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  • 1.
    Abarenkov, Kessy
    et al.
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    Adams, Rachel I.
    Univ Calif Berkeley, Plant & Microbial Biol, Berkeley, CA 94720 USA..
    Irinyi, Laszlo
    Westmead Hosp, Ctr Infect Dis & Microbiol, Mol Mycol Res Lab, Sydney Med Sch, Sydney, NSW, Australia.;Univ Sydney, Marie Bashir Inst Infect Dis & Biosecur, Sydney, NSW, Australia.;Westmead Inst Med Res, Westmead, NSW, Australia..
    Agan, Ahto
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Ambrosio, Elia
    Univ Tartu, Nat Hist Museum, Tartu, Estonia.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia.;Via Calamandrei 2, I-53035 Siena, Italy..
    Antonelli, Alexandre
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden.;Gothenburg Bot Garden, Carl Skottsbergs Gata 22A, S-41319 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, Tartu, Estonia.
    Bengtsson-Palme, Johan
    Univ Gothenburg, Sahlgrenska Acad, Dept Infect Dis, Guldhedsgatan 10, S-41346 Gothenburg, Sweden..
    Bok, Gunilla
    SP Tech Res Inst Sweden, Box 857, S-50115 Boras, Sweden..
    Cangren, Patrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Coimbra, Victor
    Univ Fed Pernambuco UFPE, Dept Micol, CCB, Av Prof Nelson Chaves S-N, BR-50670901 Recife, PE, Brazil..
    Coleine, Claudia
    Univ Tuscia, Dept Ecol & Biol Sci, I-01100 Viterbo, Italy..
    Gustafsson, Claes
    Univ Gothenburg, Herbarium GB, Box 461, S-40530 Gothenburg, Sweden..
    He, Jinhong
    Chinese Acad Sci, South China Bot Garden, 723 Xingke Rd, Guangzhou 510650, Guangdong, Peoples R China..
    Hofmann, Tobias
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Kristiansson, Erik
    Chalmers, Dept Math Sci, S-41296 Gothenburg, Sweden..
    Larsson, Ellen
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Larsson, Tomas
    Univ Gothenburg, Dept Marine Sci, Box 460, S-40530 Gothenburg, Sweden..
    Liu, Yingkui
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Martinsson, Svante
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Meyer, Wieland
    Westmead Hosp, Ctr Infect Dis & Microbiol, Mol Mycol Res Lab, Sydney Med Sch, Sydney, NSW, Australia.;Westmead Inst Med Res, Westmead, NSW, Australia..
    Panova, Marina
    Univ Gothenburg, Dept Marine Sci Tjarno, S-45296 Stromstad, Sweden..
    Pombubpa, Nuttapon
    Univ Calif Riverside, Dept Plant Pathol & Microbiol, Riverside, CA 92521 USA.;Univ Calif Riverside, Inst Integrat Genome Biol, Riverside, CA 92521 USA..
    Ritter, Camila
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Svantesson, Sten
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Scharn, Ruud
    Univ Gothenburg, Dept Earth Sci, Box 460, S-40530 Gothenburg, Sweden..
    Svensson, Ola
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Töpel, Mats
    Univ Gothenburg, Dept Marine Sci, Box 460, S-40530 Gothenburg, Sweden..
    Unterseher, Martin
    Ernst Moritz Arndt Univ Greifswald, Inst Bot & Landscape Ecol, Soldmannstr 15, D-17487 Greifswald, Germany..
    Visagie, Cobus
    Agr & Agri Food Canada, Biodivers Mycol, 960 Carling Ave, Ottawa, ON K1A 0C6, Canada.;Univ Ottawa, Dept Biol, 30 Marie Curie, Ottawa, ON K1N 6N5, Canada..
    Wurzbacher, Christian
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Taylor, Andy F. S.
    James Hutton Inst, Aberdeen AB15 8QH, Scotland.;Univ Aberdeen, Inst Biol & Environm Sci, Cruickshank Bldg, Aberdeen AB24 3UU, Scotland..
    Köljalg, Urmas
    Univ Tartu, Nat Hist Museum, Tartu, Estonia.;Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Schriml, Lynn
    Univ Maryland, Sch Med, Dept Epidemiol & Publ Hlth, Baltimore, MD 21201 USA.;Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA..
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Box 461, S-40530 Gothenburg, Sweden..
    Annotating public fungal ITS sequences from the built environment according to the MIxS-Built Environment standard - a report from a May 23-24, 2016 workshop (Gothenburg, Sweden)2016In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 16, p. 1-15Article in journal (Refereed)
    Abstract [en]

    Recent molecular studies have identified substantial fungal diversity in indoor environments. Fungi and fungal particles have been linked to a range of potentially unwanted effects in the built environment, including asthma, decay of building materials, and food spoilage. The study of the built mycobiome is hampered by a number of constraints, one of which is the poor state of the metadata annotation of fungal DNA sequences from the built environment in public databases. In order to enable precise interrogation of such data - for example, "retrieve all fungal sequences recovered from bathrooms" - a workshop was organized at the University of Gothenburg (May 23-24, 2016) to annotate public fungal barcode (ITS) sequences according to the MIxS-Built Environment annotation standard (http:// gensc.org/ mixs/). The 36 participants assembled a total of 45,488 data points from the published literature, including the addition of 8,430 instances of countries of collection from a total of 83 countries, 5,801 instances of building types, and 3,876 instances of surface-air contaminants. The results were implemented in the UNITE database for molecular identification of fungi (http://unite.ut.ee) and were shared with other online resources. Data obtained from human/animal pathogenic fungi will furthermore be verified on culture based metadata for subsequent inclusion in the ISHAM-ITS database (http:// its. mycologylab.org).

