2. Springs Dependent Species (SDS)
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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. -
LONG-LIVED AQUATIC INSECTS ACCUMULATE CALCIUM CARBONATE DEPOSITS in a MONTANE DESERT STREAM Eric K
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Papers in Natural Resources Natural Resources, School of 2016 CAUGHT BETWEEN A ROCK AND A HARD MINERAL ENCRUSTATION: LONG-LIVED AQUATIC INSECTS ACCUMULATE CALCIUM CARBONATE DEPOSITS IN A MONTANE DESERT STREAM Eric K. Moody Arizona State University Jessica R. Corman University of Nebraska - Lincoln, [email protected] Michael T. Bogan University of California - Berkeley Follow this and additional works at: http://digitalcommons.unl.edu/natrespapers Part of the Natural Resources and Conservation Commons, Natural Resources Management and Policy Commons, and the Other Environmental Sciences Commons Moody, Eric K.; Corman, Jessica R.; and Bogan, Michael T., "CAUGHT BETWEEN A ROCK AND A HARD MINERAL ENCRUSTATION: LONG-LIVED AQUATIC INSECTS ACCUMULATE CALCIUM CARBONATE DEPOSITS IN A MONTANE DESERT STREAM" (2016). Papers in Natural Resources. 796. http://digitalcommons.unl.edu/natrespapers/796 This Article is brought to you for free and open access by the Natural Resources, School of at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Papers in Natural Resources by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Western North American Naturalist 76(2), © 2016, pp. 172–179 CAUGHT BETWEEN A ROCK AND A HARD MINERAL ENCRUSTATION: LONG-LIVED AQUATIC INSECTS ACCUMULATE CALCIUM CARBONATE DEPOSITS IN A MONTANE DESERT STREAM Eric K. Moody1, Jessica R. Corman1,2, and Michael T. Bogan3 ABSTRACT.—Aquatic ecosystems overlying regions of limestone bedrock can feature active deposition of calcium carbonate in the form of travertine or tufa. Although most travertine deposits form a cement-like layer on stream sub- strates, mineral deposits can also form on benthic invertebrates. -
Multi-National Conservation of Alligator Lizards
MULTI-NATIONAL CONSERVATION OF ALLIGATOR LIZARDS: APPLIED SOCIOECOLOGICAL LESSONS FROM A FLAGSHIP GROUP by ADAM G. CLAUSE (Under the Direction of John Maerz) ABSTRACT The Anthropocene is defined by unprecedented human influence on the biosphere. Integrative conservation recognizes this inextricable coupling of human and natural systems, and mobilizes multiple epistemologies to seek equitable, enduring solutions to complex socioecological issues. Although a central motivation of global conservation practice is to protect at-risk species, such organisms may be the subject of competing social perspectives that can impede robust interventions. Furthermore, imperiled species are often chronically understudied, which prevents the immediate application of data-driven quantitative modeling approaches in conservation decision making. Instead, real-world management goals are regularly prioritized on the basis of expert opinion. Here, I explore how an organismal natural history perspective, when grounded in a critique of established human judgements, can help resolve socioecological conflicts and contextualize perceived threats related to threatened species conservation and policy development. To achieve this, I leverage a multi-national system anchored by a diverse, enigmatic, and often endangered New World clade: alligator lizards. Using a threat analysis and status assessment, I show that one recent petition to list a California alligator lizard, Elgaria panamintina, under the US Endangered Species Act often contradicts the best available science. -
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. -
Learning from the Extraordinary: How the Highly Derived Larval Eyes of the Sunburst Diving Beetle Can Give Insights Into Aspects Of
Learning from the extraordinary: How the highly derived larval eyes of the Sunburst Diving Beetle can give insights into aspects of holometabolous insect visual systems A dissertation submitted to the Division of Research and Advanced Studies of the University of Cincinnati In partial fulfillment of the requirements for the degree of Doctorate of Philosophy (Ph.D.) In the department of Biological Sciences of the College of Arts and Sciences 2011 by Nadine Stecher B.S., University of Rostock, 2001 M.S., University of Rostock, 2005 Committee Chair: Elke K. Buschbeck, Ph.D. Abstract Stemmata, the eyes of holometabolous insect larvae, vary greatly in number, structure and task. The stemmata of the Sunburst Diving Beetle, Thermonectus marmoratus, are among the most sophisticated. The predatory larvae have six eyes and a potentially light-sensitive spot (eye spot) adjacent to the stemmata. The forward-pointing tubular eyes Eye 1 (E1) and Eye 2 (E2) are involved in prey capture, and possess a biconvex lens, a cellular crystalline cone-like structure, and tiered retinal tissue. A distal and a proximal retina can be distinguished, which differ not only in morphology but possibly also in function. E1 has an additional retina which runs medially alongside the crystalline cone-like structure. Using transmission electron microscopic preparations, I described the ultrastructure of the retinas of the principal eyes E1 and E2. The proximal retinas are composed of photoreceptors with predominantly parallel microvilli, and neighboring rhabdomeres are oriented approximately orthogonally to each another. This rhabdomeric arrangement is typical for eyes that are polarization sensitive. A similar organization is observed in a portion of the medial retina of E1, but not in either of the distal retinas. -
