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  • 251.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Three new species of Dactylicapnos (Fumariaceae) and a synopsis of the D. macrocapnos complex2010In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 28, no 6, p. 656-660Article in journal (Refereed)
    Abstract [en]

    The Dactylicapnos macrocapnos complex is revised, and D. platycarpa Liden, D. odontocarpa Liden and D. macrocapnos subsp. echinosperma Liden are recognised as new taxa. The complex consists of a chain of 4 vicariant taxa from northwestern India (Garhwal) to western Bhutan (Thimphu). Dactylicapnos cordata Liden (eastern Nepal, Darjeeling) is described and contrasted with its close relative, the geographically disjunct D. burmanica (western Yunnan, Burma).

  • 252.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Music and Museums.
    ToL – IRL (Tree of Life – In Real Life)2011In: Back to Eden: challenges for contemporary gardens : conference proceedings : Katowice, Ustroń, Mikołów, 21st-23rd May 2011 / [ed] David Oldroyd, Mikołów, 2011Conference paper (Refereed)
  • 253.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Adhikari, Alister
    The real Ponerorchis nana (Orchidaceae) resurrected2016In: Pleione, ISSN 0973-9467, Vol. 10, no 2, p. 279-282Article in journal (Refereed)
  • 254.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bharali, Pankaj
    Dept of Botany, Rajiv Gandhi Univ., Rono Hills, Itanagar, Arunachal Pradesh, India.
    Impatiens pyrorhiza sp. nov. (Balsaminaceae) from east Himalaya2017In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 35, no 4, p. 411-416Article in journal (Refereed)
    Abstract [en]

    Impatiens pyrorhiza sp. nov. from the Tawang and West Kameng districts in northwest Arunachal Pradesh, India, is described and compared with related species. It is similar to I. gamblei from east Nepal and northwest Darjeeling, but differs in for example: a) rhizome extended, orange, much-branched, b) leaves with numerous teeth, c) petiole base with prominent glands, d) raceme supported by subtending leaf and e) lateral sepals without an apical divergent extended callosity. 

  • 255.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bharali, Pankaj
    Rajiv Gandhi University, Itanagar, Arunachal Pradesh, India.
    Notes on Utricularia sect. Phyllaria (Kurz) Kamieński (Lentibulariaceae) in Arunachal Pradesh2014In: Pleione, ISSN 0973-9467, Vol. 8, no 2, p. 267-270Article in journal (Refereed)
    Abstract [en]

    The article provided field observations, photo-documentation and discriminative characters forUtricularia sectionPhyllaria(Kurz) Kamieński, gathered during two recent expeditions to highaltitudes of Arunachal Pradesh (India). Four species,U. brachiata, U. christopheri, U. multicaulisand U. striatula has been enumerated along with brief discussion on their partly challengingtaxonomy.

  • 256.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bharali, Pankaj
    Das, Arup Kumar
    Rhodiola sedoides (Crassulaceae), a new species from Arunachal Pradesh, India2016In: Annales Botanici Fennici, ISSN 0003-3847, E-ISSN 1797-2442, Vol. 53, no 1-2, p. 106-108Article in journal (Refereed)
    Abstract [en]

    Rhodiola sedoides Lidén & P. Bharali (Crassulaceae), an alpine hermaphroditic spe- cies from NW Arunachal Pradesh, India, is described as new to science and compared with other low-growing, hermaphroditic and narrow-leaved alpine Rhodiola species.

  • 257.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kårehed, Jesper
    Uppsala University, Music and Museums, The Linnean Gardens of Uppsala.
    Linné och det naturliga systemet2018In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 112, no 2, p. 68-80Article in journal (Refereed)
  • 258.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Mili, Rajiv
    Saikia, Bhaskar
    New taxa of Corydalis (Papaveraceae, Fumarioidae) from Anjaw District, NE India2013In: Annales Botanici Fennici, ISSN 0003-3847, E-ISSN 1797-2442, Vol. 50, no 3, p. 172-174Article in journal (Refereed)
    Abstract [en]

    Corydalis meyori Liden, R. Mili & B. Saikia (sect. Trachycarpae) and C. pterygopetala subsp. macrocarpa Liden, R. Mili & B. Saikia (sect. Davidianae) are described as new to science. Both were collected close to Myanmar (Burma) in East Arunachal Pradesh, an area whose flora is almost unknown.

  • 259.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Morrison, David A.Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.Baldauf, SandraUppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Contributions to Botany: Dedicated to Inga Hedberg2016Collection (editor) (Other academic)
  • 260.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pathak, Mitilesh K.
    Biological survey of India.
    Studies in Dactylicapnos (Papaveraceae-Fumarioideae) part II. Revision of Dactylicapnos sect. Pogonosperma sect. nov., with D. arunachalensis sp. nov.2014In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 32, no 2, p. 176-184Article in journal (Refereed)
    Abstract [en]

    Dactylicapnos sect. Pogonosperma Liden & M. K. Pathak sect. nov. is established and revised based on morphology, and found to include four species: D. gaoligongshanensis from west Yunnan, D. arunachalensis Liden & M. K. Pathak sp. nov., endemic to central Arunachal Pradesh, D. grandifoliolata (syn. D. ventii) and D. paucinervia (K. R. Stern) Liden & M. K. Pathak comb. nov., the two latter species widespread in the east Himalayas.

  • 261.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pathak, Mitilesh K.
    Biological survey of India.
    Chowlu, Krishna
    Manipur, India.
    Saikia, Baskar
    Fumariaceae in North East India: new species and records in Corydalis DC and Dactylicapnos Wall.2013In: Nelumbo: the bulletin of the Botanical Survey of India, ISSN 0976-5069, Vol. 55, no 1-5, p. 1-20Article in journal (Refereed)
  • 262.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pavon, Daniel
    Sobre la presencia de Fumaria melillaica Pugsley (Papaveraceae) en Murcia (Espana)2016In: Flora Montiberica, ISSN 1138-5952, E-ISSN 1988-799X, Vol. 64, p. 80-83Article in journal (Refereed)
    Abstract [es]

    RESUMEN: Se cita por primera vez para Murcia Fumaria melillaica Pugsley. Se presenta una ilustración y un mapa revisado. Palabras clave: plantas vasculares, Fumaria, Papaveraceae, corología, planta rara, Murcia, España.

