Genomic Insights Into Positive Selection
Total Page:16
File Type:pdf, Size:1020Kb
Load more
Recommended publications
-
Approximating Selective Sweeps
Approximating Selective Sweeps by Richard Durrett and Jason Schweinsberg Dept. of Math, Cornell U. Corresponding Author: Richard Durrett Dept. of Mathematics 523 Malott Hall Cornell University Ithaca NY 14853 Phone: 607-255-8282 FAX: 607-255-7149 email: [email protected] 1 ABSTRACT The fixation of advantageous mutations in a population has the effect of reducing varia- tion in the DNA sequence near that mutation. Kaplan, Hudson, and Langley (1989) used a three-phase simulation model to study the effect of selective sweeps on genealogies. However, most subsequent work has simplified their approach by assuming that the number of individ- uals with the advantageous allele follows the logistic differential equation. We show that the impact of a selective sweep can be accurately approximated by a random partition created by a stick-breaking process. Our simulation results show that ignoring the randomness when the number of individuals with the advantageous allele is small can lead to substantial errors. Key words: selective sweep, hitchhiking, coalescent, random partition, paintbox construction 2 When a selectively favorable mutation occurs in a population and is subsequently fixed (i.e., its frequency rises to 100%), the frequencies of alleles at closely linked loci are altered. Alleles present on the chromosome on which the original mutation occurred will tend to increase in frequency, and other alleles will decrease in frequency. Maynard Smith and Haigh (1974) referred to this as the ‘hitchhiking effect,’ because an allele can get a lift in frequency from selection acting on a neighboring allele. They considered a situation with a neutral locus with alleles A and a and a second locus where allele B has a fitness of 1 + s relative to b. -
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. -
Joint Effects of Genetic Hitchhiking and Background Selection on Neutral Variation
Copyright 2000 by the Genetics Society of America Joint Effects of Genetic Hitchhiking and Background Selection on Neutral Variation Yuseob Kim and Wolfgang Stephan Department of Biology, University of Rochester, Rochester, New York 14627 Manuscript received December 7, 1999 Accepted for publication March 20, 2000 ABSTRACT Due to relatively high rates of strongly selected deleterious mutations, directional selection on favorable alleles (causing hitchhiking effects on linked neutral polymorphisms) is expected to occur while a deleteri- ous mutation-selection balance is present in a population. We analyze this interaction of directional selection and background selection and study their combined effects on neutral variation, using a three- locus model in which each locus is subjected to either deleterious, favorable, or neutral mutations. Average heterozygosity is measured by simulations (1) at the stationary state under the assumption of recurrent hitchhiking events and (2) as a transient level after a single hitchhiking event. The simulation results are compared to theoretical predictions. It is shown that known analytical solutions describing the hitchhiking effect without background selection can be modi®ed such that they accurately predict the joint effects of hitchhiking and background on linked, neutral variation. Generalization of these results to a more appro- priate multilocus model (such that background selection can occur at multiple sites) suggests that, in regions of very low recombination rates, stationary levels of nucleotide diversity are primarily determined by hitchhiking, whereas in regions of high recombination, background selection is the dominant force. The implications of these results on the identi®cation and estimation of the relevant parameters of the model are discussed. -
Purebred Dog Breeds Into the Twenty-First Century: Achieving Genetic Health for Our Dogs
