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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.
    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/.

    Keyword
    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.

    Keyword
    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
  • 3.
    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/.

  • 4.
    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

  • 5.
    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.

  • 6. 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.

  • 7.
    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.

  • 8.
    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)
  • 9.
    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.

  • 10.
    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)
  • 11.
    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)
  • 12.
    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.

  • 13.
    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.

  • 14.
    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.

  • 15. 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.

  • 16. 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.

  • 17.
    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.

  • 18.
    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.

  • 19.
    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.

  • 20. 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.

  • 21.
    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.

  • 22.
    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.

  • 23. 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.

  • 24. 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.

  • 25.
    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)
  • 26.
    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.

  • 27.
    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.

  • 28.
    Bálint, Miklós
    et al.
    Senckenberg Biodivers & Climate Res Ctr, Senckenberganlage 25, D-60325 Frankfurt, Germany.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Eren, A. Murat
    Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA; Univ Chicago, Dept Med, 5841 S Maryland Ave, Chicago, IL 60637 USA.
    Faust, Karoline
    Katholieke Univ Leuven, Rega Inst, Ctr Biol Dis, B-3000 Leuven, Belgium.
    Fuhrman, Jed
    Univ Southern Calif, Dept Biol Sci, MC0371, Los Angeles, CA 90089 USA.
    Lindahl, Björn
    Swedish Univ Agr Sci, Dept Soil & Environm, Box 7014, SE-75007 Uppsala, Sweden.
    O'Hara, Robert B.
    Senckenberg Biodivers & Climate Res Ctr, Senckenberganlage 25, D-60325 Frankfurt, Germany.
    Öpik, Maarja
    Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, 40 Lai St, EE-51005 Tartu, Estonia.
    Sogin, Mitchell L.
    Marine Biol Lab, Josephine Bay Paul Ctr Comparat Mol Biol & Evolut, Woods Hole, MA 02543 USA.
    Untersehe, Martin
    Ernst Moritz Arndt Univ Greifswald, Inst Bot & Landscape Ecol, Soldmannstr 15, D-17487 Greifswald, Germany.
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, 14a Ravila St, EE-50411 Tartu, Estonia.
    Millions of reads, thousands of taxa: microbial community structure and associations analyzed via marker genes2016In: FEMS Microbiology Reviews, ISSN 0168-6445, E-ISSN 1574-6976, Vol. 40, no 5, p. 686-700Article in journal (Refereed)
    Abstract [en]

    With high-throughput sequencing (HTS), we are able to explore the hidden world of microscopic organisms to an unpre-cedented level. The fast development of molecular technology and statistical methods means that microbial ecologists must keep their toolkits updated. Here, we review and evaluate some of the more widely adopted and emerging techniques for analysis of diversity and community composition, and the inference of species interactions from co-occurrence data generated by HTS of marker genes. We emphasize the importance of observational biases and statistical properties of the data and methods. The aim of the review is to critically discuss the advantages and disadvantages of established and emerging statistical methods, and to contribute to the integration of HTS-based marker gene data into community ecology.

  • 29. Caputo, Beniamino
    et al.
    Santolamazza, Federica
    Vicente, Jose L.
    Nwakanma, Davis C.
    Jawara, Musa
    Pålsson, Katinka
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Jaenson, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    White, Bradley J.
    Mancini, Emiliano
    Petrarca, Vincenzo
    Conway, David J.
    Besansky, Nora J.
    Pinto, Joao
    della Torre, Alessandra
    The "Far-West'' of Anopheles gambiae Molecular Forms2011In: PLoS ONE, ISSN 1932-6203, Vol. 6, no 2, p. e16415-Article in journal (Refereed)
    Abstract [en]

    The main Afrotropical malaria vector, Anopheles gambiae sensu stricto, is undergoing a process of sympatric ecological diversification leading to at least two incipient species (the M and S molecular forms) showing heterogeneous levels of divergence across the genome. The physically unlinked centromeric regions on all three chromosomes of these closely related taxa contain fixed nucleotide differences which have been found in nearly complete linkage disequilibrium in geographic areas of no or low M-S hybridization. Assays diagnostic for SNP and structural differences between M and S forms in the three centromeric regions were applied in samples from the western extreme of their range of sympatry, the only area where high frequencies of putative M/S hybrids have been reported. The results reveal a level of admixture not observed in the rest of the range. In particular, we found: i) heterozygous genotypes at each marker, although at frequencies lower than expected under panmixia; ii) virtually all possible genotypic combinations between markers on different chromosomes, although genetic association was nevertheless detected; iii) discordant M and S genotypes at two X-linked markers near the centromere, suggestive of introgression and inter-locus recombination. These results could be indicative either of a secondary contact zone between M and S, or of the maintenance of ancestral polymorphisms. This issue and the perspectives opened by these results in the study of the M and S incipient speciation process are discussed.

  • 30.
    Cardenas, Paco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Rapp, Hans Tore
    Disrupted spiculogenesis in deep-water Geodiidae (Porifera, Demospongiae) growing in shallow waters2013In: Invertebrate biology., ISSN 1077-8306, E-ISSN 1744-7410, Vol. 132, no 3, p. 173-194Article in journal (Refereed)
    Abstract [en]

    Environmental conditions can affect the morphology and distribution of sponges. In particular, depth is known to influence the morphology of shallow-water sponges; however, the influence of depth on deep-water sponges has never been investigated. Although boreal Geodiidae (Demospongiae, Astrophorida) are deep-water species, in fjords and along the Norwegian coast Geodia barretti, G. simplicissima, and Pachymatisma normani can occasionally be found at shallow depths (20-40m). In this study, we examine new shallow specimens from the Norwegian coast to compare their morphological and molecular characteristics with those of their deep-water counterparts. Morphology was studied at the level of the organism, skeletal organization, and the spicules, and a fragment of the cytochrome oxidase 1 gene was sequenced for shallow and deep specimens. Twelve specimens of Geodia spp. and five specimens of P. normani were collected in shallow waters. The majority of the Geodia spp. were identified as G. simplicissima, a species that has not been reported since its original description in 1931. However, we propose that G. simplicissima, only found in shallow waters, is a junior synonym of G. barretti. When comparing shallow and deep-water specimens of G. barretti and P. normani, we found phenotypic differences with respect to color, external morphology, cortex organization, and, above all, spicule morphology. In shallow specimens, microrhabds, sterrasters, and triaenes were smaller and irregular or underdeveloped. Oxyasters and strongylasters were normal in form, but smaller. We hypothesize that the lower silica concentration in shallow waters is primarily responsible for the disruption of spiculogenesis in shallow-water specimens of G. barretti and P. normani. The underdeveloped sterrasters observed in shallow-water specimens provide new insights into the formation of these particular microscleres. Finally, we discuss how the colonization of shallow waters by deep-water sponges may have strongly influenced spicule evolution and speciation.