    RÉSUMÉ: Sur la présence de Fumaria melillaica Pugsley (Papaveraceae) dans la région de Murcie (Espagne). Les auteurs relatent la découverte de Fumaria melillaica Pugsley pour la région de Murcie. Ils présentent une illustration et une carte révisée. Mots clés: plantes vasculaires, chorologie, Fumaria, plante rare, Murcia, Espagne

  • 263.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Su, Zhi-Yun
    Kunming Institute of Botany, Heilongtan, Kunming.
    New species of Corydalis (Fumariaceae) from China II2007In: Novon, ISSN 1055-3177, E-ISSN 1945-6174, Vol. 17, no 4, p. 479-496Article in journal (Refereed)
    Abstract [en]

    Twenty-three species and one subspecies of Corydalis DC. (Fumariaceae) from China and Tibet are described as new to science: C. aeditua Lidén & Z. Y. Su, C. cheilosticta Z. Y. Su & Lidén, C. cryptogama Z. Y. Su & Lidén, C. dolichocentra Z. Y. Su & Lidén, C. gymnopodaZ. Y. Su & Lidén, C. heterothylax C. Y. Wu ex Z. Y. Su & Lidén, C. ischnosiphon Lidén & Z. Y. Su, C. jiulongensis Z. Y. Su & Lidén, C. lagochila Lidén & Z. Y. Su, C. longistyla Z. Y. Su & Lidén, C. lophophora Lidén & Z. Y. Su, C. madida Lidén & Z. Y. Su, C. mediterraneaZ. Y. Su & Lidén, C. milarepa Lidén & Z. Y. Su, C. nematopoda Lidén & Z. Y. Su, C. nubicola Z. Y. Su & Lidén, C. papillosa Z. Y. Su & Lidén, C. procera Lidén & Z. Y. Su, C. sarcolepis Lidén & Z. Y. Su, C. sophronitis Z. Y. Su & Lidén, C. tenuipes Lidén & Z. Y. Su,C. virginea Lidén & Z. Y. Su, C. yaoi Lidén & Z. Y. Su, and C. cheilosticta subsp. borealisLidén & Z. Y. Su. Six previously recognized subspecific taxa are raised to specific rank, and three of these are provided with new names: C. microflora (H. Chuang) Z. Y. Su & Lidén, stat. nov. [= C. flexuosa var. microflora H. Chuang], C. mucronipetala (H. Chuang) Lidén & Z. Y. Su, stat. nov. [= C. flexuosa var. mucronipetala H. Chuang], C. omeiana (C. Y. Wu & H. Chuang) Z. Y. Su & Lidén, stat. nov. [= C. flexuosa var. omeiana C. Y. Wu & H. Chuang],C. amplisepala Z. Y. Su & Lidén, nom. et stat. nov. [= C. pseudomucronata var. cristata C. Y. Wu], C. harry-smithii Lidén & Z. Y. Su, nom. et stat. nov. [= C. elata subsp. ecristata C. Y. Wu], and C. pseudomairei C. Y. Wu ex Z. Y. Su & Lidén, nom. et stat. nov. [= C. maireivar. megalantha C. Y. Wu].

  • 264.
    Lidén, Magnus
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Zhang, Ming Li
    Su, Zhi Yun
    Papaveraceae-Fumarioideae2008In: Flora of China. Vol. 7, Menispermaceae through Capparaceae / [ed] Wu Zheng Yih et al., Beijing: Science Press, 2008, p. 288-428Chapter in book (Other academic)
  • 265.
    Lindborg, Marcus
    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.
    GC-MS analysis for Polyaromatic Hydrocarbons (PAH) in Moroccan medicinal tars: An ethnobotanical study and chemical investigation of the use and safety of medicinal tars in Marrakesh and the High Atlas Mountains, Morocco2008Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 266.
    Lindeborg, Mats
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Barboutis, Christos
    Ehrenborg, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Fransson, Thord
    Jaenson, Thomas G T
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lindgren, Per-Eric
    Lundkvist, Åke
    Nyström, Fredrik
    Salaneck, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Waldenström, Jonas
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Migratory birds, ticks, and crimean-congo hemorrhagic Fever virus2012In: Emerging Infectious Diseases, ISSN 1080-6040, E-ISSN 1080-6059, Vol. 18, no 12, p. 2095-2097Article in journal (Refereed)
    Abstract [en]

    TO THE EDITOR:

    In a recently published study, Estrada-Peña et al. reported the finding of Crimean-Congo hemorrhagic fever virus (CCHFV) in adult Hyalomma lusitanicum ticks from red deer (Cervus elaphus) in Spain during 2010 (1). Phylogenetic analysis showed that the virus was most likely of African origin. Here, we present a model for the transfer of CCHFV-infected ticks by migratory birds from Africa to Europe.

