Biological Evaluation
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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. -
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, -
Earleaf Foxglove (Agalinis Auriculata)
Community Conservation Assessment for Earleaf Foxglove (Agalinis Auriculata) USDA Forest Service, Eastern Region Date Name Location This document is undergoing peer review, comments welcome This Conservation Assessment was prepared to compile the published and unpublished information and serves as a Conservation Assessment for the Eastern Region of the Forest Service. It does not represent a management decision by the U.S. Forest Service. Though the best scientific information available was used and subject experts were consulted in preparation of this document, it is expected that new information will arise. In the spirit of continuous learning and adaptive management, if you have information that will assist in conserving the subject community, please contact the Eastern Region of the Forest Service - Threatened and Endangered Species Program at 310 Wisconsin Avenue, Suite 580 Milwaukee, Wisconsin 53203. Community Conservation Assessment forEarleaf Foxglove (Agalinis Auriculata) 2 Table of Contents EXECUTIVE SUMMARY .............................................................................................. 4 ACKNOWLEDGEMENTS ............................................................................................. 4 COMMUNITY CLASSIFICATION SYSTEM AND SYNONYMS............................ 4 DESCRIPTION OF COMMUNITY............................................................................... 4 COMMUNITY ECOLOGY/ENVIRONMENTAL CONDITIONSError! Bookmark not defined. RANGE OF NATURAL VARIABILITY: COMMUNITY DISTRIBUTION AND CONDITIONS -
Checklist of Fish and Invertebrates Listed in the CITES Appendices
JOINTS NATURE \=^ CONSERVATION COMMITTEE Checklist of fish and mvertebrates Usted in the CITES appendices JNCC REPORT (SSN0963-«OStl JOINT NATURE CONSERVATION COMMITTEE Report distribution Report Number: No. 238 Contract Number/JNCC project number: F7 1-12-332 Date received: 9 June 1995 Report tide: Checklist of fish and invertebrates listed in the CITES appendices Contract tide: Revised Checklists of CITES species database Contractor: World Conservation Monitoring Centre 219 Huntingdon Road, Cambridge, CB3 ODL Comments: A further fish and invertebrate edition in the Checklist series begun by NCC in 1979, revised and brought up to date with current CITES listings Restrictions: Distribution: JNCC report collection 2 copies Nature Conservancy Council for England, HQ, Library 1 copy Scottish Natural Heritage, HQ, Library 1 copy Countryside Council for Wales, HQ, Library 1 copy A T Smail, Copyright Libraries Agent, 100 Euston Road, London, NWl 2HQ 5 copies British Library, Legal Deposit Office, Boston Spa, Wetherby, West Yorkshire, LS23 7BQ 1 copy Chadwick-Healey Ltd, Cambridge Place, Cambridge, CB2 INR 1 copy BIOSIS UK, Garforth House, 54 Michlegate, York, YOl ILF 1 copy CITES Management and Scientific Authorities of EC Member States total 30 copies CITES Authorities, UK Dependencies total 13 copies CITES Secretariat 5 copies CITES Animals Committee chairman 1 copy European Commission DG Xl/D/2 1 copy World Conservation Monitoring Centre 20 copies TRAFFIC International 5 copies Animal Quarantine Station, Heathrow 1 copy Department of the Environment (GWD) 5 copies Foreign & Commonwealth Office (ESED) 1 copy HM Customs & Excise 3 copies M Bradley Taylor (ACPO) 1 copy ^\(\\ Joint Nature Conservation Committee Report No. -
Conservation Assessment for the Kansan Spikerush Leafhopper (Dorydiella Kansana Beamer)
Conservation Assessment For The Kansan spikerush leafhopper (Dorydiella kansana Beamer) USDA Forest Service, Eastern Region January 11, 2005 James Bess OTIS Enterprises 13501 south 750 west Wanatah, Indiana 46390 This document is undergoing peer review, comments welcome This Conservation Assessment was prepared to compile the published and unpublished information on the subject taxon or community; or this document was prepared by another organization and provides information to serve as a Conservation Assessment for the Eastern Region of the Forest Service. It does not represent a management decision by the U.S. Forest Service. Though the best scientific information available was used and subject experts were consulted in preparation of this document, it is expected that new information will arise. In the spirit of continuous learning and adaptive management, if you have information that will assist in conserving the subject taxon, please contact the Eastern Region of the Forest Service - Threatened and Endangered Species Program at 310 Wisconsin Avenue, Suite 580 Milwaukee, Wisconsin 53203. TABLE OF CONTENTS EXECUTIVE SUMMARY ............................................................................................................ 1 ACKNOWLEDGEMENTS............................................................................................................ 1 NOMENCLATURE AND TAXONOMY ..................................................................................... 1 DESCRIPTION OF SPECIES....................................................................................................... -
