Paleontology
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Ancient Mitogenomes Shed Light on the Evolutionary History And
Ancient Mitogenomes Shed Light on the Evolutionary History and Biogeography of Sloths Frédéric Delsuc, Melanie Kuch, Gillian Gibb, Emil Karpinski, Dirk Hackenberger, Paul Szpak, Jorge Martinez, Jim Mead, H. Gregory Mcdonald, Ross Macphee, et al. To cite this version: Frédéric Delsuc, Melanie Kuch, Gillian Gibb, Emil Karpinski, Dirk Hackenberger, et al.. Ancient Mitogenomes Shed Light on the Evolutionary History and Biogeography of Sloths. Current Biology - CB, Elsevier, 2019. hal-02326384 HAL Id: hal-02326384 https://hal.archives-ouvertes.fr/hal-02326384 Submitted on 22 Oct 2019 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. 1 Ancient Mitogenomes Shed Light on the Evolutionary 2 History and Biogeography of Sloths 3 Frédéric Delsuc,1,13,*, Melanie Kuch,2 Gillian C. Gibb,1,3, Emil Karpinski,2,4 Dirk 4 Hackenberger,2 Paul Szpak,5 Jorge G. Martínez,6 Jim I. Mead,7,8 H. Gregory 5 McDonald,9 Ross D. E. MacPhee,10 Guillaume Billet,11 Lionel Hautier,1,12 and 6 Hendrik N. Poinar2,* 7 Author list footnotes 8 1Institut des Sciences de l’Evolution de Montpellier -
Lecture Notes: the Mathematics of Phylogenetics
Lecture Notes: The Mathematics of Phylogenetics Elizabeth S. Allman, John A. Rhodes IAS/Park City Mathematics Institute June-July, 2005 University of Alaska Fairbanks Spring 2009, 2012, 2016 c 2005, Elizabeth S. Allman and John A. Rhodes ii Contents 1 Sequences and Molecular Evolution 3 1.1 DNA structure . .4 1.2 Mutations . .5 1.3 Aligned Orthologous Sequences . .7 2 Combinatorics of Trees I 9 2.1 Graphs and Trees . .9 2.2 Counting Binary Trees . 14 2.3 Metric Trees . 15 2.4 Ultrametric Trees and Molecular Clocks . 17 2.5 Rooting Trees with Outgroups . 18 2.6 Newick Notation . 19 2.7 Exercises . 20 3 Parsimony 25 3.1 The Parsimony Criterion . 25 3.2 The Fitch-Hartigan Algorithm . 28 3.3 Informative Characters . 33 3.4 Complexity . 35 3.5 Weighted Parsimony . 36 3.6 Recovering Minimal Extensions . 38 3.7 Further Issues . 39 3.8 Exercises . 40 4 Combinatorics of Trees II 45 4.1 Splits and Clades . 45 4.2 Refinements and Consensus Trees . 49 4.3 Quartets . 52 4.4 Supertrees . 53 4.5 Final Comments . 54 4.6 Exercises . 55 iii iv CONTENTS 5 Distance Methods 57 5.1 Dissimilarity Measures . 57 5.2 An Algorithmic Construction: UPGMA . 60 5.3 Unequal Branch Lengths . 62 5.4 The Four-point Condition . 66 5.5 The Neighbor Joining Algorithm . 70 5.6 Additional Comments . 72 5.7 Exercises . 73 6 Probabilistic Models of DNA Mutation 81 6.1 A first example . 81 6.2 Markov Models on Trees . 87 6.3 Jukes-Cantor and Kimura Models . -
Marsupials As Models for Research
CSIRO PUBLISHING Introduction www.publish.csiro.au/journals/ajz Australian Journal of Zoology, 2006, 54, 137–138 Marsupials as models for research Lynne SelwoodA,B and Graeme CoulsonA ADepartment of Zoology, The University of Melbourne, Vic. 3010, Australia. BCorresponding author. Email: [email protected] Marsupials are worth studying for their intrinsic value alone. rather than by trying to determine what happens when the They are one of the three major extant mammal types, conceptuses are implanted in the uterus, as in the mouse. The Prototheria (monotremes), Metatheria (marsupials) and Renfree and Shaw group has skilfully exploited this in the Eutheria, and have provided important information about the tammar wallaby, and provided further experimental advan- evolution of mammals. They represent the major mammalian tages by developing techniques for gonad sex reversal and group on the Australian continent, and their study makes an female reproductive tract sex reversal in the neonates important contribution to our natural heritage. Such studies (Renfree et al. 2006). Using marsupials, the development of are necessary in order to stem the further loss of marsupial the scrotum, mammary glands, pouch and processus vagi- diversity due to extinction of species. In addition, the study nalis are shown to be sexually dimorphic before the testis of marsupial species has provided new insights into old prob- differentiates, and hence are independent of testicular hor- lems, because of their value as models to study a variety of mones. These studies have been extended into the molecular totally different fields. level. The study of marsupials can be seen as an example of the Studies on life history strategies of Antechinus showed importance of basic research. -
