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  • 301.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Monkey’s voyage: how improbable journeys shaped the history of life. €”by Alan de Queiroz.2014In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 63, no 5, p. 847-849Article in journal (Other academic)
  • 302.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Tree of Life: Evolution and Classification of Living Organisms .—Edited by Pablo Vargas and Rafael Zardoya; translated by Anne Louise2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 3, p. 546-548Article, book review (Other academic)
  • 303.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Understanding Evolution .— By Kostas Kampourakis2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 6, p. 1121-1122Article, book review (Other academic)
  • 304.
    Morrison, David A.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Morgan, Matthew J.
    CSIRO, Ecosyst Sci, Canberra, ACT 2601, Australia..
    Kelchner, Scot A.
    Utah State Univ, Dept Biol, Logan, UT 84322 USA..
    Molecular homology and multiple-sequence alignment: an analysis of concepts and practice2015In: Australian Systematic Botany, ISSN 1030-1887, E-ISSN 1446-5701, Vol. 28, no 1, p. 46-62Article in journal (Refereed)
    Abstract [en]

    Sequence alignment is just as much a part of phylogenetics as is tree building, although it is often viewed solely as a necessary tool to construct trees. However, alignment for the purpose of phylogenetic inference is primarily about homology, as it is the procedure that expresses homology relationships among the characters, rather than the historical relationships of the taxa. Molecular homology is rather vaguely defined and understood, despite its importance in the molecular age. Indeed, homology has rarely been evaluated with respect to nucleotide sequence alignments, in spite of the fact that nucleotides are the only data that directly represent genotype. All other molecular data represent phenotype, just as do morphology and anatomy. Thus, efforts to improve sequence alignment for phylogenetic purposes should involve a more refined use of the homology concept at a molecular level. To this end, we present examples of molecular-data levels at which homology might be considered, and arrange them in a hierarchy. The concept that we propose has many levels, which link directly to the developmental and morphological components of homology. Of note, there is no simple relationship between gene homology and nucleotide homology. We also propose terminology with which to better describe and discuss molecular homology at these levels. Our over-arching conceptual framework is then used to shed light on the multitude of automated procedures that have been created for multiple-sequence alignment. Sequence alignment needs to be based on aligning homologous nucleotides, without necessary reference to homology at any other level of the hierarchy. In particular, inference of nucleotide homology involves deriving a plausible scenario for molecular change among the set of sequences. Our clarifications should allow the development of a procedure that specifically addresses homology, which is required when performing alignment for phylogenetic purposes, but which does not yet exist.

  • 305. Morrow, Christine
    et al.
    Cardenas, Paco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Proposal for a revised classification of the Demospongiae (Porifera)2015In: Frontiers in Zoology, ISSN 1742-9994, E-ISSN 1742-9994, Vol. 12, article id 7Article in journal (Refereed)
    Abstract [en]

    Background: Demospongiae is the largest sponge class including 81% of all living sponges with nearly 7,000 species worldwide. Systema Porifera (2002) was the result of a large international collaboration to update the Demospongiae higher taxa classification, essentially based on morphological data. Since then, an increasing number of molecular phylogenetic studies have considerably shaken this taxonomic framework, with numerous polyphyletic groups revealed or confirmed and new clades discovered. And yet, despite a few taxonomical changes, the overall framework of the Systema Porifera classification still stands and is used as it is by the scientific community. This has led to a widening phylogeny/classification gap which creates biases and inconsistencies for the many end-users of this classification and ultimately impedes our understanding of today's marine ecosystems and evolutionary processes. In an attempt to bridge this phylogeny/classification gap, we propose to officially revise the higher taxa Demospongiae classification. Discussion: We propose a revision of the Demospongiae higher taxa classification, essentially based on molecular data of the last ten years. We recommend the use of three subclasses: Verongimorpha, Keratosa and Heteroscleromorpha. We retain seven (Agelasida, Chondrosiida, Dendroceratida, Dictyoceratida, Haplosclerida, Poecilosclerida, Verongiida) of the 13 orders from Systema Porifera. We recommend the abandonment of five order names (Hadromerida, Halichondrida, Halisarcida, lithistids, Verticillitida) and resurrect or upgrade six order names (Axinellida, Merliida, Spongillida, Sphaerocladina, Suberitida, Tetractinellida). Finally, we create seven new orders (Bubarida, Desmacellida, Polymastiida, Scopalinida, Clionaida, Tethyida, Trachycladida). These added to the recently created orders (Biemnida and Chondrillida) make a total of 22 orders in the revised classification. We propose the abandonment of the haplosclerid and poecilosclerid suborders. The family content of each order is also revised. Summary: The deletion of polyphyletic taxa, the use of resurrected or new names for new clades and the proposal of new family groupings will improve the comparability of studies in a wide range of scientific fields using sponges as their object of study. It is envisaged that this will lead to new and more meaningful evolutionary hypotheses for the end-users of the Demospongiae classification.

  • 306.
    Mundra, Sunil
    et al.
    Univ Ctr Svalbard, POB 156, NO-9171 Longyearbyen, Norway; Univ Oslo, Sect Genet & Evolutionary Biol, Dept Biosci, POB 1066, NO-0316 Oslo, Norway.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Eidesen, Pernille
    Univ Ctr Svalbard, POB 156, NO-9171 Longyearbyen, Norway.
    Alpine bistort (Bistorta vivipara) in edge habitat associates with fewer but distinct ectomycorrhizal fungal species: a comparative study of three contrasting soil environments in Svalbard2016In: Mycorrhiza, ISSN 0940-6360, E-ISSN 1432-1890, Vol. 26, no 8, p. 809-818Article in journal (Refereed)
    Abstract [en]

    Bistorta vivipara is a widespread arctic-alpine ectomycorrhizal (ECM) plant species. Recent findings suggest that fungal communities associated with B. vivipara roots appear random over short distances, but at larger scales, environmental filtering structure fungal communities. Habitats in highly stressful environments where specialist species with narrower niches may have an advantage represent unique opportunity to test the effect of environmental filtering. We utilised high-throughput amplicon sequencing to identify ECM communities associated with B. vivipara in Svalbard. We compared ECM communities in a core habitat where B. vivipara is frequent (Dryas-heath) with edge habitats representing extremes in terms of nutrient availability where B. vivipara is less frequent (bird-manured meadow and a nutrient-depleted mine tilling). Our analysis revealed that soil conditions in edge habitats favour less diverse but more distinct ECM fungal communities with functional traits adapted to local conditions. ECM richness was overall lower in both edge habitats, and the taxonomic compositions of ECM fungi were in line with our functional expectations. Stress-tolerant genera such as Laccaria and Hebeloma were abundant in nutrient-poor mine site whereas functional competitors genera such as Lactarius and Russula were dominant in the nutrient-rich bird-cliff site. Our results suggest that ECM communities in rare edge habitats are most likely not subsets of the larger pool of ECM fungi found in natural tundra, and they may represent a significant contribution to the overall diversity of ECM fungi in the Arctic.

