DOCSLIB.ORG

Generation Sequencing”, Is Purely My Own Unless Stated Otherwise

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Generation Sequencing”, Is Purely My Own Unless Stated Otherwise Unraveling evolution through Next Generation ​ ​ ​ ​ ​ ​ ​ ​ Sequencing Michael Westbury ​ ​ Univ.-Diss. zur Erlangung des akademischen Grades ​ ​ ​ ​ ​ ​ ​ ​ "doctor rerum naturalium" ​ ​ ​ ​ (Dr. rer. nat.) ​ ​ ​ ​ in der Wissenschaftsdisziplin "Evolutionsgenetik." ​ ​ ​ ​ ​ ​ eingereicht an der ​ ​ ​ ​ Mathematisch-Naturwissenschaftlichen Fakultät ​ ​ Institut für Biochemie und Biologie ​ ​ ​ ​ ​ ​ ​ ​ der Universität Potsdam ​ ​ ​ ​ Hauptbetreuer: Prof. Michael Hofreiter (University of Potsdam) ​ ​​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ weitere Gutachter: Associate Prof. Eline Lorenzen (Natural history museum of Denmark) and ​ Prof. Jon Waters (University of Otago, New Zealand) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Published online at the Institutional Repository of the University of Potsdam: URN urn:nbn:de:kobv:517-opus4-409981 http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409981 Declaration of authorship ​ ​ ​ ​ I, Michael Westbury, declare that the work contained within this thesis titled, “Unraveling evolution through Next Generation Sequencing”, is purely my own unless stated otherwise. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Chapter 2: ​ ​ “Complete mitochondrial genome of a bat eared fox (Otocyon megalotis), along with ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ phylogenetic considerations” ​ ​ This manuscript was published in “Mitochondrial DNA part B” in 2017 and can be found online ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ at http://dx.doi.org/10.1080/23802359.2017.1331325. I carried out the extraction lab work, data ​ ​​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ analyses and wrote the manuscript. ​ ​ ​ ​ ​ ​ ​ ​ Chapter 3: ​ ​ “A mitogenomic timetree for Darwin‘s enigmatic South American mammal Macrauchenia ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​​ patachonica” ​ This manuscript was published in “Nature communications” in 2017 under the doi ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 10.1038/ncomms15951. I carried out the majority of the lab work, including the sample that ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ yielded DNA. Sina Baleka processed some samples that were unsuccessful in yielding DNA. I ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ performed the majority of the data analyses assisted by Axel Barlow, Sina Baleka, Stefanie ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Hartmann, and Johanna L.A. Paijmans. I wrote the majority of the methods and results in the ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ manuscript. I further supplied input in the introduction and discussion of the manuscript together ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ with Ross D.E. MacPhee and Michael Hofreiter. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Chapter 4: ​ ​ “Population and conservation genomics of the world's rarest hyena species, the brown ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ hyena (Parahyena brunnea)” ​ ​ ​ ​ ​ ​ This manuscript has been submitted to “Genome research” and is also available online in the ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ preprint server “Biorxiv” under https://doi.org/10.1101/170621. I conceived the project idea ​ ​ ​ ​ ​ ​ ​ ​​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ together with Michael Hofreiter. I performed all lab work excluding the two captive samples ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ (brown and striped hyena). Love Dalén and the National Genomics Infrastructure (Stockholm) ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ processed the two captive samples. I performed all analyses apart from the sliding trees which ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Stefanie Hartmann performed. I wrote the majority of the manuscript. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Signed: Michael Westbury ​ ​ Acknowledgements Firstly, I would like to acknowledge and thank my supervisor, Prof. Michael Hofreiter, for giving me the opportunity to work on such interesting and state of art projects. Without your guidance and support, I am sure I would have been lost. I really appreciated the chances you gave me to travel all around the world, meet new people and learn new skills on the work budget. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Furthermore, I would like to thank …. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ All of the collaborators on the projects presented within this thesis. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ The Evolutionary Adaptive Genomics group, present and past members. We have grown so significantly over the years that there are too many to name. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Stefanie Hartmann for being the speediest proof reader of time and giving some valuable feedback on the thesis. ​ ​ ​ ​ ​ ​ The Potsdam Porcupines for giving me something to do apart from work. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ The Fellas over fame crew for supplying good banter in times of need and boredom and all of the lads around the world. ​ ​ ​ ​ ​ ​ A special thanks to my family, especially mum and dad who encouraged me to leave the homeland in the pursue of greater things. I am grateful that even when what I was doing seemed a bit abstract, you always were or at least pretended to be interested. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Last but not least, I would like to thank the lovely Binia De Cahsan. You helped me through the nightmare of the German bureaucratic system, supplied ample German language knowledge and put up with all of my rubbish. I greatly appreciate all the time and help you give me and wouldn’t have wanted it any other way. ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ Table of contents ​ ​ ​ ​ Summary 1 Zusammenfassung 3 Chapter 1: Introduction 6 ​ ​ ​ ​ 1.1 Traditional DNA sequencing 7 ​ ​ ​ ​ 1.2 Next generation sequencing 8 ​ ​ ​ ​ 1.2.1 Illumina technologies 9 ​ ​ 1.3 Applications of NGS 10 ​ ​ ​ ​ 1.4 Benefits of NGS within evolutionary biology 11 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 1.5 Ancient DNA 12 ​ ​ 1.6 Data analyses 14 ​ ​ 1.6.1 De novo assemblies 15 ​ ​ ​ ​ 1.6.2 Mapping assemblies 15 ​ ​ 1.6.2.1 Low coverage mapping 16 ​ ​ ​ ​ 1.6.2.2 Iterative mapping 16 ​ ​ 1.7 Thesis outline 17 ​ ​ Chapter 2: Article I 20 ​ ​ ​ ​ ​ ​ 2.1 Abstract 20 2.2 Main text 20 ​ ​ Chapter 3: Article II 24 ​ ​ ​ ​ ​ ​ 3.1 Abstract 24 3.2 Introduction 25 3.3 Results 27 3.3.1 Sample screening 27 ​ ​ 3.3.2 Validation of the iterative mapping approach using MITObim 27 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 3.3.3 Mitochondrial genome reconstruction of MAC002 28 ​ ​ ​ ​ ​ ​ ​ ​ 3.3.4 Macrauchenia mitochondrial sequence validation 29 ​ ​ ​ ​ ​ ​ 3.3.5 Phylogenetic reconstruction 30 ​ ​ 3.4 Discussion 31 3.5 Methods 33 3.5.1 Samples 33 3.5.2 DNA preparation 33 ​ ​ 3.5.3 Test sequencing and analysis 36 ​ ​ ​ ​ ​ ​ 3.5.4 Further extractions of MAC002 36 ​ ​ ​ ​ ​ ​ 3.5.5 Deep sequencing of MAC002 37 ​ ​ ​ ​ ​ ​ 3.5.6 Mitochondrial reconstruction 37 ​ ​ 3.5.7 MITObim validation 38 ​ ​ 3.5.8 MAC002 mitochondrial genome reconstruction 38 ​ ​ ​ ​ ​ ​ 3.5.9 Final sequence validation 39 ​ ​ ​ ​ 3.5.10 Retrospective mapping of other Macrauchenia and ​ ​ ​ ​ ​ ​ ​ ​​ ​ ​ Toxodon samples 40 ​ ​ 3.5.11 Phylogenetic reconstruction 40 ​ ​ Chapter 4: Article III 47 ​ ​ ​ ​ ​ ​ 4.1 Abstract 47 4.2 Introduction 48 4.3 Results 51 4.3.1 Genome reconstructions 51 ​ ​ 4.3.2 Genetic diversity 51 ​ ​ 4.3.3 Demographic history 55 ​ ​ 4.3.4 Population structure 56 ​ ​ 4.4 Discussion 61 4.4.1 