Selection Experiments and Experimental Evolution of Performance and Physiology
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1. Adaptation and the Evolution of Physiological Characters
Bennett, A. F. 1997. Adaptation and the evolution of physiological characters, pp. 3-16. In: Handbook of Physiology, Sect. 13: Comparative Physiology. W. H. Dantzler, ed. Oxford Univ. Press, New York. 1. Adaptation and the evolution of physiological characters Department of Ecology and Evolutionary Biology, University of California, ALBERT F. BENNETT 1 Irvine, California among the biological sciences (for example, behavioral CHAPTER CONTENTS science [I241). The Many meanings of "Adaptationn In general, comparative physiologists have been Criticisms of Adaptive Interpretations much more successful in, and have devoted much more Alternatives to Adaptive Explanations energy to, pursuing the former rather than the latter Historical inheritance goal (37). Most of this Handbook is devoted to an Developmentai pattern and constraint Physical and biomechanical correlation examination of mechanism-how various physiologi- Phenotypic size correlation cal systems function in various animals. Such compara- Genetic correlations tive studies are usually interpreted within a specific Chance fixation evolutionary context, that of adaptation. That is, or- Studying the Evolution of Physiological Characters ganisms are asserted to be designed in the ways they Macroevolutionary studies Microevolutionary studies are and to function in the ways they do because of Incorporating an Evolutionary Perspective into Physiological Studies natural selection which results in evolutionary change. The principal textbooks in the field (for example, refs. 33, 52, 102, 115) make explicit reference in their titles to the importance of adaptation to comparative COMPARATIVE PHYSIOLOGISTS HAVE TWO GOALS. The physiology, as did the last comparative section of this first is to explain mechanism, the study of how organ- Handbook (32). Adaptive evolutionary explanations isms are built functionally, "how animals work" (113). -
Experimental Evolution
Heredity (2008) 100, 441–442 & 2008 Nature Publishing Group All rights reserved 0018-067X/08 $30.00 www.nature.com/hdy EDITORIAL Experimental evolution Heredity (2008) 100, 441–442; doi:10.1038/hdy.2008.19 and their interactions, it should be possible to predict which genes will be altered, how they will be altered and in what order, in any defined environment. Our under- Microcosms are used in ecology and evolution to shrink standing of cell biology is as yet wholly inadequate for space and time to manageable scales. They have never the task, but the smaller genomes of viruses might be been extensively used in ecology, because many ecolo- more accessible. Bull and Molineux describe the most gists doubt that any important features of large complex ambitious attempts to date in pursuit of this grail, using systems, such as lakes, can be profitably investigated in phage T7 of E. coli. Given the detailed knowledge of T7 small chambers or vials (Carpenter, 1996). Consequently, genetics, it should be possible to introduce a specific ecology lacks any generally accepted model system genetic lesion and then predict what compensatory to facilitate the cumulative growth of understanding of mutations will be fixed so as to restore the lost function. how communities work. Evolutionary biologists have In many cases, these mutations were correctly identified been less skeptical, and at least three major schools and for very simple genomes, at least, a nearly complete have adopted microcosm methods. Perhaps the best understanding of adaptation seems to be within grasp. known is the extensive exploration of the effects of artificial selection in Drosophila (and to a lesser extent in At the same time, both Ferenci and Bull and Molineux other organisms, such as mice). -
