1 the Extended Evolutionary Synthesis: What Is the Debate About
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Toward an Extended Evolutionary Synthesis 10-13 July 2008
18th Altenberg Workshop in Theoretical Biology 2008 Toward an Extended Evolutionary Synthesis 10-13 July 2008 organized by Massimo Pigliucci and Gerd B. Müller Konrad Lorenz Institute for Evolution and Cognition Research Altenberg, Austria The topic More than 60 years have passed since the conceptual integration of several strands of evolutionary theory into what has come to be called the Modern Synthesis. Despite major advances since, in all methodological and disciplinary domains of biology, the Modern Synthesis framework has remained surprisingly static and is still regarded as the standard theoretical paradigm of evolutionary biology. But for some time now there have been calls for an expansion of the Synthesis framework through the integration of more recent achievements in evolutionary theory. The challenge for the present workshop is clear: How do we make sense, conceptually, of the astounding advances in biology since the 1940s, when the Modern Synthesis was taking shape? Not only have we witnessed the molecular revolution, from the discovery of the structure of DNA to the genomic era, we are also grappling with the increasing feeling – as reflected, for example, by the proliferation of “-omics” (proteomics, metabolomics, “interactomics,” and even “phenomics”) – that we just don't have the theoretical and analytical tools necessary to make sense of the bewildering diversity and complexity of living organisms. By contrast, in organismal biology, a number of new approaches have opened up new theoretical horizons, with new possibilities -
On the Interaction of Function, Constraint and Complexity in Evolutionary Systems
UNIVERSITY OF SOUTHAMPTON FACULTY OF PHYSICAL SCIENCES AND ENGINEERING ELECTRONICS AND COMPUTER SCIENCE Volume 1 of 1 On The Interaction Of Function, Constraint And Complexity In Evolutionary Systems by Adam Paul Davies Thesis for the degree of Doctor of Philosophy April 2014 UNIVERSITY OF SOUTHAMPTON ABSTRACT FACULTY OF PHYSICAL SCIENCES AND ENGINEERING Electronics and Computer Science Doctor of Philosophy ON THE INTERACTION OF FUNCTION, CONSTRAINT AND COMPLEXITY IN EVOLUTIONARY SYSTEMS by Adam Paul Davies Biological evolution contains a general trend of increasing complexity of the most complex organisms. But artificial evolution experiments based on the mechanisms described in the current theory generally fail to reproduce this trend; instead, they commonly show systematic trends of complexity minimisation. In this dissertation we seek evolutionary mechanisms that can explain these apparently conflicting observations. To achieve this we use a reverse engineering approach by building computational simulations of evolution. One highlighted problem is that even if complexity is beneficial, evolutionary simulations struggle with apparent roadblocks that prevent them from scaling to complexity. Another is that even without roadblocks, it is not clear what drives evolution to become more complex at all. With respect to the former, a key roadblock is how to evolve ‘irreducibly complex’ or ‘non- decomposable’ functions. Evidence from biological evolution suggests a common way to achieve this is by combining existing functions – termed ‘tinkering’ or ‘building block evolution’. But in simulation this approach generally fails to scale across multiple levels of organisation in a recursive manner. We provide a model that identifies the problem hindering recursive evolution as increasing ‘burden’ in the form of ‘internal selection’ as joined functions become more complex. -
Microevolution and the Genetics of Populations Microevolution Refers to Varieties Within a Given Type
