Cited by 986Genomics and Phylogenetic StudiesEvolution and Genetic DynamicsBacterial Genetics and Biotechnology

The DOI matches its Crossref record; 132 of the 132 references it cites were found in a registry or an index.

Prokaryotic Evolution in Light of Gene Transfer

Gogarten, J. Peter, Doolittle, W. Ford, Lawrence, Jeffrey G.·2002·Molecular Biology and Evolution

DOI 10.1093/oxfordjournals.molbev.a004046

Open this paper in CoChat — free account

Abstract

Accumulating prokaryotic gene and genome sequences reveal that the exchange of genetic information through both homology-dependent recombination and horizontal (lateral) gene transfer (HGT) is far more important, in quantity and quality, than hitherto imagined. The traditional view, that prokaryotic evolution can be understood primarily in terms of clonal divergence and periodic selection, must be augmented to embrace gene exchange as a creative force, itself responsible for much of the pattern of similarities and differences we see between prokaryotic microbes. Rather than replacing periodic selection on genetic diversity, gene loss, and other chromosomal alterations as important players in adaptive evolution, gene exchange acts in concert with these processes to provide a rich explanatory paradigm-some of whose implications we explore here. In particular, we discuss (1) the role of recombination and HGT in giving phenotypic "coherence" to prokaryotic taxa at all levels of inclusiveness, (2) the implications of these processes for the reconstruction and meaning of "phylogeny," and (3) new views of prokaryotic adaptation and diversification based on gene acquisition and exchange.

Integrity signals

Registry

Crossref · 10.1093/oxfordjournals.molbev.a004046

Cites

132 of 132 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Claims the paper makes

We couldn’t retrieve this paper’s full text, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

Animal Species and Evolution
Mayr, E. (1963) · doi:10.4159/harvard.9780674865327 · Cited by 10,175
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
Self-citation
Systematics and the Origin of Species
National Academy of Sciences (2005) · National Academies Press eBooks · doi:10.17226/11310 · Cited by 3,451
Genome sequence of enterohaemorrhagic Escherichia coli O157:H7
Perna, N. T., Plunkett, G., Burland, V., Mau, B., Glasner, J. D., Rose, D. J., Mayhew, G. F., Evans, P. S., Gregor, J., Kirkpatrick, H. A., et al. (2001) · Nature · doi:10.1038/35054089 · Cited by 2,035
Phylogenetic Classification and the Universal Tree
Doolittle, W. F. (1999) · Science · doi:10.1126/science.284.5423.2124 · Cited by 1,888
Self-citation
Evidence for lateral gene transfer between Archaea and Bacteria from genome sequence of Thermotoga maritima
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
High Frequency of Hypermutable Pseudomonas aeruginosa in Cystic Fibrosis Lung Infection
Oliver, A., Cantón, R., Campo, P., Baquero, F., & Blázquez, J. (2000) · Science · doi:10.1126/science.288.5469.1251 · Cited by 1,466
Pathogenicity Islands and the Evolution of Microbes
Hacker, J. H., & Kaper, J. B. (2000) · Annual Review of Microbiology · doi:10.1146/annurev.micro.54.1.641 · Cited by 1,298
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
Molecular archaeology of the Escherichia coli genome
Lawrence, J. G., & Ochman, H. (1998) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.95.16.9413 · Cited by 939
Self-citation

Show all 132 references

Research works printed but not linked: 1

Wright S., 1932 The roles of mutation, inbreeding, crossbreeding, and selection in evolution Proc. 6th Int. Congr. Genet1:356-366

