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Contributions to the Solution of Phylogenetic Problem in Fabales
Research Article Bartın University International Journal of Natural and Applied Sciences Araştırma Makalesi JONAS, 2(2): 195-206 e-ISSN: 2667-5048 31 Aralık/December, 2019 CONTRIBUTIONS TO THE SOLUTION OF PHYLOGENETIC PROBLEM IN FABALES Deniz Aygören Uluer1*, Rahma Alshamrani 2 1 Ahi Evran University, Cicekdagi Vocational College, Department of Plant and Animal Production, 40700 Cicekdagi, KIRŞEHIR 2 King Abdulaziz University, Department of Biological Sciences, 21589, JEDDAH Abstract Fabales is a cosmopolitan angiosperm order which consists of four families, Leguminosae (Fabaceae), Polygalaceae, Surianaceae and Quillajaceae. The monophyly of the order is supported strongly by several studies, although interfamilial relationships are still poorly resolved and vary between studies; a situation common in higher level phylogenetic studies of ancient, rapid radiations. In this study, we carried out simulation analyses with previously published matK and rbcL regions. The results of our simulation analyses have shown that Fabales phylogeny can be solved and the 5,000 bp fast-evolving data type may be sufficient to resolve the Fabales phylogeny question. In our simulation analyses, while support increased as the sequence length did (up until a certain point), resolution showed mixed results. Interestingly, the accuracy of the phylogenetic trees did not improve with the increase in sequence length. Therefore, this study sounds a note of caution, with respect to interpreting the results of the “more data” approach, because the results have shown that large datasets can easily support an arbitrary root of Fabales. Keywords: Data type, Fabales, phylogeny, sequence length, simulation. 1. Introduction Fabales Bromhead is a cosmopolitan angiosperm order which consists of four families, Leguminosae (Fabaceae) Juss., Polygalaceae Hoffmanns. -
Combined Phylogenetic Analyses Reveal Interfamilial Relationships and Patterns of floral Evolution in the Eudicot Order Fabales
Cladistics Cladistics 1 (2012) 1–29 10.1111/j.1096-0031.2012.00392.x Combined phylogenetic analyses reveal interfamilial relationships and patterns of floral evolution in the eudicot order Fabales M. Ange´ lica Belloa,b,c,*, Paula J. Rudallb and Julie A. Hawkinsa aSchool of Biological Sciences, Lyle Tower, the University of Reading, Reading, Berkshire RG6 6BX, UK; bJodrell Laboratory, Royal Botanic Gardens, Kew, Richmond, Surrey TW9 3DS, UK; cReal Jardı´n Bota´nico-CSIC, Plaza de Murillo 2, CP 28014 Madrid, Spain Accepted 5 January 2012 Abstract Relationships between the four families placed in the angiosperm order Fabales (Leguminosae, Polygalaceae, Quillajaceae, Surianaceae) were hitherto poorly resolved. We combine published molecular data for the chloroplast regions matK and rbcL with 66 morphological characters surveyed for 73 ingroup and two outgroup species, and use Parsimony and Bayesian approaches to explore matrices with different missing data. All combined analyses using Parsimony recovered the topology Polygalaceae (Leguminosae (Quillajaceae + Surianaceae)). Bayesian analyses with matched morphological and molecular sampling recover the same topology, but analyses based on other data recover a different Bayesian topology: ((Polygalaceae + Leguminosae) (Quillajaceae + Surianaceae)). We explore the evolution of floral characters in the context of the more consistent topology: Polygalaceae (Leguminosae (Quillajaceae + Surianaceae)). This reveals synapomorphies for (Leguminosae (Quillajaceae + Suri- anaceae)) as the presence of free filaments and marginal ⁄ ventral placentation, for (Quillajaceae + Surianaceae) as pentamery and apocarpy, and for Leguminosae the presence of an abaxial median sepal and unicarpellate gynoecium. An octamerous androecium is synapomorphic for Polygalaceae. The development of papilionate flowers, and the evolutionary context in which these phenotypes appeared in Leguminosae and Polygalaceae, shows that the morphologies are convergent rather than synapomorphic within Fabales. -
South African Association of Botanists
