Phylogenetic Relationships and Divergence Times in Rodents Based on Both Genes and Fossils Ryan Norris University of Vermont
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Genetic Structure of the North American Porcupine (Erethizon Dorsatum) Across Western Texas
GENETIC STRUCTURE OF THE NORTH AMERICAN PORCUPINE (ERETHIZON DORSATUM) ACROSS WESTERN TEXAS by Erica D. Thomas A Thesis Submitted in Partial Fulfillment Of the Requirements for the Degree MASTER OF SCIENCE Major Subject: Biology West Texas A&M University Canyon, Texas December 2017 Approved: Rocky Ward, PhD Date Chairman, Thesis Committee W. David Sissom, PhD Date Member, Thesis Committee William P. Johnson, M.S. Date Member, Thesis Committee W. David Sissom, PhD Date Department Head Dean, Academic College Date Angela N. Spaulding Date Dean, Graduate School ii ABSTRACT The North American porcupine (Erethizon dorsatum) is a highly mobile, generalist species with an extensive geographical distribution in North America. The porcupine was first documented in southwestern Texas in the early 20th century, but today occurs in most of the western two-thirds of the state. This species is relatively unstudied within the Great Plains ecoregion of North America, with no genetic studies having been conducted for this species in Texas. The objectives of this study were to describe population genetic metrics of porcupines across 3 ecoregions in western Texas by examining variation in 17 polymorphic microsatellites, and to confirm the applicability of the zinc finger protein sequencing method to identify sex in a population of North American porcupines. Tissue samples from 106 porcupines were collected from the High Plains, Rolling Plains, and Edwards Plateau ecoregions of western Texas. Sex was accurately identified for 92 porcupine tissue samples by directly sequencing a short portion (195 base pairs) of the zinc finger protein gene. Sixteen base pair substitutions between Zfx and Zfy chromosomes denoted the sex of individuals; heterozygous sequence for males (Zfx and Zfy), homozygous sequence for females (Zfx only). -
The Beaver's Phylogenetic Lineage Illuminated by Retroposon Reads
www.nature.com/scientificreports OPEN The Beaver’s Phylogenetic Lineage Illuminated by Retroposon Reads Liliya Doronina1,*, Andreas Matzke1,*, Gennady Churakov1,2, Monika Stoll3, Andreas Huge3 & Jürgen Schmitz1 Received: 13 October 2016 Solving problematic phylogenetic relationships often requires high quality genome data. However, Accepted: 25 January 2017 for many organisms such data are still not available. Among rodents, the phylogenetic position of the Published: 03 March 2017 beaver has always attracted special interest. The arrangement of the beaver’s masseter (jaw-closer) muscle once suggested a strong affinity to some sciurid rodents (e.g., squirrels), placing them in the Sciuromorpha suborder. Modern molecular data, however, suggested a closer relationship of beaver to the representatives of the mouse-related clade, but significant data from virtually homoplasy- free markers (for example retroposon insertions) for the exact position of the beaver have not been available. We derived a gross genome assembly from deposited genomic Illumina paired-end reads and extracted thousands of potential phylogenetically informative retroposon markers using the new bioinformatics coordinate extractor fastCOEX, enabling us to evaluate different hypotheses for the phylogenetic position of the beaver. Comparative results provided significant support for a clear relationship between beavers (Castoridae) and kangaroo rat-related species (Geomyoidea) (p < 0.0015, six markers, no conflicting data) within a significantly supported mouse-related clade (including Myodonta, Anomaluromorpha, and Castorimorpha) (p < 0.0015, six markers, no conflicting data). Most of an organism’s phylogenetic history is fossilized in their heritable genomic material. Using data from genome sequencing projects, particularly informative regions of this material can be extracted in sufficient num- bers to resolve the deepest history of speciation. -
Gliding Behavior of Japanese Giant Flying Squirrels (Petaurista Leucogenys)