Sorted by citations

Items 201–300 of 983

Fiber-Degrading Systems of Different Strains of the Genus Fibrobacter
Béra‐Maillet, C., Ribot, Y., & Forano, É. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.4.2172-2179.2004 · Cited by 93
Deriving the Genomic Tree of Life in the Presence of Horizontal Gene Transfer: Conditioned Reconstruction
Lake, J. A., & Rivera, M. C. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh061 · Cited by 93
Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations
Bhandari, V., & Gupta, R. S. (2013) · Antonie van Leeuwenhoek · doi:10.1007/s10482-013-0062-7 · Cited by 95
Microbial phylotype composition and diversity predicts plant productivity and plant–soil feedbacks
Bever, J. D., Broadhurst, L., & Thrall, P. H. (2012) · Ecology Letters · doi:10.1111/ele.12024 · Cited by 91
Gene Gain and Gene Loss in Streptococcus: Is It Driven by Habitat?
Marri, P. R., Hao, W., & Golding, G. B. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msl115 · Cited by 91
Lateral Transfer of Genes and Gene Fragments in Prokaryotes
Chan, C. X., Beiko, R. G., Darling, A. E., & Ragan, M. A. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp044 · Cited by 92
Shuffling genes around in hot environments: the unique DNA transporter ofThermus thermophilus
Averhoff, B. (2009) · FEMS Microbiology Reviews · doi:10.1111/j.1574-6976.2008.00160.x · Cited by 89
Genome mosaicism and organismal lineages
Zhaxybayeva, O., Lapierre, P., & Gogarten, J. P. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.03.009 · Cited by 91
Self-citation
Modelling bacterial speciation
Hanage, W. P., Spratt, B. G., Turner, K., & Fraser, C. (2006) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2006.1926 · Cited by 88
Stone-dwelling actinobacteria Blastococcus saxobsidens, Modestobacter marinus and Geodermatophilus obscurus proteogenomes
Sghaier, H., Hezbri, K., Ghodhbane‐Gtari, F., Pujić, P., Sen, A., Daffonchio, D. G., Boudabous, A., Tisa, L. S., Klenk, H., Armengaud, J., et al. (2015) · The ISME Journal · doi:10.1038/ismej.2015.108 · Cited by 86
From bacterial genome to functionality; case bifidobacteria
Ventura, M., Motherway, M. O., Leahy, S. C., Moreno-Muñoz, J. A., Fitzgerald, G. F., & van Sinderen, D. (2007) · International Journal of Food Microbiology · doi:10.1016/j.ijfoodmicro.2007.06.011 · Cited by 86
A paradigm shift in our view of species drives current trends in biological classification
Padial, J. M., & De la Riva, I. (2021) · Biological Reviews · doi:10.1111/brv.12676 · Cited by 85
Conserved inserts in the Hsp60 (GroEL) and Hsp70 (DnaK) proteins are essential for cellular growth
Singh, B., & Gupta, R. S. (2009) · Molecular Genetics and Genomics · doi:10.1007/s00438-008-0417-3 · Cited by 86
The Emergence of Life
Camprubí, E., de Leeuw, J. W., House, C. H., Raulin, F., Russell, M. J., Spang, A., Tirumalai, M. R., & Westall, F. (2019) · Space Science Reviews · doi:10.1007/s11214-019-0624-8 · Cited by 84
Signature proteins for the major clades of Cyanobacteria
Gupta, R. S., & Mathews, D. W. (2010) · BMC Evolutionary Biology · doi:10.1186/1471-2148-10-24 · Cited by 84
The role of laterally transferred genes in adaptive evolution
Marri, P. R., Hao, W., & Golding, G. B. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-s1-s8 · Cited by 84
Mathematical Modeling of Evolution of Horizontally Transferred Genes
Novozhilov, A. S. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi167 · Cited by 84
Type I Polyketide Synthases May Have Evolved Through Horizontal Gene Transfer
