Evolution after Gene Duplication

Katharina Dittmar de la Cruz holds both a Ph.D. in Molecular Parisitology and Entomology and a doctorate in Veterinary Medicine, both from the University of Leipzig, Germany. An expert in phylogenetics, molecular evolution, and bioinformatics, she has recently turned her attention toward examining the implications of evolutionary forces on drug design. Dr. Dittmar is an Assistant Professor at the SUNY University at Buffalo. David Liberles earned his Ph.D. in Chemistry at the California Institute of Technology working on the biochemsitry of nucleic acids. Subsequently, he has developed significant expertise in bioinformatics, computational biology and functional genomics. His broad experience includes a professorship at the Stockholm Bioinformatics Center and consultancies with Novo Nordisk and other private research and diagnostic companies. Currently he is Vice-Director of the University of Wyoming Bioinformatics Center and Assistant Professor of Molecular Biology.

Contributors vii

Preface xi

1 Understanding Gene Duplication Through Biochemistry and Population Genetics 1
David A. Liberles, Grigory Kolesov, and Katharina Dittmar

2 Functional Divergence of Duplicated Genes 23
Takashi Makino, David G. Knowles, and Aoife McLysaght

3 Duplicate Retention After Small- and Large-Scale Duplications 31
Steven Maere and Yves Van de Peer

4 Gene Dosage and Duplication 57
Fyodor A. Kondrashov

5 Myths and Realities of Gene Duplication 77
Austin L. Hughes and Robert Friedman

6 Evolution After and Before Gene Duplication? 105
Tobias Sikosek and Erich Bornberg-Bauer

7 Protein Products of Tandem Gene Duplication: A Structural View 133
William R. Taylor and Michael I. Sadowski

8 Statistical Methods for Detecting Functional Divergence of Gene Families 163
Xun Gu

9 Mapping Gene Gains and Losses Among Metazoan Full Genomes Using an Integrated Phylogenetic Framework 173
Athanasia C. Tzika, Rapha¨el Helaers, and Michel C. Milinkovitch

10 Reconciling Phylogenetic Trees 185
Oliver Eulenstein, Snehalata Huzurbazar, and David A. Liberles

11 On the Energy and Material Cost of Gene Duplication 207
Andreas Wagner

12 Fate of a Duplicate in a Network Context 215
Orkun S. Soyer

13 Evolutionary and Functional Aspects of Genetic Redundancy 229
Ran Kafri and Tzachi Pilpel

14 Phylogenomic Approach to the Evolutionary Dynamics of Gene Duplication in Birds 253
Chris L. Organ, Matthew D. Rasmussen, Maude W. Baldwin, Manolis Kellis, and Scott V. Edwards

15 Gene and Genome Duplications in Plants 269
Pamela S. Soltis, J. Gordon Burleigh, Andre S. Chanderbali, Mi-Jeong Yoo, and Douglas E. Soltis

16 Whole Genome Duplications and the Radiation of Vertebrates 299
Shigehiro Kuraku and Axel Meyer

Index 313