  • 267.
    Lindh, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    Mothers, Markets and Medicine: The role of traditional herbal medicine in primary women and child health care in the Dar es Salaam region, Tanzania.2015Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    Traditional medicine is still the most common primary healthcare used in Tanzania, especially among women. The ethnobotanical studies performed in Tanzania have not explored women’s traditional medicine, with the result that we do not know that much about it, including if women’s usage of medicinal plants create a threat against the medicinal flora’s biodiversity or not. Field studies consisting of interviews and collections of medicinal plants were carried out in the Dar es Salaam region in Tanzania before identifying the collected specimens by DNA barcoding, literature and morphology in Uppsala, Sweden. The 33 informants belonged to 15 different ethnic groups and 79% of them had migrated to Dar es Salaam. A total of 249 plant species were mentioned for women’s healthcare and 140 for children’s healthcare. The medicinal plants frequently reported as used for women’s health and childcare during structured interviews and free-listing exercises were Senna occidentalis/ Cassia abbreviata, Zanthoxylum sp., Clausena anisata, Acalypha ornata and Ximenia sp. The most salient uses of medicinal plants by women were during pregnancy, childbirth, menstruation, to induce abortion, and for cleansing infants and treating convulsions in children. Most of the fresh specimens were collected from disturbance vegetation. The informants having most interview answers in common were the market vendors, healers and herbalists and they were the only informants that mentioned species listed as vulnerable on the IUCN Red List of Threatened Species. These results were similar to the outcomes from studies of women’s traditional health care in West Africa. Out of 343 collected specimens, 19% were identified by DNA barcoding and 33% by literature sources. Out of 98 voucher samples, 61% were identified by comparisons of morphology, results from DNA analysis and literature. DNA barcoding was necessary to use as method since most medicines were sold in powdered shape. With more time and experience it should be possible to chart the majority of the medicinal plants up to species level. A difference between medicinal plant harvest for domestic and commercial use was observed where the commercial harvesting meant a greater threat to the Tanzanian medicinal plant biodiversity due to unsustainable harvesting methods. Previous studies have shown that an increased commercial harvesting and trade of plants often result in a decreased biodiversity. High population growth and quick urbanization mean that domestic harvesting of women’s medicinal plants will not be able to continue as previously and women in Tanzania will be more dependent on commercial trade for their traditional medicine.

  • 268.
    Lindholm, Anna K.
    et al.
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland..
    Dyer, Kelly A.
    Univ Georgia, Dept Genet, Athens, GA 30602 USA..
    Firman, Renee C.
    Univ Western Australia, Sch Anim Biol, Ctr Evolutionary Biol, Perth, WA 6009, Australia..
    Fishman, Lila
    Univ Montana, Div Biol Sci, Missoula, MT 59812 USA..
    Forstmeier, Wolfgang
    Max Planck Inst Ornithol, Dept Behav Ecol & Evolutionary Genet, D-82319 Seewiesen, Germany..
    Holman, Luke
    Australian Natl Univ, Res Sch Biol, Div Ecol Evolut & Genet, Canberra, ACT, Australia..
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Knief, Ulrich
    Max Planck Inst Ornithol, Dept Behav Ecol & Evolutionary Genet, D-82319 Seewiesen, Germany..
    Kokko, Hanna
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland..
    Larracuente, Amanda M.
    Univ Rochester, Dept Biol, Rochester, NY 14627 USA..
    Manser, Andri
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland..
    Montchamp-Moreau, Catherine
    Univ Paris Saclay, Univ Paris 11, CNRS, Evolut Genomes Comportement & Ecol,IRD, Gif Sur Yvette, France..
    Petrosyan, Varos G.
    Russian Acad Sci, Severtsov Inst Ecol & Evolut, Moscow 119071, Russia..
    Pomiankowski, Andrew
    UCL, Dept Genet Evolut & Environm, Gower St, London WC1E 6BT, England..
    Presgraves, Daven C.
    Univ Rochester, Dept Biol, Rochester, NY 14627 USA..
    Safronova, Larisa D.
    Russian Acad Sci, Severtsov Inst Ecol & Evolut, Moscow 119071, Russia..
    Sutter, Andreas
    Univ Zurich, Dept Evolutionary Biol & Environm Studies, Zurich, Switzerland..
    Unckless, Robert L.
    Cornell Univ, Dept Mol Biol & Genet, Ithaca, NY USA..
    Verspoor, Rudi L.
    Univ Liverpool, Inst Integrat Biol, Liverpool L69 7ZB, Merseyside, England..
    Wedell, Nina
    Univ Exeter, Biosci, Cornwall Campus, Penryn TR10 9FE, Cornwall, England..
    Wilkinson, Gerald S.
    Univ Maryland, Dept Biol, College Pk, MD 20742 USA..
    Price, Tom A. R.
    Univ Liverpool, Inst Integrat Biol, Liverpool L69 7ZB, Merseyside, England..
    The Ecology and Evolutionary Dynamics of Meiotic Drive2016In: Trends in Ecology & Evolution, ISSN 0169-5347, E-ISSN 1872-8383, Vol. 31, no 4, p. 315-326Article, review/survey (Refereed)
    Abstract [en]

    Meiotic drivers are genetic variants that selfishly manipulate the production of gametes to increase their own rate of transmission, often to the detriment of the rest of the genome and the individual that carries them. This genomic conflict potentially occurs whenever a diploid organism produces a haploid stage, and can have profound evolutionary impacts on gametogenesis, fertility, individual behaviour, mating system, population survival, and reproductive isolation. Multiple research teams are developing artificial drive systems for pest control, utilising the transmission advantage of drive to alter or exterminate target species. Here, we review current knowledge of how natural drive systems function, how drivers spread through natural populations, and the factors that limit their invasion.

  • 269.
    Liu, Jian-Kui
    et al.
    Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Peoples R China.;Guizhou Acad Agr Sci, Guizhou Inst Biotechnol, Guiyang 550006, Peoples R China.;Guizhou Acad Agr Sci, Guizhou Key Lab Agr Biotechnol, Guiyang 550006, Peoples R China..
    Hyde, Kevin D.
    Mae Fah Luang Univ, Ctr Excellence Fungal Res, Chiang Rai 57100, Thailand..
    Jeewon, Rajesh
    Univ Mauritius, Fac Sci, Dept Hlth Sci, Reduit, Mauritius..
    Phillips, Alan J. L.
    Univ Lisbon, Fac Sci, Biosyst & Integrat Sci Inst, P-1749016 Lisbon, Portugal..
    Maharachchikumbura, Sajeewa S. N.
    Sultan Qaboos Univ, Coll Agr & Marine Sci, Dept Crop Sci, POB 8, Al Khoud 123, Oman..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Liu, Zuo-Yi
    Guizhou Acad Agr Sci, Guizhou Key Lab Agr Biotechnol, Guiyang 550006, Peoples R China..
    Zhao, Qi
    Chinese Acad Sci, Kunming Inst Bot, Key Lab Plant Divers & Biogeog East Asia, Kunming 650201, Peoples R China..
    Ranking higher taxa using divergence times: a case study in Dothideomycetes2017In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 84, no 1, p. 75-99Article in journal (Refereed)
    Abstract [en]