  • 307. Mundra, Sunil
    et al.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Kauserud, Havard
    Halvorsen, Rune
    Eidensen, Pernille
    Temporal variation of Bistorta vivipara-associated ectomycorrhizal fungal communities in the High Arctic2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 24, p. 6289-6302Article in journal (Refereed)
    Abstract [en]

    Ectomycorrhizal (ECM) fungi are important for efficient nutrient uptake of several widespread arctic plant species. Knowledge of temporal variation of ECM fungi, and the relationship of these patterns to environmental variables, is essential to understand energy and nutrient cycling in Arctic ecosystems. We sampled roots of Bistorta vivipara ten times over two years; three times during the growing-season (June, July and September) and twice during winter (November and April) of both years. We found 668 ECM OTUs belonging to 25 different ECM lineages, whereof 157 OTUs persisted throughout all sampling time-points. Overall, ECM fungal richness peaked in winter and species belonging to Cortinarius, Serendipita and Sebacina were more frequent in winter than during summer. Structure of ECM fungal communities was primarily affected by spatial factors. However, after accounting for spatial effects, significant seasonal variation was evident revealing correspondence with seasonal changes in environmental conditions. We demonstrate that arctic ECM richness and community structure differ between summer (growing-season) and winter, possibly due to reduced activity of the core community, and addition of fungi adapted for winter conditions forming a winter-active fungal community. Significant month 3 year interactions were observed both for fungal richness and community composition, indicating unpredictable between-year variation. Our study indicates that addressing seasonal changes requires replication over several years.

  • 308. Mundra, Sunil
    et al.
    Halvorsen, Rune
    Kauserud, Håvard
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Institute of Ecology and Earth Sciences, Tartu University, Tartu, Estonia.
    Tedersoo, Leho
    Elberling, Bo
    Cooper, Elisabeth J.
    Eidesen, Pernille Bronken
    Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic2016In: MicrobiologyOpen, ISSN 2045-8827, E-ISSN 2045-8827, Vol. 5, no 5, p. 856-869Article in journal (Refereed)
    Abstract [en]

    Changing climate is expected to alter precipitation patterns in the Arctic, with consequences for subsurface temperature and moisture conditions, community structure, and nutrient mobilization through microbial belowground processes. Here, we address the effect of increased snow depth on the variation in species richness and community structure of ectomycorrhizal (ECM) and saprotrophic fungi. Soil samples were collected weekly from mid-July to mid-September in both control and deep snow plots. Richness of ECM fungi was higher, while saprotrophic fungi was lower in increased snow depth plots relative to controls. ECM fungal richness was related to soil NO3-N, NH4-N, and K; and saprotrophic fungi to NO3-N and pH. Small but significant changes in the composition of saprotrophic fungi could be attributed to snow treatment and sampling time, but not so for the ECM fungi. Delayed snow melt did not influence the temporal variation in fungal communities between the treatments. Results suggest that some fungal species are favored, while others are disfavored resulting in their local extinction due to long-term changes in snow amount. Shifts in species composition of fungal functional groups are likely to affect nutrient cycling, ecosystem respiration, and stored permafrost carbon.

  • 309.
    Nakhleh, Luay
    et al.
    Rice University, Houston, TX, USA.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Phylogenetic networks2016In: Encyclopedia of Evolutionary Biology: Volume 3 / [ed] Richard M. Kliman, Elsevier, 2016, p. 264-269Chapter in book (Refereed)
  • 310.
    Nguyen, Diem
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, S-75007 Uppsala, Sweden.
    Boberg, Johanna
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, S-75007 Uppsala, Sweden..
    Cleary, Michelle
    Swedish Univ Agr Sci, Southern Swedish Forest Res Ctr, S-23053 Alnarp, Sweden..
    Bruelheide, Helge
    Martin Luther Univ Halle Wittenberg, Inst Biol Geobot & Bot Garden, D-06108 Halle, Germany.;German Ctr Integrat Biodivers Res iDiv, D-04103 Leipzig, Germany..
    Hoenig, Lydia
    Martin Luther Univ Halle Wittenberg, Inst Biol Geobot & Bot Garden, D-06108 Halle, Germany..
    Koricheva, Julia
    Royal Holloway Univ London, Egham TW20 0EX, Surrey, England..
    Stenlid, Jan
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, S-75007 Uppsala, Sweden..
    Foliar fungi of Betula pendula: impact of tree species mixtures and assessment methods2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 41801Article in journal (Refereed)
    Abstract [en]

    Foliar fungi of silver birch (Betula pendula) in an experimental Finnish forest were investigated across a gradient of tree species richness using molecular high-throughput sequencing and visual macroscopic assessment. We hypothesized that the molecular approach detects more fungal taxa than visual assessment, and that there is a relationship among the most common fungal taxa detected by both techniques. Furthermore, we hypothesized that the fungal community composition, diversity, and distribution patterns are affected by changes in tree diversity. Sequencing revealed greater diversity of fungi on birch leaves than the visual assessment method. One species showed a linear relationship between the methods. Species-specific variation in fungal community composition could be partially explained by tree diversity, though overall fungal diversity was not affected by tree diversity. Analysis of specific fungal taxa indicated tree diversity effects at the local neighbourhood scale, where the proportion of birch among neighbouring trees varied, but not at the plot scale. In conclusion, both methods may be used to determine tree diversity effects on the foliar fungal community. However, high-throughput sequencing provided higher resolution of the fungal community, while the visual macroscopic assessment detected functionally active fungal species.

  • 311. 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.

  • 312.
    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.

  • 313. 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.

  • 314.
    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.

  • 315.
    Nordin, Anders
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Larsson, Björn-Owe
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Two new Aspicilia species from Fennoscandia and Russia2011In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 43, no 1, p. 27-37Article in journal (Refereed)
    Abstract [en]

    Aspicilia fluviatilis and A. granulosa, two arctic and/or (sub) alpine species with elongate +/- diverging and +/- branching marginal areoles, are described as new and compared with similar species occurring in Fennoscandia. A parsimony analysis based on ITS indicates a close relationship with the mainly coastal A. epiglypta. Aspicilia epiglypta, A. disserpens and A. sublapponica are lectotypified and A. disserpens is reduced to synonymy with A. perradiata. Aspicilia alboradiata and A. circularis are excluded from the Fennoscandian lichen biota. A key to Fennoscandian Aspicilia species with radiating thalli and/or elongate +/- diverging and +/- branching marginal areoles is also presented.

  • 316.
    Nordin, Anders
    et al.
    Uppsala University, Music and Museums, Museum of Evolution.
    Savic, Sanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Phylogeny and taxonomy of Aspicilia and Megasporaceae2010In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 102, no 6, p. 1339-1349Article in journal (Refereed)
    Abstract [en]

    Phylogenetic analyses based on nuLSU and mtSSU indicate that Megasporaceae is monophyletic. Aspicilia species were distributed among three main well supported groups and one group with low support that included the type species; a division of the family into five genera is proposed. The old names Circinaria and Sagedia are reintroduced for groups not including A. cinerea, the type of Aspicilia. The monotypic Megaspora is closely related to Circinaria, while Lobothallia is the sister group of the other Megasporaceae genera. Aspicilia recedens and A. farinosa are transferred to Lobothallia. Species of the 'Sphaerothallia group' are nested in Circinaria. Aspilidea is not a member of Megasporaceae but seems to be more closely related to Ochrolechiaceae. Aspilidea myrinii is neotypified, and lectotypes are designated for Aspicilia gibbosa, A. leprosescens and Lecanora gibbosula.

