| Foreword | p. ix |
| Preface | p. xi |
| Contributors | p. xiii |
| Plasmids and Transfer Mechanisms in Bacteria | |
| Recent History of Trans-kingdom Conjugation | p. 3 |
| Gene Cassettes and Integrons: Moving Single Genes | p. 19 |
| A Corynebacterium Plasmid Composed of Elements from Throughout the Eubacteria Kingdom | p. 29 |
| Horizontal Transfer of Naphthalene Catabolic Genes in a Toxic Waste Site | p. 37 |
| Horizontal Transmission of Genes by Agrobacterium Species | p. 45 |
| Horizontal Transfer of Proteins Between Species: Part of the Big Picture or Just a Genetic Vignette? | p. 51 |
| Transformation in Aquatic Environments | p. 63 |
| Pseudolysogeny: A Bacteriophage Strategy for Increasing Longevity in situ | p. 81 |
| Mosaic Genes and Chromosomes | |
| The Dynamics of Bacterial Genomes | p. 95 |
| Bacterial Pathogenicity Islands and Infectious Diseases | p. 111 |
| Mosaic Proteins, Not Reinventing the Wheel | p. 123 |
| Evolutionary Relationships Among Diverse Bacteriophages and Prophages: All The World's a Phage | p. 133 |
| Horizontal Gene Transfer in Bacteriophages | p. 141 |
| Horizontal Transfer of Mismatch Repair Genes and the Variable Speed of Bacterial Evolution | p. 147 |
| Eukaryotic Mobile Elements | |
| Evidence for Horizontal Transfer of P Transposable Elements | p. 161 |
| The mariner Transposons of Animals: Horizontally Jumping Genes | p. 173 |
| The Splicing of Transposable Elements: Evolution of a Nuclear Defense Against Genomic Invaders? | p. 187 |
| Transfer Mechanisms Involving Plants and Microbes | |
| Gene Transfer Through Introgressive Hybridization: History, Evolutionary Significance, and Phylogenetic Consequences | p. 199 |
| Gene Flow and Introgression from Domesticated Plants into their Wild Relatives | p. 217 |
| Search for Horizontal Gene Transfer from Transgenic Crops to Microbes | p. 237 |
| Gene Transfer in the Fungal Host-Parasite System Absidia glauca-Parasitella parasitica Depends on Infection | p. 241 |
| Automatic Eukaryotic Artificial Chromosomes: Possible Creation of Bacterial Organelles in Yeast | p. 249 |
| Bacteria as Gene Delivery Vectors for Mammalian Cells | p. 261 |
| Whole Genome Comparisons: The Emergence of the Eukaryotic Cell | |
| Gene Transfers Between Distantly Related Organisms | p. 269 |
| Horizontal Gene Transfer and its Role in the Evolution of Prokaryotes | p. 277 |
| Horizontal Gene Transfer and the Universal Tree of Life | p. 305 |
| Endosymbiotic Gene Transfer: A Special Case of Horizontal Gene Transfer Germane to Endosymbiosis, the Origins of Organelles and the Origins of Eukaryotes | p. 351 |
| Dating the Age of the Last Common Ancestor of All Living Organisms with a Protein Clock | p. 363 |
| Parallelisms and Macroevolutionary Trends | |
| Character Parallelism and Reticulation in the Origin of Angiosperms | p. 373 |
| Temporal Patterns of Plant and Metazoan Evolution Suggest Extensive Polyphyly | p. 383 |
| Graptolite Parallel Evolution and Lateral Gene Transfer | p. 397 |
| Larval Transfer in Evolution | p. 405 |
| Macroevolution, Catastrophe and Horizontal Transfer | p. 421 |
| Horizontal Gene Transfer: A New Taxonomic Principle? | p. 427 |
| Index | p. 437 |
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