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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. -
A Survey of Tricolpate (Eudicot) Phylogenetic Relationships1
American Journal of Botany 91(10): 1627±1644. 2004. A SURVEY OF TRICOLPATE (EUDICOT) PHYLOGENETIC RELATIONSHIPS1 WALTER S. JUDD2,4 AND RICHARD G. OLMSTEAD3 2Department of Botany, University of Florida, Gainesville, Florida 32611 USA; and 3Department of Biology, University of Washington, Seattle, Washington 98195 USA The phylogenetic structure of the tricolpate clade (or eudicots) is presented through a survey of their major subclades, each of which is brie¯y characterized. The tricolpate clade was ®rst recognized in 1989 and has received extensive phylogenetic study. Its major subclades, recognized at ordinal and familial ranks, are now apparent. Ordinal and many other suprafamilial clades are brie¯y diag- nosed, i.e., the putative phenotypic synapomorphies for each major clade of tricolpates are listed, and the support for the monophyly of each clade is assessed, mainly through citation of the pertinent molecular phylogenetic literature. The classi®cation of the Angiosperm Phylogeny Group (APG II) expresses the current state of our knowledge of phylogenetic relationships among tricolpates, and many of the major tricolpate clades can be diagnosed morphologically. Key words: angiosperms; eudicots; tricolpates. Angiosperms traditionally have been divided into two pri- 1992a; Chase et al., 1993; Doyle et al., 1994; Soltis et al., mary groups based on the presence of a single cotyledon 1997, 2000, 2003; KaÈllersjoÈ et al., 1998; Nandi et al., 1998; (monocotyledons, monocots) or two cotyledons (dicotyledons, Hoot et al., 1999; Savolainen et al., 2000a, b; Hilu et al., 2003; dicots). A series of additional diagnostic traits made this di- Zanis et al., 2003; Kim et al., 2004). This clade was ®rst called vision useful and has accounted for the long recognition of the tricolpates (Donoghue and Doyle, 1989), but the name these groups in ¯owering plant classi®cations. -
CHINQUAPIN the Newsletter of the Southern Appalachian Botanical Society
CHINQUAPIN The Newsletter of the Southern appalachian Botanical Society Volume 23 (4) Winter 2015 terfly to avoid egg Earl Core Student Report placement, or are there other benefits Passionflowers and a Clever Trick to possessing egg By Nichole Long-Aragon mimics? And, 4. How often have egg When most people observe butterflies in their garden, they mimics evolved in visualize a peaceful scene. Even when most botanists think of but- Passiflora? Have they terflies and their association with plants, they think of butterflies evolved in similar or sipping nectar and distributing pollen from one flower to another. different ways, and However, some of these beautiful butterflies do more than peaceful has their presence activities: they lay their eggs on plants. Once these eggs hatch, they influenced species diversification in develop into caterpillars which subsequently feed on the leaves. Authentic butterfly eggs of Heliconius hewitsoni on This causes defoliation, or sometimes even plant death. Several Passiflora pittieri. the groups that have them? species of a genus of plants well known to botanists of the eastern Thus far, my research has been able to address each of the pro- United States, the passionflowers (Passiflora), have developed a posed questions. Egg mimics may be located on the leaf, petiole, deceptive scheme to discourage this crime of passion. They trick stipule, or floral structures of the plant, and 25 species are known the butterflies with egg mimics. to have them. My study is ongoing, but they have evolved at least five times. Each mimic is unique with respect to shape, size, and location. Abundant druses are a common feature, but tissues differ in terms of cell shape, cell composition, and secretory function. -
Checklist of the Vascular Plants of San Diego County 5Th Edition