  • 2.
    Adl, Sina M.
    et al.
    Univ Saskatchewan, Dept Soil Sci, Coll Agr & Bioresources, 51 Campus Dr, Saskatoon, SK S7N 5A8, Canada.
    Bass, David
    Nat Hist Museum, Dept Life Sci, Cromwell Rd, London SW7 5BD, England;CEFAS, Barrack Rd, Weymouth DT4 8UB, Dorset, England.
    Lane, Christopher E.
    Univ Rhode Isl, Dept Biol Sci, Kingston, RI 02881 USA.
    Lukes, Julius
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic;Univ South Bohemia, Fac Sci, Ceske Budejovice 37005, Czech Republic.
    Schoch, Conrad L.
    Natl Inst Biotechnol Informat, Natl Lib Med, NIH, Bethesda, MD 20892 USA.
    Smirnov, Alexey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Agatha, Sabine
    Univ Salzburg, Dept Biosci, Hellbrunnerstr 34, A-5020 Salzburg, Austria.
    Berney, Cedric
    CNRS, UMR 7144 AD2M, Grp Evolut Protistes & Ecosyst Pelag, Stn Biol Roscoff, Pl Georges Teissier, F-29680 Roscoff, France.
    Brown, Matthew W.
    Mississippi State Univ, Dept Biol Sci, Starkville, MS 39762 USA;Mississippi State Univ, Inst Genom Biocomp & Biotechnol, Starkville, MS 39762 USA.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Farmakognosi.
    Cepicka, Ivan
    Charles Univ Prague, Dept Zool, Fac Sci, Vinicna 7, CR-12844 Prague, Czech Republic.
    Chistyakova, Lyudmila
    St Petersburg State Univ, Core Facil Ctr Culture Collect Microorganisms, St Petersburg 198504, Russia.
    del Campo, Javier
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Dunthorn, Micah
    Univ Kaiserslautern, Dept Ecol, Erwin Schroedinger St, D-67663 Kaiserslautern, Germany;Univ Duisburg Essen, Dept Eukaryot Microbiol, Univ Str 5, D-45141 Essen, Germany.
    Edvardsen, Bente
    Univ Oslo, Dept Biosci, POB 1066 Blindern, N-0316 Oslo, Norway.
    Eglit, Yana
    Dalhousie Univ, Dept Biol, Halifax B3H 4R2, NS, Canada.
    Guillou, Laure
    Univ Paris 06, Sorbonne Univ, Paris 6, CNRS,UMR 7144 AD2M,Stn Biol Roscoff, Pl Georges Teissier,,CS90074, F-29688 Roscoff, France.
    Hampl, Vladimir
    Charles Univ Prague, Dept Parasitol, Fac Sci, BIOCEV, Prumyslov 595, Vestec 25242, Czech Republic.
    Heiss, Aaron A.
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Hoppenrath, Mona
    DZMB German Ctr Marine Biodivers Res, D-26382 Wilhelmshaven, Germany.
    James, Timothy Y.
    Univ Michigan, Dept Ecol & Evolutionary Biol, Ann Arbor, MI 48109 USA.
    Karnkowska, Anna
    Univ Warsaw, Dept Mol Phylogenet & Evolut, PL-02089 Warsaw, Poland.
    Karpov, Sergey
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Kim, Eunsoo
    Amer Museum Nat Hist, Dept Invertebrate Zool, New York, NY 10024 USA.
    Kolisko, Martin
    Czech Acad Sci, Biol Ctr, Inst Parasitol, Ceske Budejovice 37005, Czech Republic.
    Kudryavtsev, Alexander
    St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia;RAS, Lab Parasit Worms & Protistol, Zool Inst, St Petersburg 199034, Russia.
    Lahr, Daniel J. G.
    Univ Sao Paulo, Dept Zool, Inst Biosci, Matao Travessa 14 Cidade Univ, BR-05508090 Sao Paulo, SP, Brazil.
    Lara, Enrique
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;CSIC, Real Jardim Bot,Plaza Murillo 2, E-28014 Madrid, Spain.
    Le Gall, Line
    Sorbonne Univ, Museum Natl Hist Nat, Inst Systemat Evolut Biodiversit, 57 Rue Cuvier,CP 39, F-75005 Paris, France.
    Lynn, Denis H.
    Univ Guelph, Dept Integrat Biol, Summerlee Sci Complex, Guelph, ON N1G 2W1, Canada;Univ British Columbia, Dept Zool, 4200-6270 Univ Blvd, Vancouver, BC V6T 1Z4, Canada.
    Mann, David G.
    Royal Bot Garden, Edinburgh EH3 5LR, Midlothian, Scotland;Inst Agrifood Res & Technol, C Poble Nou Km 5-5, E-43540 San Carlos de la Rapita, Spain.
    Massana, Ramon
    CSIC, Inst Ciencies Mar, Passeig Maritim Barceloneta 37-49, E-08003 Barcelona, Catalonia, Spain.
    Mitchell, Edward A. D.
    Univ Neuchatel, Lab Soil Biodivers, Rue Emile Argand 11, CH-2000 Neuchatel, Switzerland;Jardin Bot Neuchatel,Chemin Perthuis du Salut 58, CH-2000 Neuchatel, Switzerland.
    Morrow, Christine
    Natl Museums Northern Ireland, Dept Nat Sci, 153 Bangor Rd, Holywood BT18 0EU, England.
    Park, Jong Soo
    Kyungpook Natl Univ, Sch Earth Syst Sci, Dept Oceanog, Daegu, South Korea;Kyungpook Natl Univ, Sch Earth Syst Sci, Kyungpook Inst Oceanog, Daegu, South Korea.
    Pawlowski, Jan W.
    Univ Geneva, Dept Genet & Evolut, CH-1211 Geneva 4, Switzerland.
    Powell, Martha J.
    Univ Alabama, Dept Biol Sci, Tuscaloosa, AL 35487 USA.
    Richter, Daniel J.
    Univ Pompeu Fabra, CSIC, Inst Biol Evolut, Passeig Maritim Barceloneta 37-49, Barcelona 08003, Spain.
    Rueckert, Sonja
    Edinburgh Napier Univ, Sch Appl Sci, Edinburgh EH11 4BN, Midlothian, Scotland.
    Shadwick, Lora
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Shimano, Satoshi
    Hosei Univ, Sci Res Ctr, Chiyoda Ku, 2-17-1 Fujimi, Tokyo, Japan.
    Spiegel, Frederick W.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA.
    Torruella, Guifre
    Univ Paris XI, Lab Evolut & Systemat, F-91405 Orsay, France.
    Youssef, Noha
    Oklahoma State Univ, Dept Microbiol & Mol Genet, Stillwater, OK 74074 USA.
    Zlatogursky, Vasily V.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. St Petersburg State Univ, Fac Biol, Dept Invertebrate Zool, St Petersburg 199034, Russia.
    Zhang, Qianqian
    Chinese Acad Sci, Yantai Inst Coastal Zone Res, Yantai 264003, Peoples R China.
    Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes2019In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 66, no 1, p. 4-119Article in journal (Refereed)
    Abstract [en]

    This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.

  • 3.
    Ajawatanawong, Pravech
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mine the Gaps: Evolution of Eukaryotic Protein Indels and their Application for Testing Deep Phylogeny2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Insertions/deletions (indels) are potentially powerful evolutionary markers, but little is known about their evolution and few tools exist to effectively study them. To address this, I developed SeqFIRE, a tool for automated identification and extraction of indels from protein multiple sequence alignments. The program also extracts conserved alignment blocks, thus covering all major steps in preparing multiple sequence alignments for phylogenetic analysis.

    I then used SeqFIRE to build an indel database, using 299 single copy proteins from a broad taxonomic sampling of mainly multicellular eukaryotes. A total of 4,707 indels were extracted, of which 901 are simple (one genetic event) and 3,806 are complex (multiple events). The most abundant indels are single amino acid simple indels. Indel frequency decreases exponentially with length and shows a linear relationship with host protein size. Singleton indels reveal a strong bias towards insertions (2.31 x deletions on average). These analyses also identify 43 indels marking major clades in Plantae and Fungi (clade defining indels or CDIs), but none for Metazoa.

    In order to study the 3806 complex indels they were first classified by number of states. Analysis of the 2-state complex and simple indels combined (“bi-state indels”) confirms that insertions are over 2.5 times as frequent as deletions. Three-quarters of the complex indels had three-nine states (“slightly complex indels”). A tree-assisted search method was developed allowing me to identify 1,010 potential CDIs supporting all examined major branches of Plantae and Fungi.

    Forty-two proteins were also found to host complex indel CDIs for the deepest branches of Metazoa. After expanding the taxon set for these proteins, I identified a total of 49 non-bilaterian specific CDIs. Parsimony analysis of these indels places Ctenophora as sister taxon to all other Metazoa including Porifera. Six CDIs were also found placing Placozoa as sister to Bilateria. I conclude that slightly complex indels are a rich source of CDIs, and my tree-assisted search strategy could be automated and implemented in the program SeqFIRE to facilitate their discovery. This will have important implications for mining the phylogenomic content of the vast resource of protist genome data soon to become available.

    List of papers
    1. SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
    Open this publication in new window or tab >>SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments
    Show others...
    2012 (English)In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no W1, p. W340-W347Article in journal (Refereed) Published
    Abstract [en]

    Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

    Keywords
    Indels, Alignment, Conserved blocks
    National Category
    Bioinformatics (Computational Biology) Bioinformatics and Systems Biology
    Identifiers
    urn:nbn:se:uu:diva-179937 (URN)10.1093/nar/gks561 (DOI)000306670900056 ()
    Available from: 2012-08-27 Created: 2012-08-27 Last updated: 2018-01-12Bibliographically approved
    2. Evolution of protein indels in plants, animals and fungi
    Open this publication in new window or tab >>Evolution of protein indels in plants, animals and fungi
    2013 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 13, p. 140-Article in journal (Refereed) Published
    Abstract [en]

    Background: Insertions/deletions (indels) in protein sequences are useful as drug targets, protein structure predictors, species diagnostics and evolutionary markers. However there is limited understanding of indel evolutionary patterns. We sought to characterize indel patterns focusing first on the major groups of multicellular eukaryotes. Results: Comparisons of complete proteomes from a taxonically broad set of primarily Metazoa, Fungi and Viridiplantae yielded 299 substantial (>250aa) universal, single-copy (in-paralog only) proteins, from which 901 simple (present/absent) and 3,806 complex (multistate) indels were extracted. Simple indels are mostly small (1-7aa) with a most frequent size class of 1aa. However, even these simple looking indels show a surprisingly high level of hidden homoplasy (multiple independent origins). Among the apparently homoplasy-free simple indels, we identify 69 potential clade-defining indels (CDIs) that may warrant closer examination. CDIs show a very uneven taxonomic distribution among Viridiplante (13 CDIs), Fungi (40 CDIs), and Metazoa (0 CDIs). An examination of singleton indels shows an excess of insertions over deletions in nearly all examined taxa. This excess averages 2.31 overall, with a maximum observed value of 7.5 fold. Conclusions: We find considerable potential for identifying taxon-marker indels using an automated pipeline. However, it appears that simple indels in universal proteins are too rare and homoplasy-rich to be used for pure indel-based phylogeny. The excess of insertions over deletions seen in nearly every genome and major group examined maybe useful in defining more realistic gap penalties for sequence alignment. This bias also suggests that insertions in highly conserved proteins experience less purifying selection than do deletions.

