Maynard Smith, J., Feil, E. J. & Smith, N. H. Population structure and evolutionary dynamics of pathogenic bacteria. Bioessays 22, 1115–1122 (2000).
Garud, N. R., Good, B. H., Hallatschek, O. & Pollard, K. S. Evolutionary dynamics of bacteria in the gut microbiome within and across hosts. PLoS Biol. 17, e3000102 (2019). Using metagenomic samples form the human gut microbiome, the authors infer lineage structure from within-host polymorphisms in more than 40 species to show adaptation on short timescales can be seeded by HGT.
Google Scholar
Frazão, N., Sousa, A., Lässig, M. & Gordo, I. Horizontal gene transfer overrides mutation in Escherichia coli colonizing the mammalian gut. Proc. Natl Acad. Sci. USA 116, 17906–17915 (2019). Using the mouse microbiome as a study system, the authors show that rapid, phage-mediated HGT can transfer beneficial genes — already present in a resident strain — to an invading strain.
Google Scholar
Smith, J. M., Smith, N. H., O’Rourke, M. & Spratt, B. G. How clonal are bacteria? Proc. Natl Acad. Sci. USA 90, 4384–4388 (1993).
Google Scholar
Dykhuizen, D. E. & Green, L. Recombination in Escherichia coli and the definition of biological species. J. Bacteriol. 173, 7257–7268 (1991).
Google Scholar
Feil, E. J. et al. Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc. Natl Acad. Sci. USA 98, 182–187 (2001).
Google Scholar
Suerbaum, S. et al. Free recombination within Helicobacter pylori. PNAS 95, 12619–12624 (1998).
Google Scholar
Smillie, C. S. et al. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480, 241–244 (2011).
Google Scholar
Lozupone, C. A. et al. The convergence of carbohydrate active gene repertoires in human gut microbes. Proc. Natl Acad. Sci. USA 105, 15076–15081 (2008).
Google Scholar
Bradley, P. H., Nayfach, S. & Pollard, K. S. Phylogeny-corrected identification of microbial gene families relevant to human gut colonization. PLoS Computational Biol. 14, e1006242 (2018). The authors use phylogenetic linear regression to control for important confounders and identify genes potentially involved in adaptation to the human gut.
Andreani, N. A., Hesse, E. & Vos, M. Prokaryote genome fluidity is dependent on effective population size. ISME J. 11, 1719–1721 (2017).
Google Scholar
Mcinerney, J. O., Mcnally, A. & Connell, M. J. O. Why prokaryotes have pangenomes. Nat. Publ. Gr. 2, 1–5 (2017).
Shapiro, B. J. The population genetics of pangenomes. Nat. Microbiol. 2, 1005860 (2017).
Vos, M. & Eyre-walker, A. Are pangenomes adaptive or not? Nat. Microbiol. https://doi.org/10.1038/s41564-017-0067-5 (2017).
Google Scholar
Johnsborg, O., Eldholm, V. & Håvarstein, L. S. Natural genetic transformation: prevalence, mechanisms and function. Res. Microbiol. 158, 767–778 (2007).
Google Scholar
Johnston, C., Martin, B., Fichant, G., Polard, P. & Claverys, J. P. Bacterial transformation: distribution, shared mechanisms and divergent control. Nat. Rev. Microbiol. 12, 181–196 (2014).
Google Scholar
Pimentel, Z. T. & Zhang, Y. Evolution of the natural transformation protein, ComEC, in Bacteria. Front. Microbiol. 9, 1–10 (2018).
Roux, S., Hallam, S. J., Woyke, T. & Sullivan, M. B. Viral dark matter and virus–host interactions resolved from publicly available microbial genomes. eLife 4, 1–20 (2015).
Camarillo-Guerrero, L. F. et al. Massive expansion of human gut bacteriophage diversity. Cell 184, 1098–1109.e9 (2021).
Google Scholar
Guglielmini, J., Quintais, L., Garcillán-Barcia, M. P., de la Cruz, F. & Rocha, E. P. C. The repertoire of ice in prokaryotes underscores the unity, diversity, and ubiquity of conjugation. PLoS Genet. 7, e1002222 (2011).
Google Scholar
Dubey, G. P. & Ben-Yehuda, S. Intercellular nanotubes mediate bacterial communication. Cell 144, 590–600 (2011).
Google Scholar
Abe, K., Nomura, N. & Suzuki, S. Biofilms: hot spots of horizontal gene transfer (HGT) in aquatic environments, with a focus on a new HGT mechanism. FEMS Microbiol. Ecol. 96, 1–12 (2020).