Journal of Mammalogy, 83(2):553-562, 2002 GLIDING BEHAVIOR OF JAPANESE GIANT FLYING SQUIRRELS (PETAURISTA LEUCOGENYS) BRIAN J. STAFFORD,* RICHARD W. THORINGTON, JR., AND TAKEO KAWAMICHI Department of Anatomy, Howard University College of Medicine, 520 W Street NW, Washington, DC 20059 (BJS) Division of Mammals, Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC 20560-0108 (BJS, RWT) Department of Biology, Osaka City University, Sugimoto, Osaka, Sumiyoshi-ku 558•8585, Japan (TK) Gliding behavior of Japanese giant flying squirrels, Petaurista leucogenys, was studied at Nara Park, Japan. We observed 150 glides. We were able to calculate glide ratios on 57 glides and airspeeds on 29 glides. Glide ratios (distance/faltitude lost]) averaged 1.87, and a glide ratio of 3•3.5 seems to represent an upper performance limit for P. leucogenys. Airspeeds (4.39•9.47 m/s) were substantially lower than reported in other studies, and glide angles were higher (17.74•34.99°). Aspect ratios of the animals in mid-glide averaged 1.42. Key words: aerodynamics, flying squirrels, gliding, locomotion, musasabi, Petaurista, Pteromyinae Gliding is a common adaptation in mam- 1990; Jackson 2000; Russell and Dijkstra mals. It has evolved independently in at 2001; Scholey 1986; Stafford 1999; Thor- least 6 extant taxa: Volitantia (the dermop- ington et al. 1996 and references therein). terans and bats), Pteromyinae (true gliding Morphological studies of flying squirrels in- squirrels), Anomaluridae (scaly-tail "flying clude examinations of skeletal proportions squirrels"), Acrobates (feather-tail gliders), (Stafford 1999; Thorington and Heaney Petaurus (lesser gliding possums), and Pe- 1981), myology (Endo et al. -
Quaternary Murid Rodents of Timor Part I: New Material of Coryphomys Buehleri Schaub, 1937, and Description of a Second Species of the Genus
QUATERNARY MURID RODENTS OF TIMOR PART I: NEW MATERIAL OF CORYPHOMYS BUEHLERI SCHAUB, 1937, AND DESCRIPTION OF A SECOND SPECIES OF THE GENUS K. P. APLIN Australian National Wildlife Collection, CSIRO Division of Sustainable Ecosystems, Canberra and Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History ([email protected]) K. M. HELGEN Department of Vertebrate Zoology National Museum of Natural History Smithsonian Institution, Washington and Division of Vertebrate Zoology (Mammalogy) American Museum of Natural History ([email protected]) BULLETIN OF THE AMERICAN MUSEUM OF NATURAL HISTORY Number 341, 80 pp., 21 figures, 4 tables Issued July 21, 2010 Copyright E American Museum of Natural History 2010 ISSN 0003-0090 CONTENTS Abstract.......................................................... 3 Introduction . ...................................................... 3 The environmental context ........................................... 5 Materialsandmethods.............................................. 7 Systematics....................................................... 11 Coryphomys Schaub, 1937 ........................................... 11 Coryphomys buehleri Schaub, 1937 . ................................... 12 Extended description of Coryphomys buehleri............................ 12 Coryphomys musseri, sp.nov.......................................... 25 Description.................................................... 26 Coryphomys, sp.indet.............................................. 34 Discussion . .................................................... -
The Impact of Locomotion on the Brain Evolution of Squirrels and Close Relatives ✉ Ornella C
ARTICLE https://doi.org/10.1038/s42003-021-01887-8 OPEN The impact of locomotion on the brain evolution of squirrels and close relatives ✉ Ornella C. Bertrand 1 , Hans P. Püschel 1, Julia A. Schwab 1, Mary T. Silcox 2 & Stephen L. Brusatte1 How do brain size and proportions relate to ecology and evolutionary history? Here, we use virtual endocasts from 38 extinct and extant rodent species spanning 50+ million years of evolution to assess the impact of locomotion, body mass, and phylogeny on the size of the brain, olfactory bulbs, petrosal lobules, and neocortex. We find that body mass and phylogeny are highly correlated with relative brain and brain component size, and that locomotion strongly influences brain, petrosal lobule, and neocortical sizes. Notably, species living in 1234567890():,; trees have greater relative overall brain, petrosal lobule, and neocortical sizes compared to other locomotor categories, especially fossorial taxa. Across millions of years of Eocene- Recent environmental change, arboreality played a major role in the early evolution of squirrels and closely related aplodontiids, promoting the expansion of the neocortex and petrosal lobules. Fossoriality in aplodontiids had an opposing effect by reducing the need for large brains. 1 School of GeoSciences, University of Edinburgh, Grant Institute, Edinburgh, Scotland, UK. 2 Department of Anthropology, University of Toronto Scarborough, ✉ Toronto, ON, Canada. email: [email protected] COMMUNICATIONS BIOLOGY | (2021) 4:460 | https://doi.org/10.1038/s42003-021-01887-8 | www.nature.com/commsbio 1 ARTICLE COMMUNICATIONS BIOLOGY | https://doi.org/10.1038/s42003-021-01887-8 hat ecological and evolutionary factors affect brain size striking differences between living sciurids and aplodontiids raise in mammals? Studies have assessed the impact of the question of how this modern rodent assemblage emerged. -