Endangered Species
FEATURE: ENDANGERED SPECIES Conservation Status of Imperiled North American Freshwater and Diadromous Fishes ABSTRACT: This is the third compilation of imperiled (i.e., endangered, threatened, vulnerable) plus extinct freshwater and diadromous fishes of North America prepared by the American Fisheries Society’s Endangered Species Committee. Since the last revision in 1989, imperilment of inland fishes has increased substantially. This list includes 700 extant taxa representing 133 genera and 36 families, a 92% increase over the 364 listed in 1989. The increase reflects the addition of distinct populations, previously non-imperiled fishes, and recently described or discovered taxa. Approximately 39% of described fish species of the continent are imperiled. There are 230 vulnerable, 190 threatened, and 280 endangered extant taxa, and 61 taxa presumed extinct or extirpated from nature. Of those that were imperiled in 1989, most (89%) are the same or worse in conservation status; only 6% have improved in status, and 5% were delisted for various reasons. Habitat degradation and nonindigenous species are the main threats to at-risk fishes, many of which are restricted to small ranges. Documenting the diversity and status of rare fishes is a critical step in identifying and implementing appropriate actions necessary for their protection and management. Howard L. Jelks, Frank McCormick, Stephen J. Walsh, Joseph S. Nelson, Noel M. Burkhead, Steven P. Platania, Salvador Contreras-Balderas, Brady A. Porter, Edmundo Díaz-Pardo, Claude B. Renaud, Dean A. Hendrickson, Juan Jacobo Schmitter-Soto, John Lyons, Eric B. Taylor, and Nicholas E. Mandrak, Melvin L. Warren, Jr. Jelks, Walsh, and Burkhead are research McCormick is a biologist with the biologists with the U.S. -
Aquatic Fish Report
Aquatic Fish Report Acipenser fulvescens Lake St urgeon Class: Actinopterygii Order: Acipenseriformes Family: Acipenseridae Priority Score: 27 out of 100 Population Trend: Unknown Gobal Rank: G3G4 — Vulnerable (uncertain rank) State Rank: S2 — Imperiled in Arkansas Distribution Occurrence Records Ecoregions where the species occurs: Ozark Highlands Boston Mountains Ouachita Mountains Arkansas Valley South Central Plains Mississippi Alluvial Plain Mississippi Valley Loess Plains Acipenser fulvescens Lake Sturgeon 362 Aquatic Fish Report Ecobasins Mississippi River Alluvial Plain - Arkansas River Mississippi River Alluvial Plain - St. Francis River Mississippi River Alluvial Plain - White River Mississippi River Alluvial Plain (Lake Chicot) - Mississippi River Habitats Weight Natural Littoral: - Large Suitable Natural Pool: - Medium - Large Optimal Natural Shoal: - Medium - Large Obligate Problems Faced Threat: Biological alteration Source: Commercial harvest Threat: Biological alteration Source: Exotic species Threat: Biological alteration Source: Incidental take Threat: Habitat destruction Source: Channel alteration Threat: Hydrological alteration Source: Dam Data Gaps/Research Needs Continue to track incidental catches. Conservation Actions Importance Category Restore fish passage in dammed rivers. High Habitat Restoration/Improvement Restrict commercial harvest (Mississippi River High Population Management closed to harvest). Monitoring Strategies Monitor population distribution and abundance in large river faunal surveys in cooperation -
Louisiana's Animal Species of Greatest Conservation Need (SGCN)
Louisiana's Animal Species of Greatest Conservation Need (SGCN) ‐ Rare, Threatened, and Endangered Animals ‐ 2020 MOLLUSKS Common Name Scientific Name G‐Rank S‐Rank Federal Status State Status Mucket Actinonaias ligamentina G5 S1 Rayed Creekshell Anodontoides radiatus G3 S2 Western Fanshell Cyprogenia aberti G2G3Q SH Butterfly Ellipsaria lineolata G4G5 S1 Elephant‐ear Elliptio crassidens G5 S3 Spike Elliptio dilatata G5 S2S3 Texas Pigtoe Fusconaia askewi G2G3 S3 Ebonyshell Fusconaia ebena G4G5 S3 Round Pearlshell Glebula rotundata G4G5 S4 Pink Mucket Lampsilis abrupta G2 S1 Endangered Endangered Plain Pocketbook Lampsilis cardium G5 S1 Southern Pocketbook Lampsilis ornata G5 S3 Sandbank Pocketbook Lampsilis satura G2 S2 Fatmucket Lampsilis siliquoidea G5 S2 White Heelsplitter Lasmigona complanata G5 S1 Black Sandshell Ligumia recta G4G5 S1 Louisiana Pearlshell Margaritifera hembeli G1 S1 Threatened Threatened Southern Hickorynut Obovaria jacksoniana G2 S1S2 Hickorynut Obovaria olivaria G4 S1 Alabama Hickorynut Obovaria unicolor G3 S1 Mississippi Pigtoe Pleurobema beadleianum G3 S2 Louisiana Pigtoe Pleurobema riddellii G1G2 S1S2 Pyramid Pigtoe Pleurobema rubrum G2G3 S2 Texas Heelsplitter Potamilus amphichaenus G1G2 SH Fat Pocketbook Potamilus capax G2 S1 Endangered Endangered Inflated Heelsplitter Potamilus inflatus G1G2Q S1 Threatened Threatened Ouachita Kidneyshell Ptychobranchus occidentalis G3G4 S1 Rabbitsfoot Quadrula cylindrica G3G4 S1 Threatened Threatened Monkeyface Quadrula metanevra G4 S1 Southern Creekmussel Strophitus subvexus -
