Chapter 3: Small Mammals, Reptiles, and Amphibians
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Molecular Systematics of Spiny Pocket Mice (Subfamily Heteromyinae) Inferred from Mitochondrial and Nuclear Sequence Data
Brigham Young University BYU ScholarsArchive Theses and Dissertations 2009-04-17 Molecular Systematics of Spiny Pocket Mice (Subfamily Heteromyinae) Inferred from Mitochondrial and Nuclear Sequence Data Melina Crystal Williamson Brigham Young University - Provo Follow this and additional works at: https://scholarsarchive.byu.edu/etd Part of the Biology Commons BYU ScholarsArchive Citation Williamson, Melina Crystal, "Molecular Systematics of Spiny Pocket Mice (Subfamily Heteromyinae) Inferred from Mitochondrial and Nuclear Sequence Data" (2009). Theses and Dissertations. 1718. https://scholarsarchive.byu.edu/etd/1718 This Thesis is brought to you for free and open access by BYU ScholarsArchive. It has been accepted for inclusion in Theses and Dissertations by an authorized administrator of BYU ScholarsArchive. For more information, please contact [email protected], [email protected]. MOLECULAR SYSTEMATICS OF SPINY POCKET MICE (SUBFAMILY HETEROMYINAE) INFERRED FROM MITOCHONDRIAL AND NUCLEAR SEQUENCE DATA by Melina C. Williamson A thesis submitted to the faculty of Brigham Young University in partial fulfillment of the requirements for the degree of Master of Science Department of Biology Brigham Young University August 2009 BRIGHAM YOUNG UNIVERSITY GRADUATE COMMITTEE APPROVAL of a thesis submitted by Melina C. Williamson This thesis has been read by each member of the following graduate committee and by majority vote has been found to be satisfactory. Date Duke S. Rogers, Chair Date Leigh A. Johnson Date Jack W. Sites, Jr. BRIGHAM YOUNG UNIVERSITY As chair of the candidate’s graduate committee, I have read the thesis of Melina C. Williamson in its final form and have found that (1) its format, citations, and bibliographical style are consistent and acceptable and fulfill university and department style requirements; (2) its illustrative materials including figures, tables, and charts are in place; and (3) the final manuscript is satisfactory to the graduate committee and is ready for submission to the university library. -
Classification of Mammals 61
© Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FORCHAPTER SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION Classification © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC 4 NOT FORof SALE MammalsOR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC © Jones & Bartlett Learning, LLC NOT FOR SALE OR DISTRIBUTION NOT FOR SALE OR DISTRIBUTION © Jones & Bartlett Learning, LLC. NOT FOR SALE OR DISTRIBUTION. 2ND PAGES 9781284032093_CH04_0060.indd 60 8/28/13 12:08 PM CHAPTER 4: Classification of Mammals 61 © Jones Despite& Bartlett their Learning,remarkable success, LLC mammals are much less© Jones stress & onBartlett the taxonomic Learning, aspect LLCof mammalogy, but rather as diverse than are most invertebrate groups. This is probably an attempt to provide students with sufficient information NOT FOR SALE OR DISTRIBUTION NOT FORattributable SALE OR to theirDISTRIBUTION far greater individual size, to the high on the various kinds of mammals to make the subsequent energy requirements of endothermy, and thus to the inabil- discussions of mammalian biology meaningful. -
The Herbivore Digestive System Buffalo Zebra