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THEORETICAL COMMUNICATIONS EVO/DEVO From archebiosis to evolution of organisms and informational systems Yuri Natochin1 and Tatiana Chernigovskaya2 EVO/DEVO 1Faculty of Medicine, Saint Petersburg State University, Universutetskaya nab., 7–9, Saint Petersburg, 199106, Russian Federation 2Department of the Problems of Convergence in Natural Sciences and Humanities, Laboratory for Cognitive Studies, Faculty of Liberal Arts and Sciences, Saint Petersburg State University, Universitetskaya nab., 7–9, Saint Petersburg, 190000, Russian Federation Address correspondence and requests for materials to Tatiana Chernigovskaya, [email protected] Abstract Laws of evolution seem to be relevant not only for biological domains, but for informational systems. This paper provides a sketch of a comparison of two systems — that of homeostatic systems, and that of language evolution. We argue that the patterns of evolution of functions are hierarchically organized according to four main levels: I — the primary level: a cell in biology, a phoneme in language; II — functional units: a nephron, a morpheme; III — organs: a kid- ney (a lung, a heart, etc.), a word; IV — systems: physico-chemical constancy, a sentence or a phrase. There is a set of restrictions for each domain: the linguis- tic changes have not occurred in all languages, in many cases they are still un- derway, there are ‘old’ and ‘young’ languages, etc. Such comparisons appear to be relevant and can be applied to objects as far removed as these. This allows us to speak of certain evolutionary universals. Keywords: laws of physiological evolution, history of evolutional physiology in Russia, origins of life, language evolution. Introduction: A glimpse of history Citation: Natochin, Y. -
Evolutionary Environmental Physiology (IB 150, 3 Units, Spring 2016)
Evolutionary Environmental Physiology (IB 150, 3 units, Spring 2016) Department of Integrative Biology, University of California, Berkeley COURSE INFORMATION COURSE FORMAT Two lectures (1.5h/lecture, 9:30 – 11am Tue/Thu, 110 Wheeler) and one discussion per week (2h, room and time TBA). INSTRUCTOR Caroline Williams Office: 5120 VLSB, (510) 643-9775, office hours to be advised Email: [email protected] Webpage: cmwilliamslab.com bCourses site: to be advised GSI To be advised (1 requested) PREREQUISITES Bio1A and Bio1B or equivalent ENROLLMENT Capped at 50 students for first year (8 Teams of 6-7 students), aiming to expand in future years COURSE Evolutionary physiology studies how physiological traits arise and OVERVIEW are modified during adaptation to the environment. An integrative understanding of the origin and maintenance of physiological traits, encompassing levels of biological hierarchy from molecular to ecological and biogeographic, is essential for improving human health and stewarding the natural world through the current era of rapid environmental change. This course consists of three parts: 1) big questions in evolutionary physiology and how they are addressed; 2) a student-led exploration of how environmental factors have shaped physiological evolution; and 3) predicting responses to global change using evolutionary physiology. This course will be taxonomically broad and will encompass aquatic and terrestrial systems. LEARNING This course aims to foster both content-specific knowledge and OBJECTIVES scientific enquiry and reasoning skills. As a result, this course will stimulate interest in the field of evolutionary physiology, and will also provide a solid preparation for the new (2015) MCAT examination. The specific learning objectives are listed below. -
Long-Term Experimental Evolution in Escherichia Coli. V. Effects of Recombination with Immigrant Genotypes on the Rate of Bacterial Evolution
© Birkhliuser Verlag, Basel, 1997 J. evol. bioi. 10 (1997) 743-769 1010-061X/97/050743-27 $ 1.50 + 0.20/0 I Journal of Evolutionary Biology Long-term experimental evolution in Escherichia coli. V. Effects of recombination with immigrant genotypes on the rate of bacterial evolution 1 2 3 V. Souza, P. E. Turner • and R. E. LenskF·* 1Centro de Ecologia, Universidad Nacional Aut6noma de Mexico, Coyoacim, Ciudad de Mexico, 04510, Mexico 2 Center for Microbial Ecology, Michigan State University, East Lansing MI 48824, USA 3 Current address: Department of Zoology, University of Maryland, College Park MD 20742, USA Key words: Complex selection; conjugation; Escherichia coli; experimental evolu tion; hitchhiking; migration; plasmids; recombination. Abstract This study builds upon an earlier experiment that examined the dynamics of mean fitness in evolving populations of Escherichia coli in which mutations were the sole source of genetic variation. During thousands of generations in a constant environment, the rate of improvement in mean fitness of these asexual populations slowed considerably from an initially rapid pace. In this study, we sought to determine whether sexual recombination with novel genotypes would reaccelerate the rate of adaption in these populations. To that end, treatment populations were propagated for an additional 1000 generations in the same environment as their ancestors, but they were periodically allowed to mate with an immigrant pool of genetically distinct Hfr (high frequency recombination) donors. These donors could transfer genes to the resident populations by conjugation, but the donors them selves could not grow in the experimental environment. Control populations were propagated under identical conditions, but in the absence of sexual recombination with the donors. -
