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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. -
Biological Resources Evaluation Report for Pine Acres North
Biological Resources Evaluation Report for Pine Acres North Amador County, CA Prepared by: Sycamore Environmental Consultants, Inc. 6355 Riverside Blvd., Suite C Sacramento, CA 95831-1143 Phone: 916/ 427-0703 Fax: 916/ 427-2175 Contact: R. John Little, Ph.D. Prepared for: Thomas Martin & Associates 120 Blue Ravine Road, Suite 4 Folsom, CA 95630 Phone: 916/ 985-6380 Contact: Mr. Thomas Martin 8 September 2006 Biological Resources Evaluation Pine Acres North Amador County, CA Biological Resources Evaluation Report For Pine Acres North Amador County, CA Table of Contents I. SUMMARY OF FINDINGS AND CONCLUSIONS..................................................................1 II. INTRODUCTION..........................................................................................................................1 A. Purpose of Report ......................................................................................................................1 B. Project Location.........................................................................................................................1 C. Project Applicant .......................................................................................................................1 D. Project Description ....................................................................................................................1 III. STUDY METHODS.......................................................................................................................5 A. Studies Conducted .....................................................................................................................5 -
"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. -
Tejon Ranch Botanical Survey Report
David Magney Environmental Consulting FLORA OF THE TEJON RANCH CONSERVANCY ACQUISITION AREAS, TEJON RANCH, CALIFORNIA Prepared for: TEJON RANCH CONSERVANCY July 2010 DMEC Mission Statement: To provide quality environmental consulting services, with integrity, that protect and enhance the human and natural environment. David Magney Environmental Consulting Flora of the Tejon Ranch Conservancy Acquisition Areas, Tejon Ranch, California Prepared for: Tejon Ranch Conservancy P.O. Box 216 Frazier Park, California 93225 Contact: Michael White Phone: 661/-248-2400 ext 2 Prepared by: David Magney Environmental Consulting P.O. Box 1346 Ojai, California 93024-1346 Phone: 805/646-6045 23 July 2010 DMEC Mission Statement: To provide quality environmental consulting services, with integrity, that protect and enhance the human and natural environment. This document should be cited as: David Magney Environmental Consulting. 2010. Flora of the Tejon Ranch Conservancy Acquisition Areas, Tejon Ranch, California. 23 July2010. (PN 09-0001.) Ojai, California. Prepared for Tejon Ranch Conservancy, Frazier Park, California. Tejon Ranch Conservancy – Flora of Tejon Ranch Acquisition Areas Project No. 09-0001 DMEC July 2010 TABLE OF CONTENTS Page SECTION 1. INTRODUCTION............................................................................. 1 SECTION 2. METHODS ........................................................................................ 3 Field Survey Methods .......................................................................................................... -
Likely to Have Habitat Within Iras That ALLOW Road
Item 3a - Sensitive Species National Master List By Region and Species Group Not likely to have habitat within IRAs Not likely to have Federal Likely to have habitat that DO NOT ALLOW habitat within IRAs Candidate within IRAs that DO Likely to have habitat road (re)construction that ALLOW road Forest Service Species Under NOT ALLOW road within IRAs that ALLOW but could be (re)construction but Species Scientific Name Common Name Species Group Region ESA (re)construction? road (re)construction? affected? could be affected? Bufo boreas boreas Boreal Western Toad Amphibian 1 No Yes Yes No No Plethodon vandykei idahoensis Coeur D'Alene Salamander Amphibian 1 No Yes Yes No No Rana pipiens Northern Leopard Frog Amphibian 1 No Yes Yes No No Accipiter gentilis Northern Goshawk Bird 1 No Yes Yes No No Ammodramus bairdii Baird's Sparrow Bird 1 No No Yes No No Anthus spragueii Sprague's Pipit Bird 1 No No Yes No No Centrocercus urophasianus Sage Grouse Bird 1 No Yes Yes No No Cygnus buccinator Trumpeter Swan Bird 1 No Yes Yes No No Falco peregrinus anatum American Peregrine Falcon Bird 1 No Yes Yes No No Gavia immer Common Loon Bird 1 No Yes Yes No No Histrionicus histrionicus Harlequin Duck Bird 1 No Yes Yes No No Lanius ludovicianus Loggerhead Shrike Bird 1 No Yes Yes No No Oreortyx pictus Mountain Quail Bird 1 No Yes Yes No No Otus flammeolus Flammulated Owl Bird 1 No Yes Yes No No Picoides albolarvatus White-Headed Woodpecker Bird 1 No Yes Yes No No Picoides arcticus Black-Backed Woodpecker Bird 1 No Yes Yes No No Speotyto cunicularia Burrowing -
Other Botanical Resource Assessment
