Evidence for Horizontal Gene Transfer
Direct identification of ancestor and descendant
When nearly identical sequences can be identified from two distantly related organisms, gene transfer is almost the only biological explanation. Care must be taken in these cases to exclude laboratory or analytical artifacts.
Patterns of codon usage and base composition
Lawrence and Ochman (1998) argued that of the scale of 18% of the E. coli MG1655 genome has been trasferred within the last 100 million years.
Comparative phylogenetic information
Conflict between phylogenetic trees can be evidence of horizontal gene transfer
Must distinguish between horizontal gene transfer and gene duplication (i.e., paralogy)
Another source of confusion is the fact that analyses based on insufficent or weak data will sometimes superficially appear to be in conflict.
Mechanisms for gene transfer
Viruses & RNA mediated transfer
Mobile genetic elements
gypsy, hobo, jockey, mariner, dong, roo, HMS Beagle among others.
Prokaryotes vs. Eukaryotes
Gene transfer has clearly had a substantial impact on the evolution of prokaryotic genomes
The measure of its influence on eukaryotic genomes is less clear, but some has occurred.
Heinemann & Sprague 1989 demonstrated conjugative gene transfer between a bacterium and a yeast.
Several naturally occurring examples -- rubisco genes are among the best documented.
Sexual reproduction can be considered to be a form of horizontal gene transfer
Transfer among compartments (i.e., chloroplast, mitochondrion, and nucleus) is well documented.
Segregated germ lines may reduce the inheritance of transferred material in some taxa (e.g., animals).
Evolutionary implications of gene transfer
Effects of transferred DNA can be to provide a duplicate gene or to introduce a novel function.
"Love of the dead" [Jack Heinemann in Syvanen & Kado 1998]
You are what you eat [Ford Doolittle 1998]
Gene transfer in nature and in the laboratory
Drug resistance genes encoded on plasmids
Heinemann, J. A. and Sprague, G. F., Jr. 1989. Bacterial conjugative plasmids mobilize DNA transfer between bacteria and yeast. Nature 340: 205-209.
Delwiche, C. F. and Palmer, J. D. 1996. Rampant horizontal transfer and duplication of rubisco genes in eubacteria and plastids. Mol. Biol. Evol. 13: 873-882.
Syvanen, M. and Kado, C. I. (eds) 1998. Horizontal Gene Transfer. Chapman & Hall, London, England. 474 pp.
Lawrence, J. G. and Ochman, H. 1998. Molecular archaeology of the Escherichia coli genome. Proc. Nat. Acad. Sci. USA 95: 9413-9417.
Doolittle, W. F. 1998. You are what you eat: a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends in Genetics 14: 307-311.
Adams, K. L., Song, K., Roessler, P. G., Nugent, J. M., Doyle, J. L., Doyle, J. J. and Palmer, J. D. 1999. Intracellular gene transfer in action: dual transcription and multiple silencings of nuclear and mitochondrial cox2 genes in legumes. Proc. Nat. Acad. Sci. USA 96: 13863-13868.