Chapter 8: Evolution Lesson 8.3: Microevolution and the Genetics of Populations Microevolution refers to varieties within a given type. Change happens within a group, but the descendant is clearly of the same type as the ancestor. This might better be called variation, or adaptation, but the changes are "horizontal" in effect, not "vertical." Such changes might be accomplished by "natural selection," in which a trait within the present variety is selected as the best for a given set of conditions, or accomplished by "artificial selection," such as when dog breeders produce a new breed of dog. Lesson Objectives ● Distinguish what is microevolution and how it affects changes in populations. ● Define gene pool, and explain how to calculate allele frequencies. ● State the Hardy-Weinberg theorem ● Identify the five forces of evolution. Vocabulary ● adaptive radiation ● gene pool ● migration ● allele frequency ● genetic drift ● mutation ● artificial selection ● Hardy-Weinberg theorem ● natural selection ● directional selection ● macroevolution ● population genetics ● disruptive selection ● microevolution ● stabilizing selection ● gene flow Introduction Darwin knew that heritable variations are needed for evolution to occur. However, he knew nothing about Mendel’s laws of genetics. Mendel’s laws were rediscovered in the early 1900s. Only then could scientists fully understand the process of evolution. Microevolution is how individual traits within a population change over time. In order for a population to change, some things must be assumed to be true. In other words, there must be some sort of process happening that causes microevolution. The five ways alleles within a population change over time are natural selection, migration (gene flow), mating, mutations, or genetic drift. -
Emanuele Serrelli Nathalie Gontier Editors Explanation, Interpretation
Interdisciplinary Evolution Research 2 Emanuele Serrelli Nathalie Gontier Editors Macroevolution Explanation, Interpretation and Evidence Interdisciplinary Evolution Research Volume 2 Series editors Nathalie Gontier, Lisbon, Portugal Olga Pombo, Lisbon, Portugal [email protected] About the Series The time when only biologists studied evolution has long since passed. Accepting evolution requires us to come to terms with the fact that everything that exists must be the outcome of evolutionary processes. Today, a wide variety of academic disciplines are therefore confronted with evolutionary problems, ranging from physics and medicine, to linguistics, anthropology and sociology. Solving evolutionary problems also necessitates an inter- and transdisciplinary approach, which is why the Modern Synthesis is currently extended to include drift theory, symbiogenesis, lateral gene transfer, hybridization, epigenetics and punctuated equilibria theory. The series Interdisciplinary Evolution Research aims to provide a scholarly platform for the growing demand to examine specific evolutionary problems from the perspectives of multiple disciplines. It does not adhere to one specific academic field, one specific school of thought, or one specific evolutionary theory. Rather, books in the series thematically analyze how a variety of evolutionary fields and evolutionary theories provide insights into specific, well-defined evolutionary problems of life and the socio-cultural domain. Editors-in-chief of the series are Nathalie Gontier and Olga Pombo. The -
Soft Inheritance: Challenging the Modern Synthesis
Genetics and Molecular Biology, 31, 2, 389-395 (2008) Copyright © 2008, Sociedade Brasileira de Genética. Printed in Brazil www.sbg.org.br Review Article Soft inheritance: Challenging the Modern Synthesis Eva Jablonka1 and Marion J. Lamb2 1The Cohn Institute for the History and Philosophy of Science and Ideas, Tel-Aviv University, Tel-Aviv, Israel. 211 Fernwood, Clarence Road, London, United Kingdom. Abstract This paper presents some of the recent challenges to the Modern Synthesis of evolutionary theory, which has domi- nated evolutionary thinking for the last sixty years. The focus of the paper is the challenge of soft inheritance - the idea that variations that arise during development can be inherited. There is ample evidence showing that phenotypic variations that are independent of variations in DNA sequence, and targeted DNA changes that are guided by epigenetic control systems, are important sources of hereditary variation, and hence can contribute to evolutionary changes. Furthermore, under certain conditions, the mechanisms underlying epigenetic inheritance can also lead to saltational changes that reorganize the epigenome. These discoveries are clearly incompatible with the tenets of the Modern Synthesis, which denied any significant role for Lamarckian and saltational processes. In view of the data that support soft inheritance, as well as other challenges to the Modern Synthesis, it is concluded that that synthesis no longer offers a satisfactory theoretical framework for evolutionary biology. Key words: epigenetic inheritance, hereditary variation, Lamarckism, macroevolution, microevolution. Received: March 18, 2008; Accepted: March 19, 2008. Introduction 1. Heredity occurs through the transmission of germ- There are winds of change in evolutionary biology, line genes. -