Genomic diversity 62 ​ ​ 4.4.2 Brown hyena population structure 63 ​ ​ ​ ​ ​ ​ 4.4.3 Conservation implications 64 ​ ​ 4.5 Methods 64 4.5.1 Samples 64 4.5.2 Striped hyena de novo assembly 65 ​ ​ ​ ​​ ​ ​ ​ ​ 4.5.3 Captive brown hyena sample 65 ​ ​ ​ ​ ​ ​ 4.5.4 Wild caught brown hyena samples 66 ​ ​ ​ ​ ​ ​ ​ ​ 4.5.5 Raw data treatment 66 ​ ​ ​ ​ 4.5.6 Mitochondrial genome reconstructions 66 ​ ​ ​ ​ 4.5.7 Mitochondrial analyses 67 ​ ​ 4.5.8 Low coverage nuclear genome analyses 67 ​ ​ ​ ​ ​ ​ ​ ​ 4.5.9 Brown hyena population structure 68 ​ ​ ​ ​ ​ ​ 4.5.10 Comparative population structures 69 ​ ​ ​ ​ 4.5.11 Species heterozygosity estimates 69 ​ ​ ​ ​ 4.5.12 Demographic inference 70 ​ ​ Chapter 5: Discussion 72 ​ ​ ​ ​ 5.1 Aims and importance of the thesis 72 ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ 5.2 Evolutionary insights through NGS 73 ​ ​ ​ ​ ​ ​ 5.3 Conservation 75 5.4 Bioinformatic advances 76 ​ ​ 5.5 NGS in the future 77 ​ ​ ​ ​ ​ ​ 5.6 General conclusions 79 ​ ​ Bibliography 80 Appendix A 92 ​ ​ Appendix B 117 ​ ​ List of abbreviations ​ ​ ​ ​ Bp - base pairs ​ ​ ​ ​ ​ ​ Kya - thousand years ago ​ ​ ​ ​ ​ ​ ​ ​ Ma - million years ago ​ ​ ​ ​ ​ ​ ​ ​ NGS - Next generation sequencing ​ ​ ​ ​ ​ ​ ​ ​ DNA - deoxyribonucleic acid ​ ​ ​ ​ ​ ​ Mbp - Mega bases (1,000,000bp) ​ ​ ​ ​ ​ ​ ​ ​ PCR - polymerase chain reaction ​ ​ ​ ​ ​ ​ ​ ​ RFLP - restriction fragment length polymorphisms ​ ​ ​ ​ ​ ​ ​ ​ ​ ​ SNP - single nucleotide polymorphism ​ ​ ​ ​ ​ ​ ​ ​ aDNA - ancient DNA ​ ​ ​ ​ ​ ​ Summary The sequencing of the human genome in the early 2000s led to an increased interest in cheap and fast sequencing technologies. This interest culminated in the advent of next generation sequencing (NGS). A number of different NGS platforms have arisen since then all promising to do the same thing, i.e. produce large amounts of genetic information for relatively low costs compared to more traditional methods such as Sanger sequencing. The capabilities of NGS meant that researchers were no longer bound to species for which a lot of previous work had already been done (e.g. model organisms and humans) enabling a shift in research towards more novel and diverse species of interest. This capability has greatly benefitted many fields within the
Load more

Recommended publications
  • Chapter VIII Banda Oriental and Patagonia
    CHAPTER VIII. Excursion to Colonia del Sacramiento—Value of an Estancia—Cattle, how counted—Singular Breed of Oxen—Perforated Pebbles—Shepherd Dogs —Horses Broken-in, Gauchos Riding—Character of Inhabitants—Rio Plata—Flocks of Butterflies—Aëronaut Spiders—Phosphorescence of the Sea—Port Desire—Guanaco—Port St. Julian—Geology of Patago- nia—Fossil gigantic Animal—Types of Organization constant—Change in the Zoology of America—Causes of Extinction. BANDA ORIENTAL AND PATAGONIA. HAVING been delayed for nearly a fortnight in the city, I was glad to escape on board a packet bound for Monte Video. A town in a state of blockade must always be a disagreeable place of residence; in this case moreover there were constant apprehensions from robbers within. The sentinels were the worst of all; for, from their office and from having arms in their hands, they robbed with a degree of au- thority which other men could not imitate. Our passage was a very long and tedious one. The Plata looks like a noble estuary on the map; but is in truth a poor affair. A wide ex- panse of muddy water has neither grandeur nor beauty. At one time of the day, the two shores, both of which are extremely low, could just be distinguished from the deck. On arriving at Monte Video I found that the Beagle would not sail for some time, so I prepared for a short excursion in this part of Banda Oriental. Everything which I have said about the country near Maldonado is applicable to M. Vid- eo; but the land, with the one exception of the Green Mount, 450 feet high, from which it takes its name, is far more level.