cHeckliSt of tHe vaScUlaR PlaNtS of SaN DieGo coUNty 5th edition Pinus torreyana subsp. torreyana Downingia concolor var. brevior Thermopsis californica var. semota Pogogyne abramsii Hulsea californica Cylindropuntia fosbergii Dudleya brevifolia Chorizanthe orcuttiana Astragalus deanei by Jon P. Rebman and Michael G. Simpson San Diego Natural History Museum and San Diego State University examples of checklist taxa: SPecieS SPecieS iNfRaSPecieS iNfRaSPecieS NaMe aUtHoR RaNk & NaMe aUtHoR Eriodictyon trichocalyx A. Heller var. lanatum (Brand) Jepson {SD 135251} [E. t. subsp. l. (Brand) Munz] Hairy yerba Santa SyNoNyM SyMBol foR NoN-NATIVE, NATURaliZeD PlaNt *Erodium cicutarium (L.) Aiton {SD 122398} red-Stem Filaree/StorkSbill HeRBaRiUM SPeciMeN coMMoN DocUMeNTATION NaMe SyMBol foR PlaNt Not liSteD iN THE JEPSON MANUAL †Rhus aromatica Aiton var. simplicifolia (Greene) Conquist {SD 118139} Single-leaF SkunkbruSH SyMBol foR StRict eNDeMic TO SaN DieGo coUNty §§Dudleya brevifolia (Moran) Moran {SD 130030} SHort-leaF dudleya [D. blochmaniae (Eastw.) Moran subsp. brevifolia Moran] 1B.1 S1.1 G2t1 ce SyMBol foR NeaR eNDeMic TO SaN DieGo coUNty §Nolina interrata Gentry {SD 79876} deHeSa nolina 1B.1 S2 G2 ce eNviRoNMeNTAL liStiNG SyMBol foR MiSiDeNtifieD PlaNt, Not occURRiNG iN coUNty (Note: this symbol used in appendix 1 only.) ?Cirsium brevistylum Cronq. indian tHiStle i checklist of the vascular plants of san Diego county 5th edition by Jon p. rebman and Michael g. simpson san Diego natural history Museum and san Diego state university publication of: san Diego natural history Museum san Diego, california ii Copyright © 2014 by Jon P. Rebman and Michael G. Simpson Fifth edition 2014. isBn 0-918969-08-5 Copyright © 2006 by Jon P. -
KARYOLOGICAL STUDY in the CHILEAN RHATANY Krameria Cistoidea HOOK
Vol XXX (2): 21-25; December 2019 Journal of the Argentine Society of Genetics KARYOLOGICAL STUDY IN THE CHILEAN RHATANY Krameria cistoidea HOOK. & ARN. (KRAMERIACEAE) ESTUDIO CARIOLÓGICO EN EL PACUL CHILENO Krameria cistoidea HOOK. & ARN. (KRAMERIACEAE) Palma Rojas C.1*, Jara Seguel P.2, García M.1, von Brand E.3, Araya Jaime C.1,4 ABSTRACT 1 Departamento de Biología, The karyotype of the plant species Krameria cistoidea Hook. & Arn. was studied by assessing Facultad de Ciencias, Universidad chromosome characters such as morphology, size, and C-banding pattern. The karyotype of de La Serena, Casilla 599, La K. cistoidea was composed only by metacentric chromosomes in the two populations studied. Serena, Chile. The haploid set length was 51.9±2.3 µm and the mean chromosome size was 8.68±0.78 µm. 2 Departamento de Ciencias Some similarities in chromosome morphology and size can be observed among K. cistoidea Biológicas y Químicas, Núcleo de and K. triandra, in addition to the chromosome number 2n=12 which is conserved within Estudios Ambientales, Facultad de the genus. K. cistoidea exhibited a symmetric banding pattern with large C-bands in the Recursos Naturales, Universidad telomeres of the short and long arms of all chromosomes, except the short arm of pair 1. The Católica de Temuco, Casilla 15-D, Temuco, Chile. relative length of the C-bands was 23.5% of the total haploid set length. These cytological results on K. cistoidea are the first data on quantitative karyotype morphology and C-banding 3 Departamento de Biología patterns in the genus Krameria. -
Angiosperm Phylogeny Inferred from Sequences of Four Mitochondrial Genes 1Yin-Long QIU∗ 1Libo LI 1Bin WANG 1,2Jia-Yu XUE 1Tory A
Journal of Systematics and Evolution 48 (6): 391–425 (2010) doi: 10.1111/j.1759-6831.2010.00097.x Angiosperm phylogeny inferred from sequences of four mitochondrial genes 1Yin-Long QIU∗ 1Libo LI 1Bin WANG 1,2Jia-Yu XUE 1Tory A. HENDRY 1Rui-Qi LI 1Joseph W. BROWN 1Ya n g L I U 1Geordan T. HUDSON 3Zhi-Duan CHEN 1(Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48109, USA) 2(School of Life Sciences, Nanjing University, Nanjing 210093, China) 3(Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China) Abstract An angiosperm phylogeny was reconstructed in a maximum likelihood analysis of sequences of four mitochondrial genes, atp1, matR, nad5, and