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  • 1.
    Badou, Sylvestre A.
    et al.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    De Kesel, Andre
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium.
    Raspe, Olivier
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium;Federat Wallonie Bruxelles, Rue A Lavallee 1, B-1080 Brussels, Belgium.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Guelly, Atsu K.
    Univ Lome, Fac Sci, Dept Bot & Ecol Vegetale, BP1515, Lome, Togo.
    Yorou, Nourou S.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    Two new African siblings of Pulveroboletus ravenelii (Boletaceae)2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 43, p. 115-130Article in journal (Refereed)
    Abstract [en]

    This paper sorts out the taxonomy of species affiliated with Pulveroboletus ravenelii in the Guineo-soudanian and Zambezian woodlands of Africa. Morphological and genetic characters of African Pulveroboletus collections were studied and compared to those of North American and Asian species. A phylogenetic analysis showed that the African specimens form a subclade, sister to the Asian and American taxa. Although clamp connections have previously never been reported from Pulveroboletus, all specimens of the African subclade show very small clamp connections. Two new African species, Pulveroboletus africanus sp. nov. and P. sokponianus sp. nov., are described and illustrated. Comments concerning morphology and identification, as well as distribution and ecology, are given for both species.

  • 2.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hildebrand, Falk
    Forslund, Sofia K
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Soudzilovskaia, Nadejda A
    Bodegom, Peter M
    Bengtsson-Palme, Johan
    Anslan, Sten
    Coelho, Luis Pedro
    Harend, Helery
    Huerta-Cepas, Jaime
    Medema, Marnix H
    Maltz, Mia R
    Mundra, Sunil
    Olsson, Pål Axel
    Pent, Mari
    Põlme, Sergei
    Sunagawa, Shinichi
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Bork, Peer
    Structure and function of the global topsoil microbiome.2018In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 560, no 7717, p. 233-237Article in journal (Refereed)
    Abstract [en]

    Soils harbour some of the most diverse microbiomes on Earth and are essential for both nutrient cycling and carbon storage. To understand soil functioning, it is necessary to model the global distribution patterns and functional gene repertoires of soil microorganisms, as well as the biotic and environmental associations between the diversity and structure of both bacterial and fungal soil communities1-4. Here we show, by leveraging metagenomics and metabarcoding of global topsoil samples (189 sites, 7,560 subsamples), that bacterial, but not fungal, genetic diversity is highest in temperate habitats and that microbial gene composition varies more strongly with environmental variables than with geographic distance. We demonstrate that fungi and bacteria show global niche differentiation that is associated with contrasting diversity responses to precipitation and soil pH. Furthermore, we provide evidence for strong bacterial-fungal antagonism, inferred from antibiotic-resistance genes, in topsoil and ocean habitats, indicating the substantial role of biotic interactions in shaping microbial communities. Our results suggest that both competition and environmental filtering affect the abundance, composition and encoded gene functions of bacterial and fungal communities, indicating that the relative contributions of these microorganisms to global nutrient cycling varies spatially.

  • 3. Bahram, Mohammad
    et al.
    Kõljalg, Urmas
    Courty, Pierre-Emmanuel
    Diédhiou, Abdala G.
    Kjøller, Rasmus
    Põlme, Sergei
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Veldre, Vilmar
    Tedersoo, Leho
    The distance decay of similarity in communities of ectomycorrhizal fungi in different ecosystems and scales2013In: Journal of Ecology, ISSN 0022-0477, E-ISSN 1365-2745, Vol. 101, no 5, p. 1335-1344Article in journal (Refereed)
    Abstract [en]

    Despite recent advances in understanding community ecology of ectomycorrhizal fungi, little is known about their spatial patterning and the underlying mechanisms driving these patterns across different ecosystems. * This meta-study aimed to elucidate the scale, rate and causes of spatial structure of ectomycorrhizal fungal communities in different ecosystems by analysing 16 and 55 sites at the local and global scales, respectively. We examined the distance decay of similarity relationship in species- and phylogenetic lineage-based communities in relation to sampling and environmental variables. * Tropical ectomycorrhizal fungal communities exhibited stronger distance-decay patterns compared to non-tropical communities. Distance from the equator and sampling area were the main determinants of the extent of distance decay in fungal communities. The rate of distance decay was negatively related to host density at the local scale. At the global scale, lineage-level community similarity decayed faster with latitude than with longitude. * Synthesis. Spatial processes play a stronger role and over a greater scale in structuring local communities of ectomycorrhizal fungi than previously anticipated, particularly in ecosystems with greater vegetation age and closer to the equator. Greater rate of distance decay occurs in ecosystems with lower host density that may stem from increasing dispersal and establishment limitation. The relatively strong latitude effect on distance decay of lineage-level community similarity suggests that climate affects large-scale spatial processes and may cause phylogenetic clustering of ectomycorrhizal fungi at the global scale.

  • 4.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden.
    Vanderpool, Dan
    Univ Montana, Div Biol Sci, 32 Campus Dr, Missoula, MT 59812 USA.
    Pent, Mari
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Hiltunen, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics2018In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 2, p. 155-166Article in journal (Refereed)
    Abstract [en]

    Recent advances in molecular methods have increased our understanding of various fungal symbioses. However, little is known about genomic and microbiome features of most uncultured symbiotic fungal clades. Here, we analysed the genome and microbiome of Inocybaceae (Agaricales, Basidiomycota), a largely uncultured ectomycorrhizal clade known to form symbiotic associations with a wide variety of plant species. We used metagenomic sequencing and assembly of dikaryotic fruiting-body tissues from Inocybe terrigena (Fr.) Kuyper, to classify fungal and bacterial genomic sequences, and obtained a nearly complete fungal genome containing 93% of core eukaryotic genes. Comparative genomics reveals that I. terrigena is more similar to ectomycorrhizal and brown rot fungi than to white rot fungi. The reduction in lignin degradation capacity has been independent from and significantly faster than in closely related ectomycorrhizal clades supporting that ectomycorrhizal symbiosis evolved independently in Inocybe. The microbiome of I. terrigena fruiting-bodies includes bacteria with known symbiotic functions in other fungal and non-fungal host environments, suggesting potential symbiotic functions of these bacteria in fungal tissues regardless of habitat conditions. Our study demonstrates the usefulness of direct metagenomics analysis of fruiting-body tissues for characterizing fungal genomes and microbiome.

  • 5. Bengtsson-Palme, Johan
    et al.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hartmann, Martin
    Branco, Sara
    Wang, Zheng
    Godhe, Anna
    De Wit, Pierre
    Sanchez-Garcia, Marisol
    Ebersberger, Ingo
    de Sousa, Filipe
    Amend, Anthony S.
    Jumpponen, Ari
    Unterseher, Martin
    Kristiansson, Erik
    Abarenkov, Kessy
    Bertrand, Yann J. K.
    Sanli, Kemal
    Eriksson, K. Martin
    Vik, Unni
    Veldre, Vilmar
    Nilsson, R. Henrik
    Improved software detection and extraction of ITS1 and ITS2 from ribosomal ITS sequences of fungi and other eukaryotes for analysis of environmental sequencing data2013In: Methods in Ecology and Evolution, ISSN 2041-210X, E-ISSN 2041-210X, Vol. 4, no 10, p. 914-919Article in journal (Refereed)
    Abstract [en]

