Massive Increase in Visual Range Preceded the Origin of Terrestrial
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Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution
Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman A dissertation submitted in partial satisfaction of the requirements for the degree of Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology in the Graduate Division of the University of California, Berkeley Committee in charge: Dr. Bruce G. Baldwin, Chair Dr. John P. Huelsenbeck Dr. Brent D. Mishler Dr. Kipling W. Will Fall 2017 Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution Copyright 2017 by William Allen Freyman Abstract Phylogenetic Models Linking Speciation and Extinction to Chromosome and Mating System Evolution by William Allen Freyman Doctor of Philosophy in Integrative Biology and the Designated Emphasis in Computational and Genomic Biology University of California, Berkeley Dr. Bruce G. Baldwin, Chair Key evolutionary transitions have shaped the tree of life by driving the processes of spe- ciation and extinction. This dissertation aims to advance statistical and computational ap- proaches that model the timing and nature of these transitions over evolutionary trees. These methodological developments in phylogenetic comparative biology enable formal, model- based, statistical examinations of the macroevolutionary consequences of trait evolution. Chapter 1 presents computational tools for data mining the large-scale molecular sequence datasets needed for comparative phylogenetic analyses. I describe a novel metric, the miss- ing sequence decisiveness score (MSDS), which assesses the phylogenetic decisiveness of a matrix given the pattern of missing sequence data. In Chapter 2, I introduce a class of phylogenetic models of chromosome number evolution that accommodate both anagenetic and cladogenetic change. -
Fish Locomotion: Recent Advances and New Directions
MA07CH22-Lauder ARI 6 November 2014 13:40 Fish Locomotion: Recent Advances and New Directions George V. Lauder Museum of Comparative Zoology, Harvard University, Cambridge, Massachusetts 02138; email: [email protected] Annu. Rev. Mar. Sci. 2015. 7:521–45 Keywords First published online as a Review in Advance on swimming, kinematics, hydrodynamics, robotics September 19, 2014 The Annual Review of Marine Science is online at Abstract marine.annualreviews.org Access provided by Harvard University on 01/07/15. For personal use only. Research on fish locomotion has expanded greatly in recent years as new This article’s doi: approaches have been brought to bear on a classical field of study. Detailed Annu. Rev. Marine. Sci. 2015.7:521-545. Downloaded from www.annualreviews.org 10.1146/annurev-marine-010814-015614 analyses of patterns of body and fin motion and the effects of these move- Copyright c 2015 by Annual Reviews. ments on water flow patterns have helped scientists understand the causes All rights reserved and effects of hydrodynamic patterns produced by swimming fish. Recent developments include the study of the center-of-mass motion of swimming fish and the use of volumetric imaging systems that allow three-dimensional instantaneous snapshots of wake flow patterns. The large numbers of swim- ming fish in the oceans and the vorticity present in fin and body wakes sup- port the hypothesis that fish contribute significantly to the mixing of ocean waters. New developments in fish robotics have enhanced understanding of the physical principles underlying aquatic propulsion and allowed intriguing biological features, such as the structure of shark skin, to be studied in detail. -
The Polyp and the Medusa Life on the Move
