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  • 151.
    Hill, Tobias
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Nordström, Karl J V
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Thollesson, Mikael
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Säfström, Tommy M
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Vernersson, Andreas K E
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Fredriksson, Robert
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    Schiöth, Helgi B
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Neuroscience.
    SPRIT: Identifying horizontal gene transfer in rooted phylogenetic trees2010In: BMC Evolutionary Biology, ISSN 1471-2148, Vol. 10, no 1, p. 42-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: Phylogenetic trees based on sequences from a set of taxa can be incongruent due to horizontal gene transfer (HGT). By identifying the HGT events, we can reconcile the gene trees and derive a taxon tree that adequately represents the species' evolutionary history. One HGT can be represented by a rooted Subtree Prune and Regraft (RSPR) operation and the number of RSPRs separating two trees corresponds to the minimum number of HGT events. Identifying the minimum number of RSPRs separating two trees is NP-hard, but the problem can be reduced to fixed parameter tractable. A number of heuristic and two exact approaches to identifying the minimum number of RSPRs have been proposed. This is the first implementation delivering an exact solution as well as the intermediate trees connecting the input trees. RESULTS: We present the SPR Identification Tool (SPRIT), a novel algorithm that solves the fixed parameter tractable minimum RSPR problem and its GPL licensed Java implementation. The algorithm can be used in two ways, exhaustive search that guarantees the minimum RSPR distance and a heuristic approach that guarantees finding a solution, but not necessarily the minimum one. We benchmarked SPRIT against other software in two different settings, small to medium sized trees i.e. five to one hundred taxa and large trees i.e. thousands of taxa. In the small to medium tree size setting with random artificial incongruence, SPRIT's heuristic mode outperforms the other software by always delivering a solution with a low overestimation of the RSPR distance. In the large tree setting SPRIT compares well to the alternatives when benchmarked on finding a minimum solution within a reasonable time. SPRIT presents both the minimum RSPR distance and the intermediate trees. CONCLUSIONS: When used in exhaustive search mode, SPRIT identifies the minimum number of RSPRs needed to reconcile two incongruent rooted trees. SPRIT also performs quick approximations of the minimum RSPR distance, which are comparable to, and often better than, purely heuristic solutions. Put together, SPRIT is an excellent tool for identification of HGT events and pinpointing which taxa have been involved in HGT.

  • 152.
    Hilonga, S.
    et al.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    Otieno, J. N.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    Ghorbani, Abdolbaset
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pereus, D.
    Muhimbili Univ Hlth & Allied Sci, Inst Tradit Med, POB 65001, Dar Es Salaam, Tanzania.
    Kocyan, A.
    Univ Potsdam, Biodivers Res Systemat Bot, D-14469 Potsdam, Germany.
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Oslo, Nat Hist Museum, POB 1172, NO-0318 Oslo, Norway.
    Trade of wild-harvested medicinal plant species in local markets of Tanzania and its implications for conservation2019In: South African Journal of Botany, ISSN 0254-6299, E-ISSN 1727-9321, Vol. 122, p. 214-224Article in journal (Refereed)
    Abstract [en]

    In Tanzania, about 10% of the reported 12,000 species of higher plants are estimated to be used as medicine for treating different human health problems. Most of the medicinal plants are collected from wild populations, but their trade and quantities are not properly recorded. Monitoring of trade in wild-harvested medicinal plants is challenging asmostmaterials are traded in various processed forms and most vendors practice informal trade. Yet, monitoring is important for conservation and sustainability. This study aims to assess the trade of wild-harvested medicinal plant species in local markets of Tanzania and its implications for conservation. Semi-structured interviews were used to record frequency, volume of trade and uses of wild-harvested medicinal plants in Arusha, Dodoma, Mbeya, Morogoro and Mwanza regions. Relative frequency of citation and informant consensus factor were calculated for each species and mentioned use category. Forty vendors were interviewed, and 400 out of 522 collected market samples were identified to 162 species from herbarium-deposited collections. Plant parts with the largest volume of trade were roots (3818 kg), bark (1163 kg) and leaves (492 kg). The most frequently traded species were Zanthoxylum chalybaeum Engl., Albizia anthelmintica Brongn., Zanha africana (Radlk.) Exell, Warburgia stuhlmannii and Vachellia nilotica (L.) P.J.H. Hurter & Mabb. The most popular medicinal plants in the markets are connected to local health problems including malaria, libido disorders or infertility. The high diversity of commercialized plants used for medicinal issues mainly relies on wild stock for local consumption and international trade, and this has significant implications for conservation concerns. (C) 2018 SAAB. Published by Elsevier B.V. All rights reserved.

  • 153.
    Hinsley, Amy
    et al.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Oxford, Radcliffe Observ Quarter, Dept Zool, Woodstock Rd, Oxford OX1 3PS, England..
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Oslo, Nat Hist Museum, POB 1172 Blindern, N-0318 Oslo, Norway..
    Fay, Michael F.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Royal Bot Gardens, Conservat Sci, Richmond TW7 3AE, Surrey, England.;Univ Western Australia, Sch Biol Sci, 35 Stirling Highway, Perth, WA 6009, Australia..
    Gale, Stephan W.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Kadoorie Farm & Bot Garden, Lam Kam Rd, Tai Po, Hong Kong, Peoples R China..
    Gardiner, Lauren M.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Royal Bot Gardens, Conservat Sci, Richmond TW7 3AE, Surrey, England.;Cambridge Univ Bot Gardens, Dept Plant Sci, Sainsbury Lab, Cambridge Univ Herbarium, Bateman St, Cambridge CB2 1LR, England..
    Gunasekara, Rajasinghe S.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Sri Lanka Customs, 40 Main St, Colombo 11, Sri Lanka..
    Kumar, Pankaj
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Kadoorie Farm & Bot Garden, Lam Kam Rd, Tai Po, Hong Kong, Peoples R China..
    Masters, Susanne
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Nat Biodivers Ctr, Darwinweg 2, NL-2333 CR Leiden, Netherlands.;Leiden Univ, Rapenburg 70, NL-2311 EZ Leiden, Netherlands..
    Metusala, Destario
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Indonesian Inst Sci LIPI, Purwodadi Bot Garden, Jalan Raya Surabaya Malang KM-65, Pasuruan 67163, Jawa Timur, Indonesia..
    Roberts, David L.
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Kent, Sch Anthropol & Conservat, Durrell Inst Conservat & Ecol, Marlowe Bldg, Canterbury CT2 7NR, Kent, England..
    Veldman, Sarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England..
    Wong, Shan
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Oxford, Sch Geog & Environm, South Parks Rd, Oxford OX1 3QY, England..
    Phelps, Jacob
    Royal Bot Gardens, IUCN SSC Orchid Specialist Grp, Richmond TW9 3AB, Surrey, England.;Univ Lancaster, Lancaster Environm Ctr, Lib Ave, Lancaster LA1 4YQ, England..
    A review of the trade in orchids and its implications for conservation2018In: Botanical journal of the Linnean Society, ISSN 0024-4074, E-ISSN 1095-8339, Vol. 186, no 4, p. 435-455Article, review/survey (Refereed)
    Abstract [en]

    Orchids are one of the largest plant families and are commercially traded for a variety of purposes, including as ornamental plants, medicinal products and food. These markets involve thousands of species, which may be traded legally or illegally, sustainably or unsustainably, and take place at local, national or international scales. In this review, we provide the first overview of commercial orchid trade globally and highlight the main types that involve wild-collected plants. Much of this trade is the result of illegal harvest meaning that it is little documented and is absent from official statistics, at the same time as being of growing conservation concern. We discuss the associated legal-regulatory context, identify key conservation challenges and highlight four key priorities for addressing these challenges. These are to (1) research trade dynamics and the impacts of harvest; (2) strengthen the legal trade of orchids; (3) adopt measures to reduce illegal trade; and (4) raise the profile of orchid trade among policy makers, conservationists and the public.

  • 154.
    Hoffman, Tove
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Lindeborg, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    Barboutis, Christos
    Hellen Ornithol Soc Birdlife, Athens, Greece.
    Erciyas-Yavuz, Kiraz
    Ondokuz Mayis Univ, Samsun, Turkey.
    Evander, Magnus
    Umea Univ, Umea, Sweden.
    Fransson, Thord
    Swedish Museum Nat Hist, Stockholm, Sweden.
    Figuerola, Jordi
    Estn Biol Donana, Seville, Spain;Ciber Epidemil & Salud Publ, Madrid, Spain.
    Jaenson, Thomas G.T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kiat, Yosef
    Hebrew Univ Jerusalem, Jerusalem, Israel.
    Lindgren, Per-Eric
    Linkoping Univ, Linkoping, Sweden.
    Lundkvist, Åke
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Mohamed, Nahla
    Umea Univ, Umea, Sweden.
    Moutailler, Sara
    Agence Natl Secur Sanit Alimentat, Maisons Alfort, France.
    Nystrom, Fredrik
    Linkoping Univ, Linkoping, Sweden.
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    Salaneck, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infection medicine.
    Alkhurma Hemorrhagic Fever Virus RNA in Hyalomma rufipes Ticks Infesting Migratory Birds, Europe and Asia Minor2018In: Emerging Infectious Diseases, ISSN 1080-6040, E-ISSN 1080-6059, Vol. 24, no 5, p. 879-882Article in journal (Refereed)
    Abstract [en]

    Alkhurma hemorrhagic fever virus RNA was detected in immature Hyalomma rufipes ticks infesting northward migratory birds caught in the North Mediterranean Basin. This finding suggests a role for birds in the ecology of the Alkhurma hemorrhagic fever virus and a potential mechanism for dissemination to novel regions. Increased surveillance is warranted.

