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1. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data

Author

Ørjan Karlsen, Susanne Kneitz, Rafael Henrique Nóbrega, Qiaowei Pan, Masatoshi Nakamoto, Elodie Jouanno, Thomas Desvignes, John H. Postlethwait, Ato Takanashi, Braedan M. McCluskey, Amaury Herpin, Matthias Stöck, Alvaro S. Roco, Boudjema Imarazene, Manfred Schartl, Zhongwei Wang, Mateus Contar Adolfi, Romain Feron, Catherine Wilson, Hugues Parrinello, Takashi Sakamoto, Ingo Braasch, Christophe Klopp, Marcos Antonio de Oliveira, Frederick W. Goetz, Harry William Detrich, Robert M. Waterhouse, Ming Wen, Yann Guiguen, Mari Kawaguchi, Angel Amores, Laurent Journot, Anna Wargelius, Verena A. Kottler, Kang Du, Jennifer L. Anderson, IINRAE, Univ Lausanne, Swiss Inst Bioinformat, Hunan Normal Univ, Uppsala Univ, Univ Montpellier, INRAE, Univ Wurzburg, Texas State Univ, Univ Oregon, NOAA, Sophia Univ, Northeastern Univ, Universidade Estadual Paulista (Unesp), Tokyo Univ Marine Sci & Technol, Inst Marine Res, Chinese Acad Sci, IGB, Michigan State Univ, Laboratoire de Physiologie et Génomique des Poissons (LPGP), Structure Fédérative de Recherche en Biologie et Santé de Rennes ( Biosit : Biologie - Santé - Innovation Technologique )-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Department of Ecology and Evolution, University of Lausanne, Université de Lausanne (UNIL), Swiss Institute of Bioinformatics [Lausanne] (SIB), State Key Laboratory of Developmental Biology of Freshwater Fish, Hunan University [Changsha] (HNU), Department of Systematic Biology [Uppsala], Evolutionary Biology Centre (EBC), Uppsala University-Uppsala University, Institut de Génomique Fonctionnelle (IGF), Université de Montpellier (UM)-Université Montpellier 1 (UM1)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Université Montpellier 2 - Sciences et Techniques (UM2)-Centre National de la Recherche Scientifique (CNRS), Système d'Information des GENomes des Animaux d'Elevage (SIGENAE), Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Physiological Chemistry, Biocenter, University of Würzburg = Universität Würzburg, The Xiphophorus Genetic Stock Center, Department of Chemistry and Biochemistry, Texas State University, Institute of Neuroscience, University of Oregon, Eugene, University of Oregon [Eugene], Tokyo University of Marine Science and Technology (TUMSAT), Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Oceanic and Atmospheric Administration (NOAA), Sophia University, Tokyo, Faculty of Science and Technology, Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Institute of Marine Research [Bergen] (IMR), University of Bergen (UiB), Institute of Hydrobiology [Wuhan], Chinese Academy of Sciences [Beijing] (CAS), Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB), Department of Integrative Biology, Michigan State University, Michigan State University [East Lansing], Michigan State University System-Michigan State University System, This project was supported by funds from the 'Agence Nationale de la Recherche', the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project,2014-2016, SCHA 408/10-1, MS), the National Institutes of Health (USA) grant R01GM085318, JHP), and the National Science Foundation (USA) Office of Polar Programs (grants PLR-1247510 and PLR-1444167 to HWD and grant OPP-1543383 to JHP, TD, and HWD). The MGX core sequencing facility was supported by France Genomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). RF was partially supported by Swiss National Science Foundation grant PP00P3_170664 to RMW., ANR-13-ISV7-0005,PhyloSex,Evolution des déterminants majeurs du sexe chez les poissons.(2013), ANR-10-INBS-0009,France-Génomique,Organisation et montée en puissance d'une Infrastructure Nationale de Génomique(2010), Department of Ecology and Evolution [Lausanne], Institute of Neuroscience, University of Oregon, Eugene, Oregon, Department of Materials and Life Sciences, Sophia University [Tokyo], Department of Structural and Functional Biology, Department of Aquatic Marine Biosciences, Developmental Biochemistry, Biocenter, Julius-Maximilians-Universität Würzburg [Wurtzbourg, Allemagne] (JMU), and This project was supported by funds from the 'Agence Nationale de la Recherche', the 'Deutsche Forschungsgemeinschaft' (ANR/DFG, PhyloSex project, 2014-2016, SCHA 408/10-1, MS), the National Institutes of Health (USA) grants R01GM085318 and R35GM139635, JHP), and the National Science Foundation (USA) Office of Polar Programs (grants PLR-1247510 and PLR-1444167 to HWD and grant OPP-1543383 to JHP, TD, and HWD). The MGX core sequencing facility was supported by France Genomique National infrastructure, funded as part of 'Investissement d’avenir' program managed by Agence Nationale pour la Recherche (contract ANR-10-INBS-09). RF was partially supported by Swiss National Science Foundation grant PP00P3_170664 to RMW.