The Polyp and the Medusa Life on the Move Millions of years ago, unlikely pioneers sparked a revolution. Cnidarians set animal life in motion. So much of what we take for granted today began with Cnidarians. FROM SHAPE OF LIFE The Polyp and the Medusa Life on the Move Take a moment to follow these instructions: Raise your right hand in front of your eyes. Make a fist. Make the peace sign with your first and second fingers. Make a fist again. Open your hand. Read the next paragraph. What you just did was exhibit a trait we associate with all animals, a trait called, quite simply, movement. And not only did you just move your hand, but you moved it after passing the idea of movement through your brain and nerve cells to command the muscles in your hand to obey. To do this, your body needs muscles to move and nerves to transmit and coordinate movement, whether voluntary or involuntary. The bit of business involved in making fists and peace signs is pretty complex behavior, but it pales by comparison with the suites of thought and movement associated with throwing a curve ball, walking, swimming, dancing, breathing, landing an airplane, running down prey, or fleeing a predator. But whether by thought or instinct, you and all animals except sponges have the ability to move and to carry out complex sequences of movement called behavior. In fact, movement is such a basic part of being an animal that we tend to define animalness as having the ability to move and behave. -
Genetic Change and Rates of Cladogenesis
GENETIC CHANGE AND RATES OF CLADOGENESIS JOHN C. AVISE* AND FRANCISCO J. AYALA Depariment of Genetics, University of Californiu, Davis, California 95616 Manuscript received May 12, 1975 Revised copy received July 28, 1975 ABSTRACT Models are introduced which predict ratios of mean levels of genetic divergence in species-rich versus species-poor phylads under two competing assumptions: (1) genetic differentiation is a function of time, unrelated to the number of cladogenetic events and (2) genetic differentiation is proportional to the number of speciation events in the group. The models are simple, general, and biologically real, but not precise. They lead to qualitatively distinct predic- tions about levels of genetic divergence depending upon the relationship between rates of speciation and amount of genetic change. When genetic dis- tance between species is a function of time, mean genetic distances in speciose and depauperate phylads of equal evolutionary age are very similar. On the contrary, when genetic distance is a function of the number of speciations in the history of a phylad, the ratio of mean genetic distances separating species in speciose versus depauperate phylads is greater than one, and increases rapidly as the frequency of speciations in one group relative to the other increases. The models may be tested with data from natural populations to assess (1) possible correlations between rates of anagenesis and cladogenesis and (2) the amount of genetic differentiation accompanying the speciation process. The data collected in electrophoretic surveys and other kinds of studies can be used to test the predictions of the models. For this purpose genetic distances need to be measured in speciose and depauperate phylads of equal evolutionary age. -
Amphibious Fishes: Terrestrial Locomotion, Performance, Orientation, and Behaviors from an Applied Perspective by Noah R
AMPHIBIOUS FISHES: TERRESTRIAL LOCOMOTION, PERFORMANCE, ORIENTATION, AND BEHAVIORS FROM AN APPLIED PERSPECTIVE BY NOAH R. BRESSMAN A Dissertation Submitted to the Graduate Faculty of WAKE FOREST UNIVESITY GRADUATE SCHOOL OF ARTS AND SCIENCES in Partial Fulfillment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY Biology May 2020 Winston-Salem, North Carolina Approved By: Miriam A. Ashley-Ross, Ph.D., Advisor Alice C. Gibb, Ph.D., Chair T. Michael Anderson, Ph.D. Bill Conner, Ph.D. Glen Mars, Ph.D. ACKNOWLEDGEMENTS I would like to thank my adviser Dr. Miriam Ashley-Ross for mentoring me and providing all of her support throughout my doctoral program. I would also like to thank the rest of my committee – Drs. T. Michael Anderson, Glen Marrs, Alice Gibb, and Bill Conner – for teaching me new skills and supporting me along the way. My dissertation research would not have been possible without the help of my collaborators, Drs. Jeff Hill, Joe Love, and Ben Perlman. Additionally, I am very appreciative of the many undergraduate and high school students who helped me collect and analyze data – Mark Simms, Tyler King, Caroline Horne, John Crumpler, John S. Gallen, Emily Lovern, Samir Lalani, Rob Sheppard, Cal Morrison, Imoh Udoh, Harrison McCamy, Laura Miron, and Amaya Pitts. I would like to thank my fellow graduate student labmates – Francesca Giammona, Dan O’Donnell, MC Regan, and Christine Vega – for their support and helping me flesh out ideas. I am appreciative of Dr. Ryan Earley, Dr. Bruce Turner, Allison Durland Donahou, Mary Groves, Tim Groves, Maryland Department of Natural Resources, UF Tropical Aquaculture Lab for providing fish, animal care, and lab space throughout my doctoral research. -
