The DOI matches its Crossref record; 122 of the 123 references it cites were found in a registry or an index.
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.
Overview
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
Verification
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?
In the citing paper
“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.
Citations
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 8,895
Ohno, S. (1970) · doi:10.1007/978-3-642-86659-3 · Cited by 7,833
Darwin, C. R., Darwin, C. R., & Edmonds & Remnants (1859) · J. Murray eBooks · doi:10.5962/bhl.title.59991 · Cited by 7,020
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
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 5,696
(1977) · Cited by 4,052
Genetics and the Origin of Species
Dobzhansky, T. (1952) · AIBS Bulletin · doi:10.1093/aibsbulletin/2.2.14-b · Cited by 3,962
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
Bird, A. (2007) · Nature · doi:10.1038/nature05913 · Cited by 3,011
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
Flagged first, then by citations
1 of the 123 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 201–300 of 378
Zeng, L., Gao, J., Cui, Y., Zhao, Y., Guo, Y., Yuan, Y., & Xu, H. (2024) · Chemical Engineering Journal · doi:10.1016/j.cej.2024.151469 · Cited by 8
Dufour, Y. S., & Donohue, T. J. (2012) · Advances in microbial physiology/Advances in Microbial Physiology · doi:10.1016/b978-0-12-394423-8.00001-9 · Cited by 8
“is frequent among bacteria (Boto, 2010), thus, overestimating the contribution from gene duplication.”
BackgroundAssessing the effects of a sequestered germline on interdomain lateral gene transfer in Metazoa
Jensen, L., Grant, J. R., Laughinghouse, H. D., & Katz, L. A. (2016) · Evolution · doi:10.1111/evo.12935 · Cited by 8
Daugavet, M., Shabelnikov, S., & Podgornaya, O. I. (2020) · BMC Bioinformatics · doi:10.1186/s12859-020-03599-y · Cited by 8
“Another way of gene flow is horizontal gene transfer (HGT), which means the acquisition of DNA from non-related species [1].”
BackgroundEvolutionary change and phylogenetic relationships in light of horizontal gene transfer
Boto, L. (2015) · Journal of Biosciences · doi:10.1007/s12038-015-9514-8 · Cited by 9
“On the other side, others authors (Doolittle 1999; Doolittle and Bapteste 2007; Bapteste et al. 2009) oppose fiercely the idea that evolution, at least in the bacterial world, may be depicted as a tree, and defend their position with the argument that a small number of core genes cannot reflect the complex evolutionar…”
InfluentialSelf-citationSzczepankowska, A. K., Prestel, E., Mariadassou, M., Bardowski, J. K., & Bidnenko, E. (2011) · PLoS ONE · doi:10.1371/journal.pone.0026942 · Cited by 8
“that recent horizontal gene transfers tend to involve closely related organisms and ancient events involved transfer between more distant organisms [46–48].”
BackgroundAnalysis of the 3′ ends of tRNA as the cause of insertion sites of foreign DNA in Prochlorococcus
Liu, H., & Zhu, J. Z. (2010) · Journal of Zhejiang University SCIENCE B · doi:10.1631/jzus.b0900417 · Cited by 8
Mozhayskiy, V., & Tagkopoulos, I. (2011) · Lecture notes in computer science · doi:10.1007/978-3-642-21260-4_26 · Cited by 8
“Although largely ignored in the past, recent phylogenetic evidence suggests that its impact on bacterial evolution is significant and should be investigated more thoroughly [1, 2].”
BackgroundAbiotic Gene Transfer: Rare or Rampant?
Kotnik, T., & Weaver, J. C. (2016) · The Journal of Membrane Biology · doi:10.1007/s00232-016-9897-y · Cited by 9
“While— as cited above—their discoveries date to 1974 and 1989, respectively, many prominent reviews of natural HGT mechanisms left them unmentioned even over the last decade (Chen et al. 2005; Thomas and Nielsen 2005; Boto 2010; Syvanen 2012).”