  • 31.
    Cardenas, Paco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Rapp, Hans Tore
    Klitgaard, Anne Birgitte
    Best, Megan
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tendal, Ole Secher
    Taxonomy, biogeography and DNA barcodes of Geodia species (Porifera, Demospongiae, Tetractinellida) in the Atlantic boreo-arctic region2013In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 169, no 2, p. 251-311Article in journal (Refereed)
    Abstract [en]

    Geodia species north of 60 degrees N in the Atlantic appeared in the literature for the first time when Bowerbank described Geodia barretti and G.macandrewii in 1858 from western Norway. Since then, a number of species have been based on material from various parts of the region: G.simplex, Isops phlegraei, I.pallida, I.sphaeroides, Synops pyriformis, G.parva, G.normani, G.atlantica, Sidonops mesotriaena (now called G.hentscheli), and G.simplicissima. In addition to these 12 nominal species, four species described from elsewhere are claimed to have been identified in material from the northeast Atlantic, namely G.nodastrella and G.cydonium (and its synonyms Cydonium muelleri and Geodia gigas). In this paper, we revise the boreo-arctic Geodia species using morphological, molecular, and biogeographical data. We notably compare northwest and northeast Atlantic specimens. Biological data (reproduction, biochemistry, microbiology, epibionts) for each species are also reviewed. Our results show that there are six valid species of boreo-arctic Atlantic Geodia while other names are synonyms or mis-identifications. Geodia barretti, G.atlantica, G.macandrewii, and G.hentscheli are well established and widely distributed. The same goes for Geodia phlegraei, but this species shows a striking geographical and bathymetric variation, which led us to recognize two species, G.phlegraei and G.parva (here resurrected). Some Geodia are arctic species (G.hentscheli, G.parva), while others are typically boreal (G.atlantica, G.barretti, G.phlegraei, G.macandrewii). No morphological differences were found between specimens from the northeast and northwest Atlantic, except for G.parva. The Folmer cytochrome oxidase subunit I (COI) fragment is unique for every species and invariable over their whole distribution range, except for G.barretti which had two haplotypes. 18S is unique for four species but cannot discriminate G.phlegraei and G.parva. Two keys to the boreo-arctic Geodia are included, one based on external morphology, the other based on spicule morphology.

  • 32. Carr, M.
    et al.
    Leadbeater, B. S. C.
    Hassan, R.
    Nelson, M.
    Baldauf, Sandra L.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Molecular phylogeny of choanoflagellates, the sister group to Metazoa2008In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 105, no 43, p. 16641-16646Article in journal (Refereed)
    Abstract [en]

    Choanoflagellates are single-celled aquatic flagellates with a unique morphology consisting of a cell with a single flagellum surrounded by a "collar" of microvilli. They have long interested evolutionary biologists because of their striking resemblance to the collared cells (choanocytes) of sponges. Molecular phylogeny has confirmed a close relationship between choanoflagellates and Metazoa, and the first choanoflagellate genome sequence has recently been published. However, molecular phylogenetic studies within choanoflagellates are still extremely limited. Thus, little is known about choanoflagellate evolution or the exact nature of the relationship between choanoflagellates and Metazoa. We have sequenced four genes from a broad sampling of the morphological diversity of choanoflagellates including most species currently available in culture. Phylogenetic analyses of these sequences, alone and in combination, reject much of the traditional taxonomy of the group. The molecular data also strongly support choanoflagellate monophyly rejecting proposals that Metazoa were derived from a true choanoflagellate ancestor. Mapping of a complementary matrix of morphological and ecological traits onto the phylogeny allows a reinterpretation of choanoflagellate character evolution and predicts the nature of their last common ancestor.

  • 33.
    Carr, Martin
    et al.
    Department of Biology, University of York.
    Nelson, Michaela
    Department of Biology, University of York.
    Leadbeater, Barry
    School of Biosciences, University of Birmingham.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Three Families of LTR Retrotransposons are Present in the Genome of the Choanoflagellate Monosiga brevicollis2008In: Protist, ISSN 1434-4610, E-ISSN 1618-0941, Vol. 159, no 4, p. 579-590Article in journal (Refereed)
    Abstract [en]

    The choanoflagellates are a ubiquitous group of nanoflagellates and the sister group of Metazoa. Examination of the initial draft version of the first choanoflagellate genome, that of Monosiga brevicollis, reveals the presence of three novel families of long terminal repeat (LTR) retrotransposons and an apparent absence of non-LTR retrotransposons and transposons. One of the newly discovered LTR families falls in the chromovirus clade of the Ty3/gypsy group while the other two families are closely related members of the Ty1/copia group. Examination of EST sequences and nucleotide analyses show that all three families are transcriptionally active and potentially functional within the genome of M. brevicollis.

  • 34.
    Cavender, James C.
    et al.
    Ohio Univ, Dept Environm & Plant Biol, Athens, OH 45701 USA..
    Landolt, John C.
    Shepherd Univ, Dept Biol, Shepherdstown, WV 25443 USA..
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Perrigo, Allison
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Vadell, Eduardo M.
    JF Kennedy Univ, Escuela Farm & Bioquim, Buenos Aires, DF, Argentina..
    Stephenson, Steven L.
    Univ Arkansas, Dept Biol Sci, Fayetteville, AR 72701 USA..
    New species of Polysphondylium from Madagascar2016In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 108, no 1, p. 80-109Article in journal (Refereed)
    Abstract [en]

    Two series of samples collected for isolation of dictyostelid cellular slime molds (dictyostelids) in Madagascar yielded a relatively large number of isolates of Polysphondylium. Most of these turned out to be species new to science that show varying degrees of clustering from unclustered to coremiform as well as an ability to migrate. Migratory ability (phototaxis) is a common feature of species assigned to Group 2 of the Polysphondylia and is common in the new species from Madagascar. Another common feature, clustering, appears to be a strategy for keeping fruiting bodies erect for a longer time in a climate that is relatively dry, whereas migratory ability may function seasonally when there is more rainfall. Thirteen species are described herein. Each of these is characterized by a particular set of distinguishing features, and collectively they expand our concept of the genus Polysphondylium.

  • 35. Cavender, James C.
    et al.
    Vadell, Eduardo M.
    Landolt, John C.
    Winsett, Katherine E.
    Stephenson, Steven L.
    Rollins, Adam W.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    New small dictyostelids from seasonal rainforests of Central America2013In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 105, no 3, p. 610-635Article in journal (Refereed)
    Abstract [en]

    Ten small dictyostelids isolated from samples collected from the surface humus layer of seasonal rainforests of Belize and Guatemala were studied morphologically, and nine were found to represent distinct species, all with an average height of < 2 mm (0.5-3.5 mm). Although their fruiting bodies (sorocarps) closely resemble one another, the nine species differ in their patterns of aggregation, stream pattern, branching development, formation of microcysts, spore shape, presence or absence of spore granules and their distribution, as well as in the shapes and behavior of their sorogens and myxamoebae. These stable morphological features were sufficient to recognize nine new species of small dictyostends, one with two varieties. SSU rDNA sequences were generated for all these new isolates, and phylogenetic analyses of these sequences show these new isolates belong to Dictyostelid group 3. As a result of this and other recent studies, the concept of what constitutes a species in the dictyostelids has become much more restricted and well defined, in as much as some of the morphological and behavioral patterns now being observed were overlooked in the past. The extent, flow direction and conformation of streaming within the group varies from simple aggregation mounds with no streams to short streams, to somewhat longer streams and finally to well developed streams. Each of these is characterized by a particular set of distinguishing features.

