Springs and Springs-Dependent Taxa of the Colorado River Basin, Southwestern North America: Geography, Ecology and Human Impacts
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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. -
Schriever, Bogan, Boersma, Cañedo-Argüelles, Jaeger, Olden, and Lytle
Schriever, Bogan, Boersma, Cañedo-Argüelles, Jaeger, Olden, and Lytle. Hydrology shapes taxonomic and functional structure of desert stream invertebrate communities. Freshwater Science Vol. 34, No. 2 Appendix S1. References for trait state determination. Order Family Taxon Body Voltinism Dispersal Respiration FFG Diapause Locomotion Source size Amphipoda Crustacea Hyalella 3 3 1 2 2 2 3 1, 2 Annelida Hirudinea Hirudinea 2 2 3 3 6 2 5 3 Anostraca Anostraca Anostraca 2 3 3 2 4 1 5 1, 3 Basommatophora Ancylidae Ferrissia 1 2 1 1 3 3 4 1 Ancylidae Ancylidae 1 2 1 1 3 3 4 3, 4 Class:Arachnida subclass:Acari Acari 1 2 3 1 5 1 3 5,6 Coleoptera Dryopidae Helichus lithophilus 1 2 4 3 3 3 4 1,7, 8 Helichus suturalis 1 2 4 3 3 3 4 1 ,7, 9, 8 Helichus triangularis 1 2 4 3 3 3 4 1 ,7, 9,8 Postelichus confluentus 1 2 4 3 3 3 4 7,9,10, 8 Postelichus immsi 1 2 4 3 3 3 4 7,9, 10,8 Dytiscidae Agabus 1 2 4 3 6 1 5 1,11 Desmopachria portmanni 1 3 4 3 6 3 5 1,7,10,11,12 Hydroporinae 1 3 4 3 6 3 5 1 ,7,9, 11 Hygrotus patruelis 1 3 4 3 6 3 5 1,11 Hygrotus wardi 1 3 4 3 6 3 5 1,11 Laccophilus fasciatus 1 2 4 3 6 3 5 1, 11,13 Laccophilus maculosus 1 3 4 3 6 3 5 1, 11,13 Laccophilus mexicanus 1 2 4 3 6 3 5 1, 11,13 Laccophilus oscillator 1 2 4 3 6 3 5 1, 11,13 Laccophilus pictus 1 2 4 3 6 3 5 1, 11,13 Liodessus obscurellus 1 3 4 3 6 3 5 1 ,7,11 Neoclypeodytes cinctellus 1 3 4 3 7 3 5 14,15,1,10,11 Neoclypeodytes fryi 1 3 4 3 7 3 5 14,15,1,10,11 Neoporus 1 3 4 3 7 3 5 14,15,1,10,11 Rhantus atricolor 2 2 4 3 6 3 5 1,16 Schriever, Bogan, Boersma, Cañedo-Argüelles, Jaeger, Olden, and Lytle. -
Seasonal Flooding Affects Habitat and Landscape Dynamics of a Gravel
Seasonal flooding affects habitat and landscape dynamics of a gravel-bed river floodplain Katelyn P. Driscoll1,2,5 and F. Richard Hauer1,3,4,6 1Systems Ecology Graduate Program, University of Montana, Missoula, Montana 59812 USA 2Rocky Mountain Research Station, Albuquerque, New Mexico 87102 USA 3Flathead Lake Biological Station, University of Montana, Polson, Montana 59806 USA 4Montana Institute on Ecosystems, University of Montana, Missoula, Montana 59812 USA Abstract: Floodplains are comprised of aquatic and terrestrial habitats that are reshaped frequently by hydrologic processes that operate at multiple spatial and temporal scales. It is well established that hydrologic and geomorphic dynamics are the primary drivers of habitat change in river floodplains over extended time periods. However, the effect of fluctuating discharge on floodplain habitat structure during seasonal flooding is less well understood. We collected ultra-high resolution digital multispectral imagery of a gravel-bed river floodplain in western Montana on 6 dates during a typical seasonal flood pulse and used it to quantify changes in habitat abundance and diversity as- sociated with annual flooding. We observed significant changes in areal abundance of many habitat types, such as riffles, runs, shallow shorelines, and overbank flow. However, the relative abundance of some habitats, such as back- waters, springbrooks, pools, and ponds, changed very little. We also examined habitat transition patterns through- out the flood pulse. Few habitat transitions occurred in the main channel, which was dominated by riffle and run habitat. In contrast, in the near-channel, scoured habitats of the floodplain were dominated by cobble bars at low flows but transitioned to isolated flood channels at moderate discharge. -
Modifying Wepp to Improve Streamflow Simulation in a Pacific Northwest Watershed
