Population Evolution
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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. -
Allele Frequency–Based and Polymorphism-Versus
View metadata, citation and similar papers at core.ac.uk brought to you by CORE Allele Frequency–Based and Polymorphism-Versus- provided by PubMed Central Divergence Indices of Balancing Selection in a New Filtered Set of Polymorphic Genes in Plasmodium falciparum Lynette Isabella Ochola,1 Kevin K. A. Tetteh,2 Lindsay B. Stewart,2 Victor Riitho,1 Kevin Marsh,1 and David J. Conway*,2 1Kenya Medical Research Institute, Centre for Geographic Medicine Research Coast, Kilifi, Kenya 2Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom *Corresponding author: E-mail: [email protected], [email protected]. Associate editor: John H. McDonald Research article Abstract Signatures of balancing selection operating on specific gene loci in endemic pathogens can identify candidate targets of naturally acquired immunity. In malaria parasites, several leading vaccine candidates convincingly show such signatures when subjected to several tests of neutrality, but the discovery of new targets affected by selection to a similar extent has been slow. A small minority of all genes are under such selection, as indicated by a recent study of 26 Plasmodium falciparum merozoite- stage genes that were not previously prioritized as vaccine candidates, of which only one (locus PF10_0348) showed a strong signature. Therefore, to focus discovery efforts on genes that are polymorphic, we scanned all available shotgun genome sequence data from laboratory lines of P. falciparum and chose six loci with more than five single nucleotide polymorphisms per kilobase (including PF10_0348) for in-depth frequency–based analyses in a Kenyan population (allele sample sizes .50 for each locus) and comparison of Hudson–Kreitman–Aguade (HKA) ratios of population diversity (p) to interspecific divergence (K) from the chimpanzee parasite Plasmodium reichenowi. -
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. -
NOTES – CH 17 – Evolution of Populations
NOTES – CH 17 – Evolution of Populations ● Vocabulary – Fitness – Genetic Drift – Punctuated Equilibrium – Gene flow – Adaptive radiation – Divergent evolution – Convergent evolution – Gradualism 17.1 – Genes & Variation ● Darwin developed his theory of natural selection without knowing how heredity worked…or how variations arise ● VARIATIONS are the raw materials for natural selection ● All of the discoveries in genetics fit perfectly into evolutionary theory! Genotype & Phenotype ● GENOTYPE : the particular combination of alleles an organism carries ● an organism’s genotype, together with environmental conditions, produces its PHENOTYPE ● PHENOTYPE : all physical, physiological, and behavioral characteristics of an organism (i.e. eye color, height ) Natural Selection ● NATURAL SELECTION acts directly on… …PHENOTYPES ! ● How does that work?...some individuals have phenotypes that are better suited to their environment…they survive & produce more offspring (higher fitness!) ● organisms with higher fitness pass more copies of their genes to the next generation! Do INDIVIDUALS evolve? ● NO! ● Individuals are born with a certain set of genes (and therefore phenotypes) ● If one or more of their phenotypes (i.e. tooth shape, flower color, etc.) are poorly adapted, they may be unable to survive and reproduce ● An individual CANNOT evolve a new phenotype in response to its environment So, EVOLUTION acts on… ● POPULATIONS! ● POPULATION = all members of a species that live in a particular area ● In a population, there exists a RANGE of phenotypes ● NATURAL SELECTION acts on this range of phenotypes the most “fit” are selected for survival and reproduction 17.2: Evolution as Genetic Change in Populations Mechanisms of Evolution (How evolution happens) 1) Natural Selection (from Darwin) 2) Mutations 3) Migration (Gene Flow) 4) Genetic Drift DEFINITIONS: ● SPECIES: group of organisms that breed with one another and produce fertile offspring. -
Intro Forensic Stats
Popstats Unplugged 14th International Symposium on Human Identification John V. Planz, Ph.D. UNT Health Science Center at Fort Worth Forensic Statistics From the ground up… Why so much attention to statistics? Exclusions don’t require numbers Matches do require statistics Problem of verbal expression of numbers Transfer evidence Laboratory result 1. Non-match - exclusion 2. Inconclusive- no decision 3. Match - estimate frequency Statistical Analysis Focus on the question being asked… About “Q” sample “K” matches “Q” Who else could match “Q" partial profile, mixtures Match – estimate frequency of: Match to forensic evidence NOT suspect DNA profile Who is in suspect population? So, what are we really after? Quantitative statement that expresses the rarity of the DNA profile Estimate genotype frequency 1. Frequency at each locus Hardy-Weinberg Equilibrium 2. Frequency across all loci Linkage Equilibrium Terminology Genetic marker variant = allele DNA profile = genotype Database = table that provides frequency of alleles in a population Population = some assemblage of individuals based on some criteria for inclusion Where Do We Get These Numbers? 