    Keywords
    Indels, Rare genomic changes, Phylogeny, Insertion/deletion, Multiple sequence alignment, Eukaryote evolution, Indel profiles
    National Category
    Natural Sciences
    Identifiers
    urn:nbn:se:uu:diva-204971 (URN)10.1186/1471-2148-13-140 (DOI)000321461800001 ()
    Available from: 2013-08-16 Created: 2013-08-13 Last updated: 2017-12-06Bibliographically approved
    3. An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa
    Open this publication in new window or tab >>An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa
    2014 (English)Article in journal (Refereed) Submitted
    Abstract [en]

    Insertions/deletions (indels) in protein sequences are potential powerful evolutionary markers. However, these characters have rarely been explored systematically at deep phylogenetic levels. Previous analyses of simple (2-state) clade defining indels (CDIs) in universal eukaryotic proteins found none to support any major animal clade. We hypothesized that CDIs might still be found in the remaining population of indels, which we term complex indels. Here, we propose a method for analyzing the simplest class of complex indels the “slightly complex indels”, and use these to investigate deep branches in animal phylogeny. Complex indels with two states, called bi-state indels, show similar evolutionary patterns to singleton simple indels and confirms that insertion mutations are more common than deletions. Exploration of CDIs in 2- to 9-state complex indels shows strong support for all examined branches of fungi and Archaeplastida. Surprisingly, we also found CDIs supporting major branches in animals, particular in vertebrates. We then expanded the search to non-bilaterial animals (Porifera, Cnidaria and Ctenophora). The phylogenetic tree reconstructed by CDIs places the Ctenophore Mnemiopsis leidyi as the deepest branch of animals with 6 CDIs support. Trichoplax adhaerens is closely related to the Bilateria. Moreover, the indel phylogeny shows Nematostella vectensis and Hydra magnipapillata are paraphyletic group and position of Cnidarian branches seems to be problematic in the indel phylogeny because of homoplasy. This might be solved if we discover CDIs from animal specific proteins, which emerged after the universal orthologous proteins.Evolutionary Patterns in Slightly Complex Protein Insertions/Deletions (Indels) and Their Application to the Study of Deep Phylogeny in Metazoa

    National Category
    Other Biological Topics
    Identifiers
    urn:nbn:se:uu:diva-216842 (URN)
    Available from: 2014-01-27 Created: 2014-01-27 Last updated: 2014-04-17Bibliographically approved
  • 4.
    Ajawatanawong, Pravech
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Atkinson, Gemma C.
    Watson-Haigh, Nathan S.
    MacKenzie, Bryony
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    SeqFIRE: a web application for automated extraction of indel regions and conserved blocks from protein multiple sequence alignments2012In: Nucleic Acids Research, ISSN 0305-1048, E-ISSN 1362-4962, Vol. 40, no W1, p. W340-W347Article in journal (Refereed)
    Abstract [en]

    Analyses of multiple sequence alignments generally focus on well-defined conserved sequence blocks, while the rest of the alignment is largely ignored or discarded. This is especially true in phylogenomics, where large multigene datasets are produced through automated pipelines. However, some of the most powerful phylogenetic markers have been found in the variable length regions of multiple alignments, particularly insertions/deletions (indels) in protein sequences. We have developed Sequence Feature and Indel Region Extractor (SeqFIRE) to enable the automated identification and extraction of indels from protein sequence alignments. The program can also extract conserved blocks and identify fast evolving sites using a combination of conservation and entropy. All major variables can be adjusted by the user, allowing them to identify the sets of variables most suited to a particular analysis or dataset. Thus, all major tasks in preparing an alignment for further analysis are combined in a single flexible and user-friendly program. The output includes a numbered list of indels, alignments in NEXUS format with indels annotated or removed and indel-only matrices. SeqFIRE is a user-friendly web application, freely available online at www.seqfire.org/.

  • 5.
    Ajawatanawong, Pravech
    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.
    An automatable method for high throughput analysis of evolutionary patterns in slightly complex indels and its application to the deep phylogeny of Metazoa2014Article in journal (Refereed)
    Abstract [en]

    Insertions/deletions (indels) in protein sequences are potential powerful evolutionary markers. However, these characters have rarely been explored systematically at deep phylogenetic levels. Previous analyses of simple (2-state) clade defining indels (CDIs) in universal eukaryotic proteins found none to support any major animal clade. We hypothesized that CDIs might still be found in the remaining population of indels, which we term complex indels. Here, we propose a method for analyzing the simplest class of complex indels the “slightly complex indels”, and use these to investigate deep branches in animal phylogeny. Complex indels with two states, called bi-state indels, show similar evolutionary patterns to singleton simple indels and confirms that insertion mutations are more common than deletions. Exploration of CDIs in 2- to 9-state complex indels shows strong support for all examined branches of fungi and Archaeplastida. Surprisingly, we also found CDIs supporting major branches in animals, particular in vertebrates. We then expanded the search to non-bilaterial animals (Porifera, Cnidaria and Ctenophora). The phylogenetic tree reconstructed by CDIs places the Ctenophore Mnemiopsis leidyi as the deepest branch of animals with 6 CDIs support. Trichoplax adhaerens is closely related to the Bilateria. Moreover, the indel phylogeny shows Nematostella vectensis and Hydra magnipapillata are paraphyletic group and position of Cnidarian branches seems to be problematic in the indel phylogeny because of homoplasy. This might be solved if we discover CDIs from animal specific proteins, which emerged after the universal orthologous proteins.Evolutionary Patterns in Slightly Complex Protein Insertions/Deletions (Indels) and Their Application to the Study of Deep Phylogeny in Metazoa

  • 6.
    Ajawatanawong, Pravech
    et al.
    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.
    Evolution of protein indels in plants, animals and fungi2013In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 13, p. 140-Article in journal (Refereed)
    Abstract [en]

    Background: Insertions/deletions (indels) in protein sequences are useful as drug targets, protein structure predictors, species diagnostics and evolutionary markers. However there is limited understanding of indel evolutionary patterns. We sought to characterize indel patterns focusing first on the major groups of multicellular eukaryotes. Results: Comparisons of complete proteomes from a taxonically broad set of primarily Metazoa, Fungi and Viridiplantae yielded 299 substantial (>250aa) universal, single-copy (in-paralog only) proteins, from which 901 simple (present/absent) and 3,806 complex (multistate) indels were extracted. Simple indels are mostly small (1-7aa) with a most frequent size class of 1aa. However, even these simple looking indels show a surprisingly high level of hidden homoplasy (multiple independent origins). Among the apparently homoplasy-free simple indels, we identify 69 potential clade-defining indels (CDIs) that may warrant closer examination. CDIs show a very uneven taxonomic distribution among Viridiplante (13 CDIs), Fungi (40 CDIs), and Metazoa (0 CDIs). An examination of singleton indels shows an excess of insertions over deletions in nearly all examined taxa. This excess averages 2.31 overall, with a maximum observed value of 7.5 fold. Conclusions: We find considerable potential for identifying taxon-marker indels using an automated pipeline. However, it appears that simple indels in universal proteins are too rare and homoplasy-rich to be used for pure indel-based phylogeny. The excess of insertions over deletions seen in nearly every genome and major group examined maybe useful in defining more realistic gap penalties for sequence alignment. This bias also suggests that insertions in highly conserved proteins experience less purifying selection than do deletions.

  • 7. Alstrup, Vagn
    et al.
    Aptroot, Andre
    Divakar, Pradeep K.
    LaGreca, Scott
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lichens from Tanzania and Kenya III: Macrolichens and calicioid lichens2010In: Cryptogamie Mycologie, ISSN 0181-1584, E-ISSN 1776-100X, Vol. 31, no 3, p. 333-351Article in journal (Refereed)
    Abstract [en]

    156 species of macrolichens and calicioid lichens are reported from Tanzania and Kenya. 28 species are new for Tanzania and 2 for Kenya. New for Africa are Hypotrachyna novella, H. physcioides, Melanelia panniformis, Physcidia squamulosa, and Xanthoparmelia microspora.

  • 8.
    Ament-Velasquez, Sandra Lorena
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Figuet, E.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Ballenghien, M.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Zattara, E. E.
    Indiana Univ, Dept Biol, 107 S Indiana Ave, Bloomington, IN 47405 USA.;Smithsonian Inst, Natl Museum Nat Hist, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA..
    Norenburg, J. L.
    Smithsonian Inst, Natl Museum Nat Hist, Dept Invertebrate Zool, 10th St & Constitut Ave NW, Washington, DC 20560 USA..
    Fernandez-Alvarez, F. A.
    CSIC Barcelona, Inst Ciencies Mar, Barcelona 08003, Spain..
    Bierne, J.
    Univ Reims, Lab Biol Cellulaire & Mol, 9 Blvd Paix, F-51100 Reims, France..
    Bierne, N.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Galtier, N.
    Univ Montpellier, Inst Evolutionary Sci, CNRS, IRD,EPHE, Pl Eugene Bataillon, F-34095 Montpellier, France..
    Population genomics of sexual and asexual lineages in fissiparous ribbon worms (Lineus, Nemertea): hybridization, polyploidy and the Meselson effect2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 14, p. 3356-3369Article in journal (Refereed)
    Abstract [en]

    Comparative population genetics in asexual vs. sexual species offers the opportunity to investigate the impact of asexuality on genome evolution. Here, we analyse coding sequence polymorphism and divergence patterns in the fascinating Lineus ribbon worms, a group of marine, carnivorous nemerteans with unusual regeneration abilities, and in which asexual reproduction by fissiparity is documented. The population genomics of the fissiparous L. pseudolacteus is characterized by an extremely high level of heterozygosity and unexpectedly elevated pi(N)/pi(S) ratio, in apparent agreement with theoretical expectations under clonal evolution. Analysis of among-species allele sharing and read-count distribution, however, reveals that L. pseudolacteus is a triploid hybrid between Atlantic populations of L. sanguineus and L. lacteus. We model and quantify the relative impact of hybridity, polyploidy and asexuality on molecular variation patterns in L. pseudolacteus and conclude that (i) the peculiarities of L. pseudolacteus population genomics result in the first place from hybridization and (ii) the accumulation of new mutations through the Meselson effect is more than compensated by processes of heterozygosity erosion, such as gene conversion or gene copy loss. This study illustrates the complexity of the evolutionary processes associated with asexuality and identifies L. pseudolacteus as a promising model to study the first steps of polyploid genome evolution in an asexual context.