Bárdy, P. et al. Structure and mechanism of DNA delivery of a gene transfer agent. Nat. Commun. 11, 3034 (2020).
Google Scholar
Hasegawa, H., Suzuki, E. & Maeda, S. Horizontal plasmid transfer by transformation in Escherichia coli: environmental factors and possible mechanisms. Front. Microbiol. 9, 1–6 (2018).
Seitz, P. & Blokesch, M. Cues and regulatory pathways involved in natural competence and transformation in pathogenic and environmental Gram-negative bacteria. FEMS Microbiol. Rev. 37, 336–363 (2013).
Google Scholar
Wall, D. Kin recognition in bacteria. Annu. Rev. Microbiol. 70, 143–160 (2016).
Google Scholar
Frye, S. A., Nilsen, M., Tønjum, T. & Ambur, O. H. Dialects of the DNA uptake sequence in Neisseriaceae. PLoS Genet. https://doi.org/10.1371/journal.pgen.1003458 (2013).
Google Scholar
Redfield, R. J. et al. Evolution of competence and DNA uptake specificity in the Pasteurellaceae. BMC Evol. Biol. 6, 1–15 (2006).
Dion, M. B., Oechslin, F. & Moineau, S. Phage diversity, genomics and phylogeny. Nat. Rev. Microbiol. https://doi.org/10.1038/s41579-019-0311-5 (2020).
Google Scholar
Siguier, P., Gourbeyre, E. & Chandler, M. Bacterial insertion sequences: their genomic impact and diversity. FEMS Microbiol. Rev. 38, 865–891 (2014).
Google Scholar
Vulić, M., Dionisio, F., Taddei, F. & Radman, M. Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria. Proc. Natl Acad. Sci. USA 94, 9763–9767 (1997).
Google Scholar
Majewski, J. et al. Barriers to genetic exchange between bacterial species: Streptococcus pneumoniae transformation. J. Bacteriol. 182, 1016–1023 (2000).
Google Scholar
Wyres, K. L. et al. Pneumococcal capsular switching: a historical perspective. J. Infect. Dis. 207, 439–449 (2013).
Google Scholar
Hallet, B. & Sherratt, D. J. Transposition and site-specific recombination: adapting DNA cut-and-paste mechanisms to a variety of genetic rearrangements. FEMS Microbiol. Rev. 21, 157–178 (1997).
Google Scholar
Durrant, M. G., Li, M. M., Siranosian, B. A., Montgomery, S. B. & Bhatt, A. S. A bioinformatic analysis of integrative mobile genetic elements highlights their role in bacterial adaptation. Cell Host Microbe 27, 140–153.e9 (2020).
Google Scholar
Rajeev, L., Malanowska, K. & Gardner, J. F. Challenging a paradigm: the role of DNA homology in tyrosine recombinase reactions. Microbiol. Mol. Biol. Rev. 73, 300–309 (2009).
Google Scholar
Hickman, A. B., Chandler, M. & Dyda, F. Integrating prokaryotes and eukaryotes: DNA transposases in light of structure. Crit. Rev. Biochem. Mol. Biol. 45, 50–69 (2010).
Google Scholar
Oliveira, P. H., Touchon, M., Cury, J. & Rocha, E. P. C. The chromosomal organization of horizontal gene transfer in bacteria. Nat. Commun. 8, 1–10 (2017).
Wadsworth, C. B., Arnold, B. J., Sater, M. R. A. & Grad, Y. Azithromycin resistance through interspecific acquisition of an epistasis-dependent efflux pump component and transcriptional regulator in Neisseria gonorrhoeae. mBio 9, 1–17 (2018).
Arevalo, P., VanInsberghe, D., Elsherbini, J., Gore, J. & Polz, M. F. A reverse ecology approach based on a biological definition of microbial populations. Cell 178, 820–834.e14 (2019). The authors create a metric of recent gene flow to define ecological populations and discover genes that have experienced positive selection across populations.
Google Scholar
Croucher, N. J. et al. Horizontal DNA transfer mechanisms of bacteria as weapons of intragenomic conflict. PLoS Biol. 14, 1–42 (2016). A model of transformation with known bias towards the acquisition of shorter alleles suggests HGT may effectively purge bacterial genomes of parasitic MGEs.
Apagyi, K. J., Fraser, C. & Croucher, N. J. Transformation asymmetry and the evolution of the bacterial accessory genome. Mol. Biol. Evol. 35, 575–581 (2018).
