Species Using RAPD Markers
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Outline of Angiosperm Phylogeny
Outline of angiosperm phylogeny: orders, families, and representative genera with emphasis on Oregon native plants Priscilla Spears December 2013 The following listing gives an introduction to the phylogenetic classification of the flowering plants that has emerged in recent decades, and which is based on nucleic acid sequences as well as morphological and developmental data. This listing emphasizes temperate families of the Northern Hemisphere and is meant as an overview with examples of Oregon native plants. It includes many exotic genera that are grown in Oregon as ornamentals plus other plants of interest worldwide. The genera that are Oregon natives are printed in a blue font. Genera that are exotics are shown in black, however genera in blue may also contain non-native species. Names separated by a slash are alternatives or else the nomenclature is in flux. When several genera have the same common name, the names are separated by commas. The order of the family names is from the linear listing of families in the APG III report. For further information, see the references on the last page. Basal Angiosperms (ANITA grade) Amborellales Amborellaceae, sole family, the earliest branch of flowering plants, a shrub native to New Caledonia – Amborella Nymphaeales Hydatellaceae – aquatics from Australasia, previously classified as a grass Cabombaceae (water shield – Brasenia, fanwort – Cabomba) Nymphaeaceae (water lilies – Nymphaea; pond lilies – Nuphar) Austrobaileyales Schisandraceae (wild sarsaparilla, star vine – Schisandra; Japanese -
Untangling Phylogenetic Patterns and Taxonomic Confusion in Tribe Caryophylleae (Caryophyllaceae) with Special Focus on Generic
TAXON 67 (1) • February 2018: 83–112 Madhani & al. • Phylogeny and taxonomy of Caryophylleae (Caryophyllaceae) Untangling phylogenetic patterns and taxonomic confusion in tribe Caryophylleae (Caryophyllaceae) with special focus on generic boundaries Hossein Madhani,1 Richard Rabeler,2 Atefeh Pirani,3 Bengt Oxelman,4 Guenther Heubl5 & Shahin Zarre1 1 Department of Plant Science, Center of Excellence in Phylogeny of Living Organisms, School of Biology, College of Science, University of Tehran, P.O. Box 14155-6455, Tehran, Iran 2 University of Michigan Herbarium-EEB, 3600 Varsity Drive, Ann Arbor, Michigan 48108-2228, U.S.A. 3 Department of Biology, Faculty of Sciences, Ferdowsi University of Mashhad, P.O. Box 91775-1436, Mashhad, Iran 4 Department of Biological and Environmental Sciences, University of Gothenburg, Box 461, 40530 Göteborg, Sweden 5 Biodiversity Research – Systematic Botany, Department of Biology I, Ludwig-Maximilians-Universität München, Menzinger Str. 67, 80638 München, Germany; and GeoBio Center LMU Author for correspondence: Shahin Zarre, [email protected] DOI https://doi.org/10.12705/671.6 Abstract Assigning correct names to taxa is a challenging goal in the taxonomy of many groups within the Caryophyllaceae. This challenge is most serious in tribe Caryophylleae since the supposed genera seem to be highly artificial, and the available morphological evidence cannot effectively be used for delimitation and exact determination of taxa. The main goal of the present study was to re-assess the monophyly of the genera currently recognized in this tribe using molecular phylogenetic data. We used the sequences of nuclear ribosomal internal transcribed spacer (ITS) and the chloroplast gene rps16 for 135 and 94 accessions, respectively, representing all 16 genera currently recognized in the tribe Caryophylleae, with a rich sampling of Gypsophila as one of the most heterogeneous groups in the tribe. -
Desmodium Cuspidatum (Muhl.) Loudon Large-Bracted Tick-Trefoil