The Yeast Sup35nm Domain Propagates As a Prion in Mammalian Cells Carmen Krammera, Dmitry Kryndushkinb, Michael H
The yeast Sup35NM domain propagates as a prion in mammalian cells Carmen Krammera, Dmitry Kryndushkinb, Michael H. Suhrec, Elisabeth Kremmerd, Andreas Hofmanne, Alexander Pfeifere, Thomas Scheibelc, Reed B. Wicknerb, Hermann M. Scha¨ tzla, and Ina Vorberga,1 aInstitute of Virology, Technische Universita¨t Mu¨ nchen, Trogerstrasse 30, 81675 Munich, Germany; bLaboratory of Biochemistry and Genetics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892; cLehrstuhl fu¨r Biomaterialien, Geba¨ude FAN/D, Universita¨t Bayreuth, Universita¨tsstrasse 30, 95447 Bayreuth, Germany; dInstitute of Molecular Immunology, Helmholtz Zentrum Mu¨nchen, Marchioninistrasse 25, 81377 Munich, Germany; and eInstitute of Pharmacology and Toxicology, Universita¨t Bonn, Reuterstrasse 2b, 53113 Bonn, Germany Contributed by Reed B. Wickner, November 13, 2008 (sent for review October 13, 2008) Prions are infectious, self-propagating amyloid-like protein aggre- for Sup35p aggregation (12). Stable maintenance of yeast prions gates of mammals and fungi. We have studied aggregation propen- relies on the activity of a variety of molecular chaperones (13). sities of a yeast prion domain in cell culture to gain insights into Deletion of the heat shock protein Hsp104 cures all known naturally general mechanisms of prion replication in mammalian cells. Here, we occurring yeast prions, strongly emphasizing its crucial role in prion report the artificial transmission of a yeast prion across a phylogenetic biogenesis (14). In concert with other heat shock factors, Hsp104 is kingdom. HA epitope-tagged yeast Sup35p prion domain NM was capable of disaggregating aberrant protein aggregates, and thereby stably expressed in murine neuroblastoma cells. Although cytosoli- likely generates prion seeds that can be passed on to daughter cells cally expressed NM-HA remained soluble, addition of fibrils of bac- (5, 15). -
Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt
Bryn Mawr College Scholarship, Research, and Creative Work at Bryn Mawr College Biology Faculty Research and Scholarship Biology 2013 Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt Gregory K. Davis Bryn Mawr College, [email protected] Caleb Trujillo Mark Terry Donald P. French See next page for additional authors Let us know how access to this document benefits ouy . Follow this and additional works at: http://repository.brynmawr.edu/bio_pubs Part of the Biology Commons Custom Citation Hiatt A, Davis GK, Trujillo C, Terry M, French DP, Price RM and Perez KE . "Getting to evo-devo: concepts and challenges for students learning evolutionary developmental biology". CBE-Life Sciences Education 12 (2013): 494-508. This paper is posted at Scholarship, Research, and Creative Work at Bryn Mawr College. http://repository.brynmawr.edu/bio_pubs/10 For more information, please contact [email protected]. Authors Anna Hiatt, Gregory K. Davis, Caleb Trujillo, Mark Terry, Donald P. French, Rebecca M. Price, and Kathryn E. Perez This article is available at Scholarship, Research, and Creative Work at Bryn Mawr College: http://repository.brynmawr.edu/ bio_pubs/10 CBE—Life Sciences Education Vol. 12, 494–508, Fall 2013 Article Getting to Evo-Devo: Concepts and Challenges for Students Learning Evolutionary Developmental Biology Anna Hiatt,*† Gregory K. Davis,‡ Caleb Trujillo,§ Mark Terry, Donald P. French,* Rebecca M. Price,¶ and Kathryn E. Perez** *Department of Zoology, Oklahoma -
Genetic Drift Lab
