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Selective Sweep Biotechnology Intelligence Unit Medical Intelligence Unit Molecular Biology Intelligence Unit MOLECULAR BIOLOGY INTELLIGENCE UNIT MOLECULAR BIOLOGY INTELLIGENCE UNIT Landes Bioscience, a bioscience publisher, is making a transition to the internet as Dmitry Nurminsky Eurekah.com. NURMINSKY INTELLIGENCE UNITS Selective Sweep Biotechnology Intelligence Unit Medical Intelligence Unit Molecular Biology Intelligence Unit Neuroscience Intelligence Unit MBIU Tissue Engineering Intelligence Unit The chapters in this book, as well as the chapters of all of the five Intelligence Unit series, are available at our website. S elective Sweep elective ISBN 0-306-48235-5 9780306 482359 MOLECULAR BIOLOGY INTELLIGENCE UNIT MOLECULAR BIOLOGY INTELLIGENCE UNIT Landes Bioscience, a bioscience publisher, is making a transition to the internet as Dmitry Nurminsky Eurekah.com. NURMINSKY INTELLIGENCE UNITS Selective Sweep Biotechnology Intelligence Unit Medical Intelligence Unit Molecular Biology Intelligence Unit Neuroscience Intelligence Unit MBIU Tissue Engineering Intelligence Unit The chapters in this book, as well as the chapters of all of the five Intelligence Unit series, are available at our website. S elective Sweep elective ISBN 0-306-48235-5 9780306 482359 MOLECULAR BIOLOGY INTELLIGENCE UNIT Selective Sweep Dmitry Nurminsky, Ph.D. Department of Anatomy and Cellular Biology Tufts University School of Medicine Boston, Massachusetts, U.S.A. LANDES BIOSCIENCE / EUREKAH.COM KLUWER ACADEMIC / PLENUM PUBLISHERS GEORGETOWN, TEXAS NEW YORK, NEW YORK U.S.A. U.S.A. SELECTIVE SWEEP Molecular Biology Intelligence Unit Landes Bioscience / Eurekah.com Kluwer Academic / Plenum Publishers Copyright ©2005 Eurekah.com and Kluwer Academic / Plenum Publishers All rights reserved. No part of this book may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopy, recording, or any information storage and retrieval system, without permission in writing from the publisher. Printed in the U.S.A. Kluwer Academic / Plenum Publishers, 233 Spring Street, New York, New York, U.S.A. 10013 http://www.wkap.nl Please address all inquiries to the Publishers: Landes Bioscience / Eurekah.com, 810 South Church Street, Georgetown, Texas, U.S.A. 78626 Phone: 512/ 863 7762; FAX: 512/ 863 0081 http://www.eurekah.com http://www.landesbioscience.com ISBN: 0-306-48235-5 Selective Sweep edited by Dmitry Nurminsky, Landes / Kluwer dual imprint / Landes series: Molecular Biology Intelligence Unit While the authors, editors and publisher believe that drug selection and dosage and the specifications and usage of equipment and devices, as set forth in this book, are in accord with current recommend- ations and practice at the time of publication, they make no warranty, expressed or implied, with respect to material described in this book. In view of the ongoing research, equipment development, changes in governmental regulations and the rapid accumulation of information relating to the biomedical sciences, the reader is urged to carefully review and evaluate the information provided herein. Library of Congress Cataloging-in-Publication Data Selective sweep / [edited by] Dmitry Nurminsky. p. ; cm. -- (Molecular biology intelligence unit) Includes bibliographical references and index. ISBN 0-306-48235-5 1. Mutation (Biology) 2. Population genetics. 3. Natural selection. I. Nurminsky, Dmitry. II. Series: Molecular biology intelligence unit (Unnumbered) [DNLM: 1. Selection (Genetics) 2. Evolution, Molecular. 3. Mutation. QH 455 S464 2005] QH460.S454 2005 576.5'49--dc22 2004023424 CONTENTS Preface ................................................................................................. vii 1. Inferring Evolutionary History through Inter- and Intraspecific DNA Sequence Comparison: The Drosophila janus and ocnus Genes .............. 1 John Parsch, Colin D. Meiklejohn and Daniel L. Hartl Detecting Selection by Inter- and Intraspecific DNA Sequence Comparison ...................................................................................... 1 Molecular Evolution of the janus and ocnus Genes in the D. melanogaster Species Subgroup...................................................... 3 DNA Sequence Polymorphism in the janus-ocnus Region of D. simulans .................................................................................... 5 Distinguishing between Demographics and Selection ............................ 8 Identifying Specific Targets of Positive Selection ................................. 10 2. Rapid Evolution of Sex-Related Genes: Sexual Conflict or Sex-Specific Adaptations? ........................................ 13 Alberto Civetta and Rama S. Singh Are Males Conflicting with Females or Coadapting to Them? ............. 