Michael O. Woodburne1,* Alberto L. Cione2,**, and Eduardo P. Tonni2,***
Woodburne, M.O.; Cione, A.L.; and Tonni, E.P., 2006, Central American provincialism and the 73 Great American Biotic Interchange, in Carranza-Castañeda, Óscar, and Lindsay, E.H., eds., Ad- vances in late Tertiary vertebrate paleontology in Mexico and the Great American Biotic In- terchange: Universidad Nacional Autónoma de México, Instituto de Geología and Centro de Geociencias, Publicación Especial 4, p. 73–101. CENTRAL AMERICAN PROVINCIALISM AND THE GREAT AMERICAN BIOTIC INTERCHANGE Michael O. Woodburne1,* Alberto L. Cione2,**, and Eduardo P. Tonni2,*** ABSTRACT The age and phyletic context of mammals that dispersed between North and South America during the past 9 m.y. is summarized. The presence of a Central American province of cladogenesis and faunal differentiation is explored. One apparent aspect of such a province is to delay dispersals of some taxa northward from Mexico into the continental United States, largely during the Blancan. Examples are recognized among the various xenar- thrans, and cervid artiodactyls. Whereas the concept of a Central American province has been mentioned in past investigations it is upgraded here. Paratoceras (protoceratid artio- dactyl) and rhynchotheriine proboscideans provide perhaps the most compelling examples of Central American cladogenesis (late Arikareean to early Barstovian and Hemphillian to Rancholabrean, respectively), but this category includes Hemphillian sigmodontine rodents, and perhaps a variety of carnivores and ungulates from Honduras in the medial Miocene, as well as peccaries and equids from Mexico. For South America, Mexican canids and hy- drochoerid rodents may have had an earlier development in Mexico. Remarkably, the first South American immigrants to Mexico (after the Miocene heralds; the xenarthrans Plaina and Glossotherium) apparently dispersed northward at the same time as the first Holarctic taxa dispersed to South America (sigmodontine rodents and the tayassuid artiodactyls). -
Checklist of Rodents and Insectivores of the Mordovia, Russia
ZooKeys 1004: 129–139 (2020) A peer-reviewed open-access journal doi: 10.3897/zookeys.1004.57359 RESEARCH ARTICLE https://zookeys.pensoft.net Launched to accelerate biodiversity research Checklist of rodents and insectivores of the Mordovia, Russia Alexey V. Andreychev1, Vyacheslav A. Kuznetsov1 1 Department of Zoology, National Research Mordovia State University, Bolshevistskaya Street, 68. 430005, Saransk, Russia Corresponding author: Alexey V. Andreychev ([email protected]) Academic editor: R. López-Antoñanzas | Received 7 August 2020 | Accepted 18 November 2020 | Published 16 December 2020 http://zoobank.org/C127F895-B27D-482E-AD2E-D8E4BDB9F332 Citation: Andreychev AV, Kuznetsov VA (2020) Checklist of rodents and insectivores of the Mordovia, Russia. ZooKeys 1004: 129–139. https://doi.org/10.3897/zookeys.1004.57359 Abstract A list of 40 species is presented of the rodents and insectivores collected during a 15-year period from the Republic of Mordovia. The dataset contains more than 24,000 records of rodent and insectivore species from 23 districts, including Saransk. A major part of the data set was obtained during expedition research and at the biological station. The work is based on the materials of our surveys of rodents and insectivo- rous mammals conducted in Mordovia using both trap lines and pitfall arrays using traditional methods. Keywords Insectivores, Mordovia, rodents, spatial distribution Introduction There is a need to review the species composition of rodents and insectivores in all regions of Russia, and the work by Tovpinets et al. (2020) on the Crimean Peninsula serves as an example of such research. Studies of rodent and insectivore diversity and distribution have a long history, but there are no lists for many regions of Russia of Copyright A.V. -
