Frequency Spectrum Neutrality Tests: One for All and All for One, Genetics, vol.183, issue.1, pp.249-258, 2009. ,
DOI : 10.1534/genetics.109.104042
Maximum-Likelihood Estimation of Demographic Parameters Using the Frequency Spectrum of Unlinked Single-Nucleotide Polymorphisms, Genetics, vol.168, issue.3, pp.1699-1712, 2004. ,
DOI : 10.1534/genetics.104.030171
Phylodynamic analysis of clinical and environmental Vibrio cholerae isolates from Haiti reveals diversification driven by positive selection, MBio, vol.5, pp.1824-1838, 2014. ,
The Temporal Dynamics of Slightly Deleterious Mutations in Escherichia coli and Shigella spp., Molecular Biology and Evolution, vol.26, issue.2, pp.345-355, 2009. ,
DOI : 10.1093/molbev/msn252
The First Steps of Adaptation of Escherichia coli to the Gut Are Dominated by Soft Sweeps, PLoS Genetics, vol.277, issue.9, p.1004182, 2014. ,
DOI : 10.1371/journal.pgen.1004182.s016
Global Population Structure and Evolution of Bordetella pertussis and Their Relationship with Vaccination, mBio, vol.5, issue.2, p.1074, 2014. ,
DOI : 10.1128/mBio.01074-14
Effect of misoriented sites on neutrality tests with outgroup, Genetics, vol.165, pp.1619-1622, 2003. ,
Approximate Bayesian computation in population genetics, Genetics, vol.162, pp.2025-2035, 2002. ,
Impermanence of bacterial clones, Proceedings of the National Academy of Sciences, vol.112, issue.29, pp.8893-8900, 2015. ,
DOI : 10.1073/pnas.1501724112
The hitchhiking effect on the site frequency spectrum of DNA polymorphisms, Genetics, vol.140, pp.783-796, 1995. ,
Bergey's manual of systematic bacteriology, 2005. ,
The Rate of Adaptive Evolution in Enteric Bacteria, Molecular Biology and Evolution, vol.23, issue.7, pp.1348-1356, 2006. ,
DOI : 10.1093/molbev/msk025
Changing patterns of infectious disease, Nature, vol.406, issue.6797, pp.762-767, 2000. ,
DOI : 10.1038/35021206
A Systematics for Discovering the Fundamental Units of Bacterial Diversity, Current Biology, vol.17, issue.10, pp.373-386, 2007. ,
DOI : 10.1016/j.cub.2007.03.032
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans, Nature Genetics, vol.41, issue.10, pp.1176-1182, 2013. ,
DOI : 10.1016/j.meegid.2007.08.001
Evolutionary and Population Genomics of the Cavity Causing Bacteria Streptococcus mutans, Molecular Biology and Evolution, vol.30, issue.4, pp.881-893, 2013. ,
DOI : 10.1093/molbev/mss278
URL : https://hal.archives-ouvertes.fr/halsde-00814175
Variable recombination dynamics during the emergence, transmission and ???disarming??? of a multidrug-resistant pneumococcal clone, BMC Biology, vol.12, issue.1, p.49, 2014. ,
DOI : 10.1186/1741-7007-12-49
Emergence of scarlet fever Streptococcus pyogenes emm12 clones in Hong Kong is associated with toxin acquisition and multidrug resistance, Nature Genetics, vol.27, issue.1, pp.84-87, 2015. ,
DOI : 10.1016/j.chom.2013.11.003
Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum, PLoS Genetics, vol.385, issue.2, p.1002511, 2012. ,
DOI : 10.1371/journal.pgen.1002511.s026
Inference of Bacterial Microevolution Using Multilocus Sequence Data, Genetics, vol.175, issue.3, pp.1251-1266, 2007. ,
DOI : 10.1534/genetics.106.063305
Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli, BMC Genomics, vol.13, issue.1, p.256, 2012. ,
DOI : 10.1186/1471-2164-13-256
BEAST: Bayesian evolutionary analysis by sampling trees, BMC Evolutionary Biology, vol.7, issue.1, p.214, 2007. ,
DOI : 10.1186/1471-2148-7-214
Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data, Genetics, vol.161, pp.1307-1320, 2002. ,
Bayesian Coalescent Inference of Past Population Dynamics from Molecular Sequences, Molecular Biology and Evolution, vol.22, issue.5, pp.1185-1192, 2005. ,
DOI : 10.1093/molbev/msi103
MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research, vol.32, issue.5, pp.1792-1797, 2004. ,
DOI : 10.1093/nar/gkh340
Four decades of transmission of a multidrug-resistant Mycobacterium tuberculosis outbreak strain, Nature Communications, vol.180, p.7119, 2015. ,
DOI : 10.1093/molbev/mss243
Eight challenges in phylodynamic inference, Epidemics, vol.10, pp.88-92, 2014. ,
DOI : 10.1016/j.epidem.2014.09.001
Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection, Genetics, vol.147, pp.915-925, 1997. ,
Targeted gene-replacement mutagenesis of dcrA, encoding an oxygen sensor of the sulfate-reducing bacterium Desulfovibrio vulgaris Hildenborough, Microbiology, vol.143, pp.1815-1826, 1997. ,
Measuring Selection Coefficients Below 10-3: Method, Questions, and Prospects, Genetics, vol.190, issue.1, pp.175-186, 2012. ,
DOI : 10.1534/genetics.111.133454
BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data, Molecular Biology and Evolution, vol.14, issue.7, pp.685-695, 1997. ,
DOI : 10.1093/oxfordjournals.molbev.a025808
URL : https://hal.archives-ouvertes.fr/lirmm-00730410
Epidemiologic data and pathogen genome sequences: a powerful synergy for public health, Genome Biology, vol.345, issue.11, p.538, 2014. ,
DOI : 10.1186/s13059-014-0538-4
Unifying the Epidemiological and Evolutionary Dynamics of Pathogens, Science, vol.303, issue.5656, pp.327-332, 2004. ,
DOI : 10.1126/science.1090727
The Evolution of the Pseudomonads, Pseudomonas syringae pathovars and related pathogens?identification, epidemiology and genomics, pp.307-319, 2008. ,
DOI : 10.1007/978-1-4020-6901-7_32
Selection intensity for codon bias, Genetics, vol.138, pp.227-234, 1994. ,
Dating of the, 1985. ,
Evolutionary dynamics of Clostridium difficile over short and long time scales, Proceedings of the National Academy of Sciences, vol.107, issue.16, pp.7527-7532, 2010. ,
DOI : 10.1073/pnas.0914322107
Bacterial Phylogenetic Reconstruction from Whole Genomes Is Robust to Recombination but Demographic Inference Is Not, mBio, vol.5, issue.6, p.2158, 2014. ,
DOI : 10.1128/mBio.02158-14
The Confounding Effect of Population Structure on Bayesian Skyline Plot Inferences of Demographic History, PLoS ONE, vol.104, issue.4, p.62992, 2013. ,
DOI : 10.1371/journal.pone.0062992.s009
A flexible forward simulator for populations subject to selection and demography, Bioinformatics, vol.24, issue.23, pp.2786-2787, 2008. ,
DOI : 10.1093/bioinformatics/btn522
Context Dependence, Ancestral Misidentification, and Spurious Signatures of Natural Selection, Molecular Biology and Evolution, vol.24, issue.8, pp.1792-1800, 2007. ,
DOI : 10.1093/molbev/msm108
Time Dependency of Molecular Rate Estimates and Systematic Overestimation of Recent Divergence Times, Molecular Biology and Evolution, vol.22, issue.7, pp.1561-1568, 2005. ,
DOI : 10.1093/molbev/msi145
Skyline-plot methods for estimating demographic history from nucleotide sequences, Molecular Ecology Resources, vol.19, issue.3, pp.423-434, 2011. ,
DOI : 10.1111/j.1755-0998.2011.02988.x
Viral Evolution in the Genomic Age, PLoS Biology, vol.24, issue.10, p.278, 2007. ,
DOI : 0737-4038(2007)024[1811:TRGSOR]2.0.CO;2
