Early Fossil Record of Euarthropoda and the Cambrian Explosion
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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. -
Decoupled Evolution of Soft and Hard Substrate Communities During the Cambrian Explosion and Great Ordovician Biodiversification Event
Decoupled evolution of soft and hard substrate communities during the Cambrian Explosion and Great Ordovician Biodiversification Event Luis A. Buatoisa,1, Maria G. Mánganoa, Ricardo A. Oleab, and Mark A. Wilsonc aDepartment of Geological Sciences, University of Saskatchewan, Saskatoon, SK, Canada S7N 5E2; bEastern Energy Resources Science Center, US Geological Survey, Reston, VA 20192; and cDepartment of Geology, The College of Wooster, Wooster, OH 44691 Edited by Steven M. Holland, University of Georgia, Athens, GA, and accepted by Editorial Board Member David Jablonski May 6, 2016 (received for review November 21, 2015) Contrasts between the Cambrian Explosion (CE) and the Great shed light on the natures of both radiations. Because there is still Ordovician Biodiversification Event (GOBE) have long been recog- controversy regarding Sepkoski’s nonstandardized curves of nized. Whereas the vast majority of body plans were established Phanerozoic taxonomic diversity (13–15), a rarefaction analysis as a result of the CE, taxonomic increases during the GOBE were was performed in an attempt to standardize diversity data. The manifested at lower taxonomic levels. Assessing changes of ichno- aims of this paper are to document the contrasting ichnodiversity diversity and ichnodisparity as a result of these two evolutionary and ichnodisparity trajectories in soft and hard substrate com- events may shed light on the dynamics of both radiations. The early munities during these two evolutionary events and to discuss the Cambrian (series 1 and 2) displayed a dramatic increase in ichnodi- possible underlying causes of this decoupled evolution. versity and ichnodisparity in softground communities. In contrast to this evolutionary explosion in bioturbation structures, only a few Results Cambrian bioerosion structures are known. -
The Ediacaran Frondose Fossil Arborea from the Shibantan Limestone of South China
Journal of Paleontology, 94(6), 2020, p. 1034–1050 Copyright © 2020, The Paleontological Society. This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/ licenses/by/4.0/), which permits unrestricted re-use, distribution, and reproduction in any medium, provided the original work is properly cited. 0022-3360/20/1937-2337 doi: 10.1017/jpa.2020.43 The Ediacaran frondose fossil Arborea from the Shibantan limestone of South China Xiaopeng Wang,1,3 Ke Pang,1,4* Zhe Chen,1,4* Bin Wan,1,4 Shuhai Xiao,2 Chuanming Zhou,1,4 and Xunlai Yuan1,4,5 1State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Palaeoenvironment, Chinese Academy of Sciences, Nanjing 210008, China <[email protected]><[email protected]> <[email protected]><[email protected]><[email protected]><[email protected]> 2Department of Geosciences, Virginia Tech, Blacksburg, Virginia 24061, USA <[email protected]> 3University of Science and Technology of China, Hefei 230026, China 4University of Chinese Academy of Sciences, Beijing 100049, China 5Center for Research and Education on Biological Evolution and Environment, Nanjing University, Nanjing 210023, China Abstract.—Bituminous limestone of the Ediacaran Shibantan Member of the Dengying Formation (551–539 Ma) in the Yangtze Gorges area contains a rare carbonate-hosted Ediacara-type macrofossil assemblage. This assemblage is domi- nated by the tubular fossil Wutubus Chen et al., 2014 and discoidal fossils, e.g., Hiemalora Fedonkin, 1982 and Aspidella Billings, 1872, but frondose organisms such as Charnia Ford, 1958, Rangea Gürich, 1929, and Arborea Glaessner and Wade, 1966 are also present. -
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. -
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. -
The Geologic Time Scale Is the Eon
Exploring Geologic Time Poster Illustrated Teacher's Guide #35-1145 Paper #35-1146 Laminated Background Geologic Time Scale Basics The history of the Earth covers a vast expanse of time, so scientists divide it into smaller sections that are associ- ated with particular events that have occurred in the past.The approximate time range of each time span is shown on the poster.The largest time span of the geologic time scale is the eon. It is an indefinitely long period of time that contains at least two eras. Geologic time is divided into two eons.The more ancient eon is called the Precambrian, and the more recent is the Phanerozoic. Each eon is subdivided into smaller spans called eras.The Precambrian eon is divided from most ancient into the Hadean era, Archean era, and Proterozoic era. See Figure 1. Precambrian Eon Proterozoic Era 2500 - 550 million