  • 36. Chalopin, Domitille
    et al.
    Volff, Jean-Nicolas
    Galiana, Delphine
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Schartl, Manfred
    Transposable elements and early evolution of sex chromosomes in fish2015In: Chromosome Research, ISSN 0967-3849, E-ISSN 1573-6849, Vol. 23, no 3, p. 545-560Article in journal (Refereed)
    Abstract [en]

    In many organisms, the sex chromosome pair can be recognized due to heteromorphy; the Y and W chromosomes have often lost many genes due to the absence of recombination during meiosis and are frequently heterochromatic. Repetitive sequences are found at a high proportion on such heterochromatic sex chromosomes and the evolution and emergence of sex chromosomes has been connected to the dynamics of repeats and transposable elements. With an amazing plasticity of sex determination mechanisms and numerous instances of independent emergence of novel sex chromosomes, fish represent an excellent lineage to investigate the early stages of sex chromosome differentiation, where sex chromosomes often are homomorphic and not heterochromatic. We have analyzed the composition, distribution, and relative age of TEs from available sex chromosome sequences of seven teleost fish. We observed recent bursts of TEs and simple repeat accumulations around young sex determination loci. More strikingly, we detected transposable element (TE) amplifications not only on the sex determination regions of the Y and W sex chromosomes, but also on the corresponding regions of the X and Z chromosomes. In one species, we also clearly demonstrated that the observed TE-rich sex determination locus originated from a TE-poor genomic region, strengthening the link between TE accumulation and emergence of the sex determination locus. Altogether, our results highlight the role of TEs in the initial steps of differentiation and evolution of sex chromosomes.

  • 37. Chang, Yue
    et al.
    Liu, Guanglong
    Guo, Lina
    Liu, Hongbo
    Yuan, Dongxia
    Xiong, Jie
    Ning, Yingzhi
    Fu, Chengjie
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Miao, Wei
    Cd-Metallothioneins in Three Additional Tetrahymena Species: Intragenic Repeat Patterns and Induction by Metal Ions2014In: Journal of Eukaryotic Microbiology, ISSN 1066-5234, E-ISSN 1550-7408, Vol. 61, no 4, p. 333-342Article in journal (Refereed)
    Abstract [en]

    Ciliate metallothioneins (MTs) possess many unique features compared to the "classic" MTs in other organisms, but they have only been studied in a small number of species. In this study, we investigated cDNAs encoding subfamily 7a metallothioneins (CdMTs) in three Tetrahymena species (T. hegewischi, T. malaccensis, and T. mobilis). Four CdMT genes (ThegMT1, ThegMT2, TmalMT1, and TmobMT1) were cloned and characterized. They share high sequence similarity to previously identified subfamily 7a MT members. Tetrahymena CdMTs exhibit a remarkably regular intragenic repeat homology. The CdMT sequences were divided into two main types of modules, which had been previously described, and which we name "A" and "B". ThegMT2 was identified as the first MT isoform solely composed of module "B". A phylogenetic analysis of individual modules of every characterized Tetrahymena CdMT rigorously documents the conclusion that modules are important units of CdMT evolution, which have undergone frequent and rapid gain/loss and shuffling. The transcriptional activity of the four newly identified genes was measured under different heavy metal exposure (Cd, Cu, Zn, Pb) using real-time quantitative PCR. The results showed that these genes were differentially induced after short (1 h) or long (24 h) metal exposure. The evolutionary diversity of Tetrahymena CdMTs is further discussed with regard to their induction by metal ions.

  • 38.
    Christerson, Linus
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
    Blomqvist, Maria
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
    Grannas, Karin
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
    Thollesson, Mikael
    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 Organismal Biology, Molecular Evolution.
    Laroucau, Karine
    Waldenström, Jonas
    Eliasson, Ingvar
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Herrmann, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
    A novel Chlamydiaceae-like bacterium found in faecal specimens from sea birds from the Bering Sea2010In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229, Vol. 2, no 4, p. 605-610Article in journal (Refereed)
    Abstract [en]

    The family Chlamydiaceae contains several bacterial pathogens of important human and veterinary medical concern, such as Chlamydia trachomatis and Chlamydophila psittaci. Within the order Chlamydiales there are also an increasing number of chlamydia-like bacteria whose biodiversity, host range and environmental spread seem to have been largely underestimated, and which are currently being investigated for their potential medical relevance. In this study we present 16S rRNA, rnpB and ompA gene sequence data congruently indicating a novel chlamydia-like bacterium found in faecal specimens from opportunistic fish-eating sea birds, belonging to the Laridae and Alcidae families, from the Bering Sea. This novel bacterium appears to be closer to the Chlamydiaceae than other chlamydia-like bacteria and is most likely a novel genus within the Chlamydiaceae family.

  • 39. Cooper, Wendy, E.
    et al.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A taxonomic revision of Trichosanthes L. (Cucurbitaceae) in Australia, including one new species from the Northern Territory2011In: Austrobaileya : a journal of plant systematics, ISSN 0155-4131, Vol. 8, no 3, p. 364-386Article in journal (Refereed)
    Abstract [en]

    Trichosanthes is represented by six species in Australia: T cucumerina L. var. cucumerina,T morrisii W.E.Cooper sp. nov., T odontosperma W.E.Cooper & A.J.Ford, T pentaphylla F.Muell. ex Benth., T pilosa Lour. and T subvelutina F.Muell. ex Cogn. Trichosanthes ovigera Blume has recently been synonymised with T pilosa and we now include T holtzei F.Muell. within this synonymy. All taxa are illustrated (with the exception of T odontosperma previously illustrated in 2010), and distinguished from other Australian species. Notes on habitat and distribution are included together with distribution maps. Three identification keys are presented, two to the sections of Trichosanthes and one to the species of Trichosanthes in Australia.

