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Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics Author(S): Kevin Weitemier, Shannon C
Hyb-Seq: Combining Target Enrichment and Genome Skimming for Plant Phylogenomics Author(s): Kevin Weitemier, Shannon C. K. Straub, Richard C. Cronn, Mark Fishbein, Roswitha Schmickl, Angela McDonnell, and Aaron Liston Source: Applications in Plant Sciences, 2(9) 2014. Published By: Botanical Society of America DOI: http://dx.doi.org/10.3732/apps.1400042 URL: http://www.bioone.org/doi/full/10.3732/apps.1400042 BioOne (www.bioone.org) is a nonprofit, online aggregation of core research in the biological, ecological, and environmental sciences. BioOne provides a sustainable online platform for over 170 journals and books published by nonprofit societies, associations, museums, institutions, and presses. Your use of this PDF, the BioOne Web site, and all posted and associated content indicates your acceptance of BioOne’s Terms of Use, available at www.bioone.org/page/terms_of_use. Usage of BioOne content is strictly limited to personal, educational, and non-commercial use. Commercial inquiries or rights and permissions requests should be directed to the individual publisher as copyright holder. BioOne sees sustainable scholarly publishing as an inherently collaborative enterprise connecting authors, nonprofit publishers, academic institutions, research libraries, and research funders in the common goal of maximizing access to critical research. Applications Applications in Plant Sciences 2014 2 ( 9 ): 1400042 in Plant Sciences P ROTOCOL NOTE H YB-SEQ: COMBINING TARGET ENRICHMENT AND GENOME 1 SKIMMING FOR PLANT PHYLOGENOMICS K EVIN W EITEMIER -
Genomic Investigations of Diversity Within the Milkweed Genus Asclepias, at Multiple Scales
AN ABSTRACT OF THE DISSERTATION OF Kevin A. Weitemier for the degree of Doctor of Philosophy in Botany and Plant Pathology presented on September 7, 2016. Title: Genomic Investigations of Diversity within the Milkweed Genus Asclepias, at Multiple Scales Abstract approved: ________________________________________________________________________ Aaron I. Liston At a time when the biodiversity on Earth is being rapidly lost, new technologies and methods in genomic analysis are fortunately allowing scientists to catalog and explore the diversity that remains more efficiently and precisely. The studies in this dissertation investigate genomic diversity within the milkweed genus, Asclepias, at multiple scales, including diversity found within a single individual, diversity within and among populations in a species, and diversity across the entire genus. These investigations contribute to our understanding of the genomic content and architecture within Asclepias and the Gentianales, patterns of population diversification in the western United States, and the evolutionary history of select loci within Asclepias, with implications across flowering plants. Chapter 2 investigates patterns of polymorphisms among paralogous copies of nuclear ribosomal DNA (nrDNA) within individual genomes, and presents a bioinformatic pipeline for characterizing polymorphisms among copies of a high-copy locus. Results are presented for intragenomic nrDNA polymorphisms across Asclepias. The 18S-26S portion of the nrDNA cistron of Asclepias syriaca served as a reference for assembly of the region from 124 samples representing 90 species of Asclepias. Reads were mapped back to each individual’s consensus and at each position reads differing from the consensus were tallied using a custom Perl script. Low frequency polymorphisms existed in all individuals (mean = 5.8%). -
Inventory of Vascular Plants at Mojave National Preserve & Manzanar Historic Site
Inventory of Vascular Plants at Mojave National Preserve & Manzanar Historic Site For U.S. National Park Service Inventory and Monitoring Program Camissonia boothii ssp. boothii Prepared by James M. André University of California Riverside, Granite Mountains Desert Research Center November 15, 2006 Contract Number: P2128020178 TABLE OF CONTENTS 1.0 INTRODUCTION 1.1 National Inventory and Monitoring Program and Mojave Network 1 1.2 Program Overview 1 1.3 Regional Context and Significance 2 1.3.1 Mojave National Preserve 2 1.3.2 Manzanar Historic Site 4 1.4 Objectives 5 2.0 METHODS 2.1 Herbarium Surveys 7 2.1.1 Database and Bibliographic Query 7 2.2 Field Surveys 7 2.2.1 Mojave National Preserve 7 2.2.2 Manzanar Historic Site 8 2.3 Voucher Specimens 8 2.4 Survey Timing 9 2.5 Field Investigators 9 3.0 RESULTS 3.1 Level of Effort 10 3.2 Summary of Findings - Manzanar Historic Site 10 3.3 Summary of Findings - Mojave National Preserve 14 3.3.1 Field Surveys 14 3.3.2 New Vascular Plant Taxa for MOJA 14 3.3.3 Special-Status Plants 33 3.3.4 Non-Native Alien Plants 40 4.0 DISCUSSION 4.1 Summary 41 4.2 Recommendations 41 Acknowledgements 43 5.0 REFERENCES 44 i List of Maps, Tables and Appendices Map 1. Distribution of all Area Searches in Priority Locations, Targeted Surveys, and Opportunistic Surveys conducted in the Mojave National Preserve, 2002 – 2005. 