Ginolhac, A., Jarrin, C., Robe, P., Perrière, G., Vogel, T. M., Simonet, P., & Nalin, R. (2005) · Journal of Molecular Evolution · doi:10.1007/s00239-004-0161-1 · Cited by 84
Gene Organization: Selection, Selfishness, and Serendipity
Lawrence, J. G. (2003) · Annual Review of Microbiology · doi:10.1146/annurev.micro.57.030502.090816 · Cited by 83
Self-citation
The Phylogeny ofRickettsiaUsing Different Evolutionary Signatures: How Tree-Like is Bacterial Evolution?
Murray, G. G. R., Weinert, L. A., Rhule, E., & Welch, J. J. (2015) · Systematic Biology · doi:10.1093/sysbio/syv084 · Cited by 82
Successful Lateral Transfer Requires Codon Usage Compatibility Between Foreign Genes and Recipient Genomes
Medrano-Soto, A., Moreno‐Hagelsieb, G., Vinuesa, P., Christen, J. A., & Collado‐Vides, J. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh202 · Cited by 84
Evolution of Transcription Regulatory Genes Is Linked to Niche Specialization in the Bacterial Pathogen Streptococcus pyogenes
Bessen, D. E., Manoharan, A., Luo, F. H., Wertz, J. E., & Robinson, D. A. (2005) · Journal of Bacteriology · doi:10.1128/jb.187.12.4163-4172.2005 · Cited by 82
Root parasitic plant Orobanche aegyptiaca and shoot parasitic plant Cuscuta australis obtained Brassicaceae-specific strictosidine synthase-like genes by horizontal gene transfer
Zhang, D., Qi, J., Yue, J., Huang, J., Sun, T., Li, S., Wen, J., Hettenhausen, C., Wu, J., Wang, L., et al. (2014) · BMC Plant Biology · doi:10.1186/1471-2229-14-19 · Cited by 81
Correlation between Exogenous Compounds and the Horizontal Transfer of Plasmid-Borne Antibiotic Resistance Genes
Liu, Y., Tong, Z., Shi, J., Jia, Y., Yang, K., & Wang, Z. (2020) · Microorganisms · doi:10.3390/microorganisms8081211 · Cited by 80
The Consistent Phylogenetic Signal in Genome Trees Revealed by Reducing the Impact of Noise
Dutilh, B., Huynen, M., Bruno, W., & Snel, B. (2004) · Journal of Molecular Evolution · doi:10.1007/s00239-003-2575-6 · Cited by 76
Bacteria, Sex, and Systematics
Franklin, L. R. (2007) · Philosophy of Science · doi:10.1086/519476 · Cited by 79
Abundant Indispensable Redundancies in Cellular Metabolic Networks
Wang, Z., & Zhang, J. (2009) · Genome Biology and Evolution · doi:10.1093/gbe/evp002 · Cited by 79
A Phylogenomic Study of Endosymbiotic Bacteria
Canbäck, B. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh122 · Cited by 79
Ancient horizontal gene transfer can benefit phylogenetic reconstruction.
Huang, J.-L., & Gogarten, J. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.05.004 · Cited by 78
Self-citation
A neutral theory of genome evolution and the frequency distribution of genes
Haegeman, B., & Weitz, J. S. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-196 · Cited by 78
Inferring and Validating Horizontal Gene Transfer Events Using Bipartition Dissimilarity
Boc, A., Philippe, H., & Makarenkov, V. (2010) · Systematic Biology · doi:10.1093/sysbio/syp103 · Cited by 77
Species Numbers in Bacteria
Dykhuizen, D. E. (2005) · PubMed · doi:10.5281/zenodo.16247400 · Cited by 77
Hosts, parasites, and horizontal gene transfer
Wijayawardena, B. K., Minchella, D. J., & DeWoody, J. A. (2013) · Trends in Parasitology · doi:10.1016/j.pt.2013.05.001 · Cited by 77
Complexity, connectivity, and duplicability as barriers to lateral gene transfer
Wellner, A., Lurie-Weinberger, M. N., & Gophna, U. (2007) · Genome biology · doi:10.1186/gb-2007-8-8-r156 · Cited by 76
Molecular Evidence for the Evolution of Metal Homeostasis Genes by Lateral Gene Transfer in Bacteria from the Deep Terrestrial Subsurface
Coombs, J. M., & Barkay, T. (2004) · Applied and Environmental Microbiology · doi:10.1128/aem.70.3.1698-1707.2004 · Cited by 77
