Horizontal gene transfer in evolution: facts and challenges
Open accessAbstract
The contribution of horizontal gene transfer to evolution has been controversial since it was suggested to be a force driving evolution in the microbial world. In this paper, I review the current standpoint on horizontal gene transfer in evolutionary thinking and discuss how important horizontal gene transfer is in evolution in the broad sense, and particularly in prokaryotic evolution. I review recent literature, asking, first, which processes are involved in the evolutionary success of transferred genes and, secondly, about the extent of horizontal gene transfer towards different evolutionary times. Moreover, I discuss the feasibility of reconstructing ancient phylogenetic relationships in the face of horizontal gene transfer. Finally, I discuss how horizontal gene transfer fits in the current neo-Darwinian evolutionary paradigm and conclude there is a need for a new evolutionary paradigm that includes horizontal gene transfer as well as other mechanisms in the explanation of evolution.
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
Increased copper tolerance in S. cerevisiae was reported to be mediated by a genomic amplification of CUP1, decreased basal levels of the copper transporters CTR2 and CCC2, and decreased activity of antioxidant enzymes.
“Increased copper tolerance was reported to be mediated by a genomic amplification of CUP1, decreased basal levels of the copper transporters CTR2 and CCC2 and decreased activity of antioxidant enzymes [117,128].”
From Adaptive laboratory evolution—Principles and applications for biotechnology (2013) · cites this paper as [117]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Cites
Application of Phylogenetic Networks in Evolutionary Studies
Huson, D. H., & Bryant, D. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msj030 · Cited by 8,751 · see citing works
Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833 · see citing works
Darwin, C. R., Darwin, C. R., & Edmonds & Remnants (1859) · J. Murray eBooks · doi:10.5962/bhl.title.59991 · Cited by 7,020 · see citing works
Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya.
Woese, C. R., Kandler, O., & Wheelis, M. L. (1990) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.87.12.4576 · Cited by 6,128 · see citing works
Darwin, C. R., Murray, J. J., Sons, W. C. A., & Evans., B. &. (1859) · Biodiversity Heritage Library (Smithsonian Institution) · doi:10.5962/bhl.title.82303 · Cited by 5,668 · see citing works
(1977) · Cited by 4,052 · see citing works
Genetics and the Origin of Species
Dobzhansky, T. (1952) · AIBS Bulletin · doi:10.1093/aibsbulletin/2.2.14-b · Cited by 3,962 · see citing works
Lateral gene transfer and the nature of bacterial innovation
Ochman, H., Lawrence, J. G., & Groisman, E. A. (2000) · Nature · doi:10.1038/35012500 · Cited by 3,816 · see citing works
Bird, A. (2007) · Nature · doi:10.1038/nature05913 · Cited by 3,011 · see citing works
Tettelin, H., Masignani, V., Cieslewicz, M. J., Donati, C., Medini, D., Ward, N. L., Angiuoli, S. V., Crabtree, J., Jones, A. L., Durkin, A. S., et al. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0506758102 · Cited by 2,728 · see citing works
Løvtrup, S., & Gould, S. J. (1978) · Systematic Zoology · doi:10.2307/2412825 · Cited by 2,359 · see citing works
Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
Carroll, S. B. (2008) · Cell · doi:10.1016/j.cell.2008.06.030 · Cited by 2,067 · see citing works
Phylogenetic Classification and the Universal Tree
Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888 · see citing works
Hybridization and adaptive radiation
D, O. S. C. (2004) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2004.01.003 · Cited by 1,861 · see citing works
Genetics and the Origin of Species
Schmidt, K. P., & Dobzhansky, T. (1938) · Copeia · doi:10.2307/1435536 · Cited by 1,756 · see citing works
Nelson, K. E., Clayton, R. A., Gill, S. R., Gwinn, M. L., Dodson, R. J., Haft, D. H., Hickey, E. K., Peterson, J. D., Nelson, W. C., Ketchum, K. A., et al. (1999) · Nature · doi:10.1038/20601 · Cited by 1,493 · see citing works
Molecules as documents of evolutionary history
Zuckerkandl, E., & Pauling, L. C. (1965) · Journal of Theoretical Biology · doi:10.1016/0022-5193(65)90083-4 · Cited by 1,359 · see citing works
Horizontal gene transfer in eukaryotic evolution
Keeling, P. J., & Palmer, J. D. (2008) · Nature Reviews Genetics · doi:10.1038/nrg2386 · Cited by 1,355 · see citing works
Blackwell, A. D. (2014) · Choice Reviews Online · doi:10.5860/choice.185702 · Cited by 1,261 · see citing works
Horizontal gene transfer among genomes: The complexity hypothesis
Jain, R., Rivera, M. C., & Lake, J. A. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.7.3801 · Cited by 1,170 · see citing works
Darwin, C. R. (1860) · The Crayon · doi:10.2307/25528056 · Cited by 1,168 · see citing works
Horizontal gene transfer in prokaryotes: Quantification and classification
Koonin, E. V., Makarova, K. S., & Aravind, L. (2001) · Annual Review of Microbiology · doi:10.1146/annurev.micro.55.1.709 · Cited by 1,126 · see citing works
Comparative genomics: the bacterial pan-genome
Tettelin, H., Riley, D., Cattuto, C., & Medini, D. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.006 · Cited by 1,120 · see citing works
Re-evaluating prokaryotic species
Gevers, D., Cohan, F. M., Lawrence, J. G., Spratt, B. G., Coenye, T., Feil, E. J., Stackebrandt, E. S., de Peer, Y. V., Vandamme, P. A. R., Thompson, F. L., et al. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1236 · Cited by 1,111 · see citing works
Horizontal gene transfer, genome innovation and evolution
Gogarten, J. P., & Townsend, J. P. (2005) · Nature Reviews Microbiology · doi:10.1038/nrmicro1204 · Cited by 1,010 · see citing works
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 · see citing works
Eukaryotic evolution, changes and challenges
Embley, T. M., & Martin, W. (2006) · Nature · doi:10.1038/nature04546 · Cited by 867 · see citing works
GENETIC EXCHANGE IN SALMONELLA
Zinder, N. D., & Lederberg, J. (1952) · Journal of Bacteriology · doi:10.1128/jb.64.5.679-699.1952 · Cited by 851 · see citing works
Widespread Lateral Gene Transfer from Intracellular Bacteria to Multicellular Eukaryotes
Hotopp, J. C. D., Clark, M. E., Oliveira, D. C. S. G., Foster, J. M., Fischer, P., Torres, M. C. M., Giebel, J. D., Kumar, N., Ishmael, N., Wang, S., et al. (2007) · Science · doi:10.1126/science.1142490 · Cited by 818 · see citing works
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
Koonin, E., & Wolf, Y. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn668 · Cited by 722 · see citing works
Robustness and evolvability: a paradox resolved
Wagner, A. (2008) · Proceedings of the Royal Society B: Biological Sciences · doi:10.1098/rspb.2007.1137 · Cited by 669 · see citing works
Gene Recombination in Escherichia Coli
Lederberg, J., & Tatum, E. L. (1946) · Nature · doi:10.1038/158558a0 · Cited by 611 · see citing works
Pattern pluralism and the Tree of Life hypothesis
Doolittle, W. F., & Bapteste, E. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0610699104 · Cited by 546 · see citing works
The ring of life provides evidence for a genome fusion origin of eukaryotes
Rivera, M. C., & Lake, J. A. (2004) · Nature · doi:10.1038/nature02848 · Cited by 546 · see citing works
DO WE NEED AN EXTENDED EVOLUTIONARY SYNTHESIS?