Subjects
0106 biological sciences, 0301 basic medicine, Male, Sex Determination Analysis, Computer science, [SDV]Life Sciences [q-bio], sex determination, Locus (genetics), Computational biology, Biology, Y chromosome, 010603 evolutionary biology, 01 natural sciences, Computational workflow, DNA sequencing, Article, Workflow, 03 medical and health sciences, Sex-determination system, Genetics, Animals, Sequencing, RAD&#8208, Computational Biology, DNA, Female, Fishes/genetics, Sequence Analysis, DNA, Sex Chromosomes, Software, RAD-Sequencing, computational workflow, fish, visualization, Ecology, Evolution, Behavior and Systematics, 030304 developmental biology, Visualization, 0303 health sciences, Fishes, Japanese Medaka, Sex determination, Restriction site, 030104 developmental biology, Fish, Identification (biology), Biotechnology
Abstract

Made available in DSpace on 2021-06-25T11:54:14Z (GMT). No. of bitstreams: 0 Previous issue date: 2021-03-09 National Institute of Health (USA) Deutsche Forschungsgemeinschaft National Science Foundation (USA) Office of Polar Programs Agence Nationale de la Recherche Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish. IINRAE, LPGP, Rennes, France Univ Lausanne, Dept Ecol & Evolut, Lausanne, Switzerland Swiss Inst Bioinformat, Lausanne, Switzerland Hunan Normal Univ, Coll Life Sci, State Key Lab Dev Biol Freshwater Fish, Changsha, Peoples R China Uppsala Univ, Dept Organismal Biol, Systemat Biol, Uppsala, Sweden Univ Montpellier, Inst Genom Fonct, INSERM, IGF,CNRS, Montpellier, France INRAE, Math & Informat Appl Toulouse, SIGENAE, Castanet Tolosan, France Univ Wurzburg, Physiol Chem, Bioctr, Wurzburg, Germany Texas State Univ, Xiphophorus Genet Stock Ctr, Dept Chem & Biochem, San Marcos, TX USA Univ Wurzburg, Dev Biochem, Bioctr, Wurzburg, Germany Univ Oregon, Inst Neurosci, Eugene, OR USA NOAA, Environm & Fisheries Sci Div, Northwest Fisheries Sci Ctr, Natl Marine Fisheries Serv, Seattle, WA USA Sophia Univ, Fac Sci & Technol, Dept Mat & Life Sci, Tokyo, Japan Northeastern Univ, Ctr Marine Sci, Dept Marine & Environm Sci, Nahant, MA 01908 USA Sao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil Tokyo Univ Marine Sci & Technol, Dept Aquat Marine Biosci, Tokyo, Japan Inst Marine Res, Bergen, Norway Chinese Acad Sci, Inst Hydrobiol, Beijing, Peoples R China IGB, Leibniz Inst Freshwater Ecol & Inland Fishe, Berlin, Germany Michigan State Univ, Dept Integrat Biol, Ecol Evolut & Behav Program, E Lansing, MI 48824 USA Sao Paulo State Univ, Inst Biosci, Dept Struct & Funct Biol, Reprod & Mol Biol Grp, Botucatu, SP, Brazil National Institute of Health (USA): R01GM085318 National Institute of Health (USA): R35GM139635 Deutsche Forschungsgemeinschaft: SCHA 408/10-1 National Science Foundation (USA) Office of Polar Programs: OPP-1543383 National Science Foundation (USA) Office of Polar Programs: PLR-1247510 National Science Foundation (USA) Office of Polar Programs: PLR-1444167 Agence Nationale de la Recherche: SCHA 408/10-1 Agence Nationale de la Recherche: ANR-10-INBS-09 Schweizerischer Nationalfonds zur Forderung der Wissenschaftlichen Forschung: PP00P3_170664

