Introduction to Population Genetics & Evolution
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Introduction to Genetics Bios 225
INTRODUCTION TO GENETICS BIOS 225 Course Description This course introduces the student to the basic concepts of inheritance, populations, mutations, and techniques used to assess each of these. Credit: 2 credits Repeatable: No Course Structure The course will be presented in different formats: Lectures with PowerPoints, self-directed learning, discussions and student assignments etc. Competencies This course emphasizes competencies to enhance skills essential for a future health care professional. • Knowledge o Demonstrate content knowledge and skills in foundational courses required by biomedical professionals o Demonstrate information literacy o Demonstrate quantitative reasoning o Demonstrate longitudinal learning through coursework • Critical Thinking o Develop the skills of self-reflection and peer assessment to improve personal performance. o Demonstrate the ability to analyze literature and written material o Demonstrate the ability to distinguish between well-reasoned and poorly reasoned arguments • Communication Skills o Demonstrate effective presentation skills to faculty and peers. o Demonstrate effective listening skills o Demonstrate effective written communication 1 Objectives: Upon completion of BIOS 225 course, the student should be able to describe: • The structure and function of purines, pyrimidines, nucleosides and nucleotides • The structure and functions of nucleic acids (DNA and RNA) • The chromosome anatomy and human karyotypes • The concepts of prokaryotic and eukaryotic DNA replication • The concepts of prokaryotic and eukaryotic RNA transcription and post-transcriptional modifications • The concepts of prokaryotic and eukaryotic protein translation and post-translational modifications • The regulations of prokaryotic and eukaryotic gene expressions • The process of genomic, chromosomal and gene mutations; and its repair mechanism • The Mendel’ hypothesis and molecular mechanisms of genetic inheritance Schedule: Dates and times to be posted at the beginning of the term on the online calendar. -
Population Size and the Rate of Evolution
Review Population size and the rate of evolution 1,2 1 3 Robert Lanfear , Hanna Kokko , and Adam Eyre-Walker 1 Ecology Evolution and Genetics, Research School of Biology, Australian National University, Canberra, ACT, Australia 2 National Evolutionary Synthesis Center, Durham, NC, USA 3 School of Life Sciences, University of Sussex, Brighton, UK Does evolution proceed faster in larger or smaller popu- mutations occur and the chance that each mutation lations? The relationship between effective population spreads to fixation. size (Ne) and the rate of evolution has consequences for The purpose of this review is to synthesize theoretical our ability to understand and interpret genomic varia- and empirical knowledge of the relationship between tion, and is central to many aspects of evolution and effective population size (Ne, Box 1) and the substitution ecology. Many factors affect the relationship between Ne rate, which we term the Ne–rate relationship (NeRR). A and the rate of evolution, and recent theoretical and positive NeRR implies faster evolution in larger popula- empirical studies have shown some surprising and tions relative to smaller ones, and a negative NeRR implies sometimes counterintuitive results. Some mechanisms the opposite (Figure 1A,B). Although Ne has long been tend to make the relationship positive, others negative, known to be one of the most important factors determining and they can act simultaneously. The relationship also the substitution rate [5–8], several novel predictions and depends on whether one is interested in the rate of observations have emerged in recent years, causing some neutral, adaptive, or deleterious evolution. Here, we reassessment of earlier theory and highlighting some gaps synthesize theoretical and empirical approaches to un- in our understanding. -
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B
Transformations of Lamarckism Vienna Series in Theoretical Biology Gerd B. M ü ller, G ü nter P. Wagner, and Werner Callebaut, editors The Evolution of Cognition , edited by Cecilia Heyes and Ludwig Huber, 2000 Origination of Organismal Form: Beyond the Gene in Development and Evolutionary Biology , edited by Gerd B. M ü ller and Stuart A. Newman, 2003 Environment, Development, and Evolution: Toward a Synthesis , edited by Brian K. Hall, Roy D. Pearson, and Gerd B. M ü ller, 2004 Evolution of Communication Systems: A Comparative Approach , edited by D. Kimbrough Oller and Ulrike Griebel, 2004 Modularity: Understanding the Development and Evolution of Natural Complex Systems , edited by Werner Callebaut and Diego Rasskin-Gutman, 2005 Compositional Evolution: The Impact of Sex, Symbiosis, and Modularity on the Gradualist Framework of Evolution , by Richard A. Watson, 2006 Biological Emergences: Evolution by Natural Experiment , by Robert G. B. Reid, 2007 Modeling Biology: Structure, Behaviors, Evolution , edited by