MODIFYING WEPP TO IMPROVE STREAMFLOW SIMULATION IN A PACIFIC NORTHWEST WATERSHED A. Srivastava, M. Dobre, J. Q. Wu, W. J. Elliot, E. A. Bruner, S. Dun, E. S. Brooks, I. S. Miller ABSTRACT. The assessment of water yield from hillslopes into streams is critical in managing water supply and aquatic habitat. Streamflow is typically composed of surface runoff, subsurface lateral flow, and groundwater baseflow; baseflow sustains the stream during the dry season. The Water Erosion Prediction Project (WEPP) model simulates surface runoff, subsurface lateral flow, soil water, and deep percolation. However, to adequately simulate hydrologic conditions with significant quantities of groundwater flow into streams, a baseflow component for WEPP is needed. The objectives of this study were (1) to simulate streamflow in the Priest River Experimental Forest in the U.S. Pacific Northwest using the WEPP model and a baseflow routine, and (2) to compare the performance of the WEPP model with and without including the baseflow using observed streamflow data. The baseflow was determined using a linear reservoir model. The WEPP- simulated and observed streamflows were in reasonable agreement when baseflow was considered, with an overall Nash- Sutcliffe efficiency (NSE) of 0.67 and deviation of runoff volume (Dv) of 7%. In contrast, the WEPP simulations without including baseflow resulted in an overall NSE of 0.57 and Dv of 47%. On average, the simulated baseflow accounted for 43% of the streamflow and 12% of precipitation annually. Integration of WEPP with a baseflow routine improved the model’s applicability to watersheds where groundwater contributes to streamflow. Keywords. Baseflow, Deep seepage, Forest watershed, Hydrologic modeling, Subsurface lateral flow, Surface runoff, WEPP. -
The Etyfish Project © Christopher Scharpf and Kenneth J
CYPRINODONTIFORMES (part 3) · 1 The ETYFish Project © Christopher Scharpf and Kenneth J. Lazara COMMENTS: v. 3.0 - 13 Nov. 2020 Order CYPRINODONTIFORMES (part 3 of 4) Suborder CYPRINODONTOIDEI Family PANTANODONTIDAE Spine Killifishes Pantanodon Myers 1955 pan(tos), all; ano-, without; odon, tooth, referring to lack of teeth in P. podoxys (=stuhlmanni) Pantanodon madagascariensis (Arnoult 1963) -ensis, suffix denoting place: Madagascar, where it is endemic [extinct due to habitat loss] Pantanodon stuhlmanni (Ahl 1924) in honor of Franz Ludwig Stuhlmann (1863-1928), German Colonial Service, who, with Emin Pascha, led the German East Africa Expedition (1889-1892), during which type was collected Family CYPRINODONTIDAE Pupfishes 10 genera · 112 species/subspecies Subfamily Cubanichthyinae Island Pupfishes Cubanichthys Hubbs 1926 Cuba, where genus was thought to be endemic until generic placement of C. pengelleyi; ichthys, fish Cubanichthys cubensis (Eigenmann 1903) -ensis, suffix denoting place: Cuba, where it is endemic (including mainland and Isla de la Juventud, or Isle of Pines) Cubanichthys pengelleyi (Fowler 1939) in honor of Jamaican physician and medical officer Charles Edward Pengelley (1888-1966), who “obtained” type specimens and “sent interesting details of his experience with them as aquarium fishes” Yssolebias Huber 2012 yssos, javelin, referring to elongate and narrow dorsal and anal fins with sharp borders; lebias, Greek name for a kind of small fish, first applied to killifishes (“Les Lebias”) by Cuvier (1816) and now a -
Forest Insect and Disease Conditions in the Southwestern Region, 2008
United States Department of Forest Insect and Agriculture Forest Disease Conditions in Service Southwestern the Southwestern Region Forestry and Forest Health Region, 2008 July 2009 PR-R3-16-5 The U.S. Department of Agriculture (USDA) prohibits discrimination in all its programs and activities on the basis of race, color, national origin, age, disability, and where applicable, sex, marital status, parental status, religion, sexual orientation, genetic information, political beliefs, reprisal, or because all or part of an individual’s income is derived from any public assistance program. (Not all prohibited bases apply to all programs.) Persons with disabilities who require alternative means for communication of program information (Braille, large print, audiotape, etc.) should contact USDA's TARGET Center at (202) 720- 2600 (voice and TTY). To file a complaint of discrimination, write to USDA, Director, Office of Civil Rights, 1400 Independence Avenue, SW, Washington, DC 20250-9410 or call (800) 795-3272 (voice) or (202) 720-6382 (TTY). USDA is an equal opportunity provider and employer. Cover photo: Pandora moth caterpillar collected on the North Kaibab Ranger District, Kaibab National Forest. Forest Insect and Disease Conditions in the Southwestern Region, 2008 Southwestern Region Forestry and Forest Health Regional Office Salomon Ramirez, Director Allen White, Pesticide Specialist Forest Health Zones Offices Arizona Zone John Anhold, Zone Leader Mary Lou Fairweather, Pathologist Roberta Fitzgibbon, Entomologist Joel McMillin, Entomologist -