New England Plant Conservation Program Desmodium cuspidatum (Muhl.) Loudon Large-bracted Tick-trefoil Conservation and Research Plan for New England Prepared by: Lynn C. Harper Habitat Protection Specialist Massachusetts Natural Heritage and Endangered Species Program Westborough, Massachusetts For: New England Wild Flower Society 180 Hemenway Road Framingham, MA 01701 508/877-7630 e-mail: [email protected] • website: www.newfs.org Approved, Regional Advisory Council, 2002 SUMMARY Desmodium cuspidatum (Muhl.) Loudon (Fabaceae) is a tall, herbaceous, perennial legume that is regionally rare in New England. Found most often in dry, open, rocky woods over circumneutral to calcareous bedrock, it has been documented from 28 historic and eight current sites in the three states (Vermont, New Hampshire, and Massachusetts) where it is tracked by the Natural Heritage programs. The taxon has not been documented from Maine. In Connecticut and Rhode Island, the species is reported but not tracked by the Heritage programs. Two current sites in Connecticut are known from herbarium specimens. No current sites are known from Rhode Island. Although secure throughout most of its range in eastern and midwestern North America, D. cuspidatum is Endangered in Vermont, considered Historic in New Hampshire, and watch-listed in Massachusetts. It is ranked G5 globally. Very little is understood about the basic biology of this species. From work on congeners, it can be inferred that there are likely to be no problems with pollination, seed set, or germination. As for most legumes, rhizobial bacteria form nitrogen-fixing nodules on the roots of D. cuspidatum. It is unclear whether there have been any changes in the numbers or distribution of rhizobia capable of forming effective mutualisms with D. -
Moehringia Lateriflora
Report under the Article 17 of the Habitats Directive European Environment Period 2007-2012 Agency European Topic Centre on Biological Diversity Moehringia lateriflora Annex II, IV Priority No Species group Vascular plants Regions Boreal Moehringia lateriflora is a flowering plant with circumpolar distribution including Russia, China, Japan and North America. Within the European Union it occur only in the Boreal region and is very rare in Estonia and Sweden, more widespread in Finland. It grows mainly on stony shores, grazed dry or moist wooded meadows and forest edges. The species Considered "Favourable" in Estonia and Sweden, but not in Finland. Majority of the population in Sweden, but in a few sites. Overall assessment is "Unfavourable Inadequate", due to the situation in Finland. Trend stable. Main threats are changes in hydraulic conditions and lack of grazing. No changes in overall conservation status between 2001-06 and 2007-12 reports. Page 1 Species: Moehringia lateriflora Report under the Article 17 of the Habitats Directive Assessment of conservation status at the European biogeographical level Conservation status (CS) of parameters Current Trend in % in Previous Reason for Region Future CS CS region CS change Range Population Habitat prospects BOR FV FV U1 U1 U1 = 100 U1 See the endnote for more informationi Assessment of conservation status at the Member State level Page 2 Species: Moehringia lateriflora Report under the Article 17 of the Habitats Directive Assessment of conservation status at the Member State level The map shows both Conservation Status and distribution using a 10 km x 10 km grid. Conservation status is assessed at biogeographical level. -
Pollen Morphology in the Genus Bolanthus (Ser.) Reichb
Sakarya University Journal of Science SAUJS e-ISSN 2147-835X | Period Bimonthly | Founded: 1997 | Publisher Sakarya University | http://www.saujs.sakarya.edu.tr/en/ Title: Pollen morphology in the genus Bolanthus (Ser.) Reichb. (Caryophyllaceae) in Turkey Authors: Yağmur CÖMERT, Mevlüde Nur TOPAL, Murat KOÇ Recieved: 2020-08-14 16:59:23 Accepted: 2020-10-27 12:43:05 Article Type: Research Article Volume: 25 Issue: 1 Month: February Year: 2021 Pages: 40-54 How to cite Yağmur CÖMERT, Mevlüde Nur TOPAL, Murat KOÇ; (2021), Pollen morphology in the genus Bolanthus (Ser.) Reichb. (Caryophyllaceae) in Turkey . Sakarya University Journal of Science, 25(1), 40-54, DOI: https://doi.org/10.16984/saufenbilder.780724 Access link http://www.saujs.sakarya.edu.tr/en/pub/issue/58068/780724 New submission to SAUJS https://dergipark.org.tr/en/journal/1115/submission/step/manuscript/new Sakarya University Journal of Science 25(1), 40-54, 2021 Pollen morphology in the genus Bolanthus (Ser.) Reichb. (Caryophyllaceae) in Turkey Yağmur CÖMERT*1, Mevlüde Nur TOPAL1, Murat KOÇ1 Abstract Bolanthus including 11 species and all endemic in Turkey. Pollen morphology that belong to the genus Bolanthus were investigated using light microscopy (LM) and scanning electron microscopy (SEM). In this study, all of 11 species in Bolanthus were studied. Pollen of seven species were determined from Turkey and reported for the first time. Pollen shape has two different ornamentation at genus Bolanthus as prolate-spheroidal and oblate-spheroidal. Pollen grains are polipantoporate and isopolar symmetrical. The pollen ornamentation is scabrate-perforate. Pollen diameter, pore diameter, pore numbers, exine thickness, operculum diameter, distance between two pores, spinule numbers, punctum numbers are varying characters between Bolanthus species. -
