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References from How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality. Local targets link to admitted publications; unresolved targets remain external evidence.
Insights from genomic comparisons of genetically monomorphic bacterial pathogens
10.1098/rstb.2011.0303 · 2012 · External reference
Evolution, population structure, and phylogeography of genetically monomorphic bacterial pathogens
10.1146/annurev.micro.62.081307.162832 · 2008 · External reference
Parallel in vivo experimental evolution reveals that increased stress resistance was key for the emergence of persistent tuberculosis bacilli
10.1038/s41564-021-00938-4 · 2021 · External reference
Mutational Meltdown in Primary Endosymbionts: Selection Limits Muller's Ratchet
10.1371/journal.pone.0004969 · 2009 · External reference
Codon usage in the Mycobacterium tuberculosis complex
10.1099/00221287-142-4-915 · 1996 · External reference
The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp.
10.1093/molbev/msn252 · 2009 · External reference
Impact of recombination on the base composition of bacteria and archaea
10.1093/molbev/msx189 · 2017 · External reference
Impermanence of bacterial clones
10.1073/pnas.1501724112 · 2015 · External reference
Factors driving effective population size and pan-genome evolution in bacteria
10.1186/s12862-018-1272-4 · 2018 · External reference
Key experimental evidence of chromosomal DNA transfer among selected tuberculosis-causing mycobacteria
10.1073/pnas.1604921113 · 2016 · External reference
Pre-Columbian mycobacterial genomes reveal seals as a source of New World human tuberculosis
10.1038/nature13591 · 2014 · External reference
Co-evolution of Mycobacterium tuberculosis and Homo sapiens
10.1111/imr.12264 · 2015 · External reference
A new phylogenetic framework for the animal-adapted Mycobacterium tuberculosis complex
10.3389/fmicb.2018.02820 · 2018 · External reference
Evolution of intracellular pathogens
10.1146/annurev.micro.61.080706.093305 · 2008 · External reference
The effect of deleterious mutations on neutral molecular variation
10.1111/j.0014-3820.2002.tb00188.x · 1993 · External reference
Effective population size and patterns of molecular evolution and variation
10.1038/nrg2526 · 2009 · External reference
The effects of deleterious mutations on evolution at linked sites
10.1534/genetics.111.134288 · 2012 · External reference
Gene evolutionary trajectories in Mycobacterium tuberculosis reveal temporal signs of selection.
10.1073/pnas.2113600119 · 2022 · External reference
Genomic determinants of speciation and spread of the Mycobacterium tuberculosis complex
10.1101/314559 · 2019 · External reference
A polymorphic gene within the Mycobacterium smegmatis esx1 locus determines mycobacterial self-identity and conjugal compatibility
10.1128/mbio.00213-22 · 2022 · External reference
Mycobacterium tuberculosis progresses through two phases of latent infection in humans
10.1038/s41467-020-18699-9 · 2020 · External reference
Massive gene decay in the leprosy bacillus
10.1038/35059006 · 2001 · External reference
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence
10.1038/31159 · 1998 · External reference
Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes
10.1038/ng.1038 · 2012 · External reference
Out-of-Africa migration and Neolithic coexpansion of Mycobacterium tuberculosis with modern humans
10.1038/ng.2744 · 2013 · External reference
Genotyping of genetically monomorphic bacteria: DNA sequencing in Mycobacterium tuberculosis highlights the limitations of current methodologies
10.1371/journal.pone.0007815 · 2009 · External reference
Within-host evolution selects for a dominant genotype of Mycobacterium tuberculosis while T cells increase pathogen genetic diversity
10.1371/journal.ppat.1006111 · 2016 · External reference
Genome-wide association studies of global Mycobacterium tuberculosis resistance to 13 antimicrobials in 10,228 genomes identify new resistance mechanisms
10.1371/journal.pbio.3001755 · 2022 · External reference
10.24072/pcjournal.72 · 2022 · Admitted local publication
The effect of strong purifying selection on genetic diversity
10.1534/genetics.118.301058 · 2018 · External reference
Origins and evolution of antibiotic resistance.