South African Journal of Botany 2003, 69(2): 224–268 Copyright © NISC Pty Ltd Printed in South Africa — All rights reserved SOUTH AFRICAN JOURNAL OF BOTANY ISSN 0254–6299 Conference Abstracts South African Association of Botanists Abstracts of papers and posters presented at the 29th Annual Congress of the South African Association of Botanists and the International Society for Ethnopharmacology held at the University of Pretoria, 8–11 January 2003 The presenter of multi-authored papers is underlined $ Awards made to students Plenary Lectures ability of immense biological resources in Africa have provided a feasible platform for the establishment of a ‘biology-industrial pro- Ethnopharmacology as source of new drug paradigms: gramme’, which focuses on biodiscovery. In this approach, biodi- the case of an Amazonian ‘brain tonic’ versity functions not as raw materials or industrial feedstock but more importantly as an informational input to research development EE Elisabetsky1,3, IR Siqueira2,3, AL Silva1,4, DS Nunes5 and CA processes. Biodiscovery is an inclusive term to describe the collec- Netto2,3 tion of biological resources for the identification of valuable molecu- 1 Laboratório de Etnofarmacologia, Deptamento de Farmacologia, lar or genetic information about those biological resources and to Universidade Federal do Rio Grande do Sul, CP 5072, 90041-970, Porto utilise that information in the development of bio-products. Africa Alegre, Rio Grande do Sul, Brazil possesses a unique advantage in the development of plant genetic 2 Deptamento de Bioquímica e PPGs, Universidade Federal do Rio Grande materials into consumer goods because of the long history and do Sul, CP 5072, 90041-970, Porto Alegre, Rio Grande do Sul, Brazil widespread use of traditional medicine in the continent. -
Systematics of Hermannia L. (Malvaceae): a Taxonomic Revision of the Genus
Systematics of Hermannia L. (Malvaceae): A Taxonomic Revision of the Genus. by David Gwynne-Evans Thesis presented for the degree of DOCTOR OF PHILOSOPHY In the DEPARTMENT OF BOTANY UNIVERSITY OF CAPE TOWN 31 Oct 2015 University of Cape Town Supervised by Prof. Terry Hedderson The copyright of this thesis vests in the author. No quotation from it or information derived from it is to be published without full acknowledgement of the source. The thesis is to be used for private study or non- commercial research purposes only. Published by the University of Cape Town (UCT) in terms of the non-exclusive license granted to UCT by the author. University of Cape Town CONTENTS Systematics of Hermannia L. (Malvaceae): ....................................................................... i A Taxonomic Revision of the Genus. ................................................................................. i Contents ......................................................................................................................... ii List of Figures ............................................................................................................. xiii List of Tables .............................................................................................................. xxii Acknowledgements ................................................................................................... xxiii Abstract ....................................................................................................................... xxv -
The Endemic Flora of the Cape Peninsula, South Africa
South African Journal of Botany 72 (2006) 205 – 210 www.elsevier.com/locate/sajb The endemic flora of the Cape Peninsula, South Africa N.A. Helme a,*, T.H. Trinder-Smith b a Nick Helme Botanical Surveys, PO Box 22652, Scarborough 7975, South Africa b Bolus Herbarium, Department of Botany, University of Cape Town, Private Bag, Rondebosch 7700, South Africa Received 27 June 2005; accepted 13 July 2005 Abstract The Cape Peninsula is a well known area of exceptional plant diversity and endemism within the Cape Floristic Region, but an accurate and complete listing of the endemic seed plant species has been lacking. Here, we present a list of the 158 species and 3 subspecies that are currently regarded as Cape Peninsula endemics, with discussion on the profile of the endemic flora, plant hotspots within the area, and conservation issues. Endemics constitute 7% of the total Peninsula flora. 76% of the endemic species fall within only 10 families, with Erica being the genus with the greatest number of endemic species on the Peninsula (39). The Peninsula is identified as a centre of endemism for Roella, Tetraria, Serruria, and Muraltia. Many families are notably under-represented in terms of endemic species on the Peninsula, including Geraniaceae, Oxalidaceae, Thymelaeaceae, Apiaceae, Hyacinthaceae, Poaceae, Rhamnaceae, Rutaceae, Orchidaceae, and Asteraceae. 62% of the endemics are shrubs or dwarf shrubs. 41% of the endemics are currently Red Data Book listed, but the Table Mountain National Park conserves a large percentage of the montane habitat, as well as significant lowland habitat in the extreme south. D 2005 SAAB. -