  • 155.
    Hosken, David J.
    et al.
    Univ Exeter, Ctr Ecol & Conservat, Penryn TR109EZ, Cornwall, England.
    Archer, C. Ruth
    Univ Exeter, Ctr Ecol & Conservat, Penryn TR109EZ, Cornwall, England.
    Mank, Judith E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England;Univ British Columbia, Dept Zool, Vancouver, BC V6T 1Z4, Canada.
    Sexual conflict2019In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 29, no 11, p. R451-R455Article, review/survey (Refereed)
  • 156.
    Hua, Wenjing
    et al.
    McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada.
    Vogan, Aaron A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada.
    Xu, Jianping
    McMaster Univ, Dept Biol, Hamilton, ON L8S 4K1, Canada.
    Genotypic and Phenotypic Analyses of Two "Isogenic" Strains of the Human Fungal Pathogen Cryptococcus neoformans var. neoformans2019In: Mycopathologia, ISSN 0301-486X, E-ISSN 1573-0832, Vol. 184, no 2, p. 195-212Article in journal (Refereed)
    Abstract [en]

    The Cryptococcus neoformans species complex is a model organism for fungal studies. Many studies have used two strains, JEC20 and JEC21, and their derivatives. These two strains were obtained through 10 rounds of backcrosses and have been assumed near identical except at the mating-type locus. Here we obtained and compared the JEC20 genome sequence with the published JEC21 genome. Our comparison revealed 5322 single nucleotide polymorphisms (SNPs) with the majority (N=3816, 71.7%) located in three genomic regions, including the previously noted mating-type region. The remaining 1506 SNPs (28.3%) were distributed throughout all 14 chromosomes, predominantly at chromosomal ends. To study the potential effects of these three SNP-rich regions on phenotypes, 24 progenies from the JEC20xJEC21 cross representing eight recombinant genotypes were analyzed for their mating ability, melanin production, capsule formation, and growths at 30 degrees C and 40 degrees C. Significant phenotypic variations were found among the progeny. However, the observed phenotypic variations could not be explained by the three SNP-rich regions. Further genome sequencing of our JEC21 and the 24 progenies revealed only six segregating SNPs outside of the three SNP-rich regions between JEC20 and JEC21, a result indicating that the 1500 SNPs identified in the published JEC21 genome might be caused by sequencing errors and/or strain mixing. However, the six SNPs and the three SNP-rich regions could not explain the observed phenotypic variations. Our analyses suggest that spontaneous mutations accumulated under laboratory conditions could have significant effects on phenotypes and on our interpretations of experimental results.

  • 157.
    Hussein, Juma
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tibuhwa, Donatha Damian
    University of Dar es Salaam, Department of molecular Biology and Biotechnology.
    Tibell, Sanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Phylogenetic position and taxonomy of Kusaghiporia usambarensis gen. et sp. nov. (Polyporales)2018In: Mycology, ISSN 2150-1203Article in journal (Refereed)
    Abstract [en]

    A large polyporoid mushroom from the West Usambara Mountains in North-eastern Tanzania produces dark brown, up to 60-cm large fruiting bodies that at maturity may weigh more than 10 kg. It has a high rate of mycelial growth and regeneration and was found growing on both dry and green leaves of shrubs; attached to the base of living trees, and it was also observed to degrade dead snakes and insects accidentally coming into contact with it. Phylogenetic analyses based on individual and concatenated data sets of nrLSU, nrSSU and the RPB2 and TEF1 genes showed it, together with Laetiporus, Phaeolus, Pycnoporellus and Wolfiporia, to form a monophyletic group in Polyporales. Based on morphological features and molecular data, it is described as Kusaghiporia usambarensis.

  • 158. Hyde, Kevin D
    et al.
    Udayanga, Dhanushka
    Manamgoda, Dimuthu S
    Tedersoo, Leho
    Larsson, Ellen
    Göteborgs Universitet.
    Abarenkov, Kessy
    Bertrand, Yann JK
    Göteborgs Universitet.
    Oxelman, Bengt
    Göteborgs Universitet.
    Hartmann, Martin
    Kauserud, Håvard
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kristiansson, Erik
    Nilsson, R. Henrik
    Göteborgs Universitet.
    Incorporating molecular data in fungal systematics: a guide for aspiring researchers2013In: Current Research in Environmental & Applied Mycology, ISSN 2229-2225, Vol. 3, no 1, p. 1-32Article in journal (Refereed)
  • 159.
    Ickert-Bond, Stephanie M.
    et al.
    University of Alaska, Fairbanks.
    Rydin, Catarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Micromorphology of the seed envelope of Ephedra L. (Gnetales) and its relevance for the timing of evolutionary events2011In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 172, no 1, p. 36-48Article in journal (Refereed)
    Abstract [en]

    Micromorphology of the seed envelope of Ephedra (Gnetales) is known to be variable, but variation patternshave never been systematically documented. We test the usefulness of this feature for species determination and subclade delimitation in Ephedra and investigate the relationship of this character to infrageneric evolutionarypatterns. Most species have a basically smooth seed envelope, which in some species appears slightly striate or reticulate due to convex or depressed outer periclinal cell walls. Ephedra rhytidosperma from China and Ephedra torreyana from North America have transverse lamellae formed by the epidermis. A papillate surfaceis found in respective close relatives of these two species. Micromorphology of the seed envelope is generally not useful for species identification or subclade delineation. The amount of variation is low, and intraspecific variation, which in some cases seems to be correlated with hybridization and/or introgression, complicates species recognition. Furthermore, parallel evolution of similar micromorphological patterns in unrelated subclades of Ephedra is evident and cannot be explained by similar seed dispersal mechanisms. The Asian species with transverse lamellae or papillae on the seed are dispersed by frugivores whereas similar American species are anemochoric. Transverse ridges occur in several Early Cretaceous fossil seeds with affinity to Ephedra. However, our results indicate that the resemblance between these fossils and extant taxa with similar features is superficial and convergent. In line with other recent studies, we find that Cretaceous ephedroids are extinct stem relatives to the extant clade.

  • 160.
    Idnurm, Alexander
    et al.
    Univ Melbourne, Sch Biosci, Melbourne, Vic 3010, Australia..
    Hood, Michael E.
    Amherst Coll, Dept Biol, Amherst, MA 01002 USA..
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Giraud, Tatiana
    Univ Paris 11, Lab Ecol Systemat & Evolut, UMR 8079, F-91405 Orsay, France.;CNRS, F-91405 Orsay, France..
    Contrasted patterns in mating-type chromosomes in fungi: Hotspots versus coldspots of recombination2015In: Mycologist, ISSN 1749-4613, E-ISSN 1878-0253, Vol. 29, no 3-4, p. 220-229Article, review/survey (Refereed)
    Abstract [en]

    It is striking that, while central to sexual reproduction, the genomic regions determining sex or mating-types are often characterized by suppressed recombination that leads to a decrease in the efficiency of selection, shelters genetic load, and inevitably contributes to their genic degeneration. Research on model and lesser-explored fungi has revealed similarities in recombination suppression of the genomic regions involved in mating compatibility across eukaryotes, but fungi also provide opposite examples of enhanced recombination in the genomic regions that determine their mating types. These contrasted patterns of genetic recombination (sensu lato, including gene conversion and ectopic recombination) in regions of the genome involved in mating compatibility point to important yet complex processes occurring in their evolution. A number of pieces in this puzzle remain to be solved, in particular on the unclear selective forces that may cause the patterns of recombination, prompting theoretical developments and experimental studies. This review thus points to fungi as a fascinating group for studying the various evolutionary forces at play in the genomic regions involved in mating compatibility.

  • 161.
    Irisarri, Iker
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany.
    Baurain, Denis
    Univ Liege, InBioS Eukaryot Phylogen, Dept Life Sci & PhytoSYST, B-4000 Liege, Belgium.
    Brinkmann, Henner
    Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany.
    Delsuc, Frédéric
    Univ Montpellier, Inst Sci Evolut, UMR 5554, CNRS,IRD,EPHE, F-34095 Montpellier, France.
    Sire, Jean-Yves
    Sorbonne Univ, Inst Biol Paris Seine, UMR7138, F-75005 Paris, France.
    Kupfer, Alexander
    Stuttgart State Museum Nat Hist, Dept Zool, D-70191 Stuttgart, Germany.
    Petersen, Jörn
    Leibniz Inst DSMZ German Collect Microorgan & Cell, D-38124 Braunschweig, Germany.
    Jarek, Michael
    Helmholtz Ctr Infect Res, Dept Genome Analyt, D-38124 Braunschweig, Germany.
    Meyer, Axel
    Univ Konstanz, Dept Biol, Lehrstuhl Zool & Evolut Biol, Univ Str 10, D-78464 Constance, Germany.
    Vences, Miguel
    Braunschweig Univ Technol, Zool Inst, D-38106 Braunschweig, Germany.
    Philippe, Hervé
    Ctr Biodivers Theory & Modelling, UMR CNRS 5321, Stn Theoret & Expt Ecol, F-09200 Moulis, France; Univ Montreal, Dept Biochim, Montreal, PQ H3C 3J7, Canada.
    Phylotranscriptomic consolidation of the jawed vertebrate timetree2017In: Nature Ecology & Evolution, E-ISSN 2397-334X, Vol. 1, no 9, p. 1370-1378Article in journal (Refereed)
    Abstract [en]