Pigliucci, M. (2007) · Evolution · doi:10.1111/j.1558-5646.2007.00246.x · Cited by 534 · see citing works
Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
Pál, C., Papp, B., & Lercher, M. J. (2005) · Nature Genetics · doi:10.1038/ng1686 · Cited by 505 · see citing works
Massive Horizontal Gene Transfer in Bdelloid Rotifers
Gladyshev, E. A., Meselson, M. S., & Arkhipova, I. R. (2008) · Science · doi:10.1126/science.1156407 · Cited by 493 · see citing works
Biased biological functions of horizontally transferred genes in prokaryotic genomes
Nakamura, Y., Itoh, T., Matsuda, H., & Gojobori, T. (2004) · Nature Genetics · doi:10.1038/ng1381 · Cited by 475 · see citing works
Lateral gene transfer in eukaryotes
Andersson, J. O. (2005) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-005-4539-z · Cited by 430 · see citing works
The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity
Fraser, C., Alm, E. J., Polz, M. F., Spratt, B. G., & Hanage, W. P. (2009) · Science · doi:10.1126/science.1159388 · Cited by 410 · see citing works
Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution
Dagan, T., Artzy-Randrup, Y., & Martin, W. (2008) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0800679105 · Cited by 409 · see citing works
Genome-Wide Experimental Determination of Barriers to Horizontal Gene Transfer
Sorek, R., Zhu, Y., Creevey, C. J., Francino, M. P., Bork, P., & Rubin, E. M. (2007) · Science · doi:10.1126/science.1147112 · Cited by 407 · see citing works
Horizontal gene transfer: A critical view
Kurland, C. G., Canbäck, B., & Berg, O. G. (2003) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1632870100 · Cited by 405 · see citing works
Developmental Constraints in Evolutionary Processes
Alberch, P. (1982) · Springer eBooks · doi:10.1007/978-3-642-45532-2_15 · Cited by 383 · see citing works
Genome trees and the tree of life
Wolf, Y. I., Rogozin, I. B., Grishin, N. V., & Koonin, E. V. (2002) · Trends in Genetics · doi:10.1016/s0168-9525(02)02744-0 · Cited by 362 · see citing works
Mechanistic approaches to the study of evolution: the functional synthesis
Dean, A. M., & Thornton, J. W. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2160 · Cited by 354 · see citing works
Estimating the size of the bacterial pan-genome
Lapierre, P., & Gogarten, J. P. (2009) · Trends in Genetics · doi:10.1016/j.tig.2008.12.004 · Cited by 354 · see citing works
Genomes in Flux: The Evolution of Archaeal and Proteobacterial Gene ContentPreprint
Snel, ., Bork, P., & Huynen, M. A. (2001) · Genome Research · doi:10.1101/gr.176501 · Cited by 351 · see citing works
Evolutionary Origins of Genomic Repertoires in Bacteria
Lerat, E., Daubin, V., Ochman, H., & Moran, N. A. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030130 · Cited by 338 · see citing works
Phylogenetic analyses of cyanobacterial genomes: Quantification of horizontal gene transfer eventsPreprint
Zhaxybayeva, O., Gogarten, J. P., Charlebois, R. L., Doolittle, W. F., & Papke, R. T. (2006) · Genome Research · doi:10.1101/gr.5322306 · Cited by 336 · see citing works
A Systematics for Discovering the Fundamental Units of Bacterial Diversity
Cohan, F. M., & Perry, E. B. (2007) · Current Biology · doi:10.1016/j.cub.2007.03.032 · Cited by 300 · see citing works
(2006) · Kluwer Academic Publishers eBooks · doi:10.1007/0-306-48380-7_2066 · Cited by 295 · see citing works
Ancient horizontal gene transfer
Brown, J. R. (2003) · Nature Reviews Genetics · doi:10.1038/nrg1000 · Cited by 292 · see citing works
Dealing with incongruence in phylogenomic analyses
Galtier, N., & Daubin, V. (2008) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2008.0144 · Cited by 267 · see citing works
Hypoplasia of the exocrine tissue of the pancreas
Lumb, G. D., & Beautyman, W. (1952) · The Journal of Pathology and Bacteriology · doi:10.1002/path.1700640402 · Cited by 265 · see citing works
Andersson, J. O., Sjögren, Å. M., Davis, L. A., Embley, T. M., & Roger, A. J. (2003) · Current Biology · doi:10.1016/s0960-9822(03)00003-4 · Cited by 259 · see citing works
Darwinian evolution in the light of genomics
Koonin, E. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkp089 · Cited by 254 · see citing works
Goldenfeld, N. D., & Woese, C. R. (2007) · RePEc: Research Papers in Economics · Cited by 253 · see citing works
Hogg, J., Hu, F. Z., Janto, B., Boissy, R., Hayes, J. D., Keefe, R., Post, J. C., & Ehrlich, G. D. (2007) · Genome biology · doi:10.1186/gb-2007-8-6-r103 · Cited by 245 · see citing works
Horizontal transfer of ATPase genes — the tree of life becomes a net of life
Hilario, E., & Gogarten, J. P. (1993) · Biosystems · doi:10.1016/0303-2647(93)90038-e · Cited by 241 · see citing works
Goldenfeld, N., & Woese, C. (2007) · Nature · doi:10.1038/445369a · Cited by 236 · see citing works
Evolution of Filamentous Plant Pathogens: Gene Exchange across Eukaryotic Kingdoms
Richards, T. A., Dacks, J. B., Jenkinson, J. M., Thornton, C. R., & Talbot, N. J. (2006) · Current Biology · doi:10.1016/j.cub.2006.07.052 · Cited by 226 · see citing works
Direct Visualization of Horizontal Gene Transfer
Babić, A., Lindner, A. B., Vulić, M., Stewart, E. J., & Radman, M. (2008) · Science · doi:10.1126/science.1153498 · Cited by 221 · see citing works
Gene Transfer in Bacteria: Speciation without Species?
Lawrence, J. G. (2002) · Theoretical Population Biology · doi:10.1006/tpbi.2002.1587 · Cited by 220 · see citing works
On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales
Zhaxybayeva, O., Swithers, K. S., Lapierre, P., Fournier, G. P., Bickhart, D. M., DeBoy, R. T., Nelson, K. E., Nesbø, C. L., Doolittle, W. F., Gogarten, J. P., et al. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0901260106 · Cited by 217 · see citing works
Reconciling the many faces of lateral gene transfer
Lawrence, J. G., & Ochman, H. (2002) · Trends in Microbiology · doi:10.1016/s0966-842x(01)02282-x · Cited by 215 · see citing works
Gupta, R. S., & Singh, B. (1994) · Current Biology · doi:10.1016/s0960-9822(00)00249-9 · Cited by 207 · see citing works
The eukaryotic tree of life: endosymbiosis takes its TOL.
Lane, C. E., & Archibald, J. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.02.004 · Cited by 206 · see citing works
Horizontal gene transfer and phylogenetics
Philippe, H., & Douady, C. J. (2003) · Current Opinion in Microbiology · doi:10.1016/j.mib.2003.09.008 · Cited by 198 · see citing works
Phylogenetic Inference Using Whole Genomes
Rannala, B. H., & Yang, Z. (2008) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164407 · Cited by 186 · see citing works
Transduction of Flagellar Characters in Salmonella
Stocker, B. A. D., Zinder, N. D., & Lederberg, J. (1953) · Journal of General Microbiology · doi:10.1099/00221287-9-3-410 · Cited by 174 · see citing works
Martin, W. F., Brinkmann, H., Savonna, C., & Cerff, R. (1993) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.90.18.8692 · Cited by 171 · see citing works
Lercher, M. J., & Pál, C. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm283 · Cited by 165 · see citing works
Codon Bias and Base Composition Are Poor Indicators of Horizontally Transferred Genes
Koski, L. B., Morton, R. A., & Golding, G. B. (2001) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a003816 · Cited by 163 · see citing works
Protein-based phylogenies support a chimeric origin for the eukaryotic genome.