Google Scholar
Mira, A., Ochman, H. & Moran, N. A. Deletional bias and the evolution of bacterial genomes. Trends Genet. 17, 589–596 (2001).
Google Scholar
Kuo, C.-H. & Ochman, H. Deletional bias across the three domains of life. Genome Biol. Evol. 1, 145–152 (2009).
Google Scholar
Lawrence, J. G. & Roth, J. R. Selfish operons: horizontal transfer may drive the evolution of gene clusters. Genetics 143, 1843–1860 (1996).
Google Scholar
Hehemann, J. H. et al. Transfer of carbohydrate-active enzymes from marine bacteria to Japanese gut microbiota. Nature 464, 908–912 (2010).
Google Scholar
Campbell, A. Prophage insertion sites. Res. Microbiol. 154, 277–282 (2003).
Google Scholar
Chu, N. D. et al. A mobile element in mutS drives hypermutation in a marine Vibrio. mBio 8, 1–13 (2017).
Bobay, L. M., Rocha, E. P. C. & Touchon, M. The adaptation of temperate bacteriophages to their host genomes. Mol. Biol. Evol. 30, 737–751 (2013).
Google Scholar
Lee, H., Doak, T. G., Popodi, E., Foster, P. L. & Tang, H. Insertion sequence-caused large-scale rearrangements in the genome of Escherichia coli. Nucleic Acids Res. 44, 7109–7119 (2016).
Google Scholar
Parkhill, J. et al. Comparative analysis of the genome sequences of Bordetella pertussis, Bordetella parapertussis and Bordetella bronchiseptica. Nat. Genet. 35, 32–40 (2003).
Google Scholar
Moran, N. A. & Plague, G. R. Genomic changes following host restriction in bacteria. Curr. Opin. Genet. Dev. 14, 627–633 (2004).
Google Scholar
Hendry, T. et al. Ongoing transposon-mediated genome reduction in the luminous bacterial symbionts of deep-sea ceratioid anglerfishes. mBio https://doi.org/10.1128/mBio.01033-18 (2018).
Google Scholar
Waterworth, S. C. et al. Horizontal gene transfer to a defensive symbiont with a reduced genome in a multipartite beetle microbiome. mBio https://doi.org/10.1128/mBio.02430-19 (2020).
Google Scholar
Vos, M. et al. Rates of lateral gene transfer in prokaryotes: high but why? Trends Microbiol. 23, 598–605 (2015).
Google Scholar
Cohen, E., Kessler, D. A. & Levine, H. Recombination dramatically speeds up evolution of finite populations. Phys. Rev. Lett. 94, 1–4 (2005).
Levin, B. R. & Cornejo, O. E. The population and evolutionary dynamics of homologous gene recombination in bacteria. PLoS Genet. https://doi.org/10.1371/journal.pgen.1000601 (2009).
Google Scholar
Arnold, B. J. et al. Weak epistasis may drive adaptation in recombining bacteria. Genetics 208, 1247–1260 (2018).
Google Scholar
Moradigaravand, D. & Engelstädter, J. The effect of bacterial recombination on adaptation on fitness landscapes with limited peak accessibility. PLoS Comput. Biol. 8, 35–37 (2012).
Cooper, T. F. Recombination speeds adaptation by reducing competition between beneficial mutations in populations of Escherichia coli. PLoS Biol. 5, 1899–1905 (2007).
Winkler, J. & Kao, K. C. Harnessing recombination to speed adaptive evolution in Escherichia coli. Metab. Eng. 14, 487–495 (2012).
Google Scholar
Chu, H. Y., Sprouffske, K. & Wagner, A. The role of recombination in evolutionary adaptation of Escherichia coli to a novel nutrient. J. Evol. Biol. 30, 1692–1711 (2017).
Google Scholar
Arnold, B. et al. Fine-scale haplotype structure reveals strong signatures of positive selection in a recombining bacterial pathogen. Mol. Biol. Evol. https://doi.org/10.1093/molbev/msz225 (2019).
Google Scholar
Yahara, K. et al. The landscape of realized homologous recombination in pathogenic bacteria. Mol. Biol. Evol. 33, 456–471 (2016).
Google Scholar
Engelstädter, J. & Moradigaravand, D. Adaptation through genetic time travel? Fluctuating selection can drive the evolution of bacterial transformation. Proc. R. Soc. B Biol. Sci. 281, 20132609 (2014).