  • 40.
    Corcoran, Padraic
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology. Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, England.
    Anderson, Jennifer L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Jacobson, David J
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Sun, Yu
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution.
    Ni, Peixiang
    BGI HongKong, Hong Kong, Hong Kong, Peoples R China.
    Lascoux, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Plant Ecology and Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Introgression maintains the genetic integrity of the mating-type determining chromosome of the fungus Neurospora tetrasperma.2016In: Genome Research, ISSN 1088-9051, E-ISSN 1549-5469, Vol. 26, no 4, p. 486-498Article in journal (Refereed)
    Abstract [en]

    Genome evolution is driven by a complex interplay of factors, including selection, recombination, and introgression. The regions determining sexual identity are particularly dynamic parts of eukaryotic genomes that are prone to molecular degeneration associated with suppressed recombination. In the fungus Neurospora tetrasperma, it has been proposed that this molecular degeneration is counteracted by the introgression of nondegenerated DNA from closely related species. In this study, we used comparative and population genomic analyses of 92 genomes from eight phylogenetically and reproductively isolated lineages of N. tetrasperma, and its three closest relatives, to investigate the factors shaping the evolutionary history of the genomes. We found that suppressed recombination extends across at least 6 Mbp (similar to 63%) of the mating-type (mat) chromosome in N. tetrasperma and is associated with decreased genetic diversity, which is likely the result primarily of selection at linked sites. Furthermore, analyses of molecular evolution revealed an increased mutational load in this region, relative to recombining regions. However, comparative genomic and phylogenetic analyses indicate that the mat chromosomes are temporarily regenerated via introgression from sister species; six of eight lineages show introgression into one of their mat chromosomes, with multiple Neurospora species acting as donors. The introgressed tracts have been fixed within lineages, suggesting that they confer an adaptive advantage in natural populations, and our analyses support the presence of selective sweeps in at least one lineage. Thus, these data strongly support the previously hypothesized role of introgression as a mechanism for the maintenance of mating-type determining chromosomal regions.

  • 41.
    Cárdenas, Paco
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Who Produces Ianthelline? The Arctic Sponge Stryphnus fortis or its Sponge Epibiont Hexadella dedritifera: a Probable Case of Sponge-Sponge Contamination2016In: Journal of Chemical Ecology, ISSN 0098-0331, E-ISSN 1573-1561, Vol. 42, no 4, p. 339-347Article in journal (Refereed)
    Abstract [en]

    The bromotyrosine derivative ianthelline was isolated recently from the Atlantic boreo-arctic deep-sea sponge Stryphnus fortis, and shown to have clear antitumor and antifouling effects. However, chemosystematics, field observations, and targeted metabolic analyses (using UPLC-MS) suggest that ianthelline is not produced by S. fortis but by Hexadella dedritifera, a sponge that commonly grows on S. fortis. This case highlights the importance of combining taxonomic and ecological knowledge to the field of sponge natural products research.

  • 42.
    Cárdenas, Paco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Bergen, Dept Biol, N-5020 Bergen, Norway..
    Rapp, Hans Tore
    Univ Bergen, Dept Biol, N-5020 Bergen, Norway.;Univ Bergen, Ctr Geobiol, N-5007 Bergen, Norway.;Uni Environm, Uni Res, N-5006 Bergen, Norway..
    Demosponges from the Northern Mid-Atlantic Ridge shed more light on the diversity and biogeography of North Atlantic deep-sea sponges2015In: Journal of the Marine Biological Association of the United Kingdom, ISSN 0025-3154, E-ISSN 1469-7769, Vol. 95, no 7, p. 1475-1516Article in journal (Refereed)
    Abstract [en]

    In July-August 2004, the Mid-Atlantic Ridge Ecosystems (MAR-Eco) expedition collected Demospongiae (Porifera) from the Northern Mid-Atlantic Ridge (MAR) north of the Azores, between 41 degrees N and 61 degrees N. Demosponges were found at 10 stations, at depths ranging from 753 to 3046 m. Twenty-two species were identified: 17 Tetractinellida, one Polymastiida, one Suberitida, two Poecilosclerida and one Dendroceratida. The study of this material is an opportunity to revise the taxonomy and the North Atlantic distribution of each of these deep-sea species. Some species are particularly rare and poorly known (Tetilla longipilis, Tetilla sandalina, Craniella azorica, Polymastia corticata) and two are new to science: Forcepia (Forcepia) toxafera sp. nov. and Iotroata paravaridens sp. nov. This study suggests that the MAR is not a longitudinal barrier for the dispersal of deep-sea demosponges while on the contrary, the Charlie-Gibbs Fracture Zone (CGFZ) may be a latitudinal border for the dispersal of deep-sea demosponges, due to great depths and currents.

  • 43.
    Cárdenas, Paco
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Pharmacy, Department of Medicinal Chemistry, Division of Pharmacognosy.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A new Hymedesmia (Demospongiae, Poecilosclerida) with large sigmas off western Sweden2016In: Journal of the Marine Biological Association of the United Kingdom, ISSN 0025-3154, E-ISSN 1469-7769, Vol. 96, no 6, p. 1305-1312Article in journal (Refereed)
    Abstract [en]

    Hymedesmia (Hymedesmia) lindstroemae sp. nov. collected at 178–210 m depth off the western Swedish coast is described. This encrusting sponge is notably characterized by its unusually large sigmas. This new species brings the number of Hymedesmia (Hymedesmia) species in Swedish waters to 30. A key for all the North Atlantic Hymedesmia (Hymedesmia) species with sigmas (32 species) is included.

  • 44.
    Davis, Robert B
    et al.
    Department of Biology, University of York.
    Baladuf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mayhew, Peter J
    Department of Biology, University of York.
    The origins of species richness in the Hymenoptera: insights from a family-level supertree2010In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 10, article id 109Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The order Hymenoptera (bees, ants, wasps, sawflies) contains about eight percent of all described species, but no analytical studies have addressed the origins of this richness at family-level or above. To investigate which major subtaxa experienced significant shifts in diversification, we assembled a family-level phylogeny of the Hymenoptera using supertree methods. We used sister-group species-richness comparisons to infer the phylogenetic position of shifts in diversification.

    RESULTS: The supertrees most supported by the underlying input trees are produced using matrix representation with compatibility (MRC) (from an all-in and a compartmentalised analysis). Whilst relationships at the tips of the tree tend to be well supported, those along the backbone of the tree (e.g. between Parasitica superfamilies) are generally not. Ten significant shifts in diversification (six positive and four negative) are found common to both MRC supertrees. The Apocrita (wasps, ants, bees) experienced a positive shift at their origin accounting for approximately 4,000 species. Within Apocrita other positive shifts include the Vespoidea (vespoid wasps/ants containing 24,000 spp.), Anthophila + Sphecidae (bees/thread-waisted wasps; 22,000 spp.), Bethylidae + Chrysididae (bethylid/cuckoo wasps; 5,200 spp.), Dryinidae (dryinid wasps; 1,100 spp.), and Proctotrupidae (proctotrupid wasps; 310 spp.). Four relatively species-poor families (Stenotritidae, Anaxyelidae, Blasticotomidae, Xyelidae) have undergone negative shifts. There are some two-way shifts in diversification where sister taxa have undergone shifts in opposite directions.

    CONCLUSIONS: Our results suggest that numerous phylogenetically distinctive radiations contribute to the richness of large clades. They also suggest that evolutionary events restricting the subsequent richness of large clades are common. Problematic phylogenetic issues in the Hymenoptera are identified, relating especially to superfamily validity (e.g. "Proctotrupoidea", "Mymarommatoidea"), and deeper apocritan relationships. Our results should stimulate new functional studies on the causes of the diversification shifts we have identified. Possible drivers highlighted for specific adaptive radiations include key anatomical innovations, the exploitation of rich host groups, and associations with angiosperms. Low richness may have evolved as a result of geographical isolation, specialised ecological niches, and habitat loss or competition.