Genetic Drift Lab Small population sizes are more strongly influenced by random events than large populations. This means that the genetic frequencies of alleles in small populations are more likely to vary from one generation to the next from the original population. Often, genetic variation is rapidly lost in small populations and random events can create rapid genetic changes or microevolution in such cases. Populations may be subject to this random genetic drift (rapid movement of allele frequencies) by one of two events that reduce population size. 1. Bottlenecks - an incident reduces the overall number of individuals in a population and only a few survive to produce the next generation. Evidence of bottlenecks have been discovered in many species, such as cheetahs and the northern elephant seal. 2. Founder effect - a small number of individuals disperse and colonize new habitat, founding a new population. Organisms colonizing new habitats, such as islands, or migrating to new areas are also common. In both cases the surviving or founding individuals will often vary in genetic frequency from the parental populations (original sources). Also, small subsequent population size plays a big role in additional changes to the gene frequencies. I. Simulation of random events (coin tosses): Each student flips a coin 10 times. What are the expected number of heads for 10 flips? How many heads did you obtain for your 10 flips? _______ # students in your class ___________ # times heads appeared out of 10 trials for all students: 0 _____ 1 ______ 2 _______ 3 ______ 4 ______ 5 ______ 6 _____ 7 _______ 8 ______ 9 ______ 10 ______ How many total times did the replications meet the expected number of heads _______ How many times did the replications not meet this? __________ II. -
Evolution—The Extended Synthesis
EVOLUTION—THE EXTENDED SYNTHESIS edited by Massimo Pigliucci and Gerd B. Müller The MIT Press Cambridge, Massachusetts London, England © 2010 Massachusetts Institute of Technology All rights reserved. No part of this book may be reproduced in any form by any electronic or mechanical means (including photocopying, recording, or information storage and retrieval) without permission in writing from the publisher. MIT Press books may be purchased at special quantity discounts for business or sales promotional use. For information, please email [email protected] or write to Special Sales Department, The MIT Press, 55 Hayward Street, Cambridge, MA 02142. This book was set in Times Roman by Toppan Best-set Premedia Limited. Printed and bound in the United States of America. Library of Congress Cataloging-in-Publication Data Evolution—the extended synthesis / edited by Massimo Pigliucci and Gerd B. Müller. p. cm. Includes bibliographical references and index. ISBN 978-0-262-51367-8 (pbk. : alk. paper) 1. Evolution (Biology) 2. Evolutionary genetics. 3. Developmental biology. I. Pigliucci, Massimo, 1964– II. Müller, Gerd B. QH366.2.E8627 2010 576.8—dc22 2009024587 10 9 8 7 6 5 4 3 2 1 Index Abir-Am, Pnina, 445 Average effects, 87 Abstract gene model, 102 Avital, E., 165 Accommodation, 298, 324, 366. See also Phenotypic and genetic Badyaev, A. V., 365 accommodation Baldwin effect, 219, 257–258, 366, 367, Activator-inhibitor systems, 290 371 Adams, Paul, 220 Baldwin, James Marc, 219, 366, 367, 371 Adaptation, 163–164, 425–427 Bat wings, 268 Adaptation and Natural Selection Beaks, fi nch, 271 (Williams), 84, 88 Behavioral inheritance, 187 Adaptive cell behaviors, 268 Benkemoun, L., 153–154 Adaptive landscapes/adaptive Biodiversity, areas for future research on topographies. -
Cross.Corrected.Pdf (1.066Mb)
iii ANALYSIS OF THE HERITABILITY OF CORTICAL INVERSIONS THROUGH SEXUAL EXCHANGE IN Paramecium tetraurelia A Senior Scholars Thesis by REBECCA KANG CROSS Submitted to Honors and Undergraduate Research Texas A&M University in partial fulfillment of the requirements for the designation as UNDERGRADUATE RESEARCH SCHOLAR May 2012 Major: Molecular and Cell Biology iii ANALYSIS OF THE HERITABILITY OF CORTICAL INVERSIONS THROUGH SEXUAL EXCHANGE IN Paramecium tetraurelia A Senior Scholars Thesis by REBECCA KANG CROSS Submitted to Honors and Undergraduate Research Texas A&M University in partial fulfillment of the requirements for the designation as UNDERGRADUATE RESEARCH SCHOLAR Approved by: Research Advisor: Karl Aufderheide Associate Drirector, Honors and Undergraduate Research: Duncan MacKenzie May 2012 Major: Molecular and Cell Biology iii ABSTRACT Analysis of the Heritability of Cortical Inversions through Sexual Exchange in Paramecium tetraurelia. (May 2012) Rebecca Kang Cross Department of Biology Texas A&M University Research Advisor: Dr. Karl Aufderheide Department of Biology Paramecium tetraurelia is a large, single-celled, ciliated protist. Short cell cycle times (4.5-5 hours) and manipulable Mendelian genetics have made it an attractive research species, particularly for developmental genetics investigations. A genetic cross between cells with inverted ciliary rows and cells with normal cortexes was performed to determine the heritability of cortical inversions through sexual exchange in P. tetraurelia. A nuclear gene, nd6, which confers trichocyst nondischarge, was used in the cross to demonstrate a Mendelian inheritance pattern. Quantitative scoring of cortical phenotypes, including the location and size of the inversion, and the total number of ciliary rows was performed for the P1, F1, and F2 generations. -