Golding, G. B., & Gupta, R. S. (1995) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a040178 · Cited by 162 · see citing works
Huang, J.-L., Mullapudi, N., Lancto, C., Scott, M. E., Abrahamsen, M., & Kissinger, J. (2004) · Genome Biology · doi:10.1186/gb-2004-5-11-r88 · Cited by 153 · see citing works
Cross-species gene transfer; implications for a new theory of evolution
Syvanen, M. (1985) · Journal of Theoretical Biology · doi:10.1016/s0022-5193(85)80291-5 · Cited by 151 · see citing works
Detection of lateral gene transfer among microbial genomes
Ragan, M. A. (2001) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00244-6 · Cited by 151 · see citing works
Horizontal gene transfer and the evolution of transcriptional regulation in Escherichia coli
Price, M. N., Dehal, P., & Arkin, A. P. (2008) · Genome biology · doi:10.1186/gb-2008-9-1-r4 · Cited by 146 · see citing works
From genome to aetiology in a multifactorial disease, type 1 diabetes
Todd, J. A. (1999) · Bioessays · doi:10.1002/(sici)1521-1878(199902)21:2 · Cited by 145 · see citing works
Global extent of horizontal gene transfer
Choi, I., & Kim, S. (2007) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0611557104 · Cited by 139 · see citing works
The Cobweb of Life Revealed by Genome-Scale Estimates of Horizontal Gene Transfer
Ge, F., Wang, L., & Kim, J. (2005) · PLoS Biology · doi:10.1371/journal.pbio.0030316 · Cited by 133 · see citing works
Fournier, G. P., & Gogarten, J. P. (2007) · Journal of Bacteriology · doi:10.1128/jb.01382-07 · Cited by 128 · see citing works
Mobile elements in archaeal genomes
Brügger, K., Redder, P., She, Q., Confalonieri, F., Zivanovic, Y., & Garrett, R. A. (2002) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2002.tb10999.x · Cited by 112 · see citing works
The prokaryotic tree of life: past, present…and future?
McInerney, J. O., Cotton, J. A., & Pisani, D. (2008) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2008.01.008 · Cited by 108 · see citing works
Genomics, environmental genomics and the issue of microbial species
Ward, D. M., Cohan, F. M., Bhaya, D., Heidelberg, J. F., Kühl, M., & Grossman, A. R. (2007) · Heredity · doi:10.1038/sj.hdy.6801011 · Cited by 103 · see citing works
Bapteste, E. P., Susko, E., Leigh, J., Ruiz‐Trillo, I., Bucknam, J., & Doolittle, W. F. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm229 · Cited by 99 · see citing works
Archaeal genomics: Do archaea have a mixed heritage?
Doolittle, W. F., & Logsdon, J. M. (1998) · Current Biology · doi:10.1016/s0960-9822(98)70127-7 · Cited by 96 · see citing works
What was the evolutionary synthesis?
Mayr, E. W. (1993) · Trends in Ecology & Evolution · doi:10.1016/0169-5347(93)90128-c · Cited by 92 · see citing works
The fate of new bacterial genes
Kuo, C., & Ochman, H. (2008) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2008.00140.x · Cited by 85 · see citing works
Boussau, B., Guéguen, L., & Gouy, M. (2008) · BMC Evolutionary Biology · doi:10.1186/1471-2148-8-272 · Cited by 83 · see citing works
Ancient horizontal gene transfer can benefit phylogenetic reconstruction
Huang, J., & Gogarten, J. P. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.05.004 · Cited by 78 · see citing works
Retroids in Archaea: Phylogeny and Lateral Origins
Rest, J. S. (2003) · Molecular Biology and Evolution · doi:10.1093/molbev/msg135 · Cited by 76 · see citing works
Lateral gene transfer challenges principles of microbial systematics
Bapteste, E. P., & Boucher, Y. (2008) · Trends in Microbiology · doi:10.1016/j.tim.2008.02.005 · Cited by 66 · see citing works
Kanhere, A., & Vingron, M. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-9 · Cited by 62 · see citing works
Lateral and oblique gene transfer
Ochman, H. (2001) · Current Opinion in Genetics & Development · doi:10.1016/s0959-437x(00)00243-4 · Cited by 60 · see citing works
Horizontal gene transfer depends on gene content of the host
Pál, C., Papp, B., & Lercher, M. J. (2005) · Bioinformatics · doi:10.1093/bioinformatics/bti1136 · Cited by 60 · see citing works
Mobile elements in archaeal genomes
Brügger, K. (2002) · FEMS Microbiology Letters · doi:10.1016/s0378-1097(01)00504-3 · Cited by 60 · see citing works
Horizontal gene transfer of two cytoskeletal elements from a eukaryote to a cyanobacterium
Guljamow, A., Jenke‐Kodama, H., Saumweber, H., Quillardet, P., Frangeul, L., Castets, A. M., Bouchier, C., de Marsac, N. T., & Dittmann, E. (2007) · Current Biology · doi:10.1016/j.cub.2007.06.063 · Cited by 58 · see citing works
Paradigm change in evolutionary microbiology
O’Malley, M. A., & Boucher, Y. (2005) · Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences · doi:10.1016/j.shpsc.2004.12.002 · Cited by 56 · see citing works
What tangled web: barriers to rampant horizontal gene transfer
Kurland, C. G. (2005) · BioEssays · doi:10.1002/bies.20258 · Cited by 51 · see citing works
A phylogenetic approach to the identification of phosphoglucomutase genes
Whitehouse, D. B., Tomkins, J., Lovegrove, J. U., Hopkinson, D. A., & McMillan, W. O. (1998) · Molecular Biology and Evolution · doi:10.1093/oxfordjournals.molbev.a025942 · Cited by 48 · see citing works
Concerted gene recruitment in early plant evolution
Huang, J., & Gogarten, J. P. (2008) · Genome biology · doi:10.1186/gb-2008-9-7-r109 · Cited by 48 · see citing works
Evolutionary patterns in prokaryotic genomes.
Rocha, E. (2008) · Current Opinion in Microbiology · doi:10.1016/j.mib.2008.09.007 · Cited by 43 · see citing works
Nedelcu, A. M., MILES, I. H., FAGIR, A. M., & Karol, K. G. (2008) · Journal of Evolutionary Biology · doi:10.1111/j.1420-9101.2008.01605.x · Cited by 43 · see citing works
Distant horizontal gene transfer is rare for multiple families of prokaryotic insertion sequences
Wagner, A., & de la Chaux, N. (2008) · Molecular Genetics and Genomics · doi:10.1007/s00438-008-0373-y · Cited by 39 · see citing works
Feder, M. E. (2007) · Journal of Experimental Biology · doi:10.1242/jeb.02725 · Cited by 38 · see citing works
Have archaeal genes contributed to bacterial virulence?
Gophna, U., Charlebois, R. L., & Doolittle, W. F. (2004) · Trends in Microbiology · doi:10.1016/j.tim.2004.03.002 · Cited by 36 · see citing works
Gene amelioration demonstrated: the journey of nascent genes in bacteria
Marri, P. R., & Golding, G. B. (2008) · Genome · doi:10.1139/g07-105 · Cited by 34 · see citing works
Uncovering rate variation of lateral gene transfer during bacterial genome evolution
Hao, W., & Golding, B. (2008) · BMC Genomics · doi:10.1186/1471-2164-9-235 · Cited by 34 · see citing works
Revisiting the concept of lineage in prokaryotes: a phylogenetic perspective
Boucher, Y., & Bapteste, E. P. (2009) · BioEssays · doi:10.1002/bies.200800216 · Cited by 31 · see citing works
Watkins, R. F., & Gray, M. W. (2006) · Journal of Molecular Evolution · doi:10.1007/s00239-006-0031-0 · Cited by 29 · see citing works
Genomics: Lessons from the Aeropyrum pernix genome
Faguy David, M., & Doolittle, W. F. (1999) · Current Biology · doi:10.1016/s0960-9822(00)80074-3 · Cited by 27 · see citing works
Saunders, N. J. S. G., Hood, D. W., & Moxon, E. R. (1999) · Current Biology · doi:10.1016/s0960-9822(99)80108-0 · Cited by 26 · see citing works
Systematic overestimation of gene gain through false diagnosis of gene absence.