years ago Archaean Era 3800 - 2500 million years ago Hadean Era 4600 - 3800 million years ago Figure 1. Eras of the Precambrian Eon Single-celled and simple multicelled organisms first developed during the Precambrian eon. There are many fos- sils from this time because the sea-dwelling creatures were trapped in sediments and preserved. The Phanerozoic eon is subdivided into three eras – the Paleozoic era, Mesozoic era, and Cenozoic era. An era is often divided into several smaller time spans called periods. For example, the Paleozoic era is divided into the Cambrian, Ordovician, Silurian, Devonian, Carboniferous,and Permian periods. Paleozoic Era Permian Period 300 - 250 million years ago Carboniferous Period 350 - 300 million years ago Devonian Period 400 - 350 million years ago Silurian Period 450 - 400 million years ago Ordovician Period 500 - 450 million years ago Cambrian Period 550 - 500 million years ago Figure 2. -
1 Integrative Biology 200 "PRINCIPLES OF
Integrative Biology 200 "PRINCIPLES OF PHYLOGENETICS" Spring 2018 University of California, Berkeley B.D. Mishler March 14, 2018. Classification II: Phylogenetic taxonomy including incorporation of fossils; PhyloCode I. Phylogenetic Taxonomy - the argument for rank-free classification A number of recent calls have been made for the reformation of the Linnaean hierarchy (e.g., De Queiroz & Gauthier, 1992). These authors have emphasized that the existing system is based in a non-evolutionary world-view; the roots of the Linnaean hierarchy are in a specially- created world-view. Perhaps the idea of fixed, comparable ranks made some sense under that view, but under an evolutionary world view they don't make sense. There are several problems with the current nomenclatorial system: 1. The current system, with its single type for a name, cannot be used to precisely name a clade. E.g., you may name a family based on a certain type specimen, and even if you were clear about what node you meant to name in your original publication, the exact phylogenetic application of your name would not be clear subsequently, after new clades are added. 2. There are not nearly enough ranks to name the thousands of levels of monophyletic groups in the tree of life. Therefore people are increasingly using informal rank-free names for higher- level nodes, but without any clear, formal specification of what clade is meant. 3. Most aspects of the current code, including priority, revolve around the ranks, which leads to instability of usage. For example, when a change in relationships is discovered, several names often need to be changed to adjust, including those of groups whose circumscription has not changed. -
The Cambrian Explosion: a Big Bang in the Evolution of Animals
The Cambrian Explosion A Big Bang in the Evolution of Animals Very suddenly, and at about the same horizon the world over, life showed up in the rocks with a bang. For most of Earth’s early history, there simply was no fossil record. Only recently have we come to discover otherwise: Life is virtually as old as the planet itself, and even the most ancient sedimentary rocks have yielded fossilized remains of primitive forms of life. NILES ELDREDGE, LIFE PULSE, EPISODES FROM THE STORY OF THE FOSSIL RECORD The Cambrian Explosion: A Big Bang in the Evolution of Animals Our home planet coalesced into a sphere about four-and-a-half-billion years ago, acquired water and carbon about four billion years ago, and less than a billion years later, according to microscopic fossils, organic cells began to show up in that inert matter. Single-celled life had begun. Single cells dominated life on the planet for billions of years before multicellular animals appeared. Fossils from 635,000 million years ago reveal fats that today are only produced by sponges. These biomarkers may be the earliest evidence of multi-cellular animals. Soon after we can see the shadowy impressions of more complex fans and jellies and things with no names that show that animal life was in an experimental phase (called the Ediacran period). Then suddenly, in the relatively short span of about twenty million years (given the usual pace of geologic time), life exploded in a radiation of abundance and diversity that contained the body plans of almost all the animals we know today. -
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 Origin and Evolution of Arthropods Graham E