Manfred D. Laubichler and Gerd B. M ü ller, 2007 Evolution of Communicative Flexibility: Complexity, Creativity, and Adaptability in Human and Animal Communication , edited by Kimbrough D. Oller and Ulrike Griebel, 2008 Functions in Biological and Artifi cial Worlds: Comparative Philosophical Perspectives , edited by Ulrich Krohs and Peter Kroes, 2009 Cognitive Biology: Evolutionary and Developmental Perspectives on Mind, Brain, and Behavior , edited by Luca Tommasi, Mary A. Peterson, and Lynn Nadel, 2009 Innovation in Cultural Systems: Contributions from Evolutionary Anthropology , edited by Michael J. O ’ Brien and Stephen J. Shennan, 2010 The Major Transitions in Evolution Revisited , edited by Brett Calcott and Kim Sterelny, 2011 Transformations of Lamarckism: From Subtle Fluids to Molecular Biology , edited by Snait B. -
Evolution by Natural Selection, Formulated Independently by Charles Darwin and Alfred Russel Wallace
UNIT 4 EVOLUTIONARY PATT EVOLUTIONARY E RNS AND PROC E SS E Evolution by Natural S 22 Selection Natural selection In this chapter you will learn that explains how Evolution is one of the most populations become important ideas in modern biology well suited to their environments over time. The shape and by reviewing by asking by applying coloration of leafy sea The rise of What is the evidence for evolution? Evolution in action: dragons (a fish closely evolutionary thought two case studies related to seahorses) 22.1 22.4 are heritable traits that with regard to help them to hide from predators. The pattern of evolution: The process of species have changed evolution by natural and are related 22.2 selection 22.3 keeping in mind Common myths about natural selection and adaptation 22.5 his chapter is about one of the great ideas in science: the theory of evolution by natural selection, formulated independently by Charles Darwin and Alfred Russel Wallace. The theory explains how T populations—individuals of the same species that live in the same area at the same time—have come to be adapted to environments ranging from arctic tundra to tropical wet forest. It revealed one of the five key attributes of life: Populations of organisms evolve. In other words, the heritable characteris- This chapter is part of the tics of populations change over time (Chapter 1). Big Picture. See how on Evolution by natural selection is one of the best supported and most important theories in the history pages 516–517. of scientific research. -
IN EVOLUTION JACK LESTER KING UNIVERSITY of CALIFORNIA, SANTA BARBARA This Paper Is Dedicated to Retiring University of California Professors Curt Stern and Everett R
THE ROLE OF MUTATION IN EVOLUTION JACK LESTER KING UNIVERSITY OF CALIFORNIA, SANTA BARBARA This paper is dedicated to retiring University of California Professors Curt Stern and Everett R. Dempster. 1. Introduction Eleven decades of thought and work by Darwinian and neo-Darwinian scientists have produced a sophisticated and detailed structure of evolutionary ,theory and observations. In recent years, new techniques in molecular biology have led to new observations that appear to challenge some of the basic theorems of classical evolutionary theory, precipitating the current crisis in evolutionary thought. Building on morphological and paleontological observations, genetic experimentation, logical arguments, and upon mathematical models requiring simplifying assumptions, neo-Darwinian theorists have been able to make some remarkable predictions, some of which, unfortunately, have proven to be inaccurate. Well-known examples are the prediction that most genes in natural populations must be monomorphic [34], and the calculation that a species could evolve at a maximum rate of the order of one allele substitution per 300 genera- tions [13]. It is now known that a large proportion of gene loci are polymorphic in most species [28], and that evolutionary genetic substitutions occur in the human line, for instance, at a rate of about 50 nucleotide changes per generation [20], [24], [25], [26]. The puzzling observation [21], [40], [46], that homologous proteins in different species evolve at nearly constant rates is very difficult to account for with classical evolutionary theory, and at the very least gives a solid indication that there are qualitative differences between the ways molecules evolve and the ways morphological structures evolve. -
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. -
Working at the Interface of Phylogenetics and Population