    The nuclear ribosomal internal transcribed spacer (ITS) region is the primary choice for molecular identification of fungi. Its two highly variable spacers (ITS1 and ITS2) are usually species specific, whereas the intercalary 5.8S gene is highly conserved. For sequence clustering and blast searches, it is often advantageous to rely on either one of the variable spacers but not the conserved 5.8S gene. To identify and extract ITS1 and ITS2 from large taxonomic and environmental data sets is, however, often difficult, and many ITS sequences are incorrectly delimited in the public sequence databases. We introduce ITSx, a Perl-based software tool to extract ITS1, 5.8S and ITS2 - as well as full-length ITS sequences - from both Sanger and high-throughput sequencing data sets. ITSx uses hidden Markov models computed from large alignments of a total of 20 groups of eukaryotes, including fungi, metazoans and plants, and the sequence extraction is based on the predicted positions of the ribosomal genes in the sequences. ITSx has a very high proportion of true-positive extractions and a low proportion of false-positive extractions. Additionally, process parallelization permits expedient analyses of very large data sets, such as a one million sequence amplicon pyrosequencing data set. ITSx is rich in features and written to be easily incorporated into automated sequence analysis pipelines. ITSx paves the way for more sensitive blast searches and sequence clustering operations for the ITS region in eukaryotes. The software also permits elimination of non-ITS sequences from any data set. This is particularly useful for amplicon-based next-generation sequencing data sets, where insidious non-target sequences are often found among the target sequences. Such non-target sequences are difficult to find by other means and would contribute noise to diversity estimates if left in the data set.

  • 6. Birkebak, Joshua M
    et al.
    Mayor, Jordan R
    Ryberg, Martin
    Department of Ecology and Evolutionary Biology, University of Tennessee.
    Matheny, P Brandon
    A systematic, morphological and ecological overview of the Clavariaceae (Agaricales).2013In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 105, no 4, p. 896-911Article in journal (Refereed)
    Abstract [en]

    The Clavariaceae is a diverse family of mushroom-forming fungi composed of species that produce simple clubs, coralloid, lamellate-stipitate, hydnoid and resupinate sporocarps. Here we present a systematic and ecological overview of the Clavariaceae based on phylogenetic analysis of sequences of the nuclear large subunit ribosomal RNA (nLSU), including nine from type collections. Forty-seven sequences from sporocarps of diverse taxa across the Clavariaceae were merged with 243 environmental sequences from GenBank and analyzed phylogenetically to determine major clades within the family. Four major clades or lineages were recovered: (i) Mucronella, (ii) Ramariopsis-Clavulinopsis, (iii) Hyphodontiella and (iv) Clavaria-Camarophyllopsis-Clavicorona. Clavaria is paraphyletic, within which the lamellate and pileate-stipitate genus Camarophyllopsis is derived and composed of two independent lineages. The monotypic genus Clavicorona also appears nested within Clavaria. The monophyly of Clavaria and Camarophyllopsis, however, cannot be statistically rejected. We compared differing classification schemes for the genera Ramariopsis and Clavulinopsis, most of which are inconsistent with the molecular phylogeny and are statistically rejected. Scytinopogon, a genus classified in the Clavariaceae by several authors, shares phylogenetic affinities with the Trechisporales. Overall 126 molecular operational taxonomic units can be recognized in the Clavariaceae, roughly half of which are known only from environmental sequences, an estimate that exceeds the known number of species in the family. Stable isotope ratios of carbon and nitrogen were measured from specimens representing most major phylogenetic lineages to predict trophic strategies. These results suggest that most non-lignicolous species feature a biotrophic mode of nutrition. Ancestral state reconstruction analysis highlights the taxonomic significance of at least nine morphological traits at various depths in the family tree.

  • 7. Henrik Nilsson, R.
    et al.
    Ryberg, Martin
    Sjökvist, Elisabet
    Abarenkov, Kessy
    Rethinking taxon sampling in the light of environmental sequencing2011In: Cladistics, ISSN 0748-3007, E-ISSN 1096-0031, Vol. 27, no 2, p. 197-203Article in journal (Refereed)
  • 8.
    Herrmann, Björn
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Isaksson, Jenny
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tangrot, Jeanette
    Saleh, Isam
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine, Clinical Bacteriology.
    Versteeg, Bart
    Gravningen, Kirsten
    Bruisten, Sylvia
    Global Multilocus Sequence Type Analysis of Chlamydia trachomatis Strains from 16 Countries2015In: Journal of Clinical Microbiology, ISSN 0095-1137, E-ISSN 1098-660X, Vol. 53, no 7, p. 2172-2179Article in journal (Refereed)
    Abstract [en]

    The Uppsala University Chlamydia trachomatis multilocus sequence type (MLST) database (http://mlstdb.bmc.uu.se) is based on five target regions (non-housekeeping genes) and the ompA gene. Each target has various numbers of alleles-hctB, 89; CT058, 51; CT144, 30; CT172, 38; and pbpB, 35-derived from 13 studies. Our aims were to perform an overall analysis of all C. trachomatis MLST sequence types (STs) in the database, examine STs with global spread, and evaluate the phylogenetic capability by using the five targets. A total of 415 STs were recognized from 2,089 specimens. The addition of 49 ompA gene variants created 459 profiles. ST variation and their geographical distribution were characterized using eBURST and minimum spanning tree analyses. There were 609 samples from men having sex with men (MSM), with 4 predominating STs detected in this group, comprising 63% of MSM cases. Four other STs predominated among 1,383 heterosexual cases comprising, 31% of this group. The diversity index in ocular trachoma cases was significantly lower than in sexually transmitted chlamydia infections. Predominating STs were identified in 12 available C. trachomatis whole genomes which were compared to 22 C. trachomatis full genomes without predominating STs. No specific gene in the 12 genomes with predominating STs could be linked to successful spread of certain STs. Phylogenetic analysis showed that MLST targets provide a tree similar to trees based on whole-genome analysis. The presented MLST scheme identified C. trachomatis strains with global spread. It provides a tool for epidemiological investigations and is useful for phylogenetic analyses.

  • 9.
    Hiltunen, Markus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Grudzinska-Sterno, Magdalena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Wallerman, Ola
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Maintenance of High Genome Integrity over Vegetative Growth in the Fairy-Ring Mushroom Marasmius oreades2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 16, p. 2758-2765Article in journal (Refereed)
    Abstract [en]

    Most mutations in coding regions of the genome are deleterious, causing selection to favor mechanisms that minimize the mutational load over time [1-5]. DNA replication during cell division is a major source of new mutations. It is therefore important to limit the number of cell divisions between generations, particularly for large and long-lived organisms [6-9]. The germline cells of animals and the slowly dividing cells in plant meristems are adaptations to control the number of mutations that accumulate over generations [9-11]. Fungi lack a separated germline while harboring species with very large and long-lived individuals that appear to maintain highly stable genomes within their mycelia [8, 12, 13]. Here, we studied genomic mutation accumulation in the fairy-ring mushroom Marasmius oreades. We generated a chromosome-level genome assembly using a combination of cutting-edge DNA sequencing technologies and resequenced 40 samples originating from six individuals of this fungus. The low number of mutations recovered in the sequencing data suggests the presence of an unknown mechanism that works to maintain extraordinary genome integrity over vegetative growth in M. oreades. The highly structured growth pattern of M. oreades allowed us to estimate the number of cell divisions leading up to each sample [14, 15], and from this data, we infer an incredibly low per mitosis mutation rate (3.8 x 10(-12) mutations per site and cell division) as one of several possible explanations for the low number of identified mutations.