The Herbivore Digestive System Name__________________________ Buffalo Ruminant: The purpose of the digestion system is to ______________________________ _____________________________. Bacteria help because they can digest __________________, a sugar found in the cell walls of________________. Zebra Non- Ruminant: What is the name for the largest section of Organ Color Key a ruminant’s Mouth stomach? Esophagus __________ Stomach Small Intestine Cecum Large Intestine Background Information for the Teacher Two Strategies of Digestion in Hoofed Mammals Ruminant Non‐ruminant Representative species Buffalo, cows, sheep, goats, antelope, camels, Zebra, pigs, horses, asses, hippopotamus, rhinoceros giraffes, deer Does the animal Yes, regurgitation No regurgitation regurgitate its cud to Grass is better prepared for digestion, as grinding Bacteria can not completely digest cell walls as chew material again? motion forms small particles fit for bacteria. material passes quickly through, so stool is fibrous. Where in the system do At the beginning, in the rumen Near the end, in the cecum you find the bacteria This first chamber of its four‐part stomach is In this sac between the two intestines, bacteria digest that digest cellulose? large, and serves to store food between plant material, the products of which pass to the rumination and as site of digestion by bacteria. bloodstream. How would you Higher Nutrition Lower Nutrition compare the nutrition Reaps benefits of immediately absorbing the The digestive products made by the bacteria are obtained via digestion? products of bacterial digestion, such as sugars produced nearer the end of the line, after the small and vitamins, via the small intestine. intestine, the classic organ of nutrient absorption. -
Mammals of the California Desert
MAMMALS OF THE CALIFORNIA DESERT William F. Laudenslayer, Jr. Karen Boyer Buckingham Theodore A. Rado INTRODUCTION I ,+! The desert lands of southern California (Figure 1) support a rich variety of wildlife, of which mammals comprise an important element. Of the 19 living orders of mammals known in the world i- *- loday, nine are represented in the California desert15. Ninety-seven mammal species are known to t ':i he in this area. The southwestern United States has a larger number of mammal subspecies than my other continental area of comparable size (Hall 1981). This high degree of subspeciation, which f I;, ; leads to the development of new species, seems to be due to the great variation in topography, , , elevation, temperature, soils, and isolation caused by natural barriers. The order Rodentia may be k., 2:' , considered the most successful of the mammalian taxa in the desert; it is represented by 48 species Lc - occupying a wide variety of habitats. Bats comprise the second largest contingent of species. Of the 97 mammal species, 48 are found throughout the desert; the remaining 49 occur peripherally, with many restricted to the bordering mountain ranges or the Colorado River Valley. Four of the 97 I ?$ are non-native, having been introduced into the California desert. These are the Virginia opossum, ' >% Rocky Mountain mule deer, horse, and burro. Table 1 lists the desert mammals and their range 1 ;>?-axurrence as well as their current status of endangerment as determined by the U.S. fish and $' Wildlife Service (USWS 1989, 1990) and the California Department of Fish and Game (Calif. -
Biological Notes and Descriptions of Two New Moths Phoretic on Spiny Pocket Mice in Costa Rica (Lepidoptera, Tineoidea)
PROC. ENTOMOl. SOC. WASH. 88(1). 1986, pp. 98-109 NEOTROPICAL TlNEIDAE, U: BIOLOGICAL NOTES AND DESCRIPTIONS OF TWO NEW MOTHS PHORETIC ON SPINY POCKET MICE IN COSTA RICA (LEPIDOPTERA, TINEOIDEA) DoNALD R. DAVIS, DALE H . CLAYTON, DANIEL H . J ANZEN, AND ANNE P. BROOKE (DRD) Department of Entomology, National Museum of Natural History, Smithsonian Institution, Washington, D. C. 20560; (DHC) Committee on Evo lutionary Biology, University of Chicago, Chicago, lIIinois 60637; (DHJ) De partment of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 191 04; (APB) Museum of Vertebrate Zoology, Uni versity of Cali fomi a, Berkeley, California 94720. Abstract. - Two new species of tineid moths discovered riding on the backs of two species of spiny pocket mice (Heteromyidae) in Costa Rica are described. Amydria selvae. new species, was found on Heteromys desmarestianus Gray in the rainforest at Finca La Selva and Ptilopsaltis santarosae. new species, occurred on Liomys salvini (Thomas) in the dry forest at Santa Rosa National Park. Only female moths were observed and collected. Biological observations on both moths and their hosts in phoresy are summarized. Recent live-trapping of spiny pocket mice in Costa Rican forests has revealed the association of three species of ph ore tic moths of the family Tineidae. The life histories of the moths are still poorly understood and only the females are known to be phoretic. No males of any of the three species have been discovered. Exca vations of the burrows of the two species of spiny mice are now underway, which we hope will reveal not only the presence of males with associated immatures but also the larval biology. -