Changes in Geyser Eruption Behavior and Remotely Triggered Seismicity in Yellowstone National Park Produced by the 2002 M 7.9 Denali Fault Earthquake, Alaska
Changes in geyser eruption behavior and remotely triggered seismicity in Yellowstone National Park produced by the 2002 M 7.9 Denali fault earthquake, Alaska S. Husen* Department of Geology and Geophysics, University of Utah, Salt Lake City, Utah 84112, USA R. Taylor National Park Service, Yellowstone Center for Resources, Yellowstone National Park, Wyoming 82190, USA R.B. Smith Department of Geology and Geophysics, University of Utah, Salt Lake City, Utah 84112, USA H. Healser National Park Service, Yellowstone Center for Resources, Yellowstone National Park, Wyoming 82190, USA ABSTRACT STUDY AREA Following the 2002 M 7.9 Denali fault earthquake, clear changes in geyser activity and The Yellowstone volcanic field, Wyoming, a series of local earthquake swarms were observed in the Yellowstone National Park area, centered in Yellowstone National Park (here- despite the large distance of 3100 km from the epicenter. Several geysers altered their after called ‘‘Yellowstone’’), is one of the larg- eruption frequency within hours after the arrival of large-amplitude surface waves from est silicic volcanic systems in the world the Denali fault earthquake. In addition, earthquake swarms occurred close to major (Christiansen, 2001; Smith and Siegel, 2000). geyser basins. These swarms were unusual compared to past seismicity in that they oc- Three major caldera-forming eruptions oc- curred simultaneously at different geyser basins. We interpret these observations as being curred within the past 2 m.y., the most recent induced by dynamic stresses associated with the arrival of large-amplitude surface waves. 0.6 m.y. ago. The current Yellowstone caldera We suggest that in a hydrothermal system dynamic stresses can locally alter permeability spans 75 km by 45 km (Fig. -
Human Impacts on Geyser Basins
volume 17 • number 1 • 2009 Human Impacts on Geyser Basins The “Crystal” Salamanders of Yellowstone Presence of White-tailed Jackrabbits Nature Notes: Wolves and Tigers Geyser Basins with no Documented Impacts Valley of Geysers, Umnak (Russia) Island Geyser Basins Impacted by Energy Development Geyser Basins Impacted by Tourism Iceland Iceland Beowawe, ~61 ~27 Nevada ~30 0 Yellowstone ~220 Steamboat Springs, Nevada ~21 0 ~55 El Tatio, Chile North Island, New Zealand North Island, New Zealand Geysers existing in 1950 Geyser basins with documented negative effects of tourism Geysers remaining after geothermal energy development Impacts to geyser basins from human activities. At least half of the major geyser basins of the world have been altered by geothermal energy development or tourism. Courtesy of Steingisser, 2008. Yellowstone in a Global Context N THIS ISSUE of Yellowstone Science, Alethea Steingis- claimed they had been extirpated from the park. As they have ser and Andrew Marcus in “Human Impacts on Geyser since the park’s establishment, jackrabbits continue to persist IBasins” document the global distribution of geysers, their in the park in a small range characterized by arid, lower eleva- destruction at the hands of humans, and the tremendous tion sagebrush-grassland habitats. With so many species in the importance of Yellowstone National Park in preserving these world on the edge of survival, the confirmation of the jackrab- rare and ephemeral features. We hope this article will promote bit’s persistence is welcome. further documentation, research, and protection efforts for The Nature Note continues to consider Yellowstone with geyser basins around the world. Documentation of their exis- a broader perspective. -
December 2012 Number 1
Calochortiana December 2012 Number 1 December 2012 Number 1 CONTENTS Proceedings of the Fifth South- western Rare and Endangered Plant Conference Calochortiana, a new publication of the Utah Native Plant Society . 3 The Fifth Southwestern Rare and En- dangered Plant Conference, Salt Lake City, Utah, March 2009 . 3 Abstracts of presentations and posters not submitted for the proceedings . 4 Southwestern cienegas: Rare habitats for endangered wetland plants. Robert Sivinski . 17 A new look at ranking plant rarity for conservation purposes, with an em- phasis on the flora of the American Southwest. John R. Spence . 25 The contribution of Cedar Breaks Na- tional Monument to the conservation of vascular plant diversity in Utah. Walter Fertig and Douglas N. Rey- nolds . 