Rodent Phylogeny and a Timescale for the Evolution of Glires: Evidence from an Extensive Taxon Sampling Using Three Nuclear Genes
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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. -
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). -
A New Genus of Stem Lagomorph (Mammalia: Glires) from the Middle Eocene of the Erlian Basin, Nei Mongol, China
Acta zoologica cracoviensia, 57(1-2): 29-42, Kraków, 31 December 2014 Ó Institute of Systematics and Evolution of Animals, Pol. Acad. Sci., Kraków doi:10.3409/azc.57_1-2.29 Zoobank Account:urn:lsid:zoobank.org:pub:22E831F0-4830-4649-9740-1BD6171983DD Anewgenusofstemlagomorph(Mammalia:Glires)fromthe MiddleEoceneoftheErlianBasin,NeiMongol,China £ucja FOSTOWICZ-FRELIK andQianLI Received: 15 October 2014. Accepted: 10 December 2014. Available online: 29 December 2014. FOSTOWICZ-FRELIK £., LI Q. 2014. A new genus of stem lagomorph (Mammalia: Glires) from the Middle Eocene of the Erlian Basin, Nei Mongol, China. Acta zool. cracov., 57(1-2): 29-42. Abstract. We report the discovery of Erenlagus anielae, a new genus and species of stem lagomorph from the lower part of the Middle Eocene Irdin Manha Formation at the Huhe- boerhe locality, Erlian Basin, Nei Mongol, China. The remains consist of isolated teeth; however, the material includes all loci except the incisors and P2. The new lagomorph is characterized by a small size and high degree of unilateral hypsodonty comparable to that of Aktashmys and slightly higher than that observed in the coeval and co-occurring Stre- nulagus. Further, it shows advanced root fusion, which exceeds even that in Gobiolagus. Although phylogenetic relationships of the Eocene lagomorphs from Asia are still not fully resolved, the dental characters of Erenlagus anielae suggest that it is most closely re- lated to Lushilagus danjingensis from the Middle Eocene of Henan, China and Ak- tashmys montealbus from the late Early Eocene of Kyrgyzstan. This stratigraphically well-constrained finding represents one of the lagomorph genera that appeared in the Eo- cene Glires paleobiodiversity reservoir, the Erlian Basin in Nei Mongol. -
The Remarkable, Yet Not Extraordinary, Human Brain As a Scaled-Up Primate Brain and Its Associated Cost
The remarkable, yet not extraordinary, human brain as a scaled-up primate brain and its associated cost Suzana Herculano-Houzel1 Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, 21941-902, Rio de Janeiro, Brazil; and Instituto Nacional de Neurociência Translacional, Instituto Nacional de Ciência e Tecnologia/Ministério de Ciência e Tecnologia, 04023-900, Sao Paulo, Brazil Edited by Francisco J. Ayala, University of California, Irvine, CA, and approved April 12, 2012 (received for review February 29, 2012) Neuroscientists have become used to a number of “facts” about the The incongruity between our extraordinary cognitive abilities human brain: It has 100 billion neurons and 10- to 50-fold more glial and our not-that-extraordinary brain size has been the major cells; it is the largest-than-expected for its body among primates driving factor behind the idea that the human brain is an outlier, and mammals in general, and therefore the most cognitively able; an exception to the rules that have applied to the evolution of all it consumes an outstanding 20% of the total body energy budget other animals and brains. A largely accepted alternative expla- despite representing only 2% of body mass because of an increased nation for our cognitive superiority over other mammals has been metabolic need of its neurons; and it is endowed with an overde- our extraordinary brain size compared with our body size, that is, veloped cerebral cortex, the largest compared with brain size. our large encephalization quotient (8). Compared -
Dental Homologies and Evolutionary Transformations In
Dental homologies and evolutionary transformations in Caviomorpha (Hystricognathi, Rodentia): new data from the Paleogene of Peruvian Amazonia Myriam Boivin, Laurent Marivaux To cite this version: Myriam Boivin, Laurent Marivaux. Dental homologies and evolutionary transformations in Caviomor- pha (Hystricognathi, Rodentia): new data from the Paleogene of Peruvian Amazonia. Historical Biology, Taylor & Francis, 2020, 32 (4), pp.528-554. 10.1080/08912963.2018.1506778. hal-01870927 HAL Id: hal-01870927 https://hal.umontpellier.fr/hal-01870927 Submitted on 17 Jun 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Page 1 of 118 Historical Biology 1 2 3 Dental homologies and evolutionary transformations in Caviomorpha (Hystricognathi, 4 5 Rodentia): new data from the Paleogene of Peruvian Amazonia 6 7 8 9 10 a* a 11 Myriam Boivin and Laurent Marivaux 12 13 14 15 a Laboratoire de Paléontologie, Institut des Sciences de l’Évolution de Montpellier (ISE-M), c.c. 16 For Peer Review Only 17 18 064, Université de Montpellier, CNRS, IRD, EPHE, place Eugène Bataillon, F-34095 19 20 Montpellier Cedex 05, France. 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 *Corresponding author. -