Archival Afterlives: Life, Death, and Knowledge-Making in Early Modern British Scienti C and Medical Archives
Archival Afterlives: Life, Death, and Knowledge-Making in Early Modern British Scienti!"c and Medical Archives Kohn Centre The Royal Society 2 June 2015 Conference Description: Early modern naturalists collected, generated, and shared massive amounts of paper. Inspired by calls for the wholesale reform of natural philosophy and schooled in humanist note-taking practices, they generated correspondence, reading notes (in margins, on scraps, in notebooks), experimental and observational reports, and drafts (rough, partial, fair) of treatises intended for circulation in manuscript or further replication in print. If naturalists claimed all knowledge as their province, natural philosophy was a paper empire. In our own day, naturalists’ materials, ensconced in archives, libraries, and (occasionally) private hands, are now the foundation of a history of science that has taken a material turn towards paper, ink, pen, and !"ling systems as technologies of communication, information management, and knowledge production. Recently, the creation of such papers, and their originators’ organization of them and intentions for them have received much attention. The lives archives lived after their creators’ deaths have been explored less often. The posthumous fortunes of archives are crucial both to their survival as historical sources today and to their use as scienti!"c sources in the past. How did (often) disorderly collections of paper come to be “the archives of the Scienti!"c Revolution”? The proposed conference considers the histories of these papers from the early modern past to the digital present, including collections of material initially assembled by Samuel Hartlib, John Ray, Francis Willughby, Isaac Newton, Hans Sloane, Martin Lister, Edward Lhwyd, Robert Hooke, and Théodore de Mayerne. -
Illinois Fossils Doc 2005
State of Illinois Illinois Department of Natural Resources Illinois Fossils Illinois Department of Natural Resources he Illinois Fossils activity book from the Illinois Department of Natural Resources’ (IDNR) Division of Education is designed to supplement your curriculum in a vari- ety of ways. The information and activities contained in this publication are targeted toT grades four through eight. The Illinois Fossils resources trunk and lessons can help you T teach about fossils, too. You will find these and other supplemental items through the Web page at https://www2.illinois.gov/dnr/education/Pages/default.aspx. Contact the IDNR Division of Education at 217-524-4126 or [email protected] for more information. Collinson, Charles. 2002. Guide for beginning fossil hunters. Illinois State Geological Survey, Champaign, Illinois. Geoscience Education Series 15. 49 pp. Frankie, Wayne. 2004. Guide to rocks and minerals of Illinois. Illinois State Geological Survey, Champaign, Illinois. Geoscience Education Series 16. 71 pp. Killey, Myrna M. 1998. Illinois’ ice age legacy. Illinois State Geological Survey, Champaign, Illinois. Geoscience Education Series 14. 67 pp. Much of the material in this book is adapted from the Illinois State Geological Survey’s (ISGS) Guide for Beginning Fossil Hunters. Special thanks are given to Charles Collinson, former ISGS geologist, for the use of his fossil illustrations. Equal opportunity to participate in programs of the Illinois Department of Natural Resources (IDNR) and those funded by the U.S. Fish and Wildlife Service and other agencies is available to all individuals regardless of race, sex, national origin, disability, age, reli-gion or other non-merit factors. -
Fossil Collecting Areas in Iowa
