TY - JOUR AU - McCutcheon, J. P. AU - Moran, N. A. PY - 2012 DA - 2012// TI - Extreme genome reduction in symbiotic bacteria JO - Nat Rev Microbiol VL - 10 UR - https://doi.org/10.1038/nrmicro2670 DO - 10.1038/nrmicro2670 ID - McCutcheon2012 ER - TY - JOUR AU - Nishida, H. PY - 2012 DA - 2012// TI - Evolution of genome base composition and genome size in bacteria JO - Front Microbiol VL - 3 UR - https://doi.org/10.3389/fmicb.2012.00420 DO - 10.3389/fmicb.2012.00420 ID - Nishida2012 ER - TY - JOUR AU - Reichenberger, E. R. AU - Rosen, G. AU - Hershberg, U. AU - Hershberg, R. PY - 2015 DA - 2015// TI - Prokaryotic nucleotide composition is shaped by both phylogeny and the environment JO - Genome Biol Evol VL - 7 UR - https://doi.org/10.1093/gbe/evv063 DO - 10.1093/gbe/evv063 ID - Reichenberger2015 ER - TY - JOUR AU - Foerstner, K. U. AU - von Mering, C. AU - Hooper, S. D. AU - Bork, P. PY - 2005 DA - 2005// TI - Environments shape the nucleotide composition of genomes JO - EMBO Rep VL - 6 UR - https://doi.org/10.1038/sj.embor.7400538 DO - 10.1038/sj.embor.7400538 ID - Foerstner2005 ER - TY - JOUR AU - Hildebrand, F. AU - Meyer, A. AU - Eyre-Walker, A. PY - 2010 DA - 2010// TI - Evidence of selection upon genomic GC-content in bacteria JO - PLoS Genet VL - 6 UR - https://doi.org/10.1371/journal.pgen.1001107 DO - 10.1371/journal.pgen.1001107 ID - Hildebrand2010 ER - TY - JOUR AU - Lassalle, F. AU - Perian, S. AU - Bataillon, T. AU - Nesme, X. AU - Duret, L. AU - Daubin, V. PY - 2015 DA - 2015// TI - GC-content evolution in bacterial genomes: the biased gene conversion hypothesis expands JO - PLoS Genet VL - 11 UR - https://doi.org/10.1371/journal.pgen.1004941 DO - 10.1371/journal.pgen.1004941 ID - Lassalle2015 ER - TY - JOUR AU - Lawrence, J. G. AU - Ochman, H. PY - 1997 DA - 1997// TI - Amelioration of bacterial genomes: rates of change and exchange JO - J Mol Evol VL - 44 UR - https://doi.org/10.1007/PL00006158 DO - 10.1007/PL00006158 ID - Lawrence1997 ER - TY - JOUR AU - Moran, N. A. PY - 1996 DA - 1996// TI - Accelerated evolution and Muller's rachet in endosymbiotic bacteria JO - Proc Natl Acad Sci U S A VL - 93 UR - https://doi.org/10.1073/pnas.93.7.2873 DO - 10.1073/pnas.93.7.2873 ID - Moran1996 ER - TY - JOUR AU - Bentley, S. D. AU - Parkhill, J. PY - 2004 DA - 2004// TI - Comparative genomic structure of prokaryotes JO - Annu Rev Genet VL - 38 UR - https://doi.org/10.1146/annurev.genet.38.072902.094318 DO - 10.1146/annurev.genet.38.072902.094318 ID - Bentley2004 ER - TY - JOUR AU - Hershberg, R. