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  • 201.
    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.
    Krüger, Åsa
    Rydberg, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Abbad, Abdelaziz
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Martin, Gary
    Molecular identification of commercialized medicinal plants in southern Morocco2012In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 7, no 6, p. e39459-Article in journal (Refereed)
    Abstract [en]

    Background: Medicinal plant trade is important for local livelihoods. However, many medicinal plants are difficult to identify when they are sold as roots, powders or bark. DNA barcoding involves using a short, agreed-upon region of a genome as a unique identifier for species-ideally, as a global standard. Research Question: What is the functionality, efficacy and accuracy of the use of barcoding for identifying root material, using medicinal plant roots sold by herbalists in Marrakech, Morocco, as a test dataset. Methodology: In total, 111 root samples were sequenced for four proposed barcode regions rpoC1, psbA-trnH, matK and ITS. Sequences were searched against a tailored reference database of Moroccan medicinal plants and their closest relatives using BLAST and Blastclust, and through inference of RAxML phylograms of the aligned market and reference samples. Principal Findings: Sequencing success was high for rpoC1, psbA-trnH, and ITS, but low for matK. Searches using rpoC1 alone resulted in a number of ambiguous identifications, indicating insufficient DNA variation for accurate species-level identification. Combining rpoC1, psbA-trnH and ITS allowed the majority of the market samples to be identified to genus level. For a minority of the market samples, the barcoding identification differed significantly from previous hypotheses based on the vernacular names. Conclusions/Significance: Endemic plant species are commercialized in Marrakech. Adulteration is common and this may indicate that the products are becoming locally endangered. Nevertheless the majority of the traded roots belong to species that are common and not known to be endangered. A significant conclusion from our results is that unknown samples are more difficult to identify than earlier suggested, especially if the reference sequences were obtained from different populations. A global barcoding database should therefore contain sequences from different populations of the same species to assure the reference sequences characterize the species throughout its distributional range.

  • 202.
    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.
    Rydberg, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Krüger, Åsa
    Stockholm University.
    Abbad, Abdelazziz
    Université Cadi Ayyad.
    Martin, Gary
    The Global Diversity Foundation.
    Plant trade in Southern Morocco: Market Ethnobotany and Molecular Barcoding2010In: XIXth AETFAT Congress, Madagascar, 25-30 April 2010: abstracts, 2010Conference paper (Other academic)
  • 203.
    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.
    Rydberg, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Krüger, Åsa
    Stockholm University.
    Abderrahim, Ouarghidi
    Université Cadi Ayyad.
    Martin, Gary
    The Global Diversity Foundation.
    Marknadernas etnobotanik och DNA streckkodning i Marrakech, Marocko2010Conference paper (Other academic)
  • 204.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Oxelman, Bengt
    Göteborgs Universitet.
    Thulin, Mats
    The origin of the medicinal plant Withania somnifera and the phylogeny and biogeography of Withania (Solanaceae).2004Conference paper (Other academic)
  • 205.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Perrigo, Allison L.
    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.
    Phylogeny and biogeography of Sphaerocoma (Caryophyllaceae)2010In: XIXth AETFAT Congress, Madagascar, 25-30 April 2010: abstracts, 2010Conference paper (Other academic)
  • 206.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Perrigo, Allison
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bristly versus juicy: Phylogenetic position and taxonomy of Sphaerocoma (Caryophyllaceae)2012In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 61, no 1, p. 67-75Article in journal (Refereed)
    Abstract [en]

    The phylogenetic position of the Afro-Asian genus Sphaerocoma is investigated using DNA sequences from plastid rps16 and ndhF, as well as from nuclear ITS and RPB2. Seven accessions of Sphaerocoma, representing all three currently recognized taxa, are analyzed along with sequences from genera that have been found to be closely related to Sphaerocoma in broader studies of Caryophyllaceae. The Afro-Arabian Pollichia is indicated as sister to Sphaerocoma, and this Sphaerocoma-Pollichia clade is sister to a clade with Macaronesian Polycarpaea and the widely distributed Polycarpon prostratum. A close relationship between the anemochorous Sphaerocoma and the endozoochorous Pollichia has never previously been suggested, but some similarities in, e.g., floral characters are pointed out. Sphaerocoma is strongly supported as monophyletic, but no significant molecular variation within the genus could be detected. A new taxonomy of Sphaerocoma is proposed, where a single species with two geographically and morphologically defined subspecies are recognized: S. hookeri subsp. hookeri in coastal areas along the Red Sea in Egypt, Sudan and Saudi-Arabia, near Aden in Yemen, and in Somalia, and S. hookeri subsp. aucheri comb. & stat. nov. in coastal areas in south-eastern Yemen, Oman, United Arab Emirates, Bahrain, Iran, and Pakistan. A lectotype is designated for S. hookeri.

  • 207.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Perrigo, Allison
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Tough, tiny and terrific Caryophyllaceae, their phylogeny and biogeography2011Conference paper (Other academic)
  • 208. Kool, Anneleen
    et al.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    (2178) Proposal to reject the name Psammanthe (Caryophyllaceae)2013In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 62, no 4, p. 833-833Article in journal (Other academic)
  • 209.
    Kool, Anneleen
    et al.
    Univ Oslo, Nat Hist Museum, POB 1172 Blindern, N-0218 Oslo, Norway..
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A giant spurrey on a tiny island: On the phylogenetic position of Sanctambrosia manicata (Caryophyllaceae) and the generic circumscriptions of Spergula, Spergularia and Rhodalsine2017In: Taxon, ISSN 0040-0262, E-ISSN 1996-8175, Vol. 66, no 3, p. 615-622Article in journal (Refereed)
    Abstract [en]

    The only member of the generally herbaceous family Caryophyllaceae that may grow to a small tree is Sanctambrosia manicata, endemic to remote San Ambrosio Island, off the coast of Chile. The monospecific Sanctambrosia has been suggested to be closely related to Spergula and Spergularia (spurreys) on the basis of morphology, despite its treelike habit and gynodioecy. A plastid DNA dataset (ndhF, rps16, trnL-F) is used to investigate the relationships of Sanctambrosia and other members of Sperguleae. Sanctambrosia manicata is shown to be nested in a clade of New World and Australian Spergularia and the new combination Spergularia manicata is proposed. The volcanic San Ambrosio has been estimated to be almost three million years old, and S. manicata presumably evolved its treelike habit and gynodioecy over a short period of time. Spergula and Spergularia are monophyletic and recognizable by their number of carpels, five in Spergula and three in Spergularia. Spergularia fallax, which resembles Spergula in leaf characters, is shown to be sister to all other species of Spergularia. Minuartia subg. Rhodalsine belongs in Sperguleae and is sister to Spergula and Spergularia together, which supports the recent resurrection of Rhodalsine at the generic level.