8-2 Kihm 2011
Paludicola 8(2):75-90 March 2011 © by the Rochester Institute of Vertebrate Paleontology RODENTS FROM THE CHADRONIAN (LATEST EOCENE) MEDICINE POLE HILLS LOCAL FAUNA, NORTH DAKOTA. PART 1. EUTYPOMYIDAE, CYLINDRODONTIDAE AND PIPESTONEOMYS Allen J. Kihm Department of Geosciences, Minot State University, 500 University Ave W, Minot, ND 58707 <[email protected]> ABSTRACT The Medicine Pole Hills local fauna is a large Chadronian fauna composed of more than 4600 mammal specimens, mostly isolated teeth, derived from a limited sequence of mudball conglomerates and sandstones. The producing layer probably represents an early stage of deposition of the Chadron Formation in North Dakota, but it may not be related to any of the named members of the formation. The material described includes Eutypomys parvus, Cylindrodon collinus, Pseudocylindrodon neglectus, Ardynomys saskatchewensis and Pipestoneomys sp. The samples of E. parvus and A. saskatchewensis include teeth not previously described for these taxa. The assemblage has the greatest commonality to the middle Chadronian Calf Creek local fauna of southern Saskatchewan. This similarity does not necessarily indicate a middle Chadronian age for the Medicine Pole Hills local fauna. The lack of late early Chadronian localities with large samples of rodents may exaggerate the apparent differences between these faunas and the Medicine Pole Hills sample. The Calf Creek and Medicine Pole Hills local faunas may represent an intermediate stage between the McCarty’s Mountain and Pipestone Springs faunas of Montana. The Medicine Pole Hills fauna may be somewhat older than the Calf Creek local fauna based on the occurrence of Leptomeryx yoderi. INTRODUCTION (Murphy et al., 1993), but continuing studies of the geology, particularly the heavy minerals, suggest this This is the third in a series of papers that describe correlation is poorly supported (Webster and Kihm, the mammals of the Medicine Pole Hills local fauna of 2009). -
(Rodentia: Ctenodactylidae) from the Miocene of Israel
RESEARCH ARTICLE A Transitional Gundi (Rodentia: Ctenodactylidae) from the Miocene of Israel Raquel López-Antoñanzas1,2*, Vitaly Gutkin3, Rivka Rabinovich4, Ran Calvo5, Aryeh Grossman6,7 1 School of Earth Sciences, University of Bristol, Bristol, United Kingdom, 2 Departamento de Paleobiología, Museo Nacional de Ciencias Naturales-CSIC, Madrid, Spain, 3 The Harvey M. Krueger Family Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem, Israel, 4 National Natural History Collections, Institute of Earth Sciences and Institute of Archaeology, The Hebrew University of Jerusalem, Jerusalem, Israel, 5 Geological Survey of Israel, Jerusalem, Israel, 6 Arizona College of Osteopathic Medicine, Midwestern University, Glendale, AZ, United States of America, 7 School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, United States of America * [email protected] Abstract OPEN ACCESS We describe a new species of gundi (Rodentia: Ctenodactylidae: Ctenodactylinae), Sayi- mys negevensis, on the basis of cheek teeth from the Early Miocene of the Rotem Basin, Citation: López-Antoñanzas R, Gutkin V, Rabinovich R, Calvo R, Grossman A (2016) A Transitional Gundi southern Israel. The Rotem ctenodactylid differs from all known ctenodactylid species, (Rodentia: Ctenodactylidae) from the Miocene of including Sayimys intermedius, which was first described from the Middle Miocene of Saudi Israel. PLoS ONE 11(4): e0151804. doi:10.1371/ Arabia. Instead, it most resembles Sayimys baskini from the Early Miocene of Pakistan in journal.pone.0151804 characters of the m1-2 (e.g., the mesoflexid shorter than the metaflexid, the obliquely orien- Editor: Laurent Viriot, Team 'Evolution of Vertebrate tated hypolophid, and the presence of a strong posterolabial ledge) and the upper molars Dentition', FRANCE (e.g., the paraflexus that is longer than the metaflexus). -
Multiple Molecular Evidences for a Living Mammalian Fossil