15 Table 1. Checklist of vascular plant taxa known to occur in the Manzanar Historic Site. -
AJO PEAK to TINAJAS ALTAS: a FLORA of SOUTHWESTERN ARIZONA PART 2. the CHECKLIST ABSTRACT a Checklist Is Provided for the Mode
Felger, R.S., S. Rutman, J. Malusa, and T.R. Van Devender. 2013. Ajo Peak to Tinajas Altas: A flora of southwestern Arizona: Part 2. The checklist. Phytoneuron 2013-27: 1–30. Published 9 April 2013. ISSN 2153 733X AJO PEAK TO TINAJAS ALTAS: A FLORA OF SOUTHWESTERN ARIZONA PART 2. THE CHECKLIST RICHARD STEPHEN FELGER Herbarium, University of Arizona Tucson, Arizona 85721 [email protected] & Sky Island Alliance P.O. Box 41165 Tucson, Arizona 85717 *author for correspondence: [email protected] SUSAN RUTMAN 90 West 10th Street Ajo, Arizona 85321 JIM MALUSA School of Natural Resources and the Environment University of Arizona Tucson, Arizona 85721 [email protected] THOMAS R. VAN DEVENDER Sky Island Alliance P.O. Box 41165 Tucson, Arizona 85717 [email protected] & Herbarium, University of Arizona Tucson, Arizona 85721 ABSTRACT A checklist is provided for the modern and fossil vascular plant flora of the contiguous protected areas of Organ Pipe Cactus National Monument, Cabeza Prieta National Wildlife Refuge, and the Tinajas Altas Region in southwestern Arizona. The modern flora includes 741 native and non-native taxa. The fossil record includes more than 219 species documented by specimens recovered from packrat ( Neotoma spp.) middens spanning the last 43,000+ years. An additional checklist is provided for the approximately 135 taxa restricted to higher-elevation mountains in Organ Pipe Cactus NM. This article is the second contribution for our flora of southwestern Arizona. KEY WORDS : Sonoran Desert, vascular plant flora, Arizona, Organ Pipe Cactus National Monument, Cabeza Prieta National Wildlife Refuge, Tinajas Altas, deep history, non-native species, desert sky islands This article provides a checklist for the vascular plant flora of the three contiguous protected areas of Organ Pipe Cactus National Monument, Cabeza Prieta National Wildlife Refuge, and the Tinajas Altas Region in southwestern Arizona—the heart of the Sonoran Desert (Figure 1). -
Ajo Peak to Tinajas Altas: a Flora of Southwestern Arizona: Part 2
Felger, R.S., S. Rutman, J. Malusa, and T.R. Van Devender. 2013. Ajo Peak to Tinajas Altas: A flora of southwestern Arizona: Part 2. The checklist. Phytoneuron 2013-27: 1–30. Published 9 April 2013. ISSN 2153 733X AJO PEAK TO TINAJAS ALTAS: A FLORA OF SOUTHWESTERN ARIZONA PART 2. THE CHECKLIST RICHARD STEPHEN FELGER Herbarium, University of Arizona Tucson, Arizona 85721 [email protected] & Sky Island Alliance P.O. Box 41165 Tucson, Arizona 85717 *author for correspondence SUSAN RUTMAN 90 West 10th Street Ajo, Arizona 85321 JIM MALUSA School of Natural Resources and the Environment University of Arizona Tucson, Arizona 85721 [email protected] THOMAS R. VAN DEVENDER Sky Island Alliance P.O. Box 41165 Tucson, Arizona 85717 [email protected] & Herbarium, University of Arizona Tucson, Arizona 85721 ABSTRACT A checklist is provided for the modern and fossil vascular plant flora of the contiguous protected areas of Organ Pipe Cactus National Monument, Cabeza Prieta National Wildlife Refuge, and the Tinajas Altas Region in southwestern Arizona. The modern flora includes 741 native and non-native taxa. The fossil record includes more than 219 species documented by specimens recovered from packrat ( Neotoma spp.) middens spanning the last 43,000+ years. An additional checklist is provided for the approximately 135 taxa restricted to higher-elevation mountains in Organ Pipe Cactus NM. This article is the second contribution for our flora of southwestern Arizona. KEY WORDS : Sonoran Desert, vascular plant flora, Arizona, Organ Pipe Cactus National Monument, Cabeza Prieta National Wildlife Refuge, Tinajas Altas, deep history, non-native species, desert sky islands This article provides a checklist for the vascular plant flora of the three contiguous protected areas of Organ Pipe Cactus National Monument, Cabeza Prieta National Wildlife Refuge, and the Tinajas Altas Region in southwestern Arizona—the heart of the Sonoran Desert (Figure 1). -