Purebred Dog Breeds into the Twenty-First Century: Achieving Genetic Health for Our Dogs BY JEFFREY BRAGG WHAT IS A CANINE BREED? What is a breed? To put the question more precisely, what are the necessary conditions that enable us to say with conviction, "this group of animals constitutes a distinct breed?" In the cynological world, three separate approaches combine to constitute canine breeds. Dogs are distinguished first by ancestry , all of the individuals descending from a particular founder group (and only from that group) being designated as a breed. Next they are distinguished by purpose or utility, some breeds existing for the purpose of hunting particular kinds of game,others for the performance of particular tasks in cooperation with their human masters, while yet others owe their existence simply to humankind's desire for animal companionship. Finally dogs are distinguished by typology , breed standards (whether written or unwritten) being used to describe and to recognize dogs of specific size, physical build, general appearance, shape of head, style of ears and tail, etc., which are said to be of the same breed owing to their similarity in the foregoing respects. The preceding statements are both obvious and known to all breeders and fanciers of the canine species. Nevertheless a correct and full understanding of these simple truisms is vital to the proper functioning of the entire canine fancy and to the health and well being of the animals which are the object of that fancy. It is my purpose in this brief to elucidate the interrelationship of the above three approaches, to demonstrate how distortions and misunderstandings of that interrelationship now threaten the health of all of our dogs and the very existence of the various canine breeds, and to propose reforms which will restore both balanced breed identity and genetic health to CKC breeds. -
A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome
PLoS BIOLOGY A New Approach for Using Genome Scans to Detect Recent Positive Selection in the Human Genome Kun Tang1*, Kevin R. Thornton2, Mark Stoneking1 1 Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany, 2 Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California, United States of America Genome-wide scanning for signals of recent positive selection is essential for a comprehensive and systematic understanding of human adaptation. Here, we present a genomic survey of recent local selective sweeps, especially aimed at those nearly or recently completed. A novel approach was developed for such signals, based on contrasting the extended haplotype homozygosity (EHH) profiles between populations. We applied this method to the genome single nucleotide polymorphism (SNP) data of both the International HapMap Project and Perlegen Sciences, and detected widespread signals of recent local selection across the genome, consisting of both complete and partial sweeps. A challenging problem of genomic scans of recent positive selection is to clearly distinguish selection from neutral effects, given the high sensitivity of the test statistics to departures from neutral demographic assumptions and the lack of a single, accurate neutral model of human history. We therefore developed a new procedure that is robust across a wide range of demographic and ascertainment models, one that indicates that certain portions of the genome clearly depart from neutrality. Simulations of positive selection showed that our tests have high power towards strong selection sweeps that have undergone fixation. Gene ontology analysis of the candidate regions revealed several new functional groups that might help explain some important interpopulation differences in phenotypic traits. -
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. -
Refining the Use of Linkage Disequilibrium As A
HIGHLIGHTED ARTICLE | INVESTIGATION Refining the Use of Linkage Disequilibrium as a Robust Signature of Selective Sweeps Guy S. Jacobs,*,†,1 Timothy J. Sluckin,* and Toomas Kivisild‡ *Mathematical Sciences, University of Southampton, Southampton SO17 1BJ, United Kingdom, †Complexity Institute, Nanyang Technological University, Singapore 637723, and ‡Department of Biological Anthropology, University of Cambridge, Cambridge CB2 1QH, United Kingdom ORCID IDs: 0000-0002-4698-7758 (G.S.J.); 0000-0002-9163-0061 (T.J.S.); 0000-0002-6297-7808 (T.K.) ABSTRACT During a selective sweep, characteristic patterns of linkage disequilibrium can arise in the genomic region surrounding a selected locus. These have been used to infer past selective sweeps. However, the recombination rate is known to vary substantially along the genome for many species. We here investigate the effectiveness of current (Kelly’s ZnS and vmax) and novel statistics at inferring hard selective sweeps based on linkage disequilibrium distortions under different conditions, including a human-realistic demographic model and recombination rate variation. When the recombination rate is constant, Kelly’s ZnS offers high power, but is outperformed by a novel statistic that we test, which we call Za: We also find this statistic to be effective at detecting sweeps from standing variation. When recombination rate fluctuations are included, there is a considerable reduction in power for all linkage disequilibrium-based statistics. However, this can largely be reversed by appropriately controlling for expected linkage disequilibrium using a genetic map. To further test these different methods, we perform selection scans on well-characterized HapMap data, finding that all three statistics—vmax; Kelly’s ZnS; and Za—are able to replicate signals at regions previously identified as selection candidates based on population differentiation or the site frequency spectrum. -
