Horizontal Gene Transfer, 2009
Genomes in Flux
Methods in Molecular Biology Series, Vol. 532

Part I: Introduction 1. Gene Transfer: Who Benefits? J. Peter Gogarten and Lorraine Olendzenski Part II: Definitions, Philosophy and Implications of HGT 2. Defining the Mobilome Janet Siefert 3. The Interplay of Homologous Recombination and Horizontal Gene Transfer in Bacterial Speciation Jeffrey G. Lawrence and Adam Retchless 4. Epistemological Impacts of Horizontal Gene Transfer on Classification in Microbiology Eric Bapteste and Yan Boucher 5. Persistence Mechanisms of Conjugative Plasmids Martin Iain Bahl, Lars Hestbjerg Hansen, and Søren J. Sørensen 6. The Integron/Gene Cassette System: An Active Player in Bacterial Adaptation Mauricio Labbate, Rebecca J. Case, and Hatch W. Stokes 7. Ancient Gene Transfer as a Tool in Phylogenetic Reconstruction Jinling Huang and Peter Gogarten 8. The Tree of Life Viewed Through the Contents of Genomes Christopher H. House 9. Horizontal Gene Transfer and the Evolution of Methanogenic Pathways Greg Fournier 10. Genome Acquisition in Horizontal Gene Transfer: Symbiogenesis and Macromolecular Sequence Analysis Lynn Margulis Part III: Methods 11. Detection and Quantitative Assessment of Horizontal Gene Transfer Olga Zhaxybayeva 12. Testing Composition-Based Methods to Identify Horizontal Gene Transfer Diego Cortez, Luis Delaye, Antonio Lazcano, and Arturo Becerra 13. Testing Phylogenetic Methods to Identify Horizontal GeneTransfer Maria S. Poptsova 14. Untangling Hybrid Phylogenetic Signals: Horizontal Gene Transfer and Artifacts of Phylogenetic Reconstruction Robert G. Beiko and Mark A. Ragan 15. Construction and Use of Flow Cytometry Optimized Plasmid-Sensor Strains Martin I. Bahl, Gunnar Oregaard, Søren J. Sørensen, and Lars Hestbjerg Hansen 16. Experimental Evolution of an Essential Bacillus Gene in an E. coli Host Maia Larios-Sanz and Michael Travisano 17. Mass Action Models Describing Extant Horizontal Transfer of Plasmids: Inferences and Parameter Sensitivities Barth F. Smets and Laurant Lardon Part IV: Case Studies 18. Intradomain Transfers of Sugar Transporters Overcome Barriers to Gene Expression Kenneth Noll and Kamolwan Thirangoon 19. The Role of Horizontal Gene Transfer in Photosynthesis, Oxygen Production, and Oxygen Tolerance Jason Raymond 20. Horizontal Gene Transfer in Cyanobacterial Signature Genes Shailaja Yerrapragada, Janet L. Siefert, and George E. Fox 21. Population Genomics and the Bacterial Species Concept Margaret A. Riley and Michelle Lizotte-Waniewski 22. A Critique of Prokaryotic Species Concepts R. Thane Papke 23. What Antimicrobial Resistance has taught us about Horizontal Gene Transfer Miriam Barlow 24. Potential for Horizontal Gene Transfer in Microbial Communities of the Terrestrial Subsurface Joanna M. Coombs 25. Horizontal Gene Transfer and Mobile Genetic Elements in Marine Systems Patricia Sobecky and Tracy Hazen 26. Horizontal Gene Transfer in Metal and Radionuclide Contaminated Soils Pat Sobecky and Jonna Coombs 27. Horizontal Gene Transfer between Microbial Eukaryotes Jan Andersson 28. Horizontal Gene Transfer in Eukaryotic Parasites: a Case Study of Entamoeba histolytica and Trichomonas vaginalis Cecilia M. Alsmark, Thomas Sicheritz-Ponten, Peter Foster, Robert P. Hirt, and Martin Embley 29. Role of Horizontal Gene Transfer in the Evolution of Photosynthetic Eukaryotes and their Plastids Patrick J. Keeling 30. Role of Horizontal Gene Transfer in the Evolution of Plant Parasitism among Nematodes Makedonka Mitreva, Geert Smant, and Hans Helder