USDA Forest Service Tahoe National Forest District Yuba River Ranger District OTHER BOTANICAL RESOURCE ASSESSMENT Yuba Project 08/01/2017 Prepared by: Date: Courtney Rowe, District Botanist TABLE OF CONTENTS 1 TNF Watch List Botanical Species ........................................................................................................ 1 1.1 Introduction ................................................................................................................................ 1 1.2 Summary of Analysis Procedure .................................................................................................. 2 1.3 Project Compliance ..................................................................................................................... 2 2 Special Status Plant Communities ....................................................................................................... 5 2.1 Introduction ................................................................................................................................ 5 2.2 Project Compliance ..................................................................................................................... 5 3 Special Management Designations ..................................................................................................... 6 3.1 Introduction ................................................................................................................................ 6 3.2 Project Compliance .................................................................................................................... -
A Taxonomic Conspectus of Phrymaceae: a Narrowed Circumscriptions for Mimulus , New and Resurrected Genera, and New Names and Combinations
Barker, W.R., G.L. Nesom, P.M. Beardsley, and N.S. Fraga. 2012. A taxonomic conspectus of Phrymaceae: A narrowed circumscriptions for Mimulus , new and resurrected genera, and new names and combinations. Phytoneuron 2012-39: 1–60. Published 16 May 2012. ISSN 2153 733X A TAXONOMIC CONSPECTUS OF PHRYMACEAE: A NARROWED CIRCUMSCRIPTION FOR MIMULUS, NEW AND RESURRECTED GENERA, AND NEW NAMES AND COMBINATIONS W.R. (B ILL ) BARKER State Herbarium of South Australia, Kent Town SA 5071, AUSTRALIA; and Australian Centre for Evolutionary Biology and Biodiversity University of Adelaide Adelaide SA 5000, AUSTRALIA [email protected] GUY L. NESOM 2925 Hartwood Drive Fort Worth, Texas 76109, USA [email protected] PAUL M. BEARDSLEY Biological Sciences Department California State Polytechnic University Pomona, California 91768, USA [email protected] NAOMI S. FRAGA Rancho Santa Ana Botanic Garden Claremont, California 91711-3157, USA [email protected] ABSTRACT A revised taxonomic classification of Phrymaceae down to species level is presented, based on molecular-phylogenetic and morpho-taxonomic studies, setting a framework for ongoing work. In the concept adopted, the family includes 188 species divided into 13 genera. All species as currently understood are listed and assigned to genera and sections which in several cases have new circumscriptions requiring many new combinations. Four main clades are recognized. Clade A. An Asian-African-Australasian-centered clade of 7 genera: Mimulus L. sensu stricto (7 species) of North America, Asia to Africa, and Australasia is sister to an Australian-centered group that comprises Elacholoma (2 species), Glossostigma (5 species), Microcarpaea (2 species), Peplidium (4 species), Uvedalia (2 species) and a new monotypic genus Thyridia , described here. -
Special-Status Plants and Invasive/Noxious Weeds Technical Report
SACRAMENTO MUNICIPAL UTILITY DISTRICT UPPER AMERICAN RIVER PROJECT (FERC NO. 2101) SPECIAL-STATUS PLANTS AND INVASIVE/NOXIOUS WEEDS TECHNICAL REPORT Prepared by: Devine Tarbell & Associates, Inc. Sacramento, California Prepared for: Sacramento Municipal Utility District Sacramento, California JULY 2004 Sacramento Municipal Utility District Upper American River Project FERC Project No. 2101 TABLE OF CONTENTS Section & Description Page 1.0 INTRODUCTION .............................................................................................................. 1 2.0 BACKGROUND ................................................................................................................ 2 2.1 Special-Status Plants Study Plan ............................................................................ 2 2.2 Invasive/Noxious Weeds Study Plan...................................................................... 3 2.3 Water Year Types................................................................................................... 4 2.4 Agency Requested Information .............................................................................. 5 3.0 METHODS ......................................................................................................................... 5 3.1 Special-Status Plants............................................................................................... 5 3.2 Noxious Weeds ....................................................................................................... 6 4.0 RESULTS .......................................................................................................................... -
NORTH TABLE MOUNTAIN ECOLOGICAL RESERVE Land Management Plan
NORTH TABLE MOUNTAIN ECOLOGICAL RESERVE Land Management Plan Prepared for: December 2006 State of California The Resources Agency Department of Fish and Game NORTH TABLE MOUNTAIN ECOLOGICAL RESERVE Land Management Plan Prepared for: December 2006 State of California The Resources Agency Department of Fish and Game 8950 Cal Center Drive Building 3, Suite 300 Sacramento, CA 95826 916.564.4500 www.esassoc.com Los Angeles Oakland Orlando Petaluma Portland San Francisco Seattle Tampa 204427 ESA J MORTH TABLE MOUNTAIN ECOLOGICAL RESERVE Land Management Plan Approved by: Acting RegionalTftartager / Date _nhltn Acting Deputy Direaor for Regional Operations 'Date TABLE OF CONTENTS North Table Mountain Ecological Reserve Land Management Plan Page 1 Summary 1-1 2 Introduction 2-1 Purpose of Acquisition 2-1 Acquisition History 2-1 Purpose of This Management Plan 2-1 3 Property Description 3-1 Geographical Setting 3-1 Property Boundaries and Adjacent Lands 3-1 Geology, Soils, Climate, and Hydrology 3-1 Cultural Features 3-11 4 Vegetation Types, Habitat, and Species Descriptions 4-1 Vegetation Types and Habitats 4-1 Special-Status Species 4-5 5 Management Goals and Environmental Impacts 5-1 Definition of Terms Used in This Plan 5-1 Biological Elements: Goals, Objectives, and Environmental Impacts 5-1 Public Use Elements: Goals and Environmental Impacts 5-5 Facility Maintenance Elements: Goals and Environmental Impacts 5-6 6 Operations and Maintenance Summary 6-1 Operations and Maintenance Tasks to Implement Plan 6-1 Existing Staff and Additional Personnel -