  • 10. Hyde, Kevin D
    et al.
    Udayanga, Dhanushka
    Manamgoda, Dimuthu S
    Tedersoo, Leho
    Larsson, Ellen
    Göteborgs Universitet.
    Abarenkov, Kessy
    Bertrand, Yann JK
    Göteborgs Universitet.
    Oxelman, Bengt
    Göteborgs Universitet.
    Hartmann, Martin
    Kauserud, Håvard
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kristiansson, Erik
    Nilsson, R. Henrik
    Göteborgs Universitet.
    Incorporating molecular data in fungal systematics: a guide for aspiring researchers2013In: Current Research in Environmental & Applied Mycology, ISSN 2229-2225, Vol. 3, no 1, p. 1-32Article in journal (Refereed)
  • 11. Kennedy, Peter G
    et al.
    Matheny, P B
    Ryberg, Martin
    Henkel, Terry W
    Uehling, Jessie K
    Smith, Matthew E
    Scaling up: examining the macroecology of ectomycorrhizal fungi.2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 17, p. 4151-4Article in journal (Refereed)
    Abstract [en]

    Ectomycorrhizal (ECM) fungi play major ecological roles in temperate and tropical ecosystems. Although the richness of ECM fungal communities and the factors controlling their structure have been documented at local spatial scales, how they vary at larger spatial scales remains unclear. In this issue of Molecular Ecology, Tedersoo et al. (2012) present the results of a meta-analysis of ECM fungal community structure that sheds important new light on global-scale patterns. Using data from 69 study systems and 6021 fungal species, the researchers found that ECM fungal richness does not fit the classic latitudinal diversity gradient in which species richness peaks at lower latitudes. Instead, richness of ECM fungal communities has a unimodal relationship with latitude that peaks in temperate zones. Intriguingly, this conclusion suggests the mechanisms driving ECM fungal community richness may differ from those of many other organisms, including their plant hosts. Future research will be key to determine the robustness of this pattern and to examine the processes that generate and maintain global-scale gradients of ECM fungal richness.

  • 12. Kosentka, Pawel
    et al.
    Sprague, Sarah L
    Ryberg, Martin
    Department of Ecology and Evolutionary Biology, University of Tennessee.
    Gartz, Jochen
    May, Amanda L
    Campagna, Shawn R
    Matheny, P Brandon
    Evolution of the toxins muscarine and psilocybin in a family of mushroom-forming fungi.2013In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 8, no 5, p. e64646-Article in journal (Refereed)
    Abstract [en]

    Mushroom-forming fungi produce a wide array of toxic alkaloids. However, evolutionary analyses aimed at exploring the evolution of muscarine, a toxin that stimulates the parasympathetic nervous system, and psilocybin, a hallucinogen, have never been performed. The known taxonomic distribution of muscarine within the Inocybaceae is limited, based only on assays of species from temperate regions of the northern hemisphere. Here, we present a review of muscarine and psilocybin assays performed on species of Inocybaceae during the last fifty years. To supplement these results, we used liquid chromatography-tandem mass spectrometry (LC-MS/MS) to determine whether muscarine was present in 30 new samples of Inocybaceae, the majority of which have not been previously assayed or that originated from either the tropics or temperate regions of the southern hemisphere. Our main objective is to test the hypothesis that the presence of muscarine is a shared ancestral feature of the Inocybaceae. In addition, we also test whether species of Inocyabceae that produce psilocybin are monophyletic. Our findings suggest otherwise. Muscarine has evolved independently on several occasions, together with several losses. We also detect at least two independent transitions of muscarine-free lineages to psilocybin-producing states. Although not ancestral for the family as a whole, muscarine is a shared derived trait for an inclusive clade containing three of the seven major lineages of Inocybaceae (the Inocybe, Nothocybe, and Pseudosperma clades), the common ancestor of which may have evolved ca. 60 million years ago. Thus, muscarine represents a conserved trait followed by several recent losses. Transitions to psilocybin from muscarine-producing ancestors occurred more recently between 10-20 million years ago after muscarine loss in two separate lineages. Statistical analyses firmly reject a single origin of muscarine-producing taxa.

  • 13.
    Liu, Jian-Kui
    et al.
    Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Peoples R China.;Guizhou Acad Agr Sci, Guizhou Inst Biotechnol, Guiyang 550006, Peoples R China.;Guizhou Acad Agr Sci, Guizhou Key Lab Agr Biotechnol, Guiyang 550006, Peoples R China..
    Hyde, Kevin D.
    Mae Fah Luang Univ, Ctr Excellence Fungal Res, Chiang Rai 57100, Thailand..
    Jeewon, Rajesh
    Univ Mauritius, Fac Sci, Dept Hlth Sci, Reduit, Mauritius..
    Phillips, Alan J. L.
    Univ Lisbon, Fac Sci, Biosyst & Integrat Sci Inst, P-1749016 Lisbon, Portugal..
    Maharachchikumbura, Sajeewa S. N.
    Sultan Qaboos Univ, Coll Agr & Marine Sci, Dept Crop Sci, POB 8, Al Khoud 123, Oman..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Liu, Zuo-Yi
    Guizhou Acad Agr Sci, Guizhou Key Lab Agr Biotechnol, Guiyang 550006, Peoples R China..
    Zhao, Qi
    Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Peoples R China..
    Ranking higher taxa using divergence times: a case study in Dothideomycetes2017In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 84, no 1, p. 75-99Article in journal (Refereed)
    Abstract [en]

    The current classification system for the recognition of taxonomic ranks among fungi, especially at high-ranking level, is subjective. With the development of molecular approaches and the availability of fossil calibration data, the use of divergence times as a universally standardized criterion for ranking taxa has now become possible. We can therefore date the origin of Ascomycota lineages by using molecular clock methods and establish the divergence times for the orders and families of Dothideomycetes. We chose Dothideomycetes, the largest class of the phylum Ascomycota, which contains 32 orders, to establish ages at which points orders have split; and Pleosporales, the largest order of Dothideomycetes with 55 families, to establish family divergence times. We have assembled a multi-gene data set (LSU, SSU, TEF1 and RPB2) from 391 taxa representing most family groups of Dothideomycetes and utilized fossil calibration points solely from within the ascomycetes and a Bayesian approach to establish divergence times of Dothideomycetes lineages. Two separated datasets were analysed: (i) 272 taxa representing 32 orders of Dothideomycetes were included for the order level analysis, and (ii) 191 taxa representing 55 families of Pleosporales were included for the family level analysis. Our results indicate that divergence times (crown age) for most orders (20 out of 32, or 63%) are between 100 and 220 Mya, while divergence times for most families (39 out of 55, or 71%) are between 20 and 100 Mya. We believe that divergence times can provide additional evidence to support establishment of higher level taxa, such as families, orders and classes. Taking advantage of this added approach, we can strive towards establishing a standardized taxonomic system both within and outside Fungi. In this study we found that molecular dating coupled with phylogenetic inferences provides no support for the taxonomic status of two currently recognized orders, namely Bezerromycetales and Wiesneriomycetales and these are treated as synonyms of Tubeufiales while Asterotexiales is treated as a synonym of Asterinales. In addition, we provide an updated phylogenetic assessment of Dothideomycetes previously published as the Families of Dothideomycetes in 2013 with a further ten orders and 35 families.

