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Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Bruce G. Baldwin, Chair Dr. John P. Huelsenbeck Dr. Brent D. Mishler Dr. Kipling W. Will Fall 2017 Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Copyright 2017 by William Allen Freyman Abstract Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Dr. Bruce G. Baldwin, Chair Key evolutionary transitions have shaped the tree of life by driving the processes of spe- ciation and extinction. This dissertation aims to advance statistical and computational ap- proaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model- based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the miss- ing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. -
2015 Summary of Changes to Endangered, Threatened, And
2015 Update to State Listed Species The Department of Energy and Environmental Protection (DEEP) is required to review, at least every five years, the designation of species as endangered, threatened, or of special concern to determine whether species should be: (1) added or removed from the list; or, if necessary, (2) change the designation from one category to another. The following is a summary of the changes to the State Endangered Species list (DEEP Regulations Sections 26‐306‐4, 26‐306‐5, and 26‐306‐6) that became effective on August 5, 2015. The complete list can be found on the DEEP website. Summary of Amphibian Changes New species added Necturus maculosus, Mudpuppy added as Special Concern Summary of Reptile Changes New species added Clemmys guttata, Spotted turtle added as Special Concern Malaclemys terrapin terrapin, Northern diamondback terrapin added as Special Concern Taxonomic Changes Eumeces fasciatus, Five‐lined skink changed to Plestiodon fasciatus Liochlorophis vernalis, Smooth green snake changed to Opheodrys vernalis Summary of Bird Changes Northern diamondback terrapin Status Changes Falco sparverius, American kestrel downlisted to Special Concern Progne subis, Purple martin downlisted to Special Concern Sturnella magna, Eastern meadowlark uplisted to Threatened New species added Accipiter gentilis, Northern goshawk added as Threatened Setophaga cerulea, Cerulean warbler added as Special Concern Species delisted Anas discors, Blue‐winged teal Laterallus jamaicensis, Black rail Cerulean warbler Taxonomic changes Parula americana, Northern parula changed to Setophaga americana 1 Summary of Mammal Changes Status Changes Myotis leibii, Eastern small‐footed bat uplisted to Endangered New Species Added Myotis lucifugus, Little brown bat added as Endangered Myotis septentrionalis, Northern long‐eared bat added as Endangered (also Federally Threatened) Perimyotis subflavus, Tri‐colored bat added as Endangered Taxonomic Changes Phocoena phocoena, Harbor porpoise changed to Phocoena Northern long‐eared bat phocoena ssp. -
Bee-Friendly Flowers: Aster
Bee-Friendly Flowers: Aster Like fireworks to celebrate the coming of fall, the vibrant pinks, purples, and whites of the star flowers burst into bloom just as summer flowers fade. They are ubiquitous, lighting up meadows, woodlands, river bottoms, salt marshes, sand dunes, roadsides, and waste places. There are many native species of asters in North America, but it’s hard to put a precise number on them. The problem is that asters used to be classified with their own genus, but recent strides in DNA analysis have made scientists rethink where to put them. Plants that used to be lumped into the genus Aster are now split into Symphiotrichum, Eurybia, Solidago, and Machaeranthera just to name a few. Not all taxonomists are onboard with the change, so many botanical New England aster sources list more than one name for the same plant. Despite the confusion about what to call them, the variety of asters is enormous. Hybridization between species frequently occurs in the wild and there are a plethora of human-created hybrids and cultivars. Some have clouds of tiny flowers and some have blossoms as large as daisies. What they all have in common is that each aster flower is a composite of numerous disc and ray florets, which collectively give the appearance of a single large flower. The center holds the disc florets, which are tubular, house the nectar, and are usually yellow, orange, or brownish in color. Those near the bullseye location have both stamens and pistils and can provide pollen to visiting insects. The outer discs are all females and only have pistils to receive pollen. -
"National List of Vascular Plant Species That Occur in Wetlands: 1996 National Summary."