Zhaxybayeva, O., Nesbø, C. L., & Doolittle, W. F. (2007) · Genome biology · doi:10.1186/gb-2007-8-2-402 · Cited by 24 · see citing works
Examining Ancient Inter-domain Horizontal Gene Transfer
Almeida, F. C., Leszczyniecka, M., Fisher, P. B., & DeSalle, R. (2008) · Evolutionary Bioinformatics · doi:10.1177/117693430800400002 · Cited by 16 · see citing works
Reconciling the many faces of lateral gene transfer
Ragan, M. A. (2002) · Trends in Microbiology · doi:10.1016/s0966-842x(01)02283-1 · Cited by 15 · see citing works
Molecular mechanisms driving Darwinian evolution
Arber, W. (2007) · Mathematical and Computer Modelling · doi:10.1016/j.mcm.2007.06.003 · Cited by 10 · see citing works
Bohannon, J. (2008) · Science · doi:10.1126/science.320.5879.1031 · Cited by 9 · see citing works
GO4genome: A Prokaryotic Phylogeny Based on Genome Organization
Merkl, R., & Wiezer, A. (2009) · Journal of Molecular Evolution · doi:10.1007/s00239-009-9233-6 · Cited by 6 · see citing works
Furnham, A. F. (2011) · Palgrave Macmillan UK eBooks · doi:10.1057/9780230307209_47 · Cited by 6 · see citing works
A systematics for identifying the fundamental units of bacterial diversity
Cohan, F. M., & Perry, E. B. (2007) · Wesleyan University Digital Collections (Wesleyan University) · Cited by 2 · see citing works
Flagged first, then by citations
1 of the 123 references couldn’t be matched to a known paper.
Research works printed but not linked: 1
- Zinder N. D., Lederberg J.1952Genetic exchange in Salmonella. J. Bacteriol. 64, 679–699 [DOI] [PMC free article] [PubMed] [Google Scholar]
Cited by
Sorted by citations
Intestinal microbiome of poultry and its interaction with host and diet
Pan, D., & Yu, Z. (2013) · Gut Microbes · doi:10.4161/gmic.26945 · Cited by 895 · see citing works
“”(122) It is mediated by processes such as conjugation, transformation, and transduction and is an effective mechanism which contributes to bacterial diversification and facilitates bacterial adaptation to new environments.(123,124) In modern poultry industry, litter, which contains bacteria excreted from chickens or…”
BackgroundAdaptive laboratory evolution—Principles and applications for biotechnology
Dragosits, M., & Mattanovich, D. (2013) · Microbial Cell Factories · doi:10.1186/1475-2859-12-64 · Cited by 827 · see citing works
“Nevertheless, the role of HGT in natural evolution remains a controversial topic [133].”
BackgroundFunctional roles of melatonin in plants, and perspectives in nutritional and agricultural science
Tan, D. X., Hardeland, R., Manchester, L. C., Korkmaz, A., Ma, S., Rosales‐Corral, S., & Reiter, R. J. (2011) · Journal of Experimental Botany · doi:10.1093/jxb/err256 · Cited by 627 · see citing works
“The origin of AANAT within bacteria is unknown and difficult to identify, since horizontal gene transfer is a frequent phenomenon among bacteria, and also between bacteria and other organisms, including archaea and eucarya (Boto, 2010; Smillie et al., 2010).”
BackgroundStokes, H. W., & Gillings, M. R. (2011) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2011.00273.x · Cited by 613 · see citing works
“However, most of this literature focuses on the implications of LGT for the evolution of microbial genomes (Boto, 2010) or on issues relating to microbial phylogeny and the relevance of the species concept as it applies to prokaryotes (Bapteste et al., 2009; Gribaldo & Brochier, 2009).”
BackgroundMaldonado-Gómez, M. X., Martínez, I., Bottacini, F., O’Callaghan, A., Ventura, M., van Sinderen, D., Hillmann, B., Vangay, P., Knights, D., Hutkins, R. W., et al. (2016) · Cell Host & Microbe · doi:10.1016/j.chom.2016.09.001 · Cited by 517 · see citing works
“Horizontal gene transfer can further lead to similar genetic information being shared among bacterial taxa that are not closely related, resulting in phylogenetically distant taxa with similar traits (Boto, 2010).”
Microbial Invasions: The Process, Patterns, and Mechanisms
Mallon, C. A., van Elsas, J. D., & Salles, J. F. (2015) · Trends in Microbiology · doi:10.1016/j.tim.2015.07.013 · Cited by 488 · see citing works
“While the debate on microbial biogeography is not yet resolved, the high rates of horizontal gene transfer in microbial communities [10]; the great number of ecotypes with different physiological adaptations [11,12]; and the existing evidence of biogeographic patterns [13], especially when using multilocus sequence ty…”
BackgroundXiong, W., Sun, Y., Zhang, T., Ding, X., Li, Y., Wang, M., & Zeng, Z. (2015) · Microbial Ecology · doi:10.1007/s00248-015-0583-x · Cited by 404 · see citing works
“These genera closely related to human pathogens may enhance the probability of transferring antibiotic resistance to human pathogens, because horizontal gene transfer is more prevalent among closely related organisms than among those at phylogenetical distance [48].”
Bacterial symbionts in insects or the story of communities affecting communities
Ferrari, J., & Vavre, F. (2011) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2010.0226 · Cited by 335 · see citing works
Phylogenetic Networks: Concepts, Algorithms and Applications
Huson, D. H., Rupp, R., & Scornavacca, C. (2011) · Cited by 341 · see citing works
Boyd, E. S., & Barkay, T. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00349 · Cited by 283 · see citing works
“…other processes affect the extent of LGT [reviewed by Thomas and Nielsen (2005)] and the integration and stable inheritance of the transferred genetic material in the recipient genome [reviewed by Boto (2009)], the consequences of which are detected by phylogenetic reconstructions (Ragan, 2001).”
BackgroundTian, C. F., Zhou, Y., Zhang, Y., Li, Q. Q., Zhang, Y., Li, D. F., Wang, S., Wang, J., Gilbert, L. B., Li, Y. R., et al. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1120436109 · Cited by 239 · see citing works
“Generally speaking, recombination including LGT has been considered to preclude the reconstruction of phylogenetic relationships in the microbial world, and, on the other hand, phylogenetic incongruence has been widely used to detect recombination, particularly with ancient events (28, 29).”
BackgroundComputational approaches to species phylogeny inference and gene tree reconciliation
Nakhleh, L. K. (2013) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2013.09.004 · Cited by 209 · see citing works
“In asexual species, horizontal gene transfer (HGT) shapes the genomic repertoire and imports new genes, sometimes of beneficial consequences, into the host genome [3, 4].”
BackgroundWang, Y., Lu, J., Zhang, S., Li, J., Mao, L., Yuan, Z., Bond, P. L., & Guo, J. (2021) · The ISME Journal · doi:10.1038/s41396-021-00945-7 · Cited by 206 · see citing works
Horizontal gene transfer in the acquisition of novel traits by metazoans
Boto, L. (2014) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2013.2450 · Cited by 205 · see citing works
“In the last 20 years, horizontal gene transfer, ‘the non-genealogical transmission of genetic material from one organism to another’ according to Goldenfeld & Woese [1], has emerged as an important evolutionary force modulating the evolution of prokaryote genomes and consequently the evolution in the Bacteria and Arch…”
BackgroundSelf-citationKusari, S., & Spiteller, M. (2011) · Natural Product Reports · doi:10.1039/c1np00030f · Cited by 200 · see citing works
Causes, consequences and solutions of phylogenetic incongruence
Som, A. (2014) · Briefings in Bioinformatics · doi:10.1093/bib/bbu015 · Cited by 193 · see citing works
“It is well-known that the horizontal gene transfers are an important source of conflicts between gene trees in bacteria [63, 64].”