  • 210.
    Kool, Anneleen
    et al.
    Univ Oslo, Nat Hist Museum.
    Thulin, Mats
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A plant that Linnaeus forgot: taxonomic revision of Rhodalsine (Caryophyllaceae)2017In: Willdenowia, ISSN 0511-9618, E-ISSN 1868-6397, Vol. 47, no 3, p. 317-323Article in journal (Refereed)
    Abstract [en]

    The mainly Mediterranean genus Rhodalsine (Caryophyllaceae) is revised and a single species, R. geniculata, is recognized, distributed from the Canary Islands in the west to Somalia in the east. The history of the taxon, which was known already during the 17th century but entirely overlooked by Linnaeus, is outlined. Variation and taxonomy are discussed and illustrations and a distribution map are provided. Many names are placed in synonymy and most of the names are typified, including six lectotypes designated here.

  • 211.
    Kool, Anneleen
    et al.
    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.
    Rapid diversification of Polycarpaea (Caryophyllaceae) in the Horn of Africa region.2007Conference paper (Other academic)
  • 212.
    Kool, Anneleen
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thulin, Mats
    Sanctambrosia manicata (Caryophyllaceae), a giant spurrey on a tiny islandManuscript (preprint) (Other academic)
  • 213.
    Kool, Anneleen
    et al.
    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.
    The Horn of Africa and the recent history of a group of small Caryophyllaceae2006Conference paper (Other academic)
  • 214.
    Korall, Petra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Pryer, Kathleen
    Duke University, Durham, NC, USA.
    Global biogeography of scaly tree ferns (Cyatheaceae): evidence for Gondwanan vicariance and limited transoceanic dispersal2014In: Journal of Biogeography, ISSN 0305-0270, E-ISSN 1365-2699, Vol. 41, no 2, p. 402-413Article in journal (Refereed)
    Abstract [en]

    Aim

    Scaly tree ferns, Cyatheaceae, are a well-supported group of mostly tree-forming ferns found throughout the tropics, the subtropics and the south-temperate zone. Fossil evidence shows that the lineage originated in the Late Jurassic period. We reconstructed large-scale historical biogeographical patterns of Cyatheaceae and tested the hypothesis that some of the observed distribution patterns are in fact compatible, in time and space, with a vicariance scenario related to the break-up of Gondwana.

    Location

    Tropics, subtropics and south-temperate areas of the world.

    Methods

    The historical biogeography of Cyatheaceae was analysed in a maximum likelihood framework using Lagrange. The 78 ingroup taxa are representative of the geographical distribution of the entire family. The phylogenies that served as a basis for the analyses were obtained by Bayesian inference analyses of mainly previously published DNA sequence data using MrBayes. Lineage divergence dates were estimated in a Bayesian Markov chain Monte Carlo framework using beast.

    Results

    Cyatheaceae originated in the Late Jurassic in either South America or Australasia. Following a range expansion, the ancestral distribution of the marginate-scaled clade included both these areas, whereas Sphaeropteris is reconstructed as having its origin only in Australasia. Within the marginate-scaled clade, reconstructions of early divergences are hampered by the unresolved relationships among the Alsophila, Cyathea and Gymnosphaera lineages. Nevertheless, it is clear that the occurrence of the Cyathea and Sphaeropteris lineages in South America may be related to vicariance, whereas transoceanic dispersal needs to be inferred for the range shifts seen in Alsophila and Gymnosphaera.

    Main conclusions

    The evolutionary history of Cyatheaceae involves both Gondwanan vicariance scenarios as well as long-distance dispersal events. The number of transoceanic dispersals reconstructed for the family is rather few when compared with other fern lineages. We suggest that a causal relationship between reproductive mode (outcrossing) and dispersal limitations is the most plausible explanation for the pattern observed.

  • 215.
    Korall, Petra
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Schuettpelz, Eric
    Pryer, Kathleen M.
    Abrupt deceleration of molecular evolution linked to the origin of arborescence in ferns2010In: Evolution, ISSN 0014-3820, E-ISSN 1558-5646, Vol. 64, no 9, p. 2786-2792Article in journal (Refereed)
    Abstract [en]

    Molecular rate heterogeneity, whereby rates of molecular evolution vary among groups of organisms, is a well-documented phenomenon. Nonetheless, its causes are poorly understood. For animals, generation time is frequently cited because longer-lived species tend to have slower rates of molecular evolution than their shorter-lived counterparts. Although a similar pattern has been uncovered in flowering plants, using proxies such as growth form, the underlying process has remained elusive. Here, we find a deceleration of molecular evolutionary rate to be coupled with the origin of arborescence in ferns. Phylogenetic branch lengths within the "tree fern" clade are considerably shorter than those of closely related lineages, and our analyses demonstrate that this is due to a significant difference in molecular evolutionary rate. Reconstructions reveal that an abrupt rate deceleration coincided with the evolution of the long-lived tree-like habit at the base of the tree fern clade. This suggests that a generation time effect may well be ubiquitous across the green tree of life, and that the search for a responsible mechanism must focus on characteristics shared by all vascular plants. Discriminating among the possibilities will require contributions from various biological disciplines, but will be necessary for a full appreciation of molecular evolution.

  • 216.
    Kreziou, Anna
    et al.
    Argonafton 30, Thessaloniki, Greece.; Univ Oslo, Nat Hist Museum, N-0316 Oslo, Norway.
    de Boer, Hugo
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Nat Biodivers Ctr, Leiden, Netherlands..
    Gravendeel, Barbara
    Nat Biodivers Ctr, Leiden, Netherlands.;Univ Appl Sci Leiden, Leiden, Netherlands..
    Harvesting of salep orchids in north-western Greece continues to threaten natural populations2016In: Oryx, ISSN 0030-6053, E-ISSN 1365-3008, Vol. 50, no 3, p. 393-396Article in journal (Refereed)
    Abstract [en]

    In several eastern Mediterranean countries orchids are collected from the wild for the production of salep, a beverage made of dried orchid tubers. The drivers of this collection and trade have changed over time. We investigated which genera and species are harvested for salep production, whether any cultivation takes place, the chain of commercialization, and the economic value of tuber collection. Fieldwork and interviews in north-western Greece included 25 collectors and street vendors, the owners of two companies, and one herbal shop. The results show that several orchid species are traded for the production of salep, and none are cultivated. Tubers collected in Greece, Albania and Turkey are sold in northern Greece for EUR 55-150 per kg on average. Recent catalysts such as the increasing demand for traditional, organic and alternative foodstuffs, and the 2009 economic downturn, have led to a revival of salep consumption, with an increasing number of salep harvesters from Greece and Albania scouring the mountains for harvestable tubers, using unsustainable harvesting practices.