  • 45.
    Davis, Robert B
    et al.
    Department of Biology, University of York.
    Baldauf, Sandra L
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mayhew, Peter J
    Department of Biology, University of York.
    Many hexapod groups originated earlier and withstood extinction events better than previously realized: inferences from supertrees2010In: Proceedings of the Royal Society of London. Biological Sciences, ISSN 0962-8452, E-ISSN 1471-2954, Vol. 277, no 1687, p. 1597-1606Article in journal (Refereed)
    Abstract [en]

    Comprising over half of all described species, the hexapods are central to understanding the evolution of global biodiversity. Direct fossil evidence suggests that new hexapod orders continued to originate from the Jurassic onwards, and diversity is presently higher than ever. Previous studies also suggest that several shifts in net diversification rate have occurred at higher taxonomic levels. However, their inferred timing is phylogeny dependent. We re-examine these issues using the supertree approach to provide, to our knowledge, the first composite estimates of hexapod order-level phylogeny. The Purvis matrix representation with parsimony method provides the most optimal supertree, but alternative methods are considered. Inferring ghost ranges shows richness of terminal lineages in the order-level phylogeny to peak just before the end-Permian extinction, rather than the present day, indicating that at least 11 more lineages survived this extinction than implied by fossils alone. The major upshift in diversification is associated with the origin of wings/wing folding and for the first time, to our knowledge, significant downshifts are shown associated with the origin of species-poor taxa (e.g. Neuropterida, Zoraptera). Polyneopteran phylogeny, especially the position of Zoraptera, remains important resolve because this influences findings regarding shifts in diversification. Our study shows how combining fossil with phylogenetic information can improve macroevolutionary inferences.

  • 46.
    Davis, Robert
    et al.
    Department of Biology, University of York.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Mayhew, Peter
    University of York, Department of Biology.
    Eusociality and the success of the termites: insights from a supertree of dictyopteran families.2009In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 22, no 8, p. 1750-1761Article in journal (Refereed)
    Abstract [en]

    Sociality in insects may negatively impact on species richness. We tested whether termites have experienced shifts in diversification rates through time. Supertree methods were used to synthesize family-level relationships within termites, cockroaches and mantids. A deep positive shift in diversification rate is found within termites, but not in the cockroaches from which they evolved. The shift is responsible for most of their extant species richness suggesting that eusociality is not necessarily detrimental to species richness, and may sometimes have a positive effect. Mechanistic studies of speciation and extinction in eusocial insects are advocated.

  • 47.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    African plants as antipathogen agents: efficacy and clinical evidence2008In: Botanical Medicine in Clinical Practice / [ed] Preedy, V.R., Watson, R., CABI Publishing , 2008, p. 3-12Chapter in book (Other academic)
  • 48.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Local Awareness of Scarcity and Endangerment of Medicinal Plants in Roussenski Lom Natural Park in Northern Bulgaria2010In: Ethnobotany in the new Europe: people, health and wild plant resources / [ed] Manuel Pardo de Santayana, Andrea Pieroni, Rajindra K. Puri, New York: Berghahn Books, 2010, p. 93-111Chapter in book (Refereed)
  • 49.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Snake Gourds, Parasites and Mother Roasting: Medicinal plants, plant repellents, and Trichosanthes (Cucurbitaceae) in Lao PDR2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background. Traditional plant use was studied in Lao PDR. Research focused on medicinal plant use by the Brou, Saek and Kry ethnic groups, traditional plant repellents against parasitic arthropods and leeches, and the phylogeny and biogeography of the medicinally-important snake gourd genus (Trichosanthes, Cucurbitaceae).  Methods. The ethnobiology research used a combination of structured interviews, village surveys, botanical collecting, hydro-distillation, GC-MS analysis, literature studies, and laboratory experiments. The plant systematics research used a combination of morphological studies, molecular biology laboratory work, and phylogenetic, dating and biogeographical analysis.  Results. Informants reported the use of close to 100 species to repel arthropods and leeches, many of which have constituents with documented efficacy.  Brou, Saek and Kry informants use over 75 plant species for women’s healthcare, mainly during the postpartum period for steam sauna, steam bath, hotbed, mother roasting, medicinal decoctions and infusions, and postpartum diet.  A molecular phylogeny of Trichosanthes and Gymnopetalum using a broad sampling of ~60% of their species and 4756 nucleotides of nuclear and plastid DNA shows that Gymnopetalum is nested within Trichosanthes. Fossil-calibrated Bayesian molecular dating of the Trichosanthes phylogeny reveals an early Oligocene origin of the genus, and many of the extant sections originating and diversifying during the Miocene. Biogeographical analysis shows a likely East or South Asian origin of Trichosanthes, with lineages diversifying and spreading throughout Australasia from the early Pliocene to the Pleistocene.  Discussion. Traditional plant use in Lao PDR is common and widespread. The presence among the repellent species of economical alternatives to costly synthetic repellents is tenable, and the subject of ongoing studies.  Postpartum traditions and medicinal plant use are essential parts of childbirth and postpartum recovery in these ethnic groups, and many other groups in Lao PDR. Efforts to improve maternal healthcare and reduce maternal and infant mortality need to integrate these traditions with modern notions of healthcare to achieve wider adoption. Documenting all possible uses of commonly used medicinal plant species shows that similarity in use between these ethnic groups is relatively low considering that they share, and have shared for many generations, the same environment and resources. A lack of effective cures leads to a process of continuous innovation, where effective cures are shared between cultures, but remedies of only cultural importance, or those under evaluation are culture-specific.  The Trichosanthes phylogeny implies the merging of Gymnopetalum into Trichosanthes, and this is done using available names or new combinations. A synopsis of Trichosanthes, the new combinations, and a revision of the species in Australia, are made and presented.  Conclusions. Traditional plant use is widespread in Lao PDR, and of significance to many people as a source of primary healthcare and inexpensive repellents. The important medicinal plant genus Trichosanthes includes Gymnopetalum, and has a complex biogeographic history with multiple colonization events of Australasia.

    List of papers
    1. Plants used during pregnancy, childbirth and postpartum healthcare in Lao PDR: A comparative study of the Brou, Saek and Kry ethnic groups
    Open this publication in new window or tab >>Plants used during pregnancy, childbirth and postpartum healthcare in Lao PDR: A comparative study of the Brou, Saek and Kry ethnic groups
    2009 (English)In: Journal of Ethnobiology and Ethnomedicine, ISSN 1746-4269, E-ISSN 1746-4269, Vol. 5, p. 25-Article in journal (Refereed) Published
    Abstract [en]

    Background

    In many Southeast Asian cultures the activities and diet during the postpartum period are culturally dictated and a period of confinement is observed. Plants play an important role in recovery during the postpartum period in diet, traditional medicine, steam bath and mother roasting (where mother and child placed on a bed above a brazier with charcoal embers on which aromatic plants are laid). This research focuses on the use of plants during pregnancy, parturition, postpartum recovery and infant healthcare among three ethnic groups, the Brou, Saek and Kry. It aims to identify culturally important traditions that may facilitate implementation of culturally appropriate healthcare.