Flora of the Upper Verde River, Arizona by Francis S. Coburn A
Flora of the Upper Verde River, Arizona by Francis S. Coburn A Thesis Presented in Partial Fulfillment of the Requirements for the Degree Master of Science Approved June 2015 by the Graduate Supervisory Committee: Juliet Stromberg, Co-Chair Leslie Landrum, Co-Chair Elizabeth Makings Walter Fertig ARIZONA STATE UNIVERSITY August 2015 ©2015 Francis Sterling Coburn VI All Rights Reserved ABSTRACT The Upper Verde River of central Arizona flows through a landscape of complex geology at the meeting of seven biotic communities and three physiographic provinces. This has resulted in notably diverse flora and fauna and a hub of rare and endemic plant species. The river has sustained cultures since pre-history, however current regional water use is predicted to diminish streamflow over the next century. Prior to this project, no floristic inventory had been conducted along any section of the Verde. The purpose of this study was to develop a Flora of the Upper Verde River, with the goals of documenting rare and endemic species, the composition and abundance of wetland plants, and the factors shaping plant diversity in the region. I made a total of 1856 collections and reviewed past collections to produce a checklist of 729 vascular plant taxa in 403 genera and 98 families. The most species-rich family is the Poaceae, followed by Asteraceae and Fabaceae. The flora includes 159 wetland taxa, 47 endemics, and 26 taxa of conservation concern, eight of which are Federally listed. Several new populations were found in these categories and of rarely- collected taxa including one state record, three county records and several range extensions. -
Focused Fall Special-Status Plant Survey for the Soda Mountain Solar Project, San Bernardino County, California
Focused Fall Rare Plant Survey Soda Mountain Solar Project BLM Case # CACA49584 San Bernardino County, California October-November 2012 Prepared for: Bureau of Land Management Barstow Field Office 2601 Barstow, CA 92311 Prepared by: C.S. Ecological Surveys and Assessments 11331 Star Pine Road Truckee, CA 96161 Under Contract to: Panorama Environmental Inc. One Embarcadero Center, #740 San Francisco, CA 94111 Executive Summary This report presents the results of focused botanical surveys for fall-flowering rare plants at the proposed Soda Mountain Solar Project (SMS). Transect-based complete pedestrian surveys of the approximately 4,075-acre SMS botanical survey area were conducted from October 24 through November 5, 2012. The surveys generally complied with the botanical survey guidelines of the California Department of Fish and Game (CDFG), the California Native Plant Society (CNPS), the U.S. Fish and Wildlife Service (USFWS), and the Bureau of Land Management (BLM), but differed from these protocols in that only late-season surveys were conducted. The survey work plan was approved by both BLM and CDFG prior to performing surveys. Pre-field research was conducted to select rare plant species with potential to be found within the survey area. The list of potentially occurring rare plants was derived from several sources including the California Natural Diversity Database, the CNPS On-line Inventory, and the California Consortium of Herbaria. Fifteen late summer and fall-flowering rare plant species were determined to have potential to occur within the survey area based on habitat preferences and known distribution. No federal or state-listed plant taxa were observed. -
California's Deserts, Part 1: Biology and Ecology