    Phylogenomics is extremely powerful but introduces new challenges as no agreement exists on ‘standards’ for data selection, curation and tree inference. We use jawed vertebrates (Gnathostomata) as a model to address these issues. Despite considerable efforts in resolving their evolutionary history and macroevolution, few studies have included a full phylogenetic diversity of gnathostomes, and some relationships remain controversial. We tested a new bioinformatic pipeline to assemble large and accu- rate phylogenomic datasets from RNA sequencing and found this phylotranscriptomic approach to be successful and highly cost- effective. Increased sequencing effort up to about 10 Gbp allows more genes to be recovered, but shallower sequencing (1.5 Gbp) is sufficient to obtain thousands of full-length orthologous transcripts. We reconstruct a robust and strongly supported timetree of jawed vertebrates using 7,189 nuclear genes from 100 taxa, including 23 new transcriptomes from previously unsampled key species. Gene jackknifing of genomic data corroborates the robustness of our tree and allows calculating genome-wide divergence times by overcoming gene sampling bias. Mitochondrial genomes prove insufficient to resolve the deepest relationships because of limited signal and among-lineage rate heterogeneity. Our analyses emphasize the importance of large, curated, nuclear datasets to increase the accuracy of phylogenomics and provide a reference framework for the evolutionary history of jawed vertebrates.

  • 162.
    Irwin, Nicholas
    et al.
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Tikhonenkov, Denis
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada;Russian Acad Sci, Inst Biol Inland Waters, Borok 152742, Russia.
    Hehenberger, Elisabeth
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada;Monterey Bay Aquarium Res Inst, Moss Landing, CA USA.
    Mylnikov, Alexander
    Russian Acad Sci, Inst Biol Inland Waters, Borok 152742, Russia.
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Keeling, Patrick
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada.
    Phylogenomics supports the monophyly of the Cercozoa2019In: Molecular Phylogenetics and Evolution, ISSN 1055-7903, E-ISSN 1095-9513, Vol. 130, p. 416-423Article in journal (Refereed)
    Abstract [en]

    The phylum Cercozoa consists of a diverse assemblage of amoeboid and flagellated protists that forms a major component of the supergroup, Rhizaria. However, despite its size and ubiquity, the phylogeny of the Cercozoa remains unclear as morphological variability between cercozoan species and ambiguity in molecular analyses, including phylogenomic approaches, have produced ambiguous results and raised doubts about the monophyly of the group. Here we sought to resolve these ambiguities using a 161-gene phylogenetic dataset with data from newly available genomes and deeply sequenced transcriptomes, including three new transcriptomes from Aurigamonas soils, Abollifer prolabens, and a novel species, Lapot gusevi n. gen. n. sp. Our phylogenomic analysis strongly supported a monophyletic Cercozoa, and approximately-unbiased tests rejected the paraphyletic topologies observed in previous studies. The transcriptome of L. gusevi represents the first transcriptomic data from the large and recently characterized Aquavolonidae-Treumulida-'Novel Clade 12' group, and phylogenomics supported its position as sister to the cercozoan subphylum, Endomyxa. These results provide insights into the phylogeny of the Cercozoa and the Rhizaria as a whole.

  • 163.
    Jaenson, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Antalet fästingar i Sverige ökar2011In: EPI-aktuellt, Vol. 10, no 28Article in journal (Other academic)
  • 164.
    Jaenson, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Larver av nässtyngflugan i ögat - ovanligt men allvarligt problem: Fall av human oftalmomyiasis från Dalarna och sydöstra Finland redovisas2011In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 108, no 16-17, p. 928-930Article in journal (Refereed)
  • 165.
    Jaenson, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ny fästingöverförd sjukdom2011In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 108, no 42, p. 2084-2085Article in journal (Refereed)
  • 166.
    Jaenson, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Svårdiagnosticerad sjukdom efter fästingbett2011In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 108, no 42, p. 2083-2083Article in journal (Refereed)
  • 167.
    Jaenson, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Taigafästingen nu i norra Sverige2016In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 113, no D6PPArticle in journal (Refereed)
  • 168.
    Jaenson, Thomas G. T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hjertqvist, Marika
    Bergström, Tomas
    Lundkvist, Åke
    Why is tick-borne encephalitis increasing?: A review of the key factors causing the increasing incidence of human TBE in Sweden2012In: Parasites & Vectors, ISSN 1756-3305, Vol. 5, p. 184-Article, review/survey (Refereed)
    Abstract [en]

    The highest annual incidence of human tick-borne encephalitis (TBE) in Sweden ever recorded by the Swedish Institute for Communicable Disease Control (SMI) occurred last year, 2011. The number of TBE cases recorded during 2012 up to 6th August 2012 indicates that the incidence for 2012 could exceed that of 2011. In this review of the ecology and epidemiology of TBE in Sweden our main aim is to analyse the possible reasons behind the gradually increasing incidence of human TBE during the last 20 years. The main TBE virus (TBEV) vector to humans in Sweden is the nymphal stage of the common tick Ixodes ricinus. The main mode of transmission and maintenance of TBEV in the tick population is considered to be when infective nymphs co-feed with uninfected but infectible larvae on rodents. In most locations the roe deer, Capreolus capreolus is the main host for the reproducing adult I. ricinus ticks. The high number of roe deer for more than three decades has resulted in a very large tick population. Deer numbers have, however, gradually declined from the early 1990s to the present. This decline in roe deer numbers most likely made the populations of small rodents, which are reservoir-competent for TBEV, gradually more important as hosts for the immature ticks. Consequently, the abundance of TBEV-infected ticks has increased. Two harsh winters in 2009-2011 caused a more abrupt decline in roe deer numbers. This likely forced a substantial proportion of the "host-seeking" ticks to feed on bank voles (Myodes glareolus), which at that time suddenly had become very numerous, rather than on roe deer. Thus, the bank vole population peak in 2010 most likely caused many tick larvae to feed on reservoir-competent rodents. This presumably resulted in increased transmission of TBEV among ticks and therefore increased the density of infected ticks the following year. The unusually warm, humid weather and the prolonged vegetation period in 2011 permitted nymphs and adult ticks to quest for hosts nearly all days of that year. These weather conditions stimulated many people to spend time outdoors in areas where they were at risk of being attacked by infective nymphs. This resulted in at least 284 human cases of overt TBE. The tick season of 2012 also started early with an exceptionally warm March. The abundance of TBEV-infective "hungry" ticks was presumably still relatively high. Precipitation during June and July was rich and will lead to a "good mushroom season". These factors together are likely to result in a TBE incidence of 2012 similar to or higher than that of 2011.

  • 169.
    Jaenson, Thomas G. T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Mehl, Reidar
    Försvarets mikrobiologiska laboratorium, Oslo.
    "Fågelloppor" kan ha varit fågelkvalster2010In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 107, no 29-31, p. 1791-1792Article in journal (Other (popular science, discussion, etc.))
  • 170.
    Jaenson, Thomas G. T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Varv, Kairi
    Natl Inst Hlth Dev, Dept Virol, Hiiu 42, EE-11619 Tallinn, Estonia..
    Fröjdman, Isabella
    Aalto Univ, POB 11130, FI-00076 Aalto, Finland..
    Jaaskelainen, Anu
    Univ Helsinki, Dept Virol, POB 21, FI-00014 Helsinki, Finland..
    Rundgren, Kaj
    Jarvis Vag 50, SE-95395 Nikkala, Sweden..
    Versteirt, Veerle
    Avia GIS, Precis Pest Management Unit, Risschotlei 33, BE-2980 Zoersel, Belgium..
    Estrada-Pena, Agustin
    Univ Zaragoza, Dept Parasitol, Miguel Servet 177, ES-50013 Zaragoza, Spain..
    Medlock, Jolyon M.
    Publ Hlth England, Emergency Response Dept, Med Entomol Grp, Salisbury, Wilts, England.;Hlth Protect Res Unit Emerging Infect & Zoonoses, Salisbury, Wilts, England..
    Golovljova, Irina
    Natl Inst Hlth Dev, Dept Virol, Hiiu 42, EE-11619 Tallinn, Estonia..
    First evidence of established populations of the taiga tick Ixodes persulcatus (Acari: Ixodidae) in Sweden2016In: Parasites & Vectors, ISSN 1756-3305, E-ISSN 1756-3305, Vol. 9, article id 377Article in journal (Refereed)
    Abstract [en]

    Background: The tick species Ixodes ricinus and I. persulcatus are of exceptional medical importance in the western and eastern parts, respectively, of the Palaearctic region. In Russia and Finland the range of I. persulcatus has recently increased. In Finland the first records of I. persulcatus are from 2004. The apparent expansion of its range in Finland prompted us to investigate if I. persulcatus also occurs in Sweden. Methods: Dog owners and hunters in the coastal areas of northern Sweden provided information about localities where ticks could be present. In May-August 2015 we used the cloth-dragging method in 36 localities potentially harbouring ticks in the Bothnian Bay area, province Norrbotten (NB) of northern Sweden. Further to the south in the provinces Vasterbotten (VB) and Uppland (UP) eight localities were similarly investigated. Results: Ixodes persulcatus was detected in 9 of 36 field localities in the Bothnian Bay area. Nymphs, adult males and adult females (n = 46 ticks) of I. persulcatus were present mainly in Alnus incana - Sorbus aucuparia - Picea abies - Pinus sylvestris vegetation communities on islands in the Bothnian Bay. Some of these I. persulcatus populations seem to be the most northerly populations so far recorded of this species. Dog owners asserted that their dogs became tick-infested on these islands for the first time 7-8 years ago. Moose (Alces alces), hares (Lepus timidus), domestic dogs (Canis lupus familiaris) and ground-feeding birds are the most likely carriers dispersing I. persulcatus in this area. All ticks (n = 124) from the more southern provinces of VB and UP were identified as I. ricinus. Conclusions: The geographical range of the taiga tick has recently expanded into northern Sweden. Increased information about prophylactic, anti-tick measures should be directed to people living in or visiting the coastal areas and islands of the Baltic Bay.

