L. Frost, R. Leplae, A. Summers, and A. Toussaint, Mobile genetic elements: the agents of open source evolution, Nature Reviews Microbiology, vol.11, issue.9, pp.722-732, 2005.
DOI : 10.1093/nar/gkh059

M. Vuli-c, F. Dionisio, F. Taddei, and M. Radman, Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in enterobacteria, Proceedings of the National Academy of Sciences, vol.94, issue.18, pp.9763-9767, 1997.
DOI : 10.1073/pnas.94.18.9763

X. Didelot and D. Wilson, ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes, PLOS Computational Biology, vol.172, issue.6, p.1004041, 2015.
DOI : 10.1371/journal.pcbi.1004041.s007

P. Oliveira, M. Touchon, and E. Rocha, The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts, Nucleic Acids Research, vol.42, issue.16, pp.10618-10631, 2014.
DOI : 10.1093/nar/gku734

URL : https://hal.archives-ouvertes.fr/pasteur-01374960

I. Mruk and I. Kobayashi, To be or not to be: regulation of restriction-modification systems and other toxin-antitoxin systems, Nucleic Acids Research, vol.42, issue.1, pp.70-86, 2014.
DOI : 10.1093/nar/gkt711

A. Pingoud, G. Wilson, and W. Wende, Type II restriction endonucleases???a historical perspective and more, Nucleic Acids Research, vol.42, issue.12, pp.7489-7527, 2014.
DOI : 10.1093/nar/gku447

K. Vasu, E. Nagamalleswari, and V. Nagaraja, Promiscuous restriction is a cellular defense strategy that confers fitness advantage to bacteria, Proceedings of the National Academy of Sciences, vol.109, issue.20, pp.1287-1293, 2012.
DOI : 10.1073/pnas.1119226109

R. Korona, B. Korona, and B. Levin, Sensitivity of naturally occurring coliphages to type I and type II restriction and modification, Journal of General Microbiology, vol.139, issue.6, pp.1283-1290, 1993.
DOI : 10.1099/00221287-139-6-1283

C. Thomas and K. Nielsen, Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria, Nature Reviews Microbiology, vol.84, issue.9, pp.711-721, 2005.
DOI : 10.1016/S0168-6445(98)00009-6

S. Labrie, J. Samson, and S. Moineau, Bacteriophage resistance mechanisms, Nature Reviews Microbiology, vol.153, issue.5, pp.317-327, 2010.
DOI : 10.1038/nrmicro2315

R. Korona and B. Levin, Phage-mediated selection for restriction-modification, Evolution, vol.47, issue.2, pp.565-575, 1993.

I. Kobayashi, Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution, Nucleic Acids Research, vol.29, issue.18, pp.3742-3756, 2001.
DOI : 10.1093/nar/29.18.3742

Q. Xu, R. Morgan, R. Roberts, and M. Blaser, Identification of type II restriction and modification systems in Helicobacter pylori reveals their substantial diversity among strains, Proceedings of the National Academy of Sciences, vol.97, issue.17, pp.9671-9676, 2000.
DOI : 10.1073/pnas.97.17.9671

A. Jeltsch and A. Pingoud, Horizontal gene transfer contributes to the wide distribution and evolution of type II restriction-modification systems, Journal of Molecular Evolution, vol.20, issue.Suppl, pp.91-96, 1996.
DOI : 10.1007/BF02198833

A. Seshasayee, P. Singh, and K. S. , Context-dependent conservation of DNA methyltransferases in bacteria, Nucleic Acids Research, vol.40, issue.15, pp.7066-7073, 2012.
DOI : 10.1093/nar/gks390

K. Kusano, T. Naito, N. Handa, and I. Kobayashi, Restriction-modification systems as genomic parasites in competition for specific sequences., Proceedings of the National Academy of Sciences, vol.92, issue.24, pp.11095-11099, 1995.
DOI : 10.1073/pnas.92.24.11095

X. Didelot, Recombination and Population Structure in Salmonella enterica, PLoS Genetics, vol.30, issue.7, p.1002191, 2011.
DOI : 10.1371/journal.pgen.1002191.s008

J. Doroghazi and D. Buckley, Widespread homologous recombination within and between Streptomyces species, The ISME Journal, vol.145, issue.9, pp.1136-1143, 2010.
DOI : 10.1038/ismej.2008.93

C. Fraser, W. Hanage, and B. Spratt, Recombination and the Nature of Bacterial Speciation, Science, vol.315, issue.5811, pp.476-480, 2007.
DOI : 10.1126/science.1127573

S. Budroni, Neisseria meningitidis is structured in clades associated with restriction modification systems that modulate homologous recombination, Proceedings of the National Academy of Sciences, vol.108, issue.11, pp.4494-4499, 2011.
DOI : 10.1073/pnas.1019751108

N. Croucher, Diversification of bacterial genome content through distinct mechanisms over different timescales, Nature Communications, vol.32, p.5471, 2014.
DOI : 10.1128/AEM.67.11.5190-5196.2001