Molecular Ecology (2007) 16, 839–851 doi: 10.1111/j.1365-294X.2007.03192.x WorkingBlackwell Publishing Ltd at the interface of phylogenetics and population genetics: a biogeographical analysis of Triaenops spp. (Chiroptera: Hipposideridae) A. L. RUSSELL,* J. RANIVO,†‡ E. P. PALKOVACS,* S. M. GOODMAN‡§ and A. D. YODER¶ *Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520, USA, †Département de Biologie Animale, Université d’Antananarivo, Antananarivo, BP 106, Madagascar, ‡Ecology Training Program, World Wildlife Fund, Antananarivo, BP 906 Madagascar, §The Field Museum of Natural History, Division of Mammals, 1400 South Lake Shore Drive, Chicago, IL 60605, USA, ¶Department of Ecology and Evolutionary Biology, PO Box 90338, Duke University, Durham, NC 27708, USA Abstract New applications of genetic data to questions of historical biogeography have revolutionized our understanding of how organisms have come to occupy their present distributions. Phylogenetic methods in combination with divergence time estimation can reveal biogeo- graphical centres of origin, differentiate between hypotheses of vicariance and dispersal, and reveal the directionality of dispersal events. Despite their power, however, phylo- genetic methods can sometimes yield patterns that are compatible with multiple, equally well-supported biogeographical hypotheses. In such cases, additional approaches must be integrated to differentiate among conflicting dispersal hypotheses. Here, we use a synthetic approach that draws upon the analytical strengths of coalescent and population genetic methods to augment phylogenetic analyses in order to assess the biogeographical history of Madagascar’s Triaenops bats (Chiroptera: Hipposideridae). Phylogenetic analyses of mitochondrial DNA sequence data for Malagasy and east African Triaenops reveal a pattern that equally supports two competing hypotheses. -
Muller's Ratchet As a Mechanism of Frailty and Multimorbidity
bioRxivMuller’s preprint ratchetdoi: https://doi.org/10.1101/439877 and frailty ; this version posted[Type Octoberhere] 10, 2018. The copyright holder Govindarajufor this preprint and (which Innan was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Muller’s ratchet as a mechanism of frailty and multimorbidity 2 3 Diddahally R. Govindarajua,b,1, 2, and Hideki Innanc,1,2 4 5 aDepartment of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138; 6 and bThe Institute of Aging Research, Albert Einstein College of Medicine, Bronx, 7 NY 1046, and cGraduate University for Advanced Studies, Hayama, Kanagawa, 8 240-0193, Japan 9 10 11 12 Authors contributions: D.R.G., H.I designed study, performed research, contributed new 13 analytical tools, analyzed data and wrote the paper 14 15 The authors declare no conflict of interest 16 1D.R.G., and H.I. contributed equally to this work and listed alphabetically 17 2 Correspondence: Email: [email protected]; [email protected] 18 19 Senescence | mutation accumulation | asexual reproduction | somatic cell-lineages| 20 organs and organ systems |Muller’s ratchet | fitness decay| frailty and multimorbidity 21 22 23 24 25 26 27 28 29 30 31 32 1 bioRxivMuller’s preprint ratchetdoi: https://doi.org/10.1101/439877 and frailty ; this version posted[Type Octoberhere] 10, 2018. The copyright holder Govindarajufor this preprint and (which Innan was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 33 Mutation accumulation has been proposed as a cause of senescence. -
Animal Traditions: Behavioural Inheritance in Evolution
Animal Traditions: Behavioural Inheritance in Evolution Eytan Avital and Eva Jablonka CAMBRIDGE UNIVERSITY PRESS Animal Traditions Behavioural Inheritance in Evolution Animal Traditions maintains that the assumption that the selection of genes supplies both a sufficient explanation of the evolution of behav- iour and a true description of its course is, despite its almost univer- sal acclaim, wrong. Eytan Avital and Eva Jablonka contend that evolutionary explanations must take into account the well-established fact that, in mammals and birds, the transfer of learnt information across generations is both ubiquitous and indispensable. The introduc- tion of the behavioural inheritance system into the Darwinian explanatory scheme enables the authors to offer new interpretations for common behaviours such as maternal behaviours, behavioural conflicts within families, adoption and helping. This approach offers a richer view of heredity and evolution, integrates developmental and evolutionary processes, suggests new lines for research and provides a constructive alternative to both the selfish gene and meme views of the world. It will make stimulating reading for all those interested in evolutionary biology, sociobiology, behavioural ecology and psychology. eytan avital is a lecturer in Zoology in the Department of Natural Sciences at David Yellin College of Education in Jerusalem. He is a highly experienced field biologist, and has written one zoology text and edited several others on zoology and evolution for the Israel Open university. eva jablonka is a senior lecturer in the Cohn Institute for the History and Philosophy of Science and Ideas, at Tel-Aiv University. She is the author of three books on heredity and evolution, most recently Epigenetic Inheritance and Evolution with Marion Lamb. -
Mammal Evolution