BackgroundA novel method for transforming the thermophilic bacterium Geobacillus kaustophilus
Miyano, M., Tanaka, K., Ishikawa, S., Mori, K., Miguel-Arribas, A., Meijer, W. J. J., & Yoshida, K. (2018) · Microbial Cell Factories · doi:10.1186/s12934-018-0969-9 · Cited by 8
Darvishi, F., & Hiligsmann, S. (2017) · CRC Press eBooks · doi:10.1201/9781351246101 · Cited by 27
Evolution of the connectivity and indispensability of a transferable gene: the simplicity hypothesis
Jones, C. T., Susko, E., & Bielawski, J. P. (2022) · BMC Ecology and Evolution · doi:10.1186/s12862-022-02091-w · Cited by 7
“Background Horizontal gene transfer (HGT) has played an important role in the evolution of archaea, bacteria, and even unicellular eukaryotes [6].”
BackgroundZeldes, B. M., Poehlein, A., Jain, S., Baum, C., Daniel, R., Müller, V., & Basen, M. (2023) · ISME Communications · doi:10.1038/s43705-022-00211-7 · Cited by 7
“The importance of HGT in microbial evolution remains controversial, but in certain circumstances it leads to much more rapid development of new capabilities than gradual random mutation [40].”
BackgroundClasen, F., Pierneef, R., Slippers, B., & Reva, O. N. (2018) · BMC Genomics · doi:10.1186/s12864-018-4724-8 · Cited by 7
“Horizontal gene transfer (HGT) allows organisms to rapidly adapt to fluctuating environments and different ecological pressures or opportunities [3, 4].”
BackgroundGreening, S. S., Zhang, J., Midwinter, A. C., Wilkinson, D. A., Fayaz, A., Williamson, D. A., Anderson, M. J., Gates, M. C., & French, N. P. (2021) · Epidemics · doi:10.1016/j.epidem.2021.100521 · Cited by 7
New molecular microbiology approaches in the study of Campylobacter fetus
Kienesberger, S., Gorkiewicz, G., Wolinski, H., & Zechner, E. L. (2010) · Microbial Biotechnology · doi:10.1111/j.1751-7915.2010.00173.x · Cited by 7
“The process of horizontal gene transfer (HGT) in bacteria drives genetic diversity and evolution providing also a basis for variation in the virulence repertoire as well as resistance to antibiotics and host defences (Hacker et al., 1997; Gogarten et al., 2002; Koonin and Wolf, 2008; Boto, 2010; Juhas et al., 2009).”
BackgroundXu, C., Jin, Z., Wang, H., Xie, S., Lin, X., Hodel, R. G. J., Zhang, Y., Ma, D., Liu, B., Liu, G., et al. (2023) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2023.10.21.563444 · Cited by 7
Pluralism or unity in biology: could microbes hold the secret to life?
Cleland, C. E. (2013) · Biology & Philosophy · doi:10.1007/s10539-013-9361-7 · Cited by 6
Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning
Bernardini, G., van Iersel, L. J. J., Julien, E., & Stougie, L. (2024) · Molecular Phylogenetics and Evolution · doi:10.1016/j.ympev.2024.108137 · Cited by 6
“…the phylogenetic trees inferred from different loci of the genomes often have conflicting branching patterns, due to evolutionary events like recombination, hybrid speciation, introgression or lateral gene transfer (Randal Linder and Rieseberg, 2004; Mallet, 2005; Boto, 2010; Mallet et al., 2016).”
Integron associated mobile genes
Labbate, M., Boucher, Y., Luu, I., Chowdhury, P. R., & Stokes, H. W. (2012) · Mobile Genetic Elements · doi:10.4161/mge.19510 · Cited by 6
“While all microbiologists accept LGT as a fact, there are still difficulties in reconciling the observation of its large contribution to genomes in the long-term and the likely fitness impact on a genome of acquiring one or more gene units of DNA in the short-term.(3,4) With as little as 20% of a bacterial genome bein…”
BackgroundGenomic Islands: an overview of current software and future improvements
Soares, S. D. C., Oliveira, L. D. C., Jaiswal, A. K., & Azevedo, V. (2016) · PubMed · doi:10.2390/biecoll-jib-2016-301 · Cited by 6
Embedding gene trees into phylogenetic networks by conflict resolution algorithms
Wawerka, M., Dąbkowski, D., Rutecka, N., Mykowiecka, A., & Górecki, P. (2022) · Algorithms for Molecular Biology · doi:10.1186/s13015-022-00218-8 · Cited by 6
“For example, many viruses have segmented genomes, including influenza viruses and rotaviruses [4], while horizontal gene transfer is common in bacteria [5].”