Plant and Rodent Communities of Organ Pipe Cactus National Monument
Plant and rodent communities of Organ Pipe Cactus National Monument Item Type text; Thesis-Reproduction (electronic) Authors Warren, Peter Lynd Publisher The University of Arizona. Rights Copyright © is held by the author. Digital access to this material is made possible by the University Libraries, University of Arizona. Further transmission, reproduction or presentation (such as public display or performance) of protected items is prohibited except with permission of the author. Download date 29/09/2021 16:51:51 Link to Item http://hdl.handle.net/10150/566520 PLANT AND RODENT COMMUNITIES OF ORGAN PIPE CACTUS NATIONAL.MONUMENT by Peter Lynd Warren A Thesis Submitted to the Faculty of the DEPARTMENT OF ECOLOGY AND EVOLUTIONARY BIOLOGY In Partial Fulfillment of the Requirements For the Degree of MASTER OF SCIENCE In the Graduate College THE UNIVERSITY OF ARIZONA 1 9 7 9 STATEMENT BY AUTHOR This thesis has been submitted in partial fulfillment of re quirements for an advanced degree at The University of Arizona and is deposited in the University Library to be made available to borrowers under rules of the Library. Brief quotations from this thesis are allowable without special permission, provided that accurate acknowledgment of source is made. Requests for permission for extended quotation from or reproduction of this manuscript in whole or in part may be granted by the head of the major department or the Dean of the Graduate College when in his judg ment the proposed use of the material is in the interests of scholar ship. In all other instances, however, permission must be obtained from the author. -
March Rice Rat, <I>Oryzomys Palustris</I>
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Mammalogy Papers: University of Nebraska State Museum, University of Nebraska State Museum 1-25-1985 March Rice Rat, Oryzomys palustris Hugh H. Genoways University of Nebraska - Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/museummammalogy Part of the Biodiversity Commons, Terrestrial and Aquatic Ecology Commons, and the Zoology Commons Genoways, Hugh H., "March Rice Rat, Oryzomys palustris" (1985). Mammalogy Papers: University of Nebraska State Museum. 227. http://digitalcommons.unl.edu/museummammalogy/227 This Article is brought to you for free and open access by the Museum, University of Nebraska State at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Mammalogy Papers: University of Nebraska State Museum by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. Genoways in Species of Special Concern in Pennsylvania (Genoways & Brenner, editors). Special Publication, Carnegie Museum of Natural History (1985) no. 11. Copyright 1985, Carnegie Museum of Natural History. Used by permission. 402 SPECIAL PUBLICATION CARNEGIE MUSEUM OF NATURAL HISTORY NO. 11 "'-" "~_MARSH RICE RAT (Oryzomys pa!ustris) Status Undetermined MARSH RICE RAT Oryzomys palustris Family Cricetidae Order Rodentia River Valley and in the areas surrounding its prin OTHER NAMES: Rice rat, swamp rice rat, north cipal tributaries (Hall, 1981). ern rice rat. HABITAT: The marsh rice rat is a semi-aquatic DESCRIPTION: A medium-sized rat that would species that is found in greatest abundance in the be most easily confused with smaller individuals of marshes and swamps and other wetlands ofthe Gulf the introduced Norway rat (Rattus norvegicus). -
Germination and Seedling Establishment of Spiny Hopsage (Grayia Spinosa [Hook.] Moq.)