$5.00 (Free to Members) VOL. 42, NO. 1 • JANUARY 2014 FREMONTIA JOURNAL OF THE CALIFORNIA NATIVE PLANT SOCIETY CALIFORNIA’SVOL. 42, NO. 1, JANUARY DESERTS, 2014 PARTPART 1:1: BIOLOGYBIOLOGY ANDAND FREMONTIA ECOLOGYECOLOGY CALIFORNIA NATIVE PLANT SOCIETY CNPS, 2707 K Street, Suite 1; Sacramento, CA 95816-5130 FREMONTIA Phone: (916) 447-CNPS (2677) Fax: (916) 447-2727 Web site: www.cnps.org Email: [email protected] VOL. 42, NO. 1, JANUARY 2014 Copyright © 2014 MEMBERSHIP Membership form located on inside back cover; California Native Plant Society dues include subscriptions to Fremontia and the CNPS Bulletin Bob Hass, Editor Mariposa Lily . $1,500 Family or Group . $75 Kara Moore, Managing Editor Benefactor . $600 International or Library . $75 James M. André, Patrick McIntyre, Patron . $300 Individual . $45 Advisors Plant Lover . $100 Student/Retired/Limited Income . $25 Beth Hansen-Winter, Designer CORPORATE/ORGANIZATIONAL Brad Jenkins, Cynthia Powell, and 10+ Employees . $2,500 4-6 Employees . $500 Mary Ann Showers, Proofreaders 7-10 Employees . $1,000 1-3 Employees . $150 CALIFORNIA NATIVE STAFF – SACRAMENTO CHAPTER COUNCIL PLANT SOCIETY Executive Director: Dan Gluesenkamp David Magney (Chair); Larry Levine Finance and Administration (Vice Chair); Marty Foltyn (Secretary) Dedicated to the Preservation of Manager: Cari Porter Alta Peak (Tulare): Joan Stewart Membership and Development the California Native Flora Bristlecone (Inyo-Mono): Coordinator: Stacey Flowerdew Steve McLaughlin The California Native Plant Society Conservation Program Director: (CNPS) is a statewide nonprofit organi- Greg Suba Channel Islands: David Magney zation dedicated to increasing the Rare Plant Botanist: Aaron Sims Dorothy King Young (Mendocino/ Sonoma Coast): Nancy Morin understanding and appreciation of Vegetation Program Director: East Bay: Bill Hunt California’s native plants, and to pre- Julie Evens Vegetation Ecologists: El Dorado: Sue Britting serving them and their natural habitats Kern County: Dorie Giragosian for future generations. -
Asclepias Syriaca L., 1762
Identification of Invasive Alien Species using DNA barcodes Royal Belgian Institute of Natural Sciences Royal Museum for Central Africa Rue Vautier 29, Leuvensesteenweg 13, 1000 Brussels , Belgium 3080 Tervuren, Belgium +32 (0)2 627 41 23 +32 (0)2 769 58 54 General introduction to this factsheet The Barcoding Facility for Organisms and Tissues of Policy Concern (BopCo) aims at developing an expertise forum to facilitate the identification of biological samples of policy concern in Belgium and Europe. The project represents part of the Belgian federal contribution to the European Research Infrastructure Consortium LifeWatch. Non-native species which are being introduced into Europe, whether by accident or deliberately, can be of policy concern since some of them can reproduce and disperse rapidly in a new territory, establish viable populations and even outcompete native species. As a consequence of their presence, natural and managed ecosystems can be disrupted, crops and livestock affected, and vector-borne diseases or parasites might be introduced, impacting human health and socio-economic activities. Non-native species causing such adverse effects are called Invasive Alien Species (IAS). In order to protect native biodiversity and ecosystems, and to mitigate the potential impact on human health and socio-economic activities, the issue of IAS is tackled in Europe by EU Regulation 1143/2014 of the European Parliament and Council. The IAS Regulation provides for a set of measures to be taken across all member states. The list of Invasive Alien Species of Union Concern is regularly updated. In order to implement the proposed actions, however, methods for accurate species identification are required when suspicious biological material is encountered. -
Felger, R.S., S. Rutman, and J. Malusa. 2014. Ajo Peak to Tinajas Altas: Flora of Southwestern Arizona: Part 8, Eudicots: Acanthaceae–Apocynaceae
Felger, R.S., S. Rutman, and J. Malusa. 2014. Ajo Peak to Tinajas Altas: Flora of Southwestern Arizona: Part 8, Eudicots: Acanthaceae–Apocynaceae. Phytoneuron 2014-85: 1–71. Published 28 August 2014. ISSN 2153 733X AJO PEAK TO TINAJAS ALTAS: FLORA OF SOUTHWESTERN ARIZONA PART 8. EUDICOTS: ACANTHACEAE – APOCYNACEAE RICHARD STEPHEN FELGER Herbarium, University of Arizona Tucson, Arizona 85721 & Sky Island Alliance P.O. Box 41165, Tucson, Arizona 85717 *Author for correspondence: [email protected] SUSAN RUTMAN Organ Pipe Cactus National Monument 10 Organ Pipe Drive Ajo, Arizona 85321 JIM MALUSA School of Natural Resources and the Environment University of Arizona Tucson, Arizona 85721 [email protected] ABSTRACT A floristic account is provided for seven eudicot families as part of the vascular plant flora of the contiguous protected areas of Organ Pipe Cactus National Monument, Cabeza Prieta National Wildlife Refuge, and