  • 171.
    Jaenson, Thomas GT
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hjertqvist, Marika
    Lundkvist, Åke
    År 2011 toppar TBE-incidensen: Rådjursstammens variation i storlek och vädret är nyckelfaktorer2012In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 109, no 7, p. 343-346Article in journal (Refereed)
  • 172.
    Jaenson, Thomas G.T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lindgren, Elisabet
    Karolinska institutet, Dept of Public Health.
    The range of Ixodes ricinus and the risk of contracting Lyme borreliosis will increase northwards when the vegetation period becomes longer2011In: Ticks and Tick-borne Diseases, ISSN 1877-959X, Vol. 2, no 1, p. 44-49Article in journal (Refereed)
    Abstract [en]

    In Sweden, the geographical distribution of Lyme borreliosis corresponds to that of its vector kodes ricinus. Both tick activity and the length of the vegetation period are determined by daily mean temperatures >= 5 degrees C. We analysed the correspondence between the distribution of I. ricinus in Sweden, the start date, end date, and length of the vegetation period, and the distributions of tick habitat-associated plant species. The geographical distribution oil. ricinus in Sweden corresponds to a vegetation period averaging 170 days, an early start (before May 1st) of spring, and to the distribution of black alder (Alnus glutinosa). Based on scenario models for these parameters, changes in the range and abundance of I. ricinus were projected for the periods 2011-2040, 2041-2070, and 2071-2100. We conclude that climate change during this century will probably increase the geographic range of I. ricinus as vegetation communities and mammals associated with high tick densities will increase their geographic ranges due to a markedly prolonged vegetation period. By the end of this century, the ranges of I. ricinus and Borrelia burgdorferi sensu lato may, in suitable habitats, encompass most of Sweden, Norway, and Finland as far as 70 degrees N, except the mountainous regions. This will lead to an increased Lyme borreliosis risk in northern Scandinavia.

  • 173.
    Jaenson, Thomas G.T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Petersson, Erik
    Swedish University of Agricultural Sciences.
    [Dataset for forthcoming publication]2017Data set
  • 174.
    Jaenson, Thomas G.T.
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Petersson, Erik H.
    Swedish Univ Agr Sci, Div Freshwater Res, Dept Aquat Resources, Drottningholm, Sweden.
    Jaenson, David G. E.
    Lund Univ, Dept Automat Control, Lund, Sweden.
    Kindberg, Jonas
    Swedish Univ Agr Sci, Dept Wildlife Fish & Environm Studies, Umea, Sweden.
    Pettersson, John
    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; Univ Sydney, Sch Life & Environm Sci, Charles Perkins Ctr, Marie Bashir Inst Infect Dis & Biosecur, Sydney, Australia; Univ Sydney, Sydney Med Sch, Sydney, NSW, Australia; Publ Hlth Agcy Sweden, Solna, Sweden.
    Hjertqvist, Marika
    Publ Hlth Agcy Sweden, Solna, Sweden.
    Medlock, Jolyon M.
    Publ Hlth England, Emergency Response Dept, Med Entomol Grp, Salisbury, Wilts, England; Hlth Protect Res Unit Emerging Infect & Zoonoses, Salisbury, Wilts, England.
    Bengtsson, Hans
    Swedish Meteorol & Hydrol Inst, Gothenburg, Sweden.
    The importance of wildlife in the ecology and epidemiology of the TBE virus in Sweden: incidence of human TBE correlates with abundance of deer and hares2018In: Parasites & Vectors, ISSN 1756-3305, E-ISSN 1756-3305, Vol. 11, article id 477Article in journal (Refereed)
    Abstract [en]

    Background: Tick-borne encephalitis (TBE) is one tick-transmitted disease where the human incidence has increased in some European regions during the last two decades. We aim to find the most important factors causing the increasing incidence of human TBE in Sweden. Based on a review of published data we presume that certain temperature-related variables and the population densities of transmission hosts, i.e. small mammals, and of primary tick maintenance hosts, i.e. cervids and lagomorphs, of the TBE virus vector Ixodes ricinus, are among the potentially most important factors affecting the TBE incidence. Therefore, we compare hunting data of the major tick maintenance hosts and two of their important predators, and four climatic variables with the annual numbers of human cases of neuroinvasive TBE. Data for six Swedish regions where human TBE incidence is high or has recently increased are examined by a time-series analysis. Results from the six regions are combined using a meta-analytical method.

    Results: With a one-year time lag, the roe deer (Capreolus capreolus), red deer (Cervus elaphus), mountain hare (Lepus timidus) and European hare (Lepus europaeus) showed positive covariance; the Eurasian elk (moose, Alces alces) and fallow deer (Dama dama) negative covariance; whereas the wild boar (Sus scrofa), lynx (Lynx lynx), red fox (Vulpes vulpes) and the four climate parameters showed no significant covariance with TBE incidence. All game species combined showed positive covariance.

    Conclusions: The epidemiology of TBE varies with time and geography and depends on numerous factors, i.a. climate, virus genotypes, and densities of vectors, tick maintenance hosts and transmission hosts. This study suggests that the increased availability of deer to I. ricinus over large areas of potential tick habitats in southern Sweden increased the density and range of I. ricinus and created new TBEV foci, which resulted in increased incidence of human TBE. New foci may be established by TBE virus-infected birds, or by birds or migrating mammals infested with TBEV-infected ticks. Generally, persistence of TBE virus foci appears to require presence of transmission-competent small mammals, especially mice (Apodemus spp.) or bank voles (Myodes glareolus).

  • 175.
    Jaenson, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Jaenson, David GE
    Eisen, Lars
    Petersson, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Animal Ecology.
    Lindgren, Elisabet
    Karolinska institutet.
    Changes in the geographical distribution and abundance of the tick Ixodes ricinus during the past 30 years in Sweden2012In: Parasites & Vectors, ISSN 1756-3305, Vol. 5, no 8Article in journal (Refereed)
    Abstract [en]

    Background: Ixodes ricinus is the main vector in Europe of human-pathogenic Lyme borreliosis (LB) spirochaetes, the tick-borne encephalitis virus (TBEV) and other pathogens of humans and domesticated mammals. The results of a previous 1994 questionnaire, directed at people living in Central and North Sweden (Svealand and Norrland) and aiming to gather information about tick exposure for humans and domestic animals, suggested that Ixodes ricinus ticks had become more widespread in Central Sweden and the southern part of North Sweden from the early 1980s to the early 1990s. To investigate whether the expansion of the tick's northern geographical range and the increasing abundance of ticks in Sweden were still occurring, in 2009 we performed a follow-up survey 16 years after the initial study.

    Methods: A questionnaire similar to the one used in the 1994 study was published in Swedish magazines aimed at dog owners, home owners, and hunters. The questionnaire was published together with a popular science article about the tick's biology and role as a pathogen vector in Sweden. The magazines were selected to get information from people familiar with ticks and who spend time in areas where ticks might be present.

    Results: Analyses of data from both surveys revealed that during the near 30-year period from the early 1980s to 2008, I. ricinus has expanded its distribution range northwards. In the early 1990s ticks were found in new areas along the northern coastline of the Baltic Sea, while in the 2009 study, ticks were reported for the first time from many locations in North Sweden. This included locations as far north as 66 degrees N and places in the interior part of North Sweden. During this 16-year period the tick's range in Sweden was estimated to have increased by 9.9%. Most of the range expansion occurred in North Sweden (north of 60 degrees N) where the tick's coverage area doubled from 12.5% in the early 1990s to 26.8% in 2008. Moreover, according to the respondents, the abundance of ticks had increased markedly in LB- and TBE-endemic areas in South (Gotaland) and Central Sweden.

    Conclusions: The results suggest that I. ricinus has expanded its range in North Sweden and has become distinctly more abundant in Central and South Sweden during the last three decades. However, in the northern mountain region I. ricinus is still absent. The increased abundance of the tick can be explained by two main factors: First, the high availability of large numbers of important tick maintenance hosts, i.e., cervids, particularly roe deer (Capreolus capreolus) during the last three decades. Second, a warmer climate with milder winters and a prolonged growing season that permits greater survival and proliferation over a larger geographical area of both the tick itself and deer. High reproductive potential of roe deer, high tick infestation rate and the tendency of roe deer to disperse great distances may explain the range expansion of I. ricinus and particularly the appearance of new TBEV foci far away from old TBEV-endemic localities. The geographical presence of LB in Sweden corresponds to the distribution of I. ricinus. Thus, LB is now an emerging disease risk in many parts of North Sweden. Unless countermeasures are undertaken to keep the deer populations, particularly C. capreolus and Dama dama, at the relatively low levels that prevailed before the late 1970s - especially in and around urban areas where human population density is high by e. g. reduced hunting of red fox (Vulpes vulpes) and lynx (Lynx lynx), the incidences of human LB and TBE are expected to continue to be high or even to increase in Sweden in coming decades.