A systematic method to identify genomic islands and its applications in analyzing the genomes of Corynebacterium glutamicum and Vibrio vulnificus CMCP6 chromosome I
Zhang, R., & Zhang, C. (2004) · Bioinformatics · doi:10.1093/bioinformatics/btg453 · Cited by 76
When Is A Lineage A Species? A Case Study In Myxacorys gen. nov. (Synechococcales: Cyanobacteria) With The Description of Two New Species From The Americas
Pietrasiak, N., Osorio‐Santos, K., Shalygin, S. S., Martin, M. P., & Johansen, J. R. (2019) · Journal of Phycology · doi:10.1111/jpy.12897 · Cited by 75
Inter-phylum HGT has shaped the metabolism of many mesophilic and anaerobic bacteria
Caro‐Quintero, A., & Konstantinidis, K. T. (2014) · The ISME Journal · doi:10.1038/ismej.2014.193 · Cited by 76
Phylogeny and molecular signatures (conserved proteins and indels) that are specific for the Bacteroidetes and Chlorobi species
Gupta, R. S., & Lorenzini, E. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-71 · Cited by 75
Interspecific evolution: microbial symbiosis, endosymbiosis and gene transfer
Hoffmeister, M., & Martin, W. F. (2003) · Environmental Microbiology · doi:10.1046/j.1462-2920.2003.00454.x · Cited by 75
Ancient gene duplications and the root(s) of the tree of life
Zhaxybayeva, O., Lapierre, P., & Gogarten, J. P. (2005) · PROTOPLASMA · doi:10.1007/s00709-005-0135-1 · Cited by 77
Self-citation
A Model of Horizontal Gene Transfer and the Bacterial Phylogeny Problem
Galtier, N. (2007) · Systematic Biology · doi:10.1080/10635150701546231 · Cited by 75
The molecular evolutionary history of Shigella spp. and enteroinvasive Escherichia coli
Peng, J., YANG, J., & Jin, Q. (2008) · Infection Genetics and Evolution · doi:10.1016/j.meegid.2008.10.003 · Cited by 74
The fundamental units, processes and patterns of evolution, and the Tree of Life conundrum
Koonin, E. V., & Wolf, Y. I. (2009) · Biology Direct · doi:10.1186/1745-6150-4-33 · Cited by 74
Presence of typical and atypical virulence genes in vibrio isolates belonging to the Harveyi clade
Ruwandeepika, H. A. D., Defoirdt, T., Bhowmick, P. P., Shekar, M., Bossier, P., & Karunasagar, I. (2010) · Journal of Applied Microbiology · doi:10.1111/j.1365-2672.2010.04715.x · Cited by 74
Genome beginnings: rooting the tree of life
Lake, J. A., Skophammer, R. G., Herbold, C. W., & Servin, J. A. (2009) · Philosophical Transactions of the Royal Society B Biological Sciences · doi:10.1098/rstb.2009.0035 · Cited by 74
Horizontal Gene Transfer Contributes to Plant Evolution: The Case of Agrobacterium T-DNAs
Quispe-Huamanquispe, D. G., Gheysen, G., & Kreuze, J. F. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.02015 · Cited by 74
The evolution and expression of virulence
Ebert, D., & Bull, J. J. (2007) · Oxford University Press eBooks · doi:10.1093/acprof:oso/9780199207466.003.0012 · Cited by 75
The Biogeography of Deep Time Phylogenetic Reticulation
Burbrink, F. T., & Gehara, M. (2018) · Systematic Biology · doi:10.1093/sysbio/syy019 · Cited by 73
Exploring research frontiers in microbiology: recent advances in halophilic and thermophilic extremophiles
Averhoff, B., & Müller, V. (2010) · Research in Microbiology · doi:10.1016/j.resmic.2010.05.006 · Cited by 73
Rooting the Ribosomal Tree of Life
Fournier, G. P., & Gogarten, J. P. (2010) · Molecular Biology and Evolution · doi:10.1093/molbev/msq057 · Cited by 72
Self-citation
Recombinant transfer in the basic genome of Escherichia coli
Dixit, P. D., Pang, T. Y., Studier, F. W., & Maslov, S. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1510839112 · Cited by 72
