The Structure, Development and Evolution of Reptiles
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Understanding Cladistics
Understanding Cladistics Activity for Grades 5–8 Introduction Objective At the American Museum of Natural History, In this activity, students will explore cladistics and scientists use a method called cladistics to group create a cladogram of their own. animals. They look for unique features, such as a hole in the hip socket, that the animals share. Materials Animals with like features are grouped together. A • Understanding Cladistics chart, called a cladogram, shows these relationships. • A penny, nickel, dime, and quarter for each pair Using cladistics, scientists can reconstruct genealogi- of students cal relationships and can show how animals are • 6-8 dinosaurs pictures duplicated for each group, linked to one another through a long and complex downloadable from history of evolutionary changes. amnh.org/resources/rfl/pdf/dino_16_illustrations.pdf Procedure 1. Write lion, elephant, zebra, kangaroo, koala, buffalo, raccoon, and alligator. Ask students how the animals are related and what might be a good way of grouping them into sets and subsets. Discuss students responses. Tyrannosaurus rex Apatosaurus excelsus 2. Explain to students that scientists use a method extinct extinct called cladistics to determine evolutionary relation- ships among animals. They look for features that animals share, such as four limbs, hooves, or a hole in the hip socket. Animals with like features are grouped together. Scientists make a chart called a cladogram to show these relationships. 3. Tell students that they will examine the features of various coins to determine how they are related. Remind students that cladistics is used to determine relationships among organisms, and Theropoda Sauropoda Foot with three main At least 11 or more not necessarily objects. -
Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity
Acta Biotheor (2009) 57:129–162 DOI 10.1007/s10441-008-9064-7 REGULAR ARTICLE Character Analysis in Cladistics: Abstraction, Reification, and the Search for Objectivity Rasmus Grønfeldt Winther Received: 10 October 2008 / Accepted: 17 October 2008 / Published online: 7 January 2009 Ó Springer Science+Business Media B.V. 2009 Abstract The dangers of character reification for cladistic inference are explored. The identification and analysis of characters always involves theory-laden abstraction—there is no theory-free ‘‘view from nowhere.’’ Given theory-ladenness, and given a real world with actual objects and processes, how can we separate robustly real biological characters from uncritically reified characters? One way to avoid reification is through the employment of objectivity criteria that give us good methods for identifying robust primary homology statements. I identify six such criteria and explore each with examples. Ultimately, it is important to minimize character reification, because poor character analysis leads to dismal cladograms, even when proper phylogenetic analysis is employed. Given the deep and systemic problems associated with character reification, it is ironic that philosophers have focused almost entirely on phylogenetic analysis and neglected character analysis. Keywords Characters Á Cladistics Á Phylogenetics Á Morphology Á Abstraction Á Reification Á Biological theory Á Epistemology Á Causation How are we to recognize the ‘‘true’’ characters of organisms rather than imposing upon them arbitrary divisions that obscure the very processes that we seek to understand? …No issue is of greater importance in the study of biology. –Lewontin 2001, p. xvii Are characters natural units or artifacts of observation and description? In both systematics and ecology, there is often a considerable gulf between observables and the units that play causal roles in our models. -
The Mesozoic Era Alvarez, W.(1997)