  • 217.
    Kronholm, Ilkka
    et al.
    Univ Jyvaskyla, Dept Biol & Environm Sci, Ctr Excellence Biol Interact, POB 35, FI-40014 Jyvaskyla, Finland..
    Johannesson, Hanna
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ketola, Tarmo
    Univ Jyvaskyla, Dept Biol & Environm Sci, Ctr Excellence Biol Interact, POB 35, FI-40014 Jyvaskyla, Finland..
    Epigenetic Control of Phenotypic Plasticity in the Filamentous Fungus Neurospora crassa2016In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 6, no 12, p. 4009-4022Article in journal (Refereed)
    Abstract [en]

    Phenotypic plasticity is the ability of a genotype to produce different phenotypes under different environmental or developmental conditions. Phenotypic plasticity is a ubiquitous feature of living organisms, and is typically based on variable patterns of gene expression. However, the mechanisms by which gene expression is influenced and regulated during plastic responses are poorly understood in most organisms. While modifications to DNA and histone proteins have been implicated as likely candidates for generating and regulating phenotypic plasticity, specific details of each modification and its mode of operation have remained largely unknown. In this study, we investigated how epigenetic mechanisms affect phenotypic plasticity in the filamentous fungus Neurospora crassa. By measuring reaction norms of strains that are deficient in one of several key physiological processes, we show that epigenetic mechanisms play a role in homeostasis and phenotypic plasticity of the fungus across a range of controlled environments. In general, effects on plasticity are specific to an environment and mechanism, indicating that epigenetic regulation is context dependent and is not governed by general plasticity genes. Specifically, we found that, in Neurospora, histone methylation at H3K36 affected plastic response to high temperatures, H3K4 methylation affected plastic response to pH, but H3K27 methylation had no effect. Similarly, DNA methylation had only a small effect in response to sucrose. Histone deacetylation mainly decreased reaction norm elevation, as did genes involved in histone demethylation and acetylation. In contrast, the RNA interference pathway was involved in plastic responses to multiple environments.

  • 218.
    Kruger, Åsa
    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.
    DNA-Barcoding Identification of Medicinal Roots from Morocco2008Independent thesis Advanced level (degree of Master (Two Years)), 20 credits / 30 HE creditsStudent thesis
  • 219.
    Kruys, Åsa
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    New species of Preussia with 8-celled ascospores (Sporormiaceae, Pleosporales, Ascomycota)2015In: Phytotaxa, ISSN 1179-3155, E-ISSN 1179-3163, Vol. 234, no 2, p. 143-150Article in journal (Refereed)
    Abstract [en]

    The focus of this study is on Preussia sensu lato species with 8-celled ascospores. Two new species, P. alpina and P. octocylindrospora are introduced based on morphological characters and discussed in relation to similar species in the genus. New records are provided from Sporormiella corynespora, S. octomegaspora, P. octomera and P. octonalis. This greatly expands or reduces their geographical distribution ranges, as well as substrate preferences. In addition, a key to the coprophilous species with 8-celled ascospores is provided.

  • 220.
    Kruys, Åsa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Castlebury, Lisa
    USDA ARS Systematic Mycology and Microbiology Lab.
    Molecular phylogeny of Sydowiellaceae: resolving the position of Cainiella2012In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 104, no 2, p. 419-426Article in journal (Refereed)
    Abstract [en]

    Cainiella is an ascomycete genus associated with arctic alpine plants. The systematic position of Cainiella has long been unclear, with current classifications placing the genus in either Sordariales or Xylariales. Our molecular results, based on mtSSU, ITS and nLSU rDNA data, clearly show that the genus belongs in the Sydowiellaceae (Diaporthales). The study also includes new sequences of Sydowiellaceae and contributes to a better knowledge of the phylogenetic relationships of that family.

  • 221.
    Kruys, Åsa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Eriksson, Ove E.
    Umeå University.
    Sporsäckssvampar: svampworkshop med fokus på de allra minsta2010In: Fauna och flora : populär tidskrift för biologi, ISSN 0014-8903, Vol. 105, no 3, p. 18-19Article in journal (Other (popular science, discussion, etc.))
  • 222.
    Kruys, Åsa
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Huhndorf, Sabine M
    Miller, Andrew N
    Coprophilous contributions to the phylogeny of Lasiosphaeriaceae and allied taxa within Sordariales (Ascomycota, Fungi)2015In: Fungal diversity, ISSN 1560-2745, E-ISSN 1878-9129, Vol. 10, no 1, p. 101-113Article in journal (Refereed)
    Abstract [en]

    The phylogenetic relationships of Lasiosphaeriaceae are complicated in that the family is paraphyletic and includes Sordariaceae and Chaetomiaceae, as well as several polyphyletic genera. This study focuses on the phylogenetic relationships of the coprophilous genera, Anopodium, Apodospora, Arnium, Fimetariella and Zygospermella. They are traditionally circumscribed based on ascospore characters, which have proven homoplasious in other genera within the family. Our results based on LSU nrDNA and ß–tubulin sequences distinguish four lineages ofLasiosphaeriaceae taxa. Anopodium joins the clade of morphologically similar, yellow-pigmented species of Cercophora and Lasiosphaeria. Apodospora is monophyletic and joins a larger group of taxa with unclear affinities to each other, while Arnium is polyphyletic being scattered throughout three of the four major clades of Lasiosphaeriaceae. Fimitariella is represented by a single collection and joins the clade containing Cercophora scortea and Podospora appendiculata. Zygospermellashows affinities to the Lasiosphaeris clade. Based on a combination of morphological and molecular data, Echria stat. nov. is recognized at the genus level for the former Arnium section and two new combinations are proposed: E. gigantospora and E. macrotheca.