South African Papilionoid Legumes Are Nodulated by Diverse Burkholderia with Unique Nodulation and Nitrogen-Fixation Loci
Beukes, C. W., Venter, S. N., Law, I. J., Phalane, F. L., & Steenkamp, E. T. (2013) · PLoS ONE · doi:10.1371/journal.pone.0068406 · Cited by 72
Deduction of probable events of lateral gene transfer through comparison of phylogenetic trees by recursive consolidation and rearrangement
MacLeod, D. P., Charlebois, R. L., Doolittle, F., & Bapteste, E. P. (2005) · BMC Evolutionary Biology · doi:10.1186/1471-2148-5-27 · Cited by 72
Single cell genomics indicates horizontal gene transfer and viral infections in a deep subsurface Firmicutes population
Labonté, J., Field, E. K., Lau, M. C. Y., Chivian, D. C., van Heerden, E., Wommack, K. E., Kieft, T. L., Onstott, T. C., & Stepanauskas, R. (2015) · Frontiers in Microbiology · doi:10.3389/fmicb.2015.00349 · Cited by 70
Genetic Redundancies and Their Evolutionary Maintenance
Zhang, J. (2012) · Advances in experimental medicine and biology · doi:10.1007/978-1-4614-3567-9_13 · Cited by 70
Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli
Mau, B., Glasner, J. D., Darling, A. E., & Perna, N. T. (2006) · Genome biology · doi:10.1186/gb-2006-7-5-r44 · Cited by 70
Phylogenetic Analysis of the Incidence ofluxGene Horizontal Transfer inVibrionaceae
Urbanczyk, H., Ast, J. C., Kaeding, A. J., Oliver, J. D., & Dunlap, P. V. (2008) · Journal of Bacteriology · doi:10.1128/jb.00101-08 · Cited by 71
Genetic Competence Drives Genome Diversity in Bacillus subtilis
Brito, P. H., Chevreux, B., Serra, C. R., Schyns, G., Henriques, A. O., & Pereira‐Leal, J. B. (2017) · Genome Biology and Evolution · doi:10.1093/gbe/evx270 · Cited by 72
Identification of Conserved Indels that are Useful for Classification and Evolutionary Studies
Gupta, R. S. (2014) · Methods in microbiology · doi:10.1016/bs.mim.2014.05.003 · Cited by 70
The Extent of Genome Flux and Its Role in the Differentiation of Bacterial Lineages
Nowell, R. W., Green, S., Laue, B. E., & Sharp, P. M. (2014) · Genome Biology and Evolution · doi:10.1093/gbe/evu123 · Cited by 70
Sphingomyelinase D from venoms of Loxosceles spiders: evolutionary insights from cDNA sequences and gene structure
Binford, G. J., Cordes, M. H. J., & Wells, M. A. (2005) · Toxicon · doi:10.1016/j.toxicon.2004.11.011 · Cited by 68
Hydrogen Peroxide-Dependent DNA Release and Transfer of Antibiotic Resistance Genes in Streptococcus gordonii
Itzek, A., Zheng, L., Chen, Z., Merritt, J. L., & Kreth, J. (2011) · Journal of Bacteriology · doi:10.1128/jb.05791-11 · Cited by 67
The impact of long-distance horizontal gene transfer on prokaryotic genome size
Cordero, O. X., & Hogeweg, P. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0907584106 · Cited by 72
Evolution of the RNA Polymerase B' Subunit Gene (rpoB') in Halobacteriales: a Complementary Molecular Marker to the SSU rRNA Gene
Walsh, D. A. (2004) · Molecular Biology and Evolution · doi:10.1093/molbev/msh248 · Cited by 67
Adaptive defensive mechanism of bioleaching microorganisms under extremely environmental acid stress: Advances and perspectives
Hu, W., Feng, S., Tong, Y., Zhang, H., & Yang, H. (2020) · Biotechnology Advances · doi:10.1016/j.biotechadv.2020.107580 · Cited by 69
Geobiological analysis using whole genome‐based tree building applied to the Bacteria, Archaea, and Eukarya
House, C. H., Runnegar, B. N., & Fitz‐Gibbon, S. T. (2003) · Geobiology · doi:10.1046/j.1472-4669.2003.00004.x · Cited by 68
Statistical Analysis of the Spatial Distribution of Operons in the Transcriptional Regulation Network of Escherichia coli