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

  • 270.
    Looney, Brian P.
    et al.
    Univ Tennessee, Dept Ecol & Evolutionary Biol, 332 Hesler Biol Bldg, Knoxville, TN 37996 USA..
    Ryberg, Martin
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hampe, Felix
    Univ Ghent, Dept Biol, KL Ledeganckstr 35, B-9000 Ghent, Belgium..
    Sanchez-Garcia, Marisol
    Univ Tennessee, Dept Ecol & Evolutionary Biol, 332 Hesler Biol Bldg, Knoxville, TN 37996 USA..
    Matheny, P. Brandon
    Univ Tennessee, Dept Ecol & Evolutionary Biol, 332 Hesler Biol Bldg, Knoxville, TN 37996 USA..
    Into and out of the tropics: global diversification patterns in a hyperdiverse clade of ectomycorrhizal fungi2016In: Molecular Ecology, ISSN 0962-1083, E-ISSN 1365-294X, Vol. 25, no 2, p. 630-647Article in journal (Refereed)
    Abstract [en]

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

  • 271.
    Lundh, Emma
    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.
    Plant Use in Ante- and Postpartum Health Care in Lao PDR2007Independent thesis Advanced level (degree of Master (One Year)), 20 credits / 30 HE creditsStudent thesis
  • 272.
    Lundin, Erik
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Disciplinary Domain of Science and Technology, Biology, Biology Education Centre.
    AutoPhylo, a bioinformatic tool for identifying and retrieving sequences2010Independent thesis Basic level (degree of Bachelor), 10 credits / 15 HE creditsStudent thesis
    Abstract [en]

    The task of constructing a molecular phylogenetic tree consists of finding homologous sequences, making a multiple sequence alignment, perhaps removing gaps and ambiguous positions in the alignment and finally phylogenetically inferring the tree with various evolutionary models. Often there is a need to refine the tree by removing inappropriate sequences. For each step of this process there is a tool to accomplish the task. Starting with a sequence of interest BLAST (Basic Local Alignment Search Tool) is used to find homologous sequences from various databases. Then multiple sequence alignment programs such as MUSCLE or CLUSTAL can be used to align the sequences. In the alignment there are often regions of gaps and ambiguous positions that can be identified and removed with programs such as GBlocks. Finally, using the alignment a phylogenetic tree can be reconstructed using selected methods and models. Depending on the scientific goals and data, this process generally needs to be repeated several times in order to “refine” the tree. To construct a tree of correct phylogeny “true” homologous positions in an alignment must beused. In addition, if the tree is to reconstruct the correct relationship among species (rather than just the genes), then it is also necessary to use orthologous sequences, rather than sequences that have undergone duplications (paralogs). To further complicate tree reconstruction there are technical problems such as long branch attraction (where fast evolving sequences cluster together even if they are unrelated) and horizontal gene transfer (where cells that can be unrelated exchange genes) that could mislead the phylogeny. At present there is no effective program that is sophisticated enough to correct these kinds of problems without careful manual examination. However, many of these steps are simple and repetitive. It is the goal of bioinformatics to automate as many of these simple tedious steps as possible, in order to allow large amounts of data to be processed quickly and accurately. In this paper a tool that streamlines the phylogenetic tree reconstruction process is presented. The tool, named AutoPhylo, identifies and retrieves sequences from NCBI (database collection) or a user-defined local database via BLAST searches. These sequences are then used to construct a tree that can be examined with a graphical user interface (GUI). The GUI allows the user to identify and remove unwanted sequences in order to refine the tree. The sequences are retrieved in groups that have one or more queries that limits the selection to specific species, genes or others valid NCBI queries. Some tests are applied to show that the program is useful and is able to accelerate subroutines of the process.

  • 273. Maas, Marc F.P.M.
    et al.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Debets, Alfons J.M.
    Hoekstra, Rolf. F.
    The mitochondrial plasmid pAL2-1 reduces calorie restriction mediated life span extension in the filamentous fungus Podospora anserina2004In: Fungal Genetics and Biology, Vol. 41, p. 865-871Article in journal (Refereed)
    Abstract [en]

    Calorie restriction is the only life span extending regimen known that applies to all aging organisms. Although most fungi do not appear to senesce, all natural isolates of the modular filamentous fungus Podospora anserina have a limited life span. In this paper, we show that calorie restriction extends life span also in Podospora anserina. The response to glucose limitation varies significantly among 23 natural isolates from a local population in The Netherlands, ranging from no effect up to a 5-fold life span extension. The isolate dependent effect is largely due to the presence or absence of pAL2-1 homologous plasmids. These mitochondrial plasmids are associated with reduced life span under calorie restricted conditions, suggesting a causal link. This has been substantiated using three combinations of isogenic isolates with and without plasmids. A model is proposed to explain how pAL2-1 homologues influence the response to calorie restriction.

  • 274. Martin, Gary
    et al.
    Puri, Raj
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Reyes-Garcia, Vicky
    Methods to Assess Ethnoecological Knowledge Acquistion, Distribution and Transmission: Species complexes and complex species2006In: Program of 10th International Congress of Ethnobiology, 2006Conference paper (Other (popular science, discussion, etc.))
    Abstract [en]

    We would like to take on the Thursday afternoon workshop on acquisition and transmission of knowledge. We will present methods of data gathering and analysis used by ethnoecologists, based on courses that we have given in various institutions and field projects around the world. We plan to select confirmed participants in the ICE as speakers/presenters, so we cannot give a list of speakers until we know who is coming. We expect to invite people like Viki Reyes Garcia, Tony Cunningham and others.