Ecological and Evolutionary Physiology" (BIOL 174) Winter 2007 Instructor: Theodore Garland, Jr., Professor of Biology, University of California, Riverside
Tentative Syllabus: "Ecological and Evolutionary Physiology" (BIOL 174) Winter 2007 Instructor: Theodore Garland, Jr., Professor of Biology, University of California, Riverside. Office is 109 University Lab Building; Phone 827-3524; [email protected] Office Hours: Tuesday and Wednesday, 10-11 A.M. in 109 ULB, or by appointment. Catalog Description: Interactions between organisms and their environments, emphasizing coadaptation of physiological, morphological, and behavioral phenotypes. Topics include: allometry and scaling, metabolism and locomotion, heat and water exchange, evolution of endothermy, artificial selection experiments, and phylogenetically based statistical methods. Lecture: Tuesday and Thursday, 2:10 - 3:30 P.M. in 1307 SPTHW (Spieth Hall West) Required Readings: All readings as PDF files will be posted online at http://ilearn.ucr.edu/. These should be read before class. Lectures will be posted only after class. Grading: Student Survey (10 points), Three written critiques of papers from the literature (20 points each), Mid-term Exam 1 (60 points), Mid-term Exam 2 (60 points), Final Exam (60 points). Total = 250 points. Nine points of extra credit are possible for example exam questions. Lecture Schedule and Required Readings: 1. 4 Jan. 2007 - Attendance and Introduction. Tracy, C. R., and J. S. Turner. 1982. What is physiological ecology? Bull. Ecol. Soc. Am. 63:340-347. Definitions and Opinions by: G. A. Bartholomew, A. F. Bennett, W. D. Billings, B. F. Chabot, D. M. Gates, B. Heinrich, R. B. Huey, D. H. Janzen, J. R. King, P. A. McClure, B. K. McNab, P. C. Miller, P. S. Nobel, B. R. Strain. 2. 9 Jan. 2007 - Student Survey; Historical Development of Eco Evo Phys Bennett, A. -
Darwinian Evolution in a Translation-Coupled RNA Replication System Within a Cell-Like Compartment
ARTICLE Received 28 Mar 2013 | Accepted 22 Aug 2013 | Published 3 Oct 2013 DOI: 10.1038/ncomms3494 Darwinian evolution in a translation-coupled RNA replication system within a cell-like compartment Norikazu Ichihashi1,2, Kimihito Usui1, Yasuaki Kazuta1, Takeshi Sunami1,2, Tomoaki Matsuura1,2,3 & Tetsuya Yomo1,2,4 The ability to evolve is a key characteristic that distinguishes living things from non-living chemical compounds. The construction of an evolvable cell-like system entirely from non-living molecules has been a major challenge. Here we construct an evolvable artificial cell model from an assembly of biochemical molecules. The artificial cell model contains artificial genomic RNA that replicates through the translation of its encoded RNA replicase. We perform a long-term (600-generation) replication experiment using this system, in which mutations are spontaneously introduced into the RNA by replication error, and highly replicable mutants dominate the population according to Darwinian principles. During evolution, the genomic RNA gradually reinforces its interaction with the translated replicase, thereby acquiring competitiveness against selfish (parasitic) RNAs. This study provides the first experimental evidence that replicating systems can be developed through Darwinian evolution in a cell-like compartment, even in the presence of parasitic replicators. 1 Exploratory Research for Advanced Technology, Japan Science and Technology Agency, Osaka University, Suita, Osaka 565-0871, Japan. 2 Graduate School of Information Science and Technology, Osaka University, Suita, Osaka 565-0871, Japan. 3 Graduate School of Engineering, Osaka University, Suita, Osaka 565-0871, Japan. 4 Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan. Correspondence and requests for materials should be addressed to T.Y. -
Potassium Ions Are More Effective Than Sodium Ions in Salt Induced Peptide Formation