  • 317.
    Nygren, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Strandberg, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nabholz, Benoit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gustafsson, Tim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    García, Dania
    Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, ISPV, Universitat Rovira i Virgili, 43201 Reus, Tarragona, Spain.
    Cano, José
    Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, ISPV, Universitat Rovira i Virgili, 43201 Reus, Tarragona, Spain.
    Guarro, Josep
    Unitat de Microbiologia, Facultat de Medicina i Ciències de la Salut, ISPV, Universitat Rovira i Virgili, 43201 Reus, Tarragona, Spain.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 59, no 3, p. 649-663Article in journal (Refereed)
    Abstract [en]

    The filamentous ascomycete genus Neurospora encompasses taxa with a wide range of reproductive modes. Sexual reproduction in this genus can be divided into three major modes; heterothallism (self-incompatibility), homothallism (self-compatibility) and pseudohomothallism (partial self-compatibility). In addition to the sexual pathway, most of the heterothallic taxa propagate with morphologically distinct, vegetative dissemination propagules (macroconidia), while this feature is undetected in the majority of the homothallic taxa. In this study, we used sequence information of seven nuclear gene loci from 43 taxa (295 of the possible 301 locus-by-taxon combinations) to create a phylogeny of Neurospora. The results suggest that transitions in reproductive mode have occurred at multiple times within this group of fungi. Although a homothallic ancestor would imply fewer switches in reproductive mode, we argue that the ancestor of Neurospora was likely heterothallic and that homothallism has evolved independently at least six times in the evolutionary history of the genus. Furthermore, the two pseudohomothallic taxa of Neurospora (N. tetrasperma and N. tetraspora) represent two independent origins of pseudohomothallism. Likelihood ratio tests of substitution rates among branches in the phylogeny indicate that reproductive mode is an important factor driving genome evolution in Neurospora. First, an increased level of non-synonymous/synonymous substitutions in branches delineating homothallic taxa was found, suggesting a reduced efficiency of purifying selection in these taxa. Furthermore, elevated nucleotide substitution rates were found in heterothallic, conidia-producing, lineages as compared to the homothallic non-conidiating lineages. The latter finding is likely due to the presence of conidia, i.e., a higher rate of mitotic divisions inducing mutations, and/or that the homothallic taxa have evolved a lower mutation rate to avoid genomic degeneration.

  • 318.
    Nygren, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Strandberg, Rebecka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nabholz, Benoit
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Gustafsson, Tim
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    García, Dania
    Cano, José
    Guarro, Josep
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    A comprehensive phylogeny of Neurospora reveals a link between reproductive mode and molecular evolution in fungi2011In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 59, no 3, p. 649-663Article in journal (Refereed)
    Abstract [en]

    The filamentous ascomycete genus Neurospora encompasses taxa with a wide range of reproductive modes. Sexual reproduction in this genus can be divided into three major modes; heterothallism (self-incompatibility), homothallism (self-compatibility) and pseudohomothallism (partial self-compatibility). In addition to the sexual pathway, most of the heterothallic taxa propagate with morphologically distinct, vegetative dissemination propagules (macroconidia), while this feature is undetected in the majority of the homothallic taxa. In this study, we used sequence information of seven nuclear gene loci from 43 taxa (295 of the possible 301 locus-by-taxon combinations) to create a phylogeny of Neurospora. The results suggest that transitions in reproductive mode have occurred at multiple times within this group of fungi. Although a homothallic ancestor would imply fewer switches in reproductive mode, we argue that the ancestor of Neurospora was likely heterothallic and that homothallism has evolved independently at least six times in the evolutionary history of the genus. Furthermore, the two pseudohomothallic taxa of Neurospora (N. tetrasperma and N. tetraspora) represent two independent origins of pseudohomothallism. Likelihood ratio tests of substitution rates among branches in the phylogeny indicate that reproductive mode is an important factor driving genome evolution in Neurospora. First, an increased level of non-synonymous/synonymous substitutions in branches delineating homothallic taxa was found, suggesting a reduced efficiency of purifying selection in these taxa. Furthermore, elevated nucleotide substitution rates were found in heterothallic, conidia-producing, lineages as compared to the homothallic non-conidiating lineages. The latter finding is likely due to the presence of conidia, i.e., a higher rate of mitotic divisions inducing mutations, and/or that the homothallic taxa have evolved a lower mutation rate to avoid genomic degeneration.

  • 319.
    Nygren, Kristiina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Samils, Nicklas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Stajich, Jason E
    3Department of Plant Pathology & Microbiology, University of California, Riverside, CA USA.
    Townsend, Jeffrey P
    4Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect St., New Haven, CT, USA.
    Karlsson, Magnus
    5Department of Forest Mycology and Pathology, Swedish University of Agricultural Sciences.
    Johannesson, Hanna
    Evolutionary expressed sequence tag analysis of Neurospora reveals rapid evolution of fungal reproductive genesManuscript (preprint) (Other academic)
  • 320.
    Oja, Jane
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Vahtra, Johanna
    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. Institute of Ecology and Earth Sciences University of Tartu Tartu Estonia.
    Kohout, Petr
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia; Acad Sci Czech Republ, Inst Bot, CS-25243 Pruhonice, Czech Republic.
    Kull, Tiiu
    Univ Life Sci, Inst Agr & Environm Sci Estonian, 5 Kreutzwaldi, EE-51014 Tartu, Estonia.
    Rannap, Riinu
    Univ Tartu, Inst Ecol & Earth Sci, 46 Vanemuise, EE-51014 Tartu, Estonia.
    Kõljalg, Urmas
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Tedersoo, Leho
    Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Local-scale spatial structure and community composition of orchid mycorrhizal fungi in semi-natural grasslands2017In: Mycorrhiza, ISSN 0940-6360, E-ISSN 1432-1890, Vol. 27, no 4, p. 355-367Article in journal (Refereed)
    Abstract [en]

    Orchid mycorrhizal (OrM) fungi play a crucial role in the ontogeny of orchids, yet little is known about how the structure of OrM fungal communities varies with space and environmental factors. Previous studies suggest that within orchid patches, the distance to adult orchids may affect the abundance of OrM fungi. Many orchid species grow in species-rich temperate semi-natural grasslands, the persistence of which depends on moderate physical disturbances, such as grazing and mowing. The aim of this study was to test whether the diversity, structure and composition of OrM fungal community are influenced by the orchid patches and management intensity in semi-natural grasslands. We detected putative OrM fungi from 0 to 32 m away from the patches of host orchid species (Orchis militaris and Platanthera chlorantha) in 21 semi-natural calcareous grasslands using pyrosequencing. In addition, we assessed different ecological conditions in semi-natural grasslands but primarily focused on the effect of grazing intensity on OrM fungal communities in soil. We found that investigated orchid species were mostly associated with Ceratobasidiaceae and Tulasnellaceae and, to a lesser extent, with Sebacinales. Of all the examined factors, the intensity of grazing explained the largest proportion of variation in OrM fungal as well as total fungal community composition in soil. Spatial analyses showed limited evidence for spatial clustering of OrM fungi and their dependence on host orchids. Our results indicate that habitat management can shape OrM fungal communities, and the spatial distribution of these fungi appears to be weakly structured outside the orchid patches.