10.1128/mmbr.00016-10 · 2010 · External reference
Gene expression, amino acid conservation, and hydrophobicity are the main factors shaping codon preferences in Mycobacterium tuberculosis and Mycobacterium leprae
10.1007/s002399910006 · 2000 · External reference
The population genetics of pathogenic Escherichia coli
10.1038/s41579-020-0416-x · 2021 · External reference
Genome-scale rates of evolutionary change in bacteria
10.1099/mgen.0.000094 · 2016 · External reference
Biased gene conversion and the evolution of mammalian genomic landscapes
10.1146/annurev-genom-082908-150001 · 2009 · External reference
Latent tuberculosis infection: myths, models, and molecular mechanisms
10.1128/mmbr.00010-14 · 2014 · External reference
Lack of support for the time-dependent molecular evolution hypothesis
10.1111/mec.13070 · 2015 · External reference
The distribution of fitness effects of new mutations
10.1038/nrg2146 · 2007 · External reference
Genomic analysis identifies targets of convergent positive selection in drug-resistant Mycobacterium tuberculosis
10.1038/ng.2747 · 2013 · External reference
The evolutionary advantage of recombination
10.1093/genetics/78.2.737 · 1974 · External reference
Phylogeny to function: PE/PPE protein evolution and impact on Mycobacterium tuberculosis pathogenicity
10.1111/mmi.12981 · 2015 · External reference
10.5962/bhl.title.27468
10.5962/bhl.title.27468 · 1930 · External reference
What is mutation? A chapter in the series: how microbes “jeopardize” the modern synthesis
10.1371/journal.pgen.1007995 · 2019 · External reference
Use of whole genome sequencing to estimate the mutation rate of Mycobacterium tuberculosis during latent infection
10.1038/ng.811 · 2011 · External reference
Mycobacterium tuberculosis mutation rate estimates from different lineages predict substantial differences in the emergence of drug-resistant tuberculosis
10.1038/ng.2656 · 2013 · External reference
Ecology and evolution of Mycobacterium tuberculosis
10.1038/nrmicro.2018.8 · 2018 · External reference
Variable host-pathogen compatibility in Mycobacterium tuberculosis
10.1073/pnas.0511240103 · 2006 · External reference
Mutation hot spots in mammalian mitochondrial DNA
10.1101/gr.4305906 · 2006 · External reference
The distribution of bacterial doubling times in the wild
10.1098/rspb.2018.0789 · 2018 · External reference
10.56021/9780801880087
10.56021/9780801880087 · 2004 · External reference
Recombination signal in Mycobacterium tuberculosis stems from reference-guided assemblies and alignment artefacts
10.1093/gbe/evy143 · 2018 · External reference
Blending genomes: distributive conjugal transfer in mycobacteria, a sexier form of HGT
10.1111/mmi.13971 · 2018 · External reference
Experimental evolution of Mycobacterium tuberculosis in human macrophages results in low-frequency mutations not associated with selective advantage
10.1371/journal.pone.0167989 · 2016 · External reference
Antimicrobial resistance in Mycobacterium tuberculosis: mechanistic and evolutionary perspectives
10.1093/femsre/fux011 · 2017 · External reference
SLiM 3: Forward Genetic Simulations Beyond the Wright-Fisher Model
10.1093/molbev/msy228 · 2019 · External reference
Not so simple after all: bacteria, their population genetics, and recombination
10.1101/cshperspect.a018069 · 2016 · External reference
Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not
10.1128/mbio.02158-14 · 2014 · External reference
The confounding effect of population structure on Bayesian skyline plot inferences of demographic history
10.1371/journal.pone.0062992 · 2013 · External reference
High functional diversity in Mycobacterium tuberculosis driven by genetic drift and human demography
10.1371/journal.pbio.0060311 · 2008 · External reference
Selection on codon bias
10.1146/annurev.genet.42.110807.091442 · 2008 · External reference
Evidence that mutation is universally biased towards AT in bacteria
10.1371/journal.pgen.1001115 · 2010 · External reference
Evidence of selection upon genomic GC-content in bacteria
10.1371/journal.pgen.1001107 · 2010 · External reference
Time-dependent estimates of molecular evolutionary rates: evidence and causes
10.1111/mec.13450 · 2015 · External reference
Time-dependent rates of molecular evolution
10.1111/j.1365-294x.2011.05178.x · 2011 · External reference
Skyline-plot methods for estimating demographic history from nucleotide sequences
10.1111/j.1755-0998.2011.02988.x · 2011 · External reference
Computer simulations: tools for population and evolutionary genetics
10.1038/nrg3130 · 2012 · External reference
Recommendations for improving statistical inference in population genomics
10.1371/journal.pbio.3001669 · 2022 · External reference
The effects of deleterious mutations on evolution in non-recombining genomes
10.1016/j.tig.2008.10.009 · 2009 · External reference
Is Mycobacterium tuberculosis 15,000 years old?