  • 9.
    Anderson, Jennifer L
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Nieuwenhuis, Bart P. S.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Division of Evolutionary Biology, Faculty of Biology, Ludwig- Maximilians-Universität München.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Asexual reproduction and growth rate: independent and plastic lifehistory traits in Neurospora crassa2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370Article in journal (Refereed)
  • 10.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Eremalche2012In: The Jepson manual: vascular plants of California / [ed] Bruce G. Baldwin, Berkeley: University of California Press , 2012, 2nd ed.Chapter in book (Refereed)
  • 11.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Phylogeny, Hybridization, and Evolution of Habit and Breeding System in Sidalcea and Eremalche (Malvaceae)2012In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 173, no 5, p. 532-548Article in journal (Refereed)
    Abstract [en]

    Reconstructing the phylogeny of the western North American Sidalcea-Eremalche lineage provides an opportunity to study the evolution of different fundamental traits considered to play an important role in plant evolution. These plants display different life-history strategies, such as annual and perennial habit and hermaphroditic and gynodioecious breeding systems, enabling evolutionary investigation of these traits in a phylogenetic context. Difficult species delimitations have been suggested to be caused by hybridization in combination with polyploidy. Molecular phylogenetic analyses based on sequences of the chloroplast intron rpl16 and nuclear ribosomal DNA show that the genera are strongly supported as monophyletic sister lineages, and the polytomy in Sidalcea in both data sets likely represents a rapid radiation event. Coastal California is indicated as ancestral area for Sidalcea, in agreement with earlier biogeographical hypotheses. Hybridization hypotheses gained support from the chloroplast DNA data for the hexaploid Sidalcea lineage and for S. sparsifolia and S. pedata. Sidalcea section Annuae, including the annuals, represents a paraphyletic assemblage. The shift between annual and perennial habit must have happened at least four times, but reversals to perenniality appear unlikely. At least five reversals from the gynodioecious to the hermaphroditic condition are inferred, possibly due to population bottlenecks in some lineages.

  • 12.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Potential hybridization in real data sets: complex relationships in young flowering plants2007Conference paper (Other academic)
  • 13.
    Andreasen, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Baldwin, Bruce G.
    Jespon Herbarium, University of California, Berkeley.
    Evolutionary and historical biogeographic perspectives on the genus Arnica (Asteraceae–Madieae): nuclear ribosomal DNA evidence2004Conference paper (Other academic)
  • 14.
    Andreasen, Katarina
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Manktelow, Mariette
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Sehic, Jasna
    Garkava-Gustavsson, Larisa
    Genetic identity of putative Linnaean plants: Successful DNA amplification of Linnaeus's crab apple Malus baccata2014In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 63, no 2, p. 408-416Article in journal (Other academic)
    Abstract [en]

    Advancements in molecular techniques enable us to extract DNA from historic herbarium specimens and facilitate genetic comparisons between herbarium material and living plant collections. These recent advances offer an exciting opportunity for identifying extant Linnaean plants by genetic comparisons of Linnaeus's own herbarium specimens with potentially remnant plants from his cultivations. DNA from the lectotype of Malus baccata (L.) Borkh. in the Linnaean Herbarium was successfully extracted and amplified for five of twelve loci of microsatellites. Results of genetic comparisons with M. baccata trees from Linnaeus's Hammarby, Sweden, show that the trees at Hammarby are closely related to each other, but not to the lectotype, which is closer to material from Russia. This suggests that Linnaeus received M. baccata from more than one source. Although not close to the lectotype and not represented by a specimen in the Linnaean Herbarium, the extant M. baccata at Hammarby may still represent Linnaean plants, that were grown by Linnaeus himself, or the descendants to such plants. Future studies on the almost 50 living, potential Linnaean plants may reveal an invaluable biological, scientific and cultural heritage from the era that saw the rise of systematic biology.

  • 15.
    Anslan, Sten
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, 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, Tartu, Estonia.
    Hiiesalu, Indrek
    Univ Tartu, Inst Ecol & Earth Sci, Tartu, Estonia..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, Tartu, Estonia..
    PipeCraft: Flexible open-source toolkit for bioinformatics analysis of custom high-throughput amplicon sequencing data2017In: Molecular Ecology Resources, ISSN 1755-098X, E-ISSN 1755-0998, Vol. 17, no 6, p. e234-e240Article in journal (Refereed)
    Abstract [en]

    High-throughput sequencing methods have become a routine analysis tool in environmental sciences as well as in public and private sector. These methods provide vast amount of data, which need to be analysed in several steps. Although the bioinformatics may be applied using several public tools, many analytical pipelines allow too few options for the optimal analysis for more complicated or customized designs. Here, we introduce PipeCraft, a flexible and handy bioinformatics pipeline with a user-friendly graphical interface that links several public tools for analysing amplicon sequencing data. Users are able to customize the pipeline by selecting the most suitable tools and options to process raw sequences from Illumina, Pacific Biosciences, Ion Torrent and Roche 454 sequencing platforms. We described the design and options of PipeCraft and evaluated its performance by analysing the data sets from three different sequencing platforms. We demonstrated that PipeCraft is able to process large data sets within 24hr. The graphical user interface and the automated links between various bioinformatics tools enable easy customization of the workflow. All analytical steps and options are recorded in log files and are easily traceable.

  • 16.
    Anslan, Sten
    et al.
    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. Univ Tartu, Inst Ecol & Earth Sci, 14A Ravila, EE-50411 Tartu, Estonia.
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14A Ravila, EE-50411 Tartu, Estonia..
    Seasonal and annual variation in fungal communities associated with epigeic springtails (Collembola spp.) in boreal forests2018In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 116, p. 245-252Article in journal (Refereed)
    Abstract [en]

    Soil fauna mediate nutrient cycling through engineering physical properties and altering microbial commtmities in soil. Collembola is one of the most abundant groups of soil fauna, which regulates microbial communities by consumption and dispersal. The spatial structure of associations between Collembola and soil microbes have been described in several studies, but temporal variation of these associations remains unclear. Using high throughput sequencing, we studied the fungal communities on Collembola (Entomobiya nivalis, Orchesella flavescens, Pogonognathellus longicornis) body surface, gut and their immediate habitat (topsoil samples) in four seasons across three years. The soil samples were characterized by fairly uniform relative abundance of saprotrophic and mycorrhizal fungi, whereas collembolans were associated mostly with saprotrophs. The structure of fungal communities from all substrate types exhibited comparable patterns of temporal distance decay of shnilarity. Unlike in soil, fungal richness and composition in Collembola body and gut samples exhibited seasonal and annual variation, with a significant interaction term, indicating low predictability. These results reflect spatial and temporal plasticity of the fungal communities associated with epigeic Collembola, indicating the high adaptability of collembolans to available conditions. We found that the Collembola associations with fungi (including diet) did not vary among the studied epigeic Collembola species. The detected high diversity of fungi associated with Collembola suggests that dispersal by arthropod vectors may represent a powerful alternative to aerial dispersal of fungal propagules.

  • 17. Anslan, Sten
    et al.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Temporal changes in fungal communities associated with guts and appendages of Collembola as based on culturing and high-throughput sequencing2016In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 96, p. 152-159Article in journal (Refereed)
    Abstract [en]

    Due to high abundance and feeding habits, invertebrates are of great importance for shaping microbial communities at the fine scale. Springtails (Collembola) that feed on fungal spores and mycelia may contribute to dispersal through carrying fungal propagules in their guts or on their appendages. The Collembola–fungal associations are mainly investigated by microscopy or culturing techniques, which allow identify only fungi that have distinctive morphological characteristics or that can be cultured in vitro. Here we identified the Collembola-associated fungi on the body surface and in the gut content using both culturing and high-throughput sequencing (HTS) methods. We studied three epigeic Collembola species found on the Norway spruce dominated forest stands throughout the vegetation period – Entomobrya nivalisOrchesella flavescens andPogonognathellus longicornis. We discovered over 1200 fungal operational taxonomic units (OTUs), i.e. the proxies for species, based on 97% sequence similarity of the ITS2 subregion of ribosomal DNA. Most of the fungi were saprotrophs, but we detected also mycorrhizal, parasitic and lichenized fungi. Season was the most important factor affecting fungal richness and composition, especially on body surface. Although the data matrix revealed significant effect of substrate, we were unable to detect the significant fungal community differences between body surface and gut samples of conspecifics. There were no significant differences among studied epigeic Collembola species in the preference for fungal diet. Our study demonstrates that collembolans associate with a broader range of fungi than previously observed and thus potentially play an important role in enhancing fungal colonization through dispersal activities.