    [Show full text]
  • Hyaenodontidae (Creodonta, Mammalia) and the Position of Systematics in Evolutionary Biology
    Hyaenodontidae (Creodonta, Mammalia) and the Position of Systematics in Evolutionary Biology by Paul David Polly B.A. (University of Texas at Austin) 1987 A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Paleontology in the GRADUATE DIVISION of the UNIVERSITY of CALIFORNIA at BERKELEY Committee in charge: Professor William A. Clemens, Chair Professor Kevin Padian Professor James L. Patton Professor F. Clark Howell 1993 Hyaenodontidae (Creodonta, Mammalia) and the Position of Systematics in Evolutionary Biology © 1993 by Paul David Polly To P. Reid Hamilton, in memory. iii TABLE OF CONTENTS Introduction ix Acknowledgments xi Chapter One--Revolution and Evolution in Taxonomy: Mammalian Classification Before and After Darwin 1 Introduction 2 The Beginning of Modern Taxonomy: Linnaeus and his Predecessors 5 Cuvier's Classification 10 Owen's Classification 18 Post-Darwinian Taxonomy: Revolution and Evolution in Classification 24 Kovalevskii's Classification 25 Huxley's Classification 28 Cope's Classification 33 Early 20th Century Taxonomy 42 Simpson and the Evolutionary Synthesis 46 A Box Model of Classification 48 The Content of Simpson's 1945 Classification 50 Conclusion 52 Acknowledgments 56 Bibliography 56 Figures 69 Chapter Two: Hyaenodontidae (Creodonta, Mammalia) from the Early Eocene Four Mile Fauna and Their Biostratigraphic Implications 78 Abstract 79 Introduction 79 Materials and Methods 80 iv Systematic Paleontology 80 The Four Mile Fauna and Wasatchian Biostratigraphic Zonation 84 Conclusion 86 Acknowledgments 86 Bibliography 86 Figures 87 Chapter Three: A New Genus Eurotherium (Creodonta, Mammalia) in Reference to Taxonomic Problems with Some Eocene Hyaenodontids from Eurasia (With B. Lange-Badré) 89 Résumé 90 Abstract 90 Version française abrégéé 90 Introduction 93 Acknowledgments 96 Bibliography 96 Table 3.1: Original and Current Usages of Genera and Species 99 Table 3.2: Species Currently Included in Genera Discussed in Text 101 Chapter Four: The skeleton of Gazinocyon vulpeculus n.
    [Show full text]
  • The Wild Elephant and the Method of Capturing and Taming It in Ceylon
    7^ A/cu. /U'^ ly THE WILD ELEPHANT, LONDON PRINTED BY SPOTTISWOODE AND CO. NEW-STREET SQUARE : 796 WILD ELEPHANT THE METHOD OF CAPTURING AND TAMING IT IN CEYLON. SIR EMERSON TENNENT, Bart. J.•^ 'If' K.C.S. LL.D. F.R.S. &c. AUTHOR OF " CEYLON, AN ACCOUNT OF THE ISLAND. PHYSICAL, HISTORICAL, AND TOPOGRAPHICAL," ETC. LONDON LONGMANS, GREEN, AND CO. 1867. ; TO MY INTELLIGENT COMPANION IN MANY OF THE JOURNEYS THROUGHOUT THE MOUNTAINS AND FORESTS OF CEYLON, IN THE COURSE OF WHICH MUCH OF THE INFORMATION CONTAINED IN THIS VOLUME WAS COLLECTED ; TO MAJOR SKINNER, CHIEF COMMISSIONER OF ROADS AND PUBLIC WORKS, ETC. ETC. ONE OF THE MOST EXPERIENCED AND VALUAllLE SERVANTS OF THE CROWN IT IS INSCRIBED, IN THE HOPE THAT IT ALA.Y RECALL TO HIM THE PLEASANT MEMORIES WHICH IT AWAKES IN ME. PREFACE. In this volume, the chapters descriptive of the structure and habits of the wild elephant are reprinted for the sixth time from a larger work,^ published originally in 1859. Since the appearance of the First Edition, many corrections and much additional matter have been supplied to me, chiefly from India and Ceylon, and will be found embodied in the following pages. To one of these in particular I feel bound to direct attention. In the course of a more enlarged essay on the zoology of Ceylon, 2 amongst other proofs of a geo- logical origin for that island, distinct from that of the adjacent continent of India, as evidenced by peculiarities in the flora and fauna of each respectively, I had occasion to advert to a discovery which had been recently an- ' Ceylon: An Account of the of Ceylon.