BackgroundTang, Y., Chen, H., Lin, Z., Zhang, L., Upadhyay, A., Liao, C., Merkler, D. J., & Han, Q. (2022) · Insect Science · doi:10.1111/1744-7917.13100 · Cited by 6
“Additionally, HGT is a major contributor to genomic evolution as well as a source of new traits (Boto, 2010).”
BackgroundSserwadda, I., Kidenya, B. R., Kanyerezi, S., Akaro, I. L., Mkinze, B., Mshana, S. E., Hashim, S. O., Isoe, E. M., Seni, J., Joloba, M. L., et al. (2023) · BMC Infectious Diseases · doi:10.1186/s12879-023-08579-0 · Cited by 6
“…have reported how the horizontal gene transfer, a process through which genetic information can be acquired from the environment to a bacterium or from one bacterium to another through other mechanisms other than chromosomal inheritance consequently shaping pathogen virulence evolution [52– 56].”
BackgroundStudies on Molecular Mechanisms of Prebiotic Systems
Riofrío, W. (2011) · Foundations of Science · doi:10.1007/s10699-011-9236-9 · Cited by 6
“All in all, we can assert that there is an increasing amount of evidence suggesting the importance of these phenomena for microbial evolution ( Boto 2009; Ragan and Beiko 2009).”
BackgroundBiochemistry and physiology within the framework of the extended synthesis of evolutionary biology
Vianello, A., & Passamonti, S. (2016) · Biology Direct · doi:10.1186/s13062-016-0109-6 · Cited by 6
“Boto concludes that “there is a need for a new evolutionary paradigm that includes horizontal gene transfer and other mechanisms in the explanation of evolution” [61].”
BackgroundLeave Lamarck Alone! Why the Use of the Term “Lamarckism” and Its Cognates Must Be Shunned
Tanghe, K. B. (2019) · Perspectives in biology and medicine · doi:10.1353/pbm.2019.0004 · Cited by 6
“…but they include the aforementioned epigenetic inheritance and the CRISPR immune system in prokaryotes, horizontal gene transfer, hereditary symbiosis, self-organization, and phenotypic plasticity (Boto 2010; Goldenfeld and Woese 2007; Keller 2011; Nardon and Grenier 1991; Newman and Bhat 2011).”
BackgroundInfluentialAltieri, C. (2016) · Elsevier eBooks · doi:10.1016/b978-0-08-100502-6.00015-7 · Cited by 6
Enfield, N. J. (2014) · doi:10.17169/fudocs_document_000000021399 · Cited by 6
Champagne: Whole-genome phylogenomic character matrix method places Myomorpha basal in RodentiaPreprint
Schull, J. K., Turakhia, Y., Dally, W. J., & Bejerano, G. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/803957 · Cited by 6
A method for massively scalable inference of phylogenetic networksPreprint
Kolbow, N., Kong, S., & Solís‐Lemus, C. (2025) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2025.05.05.652278 · Cited by 6
“However, growing bodies of evidence suggest that some evolutionary events, such as hybridization and horizontal gene transfer, are prevalent in the histories of many species (Boto, 2010).”
Ghelfi, A., & Isobe, S. (2024) · Computational and Structural Biotechnology Journal · doi:10.1016/j.csbj.2024.12.011 · Cited by 7
Yuan, Z., Zhang, J., & Duan, D. (2025) · International Journal of Molecular Sciences · doi:10.3390/ijms26020716 · Cited by 5
Naturally transgenic plants and the need to rethink regulatory triggers in biotechnology
Ríos, D. F., Candia, N. B., Quintana, S. A., Goberna, M. F., Nara, E., Arrúa, A. A., & Alegría, A. C. (2025) · Frontiers in Bioengineering and Biotechnology · doi:10.3389/fbioe.2025.1600610 · Cited by 5
“Horizontal gene transfer (HGT) is a widespread phenomenon across all domains of life, and has been a driving force of evolution (Keeling and Palmer, 2008; Boto, 2010; Wickell and Li, 2020).”