  • 18.
    Anslan, Sten
    et al.
    Braunschweig Univ Technol, Zool Inst, Mendelssohnstr 4, D-38106 Braunschweig, Germany.
    Nilsson, R. Henrik
    Univ Gothenburg, Dept Biol & Environm Sci, Gothenburg Global Biodivers Ctr, Box 461, S-40530 Gothenburg, Sweden.
    Wurzbacher, Christian
    Tech Univ Munich, Coulombwall 3, D-85748 Garching, Germany.
    Baldrian, Petr
    Czech Acad Sci, Inst Microbiol, Videnska 1083, Prague 14220 4, Czech Republic.
    Tedersoo, Leho
    Tartu Univ, Nat Hist Museum, 14a Ravila, Tartu 50411, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Tartu Univ, Inst Ecol & Earth Sci, 14a Ravila, EE-50411 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Ulls Vag 16, S-75651 Uppsala, Sweden.
    Great differences in performance and outcome of high-throughput sequencing data analysis platforms for fungal metabarcoding2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 39, p. 29-40Article in journal (Refereed)
    Abstract [en]

    Along with recent developments in high-throughput sequencing (HTS) technologies and thus fast accumulation of HTS data, there has been a growing need and interest for developing tools for HTS data processing and communication. In particular, a number of bioinformatics tools have been designed for analysing metabarcoding data, each with specific features, assumptions and outputs. To evaluate the potential effect of the application of different bioinformatics workflow on the results, we compared the performance of different analysis platforms on two contrasting high-throughput sequencing data sets. Our analysis revealed that the computation time, quality of error filtering and hence output of specific bioinformatics process largely depends on the platform used. Our results show that none of the bioinformatics workflows appears to perfectly filter out the accumulated errors and generate Operational Taxonomic Units, although PipeCraft, LotuS and PIPITS perform better than QIIME2 and Galaxy for the tested fungal amplicon dataset. We conclude that the output of each platform requires manual validation of the OTUs by examining the taxonomy assignment values.

  • 19. Applequist, Wendy L.
    et al.
    Callmander, Martin W.
    Davidse, Gerrit
    Sennikov, Alexander
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Vorster, Piet
    Yatskievych, George
    Apportionment of institutional votes for the Nomenclature Section: A rebuttal to Smith & al.2010In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 59, no 5, p. 1567-1570Article in journal (Refereed)
    Abstract [en]

    Smith & al. (2010) have suggested that the apportionment of institutional votes for the Nomenclature Section of the International Botanical Congress based upon taxonomic activity represents a "colonial legacy" that disadvantages developing nations, and that institutional votes should instead be distributed based at least in part upon a country's human population and the size of its flora. While we agree that increasing participation by developing-country taxonomists is an important goal, we believe that Smith & al. fail to support their claim that the current practice of plant nomenclature is harmful to developing nations. No evidence has been offered of regional biases regarding proposals to change the wording of the Code, which represent the vast majority of the votes taken at any Nomenclature Section, nor has the current process of apportionment of institutional votes been shown to be biased. The reform measures proposed by Smith & al. would, as we show, introduce explicit discrimination based on nationality into the International code of botanical nomenclature, undermining the international cooperation among taxonomists that is necessary for the smooth functioning of a universally accepted system of nomenclature. Rather than making hasty and perhaps harmful changes to the current means of voting, we suggest that the international taxonomic community should consider carefully what measures will best facilitate participation without creating new sources of injustice.

  • 20.
    Asghar, Naveed
    et al.
    Sodertorn Univ, Sch Nat Sci Technol & Environm Studies, Huddinge, Sweden.;Orebro Univ, Sch Med Sci, Orebro, Sweden.;Orebro Univ, Fac Med & Hlth, iRiSC, Orebro, Sweden..
    Pettersson, John H.-O.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Norwegian Inst Publ Hlth, Dept Infect Dis Epidemiol & Modelling, Oslo, Norway.;Natl Vet Inst, Dept Microbiol, Uppsala, Sweden..
    Dinnetz, Patrik
    Sodertorn Univ, Sch Nat Sci Technol & Environm Studies, Huddinge, Sweden..
    Andreassen, Ashild
    Norwegian Inst Publ Hlth, Div Infect Dis Control, Dept Virol, Oslo, Norway..
    Johansson, Magnus
    Orebro Univ, Sch Med Sci, Orebro, Sweden.;Orebro Univ, Fac Med & Hlth, iRiSC, Orebro, Sweden..
    Deep sequencing analysis of tick-borne encephalitis virus from questing ticks at natural foci reveals similarities between quasispecies pools of the virus2017In: Journal of General Virology, ISSN 0022-1317, E-ISSN 1465-2099, Vol. 98, no 3, p. 413-421Article in journal (Refereed)
    Abstract [en]

    Every year, tick-borne encephalitis virus (TBEV) causes severe central nervous system infection in 10 000 to 15 000 people in Europe and Asia. TBEV is maintained in the environment by an enzootic cycle that requires a tick vector and a vertebrate host, and the adaptation of TBEV to vertebrate and invertebrate environments is essential for TBEV persistence in nature. This adaptation is facilitated by the error-prone nature of the virus's RNA-dependent RNA polymerase, which generates genetically distinct virus variants called quasispecies. TBEV shows a focal geographical distribution pattern where each focus represents a TBEV hotspot. Here, we sequenced and characterized two TBEV genomes, JP-296 and JP-554, from questing Ixodes ricinus ticks at a TBEV focus in central Sweden. Phylogenetic analysis showed geographical clustering among the newly sequenced strains and three previously sequenced Scandinavian strains, Toro-2003, Saringe-2009 and Mandal-2009, which originated from the same ancestor. Among these five Scandinavian TBEV strains, only Mandal-2009 showed a large deletion within the 3' non-coding region (NCR), similar to the highly virulent TBEV strain Hypr. Deep sequencing of JP-296, JP-554 and Mandal-2009 revealed significantly high quasispecies diversity for JP-296 and JP-554, with intact 3' NCRs, compared to the low diversity in Mandal-2009, with a truncated 3' NCR. Single-nucleotide polymorphism analysis showed that 40% of the single-nucleotide polymorphisms were common between quasispecies populations of JP-296 and JP-554, indicating a putative mechanism for how TBEV persists and is maintained within its natural foci.

  • 21.
    Atkinson, Gemma
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Evolution of elongation factor G and the origins of mitochondrial and chloroplast forms2011In: Molecular biology and evolution, ISSN 0737-4038, E-ISSN 1537-1719, Vol. 28, no 3, p. 1281-1292Article in journal (Refereed)
    Abstract [en]

    Protein synthesis elongation factor G (EF-G) is an essential protein with central roles in both the elongation and ribosome recycling phases of protein synthesis. Although EF-G evolution is predicted to be conservative, recent reports suggest otherwise. We have characterized EF-G in terms of its molecular phylogeny, genomic context and patterns of amino acid substitution. We find that most bacteria carry a single "canonical" EF-G, which is phylogenetically conservative and encoded in an str operon. However, we also find a number of EF-G paralogs. These include a pair of EF-Gs that are mostly found together and in an eclectic subset of bacteria, specifically delta-proteobacteria, spirochaetes and planctomycetes (the "spd" bacteria). These spdEFGs have also given rise to the mitochondrial factors mtEFG1 and mtEFG2, which probably arrived in eukaryotes before the eukaryotic last common ancestor. Meanwhile, chloroplasts apparently use an α-proteobacterial derived EF-G, rather than the expected cyanobacterial form. The long-term co-maintenance of the spd/mtEFGs may be related to their subfunctionalization for translocation and ribosome recycling. Consistent with this, patterns of sequence conservation and site-specific evolutionary rate shifts suggest that the faster evolving spd/mtEFG2 has lost translocation function, but, surprisingly, the protein also shows little conservation of sites related to recycling activity. On the other hand, spd/mtEFG1, although more slowly evolving, shows signs of substantial remodeling. This is particularly extensive in the GTPase domain, including a highly conserved three amino acid insertion in switch I. We suggest that sub-functionalization of the spd/mtEFGs is not a simple case of specialization for subsets of original activities. Rather the duplication allows the release of one paralog from the selective constraints imposed by dual functionality thus allowing it to become more highly specialized. Thus the potential for fine-tuning afforded by subfunctionalization may explain the maintenance of EF-G paralogs.