Orig Life Evol Biosph DOI 10.1007/s11084-013-9326-5 PREBIOTIC CHEMISTRY Potassium Ions are More Effective than Sodium Ions in Salt Induced Peptide Formation Michael V. Dubina & Sergey Yu. Vyazmin & Vitali M. Boitsov & Eugene N. Nikolaev & Igor A. Popov & Alexey S. Kononikhin & Igor E. Eliseev & Yuri V. Natochin Received: 12 December 2012 /Accepted: 17 January 2013 # The Author(s) 2013. This article is published with open access at Springerlink.com Abstract Prebiotic peptide formation under aqueous conditions in the presence of metal ions is one of the plausible triggers of the emergence of life. The salt-induced peptide formation reaction has been suggested as being prebiotically relevant and was examined for the formation of peptides in NaCl solutions. In previous work we have argued that the first protocell could have emerged in KCl solution. Using HPLC-MS/MS analysis, we found that K+ is more than an order of magnitude more effective in the L-glutamic acid oligomerization with 1,1'-carbonyldiimidazole in aqueous solutions than the same concentration of Na+, which is consistent with the diffusion theory calculations. We anticipate that prebiotic peptides could have formed with K+ as the driving force, not Na+, as commonly believed. Keywords Potassium . Sodium . Prebiotic . Peptide formation . Origin of life Introduction Since Oparin’s ideas (1924; 1938) and Miller-Urey’s famous experiment (1953)onthe prebiotic synthesis of amino acids, one of the main problems of prebiotic chemistry is to “re-invent” the plausible range of indispensable physical-chemical boundary re- quirements that would enable the emergence of stable and replicable molecules on the primordial Earth (Eschenmoser 2003). -
Experimental Evolution in Vivo to Identify Selective Pressures During Pneumococcal Colonization
bioRxiv preprint doi: https://doi.org/10.1101/2020.01.15.908590; this version posted January 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Experimental Evolution in vivo to Identify Selective Pressures During Pneumococcal Colonization Vaughn S. Cooper1, Erin Honsa2,3, Hannah Rowe2, Christopher Deitrick1, Amy R. Iverson2, Jonathan J. Whittall4, Stephanie L. Neville5, Christopher A. McDevitt5 Colin Kietzman2,6, Jason W. Rosch2* 1 Department of Microbiology and Molecular Genetics, and Center for Evolutionary Biology and Medicine, University of Pittsburgh School of Medicine 2 St Jude Children’s Research Hospital, Department of Infectious Diseases 3 Current affiliation: A.T. Still University, School of Osteopathic Medicine in Arizona, 5850 E. Still Circle, Mesa, AZ, 85206 4 Department of Molecular and Biomedical Science, School of Biological Sciences, University of Adelaide, Adelaide, South Australia, Australia 5 Department of Microbiology and Immunology, The Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Victoria, Australia 6 Current affiliation: St Jude Children’s Research Hospital, Department of Developmental Neurobiology *Corresponding Author Jason Rosch, PhD. Department of Infectious Diseases St Jude Children’s Research Hospital 262 Danny Thomas Place Memphis, TN 38105 901-595-3408 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/2020.01.15.908590; this version posted January 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. Abstract (224 words) Experimental evolution is a powerful technique to understand how populations evolve from selective pressures imparted by the surrounding environment. -
Experimental Evolution Heals the Scars of Genome-Scale Recoding COMMENTARY Olivier Tenaillona,1
COMMENTARY Experimental evolution heals the scars of genome-scale recoding COMMENTARY Olivier Tenaillona,1 Much of the dramatic plot of Mary Shelley’s Frankenstein uncharged tRNA is subsequently released and the ri- resulted from the apparent scars and imperfections of bosome moves forward to expose the next codon. the creature her hero brought to life. Similarly, organisms Incorporating a nsAA therefore requires a combina- highly modified by synthetic biologists suffer from scars tion of codon, tRNA, and aaRS that act specifically and and imperfect functioning that their creators had not exclusively among themselves and the nsAA. Al- intended. However, as presented in PNAS by Wannier though every step is challenging, the use of tRNA- et al. (1), synthetic biologists can use experimental evo- aaRS from a diverged organism and the use of positive lution to rapidly heal some of these scars, as they have and negative selections to improve specificity and performed on a highly recoded Escherichia coli strain exclude interactions with other tRNA, aaRS, or amino modified to incorporate efficiently nonstandard amino acids has been quite successful (4). As a result, the acids (nsAA). machinery for the introduction of the nsAA can be One of the aims of synthetic biology is to expand carried on plasmids and easily introduced in new the range of functions natural organisms can perform. genotypes. While chemists have created myriads of new mole- Reserving exclusively a codon for the nsAA is yet cules over the last centuries, their ability to create another challenge, as it requires multiple modifica- complex molecules is surpassed by the biochemistry tions of the genome. -