  • 275.
    Mati, Evan
    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.
    Ethnobotany and Trade of Medicinal Plants in the Qaysari Market, Erbil, Kurdish Autonomous Region, Iraq2010Independent thesis Advanced level (degree of Master (Two Years)), 10 credits / 15 HE creditsStudent thesis
  • 276.
    Mati, Evan
    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.
    Natural Dyeing Plants in Kurdistan, Iraq2009Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 277. Mati, Evan
    et al.
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Contemporary Knowledge of Dye Plant Species and Natural Dye Use in Kurdish Autonomous Region, Iraq2010In: Economic Botany, ISSN 0013-0001, E-ISSN 1874-9364, Vol. 64, no 2, p. 137-148Article in journal (Refereed)
    Abstract [en]

    Contemporary knowledge of dye plant species and natural dye use in Kurdish Autonomous Region, Iraq In Kurdistan, natural dyes once played an important role in the life of nomads as they wild-crafted and traded natural dyes for their survival. They learned from their family how to find, harvest, process, and dye with natural dyes. Abandonment of weaving and the nomadic life, and recent changes in the economy have contributed to significant changes in the natural dyeing culture. Traditional knowledge of natural dyeing plants is no longer common among weavers. This study documents the surviving knowledge of dye plant species and assesses the transmission of knowledge between elderly weavers and a younger generation of weavers' apprentices. Information on dyeing and dyeing plants was elicited through a species recognition task using picture cards, a pile-sorting task, and through in-depth interviews with nomads in the mountains of the Soran district as well as weaving teachers and students in the city of Erbil, Kurdish Autonomous Region, Iraq. Consensus analysis of pile-sorting data supports the hypothesis that informants belong to a single culture. The results confirm the erosion of natural dyeing culture in Kurdistan and stress the need to stimulate knowledge transfer from the elderly, empirical generation to the younger, learning generation. The study also uncovered the existence of a keen interest among the student informants in traditional herbal medicine. If this trend is true for Kurdish urban youth in general, then it could lead to a revival and perpetuation of traditional plant knowledge.

  • 278.
    Mati, Evan
    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 and trade of medicinal plants in the Qaysari Market, Kurdish Autonomous Region, Iraq2011In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 133, no 2, p. 490-510Article in journal (Refereed)
    Abstract [en]

    Aim of study: Marketplaces epitomize a region's culture and trade, and can give a rapid insight into traditions and salience of commercialized medicinal products. The Qaysari bazaar, bordering the citadel in Erbil city in the Kurdistan Autonomous Region, Iraq, has 21 herbalist shops trading natural medicinal products, wild-crafted and cultivated from all over the Middle East and Asia Minor. Materials and methods: Freelist surveys were conducted with 18 of these herbalists to determine diversity and salience of traded traditional medicinal plants. Interviews were conducted to document use, trade volume, origin, stock and value of the reported species. Plant species were identified using a combination of morphological identification and molecular barcoding using the ITS region. Results: Vouchers were collected for a total of 158 samples, corresponding to 82 species of plants, 5 animal products, 8 types of stones, minerals or chemicals, as well as 16 mixtures of plant products. Consensus Analysis of the herbalist interviews shows strong support for a single culture of herbalist plant use. Conclusions: Most reported plant species are known to have been used since antiquity, and uses are identical or similar to previously documented uses. Herbalists report a steady year-on-year increase in trade due to the economic stability in recent times. A majority (64%) of medicinal plants is imported from outside Iraq, and the data shows that imported plants trade at a higher price than locally-sourced species, and that these species are stocked in higher volumes by the herbalists to ensure a steady supply to consumers. A strong tradition of herbal medicine exists in Kurdistan today exemplified by the diverse and vigorous trade in medicinal plants commercialized from the provinces around Erbil to countries as far away as India, Spain and Libya.

  • 279.
    Mati, Evan
    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 and trade of medicinal plants in the Qaysari Market, Kurdish Autonomous Region, Iraq.2011In: Journal of Ethnopharmacology, ISSN 0378-8741, E-ISSN 1872-7573, Vol. 133, no 2, p. 490-510Article in journal (Refereed)
    Abstract [en]

    Aim of study

    Marketplaces epitomize a region's culture and trade, and can give a rapid insight into traditions and salience of commercialized medicinal products. The Qaysari bazaar, bordering the citadel in Erbil city in the Kurdistan Autonomous Region, Iraq, has 21 herbalist shops trading natural medicinal products, wild-crafted and cultivated from all over the Middle East and Asia Minor.

    Materials and methods

    Freelist surveys were conducted with 18 of these herbalists to determine diversity and salience of traded traditional medicinal plants. Interviews were conducted to document use, trade volume, origin, stock and value of the reported species. Plant species were identified using a combination of morphological identification and molecular barcoding using the ITS region.

    Results

    Vouchers were collected for a total of 158 samples, corresponding to 82 species of plants, 5 animal products, 8 types of stones, minerals or chemicals, as well as 16 mixtures of plant products. Consensus Analysis of the herbalist interviews shows strong support for a single culture of herbalist plant use.

    Conclusions

    Most reported plant species are known to have been used since antiquity, and uses are identical or similar to previously documented uses. Herbalists report a steady year-on-year increase in trade due to the economic stability in recent times. A majority (64%) of medicinal plants is imported from outside Iraq, and the data shows that imported plants trade at a higher price than locally-sourced species, and that these species are stocked in higher volumes by the herbalists to ensure a steady supply to consumers. A strong tradition of herbal medicine exists in Kurdistan today exemplified by the diverse and vigorous trade in medicinal plants commercialized from the provinces around Erbil to countries as far away as India, Spain and Libya.