the Tinajas Altas Region in southwestern Arizona: Acanthaceae (5 genera, 7 species), Adoxaceae (1 genus, 1 species), Aizoaceae (2 genera, 3 species), Amaranthaceae (12 genera, 22 species), Anacardiaceae (1 genus, 2 species), Apiaceae (6 genera, 6 species), and Apocynaceae (5 genera, 10 species). This is the eighth contribution for this flora published in Phytoneuron and also posted open access on the website of the University of Arizona Herbarium (ARIZ). This contribution to our flora in southwestern Arizona is the eighth published in a series in Phytoneuron and also posted open access on the website of the University of Arizona Herbarium (ARIZ; Figure 1). Seven eudicot families are included in this contribution: Acanthaceae (5 genera, 7 species), Adoxaceae (1 genus, 1 species), Aizoaceae (2 genera, 3 species), Amaranthaceae (12 genera, 22 species), Anacardiaceae (1 genus, 2 species), Apiaceae (6 genera, 6 species), and Apocynaceae (5 genera, 10 species). -
View Jalisco and Zacatecas North to Chihuahua and Sonora, Reaching Its Northern Limit in Sonora 55 Spotlight on a Native Plant in the Sierra Huachinera (30.3°N)
The Plant Press THE ARIZONA NATIVE PLANT SOCIETY Volume 41, Number 2 Fall 2018 In this Issue Preliminary Floras in the Madrean Archipelago, Sonora, Mexico 6 Sierra la Elenita–la Mariquita Sky Island Complex 10 Checklist 14 Sierra la Buenos Aires Figure 1. Sierra el Tigre Sky Island. Photo courtesy Dale S. Turner. 19 Checklist The Arizona Native Plant Society’s Botany 2018 Conference explored the botanical 24 Sierra La Púrica diversity of the Madrean Sky Islands of Southern Arizona and Northern Mexico. In this 29 Checklist expanded issue of The Plant Press, prepared with the cooperation and support of the 33 Sierra Juriquipa GreaterGood.org organization, we present floras of five major Sonoran Sky Islands. 38 Checklist 43 Lower Bavispe Valley Preliminary Floras in the Madrean 49 Checklist Archipelago, Sonora, Mexico Plus by Thomas R. Van Devender1, Susan D. Carnahan2, George M. Ferguson2, 54 Arizona Native Plant Society 3 4 Botanical Adventure to the Elizabeth Makings , and José Jesús Sánchez-Escalante Chiricahua Mountains Introduction With Regular Features In 2007, Conservation International designated the Mexican Madrean Pine-oak Woodlands 2 President’s Note as a global biodiversity hotspot. This is a very large area that includes both the Sierra Madre 5 Who’s Who at AZNPS Oriental in eastern Mexico, the Sierra Madre Occidental (SMO) in western Mexico, and the Madrean Archipelago in Sonora and Arizona. The SMO extends in western Mexico from 41 Book Review Jalisco and Zacatecas north to Chihuahua and Sonora, reaching its northern limit in Sonora 55 Spotlight on a Native Plant in the Sierra Huachinera (30.3°N). -
A Report on the Flora of the Sierra De Los Ajos, Sonora, Mexico
This file was created by scanning the printed publication. Errors identified by the software have been corrected; however, some errors may remain. Another Jewel in the Crown: A Report on the Flora of the Sierra De Los Ajos, Sonora, Mexico 1 2 3 Mark Fishbein , Richard Felger , and Florentino Garza Abstract. -We report here on the flora of the Sierra de los Ajos, Sonora, Mexico, based on collections made in 1992 and 1993. The known flora of this Sky Island range contains 376 species of vascular plants in 93 families. Based on our collections and the results of floristic studies of other Sky Island ranges, we anticipate that the total flora of the Sierra de los Ajos contains over 1000 species. We have documented the only known occurrences in Mexico of two species that are candidates for listing as threatened or endangered species in the United States, various new distribution records for Mexico and Sonora, and large range extensions of a number of other plants. This work contributes to a projected flora of the Sky Island region. INTRODUCTION Islands north of the Mexico-U.S. border is surpris ing considering that the floras of New Mexico and The flora of the Sierra de los Ajos includes sev Arizona were first produced in the early part of eral notable taxa, including some that are this century (Wooton and Standley 1915, Kearney considered in danger of extinction, some that are and Peebles 1942). In fact, many of the additions far disjunct from the nearest known populations, to the flora of Arizona have come from botanical and some that show a marked extension of their exploration of the Sky Islands (e.g.