BackgroundZhu, Q., Kosoy, M., & Dittmar, K. (2014) · BMC Genomics · doi:10.1186/1471-2164-15-717 · Cited by 184 · see citing works
“Similar to phylogenetic HGT detection methods, BLAST best match is effective in detecting recent HGT events, but shows reduced sensitivity for ancient events, when donor and recipient sequences have already diverged over the long history of evolution [34].”
ResultRegulation of Bacterial Conjugation: Balancing Opportunity With Adversity
Frost, L. S., & Koraimann, G. (2010) · Future Microbiology · doi:10.2217/fmb.10.70 · Cited by 183 · see citing works
“A wide range of recipients is possible, including those of other genera or kingdoms [1,2].”
BackgroundLandscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
Khedkar, S., Smyshlyaev, G., Letunić, I., Maistrenko, O. M., Coelho, L. P., Orakov, A. N., Forslund, S. K., Hildebrand, F., Lütge, M., Schmidt, T., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac163 · Cited by 180 · see citing works
Rhizosphere microbiome manipulation for sustainable crop production
Mahmud, K., Missaoui, A., Lee, K., Ghimire, B., Presley, H., & Makaju, S. (2021) · Current Plant Biology · doi:10.1016/j.cpb.2021.100210 · Cited by 178 · see citing works
Evolution of microbes and viruses: a paradigm shift in evolutionary biology?
Koonin, E. V., & Wolf, Y. I. (2012) · Frontiers in Cellular and Infection Microbiology · doi:10.3389/fcimb.2012.00119 · Cited by 171 · see citing works
Song, W.-Z., Wemheuer, B., Zhang, S., Steensen, K., & Thomas, T. (2019) · Microbiome · doi:10.1186/s40168-019-0649-y · Cited by 160 · see citing works
“3) [57].”
Horizontal gene acquisitions by eukaryotes as drivers of adaptive evolution
Schönknecht, G., Weber, A. P. M., & Lercher, M. J. (2013) · BioEssays · doi:10.1002/bies.201300095 · Cited by 165 · see citing works
“Meanwhile, numerous eukaryotic genomes have been sequenced; the wider taxa coverage facilitates largely unbiased analyses, resulting in a rapidly increasing number of well supported cases of HGT into eukaryotes [19–21].”
BackgroundAntimicrobial Resistance in the Context of the Sustainable Development Goals: A Brief Review
Gajdács, M., Urbán, E. Z., Stájer, A., & Baráth, Z. (2021) · European Journal of Investigation in Health Psychology and Education · doi:10.3390/ejihpe11010006 · Cited by 164 · see citing works
“the progeny cells possess the resistance determinant originally “developed” by the original bacterial cells and via inter- and intra-species horizontal gene transfer (HGT); the significance of the latter is much higher, as many different resistance-determinants may reside on various mobile genetic elements (plasmids,…”
BackgroundTHE FUTURE OF OiL PaLM as a MaJOR GLOBaL CROP: OPPORTUniTiEs anD CHaLLEnGEs
Murphy, D. J. (2014) · Cited by 151 · see citing works
Ding, G., Radl, V., Schloter-Hai, B., Jechalke, S., Heuer, H., Smalla, K., & Schloter, M. (2014) · PLoS ONE · doi:10.1371/journal.pone.0092958 · Cited by 147 · see citing works
“The enrichment of these bacteria, which are phylogenetically closely related to human pathogens, may improve the chance of transferring antibiotic resistance genes to human pathogens, since horizontal gene transfer is more prevalent between closely related organisms than between those distantly related (reviewed by Bo…”
BackgroundGene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance
Baquero, F., Coque, T. M., Martínez, J. L., Aracil‐Gisbert, S., & Lanza, V. F. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.02892 · Cited by 140 · see citing works
“Horizontal accessory gene transfer, and the potential spread of antibiotic resistance genes, occurs preferentially among phylogenetically related bacteria (as is illustrated in Figure 1), even though transfer might bridge different taxonomic levels (Boto, 2009).”
BackgroundMcIntosh, F. M., Maison, N., Holtrop, G., Young, P., Stevens, V. J., Ince, J., Johnstone, A. M., Lobley, G. E., Flint, H. J., & Louis, P. (2012) · Environmental Microbiology · doi:10.1111/j.1462-2920.2012.02711.x · Cited by 132 · see citing works
Emerging strategies for engineering microbial communities
Tsoi, R., Dai, Z., & You, L. (2019) · Biotechnology Advances · doi:10.1016/j.biotechadv.2019.03.011 · Cited by 130 · see citing works
“Similarly, Brenner et al. engineered a commensal E. coli-E. coli consortium that cooperate via quorum sensing in a biofilm (Brenner and Arnold, 2011).”
Wendling, C. C., Refardt, D., & Hall, A. R. (2020) · Evolution · doi:10.1111/evo.14153 · Cited by 130 · see citing works
Adaptive Genetic Exchange: A Tangled History of Admixture and Evolutionary Innovation
Arnold, M. L., & Kunte, K. K. (2017) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2017.05.007 · Cited by 128 · see citing works
Pan-genome and phylogeny of Bacillus cereus sensu lato
Bazinet, A. L. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-017-1020-1 · Cited by 116 · see citing works
“Mobile genetic element removal For tree-based phylogenetic analyses that assume a process of vertical inheritance, the inclusion of mobile genetic elements (MGEs) that may be horizontally transferred is likely to confound the phylogenetic inference process [42].”
BackgroundInfluentialHorizontal Gene Transfer and Endophytes: An Implication for the Acquisition of Novel Traits
Tiwari, P., & Bae, H. (2020) · Plants · doi:10.3390/plants9030305 · Cited by 113 · see citing works
“species, between different domains, and across kingdoms [39].”
BackgroundReplicon-Dependent Bacterial Genome Evolution: The Case of Sinorhizobium meliloti
Galardini, M., Pini, F., Bazzicalupo, M., Biondi, E. G., & Mengoni, A. (2013) · Genome Biology and Evolution · doi:10.1093/gbe/evt027 · Cited by 112 · see citing works
Effect of the environment on horizontal gene transfer between bacteria and archaea
Fuchsman, C. A., Collins, R. E., Rocap, G., & Brazelton, W. J. (2017) · PeerJ · doi:10.7717/peerj.3865 · Cited by 109 · see citing works
Genetic cargo and bacterial species set the rate of vesicle-mediated horizontal gene transfer
Tran, F., & Boedicker, J. Q. (2017) · Scientific Reports · doi:10.1038/s41598-017-07447-7 · Cited by 107 · see citing works
Natural transformation and genome evolution in Streptococcus pneumoniae
Straume, D., Stamsås, G. A., & Håvarstein, L. S. (2014) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2014.10.020 · Cited by 101 · see citing works
Biological information systems: Evolution as cognition-based information management
Miller, W. B. (2017) · Progress in Biophysics and Molecular Biology · doi:10.1016/j.pbiomolbio.2017.11.005 · Cited by 101 · see citing works
Gupta, R. S. (2016) · FEMS Microbiology Reviews · doi:10.1093/femsre/fuw011 · Cited by 102 · see citing works
“Extensive work on studying the incidences of HGTs in the past 15–20 years has established that this process plays an important role in microbial genome evolution and no gene seems exempt from it (Olendzenski and Gogarten 1999; Koonin, Makarova and Aravind 2001; Gogarten, Doolittle and Lawrence 2002; Boucher et al. 200…”
BackgroundMethodInfluentialMultilevel populations and the evolution of antibiotic resistance through horizontal gene transfer
Andam, C. P., Fournier, G. P., & Gogarten, J. P. (2011) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2011.00274.x · Cited by 95 · see citing works
“…the exchange of genetic information between two organisms that do not share an ancestor–descendant relationship, is a mechanism that contributes significantly to the rapid creation of biological novelty that otherwise might have taken millions of years to occur (Jain et al., 2003; Boto, 2010).”
