Factors driving effective population size and pan-genome evolution in bacteria

[1]  B. Shapiro,et al.  The population genetics of pangenomes , 2017, Nature Microbiology.

[2]  J. McInerney,et al.  Reply to ‘The population genetics of pangenomes’ , 2017, Nature Microbiology.

[3]  A. Eyre-Walker,et al.  Are pangenomes adaptive or not? , 2017, Nature Microbiology.

[4]  H. Ochman,et al.  The Evolution of Bacterial Genome Architecture , 2017, Front. Genet..

[5]  E. Hesse,et al.  Prokaryote genome fluidity is dependent on effective population size , 2017, The ISME Journal.

[6]  Alan McNally,et al.  Why prokaryotes have pangenomes , 2017, Nature Microbiology.

[7]  H. Ochman,et al.  Biological Species Are Universal across Life’s Domains , 2017, Genome biology and evolution.

[8]  Michael Lynch,et al.  Genetic drift, selection and the evolution of the mutation rate , 2016, Nature Reviews Genetics.

[9]  Eugene V. Koonin,et al.  Theory of prokaryotic genome evolution , 2016, Proceedings of the National Academy of Sciences.

[10]  M. Touchon,et al.  Regulation of genetic flux between bacteria by restriction–modification systems , 2016, Proceedings of the National Academy of Sciences.

[11]  M. Touchon,et al.  Genetic and life-history traits associated with the distribution of prophages in bacteria , 2016, The ISME Journal.

[12]  A. Arkin,et al.  Weakly Deleterious Mutations and Low Rates of Recombination Limit the Impact of Natural Selection on Bacterial Genomes , 2015, mBio.

[13]  S. Gribaldo,et al.  The two-domain tree of life is linked to a new root for the Archaea , 2015, Proceedings of the National Academy of Sciences.

[14]  Daniel J. Wilson,et al.  ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes , 2015, PLoS Comput. Biol..

[15]  D. Buckley,et al.  Intraspecies comparison of Streptomyces pratensis genomes reveals high levels of recombination and gene conservation between strains of disparate geographic origin , 2014, BMC Genomics.

[16]  Bérénice Batut,et al.  Reductive genome evolution at both ends of the bacterial population size spectrum , 2014, Nature Reviews Microbiology.

[17]  L. Duret,et al.  Comparative population genomics in animals uncovers the determinants of genetic diversity , 2014, Nature.

[18]  M. Touchon,et al.  Pervasive domestication of defective prophages by bacteria , 2014, Proceedings of the National Academy of Sciences.

[19]  S. Giovannoni,et al.  Implications of streamlining theory for microbial ecology , 2014, The ISME Journal.

[20]  N. Kashtan,et al.  Single-Cell Genomics Reveals Hundreds of Coexisting Subpopulations in Wild Prochlorococcus , 2014, Science.

[21]  R. Ferreira,et al.  Effect of long-term laboratory propagation on Chlamydia trachomatis genome dynamics. , 2013, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[22]  K. Katoh,et al.  MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability , 2013, Molecular biology and evolution.

[23]  M. Syvanen,et al.  Evolutionary implications of horizontal gene transfer. , 2012, Annual review of genetics.

[24]  Thomas G. Doak,et al.  Drift-barrier hypothesis and mutation-rate evolution , 2012, Proceedings of the National Academy of Sciences.

[25]  Sean R. Eddy,et al.  Accelerated Profile HMM Searches , 2011, PLoS Comput. Biol..

[26]  M. Lynch,et al.  The repatterning of eukaryotic genomes by random genetic drift. , 2011, Annual review of genomics and human genetics.

[27]  E. Rocha,et al.  Mutational Patterns Cannot Explain Genome Composition: Are There Any Neutral Sites in the Genomes of Bacteria? , 2010, PLoS genetics.

[28]  Miklós Csuös,et al.  Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood , 2010, Bioinform..

[29]  Alexis Criscuolo,et al.  BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments , 2010, BMC Evolutionary Biology.

[30]  E. Paradis pegas: an R package for population genetics with an integrated-modular approach , 2010, Bioinform..

[31]  Eduardo P. C. Rocha,et al.  The Systemic Imprint of Growth and Its Uses in Ecological (Meta)Genomics , 2010, PLoS genetics.