10.1093/infdis/170.5.1348 · 1994 · External reference
Frequent homologous recombination events in Mycobacterium tuberculosis PE/PPE multigene families: potential role in antigenic variability
10.1128/jb.00827-08 · 2008 · External reference
Old trade, new tricks: Insights into the spontaneous mutation process from the partnering of classical mutation accumulation experiments with high-throughput genomic approaches
10.1093/gbe/evy252 · 2019 · External reference
Against storytelling of scientific results
10.1038/nmeth.2699 · 2013 · External reference
Eighteenth-century genomes show that mixed infections were common at time of peak tuberculosis in Europe
10.1038/ncomms7717 · 2015 · External reference
10.1017/cbo9780511623486
10.1017/cbo9780511623486 · 1983 · External reference
The consequences of genetic drift for bacterial genome complexity
10.1101/gr.091785.109 · 2009 · External reference
Population size and the rate of evolution
10.1016/j.tree.2013.09.009 · 2014 · External reference
The impact of selection, gene conversion, and biased sampling on the assessment of microbial demography
10.1093/molbev/msw048 · 2016 · External reference
GC-content evolution in bacterial genomes: the biased gene conversion hypothesis expands
10.1371/journal.pgen.1004941 · 2015 · External reference
Where are the pseudogenes in bacterial genomes?
10.1016/s0966-842x(01)02198-9 · 2001 · External reference
Local adaptation of Mycobacterium tuberculosis on the Tibetan Plateau
10.1073/pnas.2017831118 · 2021 · External reference
Mycobacterium tuberculosis clinical isolates carry mutational signatures of host immune environments
10.1126/sciadv.aba4901 · 2020 · External reference
Evidence for recombination in Mycobacterium tuberculosis
10.1128/jb.01062-06 · 2006 · External reference
Unresolved reference
2007 · External reference
ESX-1-Independent horizontal gene transfer by Mycobacterium tuberculosis complex strains
10.1128/mbio.00965-21 · 2021 · External reference
Digitally barcoding Mycobacterium tuberculosis reveals in vivo infection dynamics in the macaque model of tuberculosis
10.1128/mbio.00312-17 · 2017 · External reference
Analysing recombination in nucleotide sequences
10.1111/j.1755-0998.2011.03026.x · 2011 · External reference
Do bacteria have population genetics?
1995 · External reference
How clonal are bacteria?
10.1073/pnas.90.10.4384 · 1993 · External reference
The role of IS6110 in the evolution of Mycobacterium tuberculosis
10.1016/j.tube.2007.05.010 · 2007 · External reference
Mutation rate and the emergence of drug resistance in Mycobacterium tuberculosis
10.1093/jac/dkt364 · 2014 · External reference
Bayesian inference of evolutionary histories under time-dependent substitution rates
10.1093/molbev/msz094 · 2019 · External reference
Multiple merger genealogies in outbreaks of Mycobacterium tuberculosis
10.1101/2019.12.21.885723 · 2021 · External reference
The molecular clock of Mycobacterium tuberculosis
10.1371/journal.ppat.1008067 · 2019 · External reference
Local adaptation in populations of Mycobacterium tuberculosis endemic to the Indian Ocean Rim
10.1101/2020.10.20.346866 · 2021 · External reference
Transcontinental spread and evolution of Mycobacterium tuberculosis W148 European/Russian clade toward extensively drug resistant tuberculosis
10.1038/s41467-022-32455-1 · 2022 · External reference
Gene inversion potentiates bacterial evolvability and virulence
10.1038/s41467-018-07110-3 · 2018 · External reference
Universal patterns of purifying selection at noncoding positions in bacteria
10.1101/gr.6759507 · 2008 · External reference
Impact of the tree prior on estimating clock rates during epidemic outbreaks
10.1073/pnas.1713314115 · 2018 · External reference
Comparative genomic and phylogeographic analysis of Mycobacterium leprae
10.1038/ng.477 · 2009 · External reference
Evaluating the contributions of purifying selection and progeny-skew in dictating within-host Mycobacterium tuberculosis evolution