Published
2021

2. Dioecy is associated with higher diversification rates in flowering plants

Author

Jos Käfer, Anneleen Kool, Gabriel A. B. Marais, Sylvain Mousset, H. J. de Boer, Mathilde Dufay, Sexe et évolution, Département PEGASE [LBBE] (PEGASE), Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Naturalis Biodiversity Center [Leiden], Natural History Museum [Oslo], University of Oslo (UiO), Department of Systematic Biology [Uppsala], Evolutionary Biology Centre (EBC), Uppsala University-Uppsala University, Laboratoire de Génétique et Evolution des Populations Végétales, and Université de Lille, Sciences et Technologies-Centre National de la Recherche Scientifique (CNRS)

Subjects
0106 biological sciences, Pollination, Dioecy, Diversification (marketing strategy), Biology, 010603 evolutionary biology, 01 natural sciences, 03 medical and health sciences, Diversification rates, Magnoliopsida, Clade, Ecology, Evolution, Behavior and Systematics, Phylogeny, 030304 developmental biology, Abiotic component, 0303 health sciences, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Phylogenetic tree, Ecology, Reproduction, Genetic Variation, Biodiversity, 15. Life on land, Biological Evolution, Evolutionary biology, Species richness
Abstract

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

Published
2013

3. CBOL protist working group: barcoding eukaryotic richness beyond the animal, plant, and fungal kingdoms

Author

Jan Pawlowski, Stéphane Audic, Sina Adl, David Bass, Lassaâd Belbahri, Cédric Berney, Samuel S Bowser, Ivan Cepicka, Johan Decelle, Micah Dunthorn, Anna Maria Fiore-Donno, Gillian H Gile, Maria Holzmann, Regine Jahn, Miloslav Jirků, Patrick J Keeling, Martin Kostka, Alexander Kudryavtsev, Enrique Lara, Julius Lukeš, David G Mann, Edward A D Mitchell, Frank Nitsche, Maria Romeralo, Gary W Saunders, Alastair G B Simpson, Alexey V Smirnov, John L Spouge, Rowena F Stern, Thorsten Stoeck, Jonas Zimmermann, David Schindel, Colomban de Vargas, Department of genetics and evolution, Université de Genève = University of Geneva (UNIGE), Evolution des Protistes et Ecosystèmes Pélagiques (EPEP), Adaptation et diversité en milieu marin (AD2M), Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS)-Station biologique de Roscoff [Roscoff] (SBR), Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS)-Centre National de la Recherche Scientifique (CNRS), University of Saskatchewan [Saskatoon] (U of S), Department of life sciences, The Natural History Museum [London] (NHM), Laboratory of Soil Biology, Université de Neuchâtel (UNINE), Wadsworth Center, Department of Zoology, University of Kaiserslautern [Kaiserslautern], Institute of Botany and Landscape Ecology, Universität Greifswald - University of Greifswald, Department of Biochemistry and Molecular Biology, Department of Evolutionary Genetics, Botanischer Garten und Botanischer Museum Berlin-Dahlem, Institute of Parasitology [České Budějovice] (BIOLOGY CENTRE CAS), Biology Centre of the Czech Academy of Sciences (BIOLOGY CENTRE CAS), Czech Academy of Sciences [Prague] (CAS)-Czech Academy of Sciences [Prague] (CAS), Canadian Institute for Advanced Research (CIFAR), Department of invertebrate zoology, Saint Petersburg State Technical University, Saint Petersburg State Polytechnical University (SPSPU)-Saint Petersburg State Polytechnical University (SPSPU), Laboratory of Soil Biodiversity, Royal Botanic Garden [Edinburgh], Universität zu Köln = University of Cologne, Department of Systematic Biology [Uppsala], Evolutionary Biology Centre (EBC), Uppsala University-Uppsala University, University of New Brunswick (UNB), Department of Biology - Life Sciences Centre, Department of Invertebrate Zoology, National Center for Biotechnology Information (NCBI), Sir AlisterHardyFoundationforOceanScience, TheLaboratory,CitadelHill,PlymouthPL12PB,UK, Dept of Ecology, University of Kaiserslautern, Smithsonian Institution National Museum of Natural History (NMNH), Consortium for the Barcoding of Life, European ERA-net program BiodivErsA under the BioMarKs project, French ANR project [09-BLAN-0348 POSEIDON], Swiss National Science Foundation [31003A-140766], University of Geneva [Switzerland], Royal Botanical Garden Edinburgh, Royal Botanical Garden, and Universität zu Köln