    Methods

    Data were collected in 10 different villages in Khammouane province, Lao PDR, through group and individual interviews with women by female interviewers.

    Results

    A total of 55 different plant species are used in women's healthcare, of which over 90% are used in postpartum recovery. Consensus Analysis rejects the hypothesis that the three ethnic groups belong to a single culture for postpartum plant use, and multidimensional scaling reveals non-overlapping clusters per ethnic group.

    Conclusion

    Medicinal plant use is common among the Brou, Saek and Kry to facilitate childbirth, alleviate menstruation problems, assist recovery after miscarriage, mitigate postpartum haemorrhage, aid postpartum recovery, and for use in infant care. The wealth of novel insights into plant use and preparation will help to understand culturally important practices such as confinement, dietary restrictions, mother roasting and herbal steam baths and their incorporation into modern healthcare

    National Category
    Biological Sciences
    Research subject
    Systematic Botany
    Identifiers
    urn:nbn:se:uu:diva-141785 (URN)10.1186/1746-4269-5-25 (DOI)000207918700025 ()19737413 (PubMedID)
    Available from: 2011-01-12 Created: 2011-01-12 Last updated: 2017-12-11Bibliographically approved
    2. Traditions and plant use during pregnancy, childbirth and postpartum recovery by the Kry ethnic group in Lao PDR
    Open this publication in new window or tab >>Traditions and plant use during pregnancy, childbirth and postpartum recovery by the Kry ethnic group in Lao PDR
    2011 (English)In: Journal of Ethnobiology and Ethnomedicine, ISSN 1746-4269, E-ISSN 1746-4269, Vol. 7, p. 14-Article in journal (Refereed) Published
    Abstract [en]

    Background: Activities and diet during the postpartum period are culturally dictated in many Southeast Asian cultures, and a period of confinement is observed. Plants play an important role in recovery during the postpartum period in diet and traditional medicine. Little is known of the Kry, a small ethnic group whose language was recently described, concerning its traditions and use of plants during pregnancy, parturition, postpartum recovery and infant healthcare. This research aims to study those traditions and identify medicinal plant use. Methods: Data were collected in the 3 different Kry villages in Khammouane province, Lao PDR, through group and individual interviews with women by female interviewers. Results: A total of 49 different plant species are used in women's healthcare. Plant use is culturally different from the neighboring Brou and Saek ethnic groups. Menstruation, delivery and postpartum recovery take place in separate, purpose-built, huts and a complex system of spatial restrictions is observed. Conclusions: Traditions surrounding childbirth are diverse and have been strictly observed, but are undergoing a shift towards those from neighboring ethnic groups, the Brou and Saek. Medicinal plant use to facilitate childbirth, alleviate menstruation problems, assist recovery after miscarriage, mitigate postpartum haemorrhage, aid postpartum recovery, and for use in infant care, is more common than previously reported (49 species instead of 14). The wealth of novel insights into plant use and preparation will help to understand culturally important practices such as traditional delivery, spatial taboos, confinement and dietary restrictions, and their potential in modern healthcare.

    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-156106 (URN)10.1186/1746-4269-7-14 (DOI)000291981800001 ()
    Available from: 2011-07-11 Created: 2011-07-11 Last updated: 2017-12-11Bibliographically approved
    3. Steam sauna and mother roasting in Lao PDR: Practices and Chemical constituents of essential oils of plant species used in postpartum recovery
    Open this publication in new window or tab >>Steam sauna and mother roasting in Lao PDR: Practices and Chemical constituents of essential oils of plant species used in postpartum recovery
    2011 (English)In: BMC Complementary and Alternative Medicine, ISSN 1472-6882, E-ISSN 1472-6882, Vol. 11, p. 128-Article in journal (Refereed) Published
    Abstract [en]

    Background: Fundamental in traditional postpartum recovery in Lao PDR is the use of hotbeds, mother roasting, steam sauna and steam baths. During these treatments medicinal plants play a crucial role, but little has been published about how the treatments are carried out precisely, which species are used, the medicinal properties of these species, and the medicinal efficacy of their chemical constituents.

    Methods: Sixty-five interviews, in 15 rural villages, with women of 4 different ethnic groups were conducted to survey confinement rituals, and postpartum plant use and salience. Essential oils from the main species used were extracted using steam distillation and the main chemical constituents characterized using gas chromatography-mass spectrometry (GC-MS).

    Results: A total of 10 different species were used by three or more of the ethnic groups included in this study. All species were used in steam sauna and bath, but only 3 species were used in hotbed and mother roasting. Essential oils of Amomum villosum, Amomum microcarpum and Blumea balsamifera were found to contain significant amounts of the following terpenes: β-pinene, camphor, bornyl acetate, borneol, linalool, D-limonene, fenchone, terpinen-4-ol and α-terpinene.

    Conclusions: Many of these terpenes have documented antimicrobial and analgesic properties, and some have also synergistic interactions with other terpenes. The mode of application in hotbed and mother roasting differs from the documented mechanisms of action of these terpenes. Plants in these two practices are likely to serve mainly hygienic purposes, by segregating the mother from infection sources such as beds, mats, stools, cloth and towels. Steam sauna medicinal plant use through inhalation of essential oils vapors can possibly have medicinal efficacy, but is unlikely to alleviate the ailments commonly encountered during postpartum convalescence. Steam sauna medicinal plant use through dermal condensation of essential oils, and steam bath cleansing of the perineal area is possibly a pragmatic use of the reported medicinal plants, as terpene constituents have documented antimicrobial, analgesic and anti-inflammatory properties.