rps3, from 380 species that represent 376 genera and 296 families of seed plants. It is largely congruent with the phylogeny of angiosperms reconstructed from chloroplast genes atpB, matK, and rbcL, and nuclear 18S rDNA. The basalmost lineage consists of Amborella and Nymphaeales (including Hydatellaceae). Austrobaileyales follow this clade and are sister to the mesangiosperms, which include Chloranthaceae, Ceratophyllum, magnoliids, monocots, and eudicots. With the exception of Chloranthaceae being sister to Ceratophyllum, relationships among these five lineages are not well supported. In eudicots, Ranunculales, Sabiales, Proteales, Trochodendrales, Buxales, Gunnerales, Saxifragales, Vitales, Berberidopsidales, and Dilleniales form a basal grade of lines that diverged before the diversification of rosids and asterids. Within rosids, the COM (Celastrales–Oxalidales–Malpighiales) clade is sister to malvids (or rosid II), instead of to the nitrogen-fixing clade as found in all previous large-scale molecular analyses of angiosperms. Santalales and Caryophyllales are members of an expanded asterid clade. -
Rosid Radiation and the Rapid Rise of Angiosperm-Dominated Forests
Rosid radiation and the rapid rise of angiosperm-dominated forests Hengchang Wanga,b, Michael J. Moorec, Pamela S. Soltisd, Charles D. Belle, Samuel F. Brockingtonb, Roolse Alexandreb, Charles C. Davisf, Maribeth Latvisb,f, Steven R. Manchesterd, and Douglas E. Soltisb,1 aWuhan Botanical Garden, The Chinese Academy of Science, Wuhan, Hubei 430074 China; bDepartment of Botany and dFlorida Museum of Natural History, University of Florida, Gainesville, FL 32611; cBiology Department, Oberlin College, Oberlin, OH 44074-1097; eDepartment of Biological Sciences, University of New Orleans, New Orleans, LA 70148; and fDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 Communicated by Peter Crane, University of Chicago, Chicago, IL, January 4, 2009 (received for review April 1, 2008) The rosid clade (70,000 species) contains more than one-fourth of all nitrogen-fixing bacteria (nitrogen-fixing clade) and defense mech- angiosperm species and includes most lineages of extant temperate anisms such as glucosinolate production (Brassicales) and cyano- and tropical forest trees. Despite progress in elucidating relationships genic glycosides (2). Many important crops, including legumes within the angiosperms, rosids remain the largest poorly resolved (Fabaceae) and fruit crops (Rosaceae), are rosids. Furthermore, 4 major clade; deep relationships within the rosids are particularly of the 5 published complete angiosperm nuclear genome sequences enigmatic. Based on parsimony and maximum likelihood (ML) anal- are rosids (with 2 other rosids, Manihot and Ricinus, well under- yses of separate and combined 12-gene (10 plastid genes, 2 nuclear; way): Arabidopsis (Brassicaceae), Carica (Caricaceae), Populus >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening (Salicaceae), and Vitis (Vitaceae, sister to other rosids). -
Rosid Radiation and the Rapid Rise of Angiosperm-Dominated Forests
Rosid radiation and the rapid rise of angiosperm-dominated forests Hengchang Wanga,b, Michael J. Moorec, Pamela S. Soltisd, Charles D. Belle, Samuel F. Brockingtonb, Roolse Alexandreb, Charles C. Davisf, Maribeth Latvisb,f, Steven R. Manchesterd, and Douglas E. Soltisb,1 aWuhan Botanical Garden, The Chinese Academy of Science, Wuhan, Hubei 430074 China; bDepartment of Botany and dFlorida Museum of Natural History, University of Florida, Gainesville, FL 32611; cBiology Department, Oberlin College, Oberlin, OH 44074-1097; eDepartment of Biological Sciences, University of New Orleans, New Orleans, LA 70148; and fDepartment of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138 Communicated by Peter Crane, University of Chicago, Chicago, IL, January 4, 2009 (received for review April 1, 2008) The rosid clade (70,000 species) contains more than one-fourth of all nitrogen-fixing bacteria (nitrogen-fixing clade) and defense mech- angiosperm species