14 Conflict Scenarios: Balancing Selection in Rapidly Evolving Immune System Genes .................................................................... 15 External Fertilization: How Are Marine Invertebrate Sperm Surface Proteins Different from Immune System Genes? ............................. 16 Internal Fertilization: Lessons from Drosophila .................................... 16 Arm-Race vs. Sex-Specific Coadaptation: Test of Hypotheses.............. 17 3. Selective Sweep in the Evolution of a New Sperm-Specific Gene in Drosophila ....................................................................................... 22 Rob J. Kulathinal, Stanley A. Sawyer, Carlos D. Bustamante, Dmitry Nurminsky, Rita Ponce, José M. Ranz and Daniel L. Hartl The Origin of Sdic ............................................................................... 24 The Molecular Structure of Sdic .......................................................... 25 Reduced Polymorphism in the Region of Sdic ..................................... 26 The Issue of Background Selection ...................................................... 26 Further Evidence for a Selective Sweep ................................................ 27 Bayesian Analysis of Polymorphism and Divergence in the Sdic Region ........................................................................... 28 Rapid Evolution of Male-Specific Genes ............................................. 29 4. Detecting Selective Sweeps with Haplotype Tests: Hitchhiking and Haplotype Tests ........................................................ 34 Frantz Depaulis, Sylvain Mousset and Michel Veuille Available Haplotype Tests ................................................................... 37 Alternative Hypotheses ........................................................................ 40 Conditioning on S vs. θ....................................................................... 40 Intragenic Recombination ................................................................... 42 Sampling Strategy and Sliding Window .............................................. 42 Power .................................................................................................. 43 5. A Novel Test Statistic for the Identification of Local Selective Sweeps Based on Microsatellite Gene Diversity ..................... 55 Christian Schlötterer and Daniel Dieringer Material and Methods ......................................................................... 56 Results ................................................................................................. 57 Discussion ........................................................................................... 63 6. Detecting Hitchhiking from Patterns of DNA Polymorphism ............. 65 Justin C. Fay and Chung-I Wu Reduction in Levels of Variation ......................................................... 65 Skew in the Frequency Spectrum......................................................... 67 Linkage Disequilibrium ....................................................................... 70 Population Subdivision and Changes in Population Size ..................... 72 Distinguishing Background Selection and Hitchhiking in Regions of Low Recombination .................................................. 74 7. Periodic Selection and Ecological Diversity in Bacteria ........................ 78 Frederick M. Cohan The Nature of Recombination in Bacteria ........................................... 79 The Effect of Rare Recombination on Diversity within a Population ......................................................................... 80 The Origins of Permanent Divergence ................................................ 80 Effects of Periodic Selection beyond the Boundaries of the Ecotype ................................................................................. 83 Periodic Selection and Discovery of Bacterial Ecotypes........................ 86 Has Periodic Selection Occurred in Nature? ........................................ 89 8. Distribution and Abundance of Polymorphism in the Malaria Genome ........................................................................ 94 Stephen M. Rich 9. Selective Sweeps in Structured Populations—Empirical Evidence and Theoretical Studies ...................................................................... 104 Thomas Wiehe, Karl Schmid and Wolfgang Stephan Experimental Evidence ...................................................................... 105 Theoretical Studies ............................................................................ 110 Discussion ......................................................................................... 113 Index .................................................................................................. 119 EDITOR Dmitry Nurminsky
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