1 in 1,000,000 1 in 110,000,000 POPULATION DATA and Statistics DNA databases are needed for placing statistical weight on DNA profiles vWA data (N=129) 14 15 16 17 18 19 20 freq 14 9 75 15 3 0 6 16 19 1 1 46 17 23 1 14 9 72 18 6 0 3 10 4 31 19 6 1 7 3 2 2 23 20 0 0 0 3 2 0 0 5 258 Because data are not available for every genotype possible, We use allele frequencies instead of genotype frequencies to estimate rarity. -
Lecture 9: Population Genetics
Lecture 9: Population Genetics Plan of the lecture I. Population Genetics: definitions II. Hardy-Weinberg Law. III. Factors affecting gene frequency in a population. Small populations and founder effect. IV. Rare Alleles and Eugenics The goal of this lecture is to make students familiar with basic models of population genetics and to acquaint students with empirical tests of these models. It will discuss the primary forces and processes involved in shaping genetic variation in natural populations (mutation, drift, selection, migration, recombination, mating patterns, population size and population subdivision). I. Population genetics: definitions Population – group of interbreeding individuals of the same species that are occupying a given area at a given time. Population genetics is the study of the allele frequency distribution and change under the influence of the 4 evolutionary forces: natural selection, mutation, migration (gene flow), and genetic drift. Population genetics is concerned with gene and genotype frequencies, the factors that tend to keep them constant, and the factors that tend to change them in populations. All the genes at all loci in every member of an interbreeding population form gene pool. Each gene in the genetic pool is present in two (or more) forms – alleles. Individuals of a population have same number and kinds of genes (except sex genes) and they have different combinations of alleles (phenotypic variation). The applications of Mendelian genetics, chromosomal abnormalities, and multifactorial inheritance to medical practice are quite evident. Physicians work mostly with patients and families. However, as important as they may be, genes affect populations, and in the long run their effects in populations have a far more important impact on medicine than the relatively few families each physician may serve. -
1 Genepool: Exploring the Interaction Between Natural Selection and Sexual Selection
1 GenePool: Exploring The Interaction Between Natural Selection and Sexual Selection Jeffrey Ventrella Gene Pool is an artificial life simulation designed to bring some basic principles of evolution to light in an entertaining and instructive way. Most significant is the aspect of sexual selection — where mate choice is a factor in the evolution of morphology and motor-control in physically-based animated organisms. We see in the examples of deer antlers, peacock tails, and fish coloration a magnificent world of variation that makes the study of animals fascinating for us — aesthetically — driven humans that we are. But aesthetics is in the eye of the beholder. And sometimes aesthetics can run counter to the rules of basic survival. Gene Pool was designed to explore this topic. 1.0.1 History In 1996, an animated artificial life simulation, called Darwin Pond, was designed, and a paper was published describing the simulation [13]. In Darwin Pond, hundreds of physically-based organisms achieve locomotion via genetically-based motor con- trol and morphology. The ability to have more offspring is a direct outcome of two factors: 1) better ability to swim to within a critical distance to a chosen mate, and 2), the ability to attract other organisms who want to mate. Because Darwin Pond was developed at a computer game company (Rocket Sci- ence Games, Inc.) it included a significant interactive component.Rocket Science did not survive as a company, and after much effort, Darwin Pond was released from the corporate and legal complexities of the software games world, and it was published for free at, where it has remained. -
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. -
Allele Frequency Difference AFD–An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation
G C A T T A C G G C A T genes Opinion Allele Frequency Difference AFD–An Intuitive Alternative to FST for Quantifying Genetic Population Differentiation Daniel Berner Department of Environmental Sciences, Zoology, University of Basel, Vesalgasse 1, CH-4051 Basel, Switzerland; [email protected]; Tel.: +41-(0)-61-207-03-28 Received: 21 February 2019; Accepted: 12 April 2019; Published: 18 April 2019 Abstract: Measuring the magnitude of differentiation between populations based on genetic markers is commonplace in ecology, evolution, and conservation biology. The predominant differentiation metric used for this purpose is FST. Based on a qualitative survey, numerical analyses, simulations, and empirical data, I here argue that FST does not express the relationship to allele frequency differentiation between populations generally considered interpretable and desirable by researchers. In particular, FST (1) has low sensitivity when population differentiation is weak, (2) is contingent on the minor allele frequency across the populations, (3) can be strongly affected by asymmetry in sample sizes, and (4) can differ greatly among the available estimators. Together, these features can complicate pattern recognition and interpretation in population genetic and genomic analysis, as illustrated by empirical examples, and overall compromise the comparability of population differentiation among markers and study systems. I argue that a simple differentiation metric displaying intuitive properties, the absolute allele frequency difference AFD, provides a valuable alternative to FST. I provide a general definition of AFD applicable to both bi- and multi-allelic markers and conclude by making recommendations on the sample sizes needed to achieve robust differentiation estimates using AFD. -
Chapter 8 an Introduction to Population Genetics
Chapter 8 An Introduction to Population Genetics Matthew E. Andersen Department of Biological Sciences University of Nevada, Las Vegas Las Vegas, Nevada 89154-4004 Matthew Andersen received his B.A. in 1986 from Sonoma State University, California. He was an honors student for his undergraduate work and is now a doctoral student at UNLV. He has worked in biomedical research and as a pathologist's assistant. His Ph.D. research is on the molecular systematics of fish, particularly speckled dace, Rhinichthys osculus (Cyprinidae). Reprinted from: Andersen, M. E. 1993. An introduction to population genetics. Pages 141-152, in Tested studies for laboratory teaching, Volume 14 (C. A. Goldman, Editor). Proceedings of the 14th Workshop/Conference of the Association for Biology Laboratory Education (ABLE), 240 pages. - Copyright policy: http://www.zoo.utoronto.ca/able/volumes/copyright.htm Although the laboratory exercises in ABLE proceedings volumes have been tested and due consideration has been given to safety, individuals performing these exercises must assume all responsibility for risk. The Association for Biology Laboratory Education (ABLE) disclaims any liability with regards to safety in connection with the use of the exercises in its proceedings volumes. © 1993 Matthew E. Andersen 141 Association for Biology Laboratory Education (ABLE) ~ http://www.zoo.utoronto.ca/able 142 Population Genetics Contents Introduction....................................................................................................................142 Student -
The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations
Copyright 2004 by the Genetics Society of America The Allele Frequency Spectrum in Genome-Wide Human Variation Data Reveals Signals of Differential Demographic History in Three Large World Populations Gabor T. Marth,1 Eva Czabarka, Janos Murvai and Stephen T. Sherry National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894 Manuscript received April 15, 2003 Accepted for publication September 4, 2003 ABSTRACT We have studied a genome-wide set of single-nucleotide polymorphism (SNP) allele frequency measures for African-American, East Asian, and European-American samples. For this analysis we derived a simple, closed mathematical formulation for the spectrum of expected allele frequencies when the sampled populations have experienced nonstationary demographic histories. The direct calculation generates the spectrum orders of magnitude faster than coalescent simulations do and allows us to generate spectra for a large number of alternative histories on a multidimensional parameter grid. Model-fitting experiments using this grid reveal significant population-specific differences among the demographic histories that best describe the observed allele frequency spectra. European and Asian spectra show a bottleneck-shaped history: a reduction of effective population size in the past followed by a recent phase of size recovery. In contrast, the African-American spectrum shows a history of moderate but uninterrupted population expansion. These differences are expected to have profound consequences for the design of medical association studies. The analytical methods developed for this study, i.e., a closed mathematical formulation for the allele frequency spectrum, correcting the ascertainment bias introduced by shallow SNP sampling, and dealing with variable sample sizes provide a general framework for the analysis of public variation data.