  • 14.
    Looney, Brian P.
    et al.
    Univ Tennessee, Dept Ecol & Evolutionary Biol, 332 Hesler Biol Bldg, Knoxville, TN 37996 USA..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hampe, Felix
    Univ Ghent, Dept Biol, KL Ledeganckstr 35, B-9000 Ghent, Belgium..
    Sanchez-Garcia, Marisol
    Univ Tennessee, Dept Ecol & Evolutionary Biol, 332 Hesler Biol Bldg, Knoxville, TN 37996 USA..
    Matheny, P. Brandon
    Univ Tennessee, Dept Ecol & Evolutionary Biol, 332 Hesler Biol Bldg, Knoxville, TN 37996 USA..
    Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 630-647Article in journal (Refereed)
    Abstract [en]

    Ectomycorrhizal (ECM) fungi, symbiotic mutualists of many dominant tree and shrub species, exhibit a biogeographic pattern counter to the established latitudinal diversity gradient of most macroflora and fauna. However, an evolutionary basis for this pattern has not been explicitly tested in a diverse lineage. In this study, we reconstructed a mega-phylogeny of a cosmopolitan and hyperdiverse genus of ECM fungi, Russula, sampling from annotated collections and utilizing publically available sequences deposited in GenBank. Metadata from molecular operational taxonomic unit cluster sets were examined to infer the distribution and plant association of the genus. This allowed us to test for differences in patterns of diversification between tropical and extratropical taxa, as well as how their associations with different plant lineages may be a driver of diversification. Results show that Russula is most species-rich at temperate latitudes and ancestral state reconstruction shows that the genus initially diversified in temperate areas. Migration into and out of the tropics characterizes the early evolution of the genus, and these transitions have been frequent since this time. We propose the generalized diversification rate' hypothesis to explain the reversed latitudinal diversity gradient pattern in Russula as we detect a higher net diversification rate in extratropical lineages. Patterns of diversification with plant associates support host switching and host expansion as driving diversification, with a higher diversification rate in lineages associated with Pinaceae and frequent transitions to association with angiosperms.

  • 15. Nilsson, R. Henrik
    et al.
    Hyde, Kevin D.
    Pawlowska, Julia
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Aas, Anders Bjornsgard
    Alias, Siti A.
    Alves, Artur
    Anderson, Cajsa Lisa
    Antonelli, Alexandre
    Arnold, A. Elizabeth
    Bahnmann, Barbara
    Bahram, Mohammad
    Bengtsson-Palme, Johan
    Berlin, Anna
    Branco, Sara
    Chomnunti, Putarak
    Dissanayake, Asha
    Drenkhan, Rein
    Friberg, Hanna
    Froslev, Tobias Guldberg
    Halwachs, Bettina
    Hartmann, Martin
    Henricot, Beatrice
    Jayawardena, Ruvishika
    Jumpponen, Ari
    Kauserud, Havard
    Koskela, Sonja
    Kulik, Tomasz
    Liimatainen, Kare
    Lindahl, Bjorn D.
    Lindner, Daniel
    Liu, Jian-Kui
    Maharachchikumbura, Sajeewa
    Manamgoda, Dimuthu
    Martinsson, Svante
    Neves, Maria Alice
    Niskanen, Tuula
    Nylinder, Stephan
    Pereira, Olinto Liparini
    Pinho, Danilo Batista
    Porter, Teresita M.
    Queloz, Valentin
    Riit, Taavi
    Sanchez-Garcia, Marisol
    de Sousa, Filipe
    Stefanczyk, Emil
    Tadych, Mariusz
    Takamatsu, Susumu
    Tian, Qing
    Udayanga, Dhanushka
    Unterseher, Martin
    Wang, Zheng
    Wikee, Saowanee
    Yan, Jiye
    Larsson, Ellen
    Larsson, Karl-Henrik
    Koljalg, Urmas
    Abarenkov, Kessy
    Improving ITS sequence data for identification of plant pathogenic fungi2014In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 67, no 1, p. 11-19Article in journal (Refereed)
    Abstract [en]

    Plant pathogenic fungi are a large and diverse assemblage of eukaryotes with substantial impacts on natural ecosystems and human endeavours. These taxa often have complex and poorly understood life cycles, lack observable, discriminatory morphological characters, and may not be amenable to in vitro culturing. As a result, species identification is frequently difficult. Molecular (DNA sequence) data have emerged as crucial information for the taxonomic identification of plant pathogenic fungi, with the nuclear ribosomal internal transcribed spacer (ITS) region being the most popular marker. However, international nucleotide sequence databases are accumulating numerous sequences of compromised or low-resolution taxonomic annotations and substandard technical quality, making their use in the molecular identification of plant pathogenic fungi problematic. Here we report on a concerted effort to identify high-quality reference sequences for various plant pathogenic fungi and to re-annotate incorrectly or insufficiently annotated public ITS sequences from these fungal lineages. A third objective was to enrich the sequences with geographical and ecological metadata. The results - a total of 31,954 changes - are incorporated in and made available through the UNITE database for molecular identification of fungi (including standalone FASTA files of sequence data for local BLAST searches, use in the next-generation sequencing analysis platforms QIIME and mothur, and related applications. The present initiative is just a beginning to cover the wide spectrum of plant pathogenic fungi, and we invite all researchers with pertinent expertise to join the annotation effort.

  • 16.
    Nilsson, R. Henrik
    et al.
    University of Gothenburg, Department of Biological and Environmental Sciences; Gothenburg Global Biodiversity Centre.
    Sánchez-García, Marisol
    Clark University, Department of Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. University of Tennessee.
    Abarenkov, Kessy
    University of Tartu, Natural History Museum.
    Wurzbacher, Christian
    University of Gothenburg, Department of Biological and Environmental Sciences; Gothenburg Global Biodiversity Centre.
    Kristiansson, Erik
    Chalmers University of Technology, Department of Mathematical Statistics.
    Read quality-based trimming of the distal ends of public fungal DNA sequences is nowhere near satisfactory2017In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, Vol. 26, p. 13-24Article in journal (Refereed)
    Abstract [en]

    DNA sequences are increasingly used for taxonomic and functional assessment of environmental communities. In mycology, the nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen marker for such pursuits. Molecular identification is associated with many challenges, one of which is low read quality of the reference sequences used for inference of taxonomic and functional properties of the newly sequenced community (or single taxon). This study investigates whether public fungal ITS sequences are subjected to sufficient trimming in their distal (5’ and 3’) ends prior to deposition in the public repositories. We examined 86 species (and 10,584 sequences) across the fungal tree of life, and we found that on average 13.1% of the sequences were poorly trimmed in one or both of their 5’ and 3’ ends. Deposition of poorly trimmed entries was found to continue through 2016. Poorly trimmed reference sequences add noise and mask biological signal in sequence similarity searches and phylogenetic analyses, and we provide a set of recommendations on how to manage the sequence trimming problem.