Lineages, Splits and Divergence Challenge Whether the Terms Anagenesis and Cladogenesis Are Necessary
Biological Journal of the Linnean Society, 2015, , – . With 2 figures. Lineages, splits and divergence challenge whether the terms anagenesis and cladogenesis are necessary FELIX VAUX*, STEVEN A. TREWICK and MARY MORGAN-RICHARDS Ecology Group, Institute of Agriculture and Environment, Massey University, Palmerston North, New Zealand Received 3 June 2015; revised 22 July 2015; accepted for publication 22 July 2015 Using the framework of evolutionary lineages to separate the process of evolution and classification of species, we observe that ‘anagenesis’ and ‘cladogenesis’ are unnecessary terms. The terms have changed significantly in meaning over time, and current usage is inconsistent and vague across many different disciplines. The most popular definition of cladogenesis is the splitting of evolutionary lineages (cessation of gene flow), whereas anagenesis is evolutionary change between splits. Cladogenesis (and lineage-splitting) is also regularly made synonymous with speciation. This definition is misleading as lineage-splitting is prolific during evolution and because palaeontological studies provide no direct estimate of gene flow. The terms also fail to incorporate speciation without being arbitrary or relative, and the focus upon lineage-splitting ignores the importance of divergence, hybridization, extinction and informative value (i.e. what is helpful to describe as a taxon) for species classification. We conclude and demonstrate that evolution and species diversity can be considered with greater clarity using simpler, more transparent terms than anagenesis and cladogenesis. Describing evolution and taxonomic classification can be straightforward, and there is no need to ‘make words mean so many different things’. © 2015 The Linnean Society of London, Biological Journal of the Linnean Society, 2015, 00, 000–000. -
Tetrapod Biostratigraphy and Biochronology of the Triassic–Jurassic Transition on the Southern Colorado Plateau, USA
Palaeogeography, Palaeoclimatology, Palaeoecology 244 (2007) 242–256 www.elsevier.com/locate/palaeo Tetrapod biostratigraphy and biochronology of the Triassic–Jurassic transition on the southern Colorado Plateau, USA Spencer G. Lucas a,⁎, Lawrence H. Tanner b a New Mexico Museum of Natural History, 1801 Mountain Rd. N.W., Albuquerque, NM 87104-1375, USA b Department of Biology, Le Moyne College, 1419 Salt Springs Road, Syracuse, NY 13214, USA Received 15 March 2006; accepted 20 June 2006 Abstract Nonmarine fluvial, eolian and lacustrine strata of the Chinle and Glen Canyon groups on the southern Colorado Plateau preserve tetrapod body fossils and footprints that are one of the world's most extensive tetrapod fossil records across the Triassic– Jurassic boundary. We organize these tetrapod fossils into five, time-successive biostratigraphic assemblages (in ascending order, Owl Rock, Rock Point, Dinosaur Canyon, Whitmore Point and Kayenta) that we assign to the (ascending order) Revueltian, Apachean, Wassonian and Dawan land-vertebrate faunachrons (LVF). In doing so, we redefine the Wassonian and the Dawan LVFs. The Apachean–Wassonian boundary approximates the Triassic–Jurassic boundary. This tetrapod biostratigraphy and biochronology of the Triassic–Jurassic transition on the southern Colorado Plateau confirms that crurotarsan extinction closely corresponds to the end of the Triassic, and that a dramatic increase in dinosaur diversity, abundance and body size preceded the end of the Triassic. © 2006 Elsevier B.V. All rights reserved. Keywords: Triassic–Jurassic boundary; Colorado Plateau; Chinle Group; Glen Canyon Group; Tetrapod 1. Introduction 190 Ma. On the southern Colorado Plateau, the Triassic– Jurassic transition was a time of significant changes in the The Four Corners (common boundary of Utah, composition of the terrestrial vertebrate (tetrapod) fauna. -
Animal Origins and the Evolution of Body Plans 621
