Selective Sweep - Dmitry Nurminsky.pdf

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MOLECULAR BIOLOGY INTELLIGENCE UNIT
Dmitry Nurminsky
Selective Sweep
MBIU
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MOLECULAR BIOLOGY INTELLIGENCE UNIT
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ISBN 0-306-48235-5
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M OLECULAR B IOLOGY
U NIT
Selective Sweep
Dmitry Nurminsky, Ph.D.
Department of Anatomy and Cellular Biology
Tufts University School of Medicine
Boston, Massachusetts, U.S.A.
L ANDES B IOSCIENCE / E UREKAH . COM
G EORGETOWN , T EXAS
U.S.A.
K LUWER A CADEMIC / P LENUM P UBLISHERS
N EW Y ORK , N EW Y ORK
U.S.A.
I NTELLIGENCE
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S ELECTIVE S WEEP
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
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Please address all inquiries to the Publishers:
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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
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