On the Unfounded Enthusiasm for Soft Selective Sweeps III: the Supervised Machine Learning Algorithm That Isn’T
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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. -
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. -
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. -
Soft Sweeps II—Molecular Population Genetics of Adaptation from Recurrent Mutation Or Migration
Soft Sweeps II—Molecular Population Genetics of Adaptation from Recurrent Mutation or Migration Pleuni S. Pennings and Joachim Hermisson Section of Evolutionary Biology, Department of Biology II, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany In the classical model of molecular adaptation, a favored allele derives from a single mutational origin. This ignores that beneficial alleles can enter a population recurrently, either by mutation or migration, during the selective phase. In this case, descendants of several of these independent origins may contribute to the fixation. As a consequence, all ancestral hap- lotypes that are linked to any of these copies will be retained in the population, affecting the pattern of a selective sweep on linked neutral variation. In this study, we use analytical calculations based on coalescent theory and computer simulations to analyze molecular adaptation from recurrent mutation or migration. Under the assumption of complete linkage, we derive a robust analytical approximation for the number of ancestral haplotypes and their distribution in a sample from the population. We find that so-called ‘‘soft sweeps,’’ where multiple ancestral haplotypes appear in a sample, are likely for biologically realistic values of mutation or migration rates. Introduction When a beneficial allele rises to fixation in a popu- selected allele, ‘‘soft sweeps.’’ They are distinguished from lation, it erases genetic variation in a stretch of DNA that the classical ‘‘hard sweeps’’ where ancestral variation is is linked to it. This phenomenon is called ‘‘genetic hitchhik- maintained only through recombination. ing’’ or a ‘‘selective sweep’’ and was first described by Selective sweeps from the standing genetic variation Maynard Smith and Haigh (1974). -
JEWISH REVIEW of BOOKS Volume 5, Number 1 Spring 2014 $7.95
The New Balaboosta, Khazar DNA & Agnon’s Lost Satire JEWISH REVIEW OF BOOKS Volume 5, Number 1 Spring 2014 $7.95 The Screenwriter & the Hoodlums Ben Hecht with Stuart Schoffman Ivan Marcus Rashi with Chumash Elliott Abrams Israel’s Journalist-Prophet Steven Aschheim The Memory Man Amy Newman Smith Expulsion Chick-Lit Gavriel D. Rosenfeld George Clooney, Historian NEW AT THE Editor CENTER FOR JEWISH HISTORY Abraham Socher Senior Contributing Editor Allan Arkush Art Director Betsy Klarfeld Associate Editor Amy Newman Smith Administrative Assistant Rebecca Weiss Editorial Board Robert Alter Shlomo Avineri Leora Batnitzky Ruth Gavison Moshe Halbertal Hillel Halkin Jon D. Levenson Anita Shapira Michael Walzer J. H.H. Weiler Leon Wieseltier Ruth R. Wisse Steven J. Zipperstein Publisher Eric Cohen Associate Publisher & Director of Marketing Lori Dorr NEW SPACE The Jewish Review of Books (Print ISSN 2153-1978, The David Berg Rare Book Room is a state-of- Online ISSN 2153-1994) is a quarterly publication the-art exhibition space preserving and dis- of ideas and criticism published in Spring, Summer, playing the written word, illuminating Jewish Fall, and Winter, by Bee.Ideas, LLC., 165 East 56th Street, 4th Floor, New York, NY 10022. history over time and place. For all subscriptions, please visit www.jewishreviewofbooks.com or send $29.95 UPCOMING EXHIBITION ($39.95 outside of the U.S.) to Jewish Review of Books, Opening Sunday, March 16: By Dawn’s Early PO Box 3000, Denville, NJ 07834. Please send notifi- cations of address changes to the same address or to Light: From Subjects to Citizens (presented by the [email protected]. -
Soft Sweeps and Beyond: Understanding the Patterns and Probabilities of Selection Footprints Under Rapid Adaptation