    [Show full text]
  • Conceptual Issues in Phylogeny, Taxonomy, and Nomenclature
    Contributions to Zoology, 66 (1) 3-41 (1996) SPB Academic Publishing bv, Amsterdam Conceptual issues in phylogeny, taxonomy, and nomenclature Alexandr P. Rasnitsyn Paleontological Institute, Russian Academy ofSciences, Profsoyuznaya Street 123, J17647 Moscow, Russia Keywords: Phylogeny, taxonomy, phenetics, cladistics, phylistics, principles of nomenclature, type concept, paleoentomology, Xyelidae (Vespida) Abstract On compare les trois approches taxonomiques principales développées jusqu’à présent, à savoir la phénétique, la cladis- tique et la phylistique (= systématique évolutionnaire). Ce Phylogenetic hypotheses are designed and tested (usually in dernier terme s’applique à une approche qui essaie de manière implicit form) on the basis ofa set ofpresumptions, that is, of à les traits fondamentaux de la taxonomic statements explicite représenter describing a certain order of things in nature. These traditionnelle en de leur et particulier son usage preuves ayant statements are to be accepted as such, no matter whatever source en même temps dans la similitude et dans les relations de evidence for them exists, but only in the absence ofreasonably parenté des taxons en question. L’approche phylistique pré- sound evidence pleading against them. A set ofthe most current sente certains avantages dans la recherche de réponses aux phylogenetic presumptions is discussed, and a factual example problèmes fondamentaux de la taxonomie. ofa practical realization of the approach is presented. L’auteur considère la nomenclature A is made of the three
    [Show full text]
  • 2014BOYDANDWELSH.Pdf
    Proceedings of the 10th Conference on Fossil Resources Rapid City, SD May 2014 Dakoterra Vol. 6:124–147 ARTICLE DESCRIPTION OF AN EARLIEST ORELLAN FAUNA FROM BADLANDS NATIONAL PARK, INTERIOR, SOUTH DAKOTA AND IMPLICATIONS FOR THE STRATIGRAPHIC POSITION OF THE BLOOM BASIN LIMESTONE BED CLINT A. BOYD1 AND ED WELSH2 1Department of Geology and Geologic Engineering, South Dakota School of Mines and Technology, Rapid City, South Dakota 57701 U.S.A., [email protected]; 2Division of Resource Management, Badlands National Park, Interior, South Dakota 57750 U.S.A., [email protected] ABSTRACT—Three new vertebrate localities are reported from within the Bloom Basin of the North Unit of Badlands National Park, Interior, South Dakota. These sites were discovered during paleontological surveys and monitoring of the park’s boundary fence construction activities. This report focuses on a new fauna recovered from one of these localities (BADL-LOC-0293) that is designated the Bloom Basin local fauna. This locality is situated approximately three meters below the Bloom Basin limestone bed, a geographically restricted strati- graphic unit only present within the Bloom Basin. Previous researchers have placed the Bloom Basin limestone bed at the contact between the Chadron and Brule formations. Given the unconformity known to occur between these formations in South Dakota, the recovery of a Chadronian (Late Eocene) fauna was expected from this locality. However, detailed collection and examination of fossils from BADL-LOC-0293 reveals an abundance of specimens referable to the characteristic Orellan taxa Hypertragulus calcaratus and Leptomeryx evansi. This fauna also includes new records for the taxa Adjidaumo lophatus and Brachygaulus, a biostratigraphic verifica- tion for the biochronologically ambiguous taxon Megaleptictis, and the possible presence of new leporid and hypertragulid taxa.