Secondary and Tertiary Endosymbiosis and Kleptoplasty
Gross, J., Bhattacharya, D., Pelletreau, K. N., Rumpho, M. E., & Reyes‐Prieto, A. (2012) · Advances in photosynthesis and respiration · doi:10.1007/978-94-007-2920-9_2 · Cited by 6
Tartik, M. (2024) · Molecular Biology Reports · doi:10.1007/s11033-023-09058-0 · Cited by 4
“Although the uptaking part of the process depends on the type of cell and the nature of the DNA fragment, it is well-known that the recipient cells mostly use HR to integrate free DNA pieces obtained via HGT into their genome [39, 40].”
Predicting horizontal gene transfers with perfect transfer networks
Sánchez, A. L., & Lafond, M. (2024) · Algorithms for Molecular Biology · doi:10.1186/s13015-023-00242-2 · Cited by 4
“However, it is well-known that sequences have their limits for predicting HGT, especially in the case of ancient transfers [21].”
BackgroundUnifying duplication episode clustering and gene-species mapping inference
Górecki, P., Rutecka, N., Mykowiecka, A., & Paszek, J. (2024) · Algorithms for Molecular Biology · doi:10.1186/s13015-024-00252-8 · Cited by 4
The Major Transitions in Early Evolution
Rosslenbroich, B. (2014) · History, philosophy and theory of the life sciences · doi:10.1007/978-3-319-04141-4_4 · Cited by 4
Labbate, M., Boucher, Y., Chowdhury, P. R., & Stokes, H. W. (2011) · BMC Microbiology · doi:10.1186/1471-2180-11-253 · Cited by 4
Horizontal Gene Transfer Elements: Plasmids in Antarctic Microorganisms
Giménez, M., Azzíz, G., Gill, P. R., & Batista, S. B. (2019) · Springer polar sciences · doi:10.1007/978-3-030-02786-5_5 · Cited by 4
“HGTs play an important role modulating evolutionary processes in prokaryotes (Boto 2010).”
BackgroundPhylogeny and Evolution of RNA Structure
Gesell, T., & Schuster, P. M. (2013) · Methods in molecular biology · doi:10.1007/978-1-62703-709-9_16 · Cited by 4
Social Evolution: New HorizonsPreprint
Octavio Miramontes, A., & DeSouza, O. (2014) · arXiv (Cornell University) · doi:10.48550/arxiv.1404.6267 · Cited by 4
“genetic novelties that are more accessible to selection? or should we stick to the old idea of speciation through random mutations alone [18]? Let’s remember just one thing: HGT is a gene mixing process that occurs between different prokaryotic species and even genera [19].”
BackgroundA large‐scale evolutionary and structural analysis of CLC channels and transporters
Mishra, A., Díaz Vázquez, G., & Robertson, J. L. (2025) · Protein Science · doi:10.1002/pro.70389 · Cited by 3
“Further, archaeal sequences are scattered throughout the tree, a possible result of either very early horizontal gene transfer (Boto, 2009) or low phylogenetic signal.”
Assembly of Replicating Protocells with Primitive Metabolism
Karabaşoğlu, C., Saytas, A., Akgol, B., Mercimek, S., & Toparlak, Ö. D. (2026) · Astrobiology · doi:10.1177/15311074261435277 · Cited by 3
Galled Perfect Transfer Networks
Sánchez, A. L., & Lafond, M. (2024) · Lecture notes in computer science · doi:10.1007/978-3-031-58072-7_2 · Cited by 3
A universal and constant rate of gene content change traces pangenome flux to LUCA
Trost, K., Knopp, M. R., Wimmer, J. L. E., Tria, F. D. K., & Martin, W. F. (2024) · FEMS Microbiology Letters · doi:10.1093/femsle/fnae068 · Cited by 3
“Since LGT e v ents ar e also detectable between superking-doms, primarily between archaea and bacteria (Rest and Mindell 2003 , Gophna et al. 2004 , Boto 2010 ), the last universal common ancestor (LUCA) (Weiss et al. 2016 ) might have had the ability to under go LGT, and ther efor e a genome…”
Protein multiplicity: exemplifying an overwhelmingly likely pattern of molecular evolution?