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Reseña bibliográfica / Review La Granja 3 Las Gentianaceae: botánica, fitoquímica y actividad biológica The Gentianaceae: botany, phytochemistry and biological activity Giovanni Vidari y Paola VitaFinzi CISTRE y Departamento de Química Orgánica – Universidad de los Estudios de Pavia – Via Taramelli 10 – 27100 Pavia, Italia. Autores para correspondencia: [email protected], [email protected] Manuscrito recibido el 1 de junio de 2010. Aceptado, tras revisión el 20 de junio de 2010 Resumen Este artículo es una revisión actualizada sobre los metabolitos secundarios de la familia de las Gentianaceae. Estas plantas se emplean en la medicina tradicional de numerosos países y presentan actividad biológica inte- resante. Después de haber detallado botánicamente esta familia de plantas, que ha sido y que sigue siendo muy estudiada, se recogen los estudios fitoquímicos sobre numerosas especies. Los metabolitos característicos son los xantonas, una clase de compuestos no muy difundidos en el mundo vegetal. Son característicos también derivados de los seco-iridoides, y algunos alcaloides. Palabras claves: Gentianaceae, actividad biológica, xantonas, secoiridoides, alcaloides. Abstract This paper is a review on the secondary metabolites of the Gentianaceae family. These plants are very well known as remedies in the traditional medicine of many countries because they present a number of biological activities. After a botanical presentation of this family, that is still studied, the phytochemical research of many species are reported. The most characteristic metabolites are xanthones, a class of natural products that is not very widespread in plants. Characteristic are also the seco-iridoids and alkaloids. Keywords: Gentianaceae, biological activities, xanthones, secoiridoids, alkaloids. For ma su ge ri da de ci tar: Vidari, G., P. -
Elaiosomes and Seed Dispersal by Ants Insect–Plant Interactions
STUDENT’S GUIDE Case Study Félix Forest Elaiosomes and Royal Botanic Gardens, Kew seed dispersal by Dean Madden [Ed.] ants NCBE, University of Reading Version 2.0 CaseCase Studies elaiosomes and seed dispersal by ants Insect–plant interactions Insects evolved 400 million years ago and today they are found almost everywhere on Earth. Nearly a million species of insects have been described in the scientific literature, but this is only a fraction of the species that exist. Estimates of the number of insect species range from two to 30 million species. Many groups of insects are poorly known. The interactions that insects have with plants are a vital part of their ecology. Roughly half of all species of insects eat plants at some stage in their life cycles. Many insect species use plants as shelter and some absorb plant defence chemicals and use them to defend themselves. About 85 % of all plant species are pollinated by insects such as bees, flies, butterflies and beetles, while some plants use insects to disperse their seeds and to protect them against other insects and competitors. Within the insects, there are more than 10,000 species of ants. These have evolved complex social behaviour and numerous and varied adaptations. Ants, together with bees and termites, are one of the most important groups of insects for the ecology of numerous ecosystems. In some tropical areas such as the Amazon basin, their total biomass can be four times that of vertebrate species living there. Adrian Pingstone, Wikimedia Commons. Wikimedia Pingstone, Adrian PHOTOS Greg BY: Hume, Robin Klein and In several ant species, some of the workers Weaver ants build nests with leaves and Leaf-cutter ants collect leaves which they are used to store honeydew in their sew them together using the silk from ant bring back to their nest to use as growing abdomen, immobilising them completely. -
The Potential of South African Plants in the Development of New Medicinal Products ⁎ B.-E