  • 17. Nilsson, R. Henrik
    et al.
    Tedersoo, Leho
    Abarenkov, Kessy
    Ryberg, Martin
    Kristiansson, Erik
    Hartmann, Martin
    Schoch, Conrad L.
    Nylander, Johan A. A.
    Bergsten, Johannes
    Porter, Teresita M.
    Five simple guidelines for establishing basic authenticity and reliability of newly generated fungal ITS sequences.2012Other (Other academic)
  • 18. Nilsson, R. Henrik
    et al.
    Tedersoo, Leho
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kristiansson, Erik
    Hartmann, Martin
    Unterseher, Martin
    Porter, Teresita M.
    Bengtsson-Palme, Johan
    Walker, Donald M.
    De Sousa, Filipe
    Gamper, Hannes Andres
    Larsson, Ellen
    Larsson, Karl-Henrik
    Koljalg, Urmas
    Edgar, Robert C.
    Abarenkov, Kessy
    A Comprehensive, Automatically Updated Fungal ITS Sequence Dataset for Reference-Based Chimera Control in Environmental Sequencing Efforts2015In: Microbes and Environments, ISSN 1342-6311, E-ISSN 1347-4405, Vol. 30, no 2, p. 145-150Article in journal (Refereed)
    Abstract [en]

    The nuclear ribosomal internal transcribed spacer (ITS) region is the most commonly chosen genetic marker for the molecular identification of fungi in environmental sequencing and molecular ecology studies. Several analytical issues complicate such efforts, one of which is the formation of chimeric-artificially joined-DNA sequences during PCR amplification or sequence assembly. Several software tools are currently available for chimera detection, but rely to various degrees on the presence of a chimera-free reference dataset for optimal performance. However, no such dataset is available for use with the fungal ITS region. This study introduces a comprehensive, automatically updated reference dataset for fungal ITS sequences based on the UNITE database for the molecular identification of fungi. This dataset supports chimera detection throughout the fungal kingdom and for full-length ITS sequences as well as partial (ITS1 or ITS2 only) datasets. The performance of the dataset on a large set of artificial chimeras was above 99.5%, and we subsequently used the dataset to remove nearly 1,000 compromised fungal ITS sequences from public circulation. The dataset is available at http://unite.ut.ee/repository.php and is subject to web-based third-party curation.

  • 19.
    Nilsson, R. Henrik
    et al.
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Ulikooli 18, EE-50090 Tartu, Estonia..
    Coimbra, Victor R. M.
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden.;Univ Fed Pernambuco UFPE, Ctr Ciencias Biol CCB, Dept Micol, Av Prof Nelson Chaves S-N, BR-50760901 Recife, PE, Brazil..
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Tedersoo, Leho
    Univ Tartu, Inst Ecol & Earth Sci, Ulikooli 18, EE-50090 Tartu, Estonia..
    Eriksson, Jonna
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Ritter, Camila Duarte
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Svantesson, Sten
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Sanchez-Garcia, Marisol
    Univ Tennessee, Dept Ecol & Evolutionary Biol, Knoxville, TN 37996 USA..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kristiansson, Erik
    Univ Gothenburg, Chalmers Univ Technol, Dept Math Sci, S-41296 Gothenburg, Sweden..
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Top 50 most wanted fungi2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 12, p. 29-40Article in journal (Refereed)
    Abstract [en]

    Environmental sequencing regularly recovers fungi that cannot be classified to any meaningful taxonomic level beyond "Fungi". There are several examples where evidence of such lineages has been sitting in public sequence databases for up to ten years before receiving scientific attention and formal recognition. In order to highlight these unidentified lineages for taxonomic scrutiny, a search function is presented that produces updated lists of approximately genus-level clusters of fungal ITS sequences that remain unidentified at the phylum, class, and order levels, respectively. The search function (https://unite.ut.ee/top50.php) is implemented in the UNITE database for molecular identification of fungi, such that the underlying sequences and fungal lineages are open to third-party annotation. We invite researchers to examine these enigmatic fungal lineages in the hope that their taxonomic resolution will not have to wait another ten years or more.

  • 20. Orstadius, Leif
    et al.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Larsson, Ellen
    Molecular phylogenetics and taxonomy in Psathyrellaceae (Agaricales) with focus on psathyrelloid species: introduction of three new genera and 18 new species2015In: Mycological progress, ISSN 1617-416X, E-ISSN 1861-8952, Vol. 14, no 5, article id 25Article in journal (Refereed)
    Abstract [en]

    Based on traditional morphology, sequence data, and phylogenetic analyses, 18 new species are here described: Coprinellus christianopolitanus, Coprinopsis musae, C. udicola, Psathyrella arenosa, P. carminei, P. fennoscandica, P. ichnusae, P. lilliputana, P. lyckebodensis, P. madida, P. rybergii, P. sabuletorum, P. scanica, P. siccophila, P. stridvallii, P. sublatispora, P. vesterholtii, and Typhrasa nanispora. Psathyrella hololanigera and P. tenera are reported as new to Europe and P. parva as new to the Nordic countries. A four-gene dataset on Psathyrellaceae were analyzed by Maximum Parsimony, Maximum Likelihood, and Bayesian methods. Constraint analyses were performed to determine limits of /Psathyrella, and to evaluate whether the / Coprinellus, /cordisporus, and /gossypina clades could be regarded with confidence as monophyletic clades outside of the clade /Psathyrella. This was not unambiguously supported. Based on the phylogenetic results, Kauffmania is proposed as a monotypic genus for the species P. larga and Typhrasa for P. gossypina and the new described species T. nanispora. The genus Homophron is formally validated and three combinations are proposed: H. spadiceum, H. cernuum, and H. camptopodum. The genus Cystoagaricus Singer is emended and the following new combinations are proposed: C. hirtosquamulosus, C. squarrosiceps, C. olivaceogriseus, and C. silvestris. Neotypes have been selected for seven species described by Fries, and ITS sequence data for these were generated. The following new combinations are proposed: Coprinopsis canoceps, C. cineraria, C. melanthina, C. submicrospora, C. uliginicola, and Typhrasa gossypina. Brief comments are given to other species of interest. Psathyrella ornatispora were found not to belong in Psathyrellaceae. A key to 106 psathyrelloid species in Northern Europe is provided.

  • 21.
    Pent, Mari
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Hiltunen, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Poldmaa, Kadri
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Furneaux, Brendan R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hildebrand, Falk
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.
    Host genetic variation strongly influences the microbiome structure and function in fungal fruiting-bodies2018In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 20, no 5, p. 1641-1650Article in journal (Refereed)
    Abstract [en]

    Despite increasing knowledge on host-associated microbiomes, little is known about mechanisms underlying fungus-microbiome interactions. This study aimed to examine the relative importance of host genetic, geographic and environmental variations in structuring fungus-associated microbiomes. We analyzed the taxonomic composition and function of microbiomes inhabiting fungal fruiting-bodies in relation to host genetic variation, soil pH and geographic distance between samples. For this, we sequenced the metagenomes of 40 fruiting-bodies collected from six fairy rings (i.e., genets) of a sapro-trophic fungus Marasmius oreades. Our analyses revealed that fine genetic variations between host fungi could strongly affect their associated microbiome, explaining, respectively, 25% and 37% of the variation in microbiome structure and function, whereas geographic distance and soil pH remained of secondary importance. These results, together with the smaller genome size of fungi compared to other eukaryotes, suggest that fruiting-bodies are suitable for further genome-centric studies on hostmicrobiome interactions.

  • 22. Phukhamsakda, C
    et al.
    Hongsanan, S
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ariyawansa, HA
    Chomnunti, P
    Bahkali, AH
    Hyde, KD
    The evolution of Massarineae with Longipedicellataceae fam. nov.2016In: Mycosphere, ISSN 2077-7000, E-ISSN 2077-7019, Vol. 7, no 11, p. 1713-1731Article in journal (Refereed)
    Abstract [en]

    Massarineae is a suborder of Pleosporales, the latter being the largest order in Dothideomycetes. Massarineae comprises 14 families and six taxa of uncertain placement. In this study, we introduce an additional new family, Longipedicellataceae in Massarineae, which accommodates the genera Longipedicellata and Pseudoxylomyces. The family inhabits submerged culms of plants in freshwater habitats. The family can be distinguished by its very long pedicellate asci and chlamydospore-like structures, which are produced in culture. A LSU, SSU, and RPB2 dataset from representative strains used in our phylogenetic analyses shows the separation of Longipedicellataceae from the other families of Massarineae. In addition, divergence times of families in Massarineae were estimated using a molecular clock methodology. We used an Eocene fossil of Margaretbarromyces dictyosporus to estimate dates in Pleosporales with emphasis on Massarineae. In this study, the crown of Pleosporales is dated to the late Triassic (211 Mya), while the suborder Massarineae is dated to the Cretaceous (130 Mya) and family Longipedicellataceae is dated to Eocene (56 Mya).