FOSSIL COLLECTING AREAS IN IOWA The following list, although far from compete, includes a few of the better fossil collecting areas in Iowa. 1. Rockford, Floyd County (¼ mile south and ¼ mile west of the Rockford Brick and Tile Company pit, on county road “D”). Well preserved brachiopods, gastropods, and corals are most abundant in the yellowish shales that overlie the blue-gray beds. The fossils occurring here are known as the Hackberry fauna and have been described by C.L. and M.A. Fenton in a book entitled, “The Hackberry State of the Upper Devonian,” published by the MacMillan Company in 1924. 2. Bird Hill, Cerro Gordo County This is near the center of the north line of section 24, T 95N, R.19W, about 3½ miles west and ¼ mile south of the Rockford Brick and Tile Company Plant. The Hackberry fauna can be collected here also. 3. Elgin-Clermont area, Fayette County In the Elgin Member of the Maquoketa Formation large trilobites and both straight and coiled cephalopods are found. Fragments of trilobites are common, but whole specimens are rare. Road cuts along the new highway between Clermont and Elgin, the dry stream bed along county road “Y” east of Clermont, and the high-road cuts along the Turkey River southeast of Elgin are all good collecting sites. References for this area are: (1) Slocum, A.W., “Trilobites from the Maquoketa Beds of Fayette County, Iowa,” Iowa Geological Survey Annual Report, Volume 25; (2) Walter, O.T., “Trilobites of Iowa and some Related Paleozoic Forms,” Iowa Geological Survey Annual Report, Volume 31; (3) Ladd, H.S., “Stratigraphy and Paleontology of the Maquoketa Shale of Iowa,” Iowa Geological Survey Annual Report, Volume 34. -
In Defence of the Three-Domains of Life Paradigm P.T.S
van der Gulik et al. BMC Evolutionary Biology (2017) 17:218 DOI 10.1186/s12862-017-1059-z REVIEW Open Access In defence of the three-domains of life paradigm P.T.S. van der Gulik1*, W.D. Hoff2 and D. Speijer3* Abstract Background: Recently, important discoveries regarding the archaeon that functioned as the “host” in the merger with a bacterium that led to the eukaryotes, its “complex” nature, and its phylogenetic relationship to eukaryotes, have been reported. Based on these new insights proposals have been put forward to get rid of the three-domain Model of life, and replace it with a two-domain model. Results: We present arguments (both regarding timing, complexity, and chemical nature of specific evolutionary processes, as well as regarding genetic structure) to resist such proposals. The three-domain Model represents an accurate description of the differences at the most fundamental level of living organisms, as the eukaryotic lineage that arose from this unique merging event is distinct from both Archaea and Bacteria in a myriad of crucial ways. Conclusions: We maintain that “a natural system of organisms”, as proposed when the three-domain Model of life was introduced, should not be revised when considering the recent discoveries, however exciting they may be. Keywords: Eucarya, LECA, Phylogenetics, Eukaryogenesis, Three-domain model Background (English: domain) as a higher taxonomic level than The discovery that methanogenic microbes differ funda- regnum: introducing the three domains of cellular life, Ar- mentally from Bacteria such as Escherichia coli or Bacillus chaea, Bacteria and Eucarya. This paradigm was proposed subtilis constitutes one of the most important biological by Woese, Kandler and Wheelis in PNAS in 1990 [2]. -
Analytical Drawings by the Early Natural Philosopher, Robert Hooke Who Worked in Oxford in the 17Th Century
Twin visit to the Museum of the History of Science and the Oxford University Museum of Natural History Teachers’ Info Teachers’ Before your visit Two useful websites: The Museum of the History of Science website - www.mhs.ox.ac.uk The Natural History Museum website - www.oum.ox.ac.uk A valuable introduction: Booked museum introductions will give valuable Analytical background information on the Museums collections. Useful materials for this project. Black and coloured paper, white pens and pencils, scissors drawing and Prit sticks. You can also book the EasyShare cameras. Students’ Info During your visit AO1: Recording Observations, Experiences and Ideas. The sample sketchbook page with this sheet can be photocopied and will help students in the process of recording. AO2: Evaluating artefacts, understanding their contexts. Students can collect information to annotate their work by looking at object labels, talking to staff and collecting