  • 280. Merckx, Vincent S. F. T.
    et al.
    Hendriks, Kasper P.
    Beentjes, Kevin K.
    Mennes, Constantijn B.
    Becking, Leontine E.
    Peijnenburg, Katja T. C. A.
    Afendy, Aqilah
    Arumugam, Nivaarani
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Biun, Alim
    Buang, Matsain M.
    Chen, Ping-Ping
    Chung, Arthur Y. C.
    Dow, Rory
    Feijen, Frida A. A.
    Feijen, Hans
    Soest, Cobi Feijen-van
    Geml, Jozsef
    Geurts, Rene
    Gravendeel, Barbara
    Hovenkamp, Peter
    Imbun, Paul
    Ipor, Isa
    Janssens, Steven B.
    Jocque, Merlijn
    Kappes, Heike
    Khoo, Eyen
    Koomen, Peter
    Lens, Frederic
    Majapun, Richard J.
    Morgado, Luis N.
    Neupane, Suman
    Nieser, Nico
    Pereira, Joan T.
    Rahman, Homathevi
    Sabran, Suzana
    Sawang, Anati
    Schwallier, Rachel M.
    Shim, Phyau-Soon
    Smit, Harry
    Sol, Nicolien
    Spait, Maipul
    Stech, Michael
    Stokvis, Frank
    Sugau, John B.
    Suleiman, Monica
    Sumail, Sukaibin
    Thomas, Daniel C.
    van Tol, Jan
    Tuh, Fred Y. Y.
    Yahya, Bakhtiar E.
    Nais, Jamili
    Repin, Rimi
    Lakim, Maklarin
    Schilthuizen, Menno
    Evolution of endemismon a young tropical mountain2015In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 524, no 7565, p. 347-+Article in journal (Refereed)
    Abstract [en]

    Tropical mountains are hot spots of biodiversity and endemism(1-3), but the evolutionary origins of their unique biotas are poorly understood(4). In varying degrees, local and regional extinction, long-distance colonization, and local recruitment may all contribute to the exceptional character of these communities(5). Also, it is debated whether mountain endemics mostly originate from local lowland taxa, or from lineages that reach the mountain by long-range dispersal from cool localities elsewhere(6). Here we investigate the evolutionary routes to endemism by sampling an entire tropical mountain biota on the 4,095-metre-high Mount Kinabalu in Sabah, East Malaysia. We discover that most of its unique biodiversity is younger than the mountain itself (6 million years), and comprises a mix of immigrant pre-adapted lineages and descendants from local lowland ancestors, although substantial shifts from lower to higher vegetation zones in this latter group were rare. These insights could improve forecasts of the likelihood of extinction and 'evolutionary rescue'(7) in montane biodiversity hot spots under climate change scenarios.

  • 281.
    Meunier, Cécile
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Université de Montpellier.
    Les mécanismes de l'évolution2015In: BCPST 2eme année- Biologie / [ed] J. Segarra, Ellipses, Paris, France: Ellipses , 2015, 1, p. 580-677Chapter in book (Other (popular science, discussion, etc.))
  • 282.
    Meunier, Cécile
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hosseini, Sara
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Heidari, Nahid
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Maryush, Zaywa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Multilevel Selection in the Filamentous Ascomycete Neurospora tetrasperma2018In: American Naturalist, ISSN 0003-0147, E-ISSN 1537-5323, Vol. 191, no 3, p. 290-305Article in journal (Refereed)
    Abstract [en]

    The history of life has been driven by evolutionary transitions in individuality, that is, the aggregation of autonomous individuals to form a new, higher-level individual. The fungus Neurospora tetrasperma has recently undergone an evolutionary transition in individuality from homokaryosis (one single type of nuclei in the same cytoplasm) to heterokaryosis (two genetically divergent and free-ranging nuclear types). In this species, selection can act at different levels: while nuclei can compete in their replication and transmission into short-lived asexual spores, at the level of the heterokaryotic individual, cooperation between nuclear types is required to produce the long-lived sexual spores. Conflicts can arise between these two levels of selection if the coevolution between nuclear types is disrupted. Here, we investigated the extent of multilevel selection in three strains of N. tetrasperma. We assessed the ratio between nuclear types under different conditions and measured fitness traits of homo- and heterokaryotic mycelia with varying nuclear ratios. We show that the two nuclei have complementary traits, consistent with division of labor and cooperation. In one strain, for which a recent chromosomal introgression was detected, we observed the occurrence of selfish nuclei, enjoying better replication and transmission than sister nuclei at the same time as being detrimental to the heterokaryon. We hypothesize that introgression has disrupted the coevolution between nuclear types in this strain.

  • 283.
    Mirmajlessi, S. M.
    et al.
    Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Field Crops & Grassland Husb, EE-51014 Tartu, Estonia;Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Plant Protect, EE-51014 Tartu, Estonia.
    Bahram, Mohammad
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Univ Tartu, Inst Ecol & Earth Sci, Dept Bot, EE-51005 Tartu, Estonia.
    Mänd, M.
    Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Plant Protect, EE-51014 Tartu, Estonia.
    Najdabbasi, N.
    Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Plant Protect, EE-51014 Tartu, Estonia.
    Mansouripour, S.
    North Dakota State Univ, Dept Plant Pathol, Fargo, ND 58102 USA.
    Loit, E.
    Estonian Univ Life Sci, Inst Agr & Environm Sci, Dept Field Crops & Grassland Husb, EE-51014 Tartu, Estonia.
    Survey of Soil Fungal Communities in Strawberry Fields by Illumina Amplicon Sequencing2018In: Eurasian Soil Science, ISSN 1064-2293, E-ISSN 1556-195X, Vol. 51, no 6, p. 682-691Article in journal (Refereed)
    Abstract [en]

    Soil fungal pathogens are the most common cause of diseases in commercial strawberry crops worldwide. Since simultaneous infections by different pathogens can severely damage the crop, understanding the associated fungal communities can be helpful to mitigate crop loss. Herein, we used Illumina metabarcoding to assess the structure of fungal communities in five strawberry production areas in Estonia. Our analysis revealed 990 to 1430 operational taxonomic units (OTUs) per soil sample (pools of eight soil samples per production area). Based on our analyses, Ascomycota (55.5%) and Basidiomycota (25.0%) were the most OTUs-rich. Amongst the 24 most abundant OTUs, Geomyces, Rhodotorula, Verticillium and Microdochium were the most abundant genera, which were found across nearly all the soil samples. The OTUs were also clustered into three distinct groups, corresponding to different functional guilds of fungi. In addition, Fusarium solani, V. dahliae, Rhizoctonia solani and Colletotrichum truncatum were enormously abundant in the fields with disease symptoms, whereas arbuscular mycorrhizal fungi especially Rhizophagus irregularis were considerably more abundant in the fields with healthy plants. These findings provide support that mycorrhizal fungi may play an important role in suppressing pathogens. Our study for the first time shows the usefulness of Illumina technology in surveying the communities of soil fungi in strawberry fields effectively, which may improve available disease management strategies against strawberry diseases.