Flora-Lab-Manual.Pdf
LabLab MManualanual ttoo tthehe Jane Mygatt Juliana Medeiros Flora of New Mexico Lab Manual to the Flora of New Mexico Jane Mygatt Juliana Medeiros University of New Mexico Herbarium Museum of Southwestern Biology MSC03 2020 1 University of New Mexico Albuquerque, NM, USA 87131-0001 October 2009 Contents page Introduction VI Acknowledgments VI Seed Plant Phylogeny 1 Timeline for the Evolution of Seed Plants 2 Non-fl owering Seed Plants 3 Order Gnetales Ephedraceae 4 Order (ungrouped) The Conifers Cupressaceae 5 Pinaceae 8 Field Trips 13 Sandia Crest 14 Las Huertas Canyon 20 Sevilleta 24 West Mesa 30 Rio Grande Bosque 34 Flowering Seed Plants- The Monocots 40 Order Alistmatales Lemnaceae 41 Order Asparagales Iridaceae 42 Orchidaceae 43 Order Commelinales Commelinaceae 45 Order Liliales Liliaceae 46 Order Poales Cyperaceae 47 Juncaceae 49 Poaceae 50 Typhaceae 53 Flowering Seed Plants- The Eudicots 54 Order (ungrouped) Nymphaeaceae 55 Order Proteales Platanaceae 56 Order Ranunculales Berberidaceae 57 Papaveraceae 58 Ranunculaceae 59 III page Core Eudicots 61 Saxifragales Crassulaceae 62 Saxifragaceae 63 Rosids Order Zygophyllales Zygophyllaceae 64 Rosid I Order Cucurbitales Cucurbitaceae 65 Order Fabales Fabaceae 66 Order Fagales Betulaceae 69 Fagaceae 70 Juglandaceae 71 Order Malpighiales Euphorbiaceae 72 Linaceae 73 Salicaceae 74 Violaceae 75 Order Rosales Elaeagnaceae 76 Rosaceae 77 Ulmaceae 81 Rosid II Order Brassicales Brassicaceae 82 Capparaceae 84 Order Geraniales Geraniaceae 85 Order Malvales Malvaceae 86 Order Myrtales Onagraceae -
Rethinking Phylogenetics Using Caryophyllales (Angiosperms), Matk Gene and Trnk Intron As Experimental Platform
Rethinking phylogenetics using Caryophyllales (angiosperms), matK gene and trnK intron as experimental platform Sunny Sheliese Crawley Dissertation submitted to the faculty of the Virginia Polytechnic Institute and State University in partial fulfillment of the requirements for the degree of Doctor of Philosophy In Biological Sciences Khidir W. Hilu Eric P. Beers Carla V. Finkielstein Jill C. Sible December 2, 2011 Blacksburg, Virginia Keywords: (phylogeny, missing data, caryophyllids, trnK intron, matK, RNA editing, gnetophytes) Copyright 2011, Sunny Sheliese Crawley Rethinking phylogenetics using Caryophyllales (angiosperms), matK gene and trnK intron as experimental platform Sunny Sheliese Crawley ABSTRACT The recent call to reconstruct a detailed picture of the tree of life for all organisms has forever changed the field of molecular phylogenetics. Sequencing technology has improved to the point that scientists can now routinely sequence complete plastid/mitochondrial genomes and thus, vast amounts of data can be used to reconstruct phylogenies. These data are accumulating in DNA sequence repositories, such as GenBank, where everyone can benefit from the vast growth of information. The trend of generating genomic-region rich datasets has far outpaced the expasion of datasets by sampling a broader array of taxa. We show here that expanding a dataset both by increasing genomic regions and species sampled using GenBank data, despite the inherent missing DNA that comes with GenBank data, can provide a robust phylogeny for the plant order Caryophyllales (angiosperms). We also investigate the utility of trnK intron in phylogeny reconstruction at relativley deep evolutionary history (the caryophyllid order) by comparing it with rapidly evolving matK. We show that trnK intron is comparable to matK in terms of the proportion of variable sites, parsimony informative sites, the distribution of those sites among rate classes, and phylogenetic informativness across the history of the order. -
Biodiversity of the Hypersaline Urmia Lake National Park (NW Iran)