10.1111/evo.13954 · 2020 · External reference
The population genomics of within-host Mycobacterium tuberculosis
10.1038/s41437-020-00377-7 · 2021 · External reference
Accelerated evolution and Muller's rachet in endosymbiotic bacteria
10.1073/pnas.93.7.2873 · 1996 · External reference
Genomic analyses of Mycobacterium tuberculosis from human lung resections reveal a high frequency of polyclonal infections
10.1038/s41467-021-22705-z · 2021 · External reference
Signatures of selection at drug resistance loci in Mycobacterium tuberculosis
10.1101/173229 · 2017 · External reference
Dispersal of Mycobacterium tuberculosis driven by historical European trade in the South Pacific
10.3389/fmicb.2019.02778 · 2019 · External reference
The relation of recombination to mutational advance
10.1016/0027-5107(64)90047-8 · 1964 · External reference
Defying Muller’s ratchet: ancient heritable endobacteria escape extinction through retention of recombination and genome plasticity
10.1128/mbio.02057-15 · 2016 · External reference
After the bottleneck: genome-wide diversification of the Mycobacterium tuberculosis complex by mutation, recombination, and natural selection
10.1101/gr.129544.111 · 2012 · External reference
Genetic draft, selective interference, and population genetics of rapid adaptation
10.1146/annurev-ecolsys-110512-135920 · 2013 · External reference
Lineage specific histories of Mycobacterium tuberculosis dispersal in Africa and Eurasia
10.1111/mec.15120 · 2019 · External reference
Diversity of Mycobacterium tuberculosis across Evolutionary Scales
10.1371/journal.ppat.1005257 · 2015 · External reference
A new unifying theory of the pathogenesis of tuberculosis
10.1016/j.tube.2013.07.004 · 2014 · External reference
Extensive homoplasy but no evidence of convergent evolution of repeat numbers at MIRU loci in modern Mycobacterium tuberculosis lineages
10.3389/fpubh.2020.00455 · 2020 · External reference
Codon usage in highly expressed genes of Haemophillus influenzae and Mycobacterium tuberculosis: translational selection versus mutational bias
10.1016/s0378-1119(98)00257-1 · 1998 · External reference
Transition bias influences the evolution of antibiotic resistance in Mycobacterium tuberculosis
10.1371/journal.pbio.3000265 · 2019 · External reference
Evolution of tuberculosis pathogenesis
10.1146/annurev-micro-121321-093031 · 2022 · External reference
The role of selection in shaping diversity of natural M. tuberculosis populations
10.1371/journal.ppat.1003543 · 2013 · External reference
Bacterial genetic signatures of human social phenomena among M. tuberculosis from an aboriginal canadian population
10.1093/molbev/msp261 · 2010 · External reference
Muller’s ratchet in symbiont populations
10.1007/s10709-006-9007-7 · 2007 · External reference
Recombination in pe/ppe genes contributes to genetic variation in Mycobacterium tuberculosis lineages
10.1186/s12864-016-2467-y · 2016 · External reference
Drift: a historical and conceptual overview
10.1162/biot.2007.2.2.156 · 2007 · External reference
Weakly deleterious mutations and low rates of recombination limit the impact of natural selection on bacterial genomes
10.1128/mbio.01302-15 · 2015 · External reference
Weak selection on synonymous codons substantially inflates dN/dS estimates in bacteria
10.1073/pnas.2023575118 · 2021 · External reference
Prokaryotic nucleotide composition is shaped by both phylogeny and the environment
10.1093/gbe/evv063 · 2015 · External reference
Neutral theory, microbial practice: challenges in bacterial population genetics
10.1093/molbev/msy078 · 2018 · External reference
Base composition bias might result from competition for metabolic resources
10.1016/s0168-9525(02)02690-2 · 2002 · External reference
Mutational patterns cannot explain genome composition: are there any neutral sites in the genomes of bacteria?