  • 176.
    Jaenson, Thomas
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lindgren, Elisabet
    The range of Ixodes ricinus and the risk of Lyme borreliosis will increase northwards when the vegetation period becomes longer2011In: Ticks and Tick-borne Diseases, ISSN 1877-959X, E-ISSN 1877-9603, Vol. 2, no 1, p. 44-49Article in journal (Refereed)
    Abstract [en]

    In Sweden, the geographical distribution of Lyme borreliosis corresponds to that of its vector Ixodes ricinus. Both tick activity and the length of the vegetation period are determined by daily mean temperatures ≥5 °C. We analysed the correspondence between the distribution of I. ricinus in Sweden, the start date, end date, and length of the vegetation period, and the distributions of tick habitat-associated plant species. The geographical distribution of I. ricinus in Sweden corresponds to a vegetation period averaging ∼170 days, an early start (before May 1st) of spring, and to the distribution of black alder (Alnus glutinosa). Based on scenario models for these parameters, changes in the range and abundance of I. ricinus were projected for the periods 2011–2040, 2041–2070, and 2071–2100. We conclude that climate change during this century will probably increase the geographic range of I. ricinus as vegetation communities and mammals associated with high tick densities will increase their geographic ranges due to a markedly prolonged vegetation period. By the end of this century, the ranges of I. ricinus and Borrelia burgdorferi sensu lato may, in suitable habitats, encompass most of Sweden, Norway, and Finland as far as 70°N, except the mountainous regions. This will lead to an increased Lyme borreliosis risk in northern Scandinavia.

  • 177. Jahan, Sultana N.
    et al.
    Asman, Anna K. M.
    Corcoran, Padraic
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fogelqvist, Johan
    Vetukuri, Ramesh R.
    Dixelius, Christina
    Plant-mediated gene silencing restricts growth of the potato late blight pathogen Phytophthora infestans2015In: Journal of Experimental Botany, ISSN 0022-0957, E-ISSN 1460-2431, Vol. 66, no 9, p. 2785-2794Article in journal (Refereed)
    Abstract [en]

    A host-induced gene-silencing strategy for controlling potato late blight is presented, a plant disease that conventionally requires regular application of fungicides at high rates.Phytophthora infestans is an oomycete that causes severe damage to potato, and is well known for its ability to evolve rapidly in order to overcome resistant potato varieties. An RNA silencing strategy was evaluated here to clarify if small interfering RNA homologous to selected genes in P. infestans could be targeted from the plant host to reduce the magnitude of the infection. As a proof-of-concept, a hairpin RNA (hp-RNA) construct using the GFP marker gene was designed and introduced in potato. At 72 hpi, a 55-fold reduction of the signal intensity of a corresponding GFP expressing P. infestans strain on leaf samples of transgenic plants, compared with wild-type potato, was detected. This suggests that an RNA interference construct in the potato host could be processed and target a transcript of the pathogen. Three genes important in the infection process of P. infestans, PiGPB1, PiCESA2, and PiPEC, together with PiGAPDH taking part in basic cell maintenance were subsequently tested using an analogous transgenic strategy. Out of these gene candidates, the hp-PiGPB1 targeting the G protein beta-subunit (PiGPB1) important for pathogenicity resulted in most restricted disease progress. Further, Illumina sequencing of inoculated transgenic potato leaves revealed sRNAs of 24/25 nt size homologous to the PiGPB1 gene in the transgenic plants indicating post-transcriptional silencing of the target gene. The work demonstrates that a host-induced gene-silencing approach is functional against P. infestans but is highly dependent on target gene for a successful outcome. This finding broadens the arsenal of control strategies to this important plant disease.

  • 178.
    Janouskovec, Jan
    et al.
    UCL, Dept Genet Evolut & Environm, London, England.;San Diego State Univ, Dept Biol, San Diego, CA 92182 USA.;Univ British Columbia, Bot Dept, Vancouver, BC, Canada..
    Tikhonenkov, Denis V.
    Univ British Columbia, Bot Dept, Vancouver, BC, Canada.;Russian Acad Sci, Inst Biol Inland Waters, Borok, Russia..
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Science for Life Laboratory, SciLifeLab. Univ British Columbia, Bot Dept, Vancouver, BC, Canada.
    Howe, Alexis T.
    Univ British Columbia, Bot Dept, Vancouver, BC, Canada..
    Rohwer, Forest L.
    San Diego State Univ, Dept Biol, San Diego, CA 92182 USA..
    Mylnikov, Alexander P.
    Russian Acad Sci, Inst Biol Inland Waters, Borok, Russia..
    Keeling, Patrick J.
    Univ British Columbia, Bot Dept, Vancouver, BC, Canada..
    A New Lineage of Eukaryotes Illuminates Early Mitochondrial Genome Reduction2017In: Current Biology, ISSN 0960-9822, E-ISSN 1879-0445, Vol. 27, no 23, p. 3717-3724.e5Article in journal (Refereed)
    Abstract [en]

    The origin of eukaryotic cells represents a key transition in cellular evolution and is closely tied to outstanding questions about mitochondrial endosymbiosis [1, 2]. For example, gene-rich mitochondrial genomes are thought to be indicative of an ancient divergence, but this relies on unexamined assumptions about endosymbiont-to-host gene transfer [3-5]. Here, we characterize Ancoracysta twista, a new predatory flagellate that is not closely related to any known lineage in 201-protein phylogenomic trees and has a unique morphology, including a novel type of extrusome (ancoracyst). The Ancoracysta mitochondrion has a gene-rich genome with a coding capacity exceeding that of all other eukaryotes except the distantly related jakobids and Diphylleia, and it uniquely possesses heterologous, nucleus-, and mitochondrion-encoded cytochrome c maturase systems. To comprehensively examine mitochondrial genome reduction, we also assembled mitochondrial genomes from picozoans and colponemids and re-annotated existing mitochondrial genomes using hidden Markov model gene profiles. This revealed over a dozen previously overlooked mitochondrial genes at the level of eukaryotic supergroups. Analysis of trends over evolutionary time demonstrates that gene transfer to the nucleus was non-linear, that it occurred in waves of exponential decrease, and that much of it took place comparatively early, massively independently, and with lineage-specific rates. This process has led to differential gene retention, suggesting that gene-rich mitochondrial genomes are not a product of their early divergence. Parallel transfer of mitochondrial genes and their functional replacement by new nuclear factors are important in models for the origin of eukaryotes, especially as major gaps in our knowl-edge of eukaryotic diversity at the deepest level remain unfilled.

  • 179. Janouškovec, Jan
    et al.
    Gavelis, Gregory S
    Burki, Fabien
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Dinh, Donna
    Bachvaroff, Tsvetan R
    Gornik, Sebastian G
    Bright, Kelley J
    Imanian, Behzad
    Strom, Suzanne L
    Delwiche, Charles F
    Waller, Ross F
    Fensome, Robert A
    Leander, Brian S
    Rohwer, Forest L
    Saldarriaga, Juan F
    Major transitions in dinoflagellate evolution unveiled by phylotranscriptomics2017In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 114, no 2, p. E171-E180Article in journal (Refereed)
    Abstract [en]

    Dinoflagellates are key species in marine environments, but they remain poorly understood in part because of their large, complex genomes, unique molecular biology, and unresolved in-group relationships. We created a taxonomically representative dataset of dinoflagellate transcriptomes and used this to infer a strongly supported phylogeny to map major morphological and molecular transitions in dinoflagellate evolution. Our results show an early-branching position of Noctiluca, monophyly of thecate (plate-bearing) dinoflagellates, and paraphyly of athecate ones. This represents unambiguous phylogenetic evidence for a single origin of the group's cellulosic theca, which we show coincided with a radiation of cellulases implicated in cell division. By integrating dinoflagellate molecular, fossil, and biogeochemical evidence, we propose a revised model for the evolution of thecal tabulations and suggest that the late acquisition of dinosterol in the group is inconsistent with dinoflagellates being the source of this biomarker in pre-Mesozoic strata. Three distantly related, fundamentally nonphotosynthetic dinoflagellates, Noctiluca, Oxyrrhis, and Dinophysis, contain cryptic plastidial metabolisms and lack alternative cytosolic pathways, suggesting that all free-living dinoflagellates are metabolically dependent on plastids. This finding led us to propose general mechanisms of dependency on plastid organelles in eukaryotes that have lost photosynthesis; it also suggests that the evolutionary origin of bioluminescence in nonphotosynthetic dinoflagellates may be linked to plastidic tetrapyrrole biosynthesis. Finally, we use our phylogenetic framework to show that dinoflagellate nuclei have recruited DNA-binding proteins in three distinct evolutionary waves, which included two independent acquisitions of bacterial histone-like proteins.