Archaeological Data Indicate a Broader Late Holocene Distribution
Archaeological Data Indicate a Broader Late Holocene Distribution of the Sandbank Pocketbook (Unionidae: Lampsilis satura Lea 1852) in Texas Author(s): Steve Wolverton and Charles R. Randklev Source: American Malacological Bulletin, 34(2):133-137. Published By: American Malacological Society DOI: http://dx.doi.org/10.4003/006.034.0209 URL: http://www.bioone.org/doi/full/10.4003/006.034.0209 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. Amer. Malac. Bull. 34(2): 133–137 (2016) RESEARCH NOTE Archaeological Data Indicate a Broader Late Holocene Distribution of the Sandbank Pocketbook (Unionidae: Lampsilis satura Lea 1852) in Texas Steve Wolverton1 and Charles R. Randklev2 1Department of Geography and the Environment, University of North Texas, Denton, TX 76203, U.S.A. 2Institute of Renewable Natural Resources, Texas A&M University, College Station, TX 77843, U.S.A. -
Federal Register/Vol. 74, No. 44/Monday, March 9, 2009/Notices
10064 Federal Register / Vol. 74, No. 44 / Monday, March 9, 2009 / Notices Applicant: Copperhead Environmental (Rhus michauxii), bunched arrowhead March 24–26, 2009. The meeting is open Consulting, Inc., Paint Lick, (Sagittaria fasciculata), mountain sweet to the public. The meeting agenda will Kentucky, TE171516 pitcher-plant (Sarracenia jonesii), include reports from the Subcommittees The applicant requests amendment of largeflower skullcap (Scutellaria on Incentives, Legal, Science Tools & existing authorization to add authority montana), blue ridge goldenrod Procedures, and Synthesis, and to capture, handle, and release 31 (Solidago spithamaea), Virginia spirea discussion of the draft species of freshwater mussel for (Spiraea virginiana), Cooley’s Recommendations to the Secretary. presence surveys throughout the species meadowrue (Thalictrum cooleyi), and DATES: The meeting is scheduled for ranges in the eastern United States. running buffalo clover (Trifolium March 24–26, 2009, from 11 a.m. to stoloniferum) to develop and maintain Applicant: South Carolina Parks, 5:30 p.m. on March 24, 8 a.m. to 5:30 germ plasm and propagated specimens Recreation and Tourism, Columbia, p.m. on March 25, and 8 a.m. to 3:30 of plants collected from throughout South Carolina TE207117 p.m. on March 26. North Carolina, South Carolina, The applicant requests authorization ADDRESSES: U.S. Fish and Wildlife Alabama, Georgia, Florida, Tennessee, Service, 4401 N. Fairfax Drive, Rooms to harass, inspect nest cavities, and West Virginia, Virginia, and Maryland. conduct other management activities 200 A & B, Arlington, VA 22203. For Applicant: International Carnivorous with the red-cockaded woodpecker more information, see ‘‘Meeting Plant Society, Pinole, California, (Picoides borealis) throughout South Location Information.’’ TE061005 Carolina. -
Species of Greatest Conservation Need
APPENDIX A. VIRGINIA SPECIES OF GREATEST CONSERVATION NEED Taxa Common Scientific Name Tier Cons. Opp. Habitat Descriptive Habitat Notes Name Ranking Amphibians Barking Hyla gratiosa II a Forest Forests near or within The Virginia Fish and Wildlife Information System indicates treefrog shallow wetlands the loss suitable wetlands constitute the greatest threats to this species. DGIF recommends working to maintain or restore forested buffers surrounding occupied wetlands. These needs are consistent with action plan priorities to conserve and restore wetland habitats and associated buffers. Recently discovered populations within its known range, may indicate this species is more abundant than previously believed. An in-depth investigation into its status may warrant delisting. This species will be prioritized as Tier 2a. Amphibians Blue Ridge Desmognathus IV c Forest High elevation seeps, This species' distribution is very limited. Other than limiting dusky orestes streams, wet rock faces, logging activity in the occupied areas, no conservation salamander and riparian forests actions have been identified. Unless other threats or actions are identified, this species will be listed as Tier 4c. Amphibians Blue Ridge Eurycea III a Wetland Mountain streams and The needs of this species are consistent with priorities for two-lined wilderae adjacent riparian areas maintaining and enhancing riparian forests and aquatic salamander with mixed hardwood or habitats. This species will be listed as Tier 3a. spruce-fir forests up to 6000 feet. Amphibians Carpenter Lithobates III a Wetland Freshwater wetlands with The needs of this species are consistent with action plan frog virgatipes sphagnum moss priorities to preserve and restore aquatic and wetland habitats and water quality.