Cohan, F. M. Periodic selection and ecological diversity in bacteria. Selective Sweep https://doi.org/10.1007/0-387-27651-3_7 (2007).
Google Scholar
Shapiro, B. J., David, L. A., Friedman, J. & Alm, E. J. Looking for Darwin’s footprints in the microbial world. Trends Microbiol. 17, 196–204 (2009).
Google Scholar
Shapiro, B. J. et al. Population genomics of early events in the ecological differentiation of bacteria. Science 336, 48–51 (2012).
Google Scholar
Rosen, M., Davison, M., Bhaya, D. & Fisher, D. S. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science 348, 1019–1024 (2015).
Google Scholar
Bendall, M. L. et al. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations. ISME J. 10, 1589–1601 (2016).
Google Scholar
Porter, S. S., Chang, P. L., Conow, C. A., Dunham, J. P. & Friesen, M. L. Association mapping reveals novel serpentine adaptation gene clusters in a population of symbiotic Mesorhizobium. ISME J. 11, 248–262 (2017).
Google Scholar
Crits-Christoph, A., Olm, M. R., Diamond, S., Bouma-Gregson, K. & Banfield, J. F. Soil bacterial populations are shaped by recombination and gene-specific selection across a grassland meadow. ISME J. https://doi.org/10.1038/s41396-020-0655-x (2020).
Google Scholar
Woods, L. C. et al. Horizontal gene transfer potentiates adaptation by reducing selective constraints on the spread of genetic variation. Proc. Natl Acad. Sci. USA 117, 26868–26875 (2020).
Google Scholar
Miralles, R., Gerrish, P. J., Moya, A. & Elena, S. F. Clonal interference and the evolution of RNA viruses. Science 285, 1745–1747 (1999).
Google Scholar
De Visser, J. A. G. M., Zeyl, C. W., Gerrish, P. J., Blanchard, J. L. & Lenski, R. E. Diminishing returns from mutation supply rate in asexual populations. Science 283, 404–406 (1999).
Google Scholar
Good, B. H., Rouzine, I. M., Balick, D. J., Hallatschek, O. & Desai, M. M. Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proc. Natl Acad. Sci. USA 109, 4950–4955 (2012).
Google Scholar
Takeuchi, N., Cordero, O. X., Koonin, E. V. & Kaneko, K. Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection. BMC Biol. 13, 1–11 (2015). The authors show that in the presence of NFDS, genes or mutations that are unconditionally beneficial can spread through populations only via HGT, giving rise to gene-specific sweeps.
Corander, J. et al. Frequency-dependent selection in vaccine-associated pneumococcal population dynamics. Nat. Ecol. Evol. 2017, 1950–1960 (2018).
Rodriguez-Valera, F. et al. Explaining microbial population genomics through phage predation. Nat. Rev. Microbiol. 7, 828–836 (2009).
Google Scholar
Good, B. H., McDonald, M. J., Barrick, J. E., Lenski, R. E. & Desai, M. M. The dynamics of molecular evolution over 60,000 generations. Nature 551, 45–50 (2017).
Google Scholar
Ramiro, R. S., Durão, P., Bank, C. & Gordo, I. Low mutational load allows for high mutation rate variation in gut commensal bacteria. PLoS Biol. https://doi.org/10.1101/568709 (2020).
Google Scholar
Holt, R. D. Bringing the Hutchinsonian niche into the 21st century: ecological and evolutionary perspectives. Proc. Natl Acad. Sci. USA 106, 19659–19665 (2009).
Google Scholar
Cohan, F. M. Transmission in the origins of bacterial diversity, from ecotypes to phyla. Microbiol. Spectr. https://doi.org/10.1128/9781555819743.ch18 (2017).
Google Scholar
Fondi, M. et al. “Every gene is everywhere but the environment selects”: global geolocalization of gene sharing in environmental samples through network analysis. Genome Biol. Evol. 8, 1388–1400 (2016).
Google Scholar
Cohan, F. M. The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am. Nat. 143, 965–986 (1994).
Majewski, J. & Cohan, F. M. Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics 152, 1459–1474 (1999).
Google Scholar
Messer, P. W. & Petrov, D. A. Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol. Evol. https://doi.org/10.1016/j.tree.2013.08.003 (2013).
Google Scholar
Cui, Y. et al. Epidemic clones, oceanic gene pools, and Eco-LD in the free living marine pathogen Vibrio parahaemolyticus. Mol. Biol. Evol. 32, 1396–1410 (2015).