bioRxiv preprint doi: https://doi.org/10.1101/114587; this version posted March 7, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC 4.0 International license. 1 Soft sweeps and beyond: Understanding the 2 patterns and probabilities of selection footprints 3 under rapid adaptation 1∗ 2∗ 4 Joachim Hermisson & Pleuni S Pennings 1 Department of Mathematics and Max F. Perutz Laboratories, University of Vienna, [email protected] 2 Department of Biology, San Francisco State University, [email protected] ∗ both authors contributed equally 5 March 6, 2017 6 Abstract 7 1. The tempo and mode of adaptive evolution determine how natu- 8 ral selection shapes patterns of genetic diversity in DNA polymorphism 9 data. While slow mutation-limited adaptation leads to classical footprints 10 of \hard" selective sweeps, these patterns are different when adaptation 11 responds quickly to a novel selection pressure, acting either on standing 12 genetic variation or on recurrent new mutation. In the past decade, cor- 13 responding footprints of \soft" selective sweeps have been described both 14 in theoretical models and in empirical data. 15 2. Here, we summarize the key theoretical concepts and contrast model 16 predictions with observed patterns in Drosophila, humans, and microbes. 17 3. Evidence in all cases shows that \soft" patterns of rapid adaptation 18 are frequent. However, theory and data also point to a role of complex 19 adaptive histories in rapid evolution. -
1 Research Article the Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses Eran
Research Article The Missing Link of Jewish European Ancestry: Contrasting the Rhineland and the Khazarian Hypotheses Eran Israeli-Elhaik1,2 1 Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD, USA, 21208. 2 McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA, 21208. Running head: The Missing Link of Jewish European Ancestry Keywords: Jewish genome, Khazars, Rhineland, Ashkenazi Jews, population isolate, Population structure Please address all correspondence to Eran Elhaik at [email protected] Phone: 410-502-5740. Fax: 410-502-7544. 1 Abstract The question of Jewish ancestry has been the subject of controversy for over two centuries and has yet to be resolved. The “Rhineland Hypothesis” proposes that Eastern European Jews emerged from a small group of German Jews who migrated eastward and expanded rapidly. Alternatively, the “Khazarian Hypothesis” suggests that Eastern European descended from Judean tribes who joined the Khazars, an amalgam of Turkic clans that settled the Caucasus in the early centuries CE and converted to Judaism in the 8th century. The Judaized Empire was continuously reinforced with Mesopotamian and Greco-Roman Jews until the 13th century. Following the collapse of their empire, the Judeo-Khazars fled to Eastern Europe. The rise of European Jewry is therefore explained by the contribution of the Judeo-Khazars. Thus far, however, their contribution has been estimated only empirically; the absence of genome-wide data from Caucasus populations precluded testing the Khazarian Hypothesis. Recent sequencing of modern Caucasus populations prompted us to revisit the Khazarian Hypothesis and compare it with the Rhineland Hypothesis. -
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). -
1 the Genochip: a New Tool for Genetic Anthropology Eran Elhaik
The GenoChip: A New Tool for Genetic Anthropology Eran Elhaik1, Elliott Greenspan2, Sean Staats2, Thomas Krahn2, Chris Tyler-Smith3, Yali Xue3, Sergio Tofanelli4, Paolo Francalacci5, Francesco Cucca6, Luca Pagani3,7, Li Jin8, Hui Li8, Theodore G. Schurr9, Bennett Greenspan2, R. Spencer Wells10,* and the Genographic Consortium 1 Department of Mental Health, Johns Hopkins University Bloomberg School of Public Health, 615 N. Wolfe Street, Baltimore, MD 21205, USA 2 Family Tree DNA, Houston, TX 77008, USA 3 The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, UK 4 Department of Biology, University of Pisa, Italy 5 Department of Natural and Environmental Science, Evolutionary Genetics Lab, University of Sassari, Italy 6 National Research Council, Monserrato, Italy 7 Division of Biological Anthropology, University of Cambridge, UK 8 Fudan University, Shanghai, China 9 University of Pennsylvania, Philadelphia, PA 10 National Geographic Society, Washington DC, USA *Please address all correspondence to Spencer Wells at [email protected] 1 Abstract The Genographic Project is an international effort using genetic data to chart human migratory history. The project is non-profit and non-medical, and through its Legacy Fund supports locally led efforts to preserve indigenous and traditional cultures. While the first phase of the project was focused primarily on uniparentally-inherited markers on the Y-chromosome and mitochondrial DNA, the next is focusing on markers from across the entire genome to obtain a more complete understanding of human genetic variation. In this regard, genomic admixture is one of the most crucial tools that will help us to analyze the genetic makeup and shared history of human populations. -