  • 284.
    Molin, Ylva
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
    Lindeborg, Mats
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Nyström, Fredrik
    Madder, Maxime
    Hjelm, Eva
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Bacteriology.
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Jaenson, Thomas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ehrenborg, Christian
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Migratory birds, ticks and Bartonella2011In: Infection Ecology & Epidemiology, ISSN 2000-8686, Vol. 1, p. 5997-Article in journal (Refereed)
    Abstract [en]

    Bartonella spp. infections are considered to be vector-borne zoonoses; ticks are suspected vectors of bartonellae. Migratory birds can disperse ticks infected with zoonotic pathogens such as Rickettsia and tick-borne encephalitis virus and possibly also Bartonella. Thus, in the present study 386 tick specimens collected in spring 2009 from migratory birds on the Mediterranean islands Capri and Antikythera were screened for Bartonella spp. RNA. One or more ticks were found on 2.7% of the birds. Most ticks were Hyalomma rufipes nymphs and larvae with mean infestation rates of 1.7 nymphs and 0.6 larvae per infested bird. Bartonella spp. RNA was not detected in any of the tick specimens.

  • 285.
    Montesinos-Tubee, Daniel B.
    et al.
    Natl Herbarium Netherlands, Nat Biodivers Ctr, Bot Sect, Herbarium Vadense Darwinweg 2, NL-2333 CR Leiden, Netherlands.;Inst Cient Michael Owen Dillon, Av Jorge Chavez 610, Cercado, Arequipa, Peru.;Univ Nacl San Agustin Arequipa, Inst Ciencia & Gest Ambiental, Calle San Agustin 108, Arequipa, Peru..
    Cano, Asuncion
    Univ Nacl Mayor San Marcos, Museo Hist Nat, Dept Dicotiledoneas, Lab Florist, Lima, Peru.;Univ Nacl Mayor San Marcos, Fac Ciencias Biol, Inst Ciencias Biol Antonio Raimondi, Lima, Peru..
    Garcia-Llatas, Luis F.
    Univ Nacl Pedro Ruiz Gallo, Dept Bot, Lambayeque, Peru.;Inst Estudiantil Invest Biodivers Maximilian Weig, Lambayeque, Peru..
    Ju, Yingzi
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kool, Anneleen
    Univ Oslo, Nat Hist Museum, POB 1172, N-0318 Oslo, Norway..
    Paronychia sanchez-vegae (Caryophyllaceae), a new woody species of Paronychia from North Peru2018In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 334, no 1, p. 41-48Article in journal (Refereed)
    Abstract [en]

    As part of botanical expeditions in the Amazonas region of North Peru, we found plants from the Central Andes (North Peru). Based on morphology and molecular data, the Peruvian population was described and illustrated here as a new species for Science, named Paronychia sanchez-vegae. The new species is compared with its most likely closest relative, P. andina from which differs by the larger size, its woody ramified stems, the glabrous leaf surface, shorter leaf size, shorter flowers and larger size of the ovary.

  • 286.
    Morris, Jake
    et al.
    UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England.
    Darolti, Iulia
    UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England.
    Bloch, Natasha I.
    UCL, Dept Genet Evolut & Environm, London WC1E 6BT, England.
    Wright, Alison E.
    Univ Sheffield, Dept Anim & Plant Sci, Sheffield S10 2TN, S Yorkshire, 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.
    Shared and Species-Specific Patterns of Nascent Y Chromosome Evolution in Two Guppy Species2018In: Genes, ISSN 2073-4425, E-ISSN 2073-4425, Vol. 9, no 5, article id 238Article in journal (Refereed)
    Abstract [en]

    Sex chromosomes form once recombination is halted around the sex-determining locus between a homologous pair of chromosomes, resulting in a male-limited Y chromosome. We recently characterized the nascent sex chromosome system in the Trinidadian guppy (Poecilia reticulata). The guppy Y is one of the youngest animal sex chromosomes yet identified, and therefore offers a unique window into the early evolutionary forces shaping sex chromosome formation, particularly the rate of accumulation of repetitive elements and Y-specific sequence. We used comparisons between male and female genomes in P. reticulata and its sister species, Endler's guppy (P. wingei), which share an ancestral sex chromosome, to identify male-specific sequences and to characterize the degree of differentiation between the X and Y chromosomes. We identified male-specific sequence shared between P. reticulata and P. wingei consistent with a small ancestral non-recombining region. Our assembly of this Y-specific sequence shows substantial homology to the X chromosome, and appears to be significantly enriched for genes implicated in pigmentation. We also found two plausible candidates that may be involved in sex determination. Furthermore, we found that the P. wingei Y chromosome exhibits a greater signature of repetitive element accumulation than the P. reticulata Y chromosome. This suggests that Y chromosome divergence does not necessarily correlate with the time since recombination suppression. Overall, our results reveal the early stages of Y chromosome divergence in the guppy.

