by Rodrigo et al. (1993, N.Z. J. Bot. 31:257-268) to assess whether two data sets are the result of the same phylogenetic history was found to be biased, rejecting the combinability of two data sets even when they are samples of the same phylogenetic history. Combining the four pruned data sets yielded phylogenies that suggest the five lichen-forming species of Omphalina form a monophyletic group. The sister group to this symbiotic clade consists mostly of dark brown Omphalina species intermixed with species from the genera Arrhenia and Phaeothellus. The genera Omphalina and Gerronema are shown to be polyphyletic. The lichen-forming species O. ericetorum and the nonmutualistic species O. velutipes, O. epichysium, and O. sphagnicola are the best candidates for experimental work designed to gain a better understanding of mechanisms involved in symbiotic interactions and the role symbiosis has played in the evolution of fungi.

          • F Lutzoni and R Vilgalys.
          • (1995a).
          • ntegration of morphological and molecular datasets in estimating fungal phylogenies.
          • Canadian Journal of Botany
          • ,
          • 73(Suppl. 1)
          • ,
          • S649-S659.
          • FM Lutzoni and IM Brodo.
          • (1995).
          • A generic redelimitation of the Ionaspis-Hymenelia complex (lichenized ascomycotina).
          • Systematic Botany
          • ,
          • 20
          • (3)
          • ,
          • 224-258.
          • F Lutzoni and R Vilgalys.
          • (1995b).
          • Omphalina (Basidiomycota, Agaricales) as a model system for the study of coevolution in lichenized fungi.
          • Special Issue of Cryptogamic Botany
          • ,
          • 5
          • ,
          • 82-97.
          • FM Lutzoni and IM Brodo.
          • (1994).
          • Proposal to conserve the name Gyalecta suaveolens Fr. (lichenized Ascomycota) with a conserved type.
          • Taxon
          • ,
          • 43
          • (4)
          • ,
          • 657-659.
          • FM Lutzoni.
          • (1994).
          • Ionaspis alba (Ascomycotina, Hymeneliaceae), a new lichen species from eastern North America.
          • Bryologist
          • ,
          • 97
          • (4)
          • ,
          • 393-395.
          • MM Grandtner and F Lutzoni.
          • (1991).
          • References on the vegetation of Québec.
          • Excerpta Botanica Sec. B. Bd
          • ,
          • 29
          • (1)
          • ,
          • 1-24.
          • L Sirois, F Lutzoni and MM Grandtner.
          • (1988).
          • Les lichens sur serpentine et amphibolite du plateau du mont Albert, Gaspésie, Québec.
          • Canadian Journal of Botany
          • ,
          • 66
          • (5)
          • ,
          • 851-862.
          Publication Description

          At Mount Albert, many taxa are found exclusively on either serpentine or amphibolite contiguous formations, and are exclusively more noticeable within saxicolous lichens. There are more infrequent taxa on serpentine than on amphibolite. The saxicolous, muscicolous, and terricolous lichen flora and the lichenicolous fungi of the plateau include 202 taxa, most of which have an arctic affinity. Of these taxa, 36 are recorded for the first time in Quebec, 16 in Canada and 11 in North America. -from English summary

          • L Sirois, F Lutzoni and MM Grandtner.
          • (1988).
          • Lichens on serpentine and amphibolite on the plateau of Mt. Albert, Gaspesie, Quebec.
          • Canadian Journal of Botany
          • ,
          • 66
          • (5)
          • ,
          • 851-862.
          Publication Description

          At Mount Albert, many taxa are found exclusively on either serpentine or amphibolite contiguous formations, and are exclusively more noticeable within saxicolous lichens. There are more infrequent taxa on serpentine than on amphibolite. The saxicolous, muscicolous, and terricolous lichen flora and the lichenicolous fungi of the plateau include 202 taxa, most of which have an arctic affinity. Of these taxa, 36 are recorded for the first time in Quebec, 16 in Canada and 11 in North America. -from English summary

      • Papers Accepted

          • BP Hodkinson, JL Allen, L Forrest, B Goffinet, E Sérusiaux, ÓS Andrésson, V Miao, JP Bellenger and F Lutzoni.
          • (2014).
          • Lichen-symbiotic Cyanobacteria have an alternative vanadium-dependent nitrogen fixation system.
          • New Phytologist
          • .
      • Papers Submitted

          • R Darnajoux, J Constantin, J Miadlikowska, F Lutzoni and J-P Bellenger.
          • (2014).
          • Is vanadium a biometal for boreal cyanolichens?.
          • New Phytologist
          • ,
          • 202
          • (3)
          • ,
          • 765-771.
          • [web]
          • Oono, R., Lutzoni, F., Arnold, A. E., Kaye, L., U’ren, J. M., May, G., Carbone, I..
          • (2014).
          • Genetic variation in horizontally transmitted symbionts of pine needles reveals population structure in cryptic species.
          • American Naturalist
          • .
          • Miadlikowska, J., Kauff, F., Högnabba, F., Oliver, J. C., Molnár, K., Fraker, E., Gaya, E., Hafellner, J., Hofstetter, V., Gueidan, C., Kukwa, M., Lücking, M., Björk, C., Sipman, H. J. M., Burgaz, A. R., Thell, A., Passo, A., Myllys, L., Goward, T., Fernández-Brime, S., Hestmark, G., Lendemer, J., Lumbsch, H. T., Schmull, M., Schoch, C., Sérusiaux, E., Maddison, D. R., Arnold, A. E., Stenroos, S. and Lutzoni, F..
          • (2014).
          • Multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 312 genera and 66 families.
          • Molecular Phylogenetics and Evolution
          • .
      • Book Chapters

          • C Gueidan, DJ Hill, J Miadlikowska and F Lutzoni.
          • (2014).
          • Pezizomycotina: Lecanoromycetes.
          • The Mycota: A Comprehensive Treatise on Fungi As Experimental Systems for Basic and Applied Research: VII Systematics and Evolution Part B 2nd Edition
          • D. J. McLaughlin and J. W. Spatafora (Eds.),
          • Volume VII of The Mycota Part B
          • ,
          • 89-120.
          • Berlin, Germany:
          • Springer Verlag.
          • [web]
          Publication Description

          © Springer-Verlag Berlin Heidelberg 2015.Lecanoromycetes is the class of Ascomycota with the largest number of lichen-forming fungi. Members of this class are important components of most terrestrial ecosystems and occur in various habitats and on different substrates, from tropical to polar regions. Morphological, anatomical, and chemical characters have traditionally been used to classify orders, families, and genera within Lecanoromycetes. In the last two decades, molecular phylogenies have shown that traditional classification systems were not always consistent with the evolutionary history of this fungal class, resulting in changes in the delimitation of orders and families. Here, we revisit the taxonomic value of the main characters traditionally used for classification in light of current molecular phylogenies. The current delimitation of the 14 orders of Lecanoromycetes is also discussed, and recent changes in classification are highlighted.

          • F LUTZONI and R VILGALYS.
          • (1995).
          • INTEGRATION OF MORPHOLOGICAL AND MOLECULAR-DATA SETS IN ESTIMATING FUNGAL PHYLOGENIES.
          • CANADIAN JOURNAL OF BOTANY-REVUE CANADIENNE DE BOTANIQUE
          • ,
          • 73
          • ,
          • S649-S659.
          • [web]
      • Book Reviews

          • Lutzoni, F. [Review] Stefan Ekman in Opera Botanica 127, 148 pp., 1996..
          • (1999).
          • The corticolous and lignicolous species of Bacidia and Bacidina in North America.
          • The Bryologist
          • ,
          • 102
          • ,
          • 165-166.

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