Animal Origins and the Evolution 32 of Body Plans In 1822, nearly forty years before Darwin wrote The Origin of Species, a French naturalist, Étienne Geoffroy Saint-Hilaire, was examining a lob- ster. He noticed that when he turned the lobster upside down and viewed it with its ventral surface up, its central nervous system was located above its digestive tract, which in turn was located above its heart—the same relative positions these systems have in mammals when viewed dorsally. His observations led Geoffroy to conclude that the differences between arthropods (such as lobsters) and vertebrates (such as mammals) could be explained if the embryos of one of those groups were inverted during development. Geoffroy’s suggestion was regarded as preposterous at the time and was largely dismissed until recently. However, the discovery of two genes that influence a sys- tem of extracellular signals involved in development has lent new support to Geof- froy’s seemingly outrageous hypothesis. Genes that Control Development A A vertebrate gene called chordin helps to establish cells on one side of the embryo human and a lobster carry similar genes that control the development of the body as dorsal and on the other as ventral. A probably homologous gene in fruit flies, called axis, but these genes position their body sog, acts in a similar manner, but has the opposite effect. Fly cells where sog is active systems inversely. A lobster’s nervous sys- become ventral, whereas vertebrate cells where chordin is active become dorsal. How- tem runs up its ventral (belly) surface, whereas a vertebrate’s runs down its dorsal ever, when sog mRNA is injected into an embryo (back) surface. -
Lecture 6 – Integument ‐ Scale • a Scale Is a Small Rigid Plate That Grows out of an Animal’ S Skin to Provide Protection
Lecture 6 – Integument ‐ Scale • A scale is a small rigid plate that grows out of an animal’s skin to provide protection. • Scales are quite common and have evolved multiple times with varying structure and function. • Scales are generally classified as part of an organism's integumentary system. • There are various types of scales according to shape and to class of animal. • Although the meat and organs of some species of fish are edible by humans, the scales are usually not eaten. Scale structure • Fish scales Fish scales are dermally derived, specifically in the mesoderm. This fact distinguishes them from reptile scales paleontologically. Genetically, the same genes involved in tooth and hair development in mammals are also involved in scale development. Earliest scales – heavily armoured thought to be like Chondrichthyans • Fossil fishes • ion reservoir • osmotic control • protection • Weighting Scale function • Primary function is protection (armor plating) • Hydrodynamics Scales are composed of four basic compounds: ((gmoving from inside to outside in that order) • Lamellar bone • Vascular or spongy bone • Dentine (dermis) and is always associated with enamel. • Acellular enamel (epidermis) • The scales of fish lie in pockets in the dermis and are embeded in connective tissue. • Scales do not stick out of a fish but are covered by the Epithelial layer. • The scales overlap and so form a protective flexible armor capable of withstanding blows and bumping. • In some catfishes and seahorses, scales are replaced by bony plates. • In some other species there are no scales at all. Evolution of scales Placoid scale – (Chondricthyes – cartilagenous fishes) develop in dermis but protrude through epidermis. -
Giraffe Stature and Neck Elongation: Vigilance As an Evolutionary Mechanism
biology Review Giraffe Stature and Neck Elongation: Vigilance as an Evolutionary Mechanism Edgar M. Williams Faculty of Life Sciences and Education, University of South Wales, Wales CF37 1DL, UK; [email protected]; Tel.: +44-1443-483-893 Academic Editor: Chris O’Callaghan Received: 1 August 2016; Accepted: 7 September 2016; Published: 12 September 2016 Abstract: Giraffe (Giraffa camelopardalis), with their long neck and legs, are unique amongst mammals. How these features evolved is a matter of conjecture. The two leading ideas are the high browse and the sexual-selection hypotheses. While both explain many of the characteristics and the behaviour