Oak Resources Management Plan
EXHIBIT A El Dorado County Oak Resources Managenient Plan September 2017 El Dorado County Community Development Agency Long Range Planning Division 2850 Fairlane Court, Placerville, CA 95667 OAK RESOURCES MANAGEMENT PLAN Table of Contents 1.0 Introduction ................................................................................................................... l 1.1 Purpose ...................................................................................................................1 1.2 Goals and Objectives of Plan .................................................................................2 1.3 Oak Resources in El Dorado County .....................................................................3 1.3.1 Oak Woodlands ........................................................................................... .3 1.3 .2 Oak Trees .................................................................................................... .4 1.4 Economic Activity, Land, and Ecosystem Values of Oak Resources ....................4 1.5 State-level Regulations ...........................................................................................4 2.0 Oak Resources Impact Mitigation Requirements .........................................................6 2.1 Applicability, Exemptions and Mitigation Reductions ..........................................6 2.1.1 Single-Family Lot Exemption...................................................................... 6 2.1.2 Fire Safe Activities Exemption ....................................................................6 -
Sierra Nevada Framework FEIS Chapter 3
table of contrents Sierra Nevada Forest Plan Amendment – Part 4.6 4.6. Vascular Plants, Bryophytes, and Fungi4.6. Fungi Introduction Part 3.1 of this chapter describes landscape-scale vegetation patterns. Part 3.2 describes the vegetative structure, function, and composition of old forest ecosystems, while Part 3.3 describes hardwood ecosystems and Part 3.4 describes aquatic, riparian, and meadow ecosystems. This part focuses on botanical diversity in the Sierra Nevada, beginning with an overview of botanical resources and then presenting a more detailed analysis of the rarest elements of the flora, the threatened, endangered, and sensitive (TES) plants. The bryophytes (mosses and liverworts), lichens, and fungi of the Sierra have been little studied in comparison to the vascular flora. In the Pacific Northwest, studies of these groups have received increased attention due to the President’s Northwest Forest Plan. New and valuable scientific data is being revealed, some of which may apply to species in the Sierra Nevada. This section presents an overview of the vascular plant flora, followed by summaries of what is generally known about bryophytes, lichens, and fungi in the Sierra Nevada. Environmental Consequences of the alternatives are only analyzed for the Threatened, Endangered, and Sensitive plants, which include vascular plants, several bryophytes, and one species of lichen. 4.6.1. Vascular plants4.6.1. plants The diversity of topography, geology, and elevation in the Sierra Nevada combine to create a remarkably diverse flora (see Section 3.1 for an overview of landscape patterns and vegetation dynamics in the Sierra Nevada). More than half of the approximately 5,000 native vascular plant species in California occur in the Sierra Nevada, despite the fact that the range contains less than 20 percent of the state’s land base (Shevock 1996). -
Understanding the Weedy Chenopodium Complex in the North Central States
UNDERSTANDING THE WEEDY CHENOPODIUM COMPLEX IN THE NORTH CENTRAL STATES BY SUKHVINDER SINGH DISSERTATION Submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Crop Sciences in the Graduate College of the University of Illinois at Urbana-Champaign, 2010 Urbana, Illinois Doctoral Committee: Professor Patrick J. Tranel, Chair Associate Professor Aaron G. Hager Associate Professor Geoffrey A. Levin Assistant Professor Matthew E. Hudson ABSTRACT The genus Chenopodium consists of several important weed species, including Chenopodium album, C. berlandieri, C. strictum, and C. ficifolium. All of these species share similar vegetative morphology and high phenotypic plasticity, which makes it difficult to correctly identify these species. All of these weedy Chenopodium species have developed resistance to one or more classes of herbicides. An experiment was conducted to determine if there is variability in response of Chenopodium species present in the North Central states to glyphosate. Our results indicate variable responses within and among the Chenopodium species. Species such as C. berlandieri and C. ficifolium had higher levels of tolerance to glyphosate than did various accessions of C. album. In another experiment, 33 populations of Chenopodium sampled across six North Central states were screened with glyphosate. The results showed variable responses to glyphosate within and among the Chenopodium populations. In general, the Chenopodium populations from Iowa were more tolerant, but some biotypes from North Dakota, Indiana and Kansas also had significantly high tolerance to glyphosate. Given there are species other than C. album that have high tolerance to glyphosate, and there are Chenopodium populations across the North Central states that showed tolerance to glyphosate, one intriguing question was to whether the Chenopodium populations were either biotypes of C.