  • 223.
    Labbé, Lisa Sandelin
    et al.
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine.
    Tolf, Conny
    Larsson, Sara
    Wilhelmsson, Peter
    Salaneck, Erik
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology.
    Jaenson, Thomas G. T.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Lindgren, Per-Eric
    Olsen, Björn
    Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Clinical Microbiology and Infectious Medicine. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Biochemistry and Microbiology. Uppsala University, Disciplinary Domain of Medicine and Pharmacy, Faculty of Medicine, Department of Medical Sciences, Infectious Diseases.
    Waldenstrom, Jonas
    Candidatus Neoehrlichia mikurensis in Ticks from Migrating Birds in Sweden2015In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 10, no 7, article id e0133250Article in journal (Refereed)
    Abstract [en]

    Candidatus Neoehrlichia mikurensis (CNM; family Anaplasmataceae) was recently recognized as a potential tick-borne human pathogen. The presence of CNM in mammals, in host-seeking Ixodes ticks and in ticks attached to mammals and birds has been reported recently. We investigated the presence of CNM in ornithophagous ticks from migrating birds. A total of 1,150 ticks (582 nymphs, 548 larvae, 18 undetermined ticks and two adult females) collected from 5,365 birds captured in south-eastern Sweden was screened for CNM by molecular methods. The birds represented 65 different species, of which 35 species were infested with one or more ticks. Based on a combination of morphological and molecular species identification, the majority of the ticks were identified as Ixodes ricinus. Samples were initially screened by real-time PCR targeting the CNM 16S rRNA gene, and confirmed by a second real-time PCR targeting the groEL gene. For positive samples, a 1260 base pair fragment of the 16S rRNA gene was sequenced. Based upon bacterial gene sequence identification, 2.1% (24/1150) of the analysed samples were CNM-positive. Twenty-two out of 24 CNM-positive ticks were molecularly identified as I. ricinus nymphs, and the remaining two were identified as I. ricinus based on morphology. The overall CNM prevalence in I. ricinus nymphs was 4.2%. None of the 548 tested larvae was positive. CNM-positive ticks were collected from 10 different bird species. The highest CNM-prevalences were recorded in nymphs collected from common redpoll (Carduelis flammea, 3/7), thrush nightingale (Luscinia luscinia, 2/29) and dunnock (Prunella modularis, 1/17). The 16S rRNA sequences obtained in this study were all identical to each other and to three previously reported European strains, two of which were obtained from humans. It is concluded that ornithophagous ticks may be infected with CNM and that birds most likely can disperse CNM-infected ticks over large geographical areas.

  • 224.
    Lamxay, Vichith
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The Genus Amomum (Zingiberaceae) in Cambodia, Laos and Vietnam: Taxonomy and Ethnobotany, with Special Emphasis on Women's Health2011Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    The species of Amomum Roxb. (Zingiberaceae) in Cambodia, Laos and Vietnam are revised. Thirty-five species and two varieties are recognised, all names are typified, and detailed descriptions and a key are provided. Nine new species are described and one species is validated. Whilst revising Amomum for the Flore du Cambodge, du Laos et du Viêtnam, we have proposed to conserve the name Amomum villosum Lour. with a recent collection from Laos, which was not included in the protologue, as its type. Our research on the use of Amomum focuses on the use of plants during pregnancy, parturition, postpartum recovery and infant healthcare among three ethnic groups, the Brou, Saek and Kry. The investigations aim to identify culturally important traditions that may facilitate implementation of culturally appropriate healthcare. Data were collected in Khammouane province, Lao PDR, through group and individual interviews with women by female interviewers. More than 55 plant species are used in women's healthcare, of which > 90 % are used in postpartum recovery. This wealth of novel insights into plant use and preparation will help to understand culturally important practices such as confinement, dietary restrictions, mother roasting and herbal steam baths and their incorporation into modern healthcare. Through chemical analyses of Amomum we have recorded compounds with antimicrobial, analgesic and sedative effects that point to an empirical development of the traditional treatments around childbirth. Essential oils of three species used in hotbed and mother roasting, Amomum villosum Lour. Amomum microcarpum C.F.Liang & D.Fang and Blumea balsamifera (L.) DC. were found to contain significant amounts of the following terpenes: b-pinene, camphor, bornylacetate, borneol, linalool, D-limonene, fenchone, terpinen-4-ol and a-terpinene.

  • 225.
    Lamxay, Vichith
    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.
    Traditions and plant use during pregnancy, childbirth and postpartum recovery by the Kry ethnic group in Lao PDR2011In: Journal of Ethnobiology and Ethnomedicine, ISSN 1746-4269, E-ISSN 1746-4269, Vol. 7, p. 14-Article in journal (Refereed)
    Abstract [en]

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

  • 226.
    Lamxay, Vichith
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Newman, M.F.
    A revision of Amomum (Zingiberaceae) in Cambodia, Laos and Vietnam2012In: Edinburgh journal of botany, ISSN 0960-4286, E-ISSN 1474-0036, Vol. 69, no 1, p. 99-206Article in journal (Refereed)
    Abstract [en]

    The species of Amomum Roxb. (Zingiberaceae) in Cambodia, Laos and Vietnam are revised. Thirty-five species and two varieties are recognised, most names are typified, and detailed descriptions and akey are provided. Conservation assessments of all species are given. Eleven new species are described:Amomum calcaratum Lamxay & M. F. Newman, Amomum calcicolum Lamxay & M. F. Newman, Amomumcelsum Lamxay & M. F. Newman, Amomum chevalieri Gagnep. ex Lamxay, Amomum chryseum Lamxay & M. F. Newman, Amomum glabrifolium Lamxay & M. F. Newman, Amomum plicatum Lamxay & M. F. Newman,Amomum prionocarpum Lamxay & M. F. Newman, Amomum rubidum Lamxay & N.S. Ly, Amomumstephanocoleum Lamxay & M. F. Newman and Amomum tenellum Lamxay & M. F. Newman.

  • 227.
    Lamxay, Vichith
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    Vongsombath, Chanda
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolution, Genomics and Systematics, Systematic Botany.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Ethnobotany, Biodiversity and Malaria in Nakai-Nam Theun NBCA, Laos: Three PhD projects2006In: Program of the Society for Economic Botany 47th Annual Meeting, 2006Conference paper (Other (popular science, discussion, etc.))
    Abstract [en]

    Starting January 2006 the Department of Biology, National University of Laos and the Department

    of Systematic Botany have started a collaboration funded to Sida-SAREC to train three Ph.D.

    students at Uppsala University. The projects evolve around ethnobotany, biodiversity studies, and

    malaria prevention in the inaccessible Nakai-Nam Theun National Biodiversity Conservation Area in

    the Annamite mountains bordering on Vietnam. The Nakai-Nam Theun NBCA was chosen for

    fieldwork, because the 2001 review of the Laos protected area system pointed out that the Nakai-

    Nam Theun National Biodiversity Conservation Area has the highest need for development,

    harbors the richest biodiversity, and would be the most effective area for improvement.

    Objectives

    The objectives are to study: 1a) The taxonomy of Amomum (Zingiberaceae) for the Flora of

    Cambodia, Laos, and Vietnam; 1b) The feasibility of micropropagation of Amomum to create a

    cash-crop alternative to wild crafting; 2a) The biodiversity of ethnobotanically used plants in the

    area; 2b) The spread of ethnobotanical knowledge between ethnic groups and mountain valleys;

    3a) The incidence of malaria, and the traditional knowledge about natural mosquito repellents; 3b)

    The effectiveness of impregnating mosquito nets with natural or chemical repellants.