  • 23.
    Rosenblad, Magnus Alm
    et al.
    Univ Gothenburg, Dept Marine Sci, Bioinformat Infrastruct Life Sci, Box 460, SE-40530 Gothenburg, Sweden..
    Martin, Maria P.
    CSIC, RJB, Dept Micol, Plaza Murillo 1, Madrid 28014, Spain..
    Tedersoo, Leho
    Univ Tartu, Inst Ecol & Earth Sci, Ulikooli 18, EE-50090 Tartu, Estonia..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, Vanemuise 46, EE-51014 Tartu, Estonia..
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden..
    Detection of signal recognition particle (SRP) RNAs in the nuclear ribosomal internal transcribed spacer 1 (ITS1) of three lineages of ectomycorrhizal fungi (Agaricomycetes, Basidiomycota)2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 13, p. 21-33Article in journal (Refereed)
    Abstract [en]

    During a routine scan for Signal Recognition Particle (SRP) RNAs in eukaryotic sequences, we surprisingly found in silico evidence in GenBank for a 265-base long SRP RNA sequence in the ITS1 region of a total of 11 fully identified species in three ectomycorrhizal genera of the Basidiomycota (Fungi): Astraeus, Russula, and Lactarius. To rule out sequence artifacts, one specimen from a species indicated to have the SRP RNA-containing ITS region in each of these genera was ordered and re-sequenced. Sequences identical to the corresponding GenBank entries were recovered, or in the case of a non-original but conspecific specimen differed by three bases, showing that these species indeed have an SRP RNA sequence incorporated into their ITS1 region. Other than the ribosomal genes, this is the first known case of non-coding RNAs in the eukaryotic ITS region, and it may assist in the examination of other types of insertions in fungal genomes.

  • 24.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Molecular operational taxonomic units as approximations of species in the light of evolutionary models and empirical data from Fungi2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 23, p. 5770-5777Article in journal (Other academic)
    Abstract [en]

    During the last couple of decades, an increasing number of studies use sequence clusters as units for taxonomic diversity. It is well known that such molecular operational taxonomic units (MOTUs) do not necessarily correspond to species, but they are treated as such when measuring diversity and testing theories. Here, I show that data from studies of molecular evolution and species diversification of fungi indicate that commonly used cut-offs are likely to lump species in many cases. At the same time, empirical studies show that the mean within-species variation is close to these cut-offs. That the within-species variation estimates are plausible is supported by coalescence modelling under a range of parameter settings. In addition, studies using crossing tests to delimit species show that there often is an overlap in within- and between-species distances. The available data therefore indicate that sequence clusters are likely to misrepresent species. However, to keep a biological relevance, MOTUs should be kept in close agreement with species. Studies using them should therefore asses how sensitive the results are to differences between MOTUs and species - something that is rarely done. An even better solution is to directly include the uncertainty in species delimitation in the analyses, but in many cases, we need to increase our knowledge of taxonomy and evolution to do this accurately. Even if the empirical data referred to here pertain to the barcoding region of rDNA in fungi, there is nothing indicating that the situation is substantially better for other taxa or genes.

  • 25.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Phylommand - a command line software package for phylogenetics [version 1; referees: awaiting peer review]2016In: F1000 Research, E-ISSN 2046-1402, Vol. 5, article id 2903Article in journal (Refereed)
    Abstract [en]

    Phylogenetics is an intrinsic part of many analyses in evolutionary biology and ecology, and as the amount of data available for these analyses is increasing rapidly the need for automated pipelines to deal with the data also increases. Phylommand is a package of four programs to create, manipulate, and/or analyze phylogenetic trees or pairwise alignments. It is built to be easily implemented in software workflows, both directly on the command prompt, and executed using scripts. Inputs can be taken from standard input or a file, and the behavior of the programs can be changed through switches. By using standard file formats for phylogenetic analyses, such as newick, nexus, phylip, and fasta, phylommand is widely compatible with other software.

  • 26. Ryberg, Martin
    et al.
    Andreasen, Mathias
    Björk, Robert G
    Weak habitat specificity in ectomycorrhizal communities associated with Salix herbacea and Salix polaris in alpine tundra.2011In: Mycorrhiza, ISSN 0940-6360, E-ISSN 1432-1890, Vol. 21, no 4, p. 289-96Article in journal (Refereed)
    Abstract [en]

    This study explores mid-alpine ectomycorrhizal communities on Salix herbacea and Salix polaris in plant communities differing in nutrient status and snow conditions. Plant species were identified by tracking roots back to above ground structures while fungal species were identified using molecular methods. The fungi were identified to 34 molecular operational taxonomic units (MOTUs)/species but species accumulation curves indicated that the communities were only partially sampled. The estimated total species richness was 49 (±9 SD) MOTUs/species. No significant ectomycorrhizal community specificity was found between the two plant species and only weak specificity between different plant communities. Furthermore, no difference in proportion of colonized root tips could be demonstrated between plant communities. However, some fungal taxa showed tendencies to associate with specific environmental conditions. Sebacinaceae, Inocybe egenula, Russula cf. emetica, and a Tomentella sp. were found in meadow communities but not in the heath communities. Sistotrema cf. alboluteum and Tomentella cf. terrestris were only found in the dry and mesic heath communities. Classifications into exploration types showed that the contact type is more abundant in the dry heath community than the other communities. Cenococcum geophilum was the most common species but Cortinarius spp., Russula spp., Tomentella spp., and Lactarius spp. were also common. This study confirms that alpine communities are rich in ectomycorrhizal fungi including species from a wide variety of fungal lineages and also show that many dominant species have wide ecological amplitude.

  • 27. Ryberg, Martin
    et al.
    Matheny, P Brandon
    Asynchronous origins of ectomycorrhizal clades of Agaricales.2012In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 279, no 1735, p. 2003-11Article in journal (Refereed)
    Abstract [en]

    The ectomycorrhizal (ECM) symbiosis is the most widespread biotrophic nutritional mode in mushroom-forming fungi. ECM fungi include, though are not limited to, about 5000 described species of Agaricales from numerous, independently evolved lineages. Two central hypotheses suggest different explanations for the origin of ECM fungal diversity: (i) dual origins, initially with the Pinaceae in the Jurassic and later with angiosperms during the Late Cretaceous, and (ii) a simultaneous and convergent radiation of ECM lineages in response to cooling climate during the Palaeogene and advancing temperate ECM plant communities. Neither of these hypotheses is supported here. While we demonstrate support for asynchronous origins of ECM Agaricales, the timing of such events appears to have occurred more recently than suggested by the first hypothesis, first during the Cretaceous and later during the Palaeogene. We are also unable to reject models of rate constancy, which suggests that the diversity of ECM Agaricales is not a consequence of convergent rapid radiations following evolutionary transitions from saprotrophic to ECM habits. ECM lineages of Agaricales differ not only in age, but also in rates of diversification and rate of substitution at nuclear ribosomal RNA loci. These results question the biological uniformity of the ECM guild.

