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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. -
"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. -
A General Idea About Phytomelanin Layer in Some
Indian Journal of Plant Sciences ISSN: 2319-3824 (Online) An Online International Journal Available at http://www.cibtech.org/jps.htm 2013 Vol. 2 (4) October-December, pp.44-48/Jana and Mukherjee Review Article A GENERAL IDEA ABOUT PHYTOMELANIN LAYER IN SOME COMPOSITAE *Jana Bidyut Kumar and Mukherjee Sobhan Kumar Taxonomy and Biosystematics Laboratory, Department of Botany, University of Kalyani, Kalyani- 741235, Nadia, West Bengal, India *Author for Correspondence ABSTRACT The present paper deals with the general idea about the phytomelanin layer, on the surface of cypsela of some Compositae, with the help of both compound light microscope and scanning electrone microscope. Phytomelanin layer is made up of hard, black, water resistant resinous or tanniniferous or polyvinyl alcohol containing disputed substance, usually found in the cypselar wall of some members of the family Compositae belonging to the tribes-Coreopsideae, Helenieae, Heliantheae, Eupatorieae, Millerieae, Perityleae etc. Key Words: Phytomelanin Layer; Cypselar Surface; Compositae INTRODUCTION The Compositae are regarded as a fairly advanced family of the dicotyledons (Takhtajan, 1997) and are one of the largest family of angiosperms, consisting of 43 tribes, 1600- 1700 genera and 24000 species (Funk et al., 2009). Many members of the Compositae are cosmopolitan, found specially in temperate or tropical montane regions and open and / or dry habitats. Phytomelanin layer is made up of a type of hard, black, water resistant resinous or tanniniferous or polyvinyl alcohol containing disputed phytomelanin substance, usually found in the cypselar wall of some members of the family Compositae belonging to the tribes Coreopsideae (Jana and Mukherjee, 2012), Heliantheae, Eupatorieae (Pandey and Dakhal, 2001) etc. -
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. -
Characterization of Hybrids from Crosses Between Cultivated Helianthus Annuus L
Wild Species and Genetic Resources Characterization of hybrids from crosses between cultivated Helianthus annuus L. and subspecies rydbergii (Britton) Long of perennial diploid Helianthus nuttallii Miroslava M. Hristova-Cherbadzi, Michail Christov Dobroudja Agricultural Institute, General Toshevo 9520, Bulgaria, E-mail: [email protected]; [email protected] ABSTRACT The subspecies rydbergii (Britton) Long of the perennial diploid species Helianthus nuttallii was included in hybridization with the cultivated sunflower Helianthus annuus L. The investigation encompassed the period 1999-2007. H. nuttallii ssp. rydbergii could be crossed with the cultivated sunflower, but hybridization was difficult and the crossability rate was low. Seeds were obtained at both directions of crossing and hybrid plants - from the direct crosses. All F1 plants showed an annual growth cycle. The heritability in first generation was intermediate but the plants strongly resembled the wild species in their most important biomorphological traits. The polymorphism between H. annuus, H. nuttallii spp. rydbergii and their F1 hybrids was studied by RAPD. The F1 plants were also cytologically investigated. From H. nuttallii ssp. rydbergii were transferred in F1 genes that controlled such characters as, period of vegetation, plant height, type of branching, size and form of inflorescence and seeds, degree of anthocyanin coloration, seed oil content (60.84%), resistance to Plasmopara helianthi, races 300 and 700, Phomopsis helianthi, Phoma macdonaldii and Orobanche cumana. It was established that the subspecies was a source of Rf gene for CMS Pet-1 and the control was dominant and monogenic. As a result of self- pollination, sib-pollination of the F1 plants and back-crossing with cultivated sunflower, F2, BC1 were obtained. -
VASCULAR PLANTS of MINNESOTA a Checklist and Atlas