[32]  P. Keeling Functional and ecological impacts of horizontal gene transfer in eukaryotes. , 2009, Current opinion in genetics & development.

[33]  J. Andersson Gene transfer and diversification of microbial eukaryotes. , 2009, Annual review of microbiology.

[34]  J. Peter Gogarten,et al.  Intertwined Evolutionary Histories of Marine Synechococcus and Prochlorococcus marinus , 2009, Genome biology and evolution.

[35]  Howard Ochman,et al.  The consequences of genetic drift for bacterial genome complexity. , 2009, Genome research.

[36]  C. Fraser,et al.  The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity , 2009, Science.

[37]  X. Didelot,et al.  A comparison of homologous recombination rates in bacteria and archaea , 2009, The ISME Journal.

[38]  A. Danchin,et al.  Organised Genome Dynamics in the Escherichia coli Species Results in Highly Diverse Adaptive Paths , 2009, PLoS genetics.

[39]  J. Plotkin,et al.  The Population Genetics of dN/dS , 2008, PLoS genetics.

[40]  J. Rougemont,et al.  A rapid bootstrap algorithm for the RAxML Web servers. , 2008, Systematic biology.

[41]  Alex Wong,et al.  Evolution of protein-coding genes in Drosophila. , 2008, Trends in genetics : TIG.

[42]  Ziheng Yang PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[43]  Sam P. Brown,et al.  Ecology of Microbial Invasions: Amplification Allows Virus Carriers to Invade More Rapidly When Rare , 2006, Current Biology.

[44]  Alexandros Stamatakis,et al.  RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models , 2006, Bioinform..

[45]  Eduardo P C Rocha,et al.  Comparisons of dN/dS are time dependent for closely related bacterial genomes. , 2006, Journal of theoretical biology.

[46]  D. Presgraves,et al.  Recombination Enhances Protein Adaptation in Drosophila melanogaster , 2005, Current Biology.

[47]  Hongkai Ji,et al.  Why do human diversity levels vary at a megabase scale? , 2005, Genome research.

[48]  Emmanuelle Lerat,et al.  Recognizing the pseudogenes in bacterial genomes , 2005, Nucleic acids research.

[49]  N. Moran,et al.  Evolutionary Origins of Genomic Repertoires in Bacteria , 2005, PLoS biology.

[50]  N. Moran,et al.  Genomic changes following host restriction in bacteria. , 2004, Current opinion in genetics & development.

[51]  K. Strimmer,et al.  APE: Analyses of Phylogenetics and Evolution in R language , 2004, Bioinform..

[52]  M. Lynch,et al.  The Origins of Genome Complexity , 2003, Science.

[53]  N. Moran,et al.  Deletional bias and the evolution of bacterial genomes. , 2001, Trends in genetics : TIG.

[54]  J. Andersson,et al.  Pseudogenes, junk DNA, and the dynamics of Rickettsia genomes. , 2001, Molecular biology and evolution.

[55]  John Maynard Smith,et al.  The population genetics of bacteria , 1991, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[56]  J. Felsenstein Phylogenies and the Comparative Method , 1985, The American Naturalist.

[57]  T. Whittam,et al.  Multilocus genetic structure in natural populations of Escherichia coli. , 1983, Proceedings of the National Academy of Sciences of the United States of America.

[58]  G. A. Watterson On the number of segregating sites in genetical models without recombination. , 1975, Theoretical population biology.

[59]  T. Ohta Slightly Deleterious Mutant Substitutions in Evolution , 1973, Nature.

[60]  W. G. Hill,et al.  The effect of linkage on limits to artificial selection. , 1966, Genetical research.

[61]  Erik Kaestner,et al.  The Origins Of Genome Architecture , 2016 .

[62]  B. Charlesworth,et al.  Genetic recombination and molecular evolution. , 2009, Cold Spring Harbor symposia on quantitative biology.

[63]  B. Spratt,et al.  Recombination and the population structures of bacterial pathogens. , 2001, Annual review of microbiology.

[64]  Z. Yang,et al.  Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. , 2000, Molecular biology and evolution.

[65]  M. Riley,et al.  Evolution of the bacterial genome. , 1978, Annual review of microbiology.