  • 180.
    Jia, Qidong
    et al.
    Univ Tennessee, Grad Sch Genome Sci & Technol, Knoxville, TN 37996 USA..
    Li, Guanglin
    Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA.;Shaanxi Normal Univ, Coll Life Sci, Xian 710062, Peoples R China..
    Kollner, Tobias G.
    Max Planck Inst Chem Ecol, Dept Biochem, D-07745 Jena, Germany..
    Fu, Jianyu
    Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA.;Chinese Acad Agr Sci, Tea Res Inst, Hangzhou 310008, Zhejiang, Peoples R China..
    Chen, Xinlu
    Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA..
    Xiong, Wangdan
    Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA..
    Crandall-Stotler, Barbara J.
    Southern Illinois Univ, Dept Plant Biol, Carbondale, IL 62901 USA..
    Bowman, John L.
    Monash Univ, Sch Biol Sci, Melbourne, Vic 3800, Australia..
    Weston, David J.
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA..
    Zhang, Yong
    Beijing Genom Inst Shenzhen, Beishan Ind Zone, Shenzhen 518083, Peoples R China..
    Chen, Li
    Beijing Genom Inst Shenzhen, Beishan Ind Zone, Shenzhen 518083, Peoples R China..
    Xie, Yinlong
    Beijing Genom Inst Shenzhen, Beishan Ind Zone, Shenzhen 518083, Peoples R China..
    Li, Fay-Wei
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Rothfels, Carl J.
    Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Larsson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Graham, Sean W.
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada..
    Stevenson, Dennis W.
    New York Bot Garden, Plant Genom Program, Bronx, NY 10458 USA..
    Wong, Gane Ka-Shu
    Beijing Genom Inst Shenzhen, Beishan Ind Zone, Shenzhen 518083, Peoples R China.;Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada.;Univ Alberta, Dept Med, Edmonton, AB T6G 2E1, Canada..
    Gershenzon, Jonathan
    Max Planck Inst Chem Ecol, Dept Biochem, D-07745 Jena, Germany..
    Chen, Feng
    Univ Tennessee, Grad Sch Genome Sci & Technol, Knoxville, TN 37996 USA.;Univ Tennessee, Dept Plant Sci, Knoxville, TN 37996 USA..
    Microbial-type terpene synthase genes occur widely in nonseed land plants, but not in seed plants2016In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 113, no 43, p. 12328-12333Article in journal (Refereed)
    Abstract [en]

    The vast abundance of terpene natural products in nature is due to enzymes known as terpene synthases (TPSs) that convert acyclic prenyl diphosphate precursors into a multitude of cyclic and acyclic carbon skeletons. Yet the evolution of TPSs is not well understood at higher levels of classification. Microbial TPSs from bacteria and fungi are only distantly related to typical plant TPSs, whereas genes similar to microbial TPS genes have been recently identified in the lycophyte Selaginella moellendorffii. The goal of this study was to investigate the distribution, evolution, and biochemical functions of microbial terpene synthase-like (MTPSL) genes in other plants. By analyzing the transcriptomes of 1,103 plant species ranging from green algae to flowering plants, putative MTPSL genes were identified predominantly from nonseed plants, including liverworts, mosses, hornworts, lycophytes, and monilophytes. Directed searching for MTPSL genes in the sequenced genomes of a wide range of seed plants confirmed their general absence in this group. Among themselves, MTPSL proteins from nonseed plants form four major groups, with two of these more closely related to bacterial TPSs and the other two to fungal TPSs. Two of the four groups contain a canonical aspartate-rich "DDxxD" motif. The third group has a "DDxxxD" motif, and the fourth group has only the first two "DD" conserved in this motif. Upon heterologous expression, representative members from each of the four groups displayed diverse catalytic functions as monoterpene and sesquiterpene synthases, suggesting these are important for terpene formation in nonseed plants.

  • 181.
    Jia, Shu-Wen
    et al.
    Chinese Acad Sci, Xinjiang Inst Ecol & Geog, Key Lab Biogeog & Bioresource Arid Land, Urumqi 830011, Peoples R China.;Chinese Acad Sci, Grad Univ, Beijing 100049, Peoples R China..
    Zhang, Ming-Li
    Chinese Acad Sci, Xinjiang Inst Ecol & Geog, Key Lab Biogeog & Bioresource Arid Land, Urumqi 830011, Peoples R China.;Chinese Acad Sci, Inst Bot, Beijing 100093, Peoples R China..
    Raab-Straube, Eckhard V.
    Free Univ Berlin, Bot Garten, Konigin Luise Str 6-8, D-14195 Berlin, Germany.;Free Univ Berlin, Bot Museum Berlin Dahlem, Konigin Luise Str 6-8, D-14195 Berlin, Germany..
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Evolutionary history of Gymnocarpos (Caryophyllaceae) in the arid regions from North Africa to Central Asia2016In: Biological Journal of the Linnean Society, ISSN 0024-4066, E-ISSN 1095-8312, Vol. 119, no 2, p. 511-522Article in journal (Refereed)
    Abstract [en]

    Gymnocarpos has only about ten species distributed in the arid regions of Asia and Africa, but it exhibits a geographical disjunction between eastern Central Asia and western North Africa and Minor Asia. We sampled eight species of the genus and sequenced two chloroplast regions (rps16 and psbB-psbH), and the nuclear rDNA (ITS) to study the phylogeny and biogeography. The results of the phylogenetic analyses corroborated that Gymnocarpos is monophyletic, in the phylogenetic tree two well supported clades are recognized: clade 1 includes Gymnocarpos sclerocephalus and G. decandrus, mainly the North African group, whereas clade 2 comprises the remaining species, mainly in the Southern Arabian Peninsula. Molecular dating analysis revealed that the divergence age of Gymnocarpos was c. 31.33 Mya near the Eocene and Oligocene transition boundary, the initial diversification within Gymnocarpos dated to c. 6.69 Mya in the late Miocene, and the intraspecific diversification mostly occurred during the Quaternary climate oscillations. Ancestral area reconstruction suggested that the Southern Arabian Peninsula was the ancestral area for Gymnocarpos. Our conclusions revealed that the aridification since mid-late Miocene significantly affected the diversification of the genus in these areas.

  • 182. Jondelius, Ulf
    et al.
    Wallberg, Andreas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hooge, Matthew
    Raikova, Olga I.
    How the Worm Got its Pharynx: Phylogeny, Classification and Bayesian Assessment of Character Evolution in Acoela2011In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 60, no 6, p. 845-871Article in journal (Refereed)
    Abstract [en]

    Acoela are marine microscopic worms currently thought to be the sister taxon of all other bilaterians. Acoels have long been used as models in evolutionary scenarios, and generalized conclusions about acoel and bilaterian ancestral features are frequently drawn from studies of single acoel species. There is no extensive phylogenetic study of Acoela and the taxonomy of the 380 species is chaotic. Here we use two nuclear ribosomal genes and one mitochondrial gene in combination with 37 morphological characters in an analysis of 126 acoel terminals (about one-third of the described species) to estimate the phylogeny and character evolution of Acoela. We present an estimate of posterior probabilities for ancestral character states at 31 control nodes in the phylogeny. The overall reconstruction signal based on the shape of the posterior distribution of character states was computed for all morphological characters and control nodes to assess how well these were reconstructed. The body-wall musculature appears more clearly reconstructed than the reproductive organs. Posterior similarity to the root was calculated by averaging the divergence between the posterior distributions at the nodes and the root over all morphological characters. Diopisthoporidae is the sister group to all other acoels and has the highest posterior similarity to the root. Convolutidae, including several "model" acoels, is most divergent. Finally, we present a phylogenetic classification of Acoela down to the family level where six previous family level taxa are synonymized.

  • 183. Jones, Gareth
    et al.
    Devadatha, Bandarupalli
    Abdel-Wahab, Mohamed
    Dayarathne, Monika
    Zhang, Sheng-Nan
    Hyde, Kevin
    Liu, Jian-Kui (Jack)
    Bahkali, Ali
    Sarma, Vemuri
    Tibell, Sanja
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tibell, Leif
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Wang, Meng-Meng
    Liu, Fang
    Cai, Lei
    Phylogeny of new marine Dothideomycetesand Sordariomycetes from mangrovesand deep-sea sediments2019In: Botanica Marina, ISSN 0006-8055, E-ISSN 1437-4323Article in journal (Refereed)
  • 184.
    Julin, Madeleine
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Tar production – traditional medicine and potential threat to biodiversity in the Marrakesh region: An ethnobotanical study2008Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 185. Kaefer, J.
    et al.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mousset, S.
    Kool, A.
    Dufay, M.
    Marais, G. A. B.
    Dioecy is associated with higher diversification rates in flowering plants2014In: Journal of Evolutionary Biology, ISSN 1010-061X, E-ISSN 1420-9101, Vol. 27, no 7, p. 1478-1490Article in journal (Refereed)
    Abstract [en]

    In angiosperms, dioecious clades tend to have fewer species than their nondioecious sister clades. This departure from the expected equal species richness in the standard sister clade test has been interpreted as implying that dioecious clades diversify less and has initiated a series of studies suggesting that dioecy might be an 'evolutionary dead end. However, two of us recently showed that the equal species richness null hypothesis is not valid in the case of derived char acters, such as dioecy, and proposed a new test for sister clade comparisons; preliminary results, using a data set available in the litterature, indicated that dioecious clades migth diversify more than expected. However, it is crucial for this new test to distinguish between ancestral and derived cases of dioecy, a criterion that was not taken into account in the available data set. Here, we present a new data set that was obtained by searching the phylogenetic literature on more than 600 completely dioecious angiosperm genera and identifying 115 sister clade pairs for which dioecy is likely to be derived (including > 50% of the dioecious species). Applying the new sister clade test to this new dataset, we confirm the preliminary result that dioecy is associated with an increased diversification rate, a result that does not support the idea that dioecy is an evolutionary dead end in angiosperms. The traits usually associated with dioecy, that is, an arborescent growth form, abiotic pollination, fleshy fruits or a tropical distribution, do not influence the diversification rate. Rather than a low diversification rate, the observed species richness patterns of dioecious clades seem to be better explained by a low transition rate to dioecy and frequent losses.