Ecography ECOG-02578 Pinkert, S., Brandl, R
Ecography ECOG-02578 Pinkert, S., Brandl, R. and Zeuss, D. 2016. Colour lightness of dragonfly assemblages across North America and Europe. – Ecography doi: 10.1111/ecog.02578 Supplementary material Appendix 1 Figures A1–A12, Table A1 and A2 1 Figure A1. Scatterplots between female and male colour lightness of 44 North American (Needham et al. 2000) and 19 European (Askew 1988) dragonfly species. Note that colour lightness of females and males is highly correlated. 2 Figure A2. Correlation of the average colour lightness of European dragonfly species illustrated in both Askew (1988) and Dijkstra and Lewington (2006). Average colour lightness ranges from 0 (absolute black) to 255 (pure white). Note that the extracted colour values of dorsal dragonfly drawings from both sources are highly correlated. 3 Figure A3. Frequency distribution of the average colour lightness of 152 North American and 74 European dragonfly species. Average colour lightness ranges from 0 (absolute black) to 255 (pure white). Rugs at the abscissa indicate the value of each species. Note that colour values are from different sources (North America: Needham et al. 2000, Europe: Askew 1988), and hence absolute values are not directly comparable. 4 Figure A4. Scatterplots of single ordinary least-squares regressions between average colour lightness of 8,127 North American dragonfly assemblages and mean temperature of the warmest quarter. Red dots represent assemblages that were excluded from the analysis because they contained less than five species. Note that those assemblages that were excluded scatter more than those with more than five species (c.f. the coefficients of determination) due to the inherent effect of very low sampling sizes. -
A Checklist of North American Odonata
A Checklist of North American Odonata Including English Name, Etymology, Type Locality, and Distribution Dennis R. Paulson and Sidney W. Dunkle 2009 Edition (updated 14 April 2009) A Checklist of North American Odonata Including English Name, Etymology, Type Locality, and Distribution 2009 Edition (updated 14 April 2009) Dennis R. Paulson1 and Sidney W. Dunkle2 Originally published as Occasional Paper No. 56, Slater Museum of Natural History, University of Puget Sound, June 1999; completely revised March 2009. Copyright © 2009 Dennis R. Paulson and Sidney W. Dunkle 2009 edition published by Jim Johnson Cover photo: Tramea carolina (Carolina Saddlebags), Cabin Lake, Aiken Co., South Carolina, 13 May 2008, Dennis Paulson. 1 1724 NE 98 Street, Seattle, WA 98115 2 8030 Lakeside Parkway, Apt. 8208, Tucson, AZ 85730 ABSTRACT The checklist includes all 457 species of North American Odonata considered valid at this time. For each species the original citation, English name, type locality, etymology of both scientific and English names, and approxi- mate distribution are given. Literature citations for original descriptions of all species are given in the appended list of references. INTRODUCTION Before the first edition of this checklist there was no re- Table 1. The families of North American Odonata, cent checklist of North American Odonata. Muttkows- with number of species. ki (1910) and Needham and Heywood (1929) are long out of date. The Zygoptera and Anisoptera were cov- Family Genera Species ered by Westfall and May (2006) and Needham, West- fall, and May (2000), respectively, but some changes Calopterygidae 2 8 in nomenclature have been made subsequently. Davies Lestidae 2 19 and Tobin (1984, 1985) listed the world odonate fauna Coenagrionidae 15 103 but did not include type localities or details of distri- Platystictidae 1 1 bution. -
Coleoptera: Dytiscidae) on Larval Culex Quinquefasciatus (Diptera: Culicidae)
The University of Southern Mississippi The Aquila Digital Community Honors Theses Honors College Spring 5-2014 Differences In Consumption Rates Between Juvenile and Adult Laccophilus fasciatus rufus (Coleoptera: Dytiscidae) On Larval Culex quinquefasciatus (Diptera: Culicidae) Carmen E. Bofill University of Southern Mississippi Follow this and additional works at: https://aquila.usm.edu/honors_theses Part of the Biology Commons Recommended Citation Bofill, Carmen E., "Differences In Consumption Rates Between Juvenile and Adult Laccophilus fasciatus rufus (Coleoptera: Dytiscidae) On Larval Culex quinquefasciatus (Diptera: Culicidae)" (2014). Honors Theses. 254. https://aquila.usm.edu/honors_theses/254 This Honors College Thesis is brought to you for free and open access by the Honors College at The Aquila Digital Community. It has been accepted for inclusion in Honors Theses by an authorized administrator of The Aquila Digital Community. For more information, please contact [email protected]. The University of Southern Mississippi Differences in consumption rates between juvenile and adult Laccophilus fasciatus rufus (Coleoptera: Dytiscidae) on larval Culex quinquefasciatus (Diptera: Culicidae) by Carmen Bofill A Thesis Submitted to the Honors College of The University of Southern Mississippi in Partial Fulfillment of the Requirements for the Degree of Bachelor of Science in the Department of Biological Sciences May 2014 ii Approved by ______________________________ Donald Yee, Ph.D., Thesis Adviser Assistant Professor of Biology ______________________________ Shiao Wang, Ph.D., Chair Department of Biological Sciences ______________________________ David R. Davies, Ph.D., Dean Honors College iii Abstract With the increase of global temperature and human populations, prevalence of vector-borne diseases is becoming an issue for public health. Over the years these vectors have been notorious for developing resistance to human regulated insecticides. -