T. Nandi, sequencing identifies genomic clades with distinct recombination, accessory, and epigenetic profiles, Genome Research, vol.25, issue.1, pp.129-141, 2015.
DOI : 10.1101/gr.177543.114

G. Roberts, Impact of target site distribution for Type I restriction enzymes on the evolution of methicillin-resistant Staphylococcus aureus (MRSA) populations, Nucleic Acids Research, vol.41, issue.15, pp.7472-7484, 2013.
DOI : 10.1093/nar/gkt535

C. Chan, R. Beiko, and M. Ragan, Detecting recombination in evolving nucleotide sequences, BMC Bioinformatics, vol.7, issue.1, p.412, 2006.
DOI : 10.1186/1471-2105-7-412

M. Csurös, Count: Evolutionary analysis of phylogenetic profiles with parsimony and likelihood, Bioinformatics, vol.26, issue.15, pp.1910-1912, 2010.

R. Roberts, T. Vincze, J. Posfai, and D. Macelis, REBASE--a database for DNA restriction and modification: enzymes, genes and genomes, Nucleic Acids Research, vol.38, issue.Database, pp.234-236, 2010.
DOI : 10.1093/nar/gkp874

C. Johnston, B. Martin, G. Fichant, P. Polard, and J. Claverys, Bacterial transformation: distribution, shared mechanisms and divergent control, Nature Reviews Microbiology, vol.16, issue.3, pp.181-196, 2014.
DOI : 10.1038/nrmicro3199

URL : https://hal.archives-ouvertes.fr/hal-01117850

T. Treangen and E. Rocha, Horizontal Transfer, Not Duplication, Drives the Expansion of Protein Families in Prokaryotes, PLoS Genetics, vol.13, issue.1, p.1001284, 2011.
DOI : 10.1371/journal.pgen.1001284.s007

URL : https://hal.archives-ouvertes.fr/pasteur-00578535

O. Cordero and P. Hogeweg, The impact of long-distance horizontal gene transfer on prokaryotic genome size, Proceedings of the National Academy of Sciences, vol.106, issue.51, pp.21748-21753, 2009.
DOI : 10.1073/pnas.0907584106

M. Touchon and E. Rocha, Causes of Insertion Sequences Abundance in Prokaryotic Genomes, Molecular Biology and Evolution, vol.24, issue.4, pp.969-981, 2007.
DOI : 10.1093/molbev/msm014

L. Bobay, E. Rocha, and M. Touchon, The Adaptation of Temperate Bacteriophages to Their Host Genomes, Molecular Biology and Evolution, vol.30, issue.4, pp.737-751, 2013.
DOI : 10.1093/molbev/mss279

URL : https://hal.archives-ouvertes.fr/pasteur-01374945

J. Guglielmini, L. Quintais, M. Garcillán-barcia, F. De-la-cruz, and E. Rocha, The Repertoire of ICE in Prokaryotes Underscores the Unity, Diversity, and Ubiquity of Conjugation, PLoS Genetics, vol.22, issue.8, p.1002222, 2011.
DOI : 10.1371/journal.pgen.1002222.s002

URL : https://hal.archives-ouvertes.fr/pasteur-00647077

W. Arber, Genetic variation: molecular mechanisms and impact on microbial evolution, FEMS Microbiology Reviews, vol.24, issue.1, pp.1-7, 2000.
DOI : 10.1111/j.1574-6976.2000.tb00529.x

K. Vasu and V. Nagaraja, Diverse Functions of Restriction-Modification Systems in Addition to Cellular Defense, Microbiology and Molecular Biology Reviews, vol.77, issue.1, pp.53-72, 2013.
DOI : 10.1128/MMBR.00044-12

A. Corvaglia, A type III-like restriction endonuclease functions as a major barrier to horizontal gene transfer in clinical Staphylococcus aureus strains, Proceedings of the National Academy of Sciences, vol.107, issue.26, pp.11954-11958, 2010.
DOI : 10.1073/pnas.1000489107

E. Rocha, E. Cornet, and B. Michel, Comparative and Evolutionary Analysis of the Bacterial Homologous Recombination Systems, PLoS Genetics, vol.188, issue.2, p.15, 2005.
DOI : 0378-1097(2000)188[0209:COGAGC]2.0.CO;2

S. Halary, J. Leigh, B. Cheaib, P. Lopez, and E. Bapteste, Network analyses structure genetic diversity in independent genetic worlds, Proceedings of the National Academy of Sciences, vol.107, issue.1, pp.127-132, 2010.
DOI : 10.1073/pnas.0908978107

E. Skippington and M. Ragan, Lateral genetic transfer and the construction of genetic exchange communities, FEMS Microbiology Reviews, vol.35, issue.5, pp.707-735, 2011.
DOI : 10.1111/j.1574-6976.2010.00261.x

O. Popa, E. Hazkani-covo, G. Landan, W. Martin, and T. Dagan, Directed networks reveal genomic barriers and DNA repair bypasses to lateral gene transfer among prokaryotes, Genome Research, vol.21, issue.4, pp.599-609, 2011.
DOI : 10.1101/gr.115592.110