Alles Introductory Biology: Illustrated Lecture Presentations Instructor David L. Alles Western Washington University ----------------------- Part Three: The Integration of Biological Knowledge Vertebrate Evolution in the Late Paleozoic and Mesozoic Eras ----------------------- Vertebrate Evolution in the Late Paleozoic and Mesozoic • Amphibians to Reptiles Internal Fertilization, the Amniotic Egg, and a Water-Tight Skin • The Adaptive Radiation of Reptiles from Scales to Hair and Feathers • Therapsids to Mammals • Dinosaurs to Birds Ectothermy to Endothermy The Evolution of Reptiles The Phanerozoic Eon 444 365 251 Paleozoic Era 542 m.y.a. 488 416 360 299 Camb. Ordov. Sil. Devo. Carbon. Perm. Cambrian Pikaia Fish Fish First First Explosion w/o jaws w/ jaws Amphibians Reptiles 210 65 Mesozoic Era 251 200 180 150 145 Triassic Jurassic Cretaceous First First First T. rex Dinosaurs Mammals Birds Cenozoic Era Last Ice Age 65 56 34 23 5 1.8 0.01 Paleo. Eocene Oligo. Miocene Plio. Ple. Present Early Primate First New First First Modern Cantius World Monkeys Apes Hominins Humans A modern Amphibian—the toad A modern day Reptile—a skink, note the finely outlined scales. A Comparison of Amphibian and Reptile Reproduction The oldest known reptile is Hylonomus lyelli dating to ~ 320 m.y.a.. The earliest or stem reptiles radiated into therapsids leading to mammals, and archosaurs leading to all the other reptile groups including the thecodontians, ancestors of the dinosaurs. Dimetrodon, a Mammal-like Reptile of the Early Permian Dicynodonts were a group of therapsids of the late Permian. Web Reference http://www.museums.org.za/sam/resource/palaeo/cluver/index.html Therapsids experienced an adaptive radiation during the Permian, but suffered heavy extinctions during the end Permian mass extinction. -
Crown Clades in Vertebrate Nomenclature
2008 POINTS OF VIEW 173 Wiens, J. J. 2001. Character analysis in morphological phylogenetics: Wilkins, A. S. 2002. The evolution of developmental pathways. Sinauer Problems and solutions. Syst. Biol. 50:689–699. Associates, Sunderland, Massachusetts. Wiens, J. J., and R. E. Etheridge. 2003. Phylogenetic relationships of Wright, S. 1934a. An analysis of variability in the number of digits in hoplocercid lizards: Coding and combining meristic, morphometric, an inbred strain of guinea pigs. Genetics 19:506–536. and polymorphic data using step matrices. Herpetologica 59:375– Wright, S. 1934b. The results of crosses between inbred strains 398. of guinea pigs differing in number of digits. Genetics 19:537– Wiens, J. J., and M. R. Servedio. 1997. Accuracy of phylogenetic analysis 551. including and excluding polymorphic characters. Syst. Biol. 46:332– 345. Wiens, J. J., and M. R. Servedio. 1998. Phylogenetic analysis and in- First submitted 28 June 2007; reviews returned 10 September 2007; traspecific variation: Performance of parsimony, likelihood, and dis- final acceptance 18 October 2007 tance methods. Syst. Biol. 47:228–253. Associate Editor: Norman MacLeod Syst. Biol. 57(1):173–181, 2008 Copyright c Society of Systematic Biologists ISSN: 1063-5157 print / 1076-836X online DOI: 10.1080/10635150801910469 Crown Clades in Vertebrate Nomenclature: Correcting the Definition of Crocodylia JEREMY E. MARTIN1 AND MICHAEL J. BENTON2 1UniversiteL´ yon 1, UMR 5125 PEPS CNRS, 2, rue Dubois 69622 Villeurbanne, France; E-mail: [email protected] 2Department of Earth Sciences, University of Bristol, Bristol, BS9 1RJ, UK; E-mail: [email protected] Downloaded By: [Martin, Jeremy E.] At: 19:32 25 February 2008 Acrown group is defined as the most recent common Dyke, 2002; Forey, 2002; Monsch, 2005; Rieppel, 2006) ancestor of at least two extant groups and all its descen- but rather expresses dissatisfaction with the increasingly dants (Gauthier, 1986). -
Cladistics: Definition of Terms Amniotic Egg: Includes Several Extensive Membranes, the Amnion, Chorion, and Allantois
Cladistics: Definition of Terms Amniotic egg: includes several extensive membranes, the amnion, chorion, and allantois. The egg is contained in an amniotic sac, as, for example, in the human fetus. Clade: a group of organisms including their common ancestor and all descendants that have evolved from that common ancestor. Cladistics: a system of classification based on shared derived characters that arranges organisms only by their branching in an evolutionary tree. Cladogram: a tree-shaped diagram used to illustrate evolutionary relationships among species by analyz- ing certain kinds of characters, or physical features, � � � � in the organisms. A cladogram starts with the root, which then splits several times. As you follow along �������� Outgroup ������ on a cladogram, it will split at nodes into two or more internodes. The node represents a speciation ������� event (the formation of a new species). The line ��������� between two speciation events, the internode, rep- ���� resents at least one hypothetical ancestor. Described ���� species (either from the present or from the fossil record), known as terminal taxa, appear at the tips or ends of the branches. Characters that are used to define a group or clade (shared derived characters) can be drawn on the internode leading to the node defining the clade. Characters: physical features shared by a group of organisms. These characters correspond to the specific traits of an organism. For example, if the character is vertebrae, then one of the traits of a particular species is the presence or absence of vertebrae. Characters that are new, and not present in an outgroup or ancestor, are called derived. Characters that are present in an ancestor of a studied group are called ancestral. -
Evolution of Reptiles
Evolution of Reptiles: Reptiles were 1st vertebrates to make a complete transition to life on land (more food & space) Arose from ancestral reptile group called cotylosaurs (small, lizard like reptile) Cotylosaurs adapted to other environments in Permian period 1. Pterosaurs – flying reptiles 2. Ichthyosaurs & plesiosaurs – marine reptiles 3. Thecodonts – small, land reptiles that walked on back legs Mesozoic Era called “age of reptiles” Dinosaurs dominated life on land for 160 million years Brachiosaurs were largest dinosaurs Herbivores included Brontosaurus & Diplodocus, while Tyrannosaurus were carnivores Dinosaurs became extinct at end of Cretaceous period Mass extinction of many animal species possibly due to impact of huge asteroid with earth; Asteroid Impact Theory Amniote (shelled) egg allowed reptiles to live & reproduce on land Amniote Egg: Egg had protective membranes & porous shell enclosing the embryo Has 4 specialized membranes — amnion, yolk sac, allantois, & chorion Amnion is a thin membrane surrounding a salty fluid in which the embryo “floats” Yolk sac encloses the yolk or protein-rich food supply for embryo Allantois stores nitrogenous wastes made by embryo until egg hatches Chorion lines the inside of the shell & regulates oxygen & carbon dioxide exchange Shell leathery & waterproof Internal fertilization occurs in female before shell is formed Terrestrial Adaptations: Dry, watertight skin covered by scales made of a protein called keratin to prevent desiccation (water loss) Toes with claws to -
29 | Vertebrates 791 29 | VERTEBRATES
Chapter 29 | Vertebrates 791 29 | VERTEBRATES Figure 29.1 Examples of critically endangered vertebrate species include (a) the Siberian tiger (Panthera tigris), (b) the mountain gorilla (Gorilla beringei), and (c) the Philippine eagle (Pithecophega jefferyi). (credit a: modification of work by Dave Pape; credit b: modification of work by Dave Proffer; credit c: modification of work by "cuatrok77"/Flickr) Chapter Outline 29.1: Chordates 29.2: Fishes 29.3: AmphiBians 29.4: Reptiles 29.5: Birds 29.6: Mammals 29.7: The Evolution of Primates Introduction Vertebrates are among the most recognizable organisms of the animal kingdom. More than 62,000 vertebrate species have been identified. The vertebrate species now living represent only a small portion of the vertebrates that have existed. The best-known extinct vertebrates are the dinosaurs, a unique group of reptiles, which reached sizes not seen before or after in terrestrial animals. They were the dominant terrestrial animals for 150 million years, until they died out in a mass extinction near the end of the Cretaceous period. Although it is not known with certainty what caused their extinction, a great deal is known about the anatomy of the dinosaurs, given the preservation of skeletal elements in the fossil record. Currently, a number of vertebrate species face extinction primarily due to habitat loss and pollution. According to the International Union for the Conservation of Nature, more than 6,000 vertebrate species are classified as threatened. Amphibians and mammals are the classes with the greatest percentage of threatened species, with 29 percent of all amphibians and 21 percent of all mammals classified as threatened. -
Application of Cladistics to the Analysis of Genotype-Phenotype Relationships