INSIGHT REVIEW NATURE|Vol 457|12 February 2009|doi:10.1038/nature07890 The origin and evolution of arthropods Graham E. Budd1 & Maximilian J. Telford2 The past two decades have witnessed profound changes in our understanding of the evolution of arthropods. Many of these insights derive from the adoption of molecular methods by systematists and developmental biologists, prompting a radical reordering of the relationships among extant arthropod classes and their closest non-arthropod relatives, and shedding light on the developmental basis for the origins of key characteristics. A complementary source of data is the discovery of fossils from several spectacular Cambrian faunas. These fossils form well-characterized groupings, making the broad pattern of Cambrian arthropod systematics increasingly consensual. The arthropods are one of the most familiar and ubiquitous of all ani- Arthropods are monophyletic mal groups. They have far more species than any other phylum, yet Arthropods encompass a great diversity of animal taxa known from the living species are merely the surviving branches of a much greater the Cambrian to the present day. The four living groups — myriapods, diversity of extinct forms. One group of crustacean arthropods, the chelicerates, insects and crustaceans — are known collectively as the barnacles, was studied extensively by Charles Darwin. But the origins Euarthropoda. They are united by a set of distinctive features, most and the evolution of arthropods in general, embedded in what is now notably the clear segmentation of their bodies, a sclerotized cuticle and known as the Cambrian explosion, were a source of considerable con- jointed appendages. Even so, their great diversity has led to consider- cern to him, and he devoted a substantial and anxious section of On able debate over whether they had single (monophyletic) or multiple the Origin of Species1 to discussing this subject: “For instance, I cannot (polyphyletic) origins from a soft-bodied, legless ancestor. -
Durham Research Online
Durham Research Online Deposited in DRO: 23 May 2017 Version of attached le: Accepted Version Peer-review status of attached le: Peer-reviewed Citation for published item: Betts, Marissa J. and Paterson, John R. and Jago, James B. and Jacquet, Sarah M. and Skovsted, Christian B. and Topper, Timothy P. and Brock, Glenn A. (2017) 'Global correlation of the early Cambrian of South Australia : shelly fauna of the Dailyatia odyssei Zone.', Gondwana research., 46 . pp. 240-279. Further information on publisher's website: https://doi.org/10.1016/j.gr.2017.02.007 Publisher's copyright statement: c 2017 This manuscript version is made available under the CC-BY-NC-ND 4.0 license http://creativecommons.org/licenses/by-nc-nd/4.0/ Additional information: Use policy The full-text may be used and/or reproduced, and given to third parties in any format or medium, without prior permission or charge, for personal research or study, educational, or not-for-prot purposes provided that: • a full bibliographic reference is made to the original source • a link is made to the metadata record in DRO • the full-text is not changed in any way The full-text must not be sold in any format or medium without the formal permission of the copyright holders. Please consult the full DRO policy for further details. Durham University Library, Stockton Road, Durham DH1 3LY, United Kingdom Tel : +44 (0)191 334 3042 | Fax : +44 (0)191 334 2971 https://dro.dur.ac.uk Accepted Manuscript Global correlation of the early Cambrian of South Australia: Shelly fauna of the Dailyatia odyssei Zone Marissa J. -
Page - Paleo Lab 06 - the Cambrian Explosion of Life
page - Paleo Lab 06 - The Cambrian Explosion of Life An Introduction to Index Fossils CLASSIFICATION AND TAXONOMY Geologists follow the lead of biologists in the classification and naming of organisms (taxonomy after taxon = name). Since its introduction early in the 18th century, the system devised by Linnaeus has been used to categorize organisms and to affix a formal name to each species. Major classification categories or groupings are listed below on the left with an example using the species of the common house cat to show how the system may be used: KINGDOM Animalia PHYLUM Chordata CLASS Mammalia ORDER Carnivora FAMILY Felidae GENUS Felis SPECIES domestica The basic unit of the system is the species, and each category above it includes the divisions below. A two part (binomial) formal designation for each species, following the scheme of Linnaeus, is composed of the capitalized name of the genus (plural = genera) followed by the uncapitalized name of the species (plural = species). Note that the binomial is printed in a special way (italics) to distinguish it. After at least 5000 years of domestication, man has drawn out of that species such a variety of traits through selection and cross-breeding that it may be more difficult to realize that all such cats belong to the same species than it is to recognize that they share the same genus with the lion (Felis leo), leopard (Felis pardus), jaguar (Felis onca), tiger (Felis tigris), and the cougar or puma (Felis concolor). All wildcats belong to the same genus but are classified in three separate species found in Europe, Africa, and the Americas (the ocelot), Felis sylvestris, F.