  • 321. Ollerton, Jeff
    et al.
    Dötterl, Stefan
    Ghorpadé, Kumar
    Heiduk, Annemarie
    Liede-Schumann, Sigrid
    Masinde, Siro
    Meve, Ulrich
    Peter, Craig
    Prieto-Benítez, Samuel
    Punekar, Sachin
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Whittington, Andrew
    Diversity of Diptera families that pollinate Ceropegia (Apocynaceae) trap flowers: An update in light of new data and phylogenetic analyses2017In: Flora: Morphologie, Geobotanik, Oekophysiologie, ISSN 0367-2530, E-ISSN 1618-0585, Vol. 234, p. 233-244Article in journal (Refereed)
    Abstract [en]

    Pollination by flies (Diptera) has been important to the diversification and ecology of the flowering plants, but is poorly understood in contrast to pollination by other groups such as bees, butterflies and birds. Within the Apocynaceae the genera Ceropegia and Riocreuxia temporarily trap flies, releasing them after a fixed, species-specific period of time, during which pollination and/or pollen removal occurs. This "trap flower" pollination system shows convergent evolution with unrelated species in other families and fascinated Stefan Vogel for much of his career, leading to ground-breaking work on floral function in Ceropegia (Apocynaceae). In this new study we extend the work of the latest broad analysis published by some of the authors (Ollerton et al., 2009 − Annals of Botany). This incorporates previously unpublished data from India and Africa, as well as recently published information, on the diversity of pollinators exploited by Ceropegia. The analyses are based on a more accurate phylogenetic understanding of the relationships between the major groups, and significantly widens the biogeographic scope of our understanding of fly pollination within Ceropegia. Information about the pollinators of 69 taxa (species, subspecies and natural varieties) of Ceropegia is now available. Twenty five families of Diptera are known to visit the flowers of Ceropegia, of which sixteen are confirmed as pollinators. Most taxa are pollinated by species from a single family. Overall, there were no major biogeographic differences in the types of Diptera that were used in particular regions, though some subtle differences were apparent. Likewise there were no differences between the two major clades of Ceropegia, but clear differences when comparing the range of Diptera exploited by Ceropegia with that of the stapeliads. This clade, one of the largest in the Asclepiadoideae, is a fascinating example of a species radiation driven by an apparently relatively uniform set of pollinators.

  • 322.
    Onsbring, Henning
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Jamy, Mahwash
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ettema, Thijs J. G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    RNA Sequencing of Stentor Cell Fragments Reveals Transcriptional Changes during Cellular Regeneration2018In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 28, no 8, p. 1281-1288.e3Article in journal (Refereed)
    Abstract [en]

    While ciliates of the genus Stentor are known for their ability to regenerate when their cells are damaged or even fragmented, the physical and molecular mechanisms underlying this process are poorly understood. To identify genes involved in the regenerative capability of Stentor cells, RNA sequencing of individual Stentor polymorphus cell fragments was performed. After splitting a cell over the anterior-posterior axis, the posterior fragment has to regenerate the oral apparatus, while the anterior part needs to regenerate the hold fast. Altogether, differential expression analysis of both posterior and anterior S. polymorphus cell fragments for four different post-split time points revealed over 10,000 upregulated genes throughout the regeneration process. Among these, genes involved in cell signaling, microtubule-based movement, and cell cycle regulation seemed to be particularly important during cellular regeneration. We identified roughly nine times as many upregulated genes in regenerating S. polymorphus posterior fragments as compared to anterior fragments, indicating that regeneration of the anterior oral apparatus is a complex process that involves many genes. Our analyses identified several expanded groups of genes, such as dual-specific tyrosine-(Y)-phosphorylation-regulated kinases and MORN domain-containing proteins that seemingly act as key regulators of cellular regeneration. In agreement with earlier morphological and cell biological studies [1, 2], our differential expression analyses indicate that cellular regeneration and vegetative division share many similarities.

  • 323.
    Onut-Brännström, Ioana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ament-Velásquez, Sandra Lorena
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hiltunen, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Resl, Philipp
    Vanderpool, Dan
    Yamamoto, Yoshikazu
    Spribille, Toby
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Constraints to sex by a single mating type? Genomic and population analyses reveal insight into the reproductive biology of ThamnoliaManuscript (preprint) (Other academic)
  • 324.
    Onuţ-Brännström, Ioana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Benjamin, Mitchell
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Starri, Heiðmarsson
    Icelandic Institute of Natural History, Borgir Nordurslod, Iceland.
    Andersson, Martin G.I.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Lindström, Eva S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sharing of photobionts in sympatric populations of Thamnolia and Cetraria lichens: evidence from high-throughput sequencing2018In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 8, article id 4406Article in journal (Refereed)
    Abstract [en]

    In this study, we explored the diversity of green algal symbionts (photobionts) in sympatric populations of the cosmopolitan lichen-forming fungi Thamnolia and Cetraria. We sequenced with both Sanger and Ion Torrent High-Throughput Sequencing technologies the photobiont ITS-region of 30 lichen thalli from two islands: Iceland and Öland. While Sanger recovered just one photobiont genotype from each thallus, the Ion Torrent data recovered 10–18 OTUs for each pool of 5 lichen thalli, suggesting that individual lichens can contain heterogeneous photobiont populations. Both methods showed evidence for photobiont sharing between Thamnolia and Cetraria on Iceland. In contrast, our data suggest that on Öland the two mycobionts associate with distinct photobiont communities, with few shared OTUs revealed by Ion Torrent sequencing. Furthermore, by comparing our sequences with public data, we identified closely related photobionts from geographically distant localities. Taken together, we suggest that the photobiont composition in Thamnolia and Cetraria results from both photobiont-mycobiont codispersal and local acquisition during mycobiont establishment and/or lichen growth. We hypothesize that this is a successful strategy for lichens to be flexible in the use of the most adapted photobiont for the environment.

  • 325.
    Onuţ-Brännström, Ioana
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tibell, Leif
    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.
    A worldwide phylogeography of the whiteworm lichens Thamnolia reveals three lineages with distinct habitats and evolutionary histories2017In: Ecology and Evolution, ISSN 2045-7758, E-ISSN 2045-7758, Vol. 7, no 10, p. 3602-3615Article in journal (Refereed)
    Abstract [en]

    Thamnolia is a lichenized fungus with an extremely wide distribution, being encountered in arctic and alpine environments in most continents. In this study, we used molecular markers to investigate the population structure of the fungal symbiont and the associated photosynthetic partner of Thamnolia. By analyzing molecular, morphological, and chemical variation among 253 specimens covering the species distribution range, we revealed the existence of three mycobiont lineages. One lineage (Lineage A) is confined to the tundra region of Siberia and the Aleutian Islands, a second (Lineage B) is found in the high alpine region of the Alps and the Carpathians Mountains, and a third (Lineage C) has a worldwide distribution and covers both the aforementioned ecosystems. Molecular dating analysis indicated that the split of the three lineages is older than the last glacial maximum, but the distribution ranges and the population genetic analyses suggest an influence of last glacial period on the present-day population structure of each lineage. We found a very low diversity of Lineage B, but a higher and similar one in Lineages A and C. Demographic analyses suggested that Lineage C has its origin in the Northern Hemisphere, possibly Scandinavia, and that it has passed through a bottleneck followed by a recent population expansion. While all three lineages reproduce clonally, recombination tests suggest rare or past recombination in both Lineages A and C. Moreover, our data showed that Lineage C has a comparatively low photobiont specificity, being found associated with four widespread Trebouxia lineages (three of them also shared with other lichens), while Lineages A and B exclusively harbor T. simplex s. lat. Finally, we did not find support for the recognition of taxa in Thamnolia based on either morphological or chemical characters.