printed guides and postcards. After your visit A03 Developing and exploring ideas. Extra Info See the Artefact website - www.museums.ox.ac.uk/artefact. Artefact is a customized site for art students with many images. The Student and Artists’ galleries will give students ideas for developing their own work. AO4 Making connections with the work of others. The Inspirations sheet with this pack can be photocopied and will illustrate the drawings of famous artists. THE OXFORD UNIVERSITY MUSEUMS NATURAL HISTORY ASHMOLEAN @ PITT RIVERS HISTORY OF SCIENCE at the Museum of the History of Science On this page are two wonderful analytical drawings by the early natural philosopher, Robert Hooke who worked in Oxford in the 17th century. -
Rowan C. Martindale Curriculum Vitae Associate Professor (Invertebrate Paleontology) at the University of Texas at Austin
ROWAN C. MARTINDALE CURRICULUM VITAE ASSOCIATE PROFESSOR (INVERTEBRATE PALEONTOLOGY) AT THE UNIVERSITY OF TEXAS AT AUSTIN Department of Geological Sciences E-mail: [email protected] Jackson School of Geosciences Website: www.jsg.utexas.edu/martindale/ 2275 Speedway Stop C9000 Orchid ID: 0000-0003-2681-083X Austin, TX 78712-1722 Phone: 512-475-6439 Office: JSG 3.216A RESEARCH INTERESTS The overarching theme of my work is the connection between Earth and life through time, more precisely, understanding ancient (Mesozoic and Cenozoic) ocean ecosystems and the evolutionary and environmental events that shaped them. My research is interdisciplinary, (paleontology, sedimentology, biology, geochemistry, and oceanography) and focuses on: extinctions and carbon cycle perturbation events (e.g., Oceanic Anoxic Events, acidification events); marine (paleo)ecology and reef systems; the evolution of reef builders (e.g., coral photosymbiosis); and exceptionally preserved fossil deposits (Lagerstätten). ACADEMIC APPOINTMENTS Associate Professor, University of Texas at Austin September 2020 to Present Assistant Professor, University of Texas at Austin August 2014 to August 2020 Postdoctoral Researcher, Harvard University August 2012 to July 2014 Department of Organismic and Evolutionary Biology; Mentor: Dr. Andrew H. Knoll. EDUCATION Doctorate, University of Southern California 2007 to 2012 Dissertation: “Paleoecology of Upper Triassic reef ecosystems and their demise at the Triassic-Jurassic extinction, a potential ocean acidification event”. Advisor: Dr. David J. Bottjer, degree conferred August 7th, 2012. Bachelor of Science Honors Degree, Queen’s University 2003 to 2007 Geology major with a general concentration in Biology (Geological Sciences Medal Winner). AWARDS AND RECOGNITION Awards During Tenure at UT Austin • 2019 National Science Foundation CAREER Award: Awarded to candidates who are judged to have the potential to serve as academic role models in research and education. -
Some Philosophical Questions About Paleontology and Their Practica1 Consequences
ACTA GEOLOGICA HISPANICA. Concept and method in Paleontology. 16 (1981) nos 1-2, pags. 7-23 Some philosophical questions about paleontology and their practica1 consequences by Miquel DE RENZI Depto. de Geología, Facultad de Ciencias Biológicas, Universidad de Valencia. Burjassot (Valencia). This papcr attempts to objectively discuss the actual state ofpaleontology. The En aquest treball s'ha intentat fer un balanc d'alguns aspectes de I'estat de la progress of this science stood still somewhat during the latter part of the last paleontologia. La historia de la paleontologia mostra un estancarnent a les century which caused it to develop apart from the biological sciences. an area to darreries del segle passac aquest estancament va Fer que la nostra ciencia s'anes which it is naturally tied. As aconsequence, this bruought a long-term stagnation, allunyant cada cop mes de I'area de les ciencies bii~logiques,amb les qualsestava because biology, dunng this century, has made great progress and paleontology lligada naturalment AixO va portar, com a conseqüencia, un important has not During the last 20 years paleontology as a science hasrecuperatedsome endarreriment, car la biologia, durant aquest segle, ha donat un gran pas of this loss, but we as scientists need to be careful in various aspects of its endavant, mentre que aquest no ha estat el cas de lapaleontologia Al nostre pais development -i possiblement a molts d'altres- la paleontologia es, fonamentalment, un estn per datar estrats. Tanmateix, un mal estri, car la datació es basadaen les especies fossils i la seva determinació es fonamenta en el ccncepte d'especie biolbgica; els fossils pero en moltes ocasions, són utilitzats mes aviat com si fossin segells o monedes. -
Mary Anning of Lyme Regis: 19Th Century Pioneer in British Palaeontology
Headwaters Volume 26 Article 14 2009 Mary Anning of Lyme Regis: 19th Century Pioneer in British Palaeontology Larry E. Davis College of St. Benedict / St. John's University, [email protected] Follow this and additional works at: https://digitalcommons.csbsju.edu/headwaters Part of the Geology Commons, and the Paleontology Commons Recommended Citation Davis, Larry E. (2009) "Mary Anning of Lyme Regis: 19th Century Pioneer in British Palaeontology," Headwaters: Vol. 26, 96-126. Available at: https://digitalcommons.csbsju.edu/headwaters/vol26/iss1/14 This Article is brought to you for free and open access by DigitalCommons@CSB/SJU. It has been accepted for inclusion in Headwaters by an authorized editor of DigitalCommons@CSB/SJU. For more information, please contact [email protected]. LARRY E. DAVIS Mary Anning of Lyme Regis 19th Century Pioneer in British Palaeontology Ludwig Leichhardt, a 19th century German explorer noted in a letter, “… we had the pleasure of making the acquaintance of the Princess of Palaeontology, Miss Anning. She is a strong, energetic spinster of about 28 years of age, tanned and masculine in expression …” (Aurousseau, 1968). Gideon Mantell, a 19th century British palaeontologist, made a less flattering remark when he wrote in his journal, “… sallied out in quest of Mary An- ning, the geological lioness … we found her in a little dirt shop with hundreds of specimens piled around her in the greatest disorder. She, the presiding Deity, a prim, pedantic vinegar looking female; shred, and rather satirical in her conversation” (Curwin, 1940). Who was Mary Anning, this Princess of Palaeontology and Geological Lioness (Fig. -
The Paleontology Synthesis Project and Establishing a Framework for Managing National Park Service Paleontological Resource Archives and Data
Lucas, S.G. and Sullivan, R.M., eds., 2018, Fossil Record 6. New Mexico Museum of Natural History and Science Bulletin 79. 589 THE PALEONTOLOGY SYNTHESIS PROJECT AND ESTABLISHING A FRAMEWORK FOR MANAGING NATIONAL PARK SERVICE PALEONTOLOGICAL RESOURCE ARCHIVES AND DATA VINCENT L. SANTUCCI1, JUSTIN S. TWEET2 and TIMOTHY B. CONNORS3 1National Park Service, Geologic Resources Division, 1849 “C” Street, NW, Washington, D.C. 20240, [email protected]; 2National Park Service, 9149 79th Street S., Cottage Grove, MN 55016, [email protected]; 3National Park Service, Geologic Resources Division, 12795 W. Alameda Parkway, Lakewood, CO 80225, [email protected] Abstract—The National Park Service Paleontology Program maintains an extensive collection of digital and hard copy documents, publications, photographs and other archives associated with the paleontological resources documented in 268 parks. The organization and preservation of the NPS paleontology archives has been the focus of intensive data management activities by a small and dedicated team of NPS staff. The data preservation strategy complemented the NPS servicewide inventories for paleontological resources. The first phase of the data management, referred to as the NPS Paleontology Synthesis Project, compiled servicewide paleontological resource data pertaining to geologic time, taxonomy, museum repositories, holotype fossil specimens, and numerous other topics. In 2015, the second phase of data management was implemented with the creation and organization of a multi-faceted digital data system known as the NPS Paleontology Archives and NPS Paleontology Library. Two components of the NPS Paleontology Archives were designed for the preservation of both park specific and servicewide paleontological resource archives and data. A third component, the NPS Paleontology Library, is a repository for electronic copies of geology and paleontology publications, reports, and other media.