Population Genetics
Population Genetics • Study of the distribution of alleles in populations and causes of allele frequency changes Key Concepts • Diploid individuals carry two alleles at every locus Homozygous: alleles are the same Heterozygous: alleles are different • Evolution: change in allele frequencies from one generation to the next Distinguishing Among Sources of Phenotypic Variation in Populations • Discrete vs. continuous • Genotype or environment (nature vs. nurture) • Phenotypic Plasticity (revisited) Phenotypic variation - Discrete vs. Continuous Polygenic Control can create Continuous Variation Phenotypic Variation - Discrete vs. Continuous Quantitative or Continuous or Metric Variation, very often Polygenic Phenotypic variation - genotype or environment? Phenotypic variation - genotype or environment? Mechanisms of Evolutionary Change – “Microevolutionary Processes” • Mutation: Ultimate natural resource of evolution, occurs at the molecular level in DNA. • Natural Selection: A difference, on average, between the survival or fecundity of individuals with certain arrays of phenotypes as compared to individuals with alternative phenotypes. • Migration: The movement of alleles from one population to another, typically by the movement of individuals or via long-range dispersal of gametes. • Genetic Drift: Change in the frequencies of alleles in a population resulting from chance variation in the survival and/or reproductive success of individuals; results in nonadaptive evolution (e.g., bottlenecks). These combined forces affect changes at the level of individuals, populations, and species. What is Population Genetics? • The study of alleles becoming more or less common over time. • Applied Meiosis: Application of Mendel’s Law of segregation of alleles. • Hardy-Weinberg Equilibrium Principle: Acts as a null hypothesis for tracking allele and genotype frequencies in a population in the absence of evolutionary forces. -
5. EVOLUTION AS a POPULATION-GENETIC PROCESS 5 April 2020
æ 5. EVOLUTION AS A POPULATION-GENETIC PROCESS 5 April 2020 With knowledge on rates of mutation, recombination, and random genetic drift in hand, we now consider how the magnitudes of these population-genetic features dictate the paths that are open vs. closed to evolutionary exploitation in various phylogenetic lineages. Because historical contingencies exist throughout the Tree of Life, we cannot expect to derive from first principles the source of every molecular detail of cellular diversification. We can, however, use established theory to address more general issues, such as the degree of attainable molecular refinement, rates of transition from one state to another, and the degree to which nonadaptive processes (mutation and random genetic drift) contribute to phylogenetic diversification. Substantial reviews of the field of evolutionary theory appear in Charlesworth and Charlesworth (2010) and Walsh and Lynch (2018). Much of the field is con- cerned with the mechanisms maintaining genetic variation within populations, as this ultimately dictates various aspects of the short-term response to selection. Here, however, we are primarily concerned with long-term patterns of phylogenetic diver- sification, so the focus is on the divergence of mean phenotypes. This still requires some knowledge of the principles of population genetics, as evolutionary divergence is ultimately a consequence of the accrual of genetic modifications at the population level. All evolutionary change initiates as a transient phase of genetic polymor- phism, during which mutant alleles navigate the rough sea of random genetic drift, often being evaluated on various genetic backgrounds, with some paths being more accessible to natural selection than others.