35 Studying the seed bank dynamics of rare plants. Susan Meyer . 46 East meets west: Rare desert Alliums in Arizona. John L. Anderson . 56 Calochortus nuttallii (Sego lily), Spatial patterns of endemic plant spe- state flower of Utah. By Kaye cies of the Colorado Plateau. Crystal Thorne. Krause . 63 Continued on page 2 Copyright 2012 Utah Native Plant Society. All Rights Reserved. Utah Native Plant Society Utah Native Plant Society, PO Box 520041, Salt Lake Copyright 2012 Utah Native Plant Society. All Rights City, Utah, 84152-0041. www.unps.org Reserved. Calochortiana is a publication of the Utah Native Plant Society, a 501(c)(3) not-for-profit organi- Editor: Walter Fertig ([email protected]), zation dedicated to conserving and promoting steward- Editorial Committee: Walter Fertig, Mindy Wheeler, ship of our native plants. Leila Shultz, and Susan Meyer CONTENTS, continued Biogeography of rare plants of the Ash Meadows National Wildlife Refuge, Nevada. -
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. -
Biogeochemical and Metabolic Responses to the Flood Pulse in a Semi-Arid Floodplain
View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by DigitalCommons@USU 1 Running Head: Semi-arid floodplain response to flood pulse 2 3 4 5 6 Biogeochemical and Metabolic Responses 7 to the Flood Pulse in a Semi-Arid Floodplain 8 9 10 11 with 7 Figures and 3 Tables 12 13 14 15 H. M. Valett1, M.A. Baker2, J.A. Morrice3, C.S. Crawford, 16 M.C. Molles, Jr., C.N. Dahm, D.L. Moyer4, J.R. Thibault, and Lisa M. Ellis 17 18 19 20 21 22 Department of Biology 23 University of New Mexico 24 Albuquerque, New Mexico 87131 USA 25 26 27 28 29 30 31 present addresses: 32 33 1Department of Biology 2Department of Biology 3U.S. EPA 34 Virginia Tech Utah State University Mid-Continent Ecology Division 35 Blacksburg, Virginia 24061 USA Logan, Utah 84322 USA Duluth, Minnesota 55804 USA 36 540-231-2065, 540-231-9307 fax 37 [email protected] 38 4Water Resources Division 39 United States Geological Survey 40 Richmond, Virginia 23228 USA 41 1 1 Abstract: Flood pulse inundation of riparian forests alters rates of nutrient retention and 2 organic matter processing in the aquatic ecosystems formed in the forest interior. Along the 3 Middle Rio Grande (New Mexico, USA), impoundment and levee construction have created 4 riparian forests that differ in their inter-flood intervals (IFIs) because some floodplains are 5 still regularly inundated by the flood pulse (i.e., connected), while other floodplains remain 6 isolated from flooding (i.e., disconnected). -
Three New Pupfish Species, Cyprinodon (Teleostei, Cyprinodontidae), from Chihuahua, México, and Arizona, USA Author(S): W
Three New Pupfish Species, Cyprinodon (Teleostei, Cyprinodontidae), from Chihuahua, México, and Arizona, USA Author(s): W. L. Minckley, Robert Rush Miller and Steven Mark Norris Source: Copeia, Vol. 2002, No. 3 (Aug. 15, 2002), pp. 687-705 Published by: American Society of Ichthyologists and Herpetologists (ASIH) Stable URL: http://www.jstor.org/stable/1448150 . Accessed: 23/07/2014 15:57 Your use of the JSTOR archive indicates your acceptance of the Terms & Conditions of Use, available at . http://www.jstor.org/page/info/about/policies/terms.jsp . JSTOR is a not-for-profit service that helps scholars, researchers, and students discover, use, and build upon a wide range of content in a trusted digital archive. We use information technology and tools to increase productivity and facilitate new forms of scholarship. For more information about JSTOR, please contact [email protected]. American Society of Ichthyologists and Herpetologists (ASIH) is collaborating with JSTOR to digitize, preserve and extend access to Copeia. http://www.jstor.org This content downloaded from 128.123.44.23 on Wed, 23 Jul 2014 15:57:21 PM All use subject to JSTOR Terms and Conditions Copeia,2002(3), pp. 687-705 Three New Pupfish Species, Cyprinodon(Teleostei, Cyprinodontidae), from Chihuahua, Mexico, and Arizona, USA W. L. MINCKLEY,ROBERT RUSH MILLER,AND STEVENMARK NORRIS Three new species of Cyprinodon(Teleostei, Cyprinodontidae)are described,each long recognized as distinct. Cyprinodonpisteri occupies a varietyof systems and hab- itats in the Lago de Guzmin complex basin in northern Chihuahua,Mexico. It is distinguishedby its dusky to black dorsal fin and narrowor inconspicuousterminal bar on the caudal fin in mature males.