Subjects
0106 biological sciences, [SDV]Life Sciences [q-bio], Biodiversity, Protozoology, medicine.disease_cause, 01 natural sciences, DNA barcoding, ddc:590, Community Page, Naturvetenskap, Biology (General), Phylogeny, 0303 health sciences, Ecology, General Neuroscience, Protist, Eukaryota, Plants, Eukaryotic Cells, [SDE]Environmental Sciences, Taxonomy (biology), Natural Sciences, General Agricultural and Biological Sciences, Genetic Markers, QH301-705.5, Biology, 010603 evolutionary biology, Microbiology, General Biochemistry, Genetics and Molecular Biology, Microbial Ecology, 03 medical and health sciences, Species Specificity, Phylogenetics, medicine, RNA, Ribosomal, 18S, Genetics, Animals, DNA Barcoding, Taxonomic, Ecosystem, 030304 developmental biology, Internet, General Immunology and Microbiology, fungi, Genetic Variation, Genetic divergence, Multicellular organism, Species richness, Ribosomes, Zoology, Software
Abstract

Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth. Given their single-celled nature, discovering and describing new species has been difficult, and many protistan lineages contain a relatively small number of formally described species (Figure 1A), despite the critical importance of several groups as pathogens, environmental quality indicators, and markers of past environmental changes. It would seem natural to apply molecular techniques such as DNA barcoding to the taxonomy of protists to compensate for the lack of diagnostic morphological features, but this has been hampered by the extreme diversity within the group. The genetic divergence observed between and within major protistan groups greatly exceeds that found in each of the three multicellular kingdoms. No single set of molecular markers has been identified that will work in all lineages, but an international working group is now close to a solution. A universal DNA barcode for protists coupled with group-specific barcodes will enable an explosion of taxonomic research that will catalyze diverse applications.

Published
2012

4. CBOL Protist Working Group: Barcoding Eukaryotic Richness beyond the Animal, Plant, and Fungal Kingdoms

Author

Pawlowski , Jan, Audic , Stéphane, Adl , Sina, Bass , David, Belbahri , Lassaâd, Berney , Cédric, Bowser , Samuel S., Cepicka , Ivan, Decelle , Johan, Dunthorn , Micah, Fiore-Donno , Anna Maria, Gile , Gillian H., Holzmann , Maria, Jahn , Regine, Jirků , Miloslav, Keeling , Patrick J., Kostka , Martin, Kudryavtsev , Alexander, Lara , Enrique, Lukeš , Julius, Mann , David G., Mitchell , Edward A. D., Nitsche , Frank, Romeralo , Maria, Saunders , Gary W., Simpson , Alastair G. B., Smirnov , Alexey V., Spouge , John L., Stern , Rowena F., Stoeck , Thorsten, Zimmermann , Jonas, Schindel , David, Department of genetics and evolution, University of Geneva [Switzerland], Evolution des Protistes et Ecosystèmes Pélagiques ( EPEP ), Adaptation et diversité en milieu marin ( ADMM ), Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ) -Université Pierre et Marie Curie - Paris 6 ( UPMC ) -Centre National de la Recherche Scientifique ( CNRS ), University of Saskatchewan [Saskatoon] ( U of S ), Department of life sciences, The Natural History Museum [London], Laboratory of Soil Biology, University of Neuchatel, Wadsworth Center, Department of Zoology, University of Kaiserslautern [Kaiserslautern], Institute of Botany and Landscape Ecology, University of Greifswald, Department of Biochemistry and Molecular Biology, Department of Evolutionary Genetics, Botanischer Garten und Botanischer Museum Berlin-Dahlem, Institute of Parasitology, Biology Centre of the Academy of Sciences of the Czech Republic, Canadian Institute for Advanced Research ( CIAR ), Université de Montréal, Department of invertebrate zoology, Saint Petersburg State Technical University, Saint Petersburg State Polytechnical University ( SPSPU ) -Saint Petersburg State Polytechnical University ( SPSPU ), Centre des Sciences du Goût et de l'Alimentation [Dijon] ( CSGA ), Institut National de la Recherche Agronomique ( INRA ) -Université de Bourgogne ( UB ) -AgroSup Dijon - Institut National Supérieur des Sciences Agronomiques, de l'Alimentation et de l'Environnement-Centre National de la Recherche Scientifique ( CNRS ), Royal Botanical Garden Edinburgh, Royal Botanical Garden, Universität zu Köln, Department of Systematic Biology [Uppsala], Evolutionary Biology Centre ( EBC ), Uppsala University-Uppsala University, University of New Brunswick ( UNB ), Department of Biology - Life Sciences Centre, Department of Invertebrate Zoology, National Center for Biotechnology Information ( NCBI ), Sir AlisterHardyFoundationforOceanScience, TheLaboratory,CitadelHill,PlymouthPL12PB,UK, Dept of Ecology, University of Kaiserslautern, Smithsonian Institution National Museum of Natural History ( NMNH ), Consortium for the Barcoding of Life, European ERA-net program BiodivErsA under the BioMarKs project, French ANR project [09-BLAN-0348 POSEIDON], and Swiss National Science Foundation [31003A-140766]