VASCULAR PLANTS of MINNESOTA This page intentionally left blank VASCULAR PLANTS of MINNESOTA A Checklist and Atlas Gerald B. Ownbey and Thomas Morley UNIVERSITY OF MINNESOTA MINNEAPOLIS • LONDON The University of Minnesota Press gratefully acknowledges the generous assistance provided for the publication of this book by the Margaret W. Harmon Fund Minnesota Department of Transportation Minnesota Landscape Arboretum Minnesota State Horticultural Society Olga Lakela Herbarium Fund—University of Minnesota—Duluth Natural Heritage Program of the Minnesota Department of Natural Resources Copyright © 1991 by the Regents of the University of Minnesota. First paperback printing 1992 All rights reserved. No part of this publication may be reproduced, stored in a retrieval system, or transmitted, in any form or by any means, electronic, mechanical, photocopying, recording, or otherwise, without the prior written permission of the publisher. Published by the University of Minnesota Press 2037 University Avenue Southeast, Minneapolis, MN 55455 Printed in the United States of America on acid-free paper Library of Congress Cataloging-in-Publication Data Ownbey, Gerald B., 1916- Vascular plants of Minnesota : a checklist and atlas / Gerald B. Ownbey and Thomas Morley. p. cm. Includes bibliographical references and index. ISBN 0-8166-1915-8 1. Botany-Minnesota. 2. Phytogeography—Minnesota— Maps. I. Morley, Thomas. 1917- . II. Title. QK168.096 1991 91-2064 582.09776-dc20 CIP The University of Minnesota is an equal-opportunity educator and employer. Contents Introduction vii Part I. Checklist of the Vascular Plants of Minnesota 1 Pteridophytes 3 Gymnosperms 6 Angiosperms 7 Appendix 1. Excluded names 81 Appendix 2. Tables 82 Part II. Atlas of the Vascular Plants of Minnesota 83 Index of Generic and Common Names 295 This page intentionally left blank Introduction The importance of understanding the vegetation of al distributional comments. -
Appendix O – Biological Resources Technical Memorandum and Tree Removal Plan
ONE METRO WEST DRAFT FINAL ENVIRONMENTAL IMPACT REPORT – VOLUME I TECHNICAL APPENDICES Appendices Appendix O Biological Resources Technical Memorandum and Tree Removal Plan February 2020April 2021 ONE METRO WEST DRAFT FINAL ENVIRONMENTAL IMPACT REPORT – VOLUME I TECHNICAL APPENDICES Appendices This page intentionally left blank. February 2020April 2021 CARLSBAD FRESNO IRVINE LOS ANGELES PALM SPRINGS POINT RICHMOND RIVERSIDE MEMORANDUM ROSEVILLE SAN LUIS OBISPO DATE: May 30, 2019 TO: Ryan Bensley, Associate FROM: Heather Monteleone, Assistant Biologist Bo Gould, Senior Biologist SUBJECT: Biological Resources Technical Memorandum for One Metro West (LSA Project No. RSE1901) This technical memorandum serves as a biological resources assessment for the One Metro West Project (project) in Costa Mesa, California. The purpose of this assessment is to determine whether biological resources—including sensitive and/or special-status plant and wildlife species—may be present on the project site, whether such resources might be affected by the project, and to make recommendations to avoid, reduce, and/or mitigate any potentially significant impacts to biological resources, as applicable. This technical information is provided for project planning purposes and review under the California Environmental Quality Act (CEQA), California Endangered Species Act (CESA), the federal Endangered Species Act (FESA), and other pertinent regulations. PROJECT DESCRIPTION The proposed project is a mixed-use development that would consist of residential, specialty retail, creative office, and recreation uses. The vision of the project is to create a mixed-use community that would provide housing near jobs in a campus-like setting with on-site amenities, a 1.7-acre open space area, and connection to bicycle trails. -
Annotated Checklist of the Vascular Plant Flora of Grand Canyon-Parashant National Monument Phase II Report