Multiple molecular evidences for a living mammalian fossil Dorothe´ e Huchon†‡, Pascale Chevret§¶, Ursula Jordanʈ, C. William Kilpatrick††, Vincent Ranwez§, Paulina D. Jenkins‡‡, Ju¨ rgen Brosiusʈ, and Ju¨ rgen Schmitz‡ʈ †Department of Zoology, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel; §Department of Paleontology, Phylogeny, and Paleobiology, Institut des Sciences de l’Evolution, cc064, Universite´Montpellier II, Place E. Bataillon, 34095 Montpellier Cedex 5, France; ʈInstitute of Experimental Pathology, University of Mu¨nster, D-48149 Mu¨nster, Germany; ††Department of Biology, University of Vermont, Burlington, VT 05405-0086; and ‡‡Department of Zoology, The Natural History Museum, London SW7 5BD, United Kingdom Edited by Francisco J. Ayala, University of California, Irvine, CA, and approved March 18, 2007 (received for review February 11, 2007) Laonastes aenigmamus is an enigmatic rodent first described in their classification as a diatomyid suggests that Laonastes is a 2005. Molecular and morphological data suggested that it is the living fossil and a ‘‘Lazarus taxon.’’ sole representative of a new mammalian family, the Laonastidae, The two research teams also disagreed on the taxonomic and a member of the Hystricognathi. However, the validity of this position of Laonastes. According to Jenkins et al. (2), Laonastes family is controversial because fossil-based phylogenetic analyses is either the most basal group of the hystricognaths (Fig. 2A)or suggest that Laonastes is a surviving member of the Diatomyidae, nested within the hystricognaths (Fig. 2B). According to Dawson a family considered to have been extinct for 11 million years. et al. (3), Laonastes and the other Diatomyidae are the sister According to these data, Laonastes and Diatomyidae are the sister clade of the family Ctenodactylidae (i.e., gundies), a family that clade of extant Ctenodactylidae (i.e., gundies) and do not belong does not belong to the Hystricognathi, but to which it is to the Hystricognathi. -
Novitatesamerican MUSEUM PUBLISHED by the AMERICAN MUSEUM of NATURAL HISTORY CENTRAL PARK WEST at 79TH STREET NEW YORK, N.Y
NovitatesAMERICAN MUSEUM PUBLISHED BY THE AMERICAN MUSEUM OF NATURAL HISTORY CENTRAL PARK WEST AT 79TH STREET NEW YORK, N.Y. 10024 U.S.A. NUMBER 2626 JUNE 30, 1977 JOHN H. WAHLERT Cranial Foramina and Relationships of Eutypomys (Rodentia, Eutypomyidae) AMERICAN MUSEUM Novitates PUBLISHED BY THE AMERICAN MUSEUM OF NATURAL HISTORY CENTRAL PARK WEST AT 79TH STREET, NEW YORK, N.Y. 10024 Number 2626, pp. 1-8, figs. 1-3, table 1 June 30, 1977 Cranial Foramina and Relationships of Eutypomys (Rodentia, Eutypomyidae) JOHN H. WAHLERT1 ABSTRACT Derived characters of the sphenopalatine, lies had common ancestry in a stem species from interorbital, and dorsal palatine foramina are which no other rodent groups are descended. The shared by the Eutypomyidae and Castoridae. two families may be included in a monophyletic These support the hypothesis that the two fami- superfamily, Castoroidea. INTRODUCTION Eutypomys is an extinct sciuromorphous gave more characters shared with castorids; he, rodent known in North America from strata that too, found many features in common with the range in age from latest Eocene to early Miocene. ischyromyoids. Wood noted the similarity of The genus was named by Matthew (1905) based molar crown pattern to that of Paramys and ex- on the species Eutypomys thomsoni. "Progres- plained it as a parallelism that possibly indicates sive" characters of the teeth and hind feet led relationship. Wilson (1949b) pointed out that the Matthew to ally it with the beaver family, Cas- dental pattern of Eutypomys is more like that of toridae. He pointed out that it retains many sciuravids than that of paramyids. -
INSIGHTS INTO RELATIONSHIPS AMONG RODENT LINEAGES BASED on MITOCHONDRIAL GENOME SEQUENCE DATA a Dissertation by LAURENCE JOHN FR
INSIGHTS INTO RELATIONSHIPS AMONG RODENT LINEAGES BASED ON MITOCHONDRIAL GENOME SEQUENCE DATA A Dissertation by LAURENCE JOHN FRABOTTA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY December 2005 Major Subject: Zoology INSIGHTS INTO RELATIONSHIPS AMONG RODENT LINEAGES BASED ON MITOCHONDRIAL GENOME SEQUENCE DATA A Dissertation by LAURENCE JOHN FRABOTTA Submitted to the Office of Graduate Studies of Texas A&M University in partial fulfillment of the requirements for the degree of DOCTOR OF PHILOSOPHY Approved by: Chair of Committee, Rodney L. Honeycutt Committee Members, James B. Woolley John W. Bickham James R. Manhart Head of Department, Vincent M. Cassone December 2005 Major Subject: Zoology iii ABSTRACT Insights into Relationships among Rodent Lineages Based on Mitochondrial Genome Sequence Data. (December 2005) Laurence John Frabotta, B.S.; M.S., California State University, Long Beach Chair of Advisory Committee: Dr. Rodney L. Honeycutt This dissertation has two major sections. In Chapter II, complete mitochondrial (mt DNA) genome