Google Scholar
Skwark, M. et al. Interacting networks of resistance, virulence and core machinery genes identified by genome-wide epistasis analysis. PLoS Genet. https://doi.org/10.1371/journal.pgen.1006508 (2016).
Google Scholar
Pensar, J. et al. Genome-wide epistasis and co-selection study using mutual information. Nucleic Acids Res. 47, e112–e112 (2019).
Google Scholar
Puranen, S. et al. SuperDCA for genome-wide epistasis analysis. Microb. Genomics 4, e000184 (2018).
Whelan, F. J., Rusilowicz, M. & McInerney, J. O. Coinfinder: detecting significant associations and dissociations in pangenomes. Microb. Genomics 6, e000338 (2020).
Slomka, S. et al. Experimental evolution of bacillus subtilis reveals the evolutionary dynamics of horizontal gene transfer and suggests adaptive and neutral effects. Genetics 216, 543–558 (2020).
Google Scholar
Maddamsetti, R. & Lenski, R. E. Analysis of bacterial genomes from an evolution experiment with horizontal gene transfer shows that recombination can sometimes overwhelm selection. PLoS Genet. 14, 1–30 (2018).
Knöppel, A., Lind, P. A., Lustig, U., Näsvall, J. & Andersson, D. I. Minor fitness costs in an experimental model of horizontal gene transfer in bacteria. Mol. Biol. Evol. 31, 1220–1227 (2014).
Google Scholar
Collins, R. E. & Higgs, P. G. Testing the infinitely many genes model for the evolution of the bacterial core genome and pangenome. Mol. Biol. Evol. 29, 3413–3425 (2012).
Google Scholar
Baumdicker, F., Hess, W. R. & Pfaffelhuber, P. The infinitely many genes model for the distributed genome of bacteria. Genome Biol. Evol. 4, 443–456 (2012).
Google Scholar
Haegeman, B. & Weitz, J. S. A neutral theory of genome evolution and the frequency distribution of genes. BMC Genomics 13, 196 (2012).
Google Scholar
Hughes, A. L. Evidence for abundant slightly deleterious polymorphisms in bacterial populations. Genetics 169, 533–538 (2005).
Google Scholar
Van Passel, M. W. J., Marri, P. R. & Ochman, H. The emergence and fate of horizontally acquired genes in Escherichia coli. PLoS Comput. Biol. 4, e1000059 (2008).
Google Scholar
Hao, W. & Golding, G. B. The fate of laterally transferred genes: life in the fast lane to adaptation or death. Genome Res. 16, 636–643 (2006).
Google Scholar
Lerat, E., Daubin, V., Ochman, H. & Moran, N. A. Evolutionary origins of genomic repertoires in bacteria. 3, e130 (2005).
Lobkovsky, A. E., Wolf, Y. I. & Koonin, E. V. Gene frequency distributions reject a neutral model of genome evolution. Genome Biol. Evol. 5, 233–242 (2013).
Google Scholar
Sela, I., Wolf, Y. I. & Koonin, E. V. Theory of prokaryotic genome evolution. Proc. Natl Acad. Sci. USA 113, 11399–11407 (2016).
Google Scholar
Charlesworth, B. Effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. https://doi.org/10.1038/nrg2526 (2009).
Google Scholar
Cohan, F. M. & Perry, E. B. A systematics for discovering the fundamental units of bacterial diversity. Curr. Biol. 17, 373–386 (2007).
Domingo-Sananes, M. R. & McInerney, J. O. Selection-based model of prokaryote pangenomes. bioRxiv https://doi.org/10.1101/782573 (2019).
Google Scholar
Azarian, T. et al. Frequency-dependent selection can forecast evolution in Streptococcus pneumoniae. PLoS Biol. 18, e3000878 (2020). The authors provide evidence that NFDS is a pervasive evolutionary force that shapes the accessory genome of S. pneumoniae.
Google Scholar
Bobay, L. M., Touchon, M. & Rocha, E. P. C. Pervasive domestication of defective prophages by bacteria. Proc. Natl Acad. Sci. USA 111, 12127–12132 (2014). Although prophages can be considered parasitic, the authors show evidence of purifying selection within prophage genes, suggesting that they serve a beneficial purpose within their bacterial hosts.
Google Scholar
Puigbò, P., Lobkovsky, A. E., Kristensen, D. M., Wolf, Y. I. & Koonin, E. V. Genomes in turmoil: quantification of genome dynamics in prokaryote supergenomes. BMC Med. 12, 1–19 (2014).