    [Show full text]
  • Recent Polydactyle Horses ; by 0
    I 338 Scientific Intelligence. figures in this paper from the same beds several other apparently aquatic plants, a palm, and three conifers. Two of these latter, Brenclopsis Iioheneggeri and Geinitzia cretacea are indicative of an even earlier period. L. F. W. 0. Hec/icrches sur la Vegetation 'du niveau Aquitanien de Manosque; par le Marquis G. DE SAPORTA. Memoires de la Soc. Geol. do France, tome ii; I, Nympheinees, Fasc. i, Mem. No. 9, APPENDIX. pp. 22, pi. iii-vi; II, Palmiers, Fasc. 2, Mem. No. 9, pp. 23-34, pi. ix-xi.—The first of these papers treats of some important re­ cent discoveries of Nympheaceous plants in the beds of Manosque, Cerestc, and Bois rt'Asson, chiefly by local collectors, the princi­ ART. XLIII.—Recent Polydactyle Horses ; by 0. 0. MARSH. pal of whom are M. Nalin and Mile. Rostan. The flora of these deposits as previously published by the author is reviewed and IN this Journal for June, 1879, the writer made a brief the new species described and fully illustrated. These include five species of Nymphsea, one of Aneectomeria, and one of Nelumbium. summary of the facts then known to him in regard to existing Associated with these was found a Ceratophyllum (C. aquitani- horses with extra digits, especially in relation to the extinct cum), and the view is expressed that this anomalous genus is species he had discovered in the Rocky Mountains, and also really related to the Nymphajaceae. This view had already been gave figures of typical examples of existing and fossil forms.* suggested by Brongniart based on the similarity of the seeds, but Since then, he has collected much material bearing on the most authors put this genus in an apetalous order by itself, though question, particularly of extinct horses, and an illustrated Baillon places it in the Piperacese.
    [Show full text]
  • This Item Is the Archived Peer-Reviewed Author-Version Of
    This item is the archived peer-reviewed author-version of: Modern tapirs as morphofunctional analogues for locomotion in endemic eocene European perissodactyls Reference: Maclaren Jamie, Nauw elaerts Sandra.- Modern tapirs as morphofunctional analogues for locomotion in endemic eocene European perissodactyls JOURNAL OF MAMMALIAN EVOLUTION - ISSN 1064-7554 - (2019), p. 1-19 Full text (Publisher's DOI): https://doi.org/10.1007/S10914-019-09460-1 To cite this reference: https://hdl.handle.net/10067/1580640151162165141 Institutional repository IRUA 1 TITLE: 2 Modern tapirs as morphofunctional analogues for locomotion 3 in endemic Eocene European perissodactyls 4 Jamie A. MacLaren1* and Sandra Nauwelaerts1,2 5 6 1 Department of Biology, Universiteit Antwerpen, Campus Drie Eiken, Universiteitsplein, Wilrijk, 7 Antwerp, 2610 (Belgium). 8 2 Center for Research and Conservation, Koninklijke Maatschappij voor Dierkunde (KMDA), 9 Koningin Astridplein 26, Antwerp, 2018 (Belgium). 10 11 12 * Corresponding Author 13 14 15 Corresponding Author: Jamie MacLaren, Room D.1.41, Department of Biology, Universiteit 16 Antwerpen, Campus Drie Eiken, Universiteitsplein, Wilrijk, Antwerp, 2610 (Belgium) 17 18 ORCID: 19 JM (0000-0003-4177-227X) 20 SN (0000-0002-2289-4477) 21 Abstract 22 Tapirs have historically been considered as ecologically analogous to several groups of extinct 23 perissodactyls based on dental and locomotor morphology. Here, we investigate comparative 24 functional morphology between living tapirs and endemic Eocene European perissodactyls to 25 ascertain whether tapirs represent viable analogues for locomotion in palaeotheres and lophiodontids. 26 Forelimb bones from 20 species of Eocene European perissodactyls were laser scanned and 27 compared to a forelimb dataset of extant Tapirus. Bone shape was quantified using 3D geometric 28 morphometrics; coordinates were Procrustes aligned and compared using Principal Component 29 Analysis and neighbor-joining trees.