Diversity 2014, 6, 102-132; doi:10.3390/d6020102 OPEN ACCESS diversity ISSN 1424-2818 www.mdpi.com/journal/diversity Review Biodiversity of the Hypersaline Urmia Lake National Park (NW Iran) Alireza Asem 1,†,*, Amin Eimanifar 2,†,*, Morteza Djamali 3, Patricio De los Rios 4 and Michael Wink 2 1 Institute of Evolution and Marine Biodiversity, Ocean University of China, Qingdao 266003, China 2 Institute of Pharmacy and Molecular Biotechnology (IPMB), Heidelberg University, Im Neuenheimer Feld 364, Heidelberg D-69120, Germany; E-Mail: [email protected] 3 Institut Méditerranéen de Biodiversité et d'Ecologie (IMBE: UMR CNRS 7263/IRD 237/Aix- Marseille Université), Europôle Méditerranéen de l'Arbois, Pavillon Villemin BP 80, 13545, Aix-en Provence Cedex 04, France; E-Mail: [email protected] 4 Environmental Sciences School, Natural Resources Faculty, Catholic University of Temuco, Casilla 15-D, Temuco 4780000, Chile; E-Mail: [email protected] † These authors contributed equally to this work. * Authors to whom correspondence should be addressed; E-Mails: [email protected] (A.A.); [email protected] (A.E.); Tel.: +86-150-6624-4312 (A.A.); Fax: +86-532-8203-2216 (A.A.); Tel.: +49-6221-544-880 (A.E.); Fax: +49-6221-544-884 (A.E.). Received: 3 December 2013; in revised form: 13 January 2014 / Accepted: 27 January 2014 / Published: 10 February 2014 Abstract: Urmia Lake, with a surface area between 4000 to 6000 km2, is a hypersaline lake located in northwest Iran. It is the saltiest large lake in the world that supports life. Urmia Lake National Park is the home of an almost endemic crustacean species known as the brine shrimp, Artemia urmiana. -
Differential Seed Germination Responses to the Ratio of Red to Far-Red Light in Temperate and Tropical Species
Plant Ecol DOI 10.1007/s11258-013-0205-y Differential seed germination responses to the ratio of red to far-red light in temperate and tropical species Pimonrat Tiansawat • James W. Dalling Received: 9 January 2013 / Accepted: 22 April 2013 Ó Springer Science+Business Media Dordrecht 2013 Abstract Variation in vegetation density creates a that the threshold R:FR that stimulates 50 % of range of red to far-red ratios of irradiance (R:FR) maximum germination (R:FR50) was also related to potentially permitting fine-scale discrimination of seed mass and latitudinal distribution. In agreement light conditions for seed germination. However, with an earlier study, we found that for temperate taxa, remarkably few studies have explored whether R:FR the R:FR50 was significantly negatively correlated responses of germination vary among species that with seed mass. In contrast, for 22 tropical taxa, we differ in distribution and life-history traits. In this found a significant positive correlation. These oppos- study, we explored the relationships between R:FR ing relationships suggest contrasting selection pres- requirements and four species characteristics: seed sures on germination responses of tropical taxa mass, latitudinal distribution (tropical vs. temperate), (mostly trees) and temperate herbaceous plants, and seed dormancy (dormant vs. nondormant), and plant which are likely related to differences in seed longev- growth form (woody vs. nonwoody). We obtained data ity, seed burial rates, and reproductive output. on germination response to R:FR of 62 species from published literature and added new data for ten species Keywords Regeneration niche Á Light dependence Á from aseasonal tropical forests in Borneo. -
Walker Ridge and Bear Valley Area, Lake and Colusa Counties
Humboldt State University Digital Commons @ Humboldt State University Botanical Studies Open Educational Resources and Data 2018 Checklist of the Vascular Plants of the Walker Ridge and Bear Valley Area, Lake and Colusa Counties James P. Smith Jr. Humboldt State University, [email protected] Follow this and additional works at: https://digitalcommons.humboldt.edu/botany_jps Part of the Botany Commons Recommended Citation Smith, James P. Jr., "Checklist of the Vascular Plants of the Walker Ridge and Bear Valley Area, Lake and Colusa Counties" (2018). Botanical Studies. 