Identifying the Favored Mutation in a Positive Selective Sweep
HHS Public Access Author manuscript Author ManuscriptAuthor Manuscript Author Nat Methods Manuscript Author . Author manuscript; Manuscript Author available in PMC 2018 November 12. Published in final edited form as: Nat Methods. 2018 April ; 15(4): 279–282. doi:10.1038/nmeth.4606. Identifying the Favored Mutation in a Positive Selective Sweep Ali Akbari1, Joseph J. Vitti2,3, Arya Iranmehr1, Mehrdad Bakhtiari4, Pardis C. Sabeti2,3, Siavash Mirarab1, and Vineet Bafna4 1Department of Electrical & Computer Engineering, University of California San Diego, La Jolla, California, USA 2Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA 3Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA 4Department of Computer Science & Engineering, University of California San Diego, La Jolla, California, USA Abstract Methods to identify signatures of selective sweeps in population genomics data have been actively developed, but mostly do not identify the specific mutation favored by selection. We present a method, iSAFE, that uses a statistic derived solely from population genetics signals to accurately pinpoint the favored mutation in a large region (~5 Mbp). iSAFE does not require any knowledge of demography, specific phenotype under selection, or functional annotations of mutations. Human genetic data have revealed a multitude of genomic regions believed to be evolving under positive selection. Methods for detecting regions under selection from genetic variations exploit a variety of genomic signatures. Allele frequency based methods analyze the distortion in site frequency spectrums; Linkage Disequilibrium (LD) based methods use extended homozygosity in haplotypes; other methods use differences in allele frequency between populations; and finally, composite methods combine multiple test scores to improve the resolution1–3. -
Comparative Testing of DNA Segmentation Algorithms Using
Comparative Testing of DNA Segmentation Algorithms Using Benchmark Simulations Eran Elhaik,*,1 Dan Graur,1 and Kresˇimir Josic´2 1Department of Biology & Biochemistry, University of Houston 2Department of Mathematics, University of Houston *Corresponding author: E-mail: [email protected]. Associate editor: Hideki Innan Abstract Numerous segmentation methods for the detection of compositionally homogeneous domains within genomic sequences have been proposed. Unfortunately, these methods yield inconsistent results. Here, we present a benchmark consisting of Research article two sets of simulated genomic sequences for testing the performances of segmentation algorithms. Sequences in the first set are composed of fixed-sized homogeneous domains, distinct in their between-domain guanine and cytosine (GC) content variability. The sequences in the second set are composed of a mosaic of many short domains and a few long ones, distinguished by sharp GC content boundaries between neighboring domains. We use these sets to test the performance of seven segmentation algorithms in the literature. Our results show that recursive segmentation algorithms based on the Jensen–Shannon divergence outperform all other algorithms. However, even these algorithms perform poorly in certain instances because of the arbitrary choice of a segmentation-stopping criterion. Key words: isochores, GC content, segmentation algorithms, Jensen–Shannon divergence statistic, entropy, genome composition, benchmark simulations. Introduction into compositionally homogeneous domains according to predefined criteria. Segmentation methods include non- In 1976, Bernardi and colleagues (Macaya et al. 1976) put overlapping, sliding window methods (Bernardi 2001; Clay forward a theory concerning the compositional makeup of et al. 2001; International Human Genome Sequencing Con- vertebrate genomes. This description, later christened ‘‘the ´ isochore theory’’ (Cuny et al.