Warren, P. B., & ten Wolde, P. R. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.07.074 · Cited by 68
Erratum to: Molecular signatures for the phylum (class) Thermotogae and a proposal for its division into three orders (Thermotogales, Kosmotogales ord. nov. and Petrotogales ord. nov.) containing four families (Thermotogaceae, Fervidobacteriaceae fam. nov., Kosmotogaceae fam. nov. and Petrotogaceae fam. nov.) and a new genus Pseudothermotoga gen. nov. with five new combinations
Bhandari, V., & Gupta, R. S. (2015) · Antonie van Leeuwenhoek · doi:10.1007/s10482-015-0571-7 · Cited by 68
Detecting lateral gene transfers by statistical reconciliation of phylogenetic forests
Abby, S. S., Tannier, É., Gouy, M., & Daubin, V. (2010) · BMC Bioinformatics · doi:10.1186/1471-2105-11-324 · Cited by 71
Horizontal Gene Transfer in Archaea—From Mechanisms to Genome Evolution
Gophna, U., & Altman‐Price, N. (2022) · Annual Review of Microbiology · doi:10.1146/annurev-micro-040820-124627 · Cited by 66
Phylogeny and molecular signatures for the phylum Fusobacteria and its distinct subclades
Gupta, R. S., & Sethi, M. (2014) · Anaerobe · doi:10.1016/j.anaerobe.2014.06.007 · Cited by 67
The MRP Method
Baum, B. R., & Ragan, M. A. (2004) · Computational biology · doi:10.1007/978-1-4020-2330-9_2 · Cited by 65
A framework for integrating microbial dispersal modes into soil ecosystem ecology
Choudoir, M. J., & DeAngelis, K. M. (2022) · iScience · doi:10.1016/j.isci.2022.103887 · Cited by 64
Horizontal and Vertical Gene Transfer: The Life History of Pathogens
Lawrence, J. G. (2004) · KARGER eBooks · doi:10.1159/000081699 · Cited by 64
Self-citation
Functional Biogeography as Evidence of Gene Transfer in Hypersaline Microbial Communities
Parnell, J., Rompato, G., Latta, L. C., Pfrender, M. E., Nostrand, J. D. V., He, Z., Zhou, J. Z., Andersen, G. L., Champine, P., Ganesan, B., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0012919 · Cited by 64
Computational identification and analysis of orphan assembly-line polyketide synthases
O’Brien, R. V., Davis, R. W., Khosla, C., & Hillenmeyer, M. E. (2013) · The Journal of Antibiotics · doi:10.1038/ja.2013.125 · Cited by 63
Genomic Heterogeneity and Ecological Speciation within One Subspecies of Bacillus subtilis
Kopac, S., Wang, Z., Wiedenbeck, J., Sherry, J., Wu, M., & Cohan, F. M. (2014) · Applied and Environmental Microbiology · doi:10.1128/aem.00576-14 · Cited by 61
Predicted highly expressed genes in archaeal genomes
Karlin, S., Mrázek, J., Ma, J., & Brocchieri, L. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0502313102 · Cited by 61
The Rieske Protein: A Case Study on the Pitfalls of Multiple Sequence Alignments and Phylogenetic Reconstruction
Lebrun, É., Santini, J. M., Brugna, M., Ducluzeau, A., Ouchane, S., Schoepp‐Cothenet, B., Baymann, F., & Nitschke, W. (2006) · Molecular Biology and Evolution · doi:10.1093/molbev/msk010 · Cited by 60
Adaptive Evolution of Extreme Acidophile Sulfobacillus thermosulfidooxidans Potentially Driven by Horizontal Gene Transfer and Gene Loss
Zhang, X., Liu, X., Liang, Y., Guo, X. Y., Xiao, Y., Ma, L., Miao, B., Liu, H., Peng, D., Huang, W., et al. (2017) · Applied and Environmental Microbiology · doi:10.1128/aem.03098-16 · Cited by 60
Monitoring plasmid-mediated horizontal gene transfer in microbiomes: recent advances and future perspectives
Pinilla‐Redondo, R., Cyriaque, V., Jacquiod, S., Sørensen, S. J., & Riber, L. (2018) · Plasmid · doi:10.1016/j.plasmid.2018.08.002 · Cited by 60
Gene Transfer: Gene Swapping Craze Reaches Eukaryotes
Gogarten, J. P. (2003) · Current Biology · doi:10.1016/s0960-9822(02)01426-4 · Cited by 60