    [Show full text]
  • MOVING BEYOND PACHYCHOROID It Is a Spectrum That Is Poorly Defined and Has No Thematic Focus
    SPECIAL REPORT s MOVING BEYOND PACHYCHOROID It is a spectrum that is poorly defined and has no thematic focus. BY RICHARD F. SPAIDE, MD he great biologist Georges Cuvier1 helped establish the field of paleontology and devised classification systems for animals that included the order Pachydermata, or thick skin. In this order he included horse, pig, elephant, rhinoceros, and hippopotamus because he Tthought they all had a thick skin. Later, substantial differ- ences were found among these animals, most notable being that they did not have common ancestors. The attempted unifying principle, thick skin, proved illusory. The choroids in patients with central serous chorioreti- nopathy (CSC) were found to be thick compared with nor- mal eyes.2 Curiously, the choroids in the fellow eyes were typically greater than normal eyes, and the same for eyes that had resolved CSC. A link was made between choroidal vascular hyperperme- ability seen during indocyanine green (ICG) angiography, a Figure 1. An ICG angiogram of a patient with CSC. Ordinarily, the venous drainage of the hallmark finding for CSC, and increased choroidal thickness. choroid is segmental and there would be watershed zones demarcated by the dashed The choroid is also thicker for other diseases, such as Vogt- white lines. This eye does not have watershed zones and there are intervortex venous anastomoses (some of which are highlighted in yellow) crossing over the watershed zones. Koyanagi-Harada (VKH) disease.3 The term pachychoroid, pachy meaning thick, was devel- “choroidal thickening”
    [Show full text]
  • 0520237315.Pdf
    Beasts of Eden The publisher gratefully acknowledges the generous contribution to this book provided by the General Endowment Fund of the University of California Press Associates. Beasts of Eden walking whales, dawn horses, and other enigmas of mammal evolution David Rains Wallace university of california press berkeley los angeles london University of California Press Berkeley and Los Angeles, California University of California Press, Ltd. London, England © 2004 by the Regents of the University of California Library of Congress Cataloging-in-Publication Data Wallace, David Rains, 1945–. Beasts of Eden : walking whales, dawn horses, and other enigmas of mammal evolution / David Rains Wallace. p. cm. Includes bibliographical references and index. isbn 0-520-23731-5 (alk. paper). 1. Mammals—Evolution. 2. Mammals, Fossil. I. Title. ql708.5.w25 2004 599.138—dc22 2003022857 Manufactured in the United States of America 13 12 11 10 09 08 07 06 05 04 10987654 321 Printed on Ecobook 50 containing a minimum 50% post-consumer waste, processed chlorine free. The balance contains virgin pulp, including 25% Forest Stewardship Council Certified for no old growth tree cutting, processed either tcf or ecf. The sheet is acid-free and meets the minimum requirements of ansi/niso z39.48-1992 (r 1997) (Permanence of Paper). ᭺ϱ to steve fisher, who brings art to science Actually most scientific problems are far better understood by studying their history than their logic. ernst mayr quoted in Leo F. Laporte, George Gaylord Simpson: Paleontologist and Evolutionist contents list of illustrations /xi acknowledgments / xiii prologue. the fresco and the fossil /xv 1 / Pachyderms in the Catacombs /1 2 / Dr.