Intro 1996 National List of Vascular Plant Species That Occur in Wetlands The Fish and Wildlife Service has prepared a National List of Vascular Plant Species That Occur in Wetlands: 1996 National Summary (1996 National List). The 1996 National List is a draft revision of the National List of Plant Species That Occur in Wetlands: 1988 National Summary (Reed 1988) (1988 National List). The 1996 National List is provided to encourage additional public review and comments on the draft regional wetland indicator assignments. The 1996 National List reflects a significant amount of new information that has become available since 1988 on the wetland affinity of vascular plants. This new information has resulted from the extensive use of the 1988 National List in the field by individuals involved in wetland and other resource inventories, wetland identification and delineation, and wetland research. Interim Regional Interagency Review Panel (Regional Panel) changes in indicator status as well as additions and deletions to the 1988 National List were documented in Regional supplements. The National List was originally developed as an appendix to the Classification of Wetlands and Deepwater Habitats of the United States (Cowardin et al.1979) to aid in the consistent application of this classification system for wetlands in the field.. The 1996 National List also was developed to aid in determining the presence of hydrophytic vegetation in the Clean Water Act Section 404 wetland regulatory program and in the implementation of the swampbuster provisions of the Food Security Act. While not required by law or regulation, the Fish and Wildlife Service is making the 1996 National List available for review and comment. -
The Vascular Plants of Massachusetts
The Vascular Plants of Massachusetts: The Vascular Plants of Massachusetts: A County Checklist • First Revision Melissa Dow Cullina, Bryan Connolly, Bruce Sorrie and Paul Somers Somers Bruce Sorrie and Paul Connolly, Bryan Cullina, Melissa Dow Revision • First A County Checklist Plants of Massachusetts: Vascular The A County Checklist First Revision Melissa Dow Cullina, Bryan Connolly, Bruce Sorrie and Paul Somers Massachusetts Natural Heritage & Endangered Species Program Massachusetts Division of Fisheries and Wildlife Natural Heritage & Endangered Species Program The Natural Heritage & Endangered Species Program (NHESP), part of the Massachusetts Division of Fisheries and Wildlife, is one of the programs forming the Natural Heritage network. NHESP is responsible for the conservation and protection of hundreds of species that are not hunted, fished, trapped, or commercially harvested in the state. The Program's highest priority is protecting the 176 species of vertebrate and invertebrate animals and 259 species of native plants that are officially listed as Endangered, Threatened or of Special Concern in Massachusetts. Endangered species conservation in Massachusetts depends on you! A major source of funding for the protection of rare and endangered species comes from voluntary donations on state income tax forms. Contributions go to the Natural Heritage & Endangered Species Fund, which provides a portion of the operating budget for the Natural Heritage & Endangered Species Program. NHESP protects rare species through biological inventory, -
State of New York City's Plants 2018
STATE OF NEW YORK CITY’S PLANTS 2018 Daniel Atha & Brian Boom © 2018 The New York Botanical Garden All rights reserved ISBN 978-0-89327-955-4 Center for Conservation Strategy The New York Botanical Garden 2900 Southern Boulevard Bronx, NY 10458 All photos NYBG staff Citation: Atha, D. and B. Boom. 2018. State of New York City’s Plants 2018. Center for Conservation Strategy. The New York Botanical Garden, Bronx, NY. 132 pp. STATE OF NEW YORK CITY’S PLANTS 2018 4 EXECUTIVE SUMMARY 6 INTRODUCTION 10 DOCUMENTING THE CITY’S PLANTS 10 The Flora of New York City 11 Rare Species 14 Focus on Specific Area 16 Botanical Spectacle: Summer Snow 18 CITIZEN SCIENCE 20 THREATS TO THE CITY’S PLANTS 24 NEW YORK STATE PROHIBITED AND REGULATED INVASIVE SPECIES FOUND IN NEW YORK CITY 26 LOOKING AHEAD 27 CONTRIBUTORS AND ACKNOWLEGMENTS 30 LITERATURE CITED 31 APPENDIX Checklist of the Spontaneous Vascular Plants of New York City 32 Ferns and Fern Allies 35 Gymnosperms 36 Nymphaeales and Magnoliids 37 Monocots 67 Dicots 3 EXECUTIVE SUMMARY This report, State of New York City’s Plants 2018, is the first rankings of rare, threatened, endangered, and extinct species of what is envisioned by the Center for Conservation Strategy known from New York City, and based on this compilation of The New York Botanical Garden as annual updates thirteen percent of the City’s flora is imperiled or extinct in New summarizing the status of the spontaneous plant species of the York City. five boroughs of New York City. This year’s report deals with the City’s vascular plants (ferns and fern allies, gymnosperms, We have begun the process of assessing conservation status and flowering plants), but in the future it is planned to phase in at the local level for all species. -