Annotated Checklist of the Vascular Plant Flora of Grand Canyon-Parashant National Monument Phase II Report By Dr. Terri Hildebrand Southern Utah University, Cedar City, UT and Dr. Walter Fertig Moenave Botanical Consulting, Kanab, UT Colorado Plateau Cooperative Ecosystems Studies Unit Agreement # H1200-09-0005 1 May 2012 Prepared for Grand Canyon-Parashant National Monument Southern Utah University National Park Service Mojave Network TABLE OF CONTENTS Page # Introduction . 4 Study Area . 6 History and Setting . 6 Geology and Associated Ecoregions . 6 Soils and Climate . 7 Vegetation . 10 Previous Botanical Studies . 11 Methods . 17 Results . 21 Discussion . 28 Conclusions . 32 Acknowledgments . 33 Literature Cited . 34 Figures Figure 1. Location of Grand Canyon-Parashant National Monument in northern Arizona . 5 Figure 2. Ecoregions and 2010-2011 collection sites in Grand Canyon-Parashant National Monument in northern Arizona . 8 Figure 3. Soil types and 2010-2011 collection sites in Grand Canyon-Parashant National Monument in northern Arizona . 9 Figure 4. Increase in the number of plant taxa confirmed as present in Grand Canyon- Parashant National Monument by decade, 1900-2011 . 13 Figure 5. Southern Utah University students enrolled in the 2010 Plant Anatomy and Diversity course that collected during the 30 August 2010 experiential learning event . 18 Figure 6. 2010-2011 collection sites and transportation routes in Grand Canyon-Parashant National Monument in northern Arizona . 22 2 TABLE OF CONTENTS Page # Tables Table 1. Chronology of plant-collecting efforts at Grand Canyon-Parashant National Monument . 14 Table 2. Data fields in the annotated checklist of the flora of Grand Canyon-Parashant National Monument (Appendices A, B, C, and D) . -
Waterton Lakes National Park • Common Name(Order Family Genus Species)
Waterton Lakes National Park Flora • Common Name(Order Family Genus species) Monocotyledons • Arrow-grass, Marsh (Najadales Juncaginaceae Triglochin palustris) • Arrow-grass, Seaside (Najadales Juncaginaceae Triglochin maritima) • Arrowhead, Northern (Alismatales Alismataceae Sagittaria cuneata) • Asphodel, Sticky False (Liliales Liliaceae Triantha glutinosa) • Barley, Foxtail (Poales Poaceae/Gramineae Hordeum jubatum) • Bear-grass (Liliales Liliaceae Xerophyllum tenax) • Bentgrass, Alpine (Poales Poaceae/Gramineae Podagrostis humilis) • Bentgrass, Creeping (Poales Poaceae/Gramineae Agrostis stolonifera) • Bentgrass, Green (Poales Poaceae/Gramineae Calamagrostis stricta) • Bentgrass, Spike (Poales Poaceae/Gramineae Agrostis exarata) • Bluegrass, Alpine (Poales Poaceae/Gramineae Poa alpina) • Bluegrass, Annual (Poales Poaceae/Gramineae Poa annua) • Bluegrass, Arctic (Poales Poaceae/Gramineae Poa arctica) • Bluegrass, Plains (Poales Poaceae/Gramineae Poa arida) • Bluegrass, Bulbous (Poales Poaceae/Gramineae Poa bulbosa) • Bluegrass, Canada (Poales Poaceae/Gramineae Poa compressa) • Bluegrass, Cusick's (Poales Poaceae/Gramineae Poa cusickii) • Bluegrass, Fendler's (Poales Poaceae/Gramineae Poa fendleriana) • Bluegrass, Glaucous (Poales Poaceae/Gramineae Poa glauca) • Bluegrass, Inland (Poales Poaceae/Gramineae Poa interior) • Bluegrass, Fowl (Poales Poaceae/Gramineae Poa palustris) • Bluegrass, Patterson's (Poales Poaceae/Gramineae Poa pattersonii) • Bluegrass, Kentucky (Poales Poaceae/Gramineae Poa pratensis) • Bluegrass, Sandberg's (Poales -
High Frequencies of Triploids Obtained from Interspecific Crosses Involving
G3: Genes|Genomes|Genetics Early Online, published on February 7, 2017 as doi:10.1534/g3.116.036327 1 Triploid Production from Interspecific Crosses of Two Diploid Perennial Helianthus 2 with Diploid Cultivated Sunflower (Helianthus annuus L.) 3 4 Zhao Liu1*, Gerald J. Seiler2, Thomas J. Gulya2, Jiuhuan Feng3, Khalid Y. Rashid4, Xiwen Cai1, 5 Chao-Chien Jan2* 6 7 1Department of Plant Sciences, North Dakota State University, Fargo, ND 58108, USA 8 2USDA-ARS, Northern Crop Science Laboratory, Fargo, ND 58102, USA 9 3Plant Science Department, South Dakota State University, Brookings, SD 57007, USA 10 4Agriculture and Agri-Food Canada, Morden, Manitoba, R6M 1Y5, Canada 11 12 Key words: Helianthus; triploids; genomic in situ hybridization (GISH); mitotic analysis; 13 meiotic analysis 14 15 Corresponding author: Chao-Chien Jan 16 Mailing address: USDA-ARS, NCSL, 1605 Albrecht Blvd N, Fargo, ND58102-2765, USA 17 Phone: 701-239-1319 18 E-mail: [email protected] 19 20 Co-corresponding author: Zhao Liu 21 Mailing address: USDA-ARS, NCSL, 1605 Albrecht Blvd N, Fargo, ND58102-2765, USA 22 Phone: 701-239-1324 23 E-mail: [email protected] 24 1 © The Author(s) 2013. Published by the Genetics Society of America. 