Identification of Selective Sweeps, Major Genes, and Genotype by Diet Interactions Melanie D
University of Nebraska - Lincoln DigitalCommons@University of Nebraska - Lincoln Theses and Dissertations in Animal Science Animal Science Department 12-2015 Genomic Analysis of Sow Reproductive Traits: Identification of Selective Sweeps, Major Genes, and Genotype by Diet Interactions Melanie D. Trenhaile University of Nebraska-Lincoln, [email protected] Follow this and additional works at: http://digitalcommons.unl.edu/animalscidiss Part of the Meat Science Commons Trenhaile, Melanie D., "Genomic Analysis of Sow Reproductive Traits: Identification of Selective Sweeps, Major Genes, and Genotype by Diet Interactions" (2015). Theses and Dissertations in Animal Science. 114. http://digitalcommons.unl.edu/animalscidiss/114 This Article is brought to you for free and open access by the Animal Science Department at DigitalCommons@University of Nebraska - Lincoln. It has been accepted for inclusion in Theses and Dissertations in Animal Science by an authorized administrator of DigitalCommons@University of Nebraska - Lincoln. GENOMIC ANALYSIS OF SOW REPRODUCTIVE TRAITS: IDENTIFICATION OF SELECTIVE SWEEPS, MAJOR GENES, AND GENOTYPE BY DIET INTERACTIONS By Melanie Dawn Trenhaile A THESIS Presented to the Faculty of The Graduate College at the University of Nebraska In Partial Fulfillment of Requirements For the Degree of Master of Science Major: Animal Science Under the Supervision of Professor Daniel Ciobanu Lincoln, Nebraska December, 2015 GENOMIC ANALYSIS OF SOW REPRODUCTIVE TRAITS: IDENTIFICATION OF SELECTIVE SWEEPS, MAJOR GENES, AND GENOTYPE BY DIET INTERACTIONS Melanie D. Trenhaile, M.S. University of Nebraska, 2015 Advisor: Daniel Ciobanu Reproductive traits, such as litter size and reproductive longevity, are economically important. However, selection for these traits is difficult due to low heritability, polygenic nature, sex-limited expression, and expression late in life. -
Experiments on the Role of Deleterious Mutations As Stepping Stones In
Experiments on the role of deleterious mutations as PNAS PLUS stepping stones in adaptive evolution Arthur W. Covert IIIa,b,c,d, Richard E. Lenskia,c,e,1, Claus O. Wilkec,d, and Charles Ofriaa,b,c,1 aProgram in Ecology, Evolutionary Biology and Behavior, Departments of bComputer Science and Engineering and eMicrobiology and Molecular Genetics, and cBEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI 48824; and dCenter for Computational Biology, Institute for Cellular and Molecular Biology, and Department of Integrative Biology, University of Texas at Austin, Austin, TX 78712 Contributed by Richard E. Lenski, July 16, 2013 (sent for review April 22, 2013) Many evolutionary studies assume that deleterious mutations spread unless they are tightly linked (5, 6). In an asexual pop- necessarily impede adaptive evolution. However, a later mutation ulation, however, the fortuitous combination, once formed, will that is conditionally beneficial may interact with a deleterious be stably inherited, thereby providing a simple way to traverse a predecessor before it is eliminated, thereby providing access to fitness valley (5–10). adaptations that might otherwise be inaccessible. It is unknown Previous research on a variety of systems, both biological and whether such sign-epistatic recoveries are inconsequential events computational, has documented many examples of epistatic inter- or an important factor in evolution, owing to the difficulty of actions between mutations (3, 6, 11, 14–24), including a few cases monitoring the effects and fates of all mutations during experi- of mutational pairs that are individually deleterious but jointly ments with biological organisms. -
Rapid Evolution of a Skin-Lightening Allele in Southern African Khoesan