  • 326.
    Onuț-Brännström, Ioana
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The puzzle of lichen symbiosis: Pieces from Thamnolia2017Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Symbiosis brought important evolutionary novelties to life on Earth. Lichens, the symbiotic entities formed by fungi, photosynthetic organisms and bacteria, represent an example of a successful adaptation in surviving hostile environments. Yet many aspects of the lichen symbiosis remain unexplored. This thesis aims at bringing insights into lichen biology and the importance of symbiosis in adaptation. I am using as model system a successful colonizer of tundra and alpine environments, the worm lichens Thamnolia, which seem to only reproduce vegetatively through symbiotic propagules. When the genetic architecture of the mating locus of the symbiotic fungal partner was analyzed with genomic and transcriptomic data, a sexual self-incompatible life style was revealed. However, a screen of the mating types ratios across natural populations detected only one of the mating types, suggesting that Thamnolia has no potential for sexual reproduction because of lack of mating partners. Genetic data based on molecular markers revealed the existence of three morphologically cryptic Thamnolia lineages. One lineage had a clear recombination structure and was found in the tundra region of Siberia, shorelines of Scandinavia, and Aleutian Islands. The other lineage was allopatric with the previous, and was highly clonal; only two haplotypes were found across the alpine region of central and southeastern Europe. However, the third lineage was sympatric with the other two, had a worldwide distribution, and although highly clonal, showed a recombinant population structure. Our data could not reveal whether the signs of recombination resulted from rare recombination events due to the extreme low frequency of the other mating type or ancestral variation before the loss of sexual reproduction. However, investigation of Thamnolia’s green algal population showed that in different localities, different algal genotypes were associated with the same fungal genotype. Furthermore, data suggest that Thamnolia carried several algal genotypes within its thalli and shared them with other distantly related but ecologically similar fungal species.

  • 327. 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.

  • 328. Osathanunkul, Maslin
    et al.
    Madesis, Panagiotis
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bar-HRM for Authentication of Plant-Based Medicines: Evaluation of Three Medicinal Products Derived from Acanthaceae Species2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 5Article in journal (Refereed)
    Abstract [en]

    Medicinal plants are used as a popular alternative to synthetic drugs, both in developed and developing countries. The economic importance of the herbal and natural supplement industry is increasing every year. As the herbal industry grows, consumer safety is one issue that cannot be overlooked. Herbal products in Thai local markets are commonly sold without packaging or labels. Plant powders are stored in large bags or boxes, and therefore buying local herbal products poses a high risk of acquiring counterfeited, substituted and/or adulterated products. Due to these issues, a reliable method to authenticate products is needed. Here DNA barcoding was used in combination with High Resolution Melting analysis (Bar-HRM) to authenticate three medicinal Acanthaceae species (Acanthus ebracteatus, Andrographis paniculata and Rhinacanthus nasutus) commonly used in Thailand. The rbcL barcode was selected for use in primers design for HRM analysis to produce standard melting profiles of the selected species. Melting data from the HRM assay using the designed rbcL primers showed that the three chosen species could be distinguished from each other. HRM curves of all fifteen test samples indicated that three of tested products did not contain the indicated species. Two closely related species (A. paniculata and R. nasutus), which have a high level of morphological similarity, were interchanged with one another in three tested products. Incorrect information on packaging and labels of the tested herbal products was the cause of the results shown here. Morphological similarity among the species of interest also hindered the collection process. The Bar-HRM method developed here proved useful in aiding in the identification and authentication of herbal species in processed samples. In the future, species authentication through Bar-HRM could be used to promote consumer trust, as well as raising the quality of herbal products.

  • 329.
    Osathanunkul, Maslin
    et al.
    Chiang Mai Univ, Fac Sci, Dept Biol, 239 Huay Kaew Rd, Chiang Mai 50200, Thailand..
    Suwannapoom, Chatmongkon
    Chinese Acad Sci, State Key Lab Genet Resources & Evolut State, Kunming Inst Zool, Kunming 650223, Peoples R China.;Chinese Acad Sci, Yunnan Lab Mol Biol Domest Anim, Kunming Inst Zool, Kunming 650223, Peoples R China.;Univ Phayao, Sch Agr & Nat Resources, Phayao 56000, Thailand..
    Osathanunkul, Kitisak
    Maejo Univ, Fac Sci, Dept Comp Sci, Chiang Mai 50290, Thailand..
    Madesis, Panagiotis
    Ctr Res & Technol Hellas CERTH, Inst Appl Biosci, Thessaloniki, Greece..
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, POB 1172, NO-0318 Oslo, Norway..
    Evaluation of DNA barcoding coupled high resolution melting for discrimination of closely related species in phytopharmaceuticals2016In: Phytomedicine, ISSN 0944-7113, E-ISSN 1618-095X, Vol. 23, no 2, p. 156-165Article in journal (Refereed)
    Abstract [en]

    Background: Phytopharmaceuticals are increasingly popular as alternative medicines, but poorly regulated in many countries. The manufacturers of these products should be subject to strict controls regarding each product's quality and constituents. Routine testing and identification of raw materials should be performed to ensure that the raw materials used in pharmaceutical products are suitable for their intended use. Hypothesis/purpose: We have applied DNA Barcoding High Resolution Melting (Bar-HRM), an emerging method for identifying of medicinal plant species based on DNA dissociation kinetics and DNA barcoding, for the authentication of medicinal plant species. Study design: Commonly commercialized Thai medicinal plants that are widely used for medicinal purposes were used in this study. Publicly available sequences of four plastid markers were used for universal primer design. Species discrimination efficiency of the designed primers was evaluated as single and multi-locus analyses by using the primers sets. Methods: HRM analysis was performed in triplicate on each of the 26 taxa to establish the T-m for each primer set (matK, rbcLA, rbcLB, rbcLC, rpoC1, and trnL). The shapes of the melting curves were analyzed to distinguish the different plant species. Bar-HRM species identification success rates were assessed for each single-locus as well as for multi-locus combinations to establish the optimal combination of primer sets. Results: In single locus analysis the rpoC1 primer set gave the highest discrimination (53%), and in multi locus analysis this could be increased from 87% to 99% depending on the total number of regions included. Different combinations proved to be more or less effective at discrimination, depending on the genus or family examined. Conclusions: Bar-HRM has proven to be a cost-effective and reliable method for the identification of species in this study of Thai medicinal plants, and results show an identification success rate of 99% among species in the test set.