  • 186.
    Kan, Boris
    et al.
    Karolinska sjukhuset.
    Åsen, Carin
    Åsbakk, Kjetil
    Norges Veterinärhögskola, Tromsö.
    Jaenson, Thomas G.T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Misstänkta lusägg i pojkes hår avslöjade farlig parasit (Suspected louse eggs in the hair of a boy revealed dangerous parasite)2010In: Läkartidningen, ISSN 0023-7205, E-ISSN 1652-7518, Vol. 107, no 26-28, p. 1694-1697Article in journal (Refereed)
  • 187.
    Kao, Tzu-Tong
    et al.
    Duke Univ, Dept Biol, Durham, NC 27708 USA..
    Pryer, Kathleen M.
    Duke Univ, Dept Biol, Durham, NC 27708 USA..
    Turner, Melvin D.
    Duke Univ, Dept Biol, Durham, NC 27708 USA..
    White, Richard A.
    Duke Univ, Dept Biol, Durham, NC 27708 USA..
    Korall, Petra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Origins of the Endemic Scaly Tree Ferns on the Galapagos and Cocos Islands2015In: International journal of plant sciences, ISSN 1058-5893, E-ISSN 1537-5315, Vol. 176, no 9, p. 869-879Article in journal (Refereed)
    Abstract [en]

    Premise of research.Successful long-distance dispersal is rarely observed in scaly tree ferns (Cyatheaceae). Nevertheless, recent molecular evidence has suggested that the four endemic scaly tree ferns on the Galapagos Archipelago (Cyathea weatherbyana) and Cocos Island (Cyathea alfonsiana, Cyathea nesiotica, and Cyathea notabilis), two oceanic island groups west of Central and northern South America, probably each originated from different mainland America ancestors. However, the phylogenetic relationships inferred among these endemics and their mainland relatives have been unclear. This study is aimed at better resolving the relationships and tracing the origins of these island endemics.Methodology.Five plastid regions from 35 Cyathea species were analyzed to reconstruct phylogenetic relationships using parsimony, likelihood, and Bayesian approaches. We also estimated divergence times of these species, and our chronogram was used to reconstruct their biogeographical range history.Pivotal results.Our well-resolved phylogenetic tree of Cyathea, which is in agreement with previous studies, shows that when the four Galapagos and Cocos endemics are included, they each belong to separate subclades. Our biogeographical study suggests that the four endemics originated from independent colonization events from mainland America and that there was no dispersal of Cyathea between the island groups. We reveal more detailed relationships among the endemics and their respective close mainland relatives; some of these relationships differ from previous studies. Our findings are corroborated by new morphological data from ongoing stem anatomy studies.Conclusions.The four scaly tree ferns endemic to the Galapagos and Cocos Islands each did indeed originate as independent colonization events from separate sources in mainland America, and their closest relatives are identified here.

  • 188.
    Kelly, Michelle
    et al.
    Natl Inst Water & Atmospher Res Ltd, Coasts & Oceans Natl Ctr, Private Bag 99940, Auckland, New Zealand..
    Cardenas, Paco
    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.
    An unprecedented new genus and family of Tetractinellida (Porifera, Demospongiae) from New Zealand's Colville Ridge, with a new type of mitochondrial group I intron2016In: Zoological Journal of the Linnean Society, ISSN 0024-4082, E-ISSN 1096-3642, Vol. 177, no 2, p. 335-352Article in journal (Refereed)
    Abstract [en]

    A remarkable sponge with unprecedented megascleres and systematic affinities was collected recently from a previously unidentified volcano on Colville Ridge to the north-east of New Zealand. The sponge has the appearance of a tetillid sponge (family Tetillidae Sollas, 1886) with a perfectly spherical external form, radiating internal skeleton of huge oxeas and triaenes, and microspined sigmaspires as microscleres. The triaene megascleres, however, are unprecedented in their form and ornamentation; they are huge clubbed orthotriaenes the upper third of which is acanthose. Stupenda singularis gen. et sp. nov. is described here and the phylogenetic affinity and taxonomic position of this unique sponge is explored in relation to a broad range of tetractinellid sponges (order Tetractinellida Marshall, 1876) using the Folmer + Erpenbeck fragment of the cytochrome c oxidase subunit I (COI) gene and a nearly complete sequence of the 18S rDNA gene. Mitochondrial introns are rare in sponges but S. singularis gen. et sp. nov. possesses a mitochondrial group I intron at position 387 in COI; it hosts a putative LAGLIDADG endonuclease gene. This intron is the first of its kind in sponges: the self-splicing intron is homologous to a placozoan COI intron whereas the LAGLIDADG endonuclease gene may be related to Fungi LAGLIDADG endonuclease genes.

  • 189.
    Kiel, CA
    et al.
    California Academy of Sciences.
    Manktelow, M
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Daniel, TF
    California Academy of Sciences.
    Andreasen, K
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Holmqvist, P-H
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    McDade, LA
    Department of Botany. Academy of Natural Sciences.
    Bird Pollination has evolved multiple times in the Tetramerium group (Tetramerium Lineage, Justicieae, Acanthaceae).2005Conference paper (Other academic)
  • 190.
    Kleinteich, Julia
    et al.
    Univ Tubingen, Ctr Appl Geosci, Tubingen, Germany.
    Hildebrand, Falk
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, 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, Tartu, Estonia.
    Voigt, Anita Y.
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany;Jackson Lab Genom Med, Farmington, CT USA.
    Wood, Susanna A.
    Cawthron Inst, Coastal & Freshwater, Nelson, New Zealand;Univ Waikato, Environm Res Inst, Hamilton, New Zealand.
    Jungblut, Anne D.
    London Nat Hist Museum, London, England.
    Kupper, Frithjof C.
    Scottish Assoc Marine Sci, Oban, Argyll, Scotland;Univ Aberdeen, Oceanlab, Aberdeen, Scotland.
    Quesada, Antonio
    Autonomous Univ Madrid, Dept Biol, Madrid, Spain.
    Camacho, Antonio
    Univ Valencia, Cavanilles Inst Biodivers & Evolutionary Biol, Valencia, Spain.
    Pearce, David A.
    Univ Northumbria Newcastle, Fac Hlth & Life Sci, Dept Appl Sci, Newcastle Upon Tyne, Tyne & Wear, England;British Antarct Survey, Cambridge, England.
    Convey, Peter
    British Antarct Survey, Cambridge, England.
    Vincent, Warwick F.
    Univ Laval, Dept Biol, Quebec City, PQ, Canada;Univ Laval, Ctr Northern Studies, Quebec City, PQ, Canada.
    Zarfl, Christiane
    Univ Tubingen, Ctr Appl Geosci, Tubingen, Germany.
    Bork, Peer
    European Mol Biol Lab, Struct & Computat Biol, Heidelberg, Germany;Max Delbruck Ctr Mol Med, Berlin, Germany;Univ Wurzburg, Dept Bioinformat, Wurzburg, Germany.
    Dietrich, Daniel R.
    Univ Konstanz, Human & Environm Toxicol, Constance, Germany.
    Pole-to-Pole Connections: Similarities between Arctic and Antarctic Microbiomes and Their Vulnerability to Environmental Change2017In: Frontiers in Ecology and Evolution, E-ISSN 2296-701X, Vol. 5, article id 137Article in journal (Refereed)
    Abstract [en]

    The global biogeography of microorganisms remains poorly resolved, which limits the current understanding of microbial resilience toward environmental changes. Using high-throughput 16S rRNA gene amplicon sequencing, we characterized the microbial diversity of terrestrial and lacustrine biofilms from the Arctic, Antarctic and temperate regions. Our analyses suggest that bacterial community compositions at the poles are more similar to each other than they are to geographically closer temperate habitats, with 32% of all operational taxonomic units (OTUs) co-occurring in both polar regions. While specific microbial taxa were confined to distinct regions, representing potentially endemic populations, the percentage of cosmopolitan taxa was higher in Arctic (43%) than in Antarctic samples (36%). The overlap in polar microbial OTUs may be explained by natural or anthropogenically-mediated dispersal in combination with environmental filtering. Current and future changing environmental conditions may enhance microbial invasion, establishment of cosmopolitan genotypes and loss of endemic taxa.