Available online at www.sciencedirect.com South African Journal of Botany 77 (2011) 812–829 www.elsevier.com/locate/sajb Review The potential of South African plants in the development of new medicinal products ⁎ B.-E. Van Wyk Department of Botany and Plant Biotechnology, University of Johannesburg, P.O. Box 524, Auckland Park 2006, South Africa Received 2 July 2011; received in revised form 26 August 2011; accepted 26 August 2011 Abstract Southern Africa is an important focal point of botanical and cultural diversity but only a few plant species have hitherto become fully commer- cialised as medicinal products. In recent years there has been an upsurge in research and development activity, resulting in several new products and new crops. In this review, more than 90 of the best-known and most promising indigenous South African plants are listed and subjectively evaluated in the context of their potential for commercialisation as medicinal products for a variety of applications. The history of product devel- opment relating to the following species is briefly discussed and the plants and some of their products are illustrated: Agathosma betulina (buchu), Aloe ferox (bitter aloe), Artemisia afra (African wormwood), Aspalathus linearis (rooibos tea), Bulbine frutescens (burn jelly plant); Cyclopia gen- istoides (honeybush tea), Harpagophytum procumbens (devil's claw), Hoodia gordonii (hoodia, ghaap), Hypoxis hemerocallidea (“African pota- to”), Lippia javanica (fever tea), Mesembryanthemum tortuosum (=Sceletium tortuosum)(kanna, kougoed), Pelargonium sidoides (“Umckaloabo”), Siphonochilus aethiopicus (African ginger), Sutherlandia frutescens (=Lessertia frutescens) (cancer bush), Warburgia salutaris (pepperbark tree) and Xysmalobium undulatum (“Uzara”). The main factors that are apparently responsible for failure or success will be highlight- ed, especially the importance of marketing strategy, proof of concept and barriers to market entry. -
270 an In-Silico Approach for the Evaluation of Six DNA
Erzincan Üniversitesi Erzincan University Fen Bilimleri Enstitüsü Dergisi Journal of Science and Technology 2021, 14(1), 270-283 2021, 14(1), 270-283 ISSN: 1307-9085, e-ISSN: 2149-4584 DOI: 10.18185/erzifbed.786884 Araştırma Makalesi Research Article An in-silico approach for the evaluation of six DNA barcodes by using Maximum Likelihood (ML) and TaxonDNA approaches for some Polygalaceae Deniz Aygören Uluer1* 1Ahi Evran University, Çiçekdağı Vocational College, Department of Plant and Animal Production, Çiçekdağı, Kırşehir/Turkey Geliş / Received: 28/08/2020, Kabul / Accepted: 08/02/2021 Abstract Polygalaceae is a large family with a cosmopolitan distribution, comprising ca. 1,200 species in 27 genera. However, similar to many plant groups, the identification of Polygalaceae species mostly depends on floral and fruit characteristics; therefore, DNA barcoding could easily warrant the correct identification of sterile material. In the current study, the utility of six widely employed plant DNA barcode loci, namely rbcL, matK, trnL-F region (including trnL intron+trnL-F intergenic spacer), the entire ITS (ITS1+5.8S+ITS2) as well as subunits ITS1 and ITS2 have been explored by performing Maximum Likelihood (ML) and TaxonDNA analyses. The results have shown that, while none of the six loci reviewed here completely fulfils the ideal DNA barcoding criteria; yet, matK region is the most useful DNA barcode for the Polygalaceae. Keywords: DNA barcoding, ITS, matK, Polygalaceae, rbcL, trnL-F. Altı DNA bölgesinin bazı Polygalaceae’de Maximum Likelihood (ML) ve TaxonDNA yöntemleri ile in slico olarak değerlendirilmesi Öz Polygalaceae kozmopolit bir yayılıma sahip, 27 cins içinde yaklaşık 1,200 türe sahip geniş bir familyadır. -
Polygalaceae)
S.AfrJ.Bot., 1991, 57(5): 229-233 229 A re-evaluation of Nylandtia (Polygalaceae) C.T. Johnson* and F.M. Weitz Department of Botany, University of the Western Cape, Private Bag X17, Bellville, 7535 Republic of South Africa Accepted 10 June 1991 A re-evaluation of the monotypic genus Nylandtia Dumort. is presented in which two varieties, N. spinosa (L.) Dumort. var. spinosa and var. scoparia (Eckl. & Zeyh.) Johnson & Weitz, are recognized. Descriptions, synonymy, distribution data, and a key to the varieties are provided. Variation in the two varieties is covered and pollination ecology is discussed. 'n Re-evaluasie van die monotipiese genus Nylandtia Dumort. word aangebied waarin twee varieteite, N. spinosa (L.) Dumort. var. spinosa en var. scoparia (Eckl. & Zeyh.) Johnson & Weitz, erken word. Beskrywings, sinonimie, verspreidingsdata en 'n sleutel tot die varieteite word voorsien. Variasies tussen die twee varieteite word behandel en die bestuiwingsekologie word bespreek. Keywords: Nylandtia, taxonomy, morphology. ·To whom correspondence should be addressed. History and relationships related. Anatomical data (Johnson, Cyster & Spangenberg The first description referring to this species dates back to 1981) such as cyclocytic stomata, cuticle structure and 1751, when Linnaeus published his Amoenitates academi absence of extraxylary fibres, support Levyns (1949) who, cae. An identical description of the species was given by on the basis of floral structure, regarded Nylandtia as a him in 1753 when he published the name Polygala spinosa, specialized off-shoot of the sub-genus Psilocladus of though the collector or supplier of the specimen was not Muraltia. cited. The specimen that is currently housed in the Linnaean The infraspecific taxonomy in Nylandtia has been herbarium was collected by Rijk Tulbagh in May 1769 variously treated. -