  • 330.
    Osathanunkul, Maslin
    et al.
    Chiang Mai Univ, Fac Sci, Dept Biol, Chiang Mai 50200, Thailand..
    Suwannapoom, Chatmongkon
    Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources & Evolut, Kunming 650223, Peoples R China.;Chinese Acad Sci, Kunming Inst Zool, Yunnan Lab Mol Biol Domest Anim, Kunming 650223, Peoples R China.;Chiang Mai Univ, Sci & Technol Res Inst, Chiang Mai 50200, Thailand..
    Ounjai, Sarawut
    Chiang Mai Univ, Fac Sci, Dept Biol, Chiang Mai 50200, Thailand..
    Rora, Jantarika A.
    Chiang Mai Univ, Fac Sci, Dept Biol, Chiang Mai 50200, Thailand..
    Madesis, Panagiotis
    Ctr Res & Technol Hellas, Inst Appl Biosci, Thessaloniki, Greece..
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, NO-0318 Oslo, Norway..
    Refining DNA Barcoding Coupled High Resolution Melting for Discrimination of 12 Closely Related Croton Species2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 9, article id e0138888Article in journal (Refereed)
    Abstract [en]

    DNA barcoding coupled high resolution melting (Bar-HRM) is an emerging method for species discrimination based on DNA dissociation kinetics. The aim of this work was to evaluate the suitability of different primer sets, derived from selected DNA regions, for Bar-HRM analysis of species in Croton (Euphorbiaceae), one of the largest genera of plants with over 1,200 species. Seven primer pairs were evaluated (matK, rbcL1, rbcL2, rbcL3, rpoC, trnL and ITS1) from four plastid regions, matK, rbcL, rpoC, and trnL, and the nuclear ribosomal marker ITS1. The primer pair derived from the ITS1 region was the single most effective region for the identification of the tested species, whereas the rbcL1 primer pair gave the lowest resolution. It was observed that the ITS1 barcode was the most useful DNA barcoding region overall for species discrimination out of all of the regions and primers assessed. Our Bar-HRM results here also provide further support for the hypothesis that both sequence and base composition affect DNA duplex stability.

  • 331.
    Otieno, Joseph
    et al.
    Muhimbili University of Health and Allied Sciences.
    Abihudi, Siri
    Muhimbili University of Health and Allied Sciences.
    Veldman, Sarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nahashon, Michael
    van Andel, Tinde
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Vernacular dominance in folk taxonomy: acase study of ethnospecies in medicinal plant trade in Tanzania2015In: Journal of Ethnobiology and Ethnomedicine, ISSN 1746-4269, E-ISSN 1746-4269, Vol. 11, article id 10Article in journal (Refereed)
  • 332.
    Ouarghidi, Abderrahim
    et al.
    Laboratoire de Biotec-VRV, Faculty of Sciences, University of Cadi Ayyad.
    Powell, Bronwen
    School of Dietetics and Human Nutrition, McGill University.
    Martin, Gary J.
    Rachel Carson Center for Society and Environment, Ludwig Maximilian University.
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Abbad, Abdelaziz
    Laboratoire de Biotec-VRV, Faculty of Sciences, University of Cadi Ayyad.
    Species substitution in medicinal roots and possible implications for toxicity of herbal remedies in Morocco2012In: Economic Botany, ISSN 0013-0001, E-ISSN 1874-9364, Vol. 66, no 4, p. 370-382Article in journal (Refereed)
    Abstract [en]

    Herbal medicine is an integral part of health care in Morocco and is widely used by Moroccans. However, the efficacy and safety of traditional plant-based medicine in Morocco is threatened by insufficient knowledge about practices of adulteration and substitution. These issues are of particular importance when subterranean plant parts are employed. A combination of qualitative and quantitative methods was used to identify where and why confusion (accidental substitution) and intentional substitution occurs in root-based medicines sold in Marrakech. Additionally we examined local perceptions of the toxicological risks posed by substitution.         We recorded a total of 20 species (34 unique cases) of roots for which substitution or confusion was reported by either herbalists or collectors. Substitution or confusion occurred in 54.6 % of the 33 most commonly sold medicinal roots, with herbalists reporting substitution in more species than collectors. Collectors and herbalists cited poor availability of roots (in part due to overexploitation of wild resources), high demand, high prices, and lack of knowledge as factors driving substitution and confusion. Roots for which substitution was reported were significantly more difficult for herbalists to identify. Moreover, profit was higher for roots for which intentional substitution was reported. Despite the detailed knowledge held by many herbalists and a long tradition of use of herbal medicine in Morocco, doctors and pharmacists had dismissive attitudes towards traditional medicine and expressed concern about both efficacy and safety of medicinal plant use. Given the high rates of substitution and confusion documented by this study, there is an urgent need for appropriate regulation of herbal remedies in Morocco, a conclusion embraced by herbalists and Western-trained medical practitioners alike.

  • 333. Owe-Larsson, Björn
    et al.
    Nordin, Anders
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sohrabi, Mohammad
    Circinaria arida spec. nova and the ‘Aspicilia desertorum’ complex2011In: Biomonitoring, Ecology, and Systematics of Lichens: Recognizing the Lichenological Legacy of Thomas H. Nash III on his 65th Birthday / [ed] Scott T. Bates et al., Berlin/Stuttgart: J. Cramer , 2011, p. 235-246Chapter in book (Refereed)
    Abstract [en]

    Circinaria arida sp. nova is described from the Sonoran area. In the Sonoran Desert Lichen Flora 3 it was tentatively treated as Aspicilia desertorum. This name, however, is based on Lecanora desertorum, an illegitimate name introduced by Krempelhuber for both vagrant and saxicolous taxa, but usually only applied to non-vagrant, saxicolous specimens. In the analysis presented here these are shown to represent more than one taxon. For American specimens the epithet elmorei is available, and the combination Circinaria elmorei is proposed.

  • 334.
    Oxelman, Bengt
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology.
    Jonsell, Bengt
    Uppsala University, Music and Museums, The Linnean Gardens of Uppsala, Botanical Garden.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Music and Museums, The Linnean Gardens of Uppsala, Botanical Garden.
    (1476) Proposal to Conserve the Name Viscaria against Steris (Caryophyllaceae, Sileneae)2001In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 50, no 1, p. 281-282Article in journal (Refereed)
  • 335.
    Oxelman, Bengt
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Popp, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lazkov, Georgy
    Frajman, Bozo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Eggens, Frida
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Erixon, Per
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Långström, Elisabeth
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Rautenberg, Anja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Treelike and reticulate phylogeny of Sileneae and its implications on taxonomy2005In: XVII International Botanical Congress: abstracts : Vienna, Austria, Europe, Austria Center Vienna 17-23 July 2005 : 100 Years after the II IBC in Vienna 1905, 2005, p. 11-11Conference paper (Other academic)
  • 336.
    Paukov, Alexander
    et al.
    Ural Fed Univ, Inst Nat Sci, Dept Biol, Ekaterinburg, Russia..
    Nordin, Anders
    Uppsala University, Music and Museums, Museum of Evolution.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Frolov, Ivan
    Univ South Bohemia, Dept Bot, Fac Sci, Ceske Budejovice, Czech Republic..
    Vondrak, Jan
    Acad Sci, Inst Bot, Pruhonice, Czech Republic.;Czech Univ Life Sci Prague, Fac Environm Sci, Suchdol, Czech Republic..
    Aspicilia goettweigensis (Megasporaceae, lichenized Ascomycetes) – a poorly known and overlooked species in Europe and Russia2017In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 35, no 5, p. 595-601Article in journal (Refereed)
    Abstract [en]

    Aspicilia goettweigensis is a poorly known species from xerothermic siliceous rocks in Europe. It is considered to be common in the Czech Republic and it is new to Hungary and Russia. The main diagnostic character is formation of cracked, popcorn-like, areoles in the central parts of the thalli. Analysis of nrITS sequences revealed its close relationship to Aspicilia subdepressa and A. volcanica. TLC revealed stictic acid in analysed A. goettweigensis samples. A key to non-lobate Aspicilia with stictic acid known from Europe is provided.