of giraffe, neither is fully supported by the available evidence. The extended viewing horizon afforded by increased height and a need to maintain horizon vigilance, as a mechanism favouring the evolution of increased height is reviewed. In giraffe, vigilance of predators whilst feeding and drinking are important survival factors, as is the ability to interact with immediate herd members, young and male suitors. The evidence regarding giraffe vigilance behaviour is sparse and suggests that over-vigilance has a negative cost, serving as a distraction to feeding. In woodland savannah, increased height allows giraffe to see further, allowing each giraffe to increase the distance between its neighbours while browsing. Increased height allows the giraffe to see the early approach of predators, as well as bull males. It is postulated that the wider panorama afforded by an increase in height and longer neck has improved survival via allowing giraffe to browse safely over wider areas, decreasing competition within groups and with other herbivores. -
Morphology, Phylogeny, and Evolution of Diadectidae (Cotylosauria: Diadectomorpha)
Morphology, Phylogeny, and Evolution of Diadectidae (Cotylosauria: Diadectomorpha) by Richard Kissel A thesis submitted in conformity with the requirements for the degree of doctor of philosophy Graduate Department of Ecology & Evolutionary Biology University of Toronto © Copyright by Richard Kissel 2010 Morphology, Phylogeny, and Evolution of Diadectidae (Cotylosauria: Diadectomorpha) Richard Kissel Doctor of Philosophy Graduate Department of Ecology & Evolutionary Biology University of Toronto 2010 Abstract Based on dental, cranial, and postcranial anatomy, members of the Permo-Carboniferous clade Diadectidae are generally regarded as the earliest tetrapods capable of processing high-fiber plant material; presented here is a review of diadectid morphology, phylogeny, taxonomy, and paleozoogeography. Phylogenetic analyses support the monophyly of Diadectidae within Diadectomorpha, the sister-group to Amniota, with Limnoscelis as the sister-taxon to Tseajaia + Diadectidae. Analysis of diadectid interrelationships of all known taxa for which adequate specimens and information are known—the first of its kind conducted—positions Ambedus pusillus as the sister-taxon to all other forms, with Diadectes sanmiguelensis, Orobates pabsti, Desmatodon hesperis, Diadectes absitus, and (Diadectes sideropelicus + Diadectes tenuitectes + Diasparactus zenos) representing progressively more derived taxa in a series of nested clades. In light of these results, it is recommended herein that the species Diadectes sanmiguelensis be referred to the new genus -
Early Tetrapod Relationships Revisited
Biol. Rev. (2003), 78, pp. 251–345. f Cambridge Philosophical Society 251 DOI: 10.1017/S1464793102006103 Printed in the United Kingdom Early tetrapod relationships revisited MARCELLO RUTA1*, MICHAEL I. COATES1 and DONALD L. J. QUICKE2 1 The Department of Organismal Biology and Anatomy, The University of Chicago, 1027 East 57th Street, Chicago, IL 60637-1508, USA ([email protected]; [email protected]) 2 Department of Biology, Imperial College at Silwood Park, Ascot, Berkshire SL57PY, UK and Department of Entomology, The Natural History Museum, Cromwell Road, London SW75BD, UK ([email protected]) (Received 29 November 2001; revised 28 August 2002; accepted 2 September 2002) ABSTRACT In an attempt to investigate differences between the most widely discussed hypotheses of early tetrapod relation- ships, we assembled a new data matrix including 90 taxa coded for 319 cranial and postcranial characters. We have incorporated, where possible, original observations of numerous taxa spread throughout the major tetrapod clades. A stem-based (total-group) definition of Tetrapoda is preferred over apomorphy- and node-based (crown-group) definitions. This definition is operational, since it is based on a formal character analysis. A PAUP* search using a recently implemented version of the parsimony ratchet method yields 64 shortest trees. Differ- ences between these trees concern: (1) the internal relationships of aı¨stopods, the three selected species of which form a trichotomy; (2) the internal relationships of embolomeres, with Archeria