and includes most lineages of extant temperate anisms such as glucosinolate production (Brassicales) and cyano- and tropical forest trees. Despite progress in elucidating relationships genic glycosides (2). Many important crops, including legumes within the angiosperms, rosids remain the largest poorly resolved (Fabaceae) and fruit crops (Rosaceae), are rosids. Furthermore, 4 major clade; deep relationships within the rosids are particularly of the 5 published complete angiosperm nuclear genome sequences enigmatic. Based on parsimony and maximum likelihood (ML) anal- are rosids (with 2 other rosids, Manihot and Ricinus, well under- yses of separate and combined 12-gene (10 plastid genes, 2 nuclear; way): Arabidopsis (Brassicaceae), Carica (Caricaceae), Populus >18,000 bp) and plastid inverted repeat (IR; 24 genes and intervening (Salicaceae), and Vitis (Vitaceae, sister to other rosids). -
Parasitic Plants in African Agriculture
Technical Parasitic Plants in Note # 94 African Agriculture What’s Inside: Introduction Stem Parasites Root Parasites Summary of Control Options Lytton John Musselman Old Dominion University Norfolk, Virginia 23529-0266 [email protected] Photos are courtesy of the author unless otherwise indicated. Published 2019 Introduction Significance to farmers This Technical Note provides an overview of parasitic plants of agricultural significance in Africa. Parasitic weeds cause drought stress and stunted crops. Affected plants include cereal grains (e.g., sorghum [Sorghum bicolor] and maize [Zea mays]) and grain legumes (e.g., cowpea [Vigna unguiculata]) that farmers rely on for food. Damage to these and other crops is generally heightened by low soil fertility and drought stress, conditions that are faced by many African smallholders. Parasitic weeds can lead to severe yield losses, making them an important constraint to food security in many areas. Biology and botany Although parasitic plants are often thought of as weeds, they are part of a guild of highly unique plants. An understanding of their biology is essential for control and management of parasitic plants. Parasitic plants are amazingly specialized, and have remarkable adaptations. They include herbaceous plants, vines, shrubs, and trees. Some appear innocuous, with no external evidence of their parasitic nature. Others lack leaves and stems, existing only within the bodies of other plants. Parasitic plants’ reproductive strategies also vary widely, from the tiny (1 mm) flowers of some mistletoes to the meter-wide flowers of Rafflesia--the largest flower in the world. However, what all parasitic plants have in common is a haustorium (Figures 1 and 6). -
Molecular Phylogenetic and Evolutionary Studies of Parasitic Plants Daniel L
8 Molecular Phylogenetic and Evolutionary Studies of Parasitic Plants Daniel L. Nickrent, R. Joel Duff, Alison E. Colwell, Andrea D. Wolfe, Nelson D. Young, Kim E. Steiner, and Claude W. dePamphilis The parasitic nutritional mode is a frequently 1995). For the vast majority of parasitic plants, evolved adaptation in animals (Price, 1980), as negative effects upon the host are difficult to de well as in flowering plants (Kuijt, 1969). Het tect, yet others (e.g., Striga, Orobanche) are se erotrophic angiosperms can be classified as ei rious weeds of economically important crops ther mycotrophs or as haustorial parasites. The (Kuijt, 1969; Musselman, 1980; Eplee, 1981; former derive nutrients via a symbiotic relation Stewart and Press, 1990; Press and Graves, ship with mycorrhizal fungi. Haustorial para 1995). sites, in contrast, directly penetrate host tissues The degree of nutritional dependence on the via a modified root called a haustorium and host varies among haustorial parasites. Hemi thereby obtain water and nutrients. Although parasites are photosynthetic during at least one such categories are often a matter of semantics, phase of their life cycle and derive mainly water we use the term parasite in a strict sense to refer and dissolved minerals from their hosts. Oblig to haustorial parasites. Angiosperm parasites are ate hemiparasites require a host plant to com restricted to the dicot subclasses Magnoliidae, plete their life cycles whereas facultative hemi Rosidae, and Asteridae; have evolved approxi parasites do not. Hemiparasites can be found in mately 11 times; and represent approximately Laurales (Cassytha), Polygalales (Krameria), 22 families, 265 genera, and 4,000 species, that and all families of Santalales. -