Hatton, L., & Warr, G. W. (2024) · Academia Biology · doi:10.20935/acadbiol7396 · Cited by 3
Gao, Y., Han, C., & Wang, J. (2025) · Molecular Systems Design & Engineering · doi:10.1039/d5me00045a · Cited by 3
Martínez-Rosales, C., Marizcurrena, J. J., Iriarte, A., Fullana, N., Musto, H., & Castro‐Sowinski, S. (2015) · LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) · doi:10.13679/j.advps.2015.1.00088 · Cited by 3
Liu, C., Liu, B., Zhang, Y., Jiang, F., Ren, Y., Li, S., Wang, H., & Fan, W. (2018) · Gene · doi:10.1016/j.gene.2018.05.013 · Cited by 3
Carbon Cycle Implications of Soil Microbial Interactions
Ramin, K. I., & Allison, S. (2019) · Advances in environmental microbiology · doi:10.1007/978-3-030-10777-2_1 · Cited by 3
Wang, R., Li, B. J., Zhang, L., Hou, Y., Lin, H., Luo, B., Yu, G., Wang, J., & Zhu, H. (2021) · Elementa Science of the Anthropocene · doi:10.1525/elementa.2020.00095 · Cited by 3
Hinnekens, P., & Mahillon, J. (2022) · Plasmid · doi:10.1016/j.plasmid.2022.102639 · Cited by 3
A minireview on the bioinformatics analysis of mobile gene elements in microbiome research
Schwarzerová, J., Labanava, A., Rychlı́k, I., Varga, M. J., & Čejková, D. (2023) · Frontiers in Bacteriology · doi:10.3389/fbrio.2023.1275910 · Cited by 3
Why we need Info-computational Constructivism
Dodig-Crnković, G. (2014) · Chalmers Research (Chalmers University of Technology) · Cited by 3
A functional difference between native and horizontally acquired genes in bdelloid rotifers
Barbosa, E. G. G., Crisp, A., Broadbent, S. E., Carrillo, M., Boschetti, C., & Tunnacliffe, A. (2016) · Gene · doi:10.1016/j.gene.2016.06.019 · Cited by 3
Ayala‐Ruano, S., Santander‐Gordón, D., Tejera, E., Pérez‐Castillo, Y., & Armijos‐Jaramillo, V. (2019) · Ecology and Evolution · doi:10.1002/ece3.4924 · Cited by 3
“This mechanism has been rec‐ ognized as a driving evolutionary force, and it allows for gene flow between distant evolutionary taxa (Boto, 2010; Syvanen, 2012).”
BackgroundBreathing life into climate change adaptation
Stadler, F., & Houghton, L. (2019) · Journal of Industrial Ecology · doi:10.1111/jiec.12922 · Cited by 3
Bacteriome and Archaeome: The Core Family Under the Microbiomic Roof
Patrinos, G. P., Zerva, L., Arabatzis, M., Giavasis, I., & Kambouris, M. E. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-816664-2.00002-5 · Cited by 3
Soares, S. D. C., Ramos, R. T. J., Silva, W. M., Oliveira, L. C., Amorim, L. G., Hirata, R., Mattos-Guaraldi, A. L., Miyoshi, A., Silva, A., & Azevedo, V. (2013) · doi:10.13140/2.1.3206.7522 · Cited by 3
Horizontal Gene Transfer in Evolution
Boto, L. (2015) · Wiley eBooks · doi:10.1002/9780470015902.a0022835.pub2 · Cited by 3
Self-citationBerruga-Fernández, T., Huseby, D. L., Koshla, O., Shaukat, A., Katana, A., Sayed, R., Marino, G., & Hughes, D. (2026) · Molecular Biology and Evolution · doi:10.1093/molbev/msag085 · Cited by 2
“Horizontal gene transfer (HGT) between bacteria contributes significantly to bacterial evolution (Boto 2010; Arnold et al. 2022) including the spread of antimicrobial resistance and virulence determinants (Elwell and Shipley 1980; von Wintersdorff et al. 2016; Koraimann 2018).”
Next generation apomorphy: the ubiquity of taxonomically restricted genes
Nelson, P. A., & Buggs, R. J. A. (2016) · Cambridge University Press eBooks · doi:10.1017/cbo9781139236355.013 · Cited by 2
The sociology of science and generality of the DNA/RNA/protein paradigm throughout the cosmos
Wickramasinghe, N. C., Steele, E. J., Klyce, B., Tokoro, G., & Wickramasinghe, D. T. (2020) · Advances in genetics · doi:10.1016/bs.adgen.2020.03.005 · Cited by 2
Systems biology approach for analysis of mobile genetic elements in chicken gut microbiome
Schwarzerová, J., Zeman, M., Rychlı́k, I., Weckwerth, W., Provazník, I., Dolejská, M., & Čejková, D. (2022) · IEEE International Conference on Bioinformatics and Biomedicine (BIBM) · doi:10.1109/bibm55620.2022.9995414 · Cited by 2
“paradigm in evolution that includes HGT among neoDarwinian mechanisms [4, 5].”