Literature Cited
Literature Cited Robert W. Kiger, Editor This is a consolidated list of all works cited in volumes 19, 20, and 21, whether as selected references, in text, or in nomenclatural contexts. In citations of articles, both here and in the taxonomic treatments, and also in nomenclatural citations, the titles of serials are rendered in the forms recommended in G. D. R. Bridson and E. R. Smith (1991). When those forms are abbre- viated, as most are, cross references to the corresponding full serial titles are interpolated here alphabetically by abbreviated form. In nomenclatural citations (only), book titles are rendered in the abbreviated forms recommended in F. A. Stafleu and R. S. Cowan (1976–1988) and F. A. Stafleu and E. A. Mennega (1992+). Here, those abbreviated forms are indicated parenthetically following the full citations of the corresponding works, and cross references to the full citations are interpolated in the list alphabetically by abbreviated form. Two or more works published in the same year by the same author or group of coauthors will be distinguished uniquely and consistently throughout all volumes of Flora of North America by lower-case letters (b, c, d, ...) suffixed to the date for the second and subsequent works in the set. The suffixes are assigned in order of editorial encounter and do not reflect chronological sequence of publication. The first work by any particular author or group from any given year carries the implicit date suffix “a”; thus, the sequence of explicit suffixes begins with “b”. Works missing from any suffixed sequence here are ones cited elsewhere in the Flora that are not pertinent in these volumes. -
Natural Heritage Program List of Rare Plant Species of North Carolina 2012
Natural Heritage Program List of Rare Plant Species of North Carolina 2012 Edited by Laura E. Gadd, Botanist John T. Finnegan, Information Systems Manager North Carolina Natural Heritage Program Office of Conservation, Planning, and Community Affairs N.C. Department of Environment and Natural Resources 1601 MSC, Raleigh, NC 27699-1601 Natural Heritage Program List of Rare Plant Species of North Carolina 2012 Edited by Laura E. Gadd, Botanist John T. Finnegan, Information Systems Manager North Carolina Natural Heritage Program Office of Conservation, Planning, and Community Affairs N.C. Department of Environment and Natural Resources 1601 MSC, Raleigh, NC 27699-1601 www.ncnhp.org NATURAL HERITAGE PROGRAM LIST OF THE RARE PLANTS OF NORTH CAROLINA 2012 Edition Edited by Laura E. Gadd, Botanist and John Finnegan, Information Systems Manager North Carolina Natural Heritage Program, Office of Conservation, Planning, and Community Affairs Department of Environment and Natural Resources, 1601 MSC, Raleigh, NC 27699-1601 www.ncnhp.org Table of Contents LIST FORMAT ......................................................................................................................................................................... 3 NORTH CAROLINA RARE PLANT LIST ......................................................................................................................... 10 NORTH CAROLINA PLANT WATCH LIST ..................................................................................................................... 71 Watch Category -
Winter 2014-2015 (22:3) (PDF)
Contents NATIVE NOTES Page Fern workshop 1-2 Wavey-leaf basket Grass 3 Names Cacalia 4 Trip Report Sandstone Falls 5 Kate’s Mountain Clover* Trip Report Brush Creek Falls 6 Thank yous memorial 7 WEST VIRGINIA NATIVE PLANT SOCIETY NEWSLETTER News of WVNPS 8 VOLUME 22:3 WINTER 2014-15 Events, Dues Form 9 Judy Dumke-Editor: [email protected] Phone 740-894-6859 Magnoliales 10 e e e visit us at www.wvnps.org e e e . Fern Workshop University of Charleston Charleston WV January 17 2015, bad weather date January 24 2015 If you have thought about ferns, looked at them, puzzled over them or just want to know more about them join the WVNPS in Charleston for a workshop led by Mark Watson of the University of Charleston. The session will start at 10 A.M. with a scheduled end point by 12:30 P.M. A board meeting will follow. The sessions will be held in the Clay Tower Building (CTB) room 513, which is the botany lab. If you have any pressed specimens to share, or to ask about, be sure to bring them with as much information as you have on the location and habitat. Even photographs of ferns might be of interest for the session. If you have a hand lens that you favor bring it along as well. DIRECTIONS From the North: Travel I-77 South or 1-79 South into Charleston. Follow the signs to I-64 West. Take Oakwood Road Exit 58A and follow the signs to Route 61 South (MacCorkle Ave.). -
22 Foodplant Ecology of the Butterfly Chlosyne Lacinia