Wood Anatomy of Krameriaceae with Comparisons with Zygophyllaceae: Phylesis, Ecology and Systematics
Botanical Journal of the Linnean Society, 2005, 149, 257-270. With 20 figures Wood anatomy of Krameriaceae with comparisons with Zygophyllaceae: phylesis, ecology and systematics SHERWIN CARLQUIST FLS* Santa Barbara Botanic Garden, 1212 Mission Canyon Road, Santa Barbara, California 93105, USA Received March 2005; accepted for publication June 2005 Wood of nine species of Krameria (including all clades proposed within the genus) reveals a few characters related to infrageneric systematics; most relate primarily to ecology and habit. Wood of Krameria closely fits quantitative data reported for desert shrubs. Lack of vessel grouping correlates with the presence of densely pitted tracheids. Wood xeromorphy in Krameria may relate in part to hemiparasitism. Tracheid presence may also account for relatively low vessel density. Wood anatomy of six species of Zygophyllaceae (including both genera of Morkillioideae) is compared with that of Krameriaceae because recent phylogenies propose that these two families comprise the order Zygophyllales. Several wood characters appear to represent synapomorphies reflecting this relationship. Dif ferences in wood anatomy between Krameriaceae and Zygophyllaceae are believed to represent autapomorphies. Notable among these include Paedomorphic Type II rays (Krameriaceae), storying (Zygophyllaceae), presence of ves tured pits (Zygophyllaceae), and differentiation into vasicentric tracheids and fibre-tracheids (Zygophyllaceae). The latter feature is referable to the concept of fibre-tracheid dimorphism. Recognition of Krameriaceae as separate from Zygophyllaceae is supported by wood characters. Wood of Zygophyllales does not conflict with the idea that the order belongs to rosids, with Malpighiaceae as the outgroup of Zygophyllales. © 2005 The Linnean Society of London, Botanical Journal of the Linnean Society, 2005, 149, 257-270. -
Checklist of the Vascular Plants of San Diego County 5Th Edition by Jon P
i checklist of the vascular plants of san Diego county 5th edition by Jon p. rebman and Michael g. simpson san Diego natural history Museum and san Diego state university publication of: san Diego natural history Museum san Diego, california ii Copyright © 2014 by Jon P. Rebman and Michael G. Simpson Fifth edition 2014. isBn 0-918969-08-5 Copyright © 2006 by Jon P. Rebman and Michael G. Simpson © 2001 by Michael G. Simpson and Jon P. Rebman © 1996 by Michael G. Simpson, Scott C. McMillan, Brenda L. McMillan, Judy Gibson, and Jon P. Rebman. © 1995 by Michael G. Simpson, Scott C. McMillan, and Brenda L. Stone This material may not be reproduced or resold. for correspondence, write to: Dr. Jon P. Rebman, San Diego Natural History Museum, P.O. Box 121390, San Diego, CA 92112-1390 Email: [email protected] or to: Dr. Michael G. Simpson, Department of Biology, San Diego State University, San Diego, CA 92182-4614 Email: [email protected] Cover photographs are plants endemic to San Diego County, California, all taken by the authors. iii table of contents preface v alphabetical listing of families xxi san Diego county vascular plant checklist: Documented with herbarium vouchers lycophytes 1 equisetophytes 1 ophioglossoid ferns 1 leptosporangiate ferns 1 seed plants 3 conifers 3 gnetales 4 angiosperms (flowering plants) 4 Magnoliids: laurales (calycanthaceae & lauraceae) 4 Magnoliids: piperales (saururaceae) 4 ceratophyllales (ceratophyllaceae) 4 eudicots 4 Monocots 81 appendix 1: taxa reported for san Diego county but excluded 97 appendix