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On surrogate methods for detecting lateral gene transfer
Abstract
Surrogate methods for detecting lateral gene transfer are those that do not require inference of phylogenetic trees. Herein I apply four such methods to identify open reading frames (ORFs) in the genome of Escherichia coli K12 that may have arisen by lateral gene transfer. Only two of these methods detect the same ORFs more frequently than expected by chance, whereas several intersections contain many fewer ORFs than expected. Each of the four methods detects a different non-random set of ORFs. The methods may detect lateral ORFs of different relative ages; testing this hypothesis will require rigorous inference of trees.
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Cited by
Horizontal gene transfer: building the web of life
Soucy, S. M., Huang, J., & Gogarten, J. P. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3962 · Cited by 1,449
Prokaryotic Evolution in Light of Gene Transfer
Gogarten, J. P., Doolittle, W. F., & Lawrence, J. G. (2002) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a004046 · Cited by 986
The origin of new genes: Glimpses from the young and old
Long, M., Betrán, E., Thornton, K., & Wang, W. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1204 · Cited by 933
Highways of gene sharing in prokaryotes
Beiko, R. G., Harlow, T. J., & Ragan, M. A. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0504068102 · Cited by 535
Self-citationMirkin, B. G., Fenner, T. I., Galperin, M. Y., & Koonin, E. V. (2003) · BMC Evolutionary Biology · doi:10.1186/1471-2148-3-2 · Cited by 368
Metadata
- Authors
- Ragan, M.
- Venue
- FEMS Microbiology Letters
- Publisher
- Oxford University Press (OUP)
- Published
- 2001-07-24
- Volume
- 201
- Issue
- 2
- Pages
- 187-191
- ISSN
- 0378-1097 (ISSN-L)
- OpenAlex
- W2039158827
- Cited by
- 176
- References
- 0
- FWCI
- 4.13
- Type
- journal article
- Language
- en
- Open access
- closed
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