Rapid evolution of a skin-lightening allele in southern African KhoeSan Meng Lina,1,2, Rebecca L. Siforda,b,3, Alicia R. Martinc,d,e,3, Shigeki Nakagomef, Marlo Möllerg, Eileen G. Hoalg, Carlos D. Bustamanteh, Christopher R. Gignouxh,i,j, and Brenna M. Henna,2,4 aDepartment of Ecology and Evolution, State University of New York at Stony Brook, Stony Brook, NY 11794; bThe School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85287; cAnalytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114; dProgram in Medical and Population Genetics, Broad Institute, Cambridge, MA 02141; eStanley Center for Psychiatric Research, Broad Institute, Cambridge, MA 02141; fSchool of Medicine, Trinity College Dublin, Dublin 2, Ireland; gDST-NRF Centre of Excellence for Biomedical Tuberculosis Research, South African Medical Research Council Centre for Tuberculosis Research, Division of Molecular Biology and Human Genetics, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town 8000, South Africa; hDepartment of Genetics, Stanford University, Stanford, CA 94305; iColorado Center for Personalized Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO 80045; and jDepartment of Biostatistics and Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045 Edited by Nina G. Jablonski, The Pennsylvania State University, University Park, PA, and accepted by Editorial Board Member C. O. Lovejoy October 18, 2018 (received for review February 2, 2018) Skin pigmentation is under strong directional selection in northern Amhara or another group who themselves are substantially European and Asian populations. The indigenous KhoeSan popula- admixed with Near Eastern people has been proposed (13, 14). -
Review of the Current State of Genetic Testing - a Living Resource
Review of the Current State of Genetic Testing - A Living Resource Prepared by Liza Gershony, DVM, PhD and Anita Oberbauer, PhD of the University of California, Davis Editorial input by Leigh Anne Clark, PhD of Clemson University July, 2020 Contents Introduction .................................................................................................................................................. 1 I. The Basics ......................................................................................................................................... 2 II. Modes of Inheritance ....................................................................................................................... 7 a. Mendelian Inheritance and Punnett Squares ................................................................................. 7 b. Non-Mendelian Inheritance ........................................................................................................... 10 III. Genetic Selection and Populations ................................................................................................ 13 IV. Dog Breeds as Populations ............................................................................................................. 15 V. Canine Genetic Tests ...................................................................................................................... 16 a. Direct and Indirect Tests ................................................................................................................ 17 b. Single -
The Neutral Theory of Molecular Evolution
Copyright 2000 by the Genetics Society of America Perspectives Anecdotal, Historical and Critical Commentaries on Genetics Edited by James F. Crow and William F. Dove Thomas H. Jukes (1906±1999) James F. Crow Genetics Department, University of Wisconsin, Madison, Wisconsin 53706 OM Jukes accepted our invitation to write a Perspec- duced an immediate outcry from traditional students Ttives on the early history of molecular evolution, of evolution, undoubtedly abetted by the title. In the and in August 1999 he sent a rough beginning con- ensuing polemics, Kimura played the major role. King taining some now-forgotten early history. He planned an died prematurely in 1983 and Jukes wrote mainly about extensive revision and continuation, but on November 1 other things, although he did participate in one joint his death intervened. We have decided to publish his paper (Jukes and Kimura 1984). One of his interests early draft, realizing that it was but a start toward the was the evolution of the genetic code (Jukes 1983). I article that he had planned. particularly liked his showing how, in an orderly sequen- Tom, along with Jack L. King and Motoo Kimura, tial way, mutation pressure in the codon and anti-codon formulated the neutral theory of molecular evolution. could produce the unexpected codes in bacteria and Earlier, the idea had been foreshadowed by Sueoka mitochondria (Jukes 1985). He also developed a widely (1962) and Freese (1962). They had each suggested used correction for multiple undetected changes in evo- mutation pressure of near-neutral changes to account lutionary base substitutions (Jukes and Cantor 1969).