    Methods

    Study objectives 1a and 2a require extensive collection of herbarium vouchers. Objective 1b will be

    studied using micropropagation techniques through Khon Kaen University, Thailand. Objectives 2a

    and 3a will be studied using semi-structured interviews and forest walks. 3a will be done with the

    help of doctors from the Faculty of Medicine, NUOL, and 2b and 3b will be analyzed using various

    statistical methods.

    Results

    During the first three months of this project a preliminary study of the genus Amomum has been

    finished, and a few hundred herbarium vouchers have been collected in the NBCA, of which at

    least one is a new species to science.

    Conclusion

    This collaboration will hopefully initiate a lasting and ongoing tradition of ethnobotanical research in

    Laos. It will result in a better understanding of the value of plants in the livelihoods of the peoples in

    the Nakai-Nam Theun NBCA, and will hopefully improve their situation through knowledge on

    efficacy of traditionally used plants, introduction of clonal Amomum varieties, and introducing

    mosquito nets and a sustainable impregnation system based on naturally available plants. In

    addition it will result in the training of three Ph.Ds., a number of scientific publications, and probably

    a lot more.

  • 228. Landolt, John C.
    et al.
    Cavender, James C.
    Stephenson, Steven L.
    Romeralo, Maria
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Costa Rican dictyostelids, with notes on the taxonomy, phylogeny and ecology of Dictyostelium discoideum2014In: Sydowia, ISSN 0082-0598, Vol. 66, no 1, p. 129-142Article in journal (Refereed)
    Abstract [en]

    In 1962 and then over the period of 1993-2001, samples of soil/litter for isolation of cellular slime molds (dictyostelids) were collected throughout Costa Rica. Collecting sites included examples of all major forest types found in the country and ranged in elevation from 10 to 3000 m. More than 3300 clones of dictyostelids were recovered from these samples. The clones included representatives of at least 24 described species along a number of isolates that do not conform closely to any known species and thus may be new to science. Greatest diversity was found in the montane/cloud forests, whereas the average number of clones per gram was highest in moist/wet forests. Distribution of species on a country-wide basis is compared with that of Mexico, another tropical country. In addition, phylogenetic analyses of 18S rDNA sequences were carried out on 12 different isolates of Dictyostelium discoideum, a predominantly temperate species that was recorded from both Costa Rica and Mexico.

  • 229.
    Lang, Daniel
    et al.
    Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany..
    Ullrich, Kristian K.
    Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Max Planck Inst Evolutionary Biol, August Thienemann Str 2, D-24306 Plon, Germany..
    Murat, Florent
    INRA, UMR Genet Divers & Ecophysiol Cereals GDEC 1095, 5 Chemin Beaulieu, F-63100 Clermont Ferrand, France..
    Fuchs, Joerg
    Leibniz Inst Plant Genet & Crop Plant Res IPK, Corrensstr 3, D-06466 Ot Gatersleben, Stadt Seeland, Germany..
    Jenkins, Jerry
    HudsonAlpha Inst Biotechnol, Huntsville, AL USA..
    Haas, Fabian B.
    Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany..
    Piednoel, Mathieu
    Max Planck Inst Plant Breeding Res, Dept Plant Dev Biol, Carl von Linne Weg 10, D-50829 Cologne, Germany..
    Gundlach, Heidrun
    Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany..
    Van Bel, Michiel
    VIB Ctr Plant Syst Biol, Technol Pk 927, B-9052 Ghent, Belgium.;Univ Ghent, Dept Plant Biotechnol & Bioinformat, Technol Pk 927, B-9052 Ghent, Belgium..
    Meyberg, Rabea
    Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany..
    Vives, Cristina
    UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain..
    Morata, Jordi
    UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain..
    Symeonidi, Aikaterini
    Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Inst Res Biomed IRB Barcelona, Barcelona, Spain..
    Hiss, Manuel
    Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany..
    Muchero, Wellington
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA..
    Kamisugi, Yasuko
    Univ Leeds, Fac Biol Sci, Ctr Plant Sci, Leeds LS2 9JT, W Yorkshire, England..
    Saleh, Omar
    Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Humboldt Univ, Plant Mol Cell Biol, D-10115 Berlin, Germany..
    Blanc, Guillaume
    Aix Marseille Univ, Struct & Genom Informat Lab IGS, IMM FR 3479, CNRS,UMR 7256, Marseille, France..
    Decker, Eva L.
    Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany..
    van Gessel, Nico
    Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany..
    Grimwood, Jane
    HudsonAlpha Inst Biotechnol, Huntsville, AL USA.;US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA..
    Hayes, Richard D.
    US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA..
    Graham, Sean W.
    Univ British Columbia, Dept Bot, Vancouver, BC V6T 1Z4, Canada..
    Gunter, Lee E.
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA..
    McDaniel, Stuart F.
    Univ Florida, Dept Biol, Gainesville, FL 32611 USA..
    Hoernstein, Sebastian N. W.
    Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany..
    Larsson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Li, Fay-Wei
    Boyce Thompson Inst Plant Res, Ithaca, NY 14853 USA..
    Perroud, Pierre-Francois
    Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany..
    Phillips, Jeremy
    US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA..
    Ranjan, Priya
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA..
    Rokshar, Daniel S.
    US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA.;Univ Calif Berkeley, Dept Mol & Cell Biol, 229 Stanley Hall, Berkeley, CA 94720 USA..
    Rothfels, Carl J.
    Univ Calif Berkeley, Univ Herbarium, Berkeley, CA 94720 USA.;Univ Calif Berkeley, Dept Integrat Biol, Berkeley, CA 94720 USA..
    Schneider, Lucas
    Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Goethe Univ Frankfurt, Inst Transfus Med & Immunohematol, Sandhofstr 1, D-60528 Frankfurt, Germany.;German Red Cross Blood Serv, Sandhofstr 1, D-60528 Frankfurt, Germany..
    Shu, Shengqiang
    US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA..
    Stevenson, Dennis W.
    New York Bot Garden, Bronx, NY 10458 USA..
    Thummler, Fritz
    Vertis Biotechnol AG, Lise Meitner Str 30, D-85354 Freising Weihenstephan, Germany..
    Tillich, Michael
    Max Planck Inst Mol Plant Physiol, Muehlenberg 1, D-14476 Potsdam, Germany..
    Aguilar, Juan C. Villarreal
    Univ Laval, Dept Biol, Quebec City, PQ G1V 0A6, Canada..
    Widiez, Thomas
    Univ Geneva, Dept Plant Biol, Sci 3, CH-1211 Geneva 4, Switzerland.;Rutgers State Univ, Dept Plant Biol & Pathol, New Brunswick, NJ 08901 USA.;UCB Lyon 1, Lab Reprod & Dev Plantes, Univ Lyon, ENS Lyon,CNRS,INRA, F-69342 Lyon, France..
    Wong, Gane Ka-Shu
    Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E9, Canada.;Univ Alberta, Dept Med, Edmonton, AB T6G 2E1, Canada.;BGI Shenzhen, Shenzhen 518083, Peoples R China..
    Wymore, Ann
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA..
    Zhang, Yong
    Shenzhen Huahan Gene Life Technol Co Ltd, Shenzhen, Peoples R China..
    Zimmer, Andreas D.
    Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Univ Freiburg, Fac Med, Inst Human Genet, Med Ctr, Freiburg, Germany..
    Quatrano, Ralph S.
    Washington Univ, Dept Biol, Campus Box 1137, St Louis, MO 63130 USA..
    Mayer, Klaus F. X.
    Helmholtz Ctr Munich, Plant Genome & Syst Biol, D-85764 Neuherberg, Germany.;Tech Univ Munich, WZW, Munich, Germany..
    Goodstein, David
    US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA..
    Casacuberta, Josep M.
    UB, UAB, IRTA, CRAG,CSIC, Campus UAB, Barcelona 08193, Spain..
    Vandepoele, Klaas
    VIB Ctr Plant Syst Biol, Technol Pk 927, B-9052 Ghent, Belgium.;Univ Ghent, Dept Plant Biotechnol & Bioinformat, Technol Pk 927, B-9052 Ghent, Belgium..
    Reski, Ralf
    Univ Freiburg, Plant Biotechnol, Fac Biol, Schaenzlestr 1, D-79104 Freiburg, Germany.;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, Schaenzlestr 18, D-79104 Freiburg, Germany..
    Cuming, Andrew C.
    Univ Leeds, Fac Biol Sci, Ctr Plant Sci, Leeds LS2 9JT, W Yorkshire, England..
    Tuskan, Gerald A.
    Oak Ridge Natl Lab, Biosci Div, Oak Ridge, TN 37831 USA..
    Maumus, Florian
    Univ Paris Saclay, INRA, URGI, F-78026 Versailles, France..
    Salse, Jerome
    INRA, UMR Genet Divers & Ecophysiol Cereals GDEC 1095, 5 Chemin Beaulieu, F-63100 Clermont Ferrand, France..
    Schmutz, Jeremy
    HudsonAlpha Inst Biotechnol, Huntsville, AL USA.;US DOE, Joint Genome Inst, Walnut Creek, CA 94598 USA..
    Rensing, Stefan A.
    Univ Marburg, Plant Cell Biol, Fac Biol, Marburg, Germany.;Univ Freiburg, BIOSS Ctr Biol Signalling Studies, Schaenzlestr 18, D-79104 Freiburg, Germany..
    The Physcomitrella patens chromosome-scale assembly reveals moss genome structure and evolution2018In: The Plant Journal, ISSN 0960-7412, E-ISSN 1365-313X, Vol. 93, no 3, p. 515-533Article in journal (Refereed)
    Abstract [en]