25 Running title: Novel triploid production in Helianthus 2 26 ABSTRACT 27 Wild Helianthus species are a valuable genetic resource for the improvement of cultivated 28 sunflower. We report the discovery and characterization of a unique high frequency production 29 of triploids when cultivated sunflower was pollinated by specific accessions of diploid 30 Helianthus nuttallii T. &. G. and H. -
Copyright by Ruth Evangeline Timme 2006
Copyright by Ruth Evangeline Timme 2006 The Dissertation Committee for Ruth Evangeline Timme Certifies that this is the approved version of the following dissertation: Reticulate Evolution in Helianthus (Asteraceae) Committee: C. Randal Linder, Supervisor Beryl B. Simpson, Co-Supervisor Robert K. Jansen Thomas E. Juenger David M. Hillis Reticulate Evolution in Helianthus (Asteraceae) by Ruth Evangeline Timme, B.S.; M.A. Dissertation Presented to the Faculty of the Graduate School of The University of Texas at Austin in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy The University of Texas at Austin August 2006 Acknowledgements First, I want to thank both of my advisors: Randy Linder for his funding for my project and providing me with an RAship for two years, and both Randy Linder and my co-advisor, Beryl Simpson, for all their helpful advise and support during my time at UT. They both have been so willing to help at a moments notice and have been excellent advisors. I also want to thank Bob Jansen who advised my on my fourth chapter and has served as an informal third advisor for my dissertation. My other two committee members, Tom Juenger and David Hillis were also very accommodating throughout the years in scheduling committee meetings and in giving insightful comments and feedback to my research. I am also grateful to Sheri Church and Eric Baack for sending me leaf material and allowing me to use a molecular marker they had developed in the Rieseberg lab. Also Sherri Church performed two plates of sequences for the polyploids and has been very helpful in discussions regarding my project. -
FERNS and FERN ALLIES Dittmer, H.J., E.F
FERNS AND FERN ALLIES Dittmer, H.J., E.F. Castetter, & O.M. Clark. 1954. The ferns and fern allies of New Mexico. Univ. New Mexico Publ. Biol. No. 6. Family ASPLENIACEAE [1/5/5] Asplenium spleenwort Bennert, W. & G. Fischer. 1993. Biosystematics and evolution of the Asplenium trichomanes complex. Webbia 48:743-760. Wagner, W.H. Jr., R.C. Moran, C.R. Werth. 1993. Aspleniaceae, pp. 228-245. IN: Flora of North America, vol.2. Oxford Univ. Press. palmeri Maxon [M&H; Wagner & Moran 1993] Palmer’s spleenwort platyneuron (Linnaeus) Britton, Sterns, & Poggenburg [M&H; Wagner & Moran 1993] ebony spleenwort resiliens Kunze [M&H; W&S; Wagner & Moran 1993] black-stem spleenwort septentrionale (Linnaeus) Hoffmann [M&H; W&S; Wagner & Moran 1993] forked spleenwort trichomanes Linnaeus [Bennert & Fischer 1993; M&H; W&S; Wagner & Moran 1993] maidenhair spleenwort Family AZOLLACEAE [1/1/1] Azolla mosquito-fern Lumpkin, T.A. 1993. Azollaceae, pp. 338-342. IN: Flora of North America, vol. 2. Oxford Univ. Press. caroliniana Willdenow : Reports in W&S apparently belong to Azolla mexicana Presl, though Azolla caroliniana is known adjacent to NM near the Texas State line [Lumpkin 1993]. mexicana Schlechtendal & Chamisso ex K. Presl [Lumpkin 1993; M&H] Mexican mosquito-fern Family DENNSTAEDTIACEAE [1/1/1] Pteridium bracken-fern Jacobs, C.A. & J.H. Peck. Pteridium, pp. 201-203. IN: Flora of North America, vol. 2. Oxford Univ. Press. aquilinum (Linnaeus) Kuhn var. pubescens Underwood [Jacobs & Peck 1993; M&H; W&S] bracken-fern Family DRYOPTERIDACEAE [6/13/13] Athyrium lady-fern Kato, M. 1993. Athyrium, pp.