AN ABSTRACT OF THE THESIS OF Nancy L. Shaw for the degree of Doctor of Philosophy in Crop and Soil Sciences presented on March 19, 1992 Title: Germination and Seedling Establishment of Spiny Hopsage (Grayia Spinosa [Hook.] Moq.) Abstract approved:_Redactedfor Privacy von r. ULdUe Reestablishment of spiny hopsage(Grayia spinosa [Hook.] Moq.) where depleted or lost on shrub steppe sites can improve forage, plant cover, and soil stabilization. The objectives of this study were to: 1) determine direct-seeding requirements; 2) develop optimum germination pretreatments; and 3) examine dormancy mechanisms in spiny hopsage fruits and seeds. The effects of seed source, planting date,and site preparation method onseed germination and seedling establishment (SE) were examined at Birds of Prey and Reynolds Creek in southwestern Idaho. Three seed sources were planted on rough or compact seedbeds on 4 dates in 1986-87 and 3 dates in 1987-88. Exposure to cool-moist environments improved spring SE from early fall (EF) and late fall (LF) plantings. Few seedlings emerged from early (ESp) or late spring (LSp) plantings. SE was low at: 1 site in 1986-87 and atboth sites in 1987-88, probably due to lack of precipitation. For the successful 1986-87 planting, seedling density was greater on rough compared to compact seedbeds in April andMay, possiblydue to improved microclimate conditions. Growth rate varied among seed sources, but seedlings developed a deep taproot (mean length 266 mm) with few lateral roots the first season. Seeds were planted on 3 dates in 1986-87 and 1987-88, andnylon bags containing seeds were planted on 4 dates each year to study microenvironment effects on germination (G), germination rate (GR), and SE. -
Downloaded from Ensembl (Www
Lin et al. BMC Genomics 2014, 15:32 http://www.biomedcentral.com/1471-2164/15/32 RESEARCH ARTICLE Open Access Transcriptome sequencing and phylogenomic resolution within Spalacidae (Rodentia) Gong-Hua Lin1, Kun Wang2, Xiao-Gong Deng1,3, Eviatar Nevo4, Fang Zhao1, Jian-Ping Su1, Song-Chang Guo1, Tong-Zuo Zhang1* and Huabin Zhao5* Abstract Background: Subterranean mammals have been of great interest for evolutionary biologists because of their highly specialized traits for the life underground. Owing to the convergence of morphological traits and the incongruence of molecular evidence, the phylogenetic relationships among three subfamilies Myospalacinae (zokors), Spalacinae (blind mole rats) and Rhizomyinae (bamboo rats) within the family Spalacidae remain unresolved. Here, we performed de novo transcriptome sequencing of four RNA-seq libraries prepared from brain and liver tissues of a plateau zokor (Eospalax baileyi) and a hoary bamboo rat (Rhizomys pruinosus), and analyzed the transcriptome sequences alongside a published transcriptome of the Middle East blind mole rat (Spalax galili). We characterize the transcriptome assemblies of the two spalacids, and recover the phylogeny of the three subfamilies using a phylogenomic approach. Results: Approximately 50.3 million clean reads from the zokor and 140.8 million clean reads from the bamboo ratwere generated by Illumina paired-end RNA-seq technology. All clean reads were assembled into 138,872 (the zokor) and 157,167 (the bamboo rat) unigenes, which were annotated by the public databases: the Swiss-prot, Trembl, NCBI non-redundant protein (NR), NCBI nucleotide sequence (NT), Gene Ontology (GO), Cluster of Orthologous Groups (COG), and Kyoto Encyclopedia of Genes and Genomes (KEGG). -
Wildlife Ruby Lake Natillntllwildlife Refuge
I 49. 44/2: R 82/3/993 P RLE Wildlife Ruby lake NatillntllWildlife Refuge ZIMMERMAN LIBRARY UNIV. OF NEW MEXteo FEB 1 0 1994 U.S. Regional Depos1to A Refuge for Nesting and Migrating Waterfowl and Other Wildlife The Habitat Ruby Lake National Wildlife Refuge was established in The refuge, at an elevation of 6,000 feet, consists of an 1938. It encompasses 37,632 acres at the south end of extensive bulrush marsh interspersed with pockets of Ruby Valley. This land was once covered by a 200 foot open water. Fish are abundant. Islands scattered deep, 300,800-acre lake known as Franklin Lake. Today throughout provide good nesting habitat for many bird 12,000 acres of marsh remain on the refuge. Just north of species. the refuge, a 15,000-acre seasonal wetland is now referred to as Franklin Lake. Over 200 springs flow into the marsh along its west border _...)