  • 28. Ryberg, Martin
    et al.
    Matheny, Patrick Brandon
    Dealing with incomplete taxon sampling and diversification of a large clade of mushroom-forming fungi.2011In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 65, no 7, p. 1862-78Article in journal (Refereed)
    Abstract [en]

    The absence of an adequate fossil record can hinder understanding the process of diversification that underlies the evolutionary history of a given group. In such cases, investigators have used ultrametric trees derived from molecular data from extant taxa to gain insights into processes of speciation and extinction over time. Inadequate taxon sampling, however, impairs such inferences. In this study, we use simulations to investigate the effect of incomplete taxon sampling on the accumulation of lineages through time for a clade of mushroom-forming fungi, the Hebelomateae. To achieve complete taxon sampling, we use a new Bayesian approach that incorporates substitute lineages to estimate diversification rates. Unlike many studies of animals and plants, we find no evidence of a slowdown in speciation. This indicates the Hebelomateae has not undergone an adaptive radiation. Rather, these fungi have evolved under a relatively constant rate of diversification since their most recent common ancestor, which we date back to the Eocene. The estimated net diversification rate (0.08-0.19 spp./lineage/Ma) is comparable with that of many plants and animals. We suggest that continuous diversification in the Hebelomateae has been facilitated by climatic and vegetation changes throughout the Cenozoic. We also caution against modeling multiple genes as a single partition when performing phylogenetic dating analyses.

  • 29.
    Ryberg, Martin
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 463, S-40530 Gothenburg, Sweden.;Gothenburg Global Biodivers Ctr, Box 461, S-40530 Gothenburg, Sweden..
    New light on names and naming of dark taxa2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 30, p. 31-39Article in journal (Refereed)
    Abstract [en]

    A growing proportion of fungal species and lineages are known only from sequence data and cannot be linked to any physical specimen or resolved taxonomic name. Such fungi are often referred to as "dark taxa" or "dark matter fungi". As they lack a taxonomic identity in the form of a name, they are regularly ignored in many important contexts, for example in legalisation and species counts. It is therefore very urgent to find a system to also deal with these fungi. Here, issues relating to the taxonomy and nomenclature of dark taxa are discussed and a number of questions that the mycological community needs to consider before deciding on what system/s to implement are highlighted.

  • 30. Ryberg, Martin
    et al.
    Nilsson, R Henrik
    Matheny, P Brandon
    DivBayes and SubT: exploring species diversification using Bayesian statistics.2011In: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 27, no 17, p. 2439-40Article in journal (Refereed)
    Abstract [en]

    SUMMARY: DivBayes is a program to estimate diversification rates from species richness and ages of a set of clades. SubT estimates diversification rates from node heights within a clade. Both programs implement Bayesian statistics and provide the ability to account for uncertainty in the ages of taxa in the underlying data, an improvement over more commonly used maximum likelihood methods.

    AVAILABILITY: DivBayes and SubT are released as C++ source code under the GNU GPL v. 3 software license in Supplementary information 1 and 2, respectively, and at http://web.utk.edu/~kryberg/. They have been successfully compiled on various Linux, MacOS X and Windows systems.

    CONTACT: kryberg@utk.edu

    SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

  • 31. Sheedy, Elizabeth M.
    et al.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lebel, Teresa
    May, Tom W.
    Bougher, Neale L.
    Matheny, P. Brandon
    Dating the emergence of truffle-like fungi in Australia, by using an augmented meta-analysis2016In: Australian Systematic Botany, ISSN 1030-1887, E-ISSN 1446-5701, Vol. 29, no 5, p. 284-302Article in journal (Refereed)
    Abstract [en]

    Australia supports a high diversity of sequestrate (truffle-like) macrofungi. This has long been thought to be related to the predominantly or seasonally dry climate. The present study posits that if aridity were a key factor in the evolution of sequestrate fruit-bodies, most sequestrate species would have emerged in Australia only after it began to aridify, which occurred post-separation with Antarctica (c. 32 million years ago). Focusing on the high phylogenetic diversity of sequestrate taxa in the Agaricomycetes in Australia, dates of sequestrate nodes were compiled directly from published phylogenies (four lineages) or created using sequences available on GenBank that were processed in BEAST using a secondary calibration method (nine lineages). Although the morphologically diverse Hysterangiales was found to be the first group to become sequestrate, c. 83 million years ago, overall sequestration in Australia occurred more recently. Models were created and compared and support was found for an increased rate of sequestration in Australia at some point between 34 and 13 million years ago (during the Oligocene and Miocene). Although the rate of sequestration is shown to have increased in Australia after separation from Antarctica, the timing also overlaps with the radiation of potential mycorrhizal plant associates, and the emergence of specialised mycophagous marsupials. Although aridification is evidently not the sole driver of sequestration, it is still likely to have had a major influence on the diversity of sequestrate fungi in Australia. Comparisons with other regions of high sequestrate diversity will be informative.

  • 32. Tedersoo, Leho
    et al.
    Abarenkov, Kessy
    Nilsson, R Henrik
    Göteborgs Universitet.
    Schüssler, Arthur
    Grelet, Gwen-Aëlle
    Kohout, Petr
    Oja, Jane
    Bonito, Gregory M
    Veldre, Vilmar
    Jairus, Teele
    Ryberg, Martin
    University of Tennessee.
    Larsson, Karl-Henrik
    Kõljalg, Urmas
    Tidying up international nucleotide sequence databases: ecological, geographical and sequence quality annotation of its sequences of mycorrhizal fungi.2011In: PloS one, ISSN 1932-6203, Vol. 6, no 9, p. e24940-Article in journal (Refereed)
    Abstract [en]

    Sequence analysis of the ribosomal RNA operon, particularly the internal transcribed spacer (ITS) region, provides a powerful tool for identification of mycorrhizal fungi. The sequence data deposited in the International Nucleotide Sequence Databases (INSD) are, however, unfiltered for quality and are often poorly annotated with metadata. To detect chimeric and low-quality sequences and assign the ectomycorrhizal fungi to phylogenetic lineages, fungal ITS sequences were downloaded from INSD, aligned within family-level groups, and examined through phylogenetic analyses and BLAST searches. By combining the fungal sequence database UNITE and the annotation and search tool PlutoF, we also added metadata from the literature to these accessions. Altogether 35,632 sequences belonged to mycorrhizal fungi or originated from ericoid and orchid mycorrhizal roots. Of these sequences, 677 were considered chimeric and 2,174 of low read quality. Information detailing country of collection, geographical coordinates, interacting taxon and isolation source were supplemented to cover 78.0%, 33.0%, 41.7% and 96.4% of the sequences, respectively. These annotated sequences are publicly available via UNITE (http://unite.ut.ee/) for downstream biogeographic, ecological and taxonomic analyses. In European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena/), the annotated sequences have a special link-out to UNITE. We intend to expand the data annotation to additional genes and all taxonomic groups and functional guilds of fungi.