Self-citation
When integration fails: Prokaryote phylogeny and the tree of life
O’Malley, M. A. (2012) · Studies in History and Philosophy of Science Part C Studies in History and Philosophy of Biological and Biomedical Sciences · doi:10.1016/j.shpsc.2012.10.003 · Cited by 59
New Findings on Evolution of Metal Homeostasis Genes: Evidence from Comparative Genome Analysis of Bacteria and Archaea
Coombs, J. M., & Barkay, T. (2005) · Applied and Environmental Microbiology · doi:10.1128/aem.71.11.7083-7091.2005 · Cited by 59
Subinhibitory antibiotic concentrations promote the horizontal transfer of plasmid-borne resistance genes from Klebsiellae pneumoniae to Escherichia coli
Ding, M., Ye, Z., Liu, L., Wang, W., Chen, Q., Zhang, F., Wang, Y., Sjöling, Å., Martín‐Rodríguez, A. J., Hu, R., et al. (2022) · Frontiers in Microbiology · doi:10.3389/fmicb.2022.1017092 · Cited by 58
A Benchmark of Parametric Methods for Horizontal Transfers Detection
Becq, J., Churlaud, C., & Deschavanne, P. (2010) · PLoS ONE · doi:10.1371/journal.pone.0009989 · Cited by 62
Duplication is more common among laterally transferred genes than among indigenous genes
Hooper, S. D., & Berg, O. G. (2003) · Genome biology · doi:10.1186/gb-2003-4-8-r48 · Cited by 58
Plasmid pB8 is closely related to the prototype IncP-1β plasmid R751 but transfers poorly to Escherichia coli and carries a new transposon encoding a small multidrug resistance efflux protein
Schlüter, A., Heuer, H., Szczepanowski, R., Poler, S. M., Schneiker, S., Pühler, A., & Top, E. M. (2005) · Plasmid · doi:10.1016/j.plasmid.2005.03.001 · Cited by 58
The Astrobiology Primer: An Outline of General Knowledge—Version 1, 2006
Editors: L.J. Mix, J. C. A. (2006) · Astrobiology · doi:10.1089/ast.2006.6.735 · Cited by 58
Lightning-triggered electroporation and electrofusion as possible contributors to natural horizontal gene transfer
Kotnik, T. (2013) · Physics of Life Reviews · doi:10.1016/j.plrev.2013.05.001 · Cited by 58
Abundant dissolved genetic material in Arctic sea ice Part II: Viral dynamics during autumn freeze-up
Collins, R. E., & Deming, J. W. (2011) · Polar Biology · doi:10.1007/s00300-011-1008-z · Cited by 56
Gene delivery based on macrocyclic amphiphiles
Geng, W., Huang, Q., Xu, Z., Wang, R., & Guo, D. (2019) · Theranostics · doi:10.7150/thno.31914 · Cited by 56
Introduction: A Surfeit of Lampreys
Docker, M. F., Hume, J. B., & Clemens, B. J. (2014) · Springer eBooks · doi:10.1007/978-94-017-9306-3_1 · Cited by 56
Horizontal gene transfer: the path to maturity
Koonin, E. V. (2003) · Molecular Microbiology · doi:10.1046/j.1365-2958.2003.03808.x · Cited by 56
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 58
Prokaryote Genome Fluidity: Toward a System Approach of the Mobilome
Toussaint, A., & Chandler, M. (2011) · Methods in molecular biology · doi:10.1007/978-1-61779-361-5_4 · Cited by 55
Genes of ACYL CARRIER PROTEIN Family Show Different Expression Profiles and Overexpression of ACYL CARRIER PROTEIN 5 Modulates Fatty Acid Composition and Enhances Salt Stress Tolerance in Arabidopsis
Huang, J., Xue, C., Wang, H., Wang, L., Schmidt, W., Shen, R. F., & Lan, P. (2017) · Frontiers in Plant Science · doi:10.3389/fpls.2017.00987 · Cited by 55
Evolutionary aspects of whole-genome biology
Doolittle, R. F. (2005) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2005.04.001 · Cited by 55
The power of phylogenetic approaches to detect horizontally transferred genes
Poptsova, M. S., & Gogarten, J. P. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-45 · Cited by 56
Self-citation