(Dr. Sc. Nat.) Vorgelegt Der Mathematisch-Naturwissenschaftl
Zurich Open Repository and Archive University of Zurich Main Library Strickhofstrasse 39 CH-8057 Zurich www.zora.uzh.ch Year: 2012 Flowers, sex, and diversity: Reproductive-ecological and macro-evolutionary aspects of floral variation in the Primrose family, Primulaceae de Vos, Jurriaan Michiel Posted at the Zurich Open Repository and Archive, University of Zurich ZORA URL: https://doi.org/10.5167/uzh-88785 Dissertation Originally published at: de Vos, Jurriaan Michiel. Flowers, sex, and diversity: Reproductive-ecological and macro-evolutionary aspects of floral variation in the Primrose family, Primulaceae. 2012, University of Zurich, Facultyof Science. FLOWERS, SEX, AND DIVERSITY. REPRODUCTIVE-ECOLOGICAL AND MACRO-EVOLUTIONARY ASPECTS OF FLORAL VARIATION IN THE PRIMROSE FAMILY, PRIMULACEAE Dissertation zur Erlangung der naturwissenschaftlichen Doktorwürde (Dr. sc. nat.) vorgelegt der Mathematisch-naturwissenschaftliche Fakultät der Universität Zürich von Jurriaan Michiel de Vos aus den Niederlanden Promotionskomitee Prof. Dr. Elena Conti (Vorsitz) Prof. Dr. Antony B. Wilson Dr. Colin E. Hughes Zürich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s ist ein zentrales Ziel in der Evolutionsbiologie, die Muster der Vielfalt und die Prozesse, die sie erzeugen, zu verstehen. -
Springs and Springs-Dependent Taxa of the Colorado River Basin, Southwestern North America: Geography, Ecology and Human Impacts
water Article Springs and Springs-Dependent Taxa of the Colorado River Basin, Southwestern North America: Geography, Ecology and Human Impacts Lawrence E. Stevens * , Jeffrey Jenness and Jeri D. Ledbetter Springs Stewardship Institute, Museum of Northern Arizona, 3101 N. Ft. Valley Rd., Flagstaff, AZ 86001, USA; Jeff@SpringStewardship.org (J.J.); [email protected] (J.D.L.) * Correspondence: [email protected] Received: 27 April 2020; Accepted: 12 May 2020; Published: 24 May 2020 Abstract: The Colorado River basin (CRB), the primary water source for southwestern North America, is divided into the 283,384 km2, water-exporting Upper CRB (UCRB) in the Colorado Plateau geologic province, and the 344,440 km2, water-receiving Lower CRB (LCRB) in the Basin and Range geologic province. Long-regarded as a snowmelt-fed river system, approximately half of the river’s baseflow is derived from groundwater, much of it through springs. CRB springs are important for biota, culture, and the economy, but are highly threatened by a wide array of anthropogenic factors. We used existing literature, available databases, and field data to synthesize information on the distribution, ecohydrology, biodiversity, status, and potential socio-economic impacts of 20,872 reported CRB springs in relation to permanent stream distribution, human population growth, and climate change. CRB springs are patchily distributed, with highest density in montane and cliff-dominated landscapes. Mapping data quality is highly variable and many springs remain undocumented. Most CRB springs-influenced habitats are small, with a highly variable mean area of 2200 m2, generating an estimated total springs habitat area of 45.4 km2 (0.007% of the total CRB land area). -
Aquatic Ecosystems and Invertebrates of the Grand Staircase-Escalante National Monument Cooperative Agreement Number JSA990024 Annual Report of Activities for 2000
Aquatic Ecosystems and Invertebrates of the Grand Staircase-Escalante National Monument Cooperative Agreement Number JSA990024 Annual Report of Activities for 2000 Mark Vinson National Aquatic Monitoring Center Department of Fisheries and Wildlife Utah State University Logan, Utah 84322-5210 www.usu.edu/buglab 1 April 2001 i Table of contents Page Foreword ........................................................................... i Introduction ........................................................................ 1 Study area ......................................................................... 1 Long-term repeat sampling sites ........................................................ 2 Methods Locations and physical habitat ................................................... 3 Aquatic invertebrates Qualitative samples...................................................... 3 Quantitative samples ..................................................... 4 Laboratory methods ........................................................... 4 Results Sampling locations............................................................ 5 Habitat types................................................................. 6 Water temperatures ........................................................... 8 Aquatic invertebrates .......................................................... 8 Literature cited..................................................................... 13 Appendices 1. Aquatic invertebrates collected in the major habitats A. Alcove pools ......................................................