    [Show full text]
  • XLI. on the Sivatherium Giganteum, a New Fossil Ruminant Genus, From
    This article was downloaded by: [New York University] On: 31 May 2013, At: 10:13 Publisher: Taylor & Francis Informa Ltd Registered in England and Wales Registered Number: 1072954 Registered office: Mortimer House, 37-41 Mortimer Street, London W1T 3JH, UK Philosophical Magazine Series 3 Publication details, including instructions for authors and subscription information: http://www.tandfonline.com/loi/tphm14 XLI. On the Sivatherium giganteum, a new fossil Ruminant Genus, from the Valley of the Markanda, in the Siválik branch of the Sub-Himálayan Mountains Hugh Falconer M.D. & Captain P. T. Cautley Published online: 01 Jun 2009. To cite this article: Hugh Falconer M.D. & Captain P. T. Cautley (1836): XLI. On the Sivatherium giganteum, a new fossil Ruminant Genus, from the Valley of the Markanda, in the Siválik branch of the Sub-Himálayan Mountains , Philosophical Magazine Series 3, 9:53, 193-201 To link to this article: http://dx.doi.org/10.1080/14786443608636476 PLEASE SCROLL DOWN FOR ARTICLE Full terms and conditions of use: http://www.tandfonline.com/page/ terms-and-conditions This article may be used for research, teaching, and private study purposes. Any substantial or systematic reproduction, redistribution, reselling, loan, sub-licensing, systematic supply, or distribution in any form to anyone is expressly forbidden. The publisher does not give any warranty express or implied or make any representation that the contents will be complete or accurate or up to date. The accuracy of any instructions, formulae, and drug doses should be independently verified with primary sources. The publisher shall not be liable for any loss, actions, claims, proceedings, demand, or costs or damages whatsoever or howsoever caused arising directly or indirectly in connection with or arising out of the use of this material.
    [Show full text]
  • Darwin. a Reader's Guide
    OCCASIONAL PAPERS OF THE CALIFORNIA ACADEMY OF SCIENCES No. 155 February 12, 2009 DARWIN A READER’S GUIDE Michael T. Ghiselin DARWIN: A READER’S GUIDE Michael T. Ghiselin California Academy of Sciences California Academy of Sciences San Francisco, California, USA 2009 SCIENTIFIC PUBLICATIONS Alan E. Leviton, Ph.D., Editor Hallie Brignall, M.A., Managing Editor Gary C. Williams, Ph.D., Associate Editor Michael T. Ghiselin, Ph.D., Associate Editor Michele L. Aldrich, Ph.D., Consulting Editor Copyright © 2009 by the California Academy of Sciences, 55 Music Concourse Drive, San Francisco, California 94118 All rights reserved. No part of this publication may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage or retrieval system, without permission in writing from the publisher. ISSN 0068-5461 Printed in the United States of America Allen Press, Lawrence, Kansas 66044 Table of Contents Preface and acknowledgments . .5 Introduction . .7 Darwin’s Life and Works . .9 Journal of Researches (1839) . .11 Geological Observations on South America (1846) . .13 The Structure and Distribution of Coral Reefs (1842) . .14 Geological Observations on the Volcanic Islands…. (1844) . .14 A Monograph on the Sub-Class Cirripedia, With Figures of All the Species…. (1852-1855) . .15 On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life (1859) . .16 On the Various Contrivances by which British and Foreign Orchids are Fertilised by Insects, and on the Good Effects of Intercrossing (1863) . .23 The Different Forms of Flowers on Plants of the Same Species (1877) .
    [Show full text]
  • The Rise and Fall of Darwin's First Theory of Transmutation
    The Rise and Fall of Darwin's First Theory of Transmutation GEORGE GRINNELL Department of History, McMaster University Hamilton, Ontario In the four "Transmutations Notebooks," which Darwin filled for two years while living in London after returning to England from the Beagle voyage, are a host of thoughts, observations, quotations from books he was reading and from conversations with friends, such that it is difficult to know exactly which of the ideas expressed in the note- books belong to Darwin as part of "my theory," and which are simply passing thoughts to be considered and then rejected, but a statistical study of the frequency with which Darwin uses certain words indicates that during the course of the two years there were three theories of transmutation which he considered to be "mine" and that the host of other ideas which he expressed contemporaneously were either sub- sidiary to these or of only passing interest (with one major exception). 1 The question is, were these three theories complementary or were they mutually exclusive? If they were complementary, then the implication is clearly in favor of the importance of the empirical data in shaping Darwin's thought, but if they were mutually exclusive, the implication is that Darwin approached the data with a prior world view which he attempted to superimpose on the data by means of various hypothetical models and mechanisms. This paper begins with an account of Darwin's dispute with Robert Fitzroy, captain of the Beagle, over the nature and origin of the Gal~pagos finches. It describes how the dispute is settled by John Gould, ornithologist of the Zoological Society of London, when he takes Fitzroy's side by declaring the finches to be real species.
    [Show full text]