Authors: Gogarten, J. P., Doolittle, W. F., & Lawrence, J. G.
Affiliations: University of Connecticut (US)
ORCID: Gogarten, J. Peter
Doolittle, W. Ford
Lawrence, Jeffrey G.
Venue: Molecular Biology and Evolution
Publisher: Oxford University Press (OUP)
Published: 2002-12-01
Volume: 19
Issue: 12
Pages: 2226-2238
ISSN: 0737-4038 (ISSN-L)
1537-1719
DOI: 10.1093/oxfordjournals.molbev.a004046
OpenAlex: W2110105435
Cited by: 986
References: 132
Citations by year: 2026: 16 · 2025: 16 · 2024: 19 · 2023: 18 · 2022: 27 · 2021: 31 · 2020: 37 · 2019: 31 · 2018: 33 · 2017: 32 · 2016: 45 · 2015: 39 · 2014: 47 · 2013: 57 · 2012: 51
FWCI: 16.65
Type: journal article
Language: en
Open access: closed
Locations: Molecular Biology and Evolution (publishedVersion)
PubMed (publishedVersion)
Funders: David and Lucile Packard Foundation
National Aeronautics and Space Administration
Canadian Institute for Advanced Research
Canada Research Chairs
Health Canada
Canadian Institutes of Health Research
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
Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
Keywords: prokaryotic evolution, horizontal gene transfer, homologous recombination, genetic exchange, phylogeny, diversification, gene loss, clonal divergence
MeSH terms: Phylogeny, Prokaryotic Cells, Evolution, Molecular, 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

Prokaryotic Evolution in Light of Gene Transfer

Abstract

Overview

Integrity signals

Verification

Claims the paper makes

Claims other papers make about this one

Citations

Cites

Cited by

Related

Metadata

Record

About these checks