Lynch, M. Streamlining and simplification of microbial genome architecture. Annu.Rev.Microbiol. 60, 327–349 (2006).
Google Scholar
Bobay, L. & Ochman, H. Factors driving effective population size and pan-genome evolution in bacteria. BMC Evol. Biol. 18, 15 (2018).
Brito, I. L. et al. Mobile genes in the human microbiome are structured from global to individual scales. Nature 535, 435–439 (2016).
Google Scholar
Evans, T. G. Considerations for the use of transcriptomics in identifying the ‘genes that matter’ for environmental adaptation. J. Exp. Biol. 218, 1925–1935 (2015).
Google Scholar
Cain, A. K. et al. A decade of advances in transposon-insertion sequencing. Nat. Rev. Genet. 21, 526–540 (2020).
Google Scholar
Wu, M. et al. Genetic determinants of in vivo fitness and diet responsiveness in multiple human gut Bacteroides. Science (80-.) 350, aac5992 (2015).
Poulsen, B. E. et al. Defining the core essential genome of Pseudomonas aeruginosa. Proc. Natl Acad. Sci. USA 116, 10072–10080 (2019).
Google Scholar
Pál, C., Papp, B. & Lercher, M. J. Adaptive evolution of bacterial metabolic networks by horizontal gene transfer. Nat. Genet. 37, 1372–1375 (2005).
Google Scholar
Ansari, A. & Didelot, X. Inference of the properties of the recombination process from whole bacterial genomes. Genetics 196, 253–265 (2014).
Google Scholar
Lin, M. & Kussell, E. Inferring bacterial recombination rates from large-scale sequencing datasets. Nat. Methods 16, 199–204 (2019). The authors develop a fast and clever method that uses linkage information to estimate recombination rates and the diversity of the gene pool that has contributed alleles to the sample via HGT.
Google Scholar
Marttinen, P. et al. Detection of recombination events in bacterial genomes from large population samples. Nucleic Acids Res. 40, 1–12 (2012).
Didelot, X. & Wilson, D. J. ClonalFrameML: efficient inference of recombination in whole bacterial genomes. PLoS Comput. Biol. 11, 1–18 (2015).
Croucher, N. J. et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. https://doi.org/10.1371/journal.pcbi.1004041 (2015).
Mostowy, R. et al. Efficient inference of recent and ancestral recombination within bacterial populations. Mol. Biol. Evol. 34, 1167–1182 (2017).
Google Scholar
Yahara, K., Didelot, X., Ansari, M. A., Sheppard, S. K. & Falush, D. Efficient inference of recombination hot regions in bacterial genomes. Mol. Biol. Evol. 31, 1593–1605 (2014).
Google Scholar
Daubin, V., Moran, N. A. & Ochman, H. Phylogenetics and the cohesion of bacterial genomes. Science 301, 829–832 (2003).
Google Scholar
Daubin, V. & Szollosi, G. Horizontal gene transfer and the tree of life. Cold Spring Harb. Perspect. Biol. https://doi.org/10.1007/978-94-007-2941-4_37 (2016).
Google Scholar
Bertelli, C., Tilley, K. E. & Brinkman, F. S. L. Microbial genomic island discovery, visualization and analysis. Brief. Bioinform. 20, 1685–1698 (2019).
Google Scholar
Rocha, E. P. C. et al. Comparisons of dN/dS are time dependent for closely related bacterial genomes. J. Theor. Biol. 239, 226–235 (2006).
Google Scholar
Kryazhimskiy, S. & Plotkin, J. B. The population genetics of dN/dS. PLoS Genet. https://doi.org/10.1371/journal.pgen.1000304 (2008).
Google Scholar
Charlesworth, B. & Charlesworth, D. Elements of Evolutionary Genetics (Roberts and Company Publishers, 2010).
Castillo-Ramírez, S. et al. The impact of recombination on dN/dS within recently emerged bacterial clones. PLoS Pathog. https://doi.org/10.1371/journal.ppat.1002129 (2011).
Google Scholar
David, S. et al. Dynamics and impact of homologous recombination on the evolution of Legionella pneumophila. PLoS Genet. 13, 1–21 (2017).
Dillon, M., Thakur, S., Almeida, R. & Guttman, D. Recombination of ecologically and evolutionarily significant loci maintains genetic cohesion in the Pseudomonas syringae species complex. Genome Biol. https://doi.org/10.1101/227413 (2019).
Google Scholar
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