Chapter 10 Toward a Theory of Multilevel Evolution: Long-Term Information Integration Shapes the Mutational Landscape and Enhances Evolvability
1 Chapter 10 Toward a Theory of Multilevel Evolution: Long-Term Information Integration Shapes the Mutational Landscape and Enhances Evolvability Paulien Hogeweg Abstract Most of evolutionary theory has abstracted away from how information is coded in the genome and how this information is transformed into traits on which selection takes place. While in the earliest stages of biological evolution, in the RNA world, the mapping from the genotype into function was largely predefined by the physical–chemical properties of the evolving entities (RNA replicators, e.g. from sequence to folded structure and catalytic sites), in present-day organisms, the mapping itself is the result of evolution. I will review results of several in silico evolutionary studies which examine the consequences of evolving the genetic coding, and the ways this information is transformed, while adapting to prevailing environments. Such multilevel evolution leads to long-term information integration. Through genome, network, and dynamical structuring, the occurrence and/or effect of random mutations becomes nonrandom, and facilitates rapid adaptation. This is what does happen in the in silico experiments. Is it also what did happen in biological evolution? I will discuss some data that suggest that it did. In any case, these results provide us with novel search images to tackle the wealth of biological data. 1 Introduction Much of current research in biology is on the physical and biochemical basis of information processing in cells. This information processing leads to the transfor- mation of the inherited genotypic information to a living organism enough adapted to its environment to survive. P. Hogeweg () Theoretical Biology and Bioinformatics Group, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands e-mail: [email protected] O.S. -
Evolutionary Biology
EVOLUTIONARY BIOLOGY SUBDISCIPLINES OF EVOLUTIONARY BIOLOGY Behavioral Evolution • Evolution of mating systems, courtship behavior, foraging behavior, predator escape mechanisms, and cooperation. Evolutionary Developmental Biology (Evo-Devo) • Evolutionary change in the processes that translate genetic information (genotype) into its behavioral, anatomical, physiological, and biochemical characteristics (phenotype). Evolutionary Ecology • How the life histories, diets, and other ecological features of species evolve, and how these processes affect the composition and properties of communities and ecosystems, also, how species evolve in response to one another (e.g. evolution of predator-prey relationships). Evolutionary Genetics • The origin of variation; the patterns of variation within populations and species, along with the causes and consequences of these variations. Paleobiology • Large-scale evolutionary patterns in the fossil record. Examines origins and fates of lineages, major groups, and anatomical and behavioral novelties, evolutionary trends, and changes throughout geographic areas and geologic time. Evolutionary Physiology/Morphology • How physiological, biochemical, and anatomical features of an organism provide adaptation to its environment and lifeways. Also examines the history of these adaptations. Human Evolution • Many evolutionary biologists use conceptual issues of the subdisciplines to study a particular group of organisms. Of these groups, one draws special attention—the human lineage. Molecular Evolution • Investigates the history and causes of evolutionary changes in nucleotide sequences, the structure and number of genes, their physical arrangement on chromosomes, and other molecular phenomena, including the evolution of genomes. Systematics • Distinguishes and names species, infers phylogenetic relationships among species and classifies species based on their evolutionary relationships. CASE WESTERN RESERVE UNIVERSITY.