Subjects
[ SDE ] Environmental Sciences, [ SDV ] Life Sciences [q-bio], fungi
Abstract

International audience; Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth.

Published
2012

5. Mosquito (Diptera: Culicidae) repellency field tests of essential oils from plants traditionally used in Laos.

Author

Vongsombath C, Pålsson K, Björk L, Borg-Karlson AK, and Jaenson TG

Subjects
Animals, Croton chemistry, DEET, Female, Humans, Hyptis chemistry, Litsea chemistry, Male, Plant Oils chemistry, Population Density, Young Adult, Culicidae, Insect Repellents analysis, Mosquito Control, Oils, Volatile chemistry
Abstract

Essential oils of Hyptis suaveolens (Lamiaceae), Croton roxburghii (Euphorbiaceae), and Litsea cubeba (Lauraceae) were tested in the field near Vientiane city, Lao PDR, on humans for repellent activity against mosquitoes. Landing mosquitoes were collected and later identified. The most abundant mosquitoes captured belonged to the genera Armigeres, Culex, and Aedes. All the plant oils tested at concentrations of 1.7 microg/cm(2), 3.3 microg/cm(2), and 6.3 microg/cm(2) were significantly more mosquito repellent than the negative control. Croton oil was significantly repellent against mosquitoes of the three genera at the highest (6.3 microg/cm(2)) concentration tested. Litsea oil was significantly repellent against Armigeres at all (1.7 microg/cm(2), 3.3 microg/cm(2), and 6.3 microg/cm(2)) concentrations tested. Hyptis oil was significantly repellent against Armigeres at 3.3 microg/cm(2) and 6.3 microg/cm(2) and against Culex at 1.7 microg/cm(2) and 6.3 microg/cm(2). The oils were analyzed for chemical content of volatiles, mainly terpenes. Main constituents were beta-pinene, sabinene, and 1,8-cineol from oils of the green parts of H. suaveolens; alpha-pinene, beta-pinene, and alpha-phellandrene from fresh bark of C. roxburghii; and alpha-pinene, beta-phellandrene, sabinene, and 1,8-cineol from fresh fruits of L. cubeba.

Published
2012
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6. Evolution and loss of long-fringed petals: a case study using a dated phylogeny of the snake gourds, Trichosanthes (Cucurbitaceae).