G-, C-, and NOR-Stained Karyotype of the Eversmann's Hamster Allocricetulus Eversmanni and Comparison with the Karyotype of Cr
Mammal Study 30: 89–91 (2005) © the Mammalogical Society of Japan Short communication G-, C-, and NOR-stained karyotype of the Eversmann’s hamster Allocricetulus eversmanni and comparison with the karyotype of Cricetulus species (Rodentia: Cricetinae) Irina V. Kartavtseva1,* and Aleksey V. Surov2 1 Institute of Biology and Soil Science, Far East Branch of Russian Academy of Sciences, Vladivostok, Russia, 690022 2 A. N. Severtsov Institute of Ecology and Evolution, Moscow, Russia, 119071 Differential chromosomal stainings for various species chromosomes was shown using Sumner’s (1972) modi- belonging to genera in the tribe Cricetini of the Eurasian fied C-banding technique. The locations of nucleolar Cricetinae including Cricetus, Cricetulus, Tscherskia, organizer regions (NORs) of metaphase chromosomes Phodopus, and Mesocricetus are available (Gamperl et were determined after 50% aqueous AgNO3 treatment al. 1978; Kartavtseva et al. 1979; Popescu and DiPaolo for 12 hours at 50–60°C (Bloom and Goodpasture 1976). 1980; Kral et al. 1984). Hitherto, however, no differen- The karyotype consisted of 24 autosomes (2n = 26, tial chromosomes stainings for species in the genus NF = 40): four pairs of metacentrics (M) and submeta- Allocricetulus have been described and the phylogenetic centrics (SM): one pair large, one pair medium and two position of this genus in the Cricetini, based on chro- pairs small, two pairs of large subtelocentrics (ST) and mosomal data, has not been determined. six pairs of acrocentrics (A), ranging from medium-sized The Eversmann’s hamster Allocricetus eversmanni to small. The X chromosome was a medium sized sub- Brandt, 1859 occurs in dry steppes and semi-deserts metacentric (Fig. -
Relational Database Systems 1
Relational Database Systems 1 Wolf-Tilo Balke Jan-Christoph Kalo Institut für Informationssysteme Technische Universität Braunschweig www.ifis.cs.tu-bs.de Summary last week • Data models define the structural constrains and possible manipulations of data – Examples of Data Models: • Relational Model, Network Model, Object Model, etc. – Instances of data models are called schemas • Careful: Often, sloppy language is used where people call a schema also a model • We have three types of schemas: – Conceptual Schemas – Logical Schemas – Physical Schemas • We can use ER modeling for conceptual and logical schemas Relational Database Systems 1 – Wolf-Tilo Balke – Institut für Informationssysteme – TU Braunschweig 2 Summary last week • Entity Type Name • Weak Entity Type Name • Attribute name • Key Attribute name • name Multi-valued Attribute name name • Composite Attribute name • Derived Attribute name • Relationship Type name • Identifying Relationship Type name EN 3.5 Relational Database Systems 1 – Wolf-Tilo Balke – Institut für Informationssysteme – TU Braunschweig 3 Summary last week • Total participation of E2 in R E1 r E2 • Cardinality – an instance of E1 may relate to multiple instances of E2 (0,*) (1,1) E1 r E2 • Specific cardinality with min and max – an instance of E1 may relate to multiple instances of E2 (0,*) (0,1) E1 r E2 EN 3.5 Relational Database Systems 1 – Wolf-Tilo Balke – Institut für Informationssysteme – TU Braunschweig 4 3 Extended Data Modeling • Alternative ER Notations • Extended ER – Inheritance – Complex Relationships -
Phylogeny, Biogeography and Systematic Revision of Plain Long-Nosed Squirrels (Genus Dremomys, Nannosciurinae) Q ⇑ Melissa T.R
Molecular Phylogenetics and Evolution 94 (2016) 752–764 Contents lists available at ScienceDirect Molecular Phylogenetics and Evolution journal homepage: www.elsevier.com/locate/ympev Phylogeny, biogeography and systematic revision of plain long-nosed squirrels (genus Dremomys, Nannosciurinae) q ⇑ Melissa T.R. Hawkins a,b,c,d, , Kristofer M. Helgen b, Jesus E. Maldonado a,b, Larry L. Rockwood e, Mirian T.N. Tsuchiya a,b,d, Jennifer A. Leonard c a Smithsonian Conservation Biology Institute, Center for Conservation and Evolutionary Genetics, National Zoological Park, Washington DC 20008, USA b Division of Mammals, National Museum of Natural History, Smithsonian Institution, P.O. Box 37012, Washington DC 20013-7012, USA c Estación Biológica de Doñana (EBD-CSIC), Conservation and Evolutionary Genetics Group, Avda. Americo Vespucio s/n, Sevilla 41092, Spain d George Mason University, Department of Environmental