BackgroundGene duplications in prokaryotes can be associated with environmental adaptation
Bratlie, M. S., Johansen, J. A., Sherman, B. T., Huang, D. W., Lempicki, R. A., & Drabløs, F. (2010) · BMC Genomics · doi:10.1186/1471-2164-11-588 · Cited by 96 · see citing works
“The gene transfer may happen between prokaryotes and eukaryotes, but it is more likely to happen between closely related organisms [10].”
BackgroundXenogeneic Silencing and Its Impact on Bacterial Genomes
Singh, K., Milstein, J. N., & Navarre, W. W. (2016) · Annual Review of Microbiology · doi:10.1146/annurev-micro-102215-095301 · Cited by 95 · see citing works
Yang, Y., Xing, S.-C., Chen, Y., Wu, R., Wu, Y., Wang, Y., Mi, J., & Liao, X. (2020) · Journal of Hazardous Materials · doi:10.1016/j.jhazmat.2020.124149 · Cited by 95 · see citing works
Pathogenomics of fungal plant parasites: what have we learnt about pathogenesis?
Schmidt, S. M., & Panstruga, R. (2011) · Current Opinion in Plant Biology · doi:10.1016/j.pbi.2011.03.006 · Cited by 94 · see citing works
Archaeal and eukaryotic homologs of Hfq
Mura, C., Randolph, P. S., Patterson, J. A. K., & Cozen, A. E. (2013) · RNA Biology · doi:10.4161/rna.24538 · Cited by 87 · see citing works
The utility of metabolomics in natural product and biomarker characterization
Cox, D. G., Oh, J., Keasling, A. W., Colson, K., & Hamann, M. T. (2014) · Biochimica et Biophysica Acta (BBA) - General Subjects · doi:10.1016/j.bbagen.2014.08.007 · Cited by 84 · see citing works
“A prominent example would be in cases of horizontal gene transfer, commonly seen as the transfer of peripheral genes [60–62].”
A Bayesian Method for Analyzing Lateral Gene Transfer
Sjöstrand, J., Tofigh, A., Daubin, V., Arvestad, L., Sennblad, B., & Lagergren, J. (2014) · Systematic Biology · doi:10.1093/sysbio/syu007 · Cited by 84 · see citing works
“There are studied examples of laterally transferred material between all domains of life (Boto 2010).”
BackgroundAntibiotics, antibiotic resistance genes and microbial community in grouper mariculture
He, L.-X., He, L.-Y., Gao, F.-Z., Wu, D.-L., Ye, P., Cheng, Y., Chen, Z., Hu, L., Liu, Y., Chen, J., et al. (2021) · The Science of The Total Environment · doi:10.1016/j.scitotenv.2021.152042 · Cited by 84 · see citing works
Fan, X., Li, H., Chen, Q., Zhang, Y., Ye, J., Zhu, Y., & Su, J. (2019) · Frontiers in Microbiology · doi:10.3389/fmicb.2019.00194 · Cited by 81 · see citing works
“…resistant via gene mutation, or horizontal gene transfer Frontiers in Microbiology | www.frontiersin.org 1 March 2019 | Volume 10 | Article 194 (HGT) that would facilitate exchange of genetic information and contribute significantly to the evolution of bacteria (Boto, 2010; Soucy et al., 2015).”
BackgroundGiessen, T. W. (2022) · Annual Review of Biochemistry · doi:10.1146/annurev-biochem-040320-102858 · Cited by 80 · see citing works
Lopatkin, A. J., Sysoeva, T. A., & You, L. (2016) · BioEssays · doi:10.1002/bies.201600133 · Cited by 72 · see citing works
“Since its initial discovery in 1928 [1], HGT has increasingly been appreciated as a driving force in microbial evolution [2, 3].”
Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases
Adesioye, F. A., Makhalanyane, T. P., Biely, P., & Cowan, D. A. (2016) · Enzyme and Microbial Technology · doi:10.1016/j.enzmictec.2016.07.001 · Cited by 76 · see citing works
“This topology also provides strong evidence for inter- and intraspecific horizontal AcXE gene transfers, both within and between bacteria and fungi [46-48].”
BackgroundPhylogenetic Networks: A Review of Methods to Display Evolutionary History
Morrison, D. (2014) · Annual Research & Review in Biology · doi:10.9734/arrb/2014/8230 · Cited by 75 · see citing works
“transformation, transduction, or conjugation) [65,66], as shown in Fig.”
Major players on the microbial stage: why archaea are important
Jarrell, K. F., Walters, A. D., Bochiwal, C., Borgia, J. M., Dickinson, T., & Chong, J. P. J. (2011) · Microbiology · doi:10.1099/mic.0.047837-0 · Cited by 74 · see citing works
“Evidence exists for HGT among members of the same domain and across domains (Boto, 2010), but its importance in the evolution of more complex organisms is disputed (Koonin & Wolf, 2009).”
BackgroundReconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable
Pardi, F., & Scornavacca, C. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004135 · Cited by 75 · see citing works
“in bacteria [6, 7]), viral reassortment [8], or recombination (e.”
BackgroundCharacterization and Exploitation of CRISPR Loci in Bifidobacterium longum
Hidalgo-Cantabrana, C., Crawley, A. B., Sánchez, B., & Barrangou, R. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01851 · Cited by 70 · see citing works
“Transposases are responsible for the horizontal gene transfer that frequently occurs among prokaryotes, having an enormous impact in bacterial genomic evolution (Boto, 2010).”
BackgroundModern Phylogenomics: Building Phylogenetic Trees Using the Multispecies Coalescent Model
Liu, L., Anderson, C. N. K., Pearl, D. K., & Edwards, S. V. (2019) · Methods in molecular biology · doi:10.1007/978-1-4939-9074-0_7 · Cited by 68 · see citing works
Large-scale computational discovery and analysis of virus-derived microbial nanocompartments
Andreas, M. P., & Giessen, T. W. (2021) · Nature Communications · doi:10.1038/s41467-021-25071-y · Cited by 68 · see citing works
Sea Slug Kleptoplasty and Plastid Maintenance in a Metazoan
Pelletreau, K. N., Bhattacharya, D., Price, D. C., Worful, J. M., Moustafa, A., & Rumpho, M. E. (2011) · PLANT PHYSIOLOGY · doi:10.1104/pp.111.174078 · Cited by 67 · see citing works
“The most highly cited hypothesis to date, and the focus of this update, is extensive HGT from the algal nucleus to the animal, thereby supporting long-term plastid function (Olendzenski and Gogarten, 2009; Bock, 2010; Boto, 2010; Moran and Jarvik, 2010).”
BackgroundPinilla‐Redondo, R., Cyriaque, V., Jacquiod, S., Sørensen, S. J., & Riber, L. (2018) · Plasmid · doi:10.1016/j.plasmid.2018.08.002 · Cited by 60 · see citing works
Sheinman, M., Arkhipova, K., Arndt, P. F., Dutilh, B. E., Hermsen, R., & Massip, F. (2021) · eLife · doi:10.7554/elife.62719 · Cited by 61 · see citing works
“Microbial genomes are subject to loss and gain of genetic material from other microorganisms (Boto, 2010; Puigbò et al., 2014), via a variety of mechanisms: conjugation, transduction, and transformation, collectively known as horizontal gene transfer (HGT) (Soucy et al.”