  • 287.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Aristotle’s Ladder, Darwin’s Tree: The Evolution of Visual Metaphors for Biological Order. — By J. David Archibald2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 5, p. 892-895Article, book review (Other academic)
  • 288.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Biology of Evolution and Systematics: Cohesive, Concise, yet Comprehensive Introduction for Students and Professionals2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 177-178Article, book review (Other academic)
  • 289.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Biology of Evolution and Systematics: Cohesive, Concise, yet Comprehensive Introduction for Students and Professionals. By Paul Sanghera2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 1, p. 177-178Article, book review (Other academic)
  • 290.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Genealogies: Pedigrees and Phylogenies are Reticulating Networks Not Just Divergent Trees2016In: Evolutionary biology, ISSN 0071-3260, E-ISSN 1934-2845, Vol. 43, no 4, p. 456-473Article in journal (Refereed)
    Abstract [en]

    Pedigrees illustrate the genealogical relationships among individuals, and phylogenies do the same for groups of organisms (such as species, genera, etc.). Here, I provide a brief survey of current concepts and methods for calculating and displaying genealogical relationships. These relationships have long been recognized to be reticulating, rather than strictly divergent, and so both pedigrees and phylogenies are correctly treated as networks rather than trees. However, currently most pedigrees are instead presented as “family trees”, and most phylogenies are presented as phylogenetic trees. Nevertheless, the historical development of concepts shows that networks pre-dated trees in most fields of biology, including the study of pedigrees, biology theory, and biology practice, as well as in historical linguistics in the social sciences. Trees were actually introduced in order to provide a simpler conceptual model for historical relationships, since trees are a specific type of simple network. Computationally, trees and networks are a part of graph theory, consisting of nodes connected by edges. In this mathematical context they differ solely in the absence or presence of reticulation nodes, respectively. There are two types of graphs that can be called phylogenetic networks: (1) rooted evolutionary networks, and (2) unrooted affinity networks. There are quite a few computational methods for unrooted networks, which have two main roles in phylogenetics: (a) they act as a generic form of multivariate data display; and (b) they are used specifically to represent haplotype networks. Evolutionary networks are more difficult to infer and analyse, as there is no mathematical algorithm for reconstructing unique historical events. There is thus currently no coherent analytical framework for computing such networks.

  • 291.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Is Sequence Alignment an Art or a Science?2015In: Systematic Botany, ISSN 0363-6445, E-ISSN 1548-2324, Vol. 40, no 1, p. 14-26Article in journal (Refereed)
    Abstract [en]

    Aligning multiple nucleotide sequences is a prerequisite for many if not most comparative sequence analyses in evolutionary biology. These alignments are often recognized as representing the homology relations of the aligned nucleotides, but this is a necessary requirement only for phylogenetic analyses. Unfortunately, existing computer programs for sequence alignment are not based explicitly on detecting the homology of nucleotides, and so there is a notable gap in the existing bioinformatics repertoire. If homology is the goal, then current alignment procedures may be more art than science. To resolve this issue, I present a simple conceptual scheme relating the traditional criteria for homology to the features of nucleotide sequences. These relations can then be used as optimization criteria for nucleotide sequence alignments. I point out the way in which current computer programs for multiple sequence alignment relate to these criteria, noting that each of them usually implements only one criterion. This explains the apparent dissatisfaction with computerized sequence alignment in phylogenetics, as any program that truly tried to produce alignments based on homology would need to simultaneously optimize all of the criteria.

  • 292.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Multiple Sequence Alignment Methods — Edited by David J. Russell2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 4, p. 690-692Article, book review (Other academic)
  • 293.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Next Generation Systematics2017In: Systematic Biology, ISSN 1063-5157, EISSN 1076-836X, Vol. 66, no 1, p. 121-123Article, book review (Other academic)
  • 294.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pattern recognition in phylogenetics: trees and networks2016In: Pattern Recognition in Computational Molecular Biology: Techniques and Approaches / [ed] Mourad Elloumi, Costas S. Iliopoulos, Jason T. L. Wang, Albert Y. Zomaya, John Wiley & Sons, 2016, 1, p. 419-438Chapter in book (Refereed)
  • 295.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Phylogenetic analysis of pathogens2017In: Genetics and Evolution of Infectious Diseases / [ed] Michel Tibayrenc, Amsterdam: Elsevier, 2017, 2, p. 167-193Chapter in book (Refereed)
  • 296.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, Uppsala, Sweden.
    Phylogenetic networks: a new form of multivariate data summary for data mining and exploratory data analysis2014In: Wiley Interdisciplinary Reviews: Data Mining and Knowledge Discovery, ISSN 1942-4795, Vol. 4, no 4, p. 296-312Article in journal (Refereed)
    Abstract [en]

    Exploratory data analysis (EDA) involving both graphical displays and numerical summaries of data, is intended to evaluate the characteristics of the data as well as providing a form of data mining. For multivariate data, the best-known visual summaries include discriminant analysis, ordination, and clustering, particularly metric ordinations such as principal components analysis. However, these techniques have limiting mathematical assumptions that are not always realistic. Recently, network techniques have been developed in the biological field of phylogenetics that address some of these limitations. They are now widely used in biology under the name phylogenetic networks, but they are actually of general applicability to any multivariate dataset. Phylogenetic networks are fast and relatively easy to calculate, which makes them ideal as a tool for EDA. This review provides an overview of the field, with particular reference to the use of what are called splits graphs. There are several types of splits graph, which summarize the multivariate data in different ways. Example analyses are presented based on the neighbor-net graph, which seems to be the most generally useful of the available algorithms. This should encourage the more widespread use of these networks whenever a summary of a multivariate dataset is required.For further resources related to this article, please visit the WIREs website.Conflict of interest: The author has declared no conflicts of interest for this article.

  • 297.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Taxonomy of Australian Mammals. By Stephen Jackson and Colin Groves2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 2, p. 346-348Article, book review (Other academic)
  • 298.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Biology and Identification of the Coccidia (Apicomplexa) of Marsupials of the World. Donald W. Duszynski.2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 4, p. 722-724Article, book review (Other academic)
  • 299.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Book of Trees: Visualizing Branches of Knowledge — By Manuel Lima. Design for Information: an Introduction to the Histories, Theories, and Best Practices Behind Effective Information Visualizations. — By Isabel Meirelles.2015In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 64, no 3, p. 363-365Article, book review (Other academic)
  • 300.
    Morrison, David A.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Invention of Nature: The Adventures of Alexander von Humboldt, the Lost Hero of Science (UK). The Invention of Nature: Alexander von Humboldt’s New World (USA). By Andrea Wulf2016In: Systematic Biology, ISSN 1063-5157, E-ISSN 1076-836X, Vol. 65, no 6, p. 1117-1119Article, book review (Other academic)
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