BackgroundFrontiers of Fitness Landscapes: A Summary of Open Questions
Richter, H. (2013) · Emergence, complexity and computation · doi:10.1007/978-3-642-41888-4_19 · Cited by 2
Singh, P. K., Singh, P. K., Singh, R. P., & Singh, R. L. (2020) · Elsevier eBooks · doi:10.1016/b978-0-12-820595-2.00002-3 · Cited by 3
Analyzing microbial evolution through gene and genome phylogenies
Teichman, S., Lee, M., & Willis, A. D. (2023) · Biostatistics · doi:10.1093/biostatistics/kxad025 · Cited by 1
Georgakopoulos‐Soares, I., Barnea, O. Y., Mouratidis, I., Hemberg, M., & Ahituv, N. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.03.02.972422 · Cited by 2
Bacterial produce membrane-binding small molecules to regulate horizontal gene transfer in vesiclesPreprint
Tran, F., Gangan, M. S., & Boedicker, J. Q. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.04.08.487716 · Cited by 2
Pandey, M., Rajput, M., Dixit, R., Singh, P., & Shukla, V. K. (2022) · Research Square · doi:10.21203/rs.3.rs-2096480/v1 · Cited by 2
Developmental Incongruity as a Dynamical Representation of HeterochronyPreprint
Alicea, B. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.07.31.231456 · Cited by 3
“While horizontal gene transfer provides a more explicit mechanism [27-29], specific instances are no easier to empirically identify.”
BackgroundHorizontal transfer of matrix metalloproteinase genes links early animal and microbial evolution
Parsons, C., & Fournier, G. P. (2025) · Biology Direct · doi:10.1186/s13062-025-00700-4 · Cited by 1
“Furthermore, expected frequencies for duplication, loss, and transfer vary across the Tree of Life, with fixed gene duplications being more common within Eukaryotes (especially Metazoans), and HGTs being more common within microbes [52, 53].”
Islam, H., Sharma, A. K., Blair, J. C. E., & Lopatkin, A. J. (2025) · Nucleic Acids Research · doi:10.1093/nar/gkaf1507 · Cited by 1
“The absence of standardized reference databases and dedicated plasmid-specific annotation tools remains a key barrier to achieving gene-name-level resolution [ 21 ].”
Biomimetic Synthesis of Seven Halenaquinone Meroterpenoids
Hart, J. D., Lawrence, J. K., Franqui, P. N., Perrott, D. R., Yi, B., Xi, Y., Sumby, C. J., Newton, C. G., & George, J. H. (2026) · Journal of the American Chemical Society · doi:10.1021/jacs.6c06760 · Cited by 1
Hernández‐López, A. (2013) · Springer eBooks · doi:10.1007/978-3-642-38212-3_10 · Cited by 1
Phylogenetic analysis of housekeeping Archaeal proteins and early stages of Archaea evolution
Gunbin, K. V., Suslov, V., & Afonnikov, D. (2013) · Paleontological journal · doi:10.1134/s0031030113090098 · Cited by 1
“In other words, taking into account HGT is an urgent problem of reconstruction of the earliest evolutionary stages of life by comparative analysis of genomes and proteomes of bacteria, archaea, and eukaryotes (Koo nin et al., 2001; Koonin and Wolf, 2008; Gribaldo and Brochier, 2009; Boto, 2010).”
BackgroundPutting Peirce's Theory to the Test: Peircean Evolutionary Algorithms
Akhtar, J., Awais, M. M., & Koshul, B. B. (2013) · Transactions of the Charles S Peirce Society · doi:10.2979/trancharpeirsoc.49.2.77 · Cited by 1
There is no common ground between science and religion
Valdecasas, A. G., Boto, L., & Correas, A. M. (2013) · Journal of Biosciences · doi:10.1007/s12038-013-9318-7 · Cited by 1
Self-citationSagy, O., Ron Shamir, A., & Rechavi, O. (2014) · Frontiers in Genetics · doi:10.3389/fgene.2014.00275 · Cited by 1
“This is consistent with the various findings of gene exchange between organisms at all evolutionary distances (Boto, 2010; Koonin, 2010).”