    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-149972 (URN)10.1186/1472-6882-11-128 (DOI)000299843900001 ()
    Available from: 2011-03-24 Created: 2011-03-24 Last updated: 2017-12-11Bibliographically approved
    4. Comparing medicinal plant knowledge using similarity indices: A case of the Brou, Saek and Kry in Lao PDR
    Open this publication in new window or tab >>Comparing medicinal plant knowledge using similarity indices: A case of the Brou, Saek and Kry in Lao PDR
    2012 (English)In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 141, no 1, p. 481-500Article in journal (Refereed) Published
    Abstract [en]

    known traditional ecosystem services, as it provides primary healthcare, contributes to subsistence livelihoods, and for its potential value as a source of novel pharmaceuticals. People living in close contact with their surroundings for many generations are hypothesized to have developed, through trial-and-error, in-depth knowledge of ecosystems, biodiversity, and their management and utility. In the case of medicinal plant knowledge it could lead to an asymptotic climax or a constantly evolving equilibrium of cures with proven efficacy and those under assessment.Methods: An in-depth study of 97 plant species used in traditional medicine by the Brou, Saek and Kry ethnic groups in Lao PDR was made to test similarity in medicinal plant knowledge.Results: Medicinal plants were used in 99 different ways in 510 species-use combinations. Medicinal uses could be generalized into 12 use categories with 747 species-category combinations. Similarity indices show Brou and Saek plant use appears to be most similar (QS(BS): 60.0; JI(BS): 75.1) followed by Kry and Saek (QS(KS): 51.6; JI(KS): 53.4), and then Kry and Brou (QS(BK): 46.9; JI(BK): 44.1).Discussion: Intercultural similarities found are quite low, considering that all three groups share the same geographical and ecological area and have the same dependence on medicinal plants. Intercultural transmission is unimpeded but many treatments are likely to be ineffective. Comparison of the similarities found here with similarities computed from other data show that these results are homologous with other sympatric ethnic groups, and much higher than those for allopatrically living groups.Conclusion: Medicinal plant knowledge does not reach a stable climax, but appears to evolve continually by trial-and-error, as effective cures to many ailments are unavailable.

    Keyword
    Traditional plant medicine, Ethnobotany, Traditional ecological knowledge, knowledge similarity, Similarity indices, Jaccard, Sorensen
    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-168534 (URN)000304571100061 ()
    Note
    Manuscript title: Traditional Ecological Knowledge: Similarity of medicinal plant knowledge among the Brou, Saek and Kry in Lao PDRAvailable from: 2012-02-13 Created: 2012-02-13 Last updated: 2017-12-07Bibliographically approved
    5. Botanical Repellents and Pesticides Traditionally Used Against Hematophagous Invertebrates in Lao People's Democratic Republic: A Comparative Study of Plants Used in 66 Villages
    Open this publication in new window or tab >>Botanical Repellents and Pesticides Traditionally Used Against Hematophagous Invertebrates in Lao People's Democratic Republic: A Comparative Study of Plants Used in 66 Villages
    Show others...
    2010 (English)In: Journal of medical entomology, ISSN 0022-2585, E-ISSN 1938-2928, Vol. 47, no 3, p. 400-414Article in journal (Refereed) Published
    Abstract [en]

    Hematophagous parasites such as leeches, ticks, mites, lice, bedbugs, mosquitoes, and myiasis-producing fly larvae are common health problems in Lao People's Democratic Republic. Several arthropod-borne infections, e.g., malaria, dengue fever, and Japanese encephalitis, are endemic there. Effective vector control methods including the use of pesticides, insecticide-treated bed nets, and synthetic and plant-based repellents are important means of control against such invertebrates and the pathogens they may transmit or directly cause. In this study, we documented traditional knowledge on plants that are used to repel or kill hematophagous arthropods, including mosquitoes, bedbugs, human lice, mites and ticks, fly larvae, and blood-sucking leeches. Structured interviews were carried out in 66 villages comprising 17 ethnic groups, covering a range of cultures, throughout Lao People's Democratic Republic. A total of 92 plant species was recorded as traditional repellents (including plants for pesticidal usages) in 123 different plant-ectoparasite combinations. The number and species of plants, and animal taxa repelled (or killed) per plant species differed per region, village, and ethnic group. Traditional use was confirmed in the scientific literature for 74 of these plant species, and for an additional 13 species using literature on closely related species. The use of botanical repellents and pesticides from many plant species is common and widespread in the Lao countryside. In the future, the identification of the active components in certain plants to develop more optimal, inexpensive repellents, insecticides, acaricides, or antileech compounds as alternatives to synthetic repellents/pesticides against blood-feeding insects, ticks, mites, and leeches is warranted.

    Keyword
    botanical repellents, ethnobotany, leeches, mosquitoes, myiasis
    National Category
    Biological Sciences
    Identifiers
    urn:nbn:se:uu:diva-136563 (URN)10.1603/ME09273 (DOI)000277597000015 ()20496588 (PubMedID)
    Available from: 2010-12-14 Created: 2010-12-13 Last updated: 2017-12-11
    6. A Fly in the Ointment: Evaluation of Traditional Use of Plants to Repel and Kill Blowfly Larvae in Fermented Fish
    Open this publication in new window or tab >>A Fly in the Ointment: Evaluation of Traditional Use of Plants to Repel and Kill Blowfly Larvae in Fermented Fish
    2011 (English)In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 6, no 12, article id e29521Article in journal (Refereed) Published
    Abstract [en]

    Introduction: In rural areas in Laos, fly larvae infestations are common in fermenting fish. Blowflies (Chrysomyamegacephala, Diptera: Calliphoridae) are attracted to oviposit (and/or larviposit) onto fermenting fish which results ininfestations with fly larvae. Knowledge of traditional use of plants to repel larvae during the production of fermented fish iscommon and widespread in Lao PDR.

    Research Questions: How effective are the most salient species in repelling, and killing fly larvae in fermenting fish?

    Material and Methods: The three plant species most frequently reported to repel fly larvae during an ethnobotanical surveythroughout Lao PDR were tested for repellence and larvicidal activity of fly larvae infesting fermented fish. The lethality andrepellence of Tadehagi triquetrum (L.) H. Ohashi (Fabaceae), Uraria crinita (L.) Desv. ex DC. (Fabaceae) and Bambusa multiplex(Lour.) Raeusch. ex Schult. & Schult. f. (Poaceae) were tested in an experimental design using fermenting fish in Vientiane,Lao PDR.

    Results: The repellent effect of fresh material of T. triquetrum and U. crinita, and the larvicidal effect of fresh B. multiplex, issignificantly more effective than that of dried material of the same species, and the total effect (repellence and larvicidaleffect combined) for each of the three species was significantly more effective for fresh than for dry material. Fresh materialof T. triquetrum, U. crinita, or B. multiplex added on top of the fermenting fish repelled 50%, 54%, 37%, and killed 22%, 28%,and 40% of fly larvae. The total effect was not significantly different per species at 72%, 82%, and 77%, respectively.

    Discussion and Conclusions: The three most salient species are effective in repelling and killing fly larvae in the productionof fermented fish, and may be essential to augment food safety during traditional fermentation in open jars.