  • 337. Pawlowski, Jan
    et al.
    Audic, Stephane
    Adl, Sina
    Bass, David
    Belbahri, Lassaad
    Berney, Cedric
    Bowser, Samuel S.
    Cepicka, Ivan
    Decelle, Johan
    Dunthorn, Micah
    Fiore-Donno, Anna Maria
    Gile, Gillian H.
    Holzmann, Maria
    Jahn, Regine
    Jirku, Miloslav
    Keeling, Patrick J.
    Kostka, Martin
    Kudryavtsev, Alexander
    Lara, Enrique
    Lukes, Julius
    Mann, David G.
    Mitchell, Edward A. D.
    Nitsche, Frank
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Saunders, Gary W.
    Simpson, Alastair G. B.
    Smirnov, Alexey V.
    Spouge, John L.
    Stern, Rowena F.
    Stoeck, Thorsten
    Zimmermann, Jonas
    Schindel, David
    de Vargas, Colomban
    CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms2012In: PLoS biology, ISSN 1544-9173, E-ISSN 1545-7885, Vol. 10, no 11, p. e1001419-Article in journal (Refereed)
  • 338.
    Pennell, Matthew W.
    et al.
    Univ British Columbia, Dept Zool, Vancouver, BC, Canada;Univ British Columbia, Biodivers Res Ctr, Vancouver, BC, Canada.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London, England.
    Peichel, Catherine L.
    Univ Bern, Inst Ecol & Evolut, Bern, Switzerland.
    Transitions in sex determination and sex chromosomes across vertebrate species2018In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 27, no 19, p. 3950-3963Article in journal (Refereed)
    Abstract [en]

    Despite the prevalence of sexual reproduction across eukaryotes, there is a remarkable diversity of sex-determination mechanisms. The underlying causes of this diversity remain unclear, and it is unknown whether there are convergent trends in the directionality of turnover in sex-determination mechanisms. We used the recently assembled Tree of Sex database to assess patterns in the evolution of sex-determination systems in the remarkably diverse vertebrate clades of teleost fish, squamate reptiles and amphibians. Contrary to theoretical predictions, we find no evidence that the evolution of separate sexes is irreversible, as transitions from separate sexes to hermaphroditism occur at higher rates than the reverse in fish. We also find that transitions from environmental sex determination to genetic sex determination occur at higher rates than the reverse in both squamates and fish, suggesting that genetic sex determination is more stable. However, our data are not consistent with the hypothesis that heteromorphic sex chromosomes are an evolutionary trap. Rather, we find similar transition rates between homomorphic and heteromorphic sex chromosomes in both fish and amphibians, and to environmental sex determination from heteromorphic vs. homomorphic sex chromosome systems in fish. Finally, we find that transitions between male and female heterogamety occur at similar rates in amphibians and squamates, while transitions to male heterogamety occur at higher rates in fish. Together, these results provide the most comprehensive view to date of the evolution of vertebrate sex determination in a phylogenetic context, providing new insight into long-standing questions about the evolution of sexual reproduction.

  • 339.
    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.

  • 340.
    Pent, Mari
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia..
    Poldmaa, Kadri
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, Tartu, Estonia.
    Bacterial Communities in Boreal Forest Mushrooms Are Shaped Both by Soil Parameters and Host Identity2017In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, Vol. 8, article id 836Article in journal (Refereed)
    Abstract [en]

    Despite recent advances in understanding the microbiome of eukaryotes, little is known about microbial communities in fungi. Here we investigate the structure of bacterial communities in mushrooms, including common edible ones, with respect to biotic and abiotic factors in the boreal forest. Using a combination of culture-based and Illumina high-throughput sequencing, we characterized the bacterial communities in fruitbodies of fungi from eight genera spanning four orders of the class Agaricomycetes (Basidiomycota). Our results revealed that soil pH followed by fungal identity are the main determinants of the structure of bacterial communities in mushrooms. While almost half of fruitbody bacteria were also detected from soil, the abundance of several bacterial taxa differed considerably between the two environments. The effect of host identity was significant at the fungal genus and order level and could to some extent be ascribed to the distinct bacterial community of the chanterelle, representing Cantharellales-the earliest diverged group of mushroom-forming basidiomycetes. These data suggest that besides the substantial contribution of soil as a major taxa source of bacterial communities in mushrooms, the structure of these communities is also affected by the identity of the host. Thus, bacteria inhabiting fungal fruitbodies may be non-randomly selected from environment based on their symbiotic functions and/or habitat requirements.

  • 341.
    Pereus, D.
    et al.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    Otieno, J. N.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    Ghorbani, Abdolbaset
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kocyan, A.
    Univ Potsdam, Biodivers Res Systemat Bot, D-14469 Potsdam, Germany.
    Hilonga, S.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, NO-0318 Oslo, Norway.
    Diversity of Hypoxis species used in ethnomedicine in Tanzania2019In: South African Journal of Botany, ISSN 0254-6299, E-ISSN 1727-9321, Vol. 122, p. 336-341Article in journal (Refereed)
    Abstract [en]

    The corms of different Hypoxis species (Hypoxidaceae) are used for the treatment and management of a variety of human ailments and disorders in African traditional medicine. However, the used corms are morphologically similar and it is not known whether this has resulted in different species being harvested, prescribed and sold as the same species. Ethnomedicinal information regarding its use in Tanzania is scanty and the available ethnobotanical information about the plants is mostly from various studies done outside Tanzania. The objective of the study was to document the diverse uses of Hypoxis in Tanzania and study what species are used and whether preferences exist for specific species. Focus group discussions and in depth interviews with informants were done in 15 regions of Tanzania to document local uses of Hypoxis species and collect vouchers for identification. Traditional practitioners use Hypoxis to manage a variety of human illness in Tanzania, and appear to use different species indiscriminately for medicine, socio-cultural applications and for food. Medicinal uses include treatment of benign prostate hypertrophy, cancer, diabetes, gout, headache, HIV/AIDS, infertility, ringworms, stomachache, and urinary tract infections. In Tanzania, different Hypoxis species are used indiscriminately for a range of sociocultural and medicinal purposes. The reported medicinal uses could aid testing and evaluation of traditional herbal medicine and more research is needed to test their pharmacological effects. (C) 2018 SAAB. Published by Elsevier B.V. All rights reserved.

  • 342.
    Perrigo, Allison
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Diversity of dictyostelid social amoebae in high latitude habitats of Northern Sweden2013In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 58, no 1, p. 185-198Article in journal (Refereed)
    Abstract [en]

    The dictyostelid social amoebae (Dictyostelia) occur in terrestrial habitats worldwide. It has been observed previously that their diversity decreases with increasing latitude and altitude. Here we look at dictyostelid diversity in the high latitude habitats of Northern Sweden. Dictyostelids were recovered from soil samples using traditional plating methods and then identified using morphological characters and molecular sequence (small subunit ribosomal RNA) data. In total, nine species were recovered, including two new species, described herein as Dictyostelium barbibulus and Polysphondylium fuscans. The species diversity found here is discussed in relation to previous findings in the area as well as other high-latitude studies, and biogeographical patterns are examined. The total number of species found in Northern Sweden is lower than the numbers recorded for regions further south in Europe, a finding consistent with a latitudinal gradient of species diversity. Our findings highlight the benefit of using molecular data for accurate species identification in Dictyostelia and the need for a continued sampling effort to better understand their diversity and distribution, especially in high latitude habitats.