Author

de Boer HJ, Schaefer H, Thulin M, and Renner SS

Subjects
Asia, Australia, Bayes Theorem, Cell Nucleus genetics, DNA, Chloroplast genetics, DNA, Plant genetics, DNA, Ribosomal Spacer genetics, Likelihood Functions, Sequence Analysis, DNA, Trichosanthes anatomy & histology, Biological Evolution, Flowers anatomy & histology, Phylogeny, Trichosanthes genetics
Abstract

Background: The Cucurbitaceae genus Trichosanthes comprises 90-100 species that occur from India to Japan and southeast to Australia and Fiji. Most species have large white or pale yellow petals with conspicuously fringed margins, the fringes sometimes several cm long. Pollination is usually by hawkmoths. Previous molecular data for a small number of species suggested that a monophyletic Trichosanthes might include the Asian genera Gymnopetalum (four species, lacking long petal fringes) and Hodgsonia (two species with petals fringed). Here we test these groups' relationships using a species sampling of c. 60% and 4759 nucleotides of nuclear and plastid DNA. To infer the time and direction of the geographic expansion of the Trichosanthes clade we employ molecular clock dating and statistical biogeographic reconstruction, and we also address the gain or loss of petal fringes., Results: Trichosanthes is monophyletic as long as it includes Gymnopetalum, which itself is polyphyletic. The closest relative of Trichosanthes appears to be the sponge gourds, Luffa, while Hodgsonia is more distantly related. Of six morphology-based sections in Trichosanthes with more than one species, three are supported by the molecular results; two new sections appear warranted. Molecular dating and biogeographic analyses suggest an Oligocene origin of Trichosanthes in Eurasia or East Asia, followed by diversification and spread throughout the Malesian biogeographic region and into the Australian continent., Conclusions: Long-fringed corollas evolved independently in Hodgsonia and Trichosanthes, followed by two losses in the latter coincident with shifts to other pollinators but not with long-distance dispersal events. Together with the Caribbean Linnaeosicyos, the Madagascan Ampelosicyos and the tropical African Telfairia, these cucurbit lineages represent an ideal system for more detailed studies of the evolution and function of petal fringes in plant-pollinator mutualisms.

Published
2012
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7. Synopsis of Trichosanthes (Cucurbitaceae) based on recent molecular phylogenetic data.

Author

de Boer HJ and Thulin M

Abstract

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

Published
2012
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8. Steam sauna and mother roasting in Lao PDR: practices and chemical constituents of essential oils of plant species used in postpartum recovery.

Author

de Boer HJ, Lamxay V, and Björk L

Subjects
Adult, Female, Humans, Laos, Oils, Volatile chemistry, Plant Oils chemistry, Postpartum Period physiology, Steam, Terpenes chemistry, Terpenes therapeutic use, Young Adult, Balneology methods, Oils, Volatile therapeutic use, Plant Oils therapeutic use, Plants, Medicinal chemistry, Postnatal Care methods, Postpartum Period drug effects
Abstract

Background: Fundamental in traditional postpartum recovery in Lao PDR is the use of hotbeds, mother roasting, steam sauna and steam baths. During these treatments medicinal plants play a crucial role, but little has been published about how the treatments are carried out precisely, which species are used, the medicinal properties of these species, and the medicinal efficacy of their chemical constituents., Methods: Sixty-five interviews, in 15 rural villages, with women of 4 different ethnic groups were conducted to survey confinement rituals, and postpartum plant use and salience. Essential oils from the main species used were extracted using steam distillation and the main chemical constituents characterized using gas chromatography-mass spectrometry (GC-MS)., Results: A total of 10 different species were used by three or more of the ethnic groups included in this study. All species were used in steam sauna and bath, but only 3 species were used in hotbed and mother roasting. Essential oils of Amomum villosum, Amomum microcarpum and Blumea balsamifera were found to contain significant amounts of the following terpenes: β-pinene, camphor, bornyl acetate, borneol, linalool, D-limonene, fenchone, terpinen-4-ol and α-terpinene., Conclusions: Many of these terpenes have documented antimicrobial and analgesic properties, and some have also synergistic interactions with other terpenes. The mode of application in hotbed and mother roasting differs from the documented mechanisms of action of these terpenes. Plants in these two practices are likely to serve mainly hygienic purposes, by segregating the mother from infection sources such as beds, mats, stools, cloth and towels. Steam sauna medicinal plant use through inhalation of essential oils vapors can possibly have medicinal efficacy, but is unlikely to alleviate the ailments commonly encountered during postpartum convalescence. Steam sauna medicinal plant use through dermal condensation of essential oils, and steam bath cleansing of the perineal area is possibly a pragmatic use of the reported medicinal plants, as terpene constituents have documented antimicrobial, analgesic and anti-inflammatory properties.

Published
2011
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