Shigella sonnei genome sequencing and phylogenetic analysis indicate recent global dissemination from Europe, Nature Genetics, vol.28, issue.9, pp.1056-1059, 2012. ,
DOI : 10.1186/1471-2164-9-75
URL : https://hal.archives-ouvertes.fr/pasteur-01117702
Evidence for Abundant Slightly Deleterious Polymorphisms in Bacterial Populations, Genetics, vol.169, issue.2, pp.533-538, 2005. ,
DOI : 10.1534/genetics.104.036939
Evolution of protein molecules. Mammalian protein metabolism, pp.21-132, 1969. ,
Estimate of the genomic mutation rate deleterious to overall fitness in E. coli, Trends in Genetics, vol.12, issue.9, pp.694-696, 1996. ,
DOI : 10.1016/0168-9525(96)81473-9
A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences, Journal of Molecular Evolution, vol.206, issue.5, Nov., pp.111-120, 1980. ,
DOI : 10.1007/BF01731581
The neutral theory of molecular evolution, 1983. ,
Genomic analysis of emerging pathogens: methods, application and future trends, Genome Biology, vol.25, issue.11, p.541, 2014. ,
DOI : 10.1186/s13059-014-0541-9
Patterns of microbial genetic diversity and the correlation between bacterial demographic history and geohistory Genetic diversity in microorganisms, pp.123-148, 2012. ,
Exploring population size changes using SNP frequency spectra, Nature Genetics, vol.165, issue.5, pp.555-559, 2015. ,
DOI : 10.1038/nature09525
The Origins of Eukaryotic Gene Structure, Molecular Biology and Evolution, vol.23, issue.2, pp.450-468, 2006. ,
DOI : 10.1093/molbev/msj050
Microbial biogeography: putting microorganisms on the map, Nature Reviews Microbiology, vol.70, issue.2, pp.102-112, 2006. ,
DOI : 10.1038/nrmicro1341
Demographic inference using genetic data from a single individual: Separating population size variation from population structure, Theoretical Population Biology, vol.104, pp.46-58, 2015. ,
DOI : 10.1016/j.tpb.2015.06.003
URL : https://hal.archives-ouvertes.fr/hal-01087849
Evolutionary history and global spread of the Mycobacterium tuberculosis Beijing lineage, Nature Genetics, vol.150, issue.3, pp.242-249, 2015. ,
DOI : 10.1016/S1672-0229(07)60007-2
URL : https://hal.archives-ouvertes.fr/pasteur-01153552
The effects of multilocus balancing selection on neutral variability, Genetics, vol.161, pp.849-863, 2002. ,
The genealogy of samples in models with selection, Genetics, vol.145, pp.519-534, 1997. ,
IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies, Molecular Biology and Evolution, vol.32, issue.1, pp.268-274, 2015. ,
DOI : 10.1093/molbev/msu300
Statistical inferences in phylogeography, Molecular Ecology, vol.161, issue.6, pp.1034-1047, 2009. ,
DOI : 10.1111/j.1365-294X.2008.04059.x
Distinguishing migration from isolation: a Markov chain Monte Carlo approach, Genetics, vol.158, pp.885-896, 2001. ,
A Timescale for Evolution, Population Expansion, and Spatial Spread of an Emerging Clone of Methicillin-Resistant Staphylococcus aureus, PLoS Pathogens, vol.133, issue.4, p.1000855, 2010. ,
DOI : 10.1371/journal.ppat.1000855.s010
A Continuous-State Coalescent and the Impact of Weak Selection on the Structure of Gene Genealogies, Molecular Biology and Evolution, vol.27, issue.5, pp.1162-1172, 2010. ,
DOI : 10.1093/molbev/msq006
Enzyme Polymorphism and Genetic Population Structure in Escherichia coli and Shigella, Microbiology, vol.129, issue.9, pp.2715-2726, 1983. ,
DOI : 10.1099/00221287-129-9-2715
COALESCENCE IN A METAPOPULATION WITH RECURRENT LOCAL EXTINCTION AND RECOLONIZATION, Evolution, vol.28, issue.5, pp.949-961, 2003. ,
DOI : 10.1098/rstb.2001.0859