  • 343.
    Perrigo, Allison L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Diversity Underfoot: Systematics and Biogeography of the Dictyostelid Social Amoebae2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Dictyostelids (Amoebozoa) are a group of social amoebae consisting of approximately 150 species, which are found in terrestrial habitats worldwide. They are divided into eight major clades based on molecular phylogeny, and within these clades are many species complexes. Some species are seemingly cosmopolitan in distribution, while others are geographically restricted. In this thesis dictyostelids were recovered from high latitude habitats (soils in Sweden and Iceland) as well as from the soles of shoes. Morphological characters and DNA sequence analyses were used to identify isolates that were recovered and delimit new species, as well as to investigate the monophyly of Dictyostelium aureostipes. Nine species were reported from Northern Sweden and four from Iceland. Among the isolates recorded in Sweden were two new species, described as D. barbibulus and Polysphondylium fuscans. P. fuscans was among the four species recovered from footwear, contributing evidence for anthropogenic transport of dictyostelids. Ecological patterns were assessed using linear regression and generalized linear models. The ecological analyses of dictyostelids recovered from Iceland indicate that these organisms are most frequently found in soils of near-neutral pH, but also exhibit a species richness peak in moderately acidic soils. These analyses indicate that in Iceland dictyostelid species richness decreases with altitude, and in the northern hemisphere the species richness increases with decreasing latitude. A three-region analysis of the D. aureostipes species complex indicated that this species is in fact made up of at least five phylogenetically distinct clades, and in light of this the group is in need of taxonomic revision. These results indicate that the dictyostelid species richness is higher than previously known, especially in high-latitude regions, and that even seemingly well-defined species may harbour cryptic diversity. Presently, species ranges may be expanding via anthropogenic dispersal but despite this, the dictyostelids are found to exhibit biogeographic trends well known from macroorganisms, such as a latitudinal gradient of species richness.

  • 344.
    Perrigo, Allison L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Moya-Larano, Jordi
    Estacion Experimental de Zonas Aridas - CSIC, Functional and Evolutionary Ecology.
    Baldauf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Everything is not everywhere: a latitudinal gradient of protist diversityManuscript (preprint) (Other academic)
  • 345.
    Perrigo, Allison L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The  yellow  slime  mold  is  a  red  herring:  large  hidden  diversity  in  a  single  protist  morphospeciesManuscript (preprint) (Other academic)
  • 346.
    Perrigo, Allison L.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    What's on your boots: an investigation into the role we play in protist dispersal2012In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 39, no 5, p. 998-1003Article in journal (Refereed)
    Abstract [en]

    D. M. Wilkinson (2010, Journal of Biogeography, 37, 393–397) suggested that anthropogenic dispersal is an understudied and potentially important factor in terrestrial protist biogeography. We investigated human footwear as a potential vector of dictyostelids, a diverse group of amoebae that includes both geographically restricted and cosmopolitan species. Eighteen pairs of boots were examined and dictyostelids were isolated from nearly all samples larger than 5.0 g. In total, six dictyostelid isolates were recovered, corresponding to four species –Dictyostelium minutum, D. sphaerocephalum, D. leptosomopsis and a new species, Polysphondylium sp. 1. Myxogastrid amoebae and acrasid-like aggregations were also observed. Thus anthropogenic dispersal of naked amoebae appears to occur. The possible role of variations in dictyostelid fruiting body morphologies in dispersal potential is also discussed. These results support Wilkinson’s proposal and suggest that dictyostelids may be a useful group with which to study anthropogenic dispersal of terrestrial protists.

  • 347.
    Perrigo, Allison
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    What’s on your boots?: an investigation into the role we play in protistian dispersal2011Conference paper (Other academic)
  • 348.
    Persson, Claes
    et al.
    Göteborgs Universitet.
    Ståhl, BertilUppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Flora of Ecuador: 22. Myricaceae ; 23. Juglandaceae ; 24. Salicaceae ; 25A. Betulaceae ; 25B. Casuarinaceae ; 26A. Ulmaceae ; 26B. Cannabaceae2014Collection (editor) (Other academic)
  • 349. Persson, Claes
    et al.
    Ståhl, BertilUppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Flora of Ecuador: 82–84. Leguminosae – Phaseoleae, Part 1.2015Collection (editor) (Other academic)
    Abstract [en]

    The following legumegenera in Ecuador are revised: Cajanus (1 sp.), Calopogonium (3 spp.), Centrosema(9 spp.), Cologania (1 sp.), Galactia (2 spp.), Mucuna (8 spp.), Pueraria (1 sp.),Rhynchosia (7 spp.) and Teramnus (2 spp.). The species of Cajanus and Pueraria,C. cajan and P. phaseoloides, originate from Asia and have become established inseminatural, disturbed habitats. One new species, Mucuna ecuatoriana, is describedand several lectotypifications are made. Keys to all species are presented withinrespective genus along with synonymy, specimen citations, taxonomic references,and information on ecology and distribution. Many species are illustrated with eitherline drawings and/or colour photos.

  • 350.
    Pettersson, John H.-O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Origin of the Genus Flavivirus and the Ecology of Tick-Borne Pathogens2013Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The present thesis examines questions related to the temporal origin of the Flavivirus genus and the ecology of tick-borne pathogens. In the first study, we date the origin and divergence time of the Flavivirus genus. It has been argued that the first flaviviruses originated after the last glacial maximum. This has been contradicted by recent analyses estimating that the tick-borne flaviviruses emerged at least before 16,000 years ago. It has also been argued that the Powassan virus was introduced into North America at the time between the opening and splitting of the Beringian land bridge. Supported by tip date and biogeographical calibration, our results suggest that this genus originated circa 120,000 (156,100–322,700) years ago if the Tamana bat virus is included in the genus, or circa 85,000 (63,700–109,600) years ago excluding the Tamana bat virus. In the second study we estimate the prevalence of tick-borne encephalitis virus (TBEV) in host-seeking Ixodes ricinus from 29 localities in Sweden and compare our data with those of neighbouring countries. Nymphs and adult ticks were screened for TBEV using a real-time PCR assay. The mean TBEV prevalence for all tick stages combined was 0.26% for Sweden and 0.28% for all Scandinavian countries, excluding Iceland. The low prevalence of TBEV in nature may partly be explained by the fact that TBEV occurs in spatially small foci and that the inclusion of ticks from non-infected foci will reduce the prevalence estimate. In the third and fourth study, we conducted the first large-scale investigations to estimate the prevalence and geographical distribution of Anaplasma spp. and Rickettsia spp. in host-seeking larvae, nymphs and adults of I. ricinus ticks in Sweden. Ticks were collected from several localities in central and southern Sweden and were subsequently screened for the presence of Anaplasma spp. and Rickettsia spp. using a real-time PCR assay. For all active tick stages combined, the mean prevalence of Anaplasma spp. and Rickettsia spp. in I. ricinus in Sweden was estimated to 1.1% and 4.8%, respectively. It was also shown that A. phagocytophilum and R. helvetica are the main Anaplasma and Rickettsia species occurring in Sweden.

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