  • 22.
    Badou, Sylvestre A.
    et al.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    De Kesel, Andre
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium.
    Raspe, Olivier
    Meise Bot Garden, Nieuwelaan 38, B-1860 Meise, Belgium;Federat Wallonie Bruxelles, Rue A Lavallee 1, B-1080 Brussels, Belgium.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Guelly, Atsu K.
    Univ Lome, Fac Sci, Dept Bot & Ecol Vegetale, BP1515, Lome, Togo.
    Yorou, Nourou S.
    Univ Parakou, Fac Agron, Res Unit Trop Mycol & Soil Plant Fungi Interact, Lab Ecol Bot & Plant Biol, 03 BOX 125, Parakou, Benin.
    Two new African siblings of Pulveroboletus ravenelii (Boletaceae)2018In: MycoKeys, ISSN 1314-4057, E-ISSN 1314-4049, no 43, p. 115-130Article in journal (Refereed)
    Abstract [en]

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

  • 23.
    Baeten, Lander
    et al.
    Univ Ghent, Dept Environm, Gontrode, Belgium.
    Bruelheide, Helge
    Martin Luther Univ Halle Wittenberg, Inst Biol, Geobot & Bot Garden, Halle, Germany;German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany.
    van der Plas, Fons
    Univ Leipzig, Dept Systemat Bot & Funct Biodivers, Leipzig, Germany;Senckenberg Gesell Naturforsch, Biodivers & Climate Res Ctr, Frankfurt, Germany.
    Kambach, Stephan
    Martin Luther Univ Halle Wittenberg, Inst Biol, Geobot & Bot Garden, Halle, Germany;German Ctr Integrat Biodivers Res iDiv, Leipzig, Germany.
    Ratcliffe, Sophia
    Univ Leipzig, Dept Systemat Bot & Funct Biodivers, Leipzig, Germany;Natl Biodivers Network Trust, Nottingham, England.
    Jucker, Tommaso
    Univ Cambridge, Dept Plant Sci, Forest Ecol & Conservat, Cambridge, England;CSIRO Land & Water, Floreat, WA, Australia.
    Allan, Eric
    Univ Bern, Inst Plant Sci, Bern, Switzerland.
    Ampoorter, Evy
    Univ Ghent, Dept Environm, Gontrode, Belgium.
    Barbaro, Luc
    Univ Toulouse, INRA INPT, Dynafor, Auzeville, France.
    Bastias, Cristina C.
    CSIC, MNCN, Madrid, Spain.
    Bauhus, Juergen
    Univ Freiburg, Fac Environm & Nat Resources, Chair Silviculture, Freiburg, Germany.
    Benavides, Raquel
    CSIC, MNCN, Madrid, Spain.
    Bonal, Damien
    Univ Lorraine, INRA, UMR Silva, AgroParisTech, Nancy, France.
    Bouriaud, Olivier
    Stefan Cel Mare Univ Suceava, Fac Forestry, Suceava, Romania.
    Bussotti, Filippo
    Univ Firenze, Dept Agrifood & Environm Sci DISPAA, Lab Environm & Appl Bot, Florence, Italy.
    Carnol, Monique
    Univ Liege, InBioS Plant & Microbial Ecol, Liege, Belgium.
    Castagneyrol, Bastien
    INRA, UMR 1202 BIOGECO, Cestas, France;Univ Bordeaux, BIOGECO, UMR 1202, Pessac, France.
    Charbonnier, Yohan
    LPO, Le Bourg, Bourrou, France.
    Checko, Ewa
    Univ Warmia & Mazury, Dept Forestry & Forest Ecol, Olsztyn, Poland.
    Coomes, David A.
    Univ Cambridge, Dept Plant Sci, Forest Ecol & Conservat, Cambridge, England.
    Dahlgren, Jonas
    Swedish Univ Agr Sci, Dept Forest Resource Management, Umea, Sweden.
    Dawud, Seid Muhie
    Wollo Univ, Coll Agr, Dept Forestry, Dessie, Ethiopia.
    De Wandeler, Hans
    Univ Leuven, Dept Earth & Environm Sci, Leuven, Belgium.
    Domisch, Timo
    Nat Resources Inst Finland Luke, Joensuu, Finland.
    Finer, Leena
    Nat Resources Inst Finland Luke, Joensuu, Finland.
    Fischer, Markus
    Univ Bern, Inst Plant Sci, Bern, Switzerland.
    Fotelli, Mariangela
    Greek Agr Org Dimitra, Forest Res Inst Thessaloniki, Thessaloniki, Greece.
    Gessler, Arthur
    Swiss Fed Res Inst WSL, Res Unit Forest Dynam, Birmensdorf, Switzerland.
    Grossiord, Charlotte
    Los Alamos Natl Lab, Earth & Environm Sci Div, Los Alamos, NM USA.
    Guyot, Virginie
    INRA, UMR 1202 BIOGECO, Cestas, France;Univ Bordeaux, BIOGECO, UMR 1202, Pessac, France.
    Hattenschwiler, Stephan
    Univ Montpellier, Univ Paul Valery Montpellier, EPHE, CNRS,Ctr Evolutionary & Funct Ecol, Montpellier, France.
    Jactel, Herve
    INRA, UMR 1202 BIOGECO, Cestas, France;Univ Bordeaux, BIOGECO, UMR 1202, Pessac, France.
    Jaroszewicz, Bogdan
    Univ Warsaw, Bialowieza Geobotan Stn, Fac Biol, Bialowieza, Poland.
    Joly, Francois-Xavier
    Univ Montpellier, Univ Paul Valery Montpellier, EPHE, CNRS,Ctr Evolutionary & Funct Ecol, Montpellier, France.
    Koricheva, Julia
    Royal Holloway Univ London, Sch Biol Sci, Egham, Surrey, England.
    Lehtonen, Aleksi
    Nat Resources Inst Finland Luke, Helsinki, Finland.
    Mueller, Sandra
    Univ Freiburg, Dept Geobot, Fac Biol, Freiburg, Germany.
    Muys, Bart
    Nguyen, Diem
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Department of Forest Mycology and Plant Pathology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Pollastrini, Martina
    Univ Firenze, Dept Agrifood & Environm Sci DISPAA, Lab Environm & Appl Bot, Florence, Italy.
    Radoglou, Kalliopi
    Democritus Univ Thrace DUTH, Dept Forestry & Management Environm & Nat, Nea Orestiada, Greece.
    Raulund-Rasmussen, Karsten
    Univ Copenhagen, Dept Geosci & Nat Resource Managemen, Frederiksberg C, Denmark.
    Ruiz-Benito, Paloma
    Univ Alcala De Henares, Dept Ciencias Vida, Grp Ecol & Restaurac Forestal, Madrid, Spain.
    Selvi, Federico
    Univ Firenze, Dept Agrifood & Environm Sci DISPAA, Lab Environm & Appl Bot, Florence, Italy.
    Stenlid, Jan
    Swedish Univ Agr Sci, Dept Forest Mycol & Plant Pathol, Uppsala, Sweden.
    Valladares, Fernando
    CSIC, MNCN, Madrid, Spain.
    Vesterdal, Lars
    Univ Copenhagen, Dept Geosci & Nat Resource Managemen, Frederiksberg C, Denmark.
    Verheyen, Kris
    Univ Ghent, Dept Environm, Gontrode, Belgium.
    Wirth, Christian
    Max Planck Inst Biogeochem, Jena, Germany.
    Zavala, Miguel A.
    Univ Alcala De Henares, Dept Ciencias Vida, Grp Ecol & Restaurac Forestal, Madrid, Spain.
    Scherer-Lorenzen, Michael
    Identifying the tree species compositions that maximize ecosystem functioning in European forests2019In: Journal of Applied Ecology, ISSN 0021-8901, E-ISSN 1365-2664, Vol. 56, no 3, p. 733-744Article in journal (Refereed)
    Abstract [en]

    1. Forest ecosystem functioning generally benefits from higher tree species richness, but variation within richness levels is typically large. This is mostly due to the contrasting performances of communities with different compositions. Evidence-based understanding of composition effects on forest productivity, as well as on multiple other functions will enable forest managers to focus on the selection of species that maximize functioning, rather than on diversity per se.

    2. We used a dataset of 30 ecosystem functions measured in stands with different species richness and composition in six European forest types. First, we quantified whether the compositions that maximize annual above-ground wood production (productivity) generally also fulfil the multiple other ecosystem functions (multifunctionality). Then, we quantified the species identity effects and strength of interspecific interactions to identify the "best" and "worst" species composition for multifunctionality. Finally, we evaluated the real-world frequency of occurrence of best and worst mixtures, using harmonized data from multiple national forest inventories.