    The draft genome of the moss model, Physcomitrella patens, comprised approximately 2000 unordered scaffolds. In order to enable analyses of genome structure and evolution we generated a chromosome-scale genome assembly using genetic linkage as well as (end) sequencing of long DNA fragments. We find that 57% of the genome comprises transposable elements (TEs), some of which may be actively transposing during the life cycle. Unlike in flowering plant genomes, gene-and TE-rich regions show an overall even distribution along the chromosomes. However, the chromosomes are mono-centric with peaks of a class of Copia elements potentially coinciding with centromeres. Gene body methylation is evident in 5.7% of the protein-coding genes, typically coinciding with low GC and low expression. Some giant virus insertions are transcriptionally active and might protect gametes from viral infection via siRNA mediated silencing. Structure-based detection methods show that the genome evolved via two rounds of whole genome duplications (WGDs), apparently common in mosses but not in liverworts and hornworts. Several hundred genes are present in colinear regions conserved since the last common ancestor of plants. These syntenic regions are enriched for functions related to plant-specific cell growth and tissue organization. The P. patens genome lacks the TE-rich pericentromeric and gene-rich distal regions typical for most flowering plant genomes. More non-seed plant genomes are needed to unravel how plant genomes evolve, and to understand whether the P. patens genome structure is typical for mosses or bryophytes.

  • 230.
    Lantz, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Andreasen, Katarina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Bremer, Birgitta
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Evolutionary Biology, Systematic Botany.
    Nuclear rDNA ITS sequence data used to construct the first phylogeny of Vanguerieae (Rubiaceae)2002In: Plant Systematics and Evolution, ISSN 0378-2697, no 230, p. 173-187Article in journal (Refereed)
  • 231.
    Lantz, Henrik
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organism Biology, Systematic Biology.
    Johnston, P. R.
    Park, D.
    Minter, D. W.
    Molecular phylogeny reveals a core clade of Rhytismatales2011In: Mycologia, ISSN 0027-5514, E-ISSN 1557-2536, Vol. 103, no 1, p. 57-74Article in journal (Refereed)
    Abstract [en]

    Rhytismatales (Leotiomycetes, Pezizomycotina, Ascomycota) are an order of mostly plant-associated ascomycetes with a global distribution. Well known taxa include the Rhytisma tar spots on Acer spp. and several needle-cast pathogens in genera Lophodermium and Meloderma. Critical studies are lacking at all taxonomic ranks from order to species, and in particular the genus taxonomy in the order has been criticized for being unnatural. We used nuclear LSU and mitochondrial SSU sequences in Bayesian phylogenetic analyses to define a core clade of Rhytismatales sensu strict. Some of the genera traditionally placed within the Rhytismatales, Ascodichaena, Marthamyces, Mellitiosporium, Potebniamyces, Propolis and Pseudophacidium, are shown to be phylogenetically distinct, all related to various other taxa at present placed in the polyphyletic Helotiales. Within the core clade only Cudonia, Spathularia and Terriera are supported as monophyletic. The large genera Coccomyces, Hypoderma and Lophoderminum all are polyphyletic as are a few smaller genera. The traditionally used characters of ascoma and spore shape are shown to be unreliable for the delimitation of monophyletic genera but in some cases can be useful when combined with other characters. In this study we provide 72 new nrLSU and 64 new mtSSU sequences. Together with publicly available sequences data for 103 specimens representing 91 species of Rhytismatales are now available. Despite this taxon sampling intensity is still too low to propose an alternative generic taxonomy.