/ creating riparian habitat which is used by many songbirds, To Elko �� and Welle snipe, rail and small mammals. They also provide a water FRANKLIN source for larger mammals. With slight increases in LAKE elevation, wet meadows gradate into grasslands and sagebrush-rabbitbrush habitat. Pinon pines and juniper cover the slopes of the Ruby Mountains that rise to 11,000 feet along the west side of the refuge. Canyons provide habitat for a variety of wildlife. Rock cliffs provide raptors with nesting and perching sites. A mountainside of dead trees, home for ROAD cavity dwelling birds, was the result of a 1979 wildfire. BRESSMAN CABIN LOOP MAIN BOAT LANDING -4,__,,� ·�I! I N � 0 3 Miles 0 2 4 Kilometer� RANCH dead pinon tree General Key BIRDS bam ,wallow � Season 6 The following bird list includes 207 species observed on Sp - Spring (March through May) or near the refuge. -
Dipodomys Ingens)
Species Status Assessment Report for the Giant Kangaroo Rat (Dipodomys ingens) Photo by Elizabeth Bainbridge Version 1.0 August 2020 Prepared by the U.S. Fish and Wildlife Service August 2020 GKR SSA Report – August 2020 EXECUTIVE SUMMARY The U.S. Fish and Wildlife Service listed the giant kangaroo rat (Dipodomys ingens) as endangered under the Endangered Species Act in 1987 due to the threats of habitat loss and widespread rodenticide use (Service 1987, entire). The giant kangaroo rat is the largest species in the genus that contains all kangaroo rats. The giant kangaroo rat is found only in south-central California, on the western slopes of the San Joaquin Valley, the Carrizo and Elkhorn Plains, and the Cuyama Valley. The preferred habitat of the giant kangaroo rat is native, sloping annual grasslands with sparse vegetation (Grinnell, 1932; Williams, 1980). This report summarizes the results of a species status assessment (SSA) that the U. S. Fish and Wildlife Service (Service) completed for the giant kangaroo rat. To assess the species’ viability, we used the three conservation biology principles of resiliency, redundancy, and representation (together, the 3Rs). These principles rely on assessing the species at an individual, population, and species level to determine whether the species can persist into the future and avoid extinction by having multiple resilient populations distributed widely across its range. Giant kangaroo rats remain in fragmented habitat patches throughout their historical range. However, some areas where giant kangaroo rats once existed have not had documented occurrences for 30 years or more. The giant kangaroo rat is found in six geographic areas (units), representing the northern, middle, and southern portions of the range. -
Hispid Pocket Mouse Chaetodipus Hispidus
Wyoming Species Account Hispid Pocket Mouse Chaetodipus hispidus REGULATORY STATUS USFWS: No special status USFS R2: No special status USFS R4: No special status Wyoming BLM: No special status State of Wyoming: Nongame Wildlife CONSERVATION RANKS USFWS: No special status WGFD: NSSU (U), Tier III WYNDD: G5, S1S3 Wyoming Contribution: LOW IUCN: Least Concern STATUS AND RANK COMMENTS The Wyoming Natural Diversity Database has assigned Hispid Pocket Mouse (Chaetodipus hispidus) a state conservation rank ranging from S1 (Critically Imperiled) to S3 (Vulnerable) because of uncertainty about the proportion of range occupied and population trends for this species in Wyoming. NATURAL HISTORY Taxonomy: Historically, there were four recognized subspecies of Hispid Pocket Mouse, and only C. h. paradoxus was found in Wyoming 1-5. A recent DNA-based study determined that the previously accepted subspecies are neither morphologically nor genetically distinct and instead proposed new subspecies boundaries delineated by four geographically and ecologically disjunct mitochondrial clades 6. Following this taxonomic revision, Wyoming remains within the distribution of the newly defined subspecies C. h. paradoxus 6. Description: It is possible to identify Hispid Pocket Mouse in the field. It is the largest Wyoming pocket mouse species; adults weigh between 40–60 g and can reach total lengths of 200–223 mm 2. Tail, hind foot, and ear length ranges from 90–113 mm, 25–28 mm, and 12–13 mm, respectively 2. Hispid Pocket Mouse is named for its distinctly coarse dorsal pelage, which is buff to yellowish orange mixed with black hairs, thus leading to an overall brownish or even olive appearance 1, 2, 4, 5, 7.