Evolutionary uniformitarianism
Erwin, D. H. (2011) · Developmental Biology · doi:10.1016/j.ydbio.2011.01.020 · Cited by 62 · see citing works
Power, M. L., Samuel, A., Smith, J. J., Stark, J. S., Gillings, M. R., & Gordon, D. M. (2016) · Environmental Pollution · doi:10.1016/j.envpol.2016.04.013 · Cited by 56 · see citing works
Natural causes of language: Frames, biases, and cultural transmission
Enfield, N. J. (2014) · Language Science Press eBooks · doi:10.26530/oapen_533873 · Cited by 55 · see citing works
Darby, C. A., Stolzer, M., Ropp, P. J., Barker, D., & Durand, D. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw686 · Cited by 54 · see citing works
“Selective pressures are likely to change following both gene duplication (Lynch, 2007, and work cited therein) and horizontal gene transfer (Treangen and Rocha, 2011; Boto, 2010, 2016, and work cited therein).”
BackgroundHorizontal gene transfer from genetically modified plants - Regulatory considerations
Philips, J. G., Avila, E. M., & Robold, A. V. (2022) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2022.971402 · Cited by 56 · see citing works
“…the phylogenetic distance between non-related organisms increases the possibilities of genetic incompatibility, making them less likely to undergo HGT when compared with closely related organisms with compatible genomes (Bertolla and Simonet, 1999; Keese, 2008; Boto, 2010; Hibdige et al., 2021).”
BackgroundDe Novo Emergence of Peptides That Confer Antibiotic Resistance
Knopp, M. R., Guðmundsdóttir, J. S., Nilsson, T., König, F., Warsi, O., Rajer, F., Ädelroth, P., & Andersson, D. I. (2019) · mBio · doi:10.1128/mbio.00837-19 · Cited by 53 · see citing works
“Different mechanisms for the acquisition of new genes, such as horizontal gene transfer and duplication-divergence, have been observed in both natural systems and experimental settings (1, 2).”
Sterling, E. J., Gómez, A., & Porzecanski, A. L. (2010) · BioEssays · doi:10.1002/bies.201000049 · Cited by 52 · see citing works
“For example, horizontal gene transfer poses new problems to those attempting to resolve the evolutionary tree of bacterial diversity [20, 21], and we are beginning to explore its potential ecological and functional consequences [22].”
BackgroundEnvironmental shaping of codon usage and functional adaptation across microbial communities
Roller, M., Lucić, V., Nagy, I., Perica, T., & Vlahoviček, K. (2013) · Nucleic Acids Research · doi:10.1093/nar/gkt673 · Cited by 51 · see citing works
Horizontal Transfer of Non-LTR Retrotransposons from Arthropods to Flowering Plants
Gao, D., Chu, Y., Xia, H., Xu, C., Heyduk, K., Abernathy, B. L., Ozias‐Akins, P., Leebens‐Mack, J., & Jackson, S. A. (2017) · Molecular Biology and Evolution · doi:10.1093/molbev/msx275 · Cited by 52 · see citing works
“The exception to this would be if they provide some selective advantage to either themselves or the recipients, such as contributing to a biochemical network (Boto 2010; Soucy et al. 2015).”
BackgroundMultiple ancient horizontal gene transfers and duplications in lepidopteran species
Sun, B., Xiao, J., He, S., Liu, L., Murphy, R. W., & Huang, D. (2012) · Insect Molecular Biology · doi:10.1111/imb.12004 · Cited by 51 · see citing works
“A recipient can acquire novel functional genes by HGT and once acquired these genes can pass to descendants via vertical gene transfer (Boto, 2010; Hotopp, 2011).”
BackgroundGutzwiller, F., Dedeine, F., Kaiser, W., Giron, D., & López‐Vaamonde, C. (2015) · Ecology and Evolution · doi:10.1002/ece3.1580 · Cited by 49 · see citing works
“Indeed, gene transfers from symbiotic bacteria, including Wolbachia, to their insect host are known in several species (Boto 2010; Sugio et al. 2015).”
BackgroundBraga, L. P. P., Soucy, S. M., Amgarten, D., da Silva, A. M., & Setúbal, J. C. (2018) · Frontiers in Ecology and Evolution · doi:10.3389/fevo.2018.00006 · Cited by 49 · see citing works
“…by HGT, and generally, no two gene families, including 16S rDNA, share the same exact evolutionary history (Doolittle, 1999; Koonin et al., 2001; Gogarten and Townsend, 2005; Gribaldo and Brochier, 2009; Zhaxybayeva, 2009; Boto, 2010; Andam and Gogarten, 2011; Zhaxybayeva and Doolittle, 2011).”
BackgroundOrtiz‐Álvarez, R., Rı́os, A. D. L., Fernández‐Mendoza, F., Torralba‐Burrial, A., & Pérez-Ortega, S. A. (2015) · PLoS ONE · doi:10.1371/journal.pone.0132718 · Cited by 47 · see citing works
“Incongruences appear from gene duplication, gene losses, horizontal gene transfers or incomplete lineage sorting [86,87].”
BackgroundParallel evolution of genome structure and transcriptional landscape in the Epsilonproteobacteria
Porcelli, I., Reuter, M., Pearson, B. M., Wilhelm, T. E., & van Vliet, A. H. M. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-616 · Cited by 44 · see citing works
“; licensee BioMed Central Commons Attribution License (http://creativec reproduction in any medium, provided the or genome, through combinations of gene inversion, recombination, gene duplication, deletion and horizontal gene transfer [3,4].”
BIOLOGICAL TAXONOMY AND ONTOLOGY DEVELOPMENT: SCOPE AND LIMITATIONS
Franz, N. M., & Thau, D. (2010) · Biodiversity Informatics · doi:10.1038/npre.2010.4593.1 · Cited by 46 · see citing works
Palmer, M., Steenkamp, E. T., Coetzee, M. P. A., Chan, W.-Y., van Zyl, E., Maayer, P. D., Coutinho, T. A., Blom, J., Smits, T. H. M., Duffy, B., et al. (2017) · Antonie van Leeuwenhoek · doi:10.1007/s10482-017-0852-4 · Cited by 46 · see citing works
“Despite the fact that horizontal gene transfer (HGT) significantly impacts the evolution of most, if not all, bacterial groups (Woese 2000; Gogarten et al. 2002; Jain et al. 2002; Boto 2010; Cohen et al. 2011), it is now possible to infer trees that trace the shared ancestry among all the species of a genus using WGS…”
BackgroundGeorgakopoulos-Soares, I., Yizhar-Barnea, O., Mouratidis, I., Hemberg, M., & Ahituv, N. (2020) · Genome Biology · doi:10.1186/s13059-021-02459-z · Cited by 46 · see citing works
Antarctic DNA moving forward: genomic plasticity and biotechnological potential
Martínez-Rosales, C., Fullana, N., Musto, H., & Castro‐Sowinski, S. (2012) · FEMS Microbiology Letters · doi:10.1111/j.1574-6968.2012.02531.x · Cited by 43 · see citing works
Comparative Genomics of Nitrogen Cycling Pathways in Bacteria and Archaea
Albright, M., Timalsina, B., Martiny, J. B. H., & Dunbar, J. (2018) · Microbial Ecology · doi:10.1007/s00248-018-1239-4 · Cited by 43 · see citing works
Exploration of space to achieve scientific breakthroughs
Prasad, B., Richter, P. R., Vadakedath, N., Mancinelli, R. L., Krüger, M., Strauch, S. M., Grimm, D. G., Darriet, P., Chapel, J., Cohen, J., et al. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107572 · Cited by 43 · see citing works
Identifying Drivers of Parallel Evolution: A Regression Model Approach
Bailey, S. F., Guo, Q., & Bataillon, T. M. (2018) · Genome Biology and Evolution · doi:10.1093/gbe/evy210 · Cited by 42 · see citing works
“However, rates of HGT tend to be higher in bacteria, and in particular E. coli, as compared to yeast and other eukaryotes (e.g. Boto 2010).”