BackgroundResultInfluentialHarnisz, M., Korzeniewska, E., Niestępski, S., Osińska, A. D., & Nalepa, B. (2017) · E3S Web of Conferences · doi:10.1051/e3sconf/20172200063 · Cited by 1
Synergistic Interactions in Multispecies Biofilms
Ren, D. (2014) · Cited by 1
Linguistic Change and Biological Evolution
Leino, A., Syrjänen, K., & Vesakoski, O. (2020) · Springer eBooks · doi:10.1007/978-3-030-55438-5_7 · Cited by 1
Photobacterium halophilum sp. nov. and a Salt-Loving Bacterium Isolated from Marine Sediment
Kim, M., Lee, K., Cha, I., & Park, S.-J. (2022) · Diversity · doi:10.3390/d14030188 · Cited by 1
“, genome conservation) in their habits [66,67].”
Densi, A., Iyer, R., & Bhat, P. J. (2023) · Microbiology spectrum · doi:10.1128/spectrum.03847-22 · Cited by 2
Xia, Y., Zuo, S., Zheng, Y., Yang, W., Tang, X., Ke, X., Zhuo, Q., Yang, X., Li, Y., Liu, H., et al. (2023) · Reproductive Toxicology · doi:10.1016/j.reprotox.2023.108424 · Cited by 1
Amplification of Immune Genes in Ancient Stony Corals for Adapting to Unstable Marine Environments
Wu, T., Lei, Y., & Jian, Z. (2024) · Ocean-Land-Atmosphere Research · doi:10.34133/olar.0041 · Cited by 1
Fishpond microbiota, their synergism with fish and potential biotechnological applications
Kuebutornye, F. K. A., Roy, K., Folorunso, E. A., Tellbüscher, A. A., Bohatá, A., & Mráz, J. (2024) · Aquaculture · doi:10.1016/j.aquaculture.2024.741890 · Cited by 1
Topology of Reticulate Evolution
Emmett, K. (2016) · doi:10.7916/d8028rkg · Cited by 1
Ceschim, B., de Oliveira, T. B., & de Andrade, A. M. (2016) · Filosofia e História da Biologia · Cited by 1
Long Non-coding RNAs in the Human Genome Acquired by Horizontal Gene Transfer
Pierneef, R., Clasen, F., Bezuidt, O. K. I., & Reva, O. N. (2018) · The Open Bioinformatics Journal · doi:10.2174/1875036201811010182 · Cited by 1
Searching for Extraterrestrial Life Without a Definition or Universal Theory of Life
Cleland, C. E. (2019) · Cambridge University Press eBooks · doi:10.1017/9781139046893.009 · Cited by 1
Challenges for a Universal Theory of Life
Cleland, C. E. (2019) · Cambridge University Press eBooks · doi:10.1017/9781139046893.006 · Cited by 1
Nowe idee w biologii ewolucyjnej: od NDMS do EES
Garte, S. (2021) · Filozoficzne Aspekty Genezy · doi:10.53763/fag.2018.15.156 · Cited by 1
Panorama general de las adaptaciones metabólicas en el Orden Anura
Ruiz-Londoño, D., Manrique‐Barros, S., & Vidal, L. E. T. (2021) · TIP Revista Especializada en Ciencias Químico-Biológicas · doi:10.22201/fesz.23958723e.2021.352 · Cited by 1
Gabora, L. M. (2013) · Physics of Life Reviews · doi:10.1016/j.plrev.2013.05.007 · Cited by 1
“olution as discussed in the target paper. Indeed in prokaryotes this kind of non-Darwinian horizontal exchange is so rampant that it appears that no two genes have the exact same evolutionary history [2, 3, 13, 18, 19, 30, 31]. Madsen and Lipo also claim, “Nor is it required that new variation be approximated by a ran…”
BackgroundHassell, M. P. (2010) · Proceedings of the Royal Society B Biological Sciences · doi:10.1098/rspb.2010.2415 · Cited by 1
Insights into the maintenance and consequences of asexual reproduction in rotifera
Fischer, C. (2013) · Carl von Ossiezky University of Oldenburg
Metadata
- 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 of Biology and Scientific Explanation
- 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