  • 191.
    Klint, Markus
    et al.
    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 Organism Biology, Systematic Biology.
    Bongcam-Rudloff, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, The Linnaeus Centre for Bioinformatics.
    Birkelund, Svend
    University of Aarhus.
    Nilsson, Anders
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
    Herrmann, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
    Mosaic structure of intragenic repetitive elements in histone H1-like protein Hc2 varies within serovars of Chlamydia trachomatis2010In: BMC Microbiology, ISSN 1471-2180, E-ISSN 1471-2180, Vol. 10, p. 81-Article in journal (Refereed)
    Abstract [en]

    BACKGROUND: The histone-like protein Hc2 binds DNA in Chlamydia trachomatis and is known to vary in size between 165 and 237 amino acids, which is caused by different numbers of lysine-rich pentamers. A more complex structure was seen in this study when sequences from 378 specimens covering the hctB gene, which encodes Hc2, were compared. RESULTS: This study shows that the size variation is due to different numbers of 36-amino acid long repetitive elements built up of five pentamers and one hexamer. Deletions and amino acid substitutions result in 14 variants of repetitive elements and these elements are combined into 22 configurations. A protein with similar structure has been described in Bordetella but was now also found in other genera, including Burkholderia, Herminiimonas, Minibacterium and Ralstonia.Sequence determination resulted in 41 hctB variants that formed four clades in phylogenetic analysis. Strains causing the eye disease trachoma and strains causing invasive lymphogranuloma venereum infections formed separate clades, while strains from urogenital infections were more heterogeneous. Three cases of recombination were identified. The size variation of Hc2 has previously been attributed to deletions of pentamers but we show that the structure is more complex with both duplication and deletions of 36-amino acid long elements. CONCLUSIONS: The polymorphisms in Hc2 need to be further investigated in experimental studies since DNA binding is essential for the unique biphasic life cycle of the Chlamydiacae. The high sequence variation in the corresponding hctB gene enables phylogenetic analysis and provides a suitable target for the genotyping of C. trachomatis.

  • 192. Klitgaard, Bente, B.
    et al.
    Ståhl, Bertil
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Cajanus DC.: 82-84. Leguminosae - Phaseoleae, part 1.2016In: Flora of Ecuador / [ed] Persson, C. & B. Ståhl, Göteborg: Department of Biological and Environmental Sciences , 2016, p. 60-63Chapter in book (Refereed)
  • 193.
    Kohout, Petr
    et al.
    Univ Tartu, Inst Ecol & Earth Sci, EE-50411 Tartu, Estonia.;Acad Sci Czech Republ, Inst Bot, CZ-25243 Pruhonice, Czech Republic.;Charles Univ Prague, Fac Sci, Dept Expt Plant Biol, CZ-12801 Prague 2, Czech Republic..
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, EE-50411 Tartu, Estonia.
    Polme, Sergei
    Univ Tartu, Inst Ecol & Earth Sci, EE-50411 Tartu, Estonia..
    Tedersoo, Leho
    Univ Tartu, Nat Hist Museum, EE-50411 Tartu, Estonia..
    Elevation, space and host plant species structure Ericaceae root-associated fungal communities in Papua New Guinea2017In: Fungal ecology, ISSN 1754-5048, E-ISSN 1878-0083, Vol. 30, p. 112-121Article in journal (Refereed)
    Abstract [en]

    Our study aimed to identify significant predictors (spatial distance, elevation, host plant taxonomy) which shape the structure of endophytic fungal (ENDF) and putative ericoid mycorrhizal (ErMF) communities associated with roots of Ericaceae in Papua New Guinea. Roots of five Ericaceae together with one non-Ericaceae species were sampled at an experimental site and one common Ericaceae species was chosen for sampling along an elevation gradient. ENDF and putative ErMF communities were determined using the 454-sequencing approach. ENDF as well as putative ErMF communities were affected by interacting host plant. While the putative ErMF community was structured by host plants at the genus level, the ENDF community was affected by host plant subfamily level. Composition of ENDF as well as putative ErMF communities were affected by elevation. Non-Ericaceae plant species (Hypericum sp.) harbored similar communities of ENDF as well as putative ErMF as Ericaceae plants. Our study provides a first insight into ErMF and ENDF community ecology of Ericaceae in Papua New Guinea.

  • 194. Kohout, Petr
    et al.
    Doubková, Pavla
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Suda, Jan
    Tedersoo, Leho
    Voříšková, Jana
    Sudová, Radka
    Niche partitioning in arbuscular mycorrhizal communities in temperate grasslands: a lesson from adjacent serpentine and nonserpentine habitats2015In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 24, no 8, p. 1831-1843Article in journal (Refereed)
    Abstract [en]

    Arbuscular mycorrhizal fungi (AMF) represent an important soil microbial group playing a fundamental role in many terrestrial ecosystems. We explored the effects of deterministic (soil characteristics, host plant life stage, neighbouring plant communities) and stochastic processes on AMF colonization, richness and community composition in roots of Knautia arvensis(Dipsacaceae) plants from three serpentine grasslands and adjacent nonserpentine sites. Methodically, the study was based on 454-sequencing of the ITS region of rDNA. In total, we detected 81 molecular taxonomical operational units (MOTUs) belonging to the Glomeromycota. Serpentine character of the site negatively influenced AMF root colonization, similarly as higher Fe concentration. AMF MOTUs richness linearly increased along a pH gradient from 3.5 to 5.8. Contrary, K and Cr soil concentration had a negative influence on AMF MOTUs richness. We also detected a strong relation between neighbouring plant community composition and AMF MOTUs richness. Although spatial distance between the sampled sites (c. 0.3–3 km) contributed to structuring AMF communities in K. arvensis roots, environmental parameters were key factors in this respect. In particular, the composition of AMF communities was shaped by the complex of serpentine conditions, pH and available soil Ni concentration. The composition of AMF communities was also dependent on host plant life stage (vegetative vs. generative). Our study supports the dominance of deterministic factors in structuring AMF communities in heterogeneous environment composed of an edaphic mosaic of serpentine and nonserpentine soils.

  • 195.
    Kool, Anneleen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Desert Plants and Deserted Islands: Systematics and Ethnobotany in Caryophyllaceae2012Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Background. Caryophyllaceae is a large and cosmopolitic flowering plant family, however the systematics of many of its basal groups has been unclear, due to a lack of unambiguous morphology. Some members of Caryophyllaceae are used medicinally, e.g. Corrigiola roots in Morocco. Monitoring the trade in medicinal plants is complicated due to the absence of useful identification characters in plant products such as roots, bark, and powders.

    This thesis aims at elucidating the systematics and the ethnobotany of some of the basal clades in Caryophyllaceae. Methods. A comprehensive sampling from herbarium as well as market and field collected material was used in systematic studies combining morphological investigation, molecular phylogenetic and molecular dating analyses. Results. The data show that Polycarpon is polyphyletic, that Sphaerocoma is sister to Pollichia and shows some intraspecific variation, that Sanctambrosia falls within the genus Spergularia, and that both Spergula and Spergularia are monophyletic. Preliminary data suggest that Polycarpaea is polyphyletic and should be split into three larger and several smaller genera, that the members of Paronychia subgen. Anaplonychia will need to be transferred to Herniaria to maintain monophyly, and that Caryophyllaceae emerged during the Paleocene. All the major extant lineages originated in the Oligocene and diversified later. Using molecular identification it was possible to identify around 50% of the Moroccan medicinal roots to species level and an additional 30% to genus level. Discussion and conclusions. The polyphyletic Polycarpon needs to be split into at least three separate genera, but no name changes were made pending further research. The two species of Sphaerocoma were merged into one species with two subspecies. The San Ambrosio Island endemic Sanctambrosia, the only tree-like plant in Caryophyllaceae, is probably the result of a long distance dispersal event and its woody habit and gynodioecy are probably caused by inbreeding depression. Sanctambrosia manicata is transferred to Spergularia. Molecular identification put into practice on traded medicinal roots has a somewhat lower success rate than most theoretical studies, indicating that a global barcoding database would need to include reference sequences from a broad range of populations for each species.

  • 196.
    Kool, Anneleen
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Phylogeny of Withania (Solanaceae) and some notes on chromosome numbers and genome sizes.2004Conference paper (Other academic)
  • 197.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bengtson, Annika
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Polyphyly of Polycarpon (Caryophyllaceae) inferred from DNA sequence data2007In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 56, no 3, p. 775-782Article in journal (Refereed)
    Abstract [en]

    A phylogenetic study of the genus Polycarpon was made using DNA sequence data from the chloroplast rps16 intron and nuclear RPB2 regions. Polycarpon as currently recognised is shown to be polyphyletic. The South American species P. coquimbense and P. suffruticosum are more closely related to Haya obovata (Socotra) and Polycarpaea spicata (paleotropical) than to the remaining species of Polycarpon, and the widespread tropical species P. prostratum is nested with Macaronesian species of Polycarpaea. All three should therefore be ex- cluded from Polycarpon. The remaining species, the P. tetraphyllum group, has its main diversity in the Medi- terranean region. It is a polyploid complex with morphologically very similar taxa mostly separated only by partially overlapping characters. The members of this group form a strongly supported, but largely unresolved clade. It is proposed that they are all included in a widely circumscribed P. tetraphyllum. The dehiscence of the capsules in P. tetraphyllum, by valves that elastically roll inwards and finally throw out the seeds, is unique in Caryophyllaceae and provides a strong synapomorphy for Polycarpon in this new restricted sense.

  • 198.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ethnobotany at Uppsala University.2005In: Proceedings of the IVth International Congress of the Ethnobotany (ICEB 2005) / [ed] Z. Füsun Ertuğ & Ege Yayınları, 2005Conference paper (Other academic)
  • 199.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ethnobotany in the South Pare Mountains2003Conference paper (Other academic)
  • 200.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Abbad, Abdelazziz
    Université Cadi Ayyad .
    Martin, Gary
    The Global Diversity Foundation.
    Identification of threatened medicinal plants in trade: ethnobotanical, molecular and taxonomic approaches2007Conference paper (Other academic)
1234567 151 - 200 of 559
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