  • 232.
    Larsson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Systematics of Woodsia: Ferns, bioinformatics and more2014Doctoral thesis, comprehensive summary (Other academic)
    Abstract [en]

    Ferns are one of the three main clades of vascular plants. They have few easily studied morphological characters, reflected in a historically unstable classification. The fern genus Woodsia is known to have a complex evolutionary history including numerous polyploid taxa and hybrids. It is a cosmopolitan group of small rock loving ferns mainly found in montane areas.

    This thesis aims at analyzing the patterns of diploid and polyploid evolution in Woodsia and to resolve and classify the relationships of Woodsiaceae and the other families in the large fern clade Eupolypods II.

    The Eupolypods II family relationships were inferred with DNA sequences from 81 specimens representing all major lineages. This resulted in the first well supported phylogeny of this clade and revealed Woodsiaceae to be non-monophyletic. The genera previously placed in this family were reclassified into five new or resurrected families. Swedish fern genera that have changed family classification are Woodsia (hällebräknar), now in the monogeneric family Woodsiaceae, Athyrium (majbräknar), now  in Athyriaceeae and Cystopteris (stenbräknar) and Gymnocarpium (ekbräknar) now in Cystopteridaceae.

    To analyze the evolution of Woodsia, phylogenies were produced from five plastid and two nuclear regions sequenced from 188 specimens. The results show that most taxa in Woodsia are polyploid. Polyploidization is the most common mode of speciation in the genus with an estimated polyploid speciation rate of 54%. The polyploids are mostly young and many of the polyploid taxa seem to have formed multiple times. The results also address several taxonomic and biogeographic questions.

    In the process of the work we made methodological advancements and developed 20 new low copy nuclear marker regions as well as a software pipeline for finding primers in transcriptome datasets. The alignment editor software AliView was developed for handling the increasing size datasets in a user friendly way.

    In conclusion this thesis provides new insights into the complexities of the evolution of a fern genus in which much of the diversity is accommodated in young species formed through polyploidization. It provides a framework of phylogenetic relationships at different levels that both answers long standing questions and generates new ones.

  • 233.
    Larsson, Anders
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Windham, Michael
    Department of Biology, Duke University, , Durham, North Carolina, USA.
    Korall, Petra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Extensive polyploid hybridization within the fern genus Woodsia2013Conference paper (Other academic)
    Abstract [en]

    In the process of resolving the phylogeny of the cosmopolitan Woodsia ferns we have conducted the most comprehensive nuclear phylogeny of ferns. We have sequenced two nuclear regions (pgiC and RPA2) on up to 175 different specimen corresponding to some 30 species. In addition to the nuclear markers we have also sequenced 5 chloroplast regions (matK, rbcL, atpA, atpB and trnGR).

    The results show an extensive hybridization and chromosome doubling within the genus Woodsia. As many as 19 out of the 32 species we identify in the phylogeny are polyploids.

    The Scandinavian species Woodsia alpina is the allopolyploid hybrid of Woodsia ilvensis x Woodsia glabella. In this study we show that the hybrid has originated multiple times, and also that both parents have, at least once each, acted as the donor of the maternally inherited chloroplast genome.

    An extreme hybrid is Woodsia ×abbeae. It is an hybrid between the two species Woodsia ilvensis and Woodsia oregana ssp. cathcartiana separated by as much as 30-50 million years.

  • 234.
    Le, ThiThu Hien
    et al.
    Vietnam Academy of Science and Technology.
    de Boer, Hugo J.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Nong, Van Hai
    Vietnam Academy of Science and Technology.
    Le, Thanh Huong
    Vietnam Academy of Science and Technology.
    Nguyen, Mai Huong
    Vietnam Academy of Science and Technology.
    Björk, Lars
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology.
    Overview of DNA barcoding and the Barcode of Life data system2012In: Vietnamese Journal of Biotechnology, ISSN 1811-4989, Vol. 10, no 3, p. 393-405Article in journal (Refereed)
  • 235.
    Leadbeater, Barry
    et al.
    School of Biosciences, University of Birmingham.
    Hassan, Ruhana
    School of Biosciences, University of Birmingham.
    Nelson, Michaela
    Department of Biology, University of York.
    Carr, Martin
    Department of Biology, University of York.
    Baldauf, Sandra
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    A new genus, Helgoeca gen. nov., for a nudiform choanoflagellate2008In: European Journal of Protistology, ISSN 0932-4739, E-ISSN 1618-0429, Vol. 44, no 3, p. 878-889Article in journal (Refereed)
    Abstract [en]

    A new genus, Helgoeca gen. nov., has been designated to accommodate a nudiform loricate choanoflagellate (American Type Culture Collection strain ATCC 50073) that was incorrectly attributed to the tectiform genus Acanthoecopsis (=Acanthocorbis). The first indication that this species might be nudiform came from a four-gene phylogeny of the choanoflagellates which recovered ATCC 50073 within a strongly supported monophyletic clade comprising two other nudiform taxa. Fortunately an isolate of the species in question was available from the ATCC and when observed in rapidly growing culture it was immediately apparent that this species divided with the production of 'naked' motile cells; a typically nudiform character. The beaker-shaped lorica of this species consists of an outer layer of approximately 11 longitudinal costae, which terminate anteriorly as spines, and an equal or larger number of helical costae, with a left-handed conformation, each of which terminates anteriorly adjacent to the base of a spine. The pattern of costae in this species is indistinguishable from that of Acanthocorbis nana Thomsen and for this reason A. nana has been transferred to the new genus Helgoeca gen. nov., as the type species.

  • 236. Li, Fay-Wei
    et al.
    Villarreal, Juan Carlos
    Kelly, Steven
    Rothfels, Carl J.
    Melkonian, Michael
    Frangedakis, Eftychios
    Ruhsam, Markus
    Sigel, Erin M.
    Der, Joshua P.
    Pittermann, Jarmila
    Burge, Dylan O.
    Pokornyk, Lisa
    Larsson, Anders
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Chen, Tao
    Weststrand, Stina
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Thomas, Philip
    Carpenter, Eric
    Zhang, Yong
    Tian, Zhijian
    Chen, Li
    Yan, Zhixiang
    Zhu, Ying
    Sun, Xiao
    Wang, Jun
    Stevenson, Dennis W.
    Crandall-Stotler, Barbara J.
    Shaw, A. Jonathan
    Deyholos, Michael K.
    Soltis, Douglas E.
    Graham, Sean W.
    Windham, Michael D.
    Langdale, Jane A.
    Wong, Gane Ka-Shu
    Mathews, Sarah
    Pryer, Kathleen M.
    Horizontal transfer of an adaptive chimeric photoreceptor from bryophytes to ferns2014In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 111, no 18, p. 6672-6677Article in journal (Refereed)
    Abstract [en]