76. https://digitalcommons.humboldt.edu/botany_jps/76 This Flora of Northwest California-Checklists of Local Sites is brought to you for free and open access by the Open Educational Resources and Data at Digital Commons @ Humboldt State University. It has been accepted for inclusion in Botanical Studies by an authorized administrator of Digital Commons @ Humboldt State University. For more information, please contact [email protected]. A CHECKLIST OF THE VASCULAR PLANTS OF THE WALKER RIDGE - BEAR VALLEY AREA (LAKE AND COLUSA COUNTIES, CALIFORNIA) Compiled by James P. Smith, Jr. & John O. Sawyer, Jr. Department of Biological Sciences Humboldt State University Tenth Edition: 01 July 2018 Chlorogalum pomeridianum var. pomeridianum • soaproot F E R N S Dichelostemma multiflorum • wild-hyacinth Dichelostemma volubile • snake-lily, twining brodiaea Dipterostemon capitatum ssp. capitatum • blue dicks Aspidotis densa • Indian's dream Hastingsia alba • white-flowered schoenolirion Equisetum arvense • field horsetail Triteleia hyacinthina • white brodiaea Equisetum laevigatum • smooth scouring-rush Triteleia laxa • Ithuriel's spear Pellaea andromedifolia var. pubescens • coffee fern Triteleia peduncularis • long-rayed triteleia Pellaea mucronata var. -
Disparity, Diversity, and Duplications in the Caryophyllales
Research Disparity, diversity, and duplications in the Caryophyllales Stephen A. Smith1, Joseph W. Brown1, Ya Yang2, Riva Bruenn3, Chloe P. Drummond3, Samuel F. Brockington4, Joseph F. Walker1, Noah Last2, Norman A. Douglas3 and Michael J. Moore3 1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI 48103, USA; 2Department of Plant Biology, University of Minnesota-Twin Cities, 1445 Gortner Avenue, St Paul, MN 55108, USA; 3Department of Biology, Oberlin College, 119 Woodland St, Oberlin, OH 44074-1097, USA; 4Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK Summary Author for correspondence: The role played by whole genome duplication (WGD) in plant evolution is actively debated. Stephen A. Smith WGDs have been associated with advantages such as superior colonization, various adapta- Tel: +1 734 615 5510 tions, and increased effective population size. However, the lack of a comprehensive mapping Email: [email protected] of WGDs within a major plant clade has led to uncertainty regarding the potential association Received: 30 May 2017 of WGDs and higher diversification rates. Accepted: 28 July 2017 Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales, representing nearly half of the extant species. We phylogenetically New Phytologist (2017) mapped putative WGDs as identified from analyses on transcriptomic and genomic data and doi: 10.1111/nph.14772 analyzed these in conjunction with shifts in climatic occupancy and lineage diversification rate. Thirteen putative WGDs and 27 diversification shifts could be mapped onto the phylogeny. Key words: Caryophyllales, climatic occupancy, diversification rates, duplications, Of these, four WGDs were concurrent with diversification shifts, with other diversification phylogenomics. -
A Taxonomic Backbone for the Global Synthesis of Species Diversity in the Angiosperm Order Caryophyllales
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2015 A taxonomic backbone for the global synthesis of species diversity in the angiosperm order Caryophyllales Hernández-Ledesma, Patricia; Berendsohn, Walter G; Borsch, Thomas; Mering, Sabine Von; Akhani, Hossein; Arias, Salvador; Castañeda-Noa, Idelfonso; Eggli, Urs; Eriksson, Roger; Flores-Olvera, Hilda; Fuentes-Bazán, Susy; Kadereit, Gudrun; Klak, Cornelia; Korotkova, Nadja; Nyffeler, Reto; Ocampo, Gilberto; Ochoterena, Helga; Oxelman, Bengt; Rabeler, Richard K; Sanchez, Adriana; Schlumpberger, Boris O; Uotila, Pertti Abstract: The Caryophyllales constitute a major lineage of flowering plants with approximately 12500 species in 39 families. A taxonomic backbone at the genus level is provided that reflects the current state of knowledge and accepts 749 genera for the order. A detailed review of the literature of the past two decades shows that enormous progress has been made in understanding overall phylogenetic relationships in Caryophyllales. The process of re-circumscribing families in order to be monophyletic appears to be largely complete and has led to the recognition of eight new families (Anacampserotaceae, Kewaceae, Limeaceae, Lophiocarpaceae, Macarthuriaceae, Microteaceae, Montiaceae and Talinaceae), while the phylogenetic evaluation of generic concepts is still well underway. As a result of this, the number of genera has increased by more than ten percent in comparison to the last complete treatments in the Families and genera of vascular plants” series. A checklist with all currently accepted genus names in Caryophyllales, as well as nomenclatural references, type names and synonymy is presented. Notes indicate how extensively the respective genera have been studied in a phylogenetic context.