APE: Analyses of Phylogenetics and Evolution in R language, Bioinformatics, vol.20, issue.2, pp.289-290, 2004. ,
DOI : 10.1093/bioinformatics/btg412
The Role of Selection in Shaping Diversity of Natural M. tuberculosis Populations, PLoS Pathogens, vol.33, issue.8, p.1003543, 2013. ,
DOI : 10.1371/journal.ppat.1003543.s009
Temporal trends in gonococcal population genetics in a high prevalence urban community, Infection, Genetics and Evolution, vol.7, issue.2, pp.271-278, 2007. ,
DOI : 10.1016/j.meegid.2006.11.003
Adaptive Mutations in Bacteria: High Rate and Small Effects, Science, vol.317, issue.5839, pp.813-815, 2007. ,
DOI : 10.1126/science.1142284
FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix, Molecular Biology and Evolution, vol.26, issue.7, pp.1641-1650, 2009. ,
DOI : 10.1093/molbev/msp077
Molecular Epidemiology of Community-Associated Methicillin-resistant Staphylococcus aureus in the genomic era: a Cross-Sectional Study, Scientific Reports, vol.18, issue.2, 1902. ,
DOI : 10.1038/srep01902
Genealogies and weak purifying selection, Molecular Biology and Evolution, vol.16, issue.2, pp.246-252, 1999. ,
DOI : 10.1093/oxfordjournals.molbev.a026106
An integrated framework for the inference of viral population history from reconstructed genealogies, Genetics, vol.155, pp.1429-1437, 2000. ,
Statistical Properties of New Neutrality Tests Against Population Growth, Molecular Biology and Evolution, vol.19, issue.12, pp.2092-2100, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004034
Clustering Rules: A Comparison of Partitioning and Hierarchical Clustering Algorithms, Journal of Mathematical Modelling and Algorithms, vol.38, issue.5, pp.475-504, 2006. ,
DOI : 10.1007/s10852-005-9022-1
An Analysis of Determinants of Amino Acids Substitution Rates in Bacterial Proteins, Molecular Biology and Evolution, vol.21, issue.1, pp.108-116, 2004. ,
DOI : 10.1093/molbev/msh004
Comparisons of dN/dS are time dependent for closely related bacterial genomes, Journal of Theoretical Biology, vol.239, issue.2, pp.226-235, 2006. ,
DOI : 10.1016/j.jtbi.2005.08.037
Mutational Patterns Cannot Explain Genome Composition: Are There Any Neutral Sites in the Genomes of Bacteria?, PLoS Genetics, vol.23, issue.9, p.1001104, 2010. ,
DOI : 10.1371/journal.pgen.1001104.t001
URL : https://hal.archives-ouvertes.fr/pasteur-00578536
Evolutionary History of Salmonella Typhi, Science, vol.314, issue.5803, pp.1301-1304, 2006. ,
DOI : 10.1126/science.1134933
Recombination drives genome evolution in outbreak-related Legionella pneumophila isolates, Nature Genetics, vol.17, issue.11, pp.1205-1211, 2014. ,
DOI : 10.1093/bioinformatics/18.3.502
Evolution of the core genome of Pseudomonas syringae, a highly clonal, endemic plant pathogen, 2004. ,
Consequences of recombination on traditional phylogenetic analysis, Genetics, vol.156, pp.879-891, 2000. ,
phangorn: phylogenetic analysis in R, Bioinformatics, vol.27, issue.4, pp.592-593, 2011. ,
DOI : 10.1093/bioinformatics/btq706
TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing, Bioinformatics, vol.18, issue.3, pp.502-504, 2002. ,
DOI : 10.1093/bioinformatics/18.3.502
Forces that influence the evolution of codon bias, Philosophical Transactions of the Royal Society B: Biological Sciences, vol.183, issue.6, pp.1203-1212, 2010. ,
DOI : 10.1007/s00239-003-0192-z
Origin and Evolution of European Community-Acquired Methicillin-Resistant Staphylococcus aureus, mBio, vol.5, issue.5, pp.1044-01014, 2014. ,
DOI : 10.1128/mBio.01044-14