    National Category
    Agricultural Sciences Botany
    Identifiers
    urn:nbn:se:uu:diva-149968 (URN)10.1371/journal.pone.0029521 (DOI)000298665600041 ()
    Available from: 2011-03-24 Created: 2011-03-24 Last updated: 2017-12-11Bibliographically approved
    7. Evolution and loss of long-fringed petals: A case study using a dated phylogeny of the snake gourds, Trichosanthes (Cucurbitaceae)
    Open this publication in new window or tab >>Evolution and loss of long-fringed petals: A case study using a dated phylogeny of the snake gourds, Trichosanthes (Cucurbitaceae)
    2012 (English)In: BMC Evolutionary Biology, ISSN 1471-2148, E-ISSN 1471-2148, Vol. 12, p. 108-Article in journal (Refereed) Published
    Abstract [en]

    Background

    The Cucurbitaceae genus Trichosanthes comprises 90–100 species that occur from India to Japan and southeast to Australia and Fiji. Most species have large white or pale yellow petals with conspicuously fringed margins, the fringes sometimes several cm long. Pollination is usually by hawkmoths. Previous molecular data for a small number of species suggested that a monophyletic Trichosanthes might include the Asian genera Gymnopetalum (four species, lacking long petal fringes) and Hodgsonia (two species with petals fringed). Here we test these groups’ relationships using a species sampling of c. 60% and 4759 nucleotides of nuclear and plastid DNA. To infer the time and direction of the geographic expansion of the Trichosanthes clade we employ molecular clock dating and statistical biogeographic reconstruction, and we also address the gain or loss of petal fringes.

    Results

    Trichosanthes is monophyletic as long as it includes Gymnopetalum, which itself is polyphyletic. The closest relative of Trichosanthes appears to be the sponge gourds, Luffa, while Hodgsonia is more distantly related. Of six morphology-based sections in Trichosanthes with more than one species, three are supported by the molecular results; two new sections appear warranted. Molecular dating and biogeographic analyses suggest an Oligocene origin of Trichosanthes in Eurasia or East Asia, followed by diversification and spread throughout the Malesian biogeographic region and into the Australian continent.

    Conclusions

    Long-fringed corollas evolved independently in Hodgsonia and Trichosanthes, followed by two losses in the latter coincident with shifts to other pollinators but not with long-distance dispersal events. Together with the Caribbean Linnaeosicyos, the Madagascan Ampelosicyos and the tropical African Telfairia, these cucurbit lineages represent an ideal system for more detailed studies of the evolution and function of petal fringes in plant-pollinator mutualisms.

    National Category
    Biological Systematics
    Research subject
    Biology with specialization in Systematics
    Identifiers
    urn:nbn:se:uu:diva-167012 (URN)10.1186/1471-2148-12-108 (DOI)000312133600001 ()
    Available from: 2012-02-13 Created: 2012-01-19 Last updated: 2017-12-07Bibliographically approved
    8. Synopsis of Trichosanthes (Cucurbitaceae) based on recent molecular phylogenetic data
    Open this publication in new window or tab >>Synopsis of Trichosanthes (Cucurbitaceae) based on recent molecular phylogenetic data
    2012 (English)In: PhytoKeys, ISSN 1314-2011, E-ISSN 1314-2003, Vol. 12, p. 23-33Article in journal (Refereed) Published
    Abstract [en]

    The snake gourd genus, Trichosanthes, is the largest genus in the Cucurbitaceae family, with over 90 species. Recent molecular phylogenetic data have indicated that the genus Gymnopetalum is to be merged with Trichosanthes to maintain monophyly. A revised infrageneric classification of Trichosanthes including Gymnopetalum is proposed with two subgenera, (I) subg. Scotanthus comb. nov. and (II) subg. Trichosanthes, eleven sections, (i) sect. Asterospermae, (ii) sect. Cucumeroides, (iii) sect. Edulis, (iv) sect. Foliobracteola, (v) sect. Gymnopetalum, (vi) sect. Involucraria, (vii) sect. Pseudovariifera sect. nov., (viii) sect. Villosae star. nov., (ix) sect. Trichosanthes, (x) sect. Tripodanthera, and (xi) sect. Truncata. A synopsis of Trichosanthes with the 91 species recognized here is presented, including four new combinations, Trichosanthes orientalis, Trichosanthes tubiflora, Trichosanthes scabra var. pectinata, Trichosanthes scabra var. penicaudii, and a clarified nomenclature of Trichosanthes costata and Trichosanthes scabra.

    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-168535 (URN)10.3897/phytokeys.12.2952 (DOI)000305779400002 ()22645411 (PubMedID)
    Available from: 2012-02-13 Created: 2012-02-13 Last updated: 2017-12-07Bibliographically approved
    9. A taxonomic revision of Trichosanthes L. (Cucurbitaceae) in Australia, including one new species from the Northern Territory
    Open this publication in new window or tab >>A taxonomic revision of Trichosanthes L. (Cucurbitaceae) in Australia, including one new species from the Northern Territory
    2011 (English)In: Austrobaileya : a journal of plant systematics, ISSN 0155-4131, Vol. 8, no 3, p. 364-386Article in journal (Refereed) Published
    Abstract [en]

    Trichosanthes is represented by six species in Australia: T cucumerina L. var. cucumerina,T morrisii W.E.Cooper sp. nov., T odontosperma W.E.Cooper & A.J.Ford, T pentaphylla F.Muell. ex Benth., T pilosa Lour. and T subvelutina F.Muell. ex Cogn. Trichosanthes ovigera Blume has recently been synonymised with T pilosa and we now include T holtzei F.Muell. within this synonymy. All taxa are illustrated (with the exception of T odontosperma previously illustrated in 2010), and distinguished from other Australian species. Notes on habitat and distribution are included together with distribution maps. Three identification keys are presented, two to the sections of Trichosanthes and one to the species of Trichosanthes in Australia.

    National Category
    Botany
    Identifiers
    urn:nbn:se:uu:diva-165982 (URN)
    Available from: 2012-01-10 Created: 2012-01-10 Last updated: 2012-12-17Bibliographically approved
  • 50.
    de Boer, Hugo J.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Cotingting, Crystle
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Medicinal plants for women's healthcare in southeast Asia: a meta-analysis of their traditional use, chemical constituents, and pharmacology2014In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 151, no 2, p. 747-767Article in journal (Refereed)
    Abstract [en]

    Ethnopharmacological relevance

    This is an extensive review of plants used traditionally for women's healthcare in Southeast Asia and surrounding countries. Medicinal plants have a significant role in women's healthcare in many rural areas of the world. Plants with numerous efficacious observations have historically been used as a starting point in the development of new drugs, and a large percentage of modern pharmaceuticals have been derived from medicinal plants.

    Materials and methods

    A review was conducted for all plant use mentioned specifically for female healthcare, such as medicine to increase fertility, induce menstruation or abortion, ease pregnancy and parturition, reduce menstrual bleeding and postpartum hemorrhage, alleviate menstrual, parturition and postpartum pain, increase or inhibit lactation, and treat mastitis and uterine prolapse, in 200 studies focusing on medicinal plant use, either general studies or studies focusing specifically on women's healthcare.

    Results

    Nearly 2000 different plant species are reported to be used in over 5000 combinations. Most common areAchyranthes asperaArtemisia vulgarisBlumea balsamiferaCarica papayaCurcuma longaHibiscus rosa-sinensisLeonurus japonicusPsidium guajava and Ricinus communis, and each of these species had been reported in more than 10 different scientific articles.

    Conclusions

    This review provides a basis for traditional plant use in women's healthcare, and these species can be used as the starting point in the discovery of new drugs.

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