10.1371/journal.pgen.1001104 · 2010 · External reference
Comparisons of dN/dS are time dependent for closely related bacterial genomes
10.1016/j.jtbi.2005.08.037 · 2006 · External reference
Mycobacterium tuberculosis primary infection and dissemination: a critical role for alveolar epithelial cells
10.3389/fcimb.2019.00299 · 2019 · External reference
A seventeenth-century Mycobacterium tuberculosis genome supports a Neolithic emergence of the Mycobacterium tuberculosis complex
10.1186/s13059-020-02112-1 · 2020 · External reference
Inferring demography and selection in organisms characterized by skewed offspring distributions
10.1534/genetics.118.301684 · 2019 · External reference
Population genetics of pathogenic bacteria
10.1016/0882-4010(87)90032-5 · 1987 · External reference
How the tubercle bacillus got its genome: modernising, modelling, and making sense of the stories we tell
10.24072/pci.evolbiol.100644 · 2023 · External reference
Looking for Darwin's footprints in the microbial world
10.1016/j.tim.2009.02.002 · 2009 · External reference
Bottlenecks and broomsticks: the molecular evolution of Mycobacterium bovis
10.1038/nrmicro1472 · 2006 · External reference
Rapid adaptation of a complex trait during experimental evolution of Mycobacterium tuberculosis
10.7554/elife.78454 · 2022 · External reference
The genetic causes of convergent evolution
10.1038/nrg3483 · 2013 · External reference
How do monomorphic bacteria evolve? The Mycobacterium tuberculosis complex and the awkward population genetics of extreme clonality
10.5281/zenodo.8042695 · 2023 · External reference
Genomic analysis of smooth tubercle bacilli provides insights into ancestry and pathoadaptation of Mycobacterium tuberculosis
10.1038/ng.2517 · 2013 · External reference
Homoplastic single nucleotide polymorphisms contributed to phenotypic diversity in Mycobacterium tuberculosis
10.1038/s41598-020-64895-4 · 2020 · External reference
Mixed infections in tuberculosis: the missing part in a puzzle
10.1016/j.tube.2017.09.004 · 2017 · External reference
Coalescence 2.0: a multiple branching of recent theoretical developments and their applications
10.1111/mec.12755 · 2014 · External reference
10.1002/9781119836070
10.1002/9781119836070 · 2021 · External reference
Comparative analyses of selection operating on nontranslated intergenic regions of diverse bacterial species
10.1534/genetics.116.195784 · 2017 · External reference
Is predominant clonal evolution a common evolutionary adaptation to parasitism in pathogenic parasitic protozoa, fungi, bacteria, and viruses?
10.1016/bs.apar.2016.08.007 · 2017 · External reference
The within-host population dynamics of Mycobacterium tuberculosis vary with treatment efficacy
10.1186/s13059-017-1196-0 · 2017 · External reference
Comparative genomics of ESX genes from clinical isolates of Mycobacterium tuberculosis provides evidence for gene conversion and epitope variation
10.1128/iai.05344-11 · 2011 · External reference
A comparison of homologous recombination rates in bacteria and archaea
10.1038/ismej.2008.93 · 2009 · External reference
Multiple genetic paths including massive gene amplification allow Mycobacterium tuberculosis to overcome loss of ESX-3 secretion system substrates
10.1073/pnas.2112608119 · 2022 · External reference
The evolutionary landscape of the Mycobacterium tuberculosis genome
10.1016/j.gene.2012.11.033 · 2013 · External reference
Linking high GC content to the repair of double strand breaks in prokaryotic genomes
10.1371/journal.pgen.1008493 · 2019 · External reference
A generation-time effect on the rate of molecular evolution in bacteria
10.1111/evo.12597 · 2015 · External reference
Measuring the distribution of fitness effects in somatic evolution by combining clonal dynamics with dN/dS ratios
10.7554/elife.48714 · 2020 · External reference
GenomegaMap: within-species genome-wide dN/dS estimation from over 10,000 genomes
10.1093/molbev/msaa069 · 2020 · External reference
Population bottlenecks strongly affect the evolutionary dynamics of antibiotic persistence
10.1093/molbev/msab107 · 2021 · External reference
How the microbial world saved evolution from the Scylla of molecular biology and the charybdis of the Modern Synthesis
10.1128/mmbr.00002-09 · 2009 · External reference
Unresolved reference
2022 · External reference
Evolution in mendelian populations
10.4161/hv.21408 · 1931 · External reference
Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
10.1093/oxfordjournals.molbev.a025957 · 1998 · External reference
PAML 4: phylogenetic analysis by maximum likelihood
10.1093/molbev/msm088 · 2007 · External reference
10.1093/acprof:oso/9780199602605.001.0001
10.1093/acprof:oso/9780199602605.001.0001 · 2014 · External reference
Statistical methods for detecting molecular adaptation
10.1016/s0169-5347(00)01994-7 · 2000 · External reference
Genomics: leprosy—a degenerative disease of the genome
10.1016/s0960-9822(01)00213-5 · 2001 · External reference
A new nomenclature for the livestock-associated Mycobacterium tuberculosis complex based on phylogenomics
10.12688/openreseurope.14029.1 · 2021 · External reference