Strategies for the Development of Plant Systematics in a Floristically Diverse Region
Strategies for the development of plant systematics in a floristically diverse region by Janine Elizabeth Victor Submitted in partial fulfilment of the requirements for the degree Philosophiae Doctor in the Faculty of Natural & Agricultural Sciences (Plant Science) University of Pretoria Pretoria Supervisor: Prof. Dr. A.E. van Wyk Co-supervisor: Prof. Dr. G.F. Smith July 2015 DECLARATION I, Janine Elizabeth Victor, declare that the thesis/dissertation, which I hereby submit for the degree Doctorate of Philosophy at the University of Pretoria, is my own work and has not previously been submitted by me for a degree at this or any other tertiary institution. SIGNATURE: .......JtU: c!o!. ........ .. DATE: 1 July 2015 II ABSTRACT Strategies for the development of plant systematics in a floristically diverse region Janine Elizabeth Victor Submitted in partial fulfilment of the requirements for the degree Philosophiae Doctor In the Faculty of Natural & Agricultural Sciences (Department of Plant Science) University of Pretoria July 2015 Supervisor: Prof. Dr. A.E. van Wyk Co-supervisor: Prof. Dr. G.F. Smith South Africa is one of the most biologically diverse countries in the world, and harbours one of the richest floras. Vast areas of the country remain under-collected, and a large proportion of species are taxonomically problematic and under-represented in herbarium collections. These factors hinder management of biodiversity. The main intention of this study was to develop a strategy for plant taxonomic research that would meet the needs of end users, and make efficient use of scarce human and financial resources in South Africa. The development of plant taxonomy in South Africa from 1600 to 2014 is reviewed, with emphasis on the main driving factors that have influenced the research direction, techniques used, and choice of taxonomic research topic. -
Botany Appendices
ENVIRONMENTAL IMPACT ASSESSMENT FOR THE PROPOSED NUCLEAR POWER STATION (‘NUCLEAR 1’) and ASSOCIATED INFRASTRUCTURE Botany and Dune Ecology Impact Assessment APPENDICES A BARRIE LOW COASTEC J27035 UPDATED DECEMBER 2009 Nuclear 1 EIA and EMP Specialist Study for Environmental Impact Report Specialist Study: Botany and Dune Ecology Issue 3.0 / November 2009 APPENDIX 4.1.1. PLANT SPECIES RECORDED FROM DUYNEFONTEIN: INDIVIDUAL LISTS NT: Near Threatened; R: Rare, VU: vulnerable EN: Endangered, CR: Critically Endangered LC: Least Concern; DD: Data Deficient; De: Declining Report produced by the SaSFLORA database: data (C) Coastec; database design and structures (C) Reuben Roberts 1998-2008 Nuclear 1 EIA and EMP Specialist Study for Environmental Impact Report Specialist Study: Botany and Dune Ecology Issue 3.0 / November 2009 COMMUNITY K1: PRIMARY DUNES Division: Anthophyta Total named species: 24 Class: Dicotyledones Total genera: 21 Total families: 13 Total red data species: 3 AIZOACEAE Total introduced species: 2 Tetragonia decumbens Mill. APIACEAE Dasispermum suffruticosum (P.J.Bergius) B.L.Burtt ASTERACEAE Arctotheca populifolia (P.J.Bergius) Norl. Didelta carnosa (L.f.) Aiton var. tomentosa Helichrysum crispum (L.) D.Don. niveum (L.) Less. Senecio elegans L. cf. maritimus L. Tripteris dentata (Burm.f.) O.Hoffm. CRASSULACEAE Crassula cf. glomerata P.J.Bergius FABACEAE Psoralea repens L. NT GERANIACEAE Pelargonium capitatum (L.) L'Hér. MESEMBRYANTHEMACEAE Amphibolia laevis (Aiton) H.E.K.Hartmann LC Carpobrotus acinaciformis (L.) L.Bolus LC Ruschia indecora (L.Bolus) Schwantes EN MYRICACEAE Morella cordifolia (L.) Killick SCROPHULARIACEAE Hemimeris racemosa (Houtt.) Merr. LC Manulea tomentosa (L.) L. THYMELAEACEAE Passerina ericoides L. VU Division: Anthophyta Class: Monocotyledones ASPHODELACEAE Trachyandra ciliata (L.f.) Kunth LC divaricata (Jacq.) Kunth CYPERACEAE Ficinia lateralis (Vahl) Kunth Isolepis cf.