  • 33. Tedersoo, Leho
    et al.
    Bahram, Mohammad
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Otsing, Eveli
    Koljalg, Urmas
    Abarenkov, Kessy
    Global biogeography of the ectomycorrhizal/sebacina lineage (Fungi, Sebacinales) as revealed from comparative phylogenetic analyses2014In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 23, no 16, p. 4168-4183Article in journal (Refereed)
    Abstract [en]

    Compared with plants and animals, large-scale biogeographic patterns of microbes including fungi are poorly understood. By the use of a comparative phylogenetic approach and ancestral state reconstructions, we addressed the global biogeography, rate of evolution and evolutionary origin of the widely distributed ectomycorrhizal (EcM) /sebacina lineage that forms a large proportion of the Sebacinales order. We downloaded all publicly available internal transcribed spacer (ITS) sequences and metadata and supplemented sequence information from three genes to construct dated phylogenies and test biogeographic hypotheses. The /sebacina lineage evolved 45-57Myr ago that groups it with relatively young EcM taxa in other studies. The most parsimonious origin for /sebacina is inferred to be North American temperate coniferous forests. Among biogeographic traits, region and biome exhibited stronger phylogenetic signal than host family. Consistent with the resource availability (environmental energy) hypothesis, the ITS region is evolving at a faster rate in tropical than nontropical regions. Most biogeographic regions exhibited substantial phylogenetic clustering suggesting a strong impact of dispersal limitation over a large geographic scale. In northern Holarctic regions, however, phylogenetic distances and phylogenetic grouping of isolates indicate multiple recent dispersal events.

  • 34. Tedersoo, Leho
    et al.
    Bahram, Mohammad
    Toots, Märt
    Diédhiou, Abdala G
    Henkel, Terry W
    Kjøller, Rasmus
    Morris, Melissa H
    Nara, Kazuhide
    Nouhra, Eduardo
    Peay, Kabir G
    Põlme, Sergei
    Ryberg, Martin
    Smith, Matthew E
    Kõljalg, Urmas
    Towards global patterns in the diversity and community structure of ectomycorrhizal fungi.2012In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 21, no 17, p. 4160-70Article in journal (Refereed)
    Abstract [en]

    Global species richness patterns of soil micro-organisms remain poorly understood compared to macro-organisms. We use a global analysis to disentangle the global determinants of diversity and community composition for ectomycorrhizal (EcM) fungi-microbial symbionts that play key roles in plant nutrition in most temperate and many tropical forest ecosystems. Host plant family has the strongest effect on the phylogenetic community composition of fungi, whereas temperature and precipitation mostly affect EcM fungal richness that peaks in the temperate and boreal forest biomes, contrasting with latitudinal patterns of macro-organisms. Tropical ecosystems experience rapid turnover of organic material and have weak soil stratification, suggesting that poor habitat conditions may contribute to the relatively low richness of EcM fungi, and perhaps other soil biota, in most tropical ecosystems. For EcM fungi, greater evolutionary age and larger total area of EcM host vegetation may also contribute to the higher diversity in temperate ecosystems. Our results provide useful biogeographic and ecological hypotheses for explaining the distribution of fungi that remain to be tested by involving next-generation sequencing techniques and relevant soil metadata.

  • 35.
    Tedersoo, Leho
    et al.
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia;Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia;Estonian Young Acad Sci, 6 Kohtu, Tallinn, Estonia.
    Sanchez-Ramirez, Santiago
    Univ Toronto, Dept Ecol & Evolutionary Biol, 25 Willcocks St, Toronto, ON M5S 3B2, Canada.
    Koljalg, Urmas
    Univ Tartu, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Estonian Young Acad Sci, 6 Kohtu, Tallinn, Estonia.
    Doring, Markus
    Global Biodivers Informat Facil, Copenhagen, Denmark.
    Schigel, Dmitry
    Global Biodivers Informat Facil, Copenhagen, Denmark;Univ Helsinki, Dept Biosci, Helsinki, Finland.
    May, Tom
    Royal Bot Gardens Victoria, Birdwood Ave, Melbourne, Vic 3004, Australia.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Abarenkov, Kessy
    Univ Tartu, Nat Hist Museum, 14a Ravila, EE-50411 Tartu, Estonia.
    High-level classification of the Fungi and a tool for evolutionary ecological analyses2018In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 90, no 1, p. 135-159Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing studies generate vast amounts of taxonomic data. Evolutionary ecological hypotheses of the recovered taxa and Species Hypotheses are difficult to test due to problems with alignments and the lack of a phylogenetic backbone. We propose an updated phylum-and class-level fungal classification accounting for monophyly and divergence time so that the main taxonomic ranks are more informative. Based on phylogenies and divergence time estimates, we adopt phylum rank to Aphelidiomycota, Basidiobolomycota, Calcarisporiellomycota, Glomeromycota, Entomophthoromycota, Entorrhizomycota, Kickxellomycota, Monoblepharomycota, Mortierellomycota and Olpidiomycota. We accept nine subkingdoms to accommodate these 18 phyla. We consider the kingdom Nucleariae (phyla Nuclearida and Fonticulida) as a sister group to the Fungi. We also introduce a perl script and a newick-formatted classification backbone for assigning Species Hypotheses into a hierarchical taxonomic framework, using this or any other classification system. We provide an example of testing evolutionary ecological hypotheses based on a global soil fungal data set.

  • 36.
    Vowles, Tage
    et al.
    Univ Gothenburg, Dept Earth Sci, Gothenburg, Sweden; Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg, Sweden.
    Lindwall, Frida
    Univ Copenhagen, Terr Ecol, Dept Biol, Copenhagen, Denmark; Univ Copenhagen, Ctr Permafrost, Dept Geosci & Nat Resource Management, Copenhagen, Denmark.
    Ekblad, Alf
    Örebro Univ, Sch Sci & Technol, Örebro, Sweden.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Dept Bot, Inst Ecol & Earth Sci, Tartu, Estonia.
    Furneaux, Brendan R.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Björk, Robert G.
    Univ Gothenburg, Dept Earth Sci, Gothenburg, Sweden; Gothenburg Global Biodivers Ctr, Gothenburg, Sweden.
    Complex effects of mammalian grazing on extramatrical mycelial biomass in the Scandes forest-tundra ecotone2018In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 8, no 2, p. 1019-1030Article in journal (Refereed)
    Abstract [en]

    Mycorrhizal associations are widespread in high‐latitude ecosystems and are potentially of great importance for global carbon dynamics. Although large herbivores play a key part in shaping subarctic plant communities, their impact on mycorrhizal dynamics is largely unknown. We measured extramatrical mycelial (EMM) biomass during one growing season in 16‐year‐old herbivore exclosures and unenclosed control plots (ambient), at three mountain birch forests and two shrub heath sites, in the Scandes forest‐tundra ecotone. We also used high‐throughput amplicon sequencing for taxonomic identification to investigate differences in fungal species composition. At the birch forest sites, EMM biomass was significantly higher in exclosures (1.36 ± 0.43 g C/m2) than in ambient conditions (0.66 ± 0.17 g C/m2) and was positively influenced by soil thawing degree‐days. At the shrub heath sites, there was no significant effect on EMM biomass (exclosures: 0.72 ± 0.09 g C/m2; ambient plots: 1.43 ± 0.94). However, EMM biomass was negatively related to Betula nana abundance, which was greater in exclosures, suggesting that grazing affected EMM biomass positively. We found no significant treatment effects on fungal diversity but the most abundant ectomycorrhizal lineage/cortinarius, showed a near‐significant positive effect of herbivore exclusion (p = .08), indicating that herbivory also affects fungal community composition. These results suggest that herbivory can influence fungal biomass in highly context‐dependent ways in subarctic ecosystems. Considering the importance of root‐associated fungi for ecosystem carbon balance, these findings could have far‐reaching implications.

1 - 36 of 36
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