Eur. J. Epidemiol. 0392-2990 EUROPEAN Vol. 8, Suppl. to No. 2 Suppl. 1, 1992, p, 3-9 JOURNAL OF EPIDEMIOLOGY APPLICATION OF CLADISTICS TO THE ANALYSIS OF GENOTYPE-PHENOTYPE RELATIONSHIPS C.F. SING 1, M.B. HAVILAND, K.E. ZERBA and A.R. TEMPLETON The University of Michigan Medical School - Medical Science 1I M4708 ANN ARBOR - MI 48109-0618 - USA. Key words: Atherosclerosis - Cladistics - Genetics We seek to understand the relative contribution of allelic variations of a particular gene to the determination of an individual's risk ofatherosclerosis or hypertension. Work in progress is focusing on the identification and characterization of mutations in candidate genes that are known to be involved in determining the phenotypic expression of intermediate biochemical and physiological traits that are in the pathway of causation between genetic variation and variation in risk of disease. The statistical strategy described in this paper is designed to aid geneticists and molecular biologists in their search to find the DNA sequences responsible for the genetic component of variation in these traits. With this information we will have a more complete understanding of the nature of the organization of the genetic variation responsible for quantitative variation in risk of disease. It will then be possible to fully evaluate the utility of measured genetic information in predicting the risk of common diseases having a complex multifactorial etiology, such as atherosclerosis and hypertension. INTRODUCTION biological risk factor traits that influence risk of disease are continuously distributed among relatives. Numerous quantitative biological traits contribute There is no known combination of phenotypes in an to determining an individual's risk of developing a individual for which risk is totally absent or disease an common complex disease such as atherosclerosis or absolute certainty. -
A Synapomorphy-Based Multiple Sequence Alignment Method. Cladistics, 19:261
Cladistics Cladistics 19 (2003) 261–268 www.elsevier.com/locate/yclad Implied alignment: a synapomorphy-based multiple-sequence alignment method and its use in cladogram search Ward C. Wheeler* Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79thSt., New York, NY 10024-5192, USA Accepted 7 April 2003 Abstract A method to align sequence data based on parsimonious synapomorphy schemes generated by direct optimization (DO; earlier termed optimization alignment) is proposed. DO directly diagnoses sequence data on cladograms without an intervening multiple- alignment step, thereby creating topology-specific, dynamic homology statements. Hence, no multiple-alignment is required to generate cladograms. Unlike general and globally optimal multiple-alignment procedures, the method described here, implied alignment (IA), takes these dynamic homologies and traces them back through a single cladogram, linking the unaligned sequence positions in the terminal taxa via DO transformation series. These ‘‘lines of correspondence’’ link ancestor–descendent states and, when displayed as linearly arrayed columns without hypothetical ancestors, are largely indistinguishable from standard multiple alignment. Since this method is based on synapomorphy, the treatment of certain classes of insertion–deletion (indel) events may be different from that of other alignment procedures. As with all alignment methods, results are dependent on parameter assumptions such as indel cost and transversion:transition ratios. Such an IA could be used as a basis for phylogenetic search, but this would be questionable since the homologies derived from the implied alignment depend on its natal cladogram and any variance, between DO and IA + Search, due to heuristic approach. The utility of this procedure in heuristic cladogram searches using DO and the im- provement of heuristic cladogram cost calculations are discussed. -
Introduction Speciation Is a Burning Issue in Evolutionary Biology, but It
Introduction Speciation is a burning issue in evolutionary biology, but it is both fascinating and frustrating. Defining speciation depends on one’s species concept viz., typological, biological, evolutionary, recognition etc. In its simplest form, speciation is lineage splitting (ancestor-descendent sequence of populations); the resulting lineages are genetically isolated and ecologically distinct. Speciation is the process of evolutionary mechanism by which new biological species (or taxa) arise. There are two ways of new species (or taxa) origin from the pre-existing one:- i. by splitting of the parent species into two or more species (by the splitting of phylogenetic lineage) and ii. by transformation of the old species into a new one in due course of time. The Biologist O.F. Cook (1906) seems to have been the first to coin the term ‘speciation’ for the splitting of lineages (cladogenesis).The process of evolutionary mechanism by which new biological plant species (or taxa) arise, is known as plant speciation. General Mechanism of Speciation operating in nature: The mechanism of speciation is a two- staged process in which reproductive isolating mechanisms (RIM's) arise between groups of populations. Stage 1 • gene flow is interrupted between two populations. • absence of gene flow allows two populations to become genetically distinct as a result of their adaptation to different local conditions (genetic drift plays an important role here). • as populations differentiate, RIMs appear because different gene pools are not mutually coadapted. • reproductive isolation appears primarily in the form of postzygotic RIMs: hybrid failure. • these early RIMs are a byproduct of genetic differentiation, not directly promoted by natural selection. -
I. Cladistics and Phylogeny: What It Cladistics and How It Is Used to Test Phylogenetic Hypotheses
Bio 2.3 Study Guide Exam I Topics: I. Cladistics and Phylogeny: what it cladistics and how it is used to test phylogenetic hypotheses. What type of evidence is used to make decisions about cladograms and then phylogenetics? This topic applies to all of the other topics in this section of the course as it is the logical framework for the hypotheses about evolutionary relationships. Practice & Examples: given a character table make a cladogram create a character table or cladogram –good examples to practice; Fungi (all 5 phyla), the Stramenopiles, the 3 Domains, chloroplast and cyanobacteria I wouldn’t expect you to have memorized the characters of the classes Green Algae Be able to marshal an argument for or against a proposed cladogram/phylogenetic hypothesis (for example: lumping Fungi and Water Molds; Land Plants as part of Green Algae; Water Molds as part of Stramenopiles; Archea separated from Bacteria….etc) (potential essay?) Create a timeline showing the formation of the earth (solid rock), origins of life, Archea, Bacteria, Eukarya, photosynthesis and atmospheric concentrations of O2, etc II. Endosymbiosis and horizontal gene transfer: what is the impact of endosymbiosis (in our case mostly the plastids) on the evolution and ecology of the eukaryotes. How did this shape the evolution of the Eukarya- both primary and secondary endosymbiosis. This topic clearly relates to Cladistics and to Adaptation. Practice & Examples Know which phyla have primary vs. secondary endosymbiosis? Distinguish the origin of the chloroplast; cyanobacteria, green algae, red algae? What is the evidence? Can you distinguish between the host cell’s phylogeny vs. -
Tetrapod Phylogeny
© J989 Elsevier Science Publishers B. V. (Biomédical Division) The Hierarchy of Life B. Fernholm, K. Bremer and H. Jörnvall, editors 337 CHAPTER 25 Tetrapod phylogeny JACQUES GAUTHIER', DAVID CANNATELLA^, KEVIN DE QUEIROZ^, ARNOLD G. KLUGE* and TIMOTHY ROWE^ ' Deparlmenl qf Herpelology, California Academy of Sciences, San Francisco, CA 94118, U.S.A., ^Museum of Natural Sciences and Department of Biology, Louisiana State University, Baton Rouge, LA 70803, U.S.A., ^Department of ^oology and Museum of Vertebrate ^oology. University of California, Berkeley, CA 94720, U.S.A., 'Museum of ^oology and Department of Biology, University of Michigan, Ann Arbor, MI 48109, U.S.A. and ^Department of Geological Sciences, University of Texas, Austin, TX 78713, U.S.A. Introduction Early sarcopterygians were aquatic, but from the latter part of the Carboniferous on- ward that group has been dominated by terrestrial forms commonly known as the tet- rapods. Fig. 1 illustrates relationships among extant Tetrápoda [1-4J. As the clado- grams in Figs. 2•20 demonstrate, however, extant groups represent only a small part of the taxonomic and morphologic diversity of Tetrápoda. We hope to convey some appreciation for the broad outlines of tetrapod evolution during its 300+ million year history from late Mississippian to Recent times. In doing so, we summarize trees de- rived from the distribution of over 972 characters among 83 terminal taxa of Tetrápo- da. More than 90% of the terminal taxa we discuss are extinct, but all of the subter- minal taxa are represented in the extant biota. This enables us to emphasize the origins of living tetrapod groups while giving due consideration to the diversity and antiquity of the clades of which they are a part.