    3. The most productive tree species combinations also tended to express relatively high multifunctionality, although we found a relatively wide range of compositions with high- or low-average multifunctionality for the same level of productivity. Monocultures were distributed among the highest as well as the lowest performing compositions. The variation in functioning between compositions was generally driven by differences in the performance of the component species and, to a lesser extent, by particular interspecific interactions. Finally, we found that the most frequent species compositions in inventory data were monospecific stands and that the most common compositions showed below-average multifunctionality and productivity.

    4. Synthesis and applications. Species identity and composition effects are essential to the development of high-performing production systems, for instance in forestry and agriculture. They therefore deserve great attention in the analysis and design of functional biodiversity studies if the aim is to inform ecosystem management. A management focus on tree productivity does not necessarily trade-off against other ecosystem functions; high productivity and multifunctionality can be combined with an informed selection of tree species and species combinations.

  • 24.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hildebrand, Falk
    Forslund, Sofia K
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Soudzilovskaia, Nadejda A
    Bodegom, Peter M
    Bengtsson-Palme, Johan
    Anslan, Sten
    Coelho, Luis Pedro
    Harend, Helery
    Huerta-Cepas, Jaime
    Medema, Marnix H
    Maltz, Mia R
    Mundra, Sunil
    Olsson, Pål Axel
    Pent, Mari
    Põlme, Sergei
    Sunagawa, Shinichi
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tedersoo, Leho
    Bork, Peer
    Structure and function of the global topsoil microbiome.2018In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 560, no 7717, p. 233-237Article in journal (Refereed)
    Abstract [en]

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

  • 25.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, 40 Lai St, EE-50411 Tartu, Estonia.
    Kohout, Petr
    Anslan, Sten
    Harend, Helery
    Abarenkov, Kessy
    Tedersoo, Leho
    Stochastic distribution of small soil eukaryotes resulting from high dispersal and drift in a local environment2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, p. 885-896Article in journal (Refereed)
    Abstract [en]

    A central challenge in ecology is to understand the relative importance of processes that shape diversity patterns. Compared with aboveground biota, little is known about spatial patterns and processes in soil organisms. Here we examine the spatial structure of communities of small soil eukaryotes to elucidate the underlying stochastic and deterministic processes in the absence of environmental gradients at a local scale. Specifically, we focus on the fine-scale spatial autocorrelation of prominent taxonomic and functional groups of eukaryotic microbes. We collected 123 soil samples in a nested design at distances ranging from 0.01 to 64 m from three boreal forest sites and used 454 pyrosequencing analysis of Internal Transcribed Spacer for detecting Operational Taxonomic Units of major eukaryotic groups simultaneously. Among the main taxonomic groups, we found significant but weak spatial variability only in the communities of Fungi and Rhizaria. Within Fungi, ectomycorrhizas and pathogens exhibited stronger spatial structure compared with saprotrophs and corresponded to vegetation. For the groups with significant spatial structure, autocorrelation occurred at a very fine scale (<2 m). Both dispersal limitation and environmental selection had a weak effect on communities as reflected in negative or null deviation of communities, which was also supported by multivariate analysis, that is, environment, spatial processes and their shared effects explained on average <10% of variance. Taken together, these results indicate a random distribution of soil eukaryotes with respect to space and environment in the absence of environmental gradients at the local scale, reflecting the dominant role of drift and homogenizing dispersal.

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

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

  • 27.
    Bahram, Mohammad
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia;Swedish Univ Agr Sci, Dept Ecol, Uppsala, Sweden.
    Vanderpool, Dan
    Univ Montana, Div Biol Sci, 32 Campus Dr, Missoula, MT 59812 USA.
    Pent, Mari
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Hiltunen, Markus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The genome and microbiome of a dikaryotic fungus (Inocybe terrigena, Inocybaceae) revealed by metagenomics2018In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 10, no 2, p. 155-166Article in journal (Refereed)
    Abstract [en]

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

  • 28.
    Baldauf, Sandra 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.
    Fiz-Palacios, Omar
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A Deep Hidden Diversity of Dictyostelia2018In: Protist, ISSN 1434-4610, E-ISSN 1618-0941, Vol. 169, no 1, p. 64-78Article in journal (Refereed)
    Abstract [en]

    Dictyostelia is a monophyletic group of transiently multicellular (sorocarpic) amoebae, whose study is currently limited to laboratory culture. This tends to favour faster growing species with robust sorocarps, while species with smaller more delicate sorocarps constitute most of the group’s taxonomic breadth. The number of known species is also small (∼150) given Dictyostelia’s molecular depth and apparent antiquity (>600 myr). Nonetheless, dictyostelid sequences are rarely recovered in culture independent sampling (ciPCR) surveys. We developed ciPCR primers to specifically target dictyostelid small subunit (SSU or 18S) rDNA and tested them on total DNAs extracted from a wide range of soils from five continents. The resulting clone libraries show mostly dictyostelid sequences (∼90%), and phylogenetic analyses of these sequences indicate novel lineages in all four dictyostelid families and most genera. This is especially true for the species-rich Heterostelium and Dictyosteliaceae but also the less species-rich Raperosteliaceae. However, the most novel deep branches are found in two very species-poor taxa, including the deepest branch yet seen in the highly divergent Cavenderiaceae. These results confirm a deep hidden diversity of Dictyostelia, potentially including novel morphologies and developmental schemes. The primers and protocols presented here should also enable more comprehensive studies of dictyostelid ecology.

  • 29.
    Bass, David
    et al.
    Ctr Environm Fisheries & Aquaculture Sci Cefas, Barrack Rd, Weymouth, Dorset, England;Nat Hist Museum, Dept Life Sci, Cromwell Rd, London, England.
    Ward, Georgia M.
    Ctr Environm Fisheries & Aquaculture Sci Cefas, Barrack Rd, Weymouth, Dorset, England;Nat Hist Museum, Dept Life Sci, Cromwell Rd, London, England;Univ Exeter, Biosci, Exeter, Devon, England.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Ascetosporea2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 1, p. R7-R8Article in journal (Other academic)
  • 30.
    Bastiaans, Eric
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Wageningen University.
    Debets, Alfons J. M.
    Aanen, Duur K.
    Experimental evolution reveals that high relatedness protects multicellular cooperation from cheaters2016In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 7, article id 11435Article in journal (Refereed)
    Abstract [en]

    In multicellular organisms, there is a potential risk that cheating mutants gain access to the germline. Development from a single-celled zygote resets relatedness among cells to its maximum value each generation, which should accomplish segregation of cheating mutants from non-cheaters and thereby protect multicellular cooperation. Here we provide the crucial direct comparison between high- and low-relatedness conditions to test this hypothesis. We allow two variants of the fungus Neurospora crassa to evolve, one with and one without the ability to form chimeras with other individuals, thus generating two relatedness levels. While multicellular cooperation remains high in the high-relatedness lines, it significantly decreases in all replicate low-relatedness lines, resulting in an average threefold decrease in spore yield. This reduction is caused by cheating mutants with reduced investment in somatic functions, but increased competitive success when fusing with non-cheaters. Our experiments demonstrate that high-genetic relatedness is crucial to sustain multicellular cooperation.

  • 31.
    Bedarf, J. R.
    et al.
    Univ Bonn, Dept Neurol, Bonn, Germany.;German Ctr Neurodegenerat Dis Res DZNE, Bonn, Germany..
    Hildebrand, F.
    EMBL, Heidelberg, Germany..
    Coelho, L. P.
    EMBL, Heidelberg, Germany..
    Sunagawa, S.
    EMBL, Heidelberg, Germany.;Swiss Fed Inst Technol, Inst Microbiol, Vladimir Prelog 1-5-10, CH-8093 Zurich, Switzerland..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth, 40 Lai St, EE-51005 Tartu, Estonia..
    Goeser, F.
    Univ Bonn, Dept Internal Med 1, Bonn, Germany.;German Ctr Infect Res DZIF, Bonn, Germany..
    Bork, P.
    EMBL, Heidelberg, Germany.;Heidelberg Univ, MMPU, Heidelberg, Germany.;European Mol Biol Lab, Heidelberg, Germany.;Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany.;Univ Wurzburg, Dept Bioinformat, D-97074 Wurzburg, Germany.;Meyerhofstr 1, D-69117 Heidelberg, Germany..
    Wüllner, U.
    Univ Bonn, Dept Neurol, Bonn, Germany.;German Ctr Neurodegenerat Dis Res DZNE, Bonn, Germany.;Sigmund Freud Str 25, D-53127 Bonn, Germany..
    Functional implications of microbial and viral gut metagenome changes in early stage L-DOPA-naive Parkinson's disease patients2017In: Genome Medicine, ISSN 1756-994X, E-ISSN 1756-994X, Vol. 9, article id 39Article in journal (Refereed)
    Abstract [en]

    Background: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naive PD patients might also serve as a biomarker.