The effect of change in population size on DNA polymorphism, Genetics, vol.123, pp.597-601, 1989. ,
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism, Genetics, vol.123, pp.585-595, 1989. ,
Gene-specific selective sweeps in bacteria and archaea caused by negative frequency-dependent selection, BMC Biology, vol.4, issue.1, p.20, 2015. ,
DOI : 10.1186/s12915-015-0131-7
Update on RefSeq microbial genomes resources, Nucleic Acids Research, vol.43, issue.D1, pp.599-605, 2015. ,
DOI : 10.1093/nar/gku1062
Population dynamics of Neisseria gonorrhoeae in Shanghai, China: a comparative study, BMC Infectious Diseases, vol.8, issue.1, p.13, 2010. ,
DOI : 10.1186/1471-2105-8-458
Coalescence 2.0: a multiple branching of recent theoretical developments and their applications, Molecular Ecology, vol.16, issue.11, pp.2637-2652, 2014. ,
DOI : 10.1111/mec.12755
URL : https://hal.archives-ouvertes.fr/hal-01209980
The population genetics of commensal Escherichia coli, Nature Reviews Microbiology, vol.75, issue.3, pp.207-217, 2010. ,
DOI : 10.1038/nrmicro2298
Recombination and the Properties of Tajima's D in the Context of Approximate-Likelihood Calculation, Genetics, vol.171, issue.4, pp.2143-2148, 2005. ,
DOI : 10.1534/genetics.105.043786
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
The impact of the neisserial DNA uptake sequences on genome evolution and stability, Genome Biology, vol.9, issue.3, 2008. ,
DOI : 10.1186/gb-2008-9-3-r60
URL : https://hal.archives-ouvertes.fr/pasteur-00336122
Viral Phylodynamics, PLoS Computational Biology, vol.151, issue.3, p.1002947, 2013. ,
DOI : 10.1371/journal.pcbi.1002947.s002
A comparison of homologous recombination rates in bacteria and archaea, The ISME Journal, vol.16, issue.2, pp.199-208, 2009. ,
DOI : 10.1038/ismej.2008.93
Recombination and the power of statistical tests of neutrality, Genetical Research, vol.74, issue.1, pp.65-79, 1999. ,
DOI : 10.1017/S0016672399003870
Genomic signatures of human and animal disease in the zoonotic pathogen Streptococcus suis, Nature Communications, vol.27, p.6740, 2015. ,
DOI : 10.1038/ncomms7740
The Genealogy of a Sequence Subject to Purifying Selection at Multiple Sites, Molecular Biology and Evolution, vol.19, issue.8, pp.1376-1384, 2002. ,
DOI : 10.1093/oxfordjournals.molbev.a004199
Sex and virulence in Escherichia coli: an evolutionary perspective, Molecular Microbiology, vol.179, issue.5, pp.1136-1151, 2006. ,
DOI : 10.1111/j.1365-2958.2005.04985.x
URL : https://hal.archives-ouvertes.fr/hal-00174910
The rise and spread of a new pathogen: Seroresistant Moraxella catarrhalis, Genome Research, vol.17, issue.11, pp.1647-1656, 2007. ,
DOI : 10.1101/gr.6122607
URL : https://hal.archives-ouvertes.fr/hal-00173850
Phylogeographical analysis of the dominant multidrug-resistant H58 clade of Salmonella Typhi identifies inter- and intracontinental transmission events, Nature Genetics, vol.47, issue.6, pp.632-639, 2015. ,
DOI : 10.1128/AAC.02412-14
PAML 4: Phylogenetic Analysis by Maximum Likelihood, Molecular Biology and Evolution, vol.24, issue.8, pp.1586-1591, 2007. ,
DOI : 10.1093/molbev/msm088
Statistical ecology, 2013. ,
DOI : 10.1007/978-1-4757-2829-3
Transient Darwinian selection in Salmonella enterica serovar Paratyphi A during 450 years of global spread of enteric fever, Proceedings of the National Academy of Sciences, vol.111, issue.33, pp.12199-12204, 2014. ,
DOI : 10.1073/pnas.1411012111
URL : https://hal.archives-ouvertes.fr/pasteur-01104820