Mammal Evolution Geology 331 Paleontology Triassic synapsid reptiles: Therapsids or mammal-like reptiles. Note the sprawling posture. Mammal with Upright Posture From Synapsids to Mammals, a well documented transition series Carl Buell Prothero, 2007 Synapsid Teeth, less specialized Mammal Teeth, more specialized Prothero, 2007 Yanoconodon, Lower Cretaceous of China Yanoconodon, Lower Cretaceous of China, retains ear bones attached to the inside lower jaw Morganucodon Yanoconodon = articular of = quadrate of Human Ear Bones, or lower reptile upper reptile Auditory Ossicles jaw jaw Cochlea Mammals have a bony secondary palate Primary Palate Reptiles have a soft Secondary Palate secondary palate Reduction of digit bones from Hand and Foot of Permian Synapsid 2-3-4-5-3 in synapsid Seymouria ancestors to 2-3-3-3-3 in mammals Human Hand and Foot Class Mammalia - Late Triassic to Recent Superorder Tricodonta - Late Triassic to Late Cretaceous Superorder Multituberculata - Late Jurassic to Early Oligocene Superorder Monotremata - Early Cretaceous to Recent Superorder Metatheria (Marsupials) - Late Cretaceous to Recent Superorder Eutheria (Placentals) - Late Cretaceous to Recent Evolution of Mammalian Superorders Multituberculates Metatheria Eutheria (Marsupials) (Placentals) Tricodonts Monotremes . Live Birth Extinct: . .. Mammary Glands? Mammals in the Age of Dinosaurs – a nocturnal life style Hadrocodium, a lower Jurassic mammal with a “large” brain (6 mm brain case in an 8 mm skull) Were larger brains adaptive for a greater sense of smell? Big Brains and Early Mammals July 14, 2011 The Academic Minute http://www.insidehighered.com/audio/academic_pulse/big_brains_and_early_mammals Lower Cretaceous mammal from China Jawbones of a Cretaceous marsupial from Mongolia Mammal fossil from the Cretaceous of Mongolia Reconstructed Cretaceous Mammal Early Cretaceous mammal ate small dinosaurs Repenomamus robustus fed on psittacosaurs. -
Multiple Origins of Life (Extinction/Bioclade/Precambrian/Evolution/Stochastic Processes) DAVID M
Proc. Natt Acad. Sci. USA Vol. 80; pp. 2981-2984, May 1983 Evolution Multiple origins of life (extinction/bioclade/Precambrian/evolution/stochastic processes) DAVID M. RAUP* AND JAMES W. VALENTINEt *Department of the Geophysical Sciences, University of Chicago, Chicago, Illinois 60637; and tDepartment of Geological Sciences, University of California, Santa Barbara, California 93106 Contributed by David M. Raup, February 22, 1983 ABSTRACT There is some indication that life may have orig- ing a full assortment of prebiotically synthesized organic build- inated readily under primitive earth conditions. If there were ing blocks for life and conditions appropriate for life origins, it multiple origins of life, the result could have been a polyphyletic is possible that rates of bioclade origins might compare well biota today. Using simple stochastic models for diversification and enough with rates of diversification. Indeed, there has been extinction,-we conclude: (i) the probability of survival of life is low speculation that life may have been polyphyletic (1, 4). How- unless there are multiple origins, and (ii) given survival of life and ever, there is strong evidence that all living forms are de- given as many as 10 independent origins of life, the odds are that scended from a single ancestor. Biochemical and organizational all but one would have gone extinct, yielding the monophyletic biota similarities and the "universality" of the genetic code indicate we have now. The fact of the survival of our particular form of this. Therefore, the question for this paper is: If there were life does not imply that it was unique or superior. multiple bioclades early in life history, what is the probability that only one would have survived? In other words, if life The formation of life de novo is generally viewed as unlikely or orig- impossible under present earth conditions. -
Basic Population Genetics Outline
Basic Population Genetics Bruce Walsh Second Bangalore School of Population Genetics and Evolution 25 Jan- 5 Feb 2016 1 Outline • Population genetics of random mating • Population genetics of drift • Population genetics of mutation • Population genetics of selection • Interaction of forces 2 Random-mating 3 Genotypes & alleles • In a diploid individual, each locus has two alleles • The genotype is this two-allele configuration – With two alleles A and a – AA and aa are homozygotes (alleles agree) – Aa is a heterozygote (alleles are different) • With an arbitrary number of alleles A1, .., An – AiAi are homozgyotes – AiAk (for i different from k) are heterozygotes 4 Allele and Genotype Frequencies Given genotype frequencies, we can always compute allele Frequencies. For a locus with two alleles (A,a), freq(A) = freq(AA) + (1/2)freq(Aa) The converse is not true: given allele frequencies we cannot uniquely determine the genotype frequencies If we are willing to assume random mating, freq(AA) = [freq(A)]2, Hardy-Weinberg freq(Aa) = 2*freq(A)*freq(a) proportions 5 For k alleles • Suppose alleles are A1 , .. , An – Easy to go from genotype to allele frequencies – Freq(Ai) = Freq(AiAi) + (1/2) Σ freq(AiAk) • Again, assumptions required to go from allele to genotype frequencies. • With n alleles, n(n+1)/2 genotypes • Under random-mating – Freq(AiAi) = Freq(Ai)*Freq(Ai) – Freq(AiAk) =2*Freq(Ai)*Freq(Ak) 6 Hardy-Weinberg 7 Importance of HW • Under HW conditions, no – Drift (i.e., pop size is large) – Migration/mutation (i.e., no input ofvariation