    Ferns are well known for their shade-dwelling habits. Their ability to thrive under low-light conditions has been linked to the evolution of a novel chimeric photoreceptor-neochrome-that fuses red-sensing phytochrome and blue-sensing phototropin modules into a single gene, thereby optimizing phototropic responses. Despite being implicated in facilitating the diversification of modern ferns, the origin of neochrome has remained a mystery. We present evidence for neochrome in hornworts (a bryophyte lineage) and demonstrate that ferns acquired neochrome from hornworts via horizontal gene transfer (HGT). Fern neochromes are nested within hornwort neochromes in our large-scale phylogenetic reconstructions of phototropin and phytochrome gene families. Divergence date estimates further support the HGT hypothesis, with fern and hornwort neochromes diverging 179 Mya, long after the split between the two plant lineages (at least 400 Mya). By analyzing the draft genome of the hornwort Anthoceros punctatus, we also discovered a previously unidentified phototropin gene that likely represents the ancestral lineage of the neochrome phototropin module. Thus, a neochrome originating in hornworts was transferred horizontally to ferns, where it may have played a significant role in the diversification of modern ferns.

  • 237.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fjällväxter i Uppsala Botaniska Trädgård2015In: Trädgårdsamatören : medlemsblad för Sällskapet Trädgårdsamatörerna - STA, ISSN 0346-3400, Vol. 78, no 2, p. 54-58Article in journal (Other (popular science, discussion, etc.))
  • 238.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Flora of China, Illustrations. vol. 7: Menispermaceae through Capparaceae2009In: Flora of China, Illustrations. vol. 7: Menispermaceae through Capparaceae / [ed] Zhang Li Bing, beijing: Science Press, 2009, p. 294-477Chapter in book (Other academic)
  • 239.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fumariaceae2015In: Catalogue of life/ Encyclopedia of Life / [ed] Michael Hassler, Catalogue of Life , 2015Chapter in book (Other academic)
  • 240.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fumariaceae2011In: Flora of Nepal: Vol. 3, Magnoliaceae, Lauraceae, Fumariaceae, Papaveraceae, Capparaceae, Cruciferae, Crassulaceae, Saxifragaceae, Grossulariaceae. Rosaceae / [ed] Mark F. Watson et al., Edinburgh: Royal Botanic Garden , 2011, p. 49-77Chapter in book (Refereed)
  • 241.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Fumariaceae in http://www.emplantbase.org/home.html2011Other (Other academic)
  • 242.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Hemligheten är att vara hemlig ...2015In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 109, no 6, p. 339-339Article in journal (Other (popular science, discussion, etc.))
  • 243.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Kan växter vara olagliga?2015In: Trädgårdsamatören : medlemsblad för Sällskapet Trädgårdsamatörerna - STA, ISSN 0346-3400, Vol. 78, no 2, p. 81-81Article in journal (Other (popular science, discussion, etc.))
  • 244.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Klass mot klass: 2012In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 106, no 6, p. 319-319Article in journal (Other (popular science, discussion, etc.))
  • 245.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    New species, combinations, and records of Hypecoum, Dactylicapnos and Corydalis (Fumariaceae) in China2008In: Nordic Journal of Botany, ISSN 0107-055X, E-ISSN 1756-1051, Vol. 25, no 1-2, p. 1-5Article in journal (Refereed)
    Abstract [en]

    Five new species of Fumariaceae from the Flora of China area, viz. Hypecoum zhukanum (sect. Leptocarpae), Dactylicapnos gaoligongshanensis (sect. Dactylicapnos), D. leiosperma (sect. Minicalcara), Corydalis laxiflora and C. tianshanica (subgenus Cremnocapnos sect. Stricute), are described. Dactylicapnos burmanica comb. nov., D. grandifoliolata and D. macrocapnos are reported from China for the first time, and the new combinations Dactylicapnos ventii (basion.: Dicentra ventii T. C. Khanh), D. schneideri (basion.: Dicentra schneideri Fedde) and D. burmanica (basion.: Dicentra burmanica K. R. Stern) are validated. Novelties in Corydalis subgenus Corydalis will be published separately.

  • 246.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Notes on Corydalis DC. (Papaveraceae) in Eastern Himalaya with one species new to India2018In: Plant diversity in the Himalaya hotspot region.: a volume to celebrate the completion of university service of Dr. Abhaya Prasad Das / [ed] A.P. Das; Subir Bera, Dehradun: Bishen Singh Mahendra Pal Singh, 2018, p. 253-256Chapter in book (Refereed)
  • 247.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Silene indica (Caryophyllaceae) is not an Indian species2018In: Angiosperm Systematics:: Recent Trends and Emerging Issues Angiosperm systematics : felicitation volume in honour of Dr. Tariq Husain / [ed] Tariq Husain; Priyanka Agnihotri; J.S. Khuraijam, Dehradun: Bishen Singh Mahendra Pal Singh, 2018, p. 98-106Chapter in book (Refereed)
  • 248.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    Silene pseudoindica(Caryophyllaceae) a new species from Nepal, hitherto confused withS. indica2018In: Angiosperm Systematics:: Recent Trends and Emerging Issues: felicitation volume in honour of Dr. Tariq Husain / [ed] Tariq Husain; Priyanka Agnihotri; J.S. Khuraijam, Dehradun: Bishen Singh Mahendra Pal Singh, 2018, p. 91-97Chapter in book (Refereed)
  • 249.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology. Uppsala University, Music and Museums, The Linnean Gardens of Uppsala, Botanical Garden.
    Spira i spiral: blomevolution hos Pedicularis i Hengduanshan.2012In: Svensk Botanisk Tidskrift, ISSN 0039-646X, Vol. 106, no 1, p. 51-54Article in journal (Other (popular science, discussion, etc.))
  • 250.
    Lidén, Magnus
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Organismal Biology, Systematic Biology.
    The genus Dionysia (Primulaceae), a synopsis and five new species2007In: Willdenowia, ISSN 0511-9618, E-ISSN 1868-6397, Vol. 37, no 1, p. 37-61Article in journal (Refereed)
    Abstract [en]

    Five new species of Dionysia are described (D. viva, D. zschummelii, D. crista-galli, D. zetterlundii and D. tacamahaca) from the Zagros mountains of W Iran. One subspecies (D. sarvestanica subsp. spatulata), one variety (D. gaubae var. macrantha) and two sections (D.sect. Zoroasteranthos and D. sect. Mucida) are also described as new. A revised classification of the genus is suggested and a complete list of species is provided, in which some emendations to previously published data are given. A dichotomous key to the species is presented.

2345678 201 - 250 of 559
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