Table of Contents

PREFACE ix

ACKNOWLEDGMENTS xi

CONTRIBUTORS xiii

PART I GENERAL OVERVIEWS 1

1 Population Genetics and Parasite Diversity 3
Hsiao-Han Chang, Rachel F. Daniels, and Daniel L. Hartl

2 Evolution of Meiosis, Recombination, and Sexual Reproduction in Eukaryotic Microbes 17
Wenjun Li, Elizabeth Savelkoul, Joseph Heitman, and John M. Logsdon, Jr.

3 Phylogenomic Analysis 44
Andrew J. Roger, Martin Kolisko, and Alastair G. B. Simpson

4 Phylogenetics and Evolution of Virulence in the Kingdom Fungi 70
Monica A. Garcia-Solache and Arturo Casadevall

PART II POPULATION GENETICS AND EVOLUTIONARY APPROACHES 91

5 Malaria: Host Range, Diversity, and Speciation 93
Ananias A. Escalante and Francisco J. Ayala

6 From Population Genomics to Elucidated Traits in Plasmodium Falciparum 111
Sarah K. Volkman, Daniel E. Neafsey, Stephen F. Schaffner, Pardis C. Sabeti, and Dyann F. Wirth

7 Selective Sweeps in Human Malaria Parasites 124
Xin-zhuan Su and John C. Wootton

8 Evolution of Drug Resistance in Fungi 143
Jessica A. Hill, Samantha J. Hoot, Theodore C. White, and Leah E. Cowen

9 Discovery of Extant Sexual Cycles in Human Pathogenic Fungi and Their Roles in the Generation of Diversity and Virulence 168
Richard J. Bennett and Kirsten Nielsen

10 Worldwide Migrations, Host Shifts, and Reemergence of Phytophthora Infestans, the Plant Destroyer 192
Jean Beagle Ristaino

11 Experimental and Natural Evolution of the Cryptococcus Neoformans and Cryptococcus Gattii Species Complex 208
Alexander Idnurm and Jianping Xu

12 Population Genetics, Diversity, and Spread of Virulence in Toxoplasma Gondii 231
Benjamin M. Rosenthal and James W. Ajioka

PART III FORWARD AND REVERSE GENETIC SYSTEMS FOR DEFINING VIRULENCE 247

13 Genetic Crosses in Plasmodium Falciparum: Analysis of Drug Resistance 249
John C. Tan and Michael T. Ferdig

14 Genetic Mapping of Virulence in Rodent Malarias 269
Richard Carter and Richard Culleton

15 Genetic Mapping of Acute Virulence in Toxoplasma Gondii 285
L. David Sibley and John C. Boothroyd

16 Virulence in African Trypanosomes: Genetic and Molecular Approaches 307
Annette Macleod, Liam J. Morrison, and Andy Tait

17 The Evolution of Antigenic Variation in African Trypanosomes 324
Andrew P. Jackson and J. David Barry

18 Antigenic Variation, Adherence, and Virulence in Malaria 338
Joseph Smith and Kirk W. Deitsch

19 Invasion Ligand Diversity and Pathogenesis in Blood-Stage Malaria 362
Manoj T. Duraisingh, Jeffrey D. Dvorin, and Peter R. Preiser

PART IV COMPARATIVE "OMICS" APPROACHES TO DEFINING VIRULENCE 385

20 Evolution of Virulence in Oomycete Plant Pathogens 387
Paul R. J. Birch, Mary E. Coates, and Jim L. Beynon

21 Evolution and Genomics of the Pathogenic Candida Species Complex 404
Geraldine Butler, Michael Lorenz, and Neil A. R. Gow

22 Evolution of Entamoeba Histolytica Virulence 422
Upinder Singh and Christopher D. Huston

23 Sex and Virulence in Basidiomycete Pathogens 437
Guus Bakkeren, Emilia K. Kruzel, and Christina M. Hull

24 Emergence of the Chytrid Fungus Batrachochytrium Dendrobatidis and Global Amphibian Declines 461
Matthew C. Fisher, Jason E. Stajich, and Rhys A. Farrer

25 Impact of Horizontal Gene Transfer on Virulence of Fungal Pathogens of Plants 473
Barbara J. Howlett and Richard P. Oliver

26 Evolution of Plant Pathogenicity in Fusarium Species 485
Li-Jun Ma, H. Corby Kistler, and Martijn Rep

27 Genetic, Genomic, and Molecular Approaches to Define Virulence of Aspergillus Fumigatus 501
Laetitia Muszkieta, William J. Steinbach, and Jean-Paul Latge

28 Cryptosporidium: Comparative Genomics and Pathogenesis 518
Satomi Kato and Jessica C. Kissinger

INDEX 545

About the Author

Dr. David Sibley, PhD, is a faculty member at the Washington University School of Medicine, where he teaches graduate courses in microbiology and has served on the steering committee for the Molecular Microbiology program for the past 10 years. In addition to authoring over 150 publications,?Dr. Sibley is an associate editor for PLoS Pathogens, edits reviews for Cellular Microbiology, and serves on the board of reviewing editors for Science.

Dr. Barbara Howlett, PhD, is a Professor in the School of Botany at the University of Melbourne, specializing in fungal diseases of plants. She serves in an editorial capacity for PLoS Pathogens, Eukaryotic Cell, and the European Journal of Plant Pathology.

Dr. Joseph Heitman, MD, PhD is currently Chair of the Dept of Molecular Genetics and Microbiology at Duke University. Dr. Heitman has co-authored four other books on the topics of eukayrotic function and pathogenesis, and serves as an editor for numerous?publication includingEukaryotic Cell, Virulence, and the Journal of Molecular Medicine.

Reviews

“It should be of interest to evolutionary biologists, medical microbiologists and plant pathologists at postdoctoral and faculty levels.”  (Microbiology Today, 26 November 2012)