22 JOURNAL OF THE LEPIDOPTERISTS' SOCIETY 1972. Coevolution: patterns of legume predation by a lycaenid butterfly. Oecologia, in press. BRUSSARD, P. F . & P. R. EHRLICH. 1970. Contrasting population biology of two species of butterflies. Nature 227: 91-92. DETmER, V. G. 1959. Food-plant distribution and density and larval dispersal as factors affecting insect populations. Can. Entomol. 91 : 581-596. DOWNEY, J. C. & W. C. FULLER. 1961. Variation in Plebe;us icarioides (Lycaeni dae ) 1. Food-plant specificity. J. Lepid. Soc. 15( 1) : 34-52. EHRLICH, P. R. & P. H. RAVEN. 1964. Butterflies and plants: a study in coevolu tion. Evolution 18: 586-608. GILBERT, L. E. 1971. The effect of resource distribution on population structure in the butterfly Euphydryas editha: Jasper Ridge vs. Del Puerto Canyon colonies. Ph.D. dissertation, Stanford University. SINGER, M. C. 1971. Evolution of food-plant preference in the butterfly Euphydryas editha. Evolution 25: 383-389. FOODPLANT ECOLOGY OF THE BUTTERFLY CHLOSYNE LACINIA (GEYER) (NYMPHALIDAE). 1. LARVAL FOODPLANTS RAYMOND \;y. NECK D epartment of Zoology, University of Texas at Austin, Austin, Texas 78712 For several years I have studied field populations of Chlosyne lacinia ( Geyer) (N ymphalidae: Melitaeini) in central and south Texas for genetic (Neck et aI., 1971) and ecological genetic data. A considerable amount of information concerning foodplants of this species has been collected. Foodplant utilization information is an important base from which ecological studies may emerge. Such information is also invaluable in evaluating the significance of tested foodplant preferences of larvae and adults. Such studies have been under way by other investigators and will be available for comparison with natural population observa tions. -
Erigeron Speciosus (Lindl.) DC
ASPEN FLEABANE Erigeron speciosus (Lindl.) DC. Asteraceae – Aster family Corey L. Gucker & Nancy L. Shaw | 2018 ORGANIZATION NOMENCLATURE Erigeron speciosus (Lind.) DC., hereafter Names, subtaxa, chromosome number(s), hybridization. referred to as aspen fleabane, belongs to the Astereae tribe of the Asteraceae or aster family (Nesom 2006). Range, habitat, plant associations, elevation, soils. NRCS Plant Code. ERSP4 (USDA NRCS 2018). Synonyms. Erigeron conspicuus Rydberg; E. macranthus Nuttall; E. speciosus var. conspicuus (Rydberg) Breitung; E. speciosus Life form, morphology, distinguishing characteristics, reproduction. var. macranthus (Nuttall) Cronquist; E. subtrinervis Rydberg ex Porter & Britton subsp. conspicuus (Rydberg) Cronquist; Growth rate, successional status, disturbance ecology, importance to E. subtrinervis var. conspicuus (Rydberg) animals/people. Cronquist, Stenactis speciosa Lindley (Nesom 2006). Current or potential uses in restoration. Common Names. Aspen fleabane, Oregon fleabane, Oregon wild-daisy, showy daisy, showy fleabane (USDA FS 1937; Nesom 2006; AOSA 2016; USDA NRCS 2018). Seed sourcing, wildland seed collection, seed cleaning, storage, testing and marketing standards. Subtaxa. No varieties or subspecies are currently recognized by the Flora of North America (Nesom 2006). Recommendations/guidelines for producing seed. Chromosome Number. Chromosome numbers are 2n = 18, 36 (Jones and Young 1983; Welsh et al. 1987). Recommendations/guidelines for producing planting stock. Hybridization. Distributions of aspen fleabane and threenerve fleabane (E. subtrinervis) have considerable overlap, and although they are Recommendations/guidelines, wildland restoration successes/ considered at least partially reproductively failures. isolated, intermediate forms are common (Nesom 2006). Primary funding sources, chapter reviewers. DISTRIBUTION Bibliography. Aspen fleabane is widely distributed throughout western North America. In Canada, it occurs in British Columbia and Alberta. -
New York Aster
Distribution: New York aster ranges from NEW YORK ASTER Newfoundland and Nova Scotia south to Georgia, apparently to Alabama, chiefly near the coast (Tiner Symphyotrichum novi-belgii 1987). For current distribution, please consult the (L.) Nesom var. novi-belgii Plant profile page for this species on the PLANTS plant symbol = SYNON Web site. Contributed By: USDA, NRCS, National Plant Data Adaptation Center New York aster is found growing in slightly brackish and tidal fresh marshes, occasionally borders of salt marshes; inland marshes, shrub marshes, shores and other moist areas (Tiner 1987). This plant requires well-drained soil and prefers sandy, loamy and clay soils. It can grow on nutritionally poor soil, in semi- shade or no shade but prefers a sunny location. Establishment Propagation by Seed: New York aster seeds should be sown fresh in the fall or spring (Heuser 1997). Pre-chill spring sown seeds to improve germination. When the seedlings are large enough to handle, place © Don Kurz them into individual pots and plant them out in the @ PLANTS summer. Division of this species should be done in the spring. Large divisions can be planted into their Alternative Name Michaelmas daisy, Aster novi-belgii (ASNO2) permanent positions whereas smaller clumps should be kept in a cold frame until they are growing well. Uses Landscape: New York aster is an excellent upright Management perennial for a mixed bed or border. This species Divisions of New York aster should be done in the provides a color accent, bringing autumn color to the spring every three years to maintain vigor (Heuser garden.