sequences were used to construct a hypothesis for affinities of most major lineages of rodents that arose quickly in the Eocene and were well established by the end of the Oligocene. Determining the relationships among extant members of such old lineages can be difficult. Two traditional schemes on subordinal classification of rodents have persisted for over a century, dividing rodents into either two or three suborders, with relationships among families or superfamilies remaining problematic. The mtDNA sequences for four new rodent taxa (Aplodontia, Cratogeomys, Erethizon, and Hystrix), along with previously published Euarchontoglires taxa, were analyzed under parsimony, likelihood, and Bayesian criteria. -
The Naked Mole-Rat As an Animal Model in Biomedical Research: Current Perspectives
Open Access Animal Physiology Dovepress open access to scientific and medical research Open Access Full Text Article REVIEW The naked mole-rat as an animal model in biomedical research: current perspectives Laura-Nadine Schuhmacher Abstract: The naked mole-rat (NMR) is a subterranean rodent that has gained significant Zoé Husson attention from the biomedical research community in recent years as molecular mechanisms Ewan St. John Smith underlying its unusual biology start to be unraveled. With very low external mortality, NMRs have an unusually long lifespan while showing no signs of aging, such as neuro- Department of Pharmacology, University of Cambridge, Cambridge, UK degeneration or cancer. Furthermore, living underground in large colonies (100 to 300 animals), results in comparatively high carbon dioxide and low oxygen levels, from which NMRs have evolved extreme resistance to both hypoxia and hypercapnia. In this paper we have summarized the latest developments in NMR research and its impact on biomedical research, with the aim of providing a sound background that will inform and inspire further For personal use only. investigations. Keywords: naked mole-rat, longevity, cancer, hypoxia, nociception, pain Introduction The naked mole-rat (NMR) (Heterocephalus glaber) is a subterranean mammal, which has recently gained interest from scientists across a variety of research fields. Unlike the majority of mammals, NMRs are poikilothermic and eusocial, ie, are cold-blooded and have a single breeding female within a colony.1 In addition to these features, which have limited biomedical translatability, NMRs have also evolved several physiological adaptations to habituate to their extreme environmental conditions, which have led researchers to study this mammal with the hypothesis Open Access Animal Physiology downloaded from https://www.dovepress.com/ by 131.111.184.102 on 07-Sep-2017 that by understanding the extreme biology of NMRs, more will be understood about normal mammalian physiology. -
Dating Placentalia: Morphological Clocks Fail to Close the Molecular Fossil Gap
View metadata, citation and similar papers at core.ac.uk brought to you by CORE ORIGINAL ARTICLE provided by White Rose Research Online doi:10.1111/evo.12907 Dating placentalia: Morphological clocks fail to close the molecular fossil gap Mark N. Puttick,1,2 Gavin H. Thomas,3 and Michael J. Benton1 1School of Earth Sciences, Life Sciences Building, Tyndall Avenue, University of Bristol, Bristol, BS8 1TQ, United Kingdom 2E-mail: [email protected] 3Department of Animal and Plant Sciences, Alfred Denny Building, University of Sheffield, Western Bank, Sheffield, S10 2TN, United Kingdom Received January 31, 2015 Accepted March 7, 2016 Dating the origin of Placentalia has been a contentious issue for biologists and paleontologists. Although it is likely that crown- group placentals originated in the Late Cretaceous, nearly all molecular clock estimates point to a deeper Cretaceous origin. An approach with the potential to reconcile this discrepancy could be the application of a morphological clock. This would permit the direct incorporation of fossil data in node dating, and would break long internal branches of the tree, so leading to improved estimates of node ages. Here, we use a large morphological dataset and the tip-calibration approach of MrBayes. We find that the estimated date for the origin of crown mammals is much older, 130–145 million years ago (Ma), than fossil and molecular clock data (80–90 Ma). Our results suggest that tip calibration may result in estimated dates that are more ancient than those obtained from other sources of data. This can be partially overcome by constraining the ages of internal nodes on the tree; however, when this was applied to our dataset, the estimated dates were still substantially more ancient than expected.