    Methods: We performed metagenomic shotgun analyses and compared the fecal microbiomes of 31 early stage, L-DOPA-naive PD patients to 28 age-matched controls.

    Results: We found increased Verrucomicrobiaceae (Akkermansia muciniphila) and unclassified Firmicutes, whereas Prevotellaceae (Prevotella copri) and Erysipelotrichaceae (Eubacterium biforme) were markedly lowered in PD samples. The observed differences could reliably separate PD from control with a ROC-AUC of 0.84. Functional analyses of the metagenomes revealed differences in microbiota metabolism in PD involving the beta-glucuronate and tryptophan metabolism. While the abundances of prophages and plasmids did not differ between PD and controls, total virus abundance was decreased in PD participants. Based on our analyses, the intake of either a MAO inhibitor, amantadine, or a dopamine agonist (which in summary relates to 90% of PD patients) had no overall influence on taxa abundance or microbial functions.

    Conclusions: Our data revealed differences of colonic microbiota and of microbiota metabolism between PD patients and controls at an unprecedented detail not achievable through 16S sequencing. The findings point to a yet unappreciated aspect of PD, possibly involving the intestinal barrier function and immune function in PD patients. The influence of the parkinsonian medication should be further investigated in the future in larger cohorts.

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

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

  • 33.
    Bharali, Pankaj
    et al.
    Rajiv Gandhi University, Arunachal Pradesh, India.
    Das, Arup Kumar
    Rajiv Gandhi University, Arunachal Pradesh, India.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Notes on the alpine flora of Arunachal Pradesh: including several species new to India2018In: Plant diversity in the Himalaya hotspot region: volume to celebrate the completion of university service of Dr. Abhaya Prasad Das / [ed] A.P. Das; Subir Bera, Dehradun: Bishen Singh Mahendra Pal Singh , 2018, p. 163-194Chapter in book (Refereed)
  • 34.
    Bloch, Natasha, I
    et al.
    UCL, Dept Genet Evolut & Environm, London, England.
    Corral-Lopez, Alberto
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden.
    Buechel, Severine D.
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden.
    Kotrschal, Alexander
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden.
    Kolm, Niclas
    Stockholm Univ, Dept Zool Ethol, Stockholm, Sweden.
    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.
    Early neurogenomic response associated with variation in guppy female mate preference2018In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 2, no 11, p. 1772-1781Article in journal (Refereed)
    Abstract [en]

    Understanding the evolution of mate choice requires dissecting the mechanisms of female preference, particularly how these differ among social contexts and preference phenotypes. Here, we studied the female neurogenomic response after only 10 min of mate exposure in both a sensory component (optic tectum) and a decision-making component (telencephalon) of the brain. By comparing the transcriptional response between females with and without preferences for colourful males, we identified unique neurogenomic elements associated with the female preference phenotype that are not present in females without preference. A network analysis revealed different properties for this response at the sensory-processing and the decision-making levels, and we show that this response is highly centralized in the telencephalon. Furthermore, we identified an additional set of genes that vary in expression across social contexts, beyond mate evaluation. We show that transcription factors among these loci are predicted to regulate the transcriptional response of the genes we found to be associated with female preference.

  • 35. Botting, Joseph P.
    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.
    Peel, John S.
    Uppsala University, Disciplinary Domain of Science and Technology, Earth Sciences, Department of Earth Sciences, Palaeobiology.
    A Crown-Group Demosponge from the Early Cambrian Sirius Passet Biota, North Greenland2015In: Palaeontology, ISSN 0031-0239, E-ISSN 1475-4983, Vol. 58, no 1, p. 35-43Article in journal (Refereed)
    Abstract [en]

    Calibration of the divergence times of sponge lineages and understanding of their phylogenetic history are hampered by the difficulty in recognizing crown versus stem groups in the fossil record. A new specimen from the lower Cambrian (Series 2, Stage 3; approximately 515Ma) Sirius Passet Biota of North Greenland has yielded a diagnostic spicule assemblage of the extant demosponge lineages Haploscleromorpha and/or Heteroscleromorpha. The specimen has disarticulated approximately in situ, but represents an individual sponge that possessed monaxon spicules combined with a range of slightly smaller sigma, toxa and unique spiral morphologies. The combination of spicule forms, together with their relatively large size, suggests that the sponge represents the stem lineage of Haploscleromorpha+Heteroscleromorpha. This is the first crown-group demosponge described from the early Cambrian and provides the most reliable calibration point currently available for phylogenetic studies.

  • 36.
    Brännström, Ioana Onut
    et al.
    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.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thamnolia tundrae sp nov., a cryptic species and putative glacial relict2018In: The Lichenologist, ISSN 0024-2829, E-ISSN 1096-1135, Vol. 50, no 1, p. 59-75Article in journal (Refereed)
    Abstract [en]

    The lichen species of the genus Thamnolia, with their striking wormlike thalli and frequent occurrence in arctic and tundra environments, have often been debated with regard to the use of chemistry in lichen taxonomy. Phylogenetic studies have arrived at different conclusions as to the recognition of species in the genus, but in a recent study based on the analyses of six nuclear markers (genes or noncoding regions) of a worldwide sample of Thamnolia, we showed the existence of three well-supported lineages with two different chemistries and geographical distributions. Here, we present two analyses based on ITS and three markers, respectively, which were extended from the study mentioned above to include type specimens and additional Thamnolia strains and taxa. In these analyses the same three clades were retrieved. A putative DEAD-box helicase is used here for the first time as an informative phylogenetic marker to provide taxonomic resolution at species level. The distribution of morphological and chemical characters across the phylogeny was analyzed and it was concluded that three morphologically cryptic, but genetically well supported, species occur: T. vermicularis s. str., T. subuliformis s. str. and T. tundrae sp. nov. Thamnolia vermicularis s. str. contains individuals with uniform secondary chemistry (producing thamnolic acid) and a rather limited distribution in the European Alps, Tatra Mts and the Western Carpathians, a distribution which might result from glacial survival in an adjacent refugium/refugia. Thamnolia subuliformis s. str. is widely distributed in all hemispheres and the samples contain two chemotypes (either with thamnolic or squamatic acids). Thamnolia tundrae is described as new; it produces baeomycesic and squamatic acids, and has a distribution limited to the arctic tundra of Eurasia extending to the Aleutian Islands in North America. It may have survived the latest glaciation in coastal refugia near its present distribution. Thus, secondary chemistry alone is not suitable for characterizing species in Thamnolia, secondary chemistry and geographical origin are informative, and the ITS region can be confidently used for species recognition. Nomenclatural notes are given on several other names that have been used in Thamnolia.

  • 37.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A new Lineage of Eukaryotes Illuminates Eraly Mitochondrial Genome Reduction2017In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445Article in journal (Refereed)
  • 38.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala Univ, Dept Organismal Biol, Program Systemat Biol, Sci Life Lab, Norbyvagen 18D, S-75236 Uppsala, Sweden..
    Mitochondrial Evolution: Going, Going, Gone2016In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 26, no 10, p. R410-R412Article in journal (Other academic)
    Abstract [en]

    Monocercomonoides is the first example of a eukaryote lacking even the most reduced form of a mitochondrion-related organelle. This has important implications for cellular processes and our understanding of reductive mitochondrial evolution across the eukaryotic tree of life.

  • 39.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    The Convoluted Evolution of Eukaryotes With Complex Plastids2017In: Secondary Endosymbioses / [ed] Yoshihisa Hirakawa, Elsevier, 2017, p. 1-30Chapter in book (Other academic)
    Abstract [en]

    The textbook version of how plastids were established by endosymbiosis and subsequently diversified is like a well-oiled machine: a cyanobacterial endosymbiont was taken up by a heterotrophic cell and transformed over time into a bona fide photosynthetic organelle (plastid), ultimately giving rise to all plants and algae. The reality, however, is much more complicated and this chapter attempts to describe recent advances in the field of plastid evolution brought to light by disciplines such as phylogenomics, comparative genomics, and cell biology. If (almost) all plastids may ultimately trace back to the same original endosymbiotic event, the very large diversity of plastids we observe today can only be explained by multiple layers of endosymbioses. That is, plastids were passed between distantly related eukaryotic lineages multiple times, essentially creating a phylogenetic imbroglio where plastids appear monophyletic but hosts are not. The burning question then is: how can we best fit plastid and host data into a comprehensive evolutionary framework? Focusing not only on the so-called complex plastids (the product of eukaryote-to-eukaryote endosymbioses) and the lineages that host them but also on the many related plastid-lacking lineages and orphan taxa, I discuss the emergence of new models of plastid evolution. These models generalize the notion of serial endosymbioses to explain the scattered distribution of plastids in the eukaryotic tree of life. As such, they make new testable predictions as to how complex algae are connected through endosymbiotic gene transfer, but testing this will require first to determine the real magnitude of this process.

  • 40.