Science and Policy, 4400 University Drive, Fairfax, VA 20030, USA e George Mason University, Department of Biology, 4400 University Drive, Fairfax, VA 20030, USA article info abstract Article history: The plain long-nosed squirrels, genus Dremomys, are high elevation species in East and Southeast Asia. Received 25 March 2015 Here we present a complete molecular phylogeny for the genus based on nuclear and mitochondrial Revised 19 October 2015 DNA sequences. Concatenated mitochondrial and nuclear gene trees were constructed to determine Accepted 20 October 2015 the tree topology, and date the tree. All speciation events within the plain-long nosed squirrels (genus Available online 31 October 2015 Dremomys) were ancient (dated to the Pliocene or Miocene), and averaged older than many speciation events in the related Sunda squirrels, genus Sundasciurus. -
Two New Species of Shrew-Rats (Rhynchomys: Muridae: Rodentia) from Luzon Island, Philippines
Journal of Mammalogy, 100(4):1112–1129, 2019 DOI:10.1093/jmammal/gyz066 Version of Record, first published online 6 June 2019, with fixed content and layout in compliance with Art. 8.1.3.2 ICZN. Two new species of shrew-rats (Rhynchomys: Muridae: Rodentia) from Luzon Island, Philippines Downloaded from https://academic.oup.com/jmammal/article-abstract/100/4/1112/5506757 by Louisiana State University user on 05 November 2019 Eric A. Rickart,* Danilo S. Balete,† Robert M. Timm, Phillip A. Alviola, Jacob A. Esselstyn, and Lawrence R. Heaney Natural History Museum of Utah, University of Utah, Salt Lake City, UT 84108, USA (EAR) Field Museum of Natural History, 1400 S Lake Shore Drive, Chicago, IL 60605, USA (DSB, LRH) Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS 66045, USA (RMT) Institute of Biological Sciences, University of the Philippines, Los Baños, Laguna 4031, Philippines (PAA) Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, LA 70803, USA (JAE) * Correspondent: [email protected] † Deceased 1 July 2017. The murine genus Rhynchomys includes the large-bodied Philippine “shrew-rats,” highly specialized members of the vermivorous clade of Philippine murids. Four species are recognized, all of which are endemic to Luzon Island: R. soricoides from mountains within the Central Cordillera, R. isarogensis from Mt. Isarog on the Bicol Peninsula, R. banahao from Mt. Banahaw in south-central Luzon, and R. tapulao from Mt. Tapulao in the Zambales Mountains. Field surveys in 2006 and 2008 revealed two additional populations of Rhynchomys, one from Mt. -
Novltates PUBLISHED by the AMERICAN MUSEUM of NATURAL HISTORY CENTRAL PARK WEST at 79TH STREET, NEW YORK, N.Y
AMERICAN MUSEUM Novltates PUBLISHED BY THE AMERICAN MUSEUM OF NATURAL HISTORY CENTRAL PARK WEST AT 79TH STREET, NEW YORK, N.Y. 10024 Number 3064, 34 pp., 8 figures, 2 tables June 10, 1993 Philippine Rodents: Chromosomal Characteristics and Their Significance for Phylogenetic Inference Among 13 Species (Rodentia: Muridae: Murinae) ERIC A. RICKART1 AND GUY G. MUSSER2 ABSTRACT Karyotypes are reported for 13 murines be- bers of 50 and 88, respectively, indicating longing to the endemic Philippine genera Apomys, substantial chromosomal variability within that Archboldomys, Batomys, Bullimus, Chrotomys, genus. Archboldomys (2N = 26, FN = 43) has an Phloeomys, and Rhynchomys, and the widespread aberrant sex chromosome system and a karyotype genus Rattus. The karyotype of Phloeomys cum- that is substantially different from other taxa stud- ingi (2N = 44, FN = 66) differs from that of P. ied. The karyotype ofBullimus bagobus (2N = 42, pallidus (2N = 40, FN = 60), and both are chro- FN = ca. 58) is numerically similar to that of the mosomally distinct from other taxa examined. Two native Rattus everetti and the two non-native spe- species of Batomys (2N = 52), Chrotomys gon- cies ofRattus, R. tanezumi and R. exulans. Chro- zalesi (2N = 44), Rhynchomys isarogensis (2N = mosomal data corroborate some phylogenetic re- 44), and Apomys musculus (2N = 42) have FN = lationships inferred from morphology, and support 52-53 and a predominance of telocentric chro- the hypothesis that the Philippine murid fauna is mosomes. Two other species ofApomys have dip- composed of separate clades representing inde- loid numbers of30 and 44, and fundamental num- pendent ancestral invasions of the archipelago. INTRODUCTION The Philippine Islands support a remark- Heaney and Rickart, 1990; Musser and Hea- ably diverse murine rodent fauna, including ney, 1992).