BackgroundHow the space environment influences organisms: an astrobiological perspective and review
Prasad, B., Richter, P. R., Vadakedath, N., Haag, F. W. M., Strauch, S. M., Mancinelli, R. L., Schwarzwälder, A., Etcheparre, E., Gaume, N., & Lebert, M. (2021) · International Journal of Astrobiology · doi:10.1017/s1473550421000057 · Cited by 46 · see citing works
“…yield, shorter growth period, flower colour, temperature tolerance, pathogen-resistance, etc. (Mei et al ., 1998; Cyranoski, 2001; Okamura et al ., 2003; Yamaguchi et al ., 2003, 2010; Wei et al ., 2006; Zhou et al ., 2006b; Li et al ., 2007; Chengzhi, 2011; Wong et al ., 2016; Yamaguchi, 2018).”
Evidence of horizontal gene transfer by transposase gene analyses in Fervidobacterium species
Cuecas, A., Kanoksilapatham, W., & Grau, J. M. G. (2017) · PLoS ONE · doi:10.1371/journal.pone.0173961 · Cited by 41 · see citing works
Uhrig, R. G., Kerk, D., & Moorhead, G. B. G. (2013) · PLANT PHYSIOLOGY · doi:10.1104/pp.113.224378 · Cited by 38 · see citing works
“One of the hallmarks of this process is a “discordant” clustering of sequences from distant organismal sources in the same gene tree (Keeling and Palmer, 2008; Boto, 2010).”
BackgroundDalquen, D. A., Altenhoff, A., Gonnet, G. H., & Dessimoz, C. (2013) · PLoS ONE · doi:10.1371/journal.pone.0056925 · Cited by 39 · see citing works
“While exact numbers are still debated, it has been argued that the cumulative effect of LGT could be as high as 80 percent [28,29].”
Detecting horizontal gene transfer by mapping sequencing reads across species boundaries
Trappe, K., Marschall, T., & Renard, B. Y. (2016) · Bioinformatics · doi:10.1093/bioinformatics/btw423 · Cited by 40 · see citing works
Comparative Genomics Analysis of Lactobacillus mucosae from Different Niches
Jia, Y., Yang, B. K., Ross, R. P., Stanton, C., Zhang, H., Zhao, J., & Chen, W. (2020) · Genes · doi:10.3390/genes11010095 · Cited by 40 · see citing works
“In addition, transpositions have occurred at different positions of the CRISPR locus while transposases were associated with the frequent HGT in prokaryotes and had huge impacts on bacterial adaptation [70].”
BackgroundThe Microplastic-Antibiotic Resistance Connection
Marathe, N. P., & Bank, M. S. (2021) · Environmental contamination remediation and management · doi:10.1007/978-3-030-78627-4_9 · Cited by 40 · see citing works
Zheng, J., Peng, D., Ruan, L., & Sun, M. (2013) · BMC Evolutionary Biology · doi:10.1186/1471-2148-13-262 · Cited by 40 · see citing works
“Background Horizontal gene transfer (HGT) is the major driving force of bacterial evolution [1].”
The Quest for a Universal Theory of Life
Cleland, C. E. (2019) · Cambridge University Press eBooks · doi:10.1017/9781139046893 · Cited by 122 · see citing works
de la Cruz-Perera, C. I., Ren, D., Blanchet, M., Dendooven, L., Marsch, R., Sørensen, S. J., & Burmølle, M. (2012) · FEMS Microbiology Letters · doi:10.1111/1574-6968.12036 · Cited by 39 · see citing works
“Plasmids are one of the key vectors of HTG, enabling genetic exchange between bacterial cells across species and domain barriers (Poole, 2009; Boto, 2010), and they very often encode genes that confer adaptive traits to their host, such as antibiotic resistance, biodegradation pathways and virulence (de la Cruz & Davi…”
BackgroundGómez-Valero, L., & Buchrieser, C. (2019) · Genes and Immunity · doi:10.1038/s41435-019-0074-z · Cited by 39 · see citing works
Kim, M., Cha, I., Lee, K., Li, M., & Park, S.-J. (2023) · Microbiology Spectrum · doi:10.1128/spectrum.01003-23 · Cited by 38 · see citing works
“Only 279 HGT events were detected in the genus and species (Table S6 and Fig.”
BackgroundInfluentialLemaire, B., Cauwenberghe, J. V., Chimphango, S. B. M., Stirton, C. H., Honnay, O., SMETS, E. F., & Muasya, A. M. (2015) · FEMS Microbiology Ecology · doi:10.1093/femsec/fiv118 · Cited by 38 · see citing works
Horizontally Acquired Genes Are Often Shared between Closely Related Bacterial Species
Bolotin, E., & Hershberg, R. (2017) · Frontiers in Microbiology · doi:10.3389/fmicb.2017.01536 · Cited by 36 · see citing works
“Gene gain is a major driving force in the evolution of bacterial genomes (Ochman et al., 2000; Gogarten et al., 2002; Thomas and Nielsen, 2005; Boto, 2010; Vogan and Higgs, 2011; Arber, 2014).”
BackgroundInfluentialExperimental determination of evolutionary barriers to horizontal gene transfer
Kirit, H. A., Lagator, M., & Bollback, J. P. (2020) · BMC Microbiology · doi:10.1186/s12866-020-01983-5 · Cited by 34 · see citing works
“Yet, despite most transfer events resulting in fitness costs, HGT is still one of the major sources of novel genetic material in microbes (Boto, 2010; Soucy et al., 2015).”
BackgroundBhandari, V., Naushad, H. S., & Gupta, R. S. (2012) · Front. Cell. Inf. Microbio. · doi:10.3389/fcimb.2012.00098 · Cited by 33 · see citing works
“To account for the above observations and the occurrences of LGTs, it has been suggested that the prokaryotic evolution has both tree-like (at intermediate phylogenetic depths) and non-tree (or net-like) (at the base and tips) characteristics (Dagan et al., 2008; Puigbo et al., 2009, 2010; Swithers et al., 2009; Boto,…”
BackgroundMethodInfluentialHorizontal transfer of DNA methylation patterns into bacterial chromosomes
Shin, J.-E., Lin, C., & Lim, H. N. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw230 · Cited by 33 · see citing works
Katz, L. A. (2015) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2014.0324 · Cited by 33 · see citing works
- Authors
- Boto, L.
- Affiliations
- Consejo Superior de Investigaciones Científicas (ES)
- Corresponding author
- Boto, Luis
- ORCID
- Boto, Luis
- Venue
- Proceedings of the Royal Society B: Biological Sciences
- Publisher
- The Royal Society
- Published
- 2009-11-28
- Volume
- 277
- Issue
- 1683
- Pages
- 819-827
- ISSN
- 0080-4649 (ISSN-L)
- 0962-8452
- 1471-2954
- PMC
- PMC2842723
- OpenAlex
- W2108923274
- Cited by
- 379
- References
- 123
- Citations by year
- 2026: 11 · 2025: 13 · 2024: 21 · 2023: 17 · 2022: 18 · 2021: 34 · 2020: 24 · 2019: 35 · 2018: 25 · 2017: 21 · 2016: 27 · 2015: 19 · 2014: 28 · 2013: 29 · 2012: 27
- FWCI
- 1.45
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Proceedings of the Royal Society B Biological Sciences (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- DIGITAL.CSIC (Spanish National Research Council (CSIC)) (submittedVersion, other-oa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Social Sciences › Arts and Humanities › History and Philosophy of Science › Philosophy and History of Science
- Keywords
- horizontal gene transfer, prokaryotic evolution, microbial evolution, phylogenetic inference, evolutionary processes, evolutionary timescales
- MeSH terms
- Archaea, Bacteria, Biological Evolution, Phylogeny, Gene Transfer, Horizontal
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review