I. Letunic and P. Bork, Interactive Tree Of Life v2: online annotation and display of phylogenetic trees made easy, Nucleic Acids Research, vol.39, issue.suppl, pp.475-478, 2011.
DOI : 10.1093/nar/gkr201

K. Pruitt, T. Tatusova, and D. Maglott, NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins, Nucleic Acids Research, vol.35, issue.Database, pp.61-65, 2007.
DOI : 10.1093/nar/gkl842

M. Touchon, Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths, PLoS Genetics, vol.68, issue.1, p.1000344, 2009.
DOI : 10.1371/journal.pgen.1000344.s016

URL : https://hal.archives-ouvertes.fr/hal-00390293

V. Miele, S. Penel, and L. Duret, Ultra-fast sequence clustering from similarity networks with SiLiX, BMC Bioinformatics, vol.12, issue.1, p.116, 2011.
DOI : 10.1186/1471-2105-8-396

URL : https://hal.archives-ouvertes.fr/hal-00698365

S. Guindon, New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0, Systematic Biology, vol.59, issue.3, pp.307-321, 2010.
DOI : 10.1093/sysbio/syq010

URL : https://hal.archives-ouvertes.fr/lirmm-00511784

A. Stamatakis, RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies, Bioinformatics, vol.30, issue.9, pp.1312-1313, 2014.
DOI : 10.1093/bioinformatics/btu033

K. Schliep, phangorn: phylogenetic analysis in R, Bioinformatics, vol.27, issue.4, pp.592-593, 2011.
DOI : 10.1093/bioinformatics/btq706

R. Edgar, MUSCLE: A multiple sequence alignment method with reduced time and space complexity, BMC Bioinformatics, vol.5, issue.1, p.113, 2004.
DOI : 10.1186/1471-2105-5-113

I. Jakobsen and S. Easteal, A program for calculating and displaying compatibility matrices as an aid in determining reticulate evolution in molecular sequences, Bioinformatics, vol.12, issue.4, pp.291-295, 1996.
DOI : 10.1093/bioinformatics/12.4.291

J. Smith, Analyzing the mosaic structure of genes, Journal of Molecular Evolution, vol.34, issue.2, pp.126-129, 1992.
DOI : 10.1007/BF00182389

T. Bruen, H. Philippe, and D. Bryant, A Simple and Robust Statistical Test for Detecting the Presence of Recombination, Genetics, vol.172, issue.4, pp.2665-2681, 2006.
DOI : 10.1534/genetics.105.048975

S. Sawyer, Statistical tests for detecting gene conversion, Mol Biol Evol, vol.6, issue.5, pp.526-538, 1989.

E. Paradis, C. J. Strimmer, and K. , APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004.
DOI : 10.1093/bioinformatics/btg412

B. Pfeifer, U. Wittelsbürger, S. Ramos-onsins, and M. Lercher, PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses in R, Molecular Biology and Evolution, vol.31, issue.7, pp.1929-1936, 2014.
DOI : 10.1093/molbev/msu136

Y. Wolf, K. Makarova, N. Yutin, and E. Koonin, Updated clusters of orthologous genes for Archaea: a complex ancestor of the Archaea and the byways of horizontal gene transfer, Biology Direct, vol.7, issue.1, p.46, 2012.
DOI : 10.1186/1745-6150-7-46

O. Cohen and T. Pupko, Inference and Characterization of Horizontally Transferred Gene Families Using Stochastic Mapping, Molecular Biology and Evolution, vol.27, issue.3, pp.703-713, 2010.
DOI : 10.1093/molbev/msp240

A. Enright, S. Van-dongen, and C. Ouzounis, An efficient algorithm for large-scale detection of protein families, Nucleic Acids Research, vol.30, issue.7, pp.1575-1584, 2002.
DOI : 10.1093/nar/30.7.1575

K. Katoh and D. Standley, MAFFT: Iterative Refinement and Additional Methods, Methods Mol Biol, vol.1079, pp.131-146, 2014.
DOI : 10.1007/978-1-62703-646-7_8

M. Gouy, S. Guindon, and O. Gascuel, SeaView Version 4: A Multiplatform Graphical User Interface for Sequence Alignment and Phylogenetic Tree Building, Molecular Biology and Evolution, vol.27, issue.2, pp.221-224, 2010.
DOI : 10.1093/molbev/msp259

URL : https://hal.archives-ouvertes.fr/lirmm-00705187

R. Finn, J. Clements, and S. Eddy, HMMER web server: interactive sequence similarity searching, Nucleic Acids Research, vol.39, issue.suppl, pp.29-37, 2011.
DOI : 10.1093/nar/gkr367

Y. Furuta and I. Kobayashi, Mobility of DNA sequence recognition domains in DNA methyltransferases suggests epigenetics-driven adaptive evolution, Mobile Genetic Elements, vol.2, issue.6, pp.292-296, 2012.
DOI : 10.1146/annurev.es.26.110195.003125

X. Didelot and D. Falush, Inference of Bacterial Microevolution Using Multilocus Sequence Data, Genetics, vol.175, issue.3, pp.1251-1266, 2007.
DOI : 10.1534/genetics.106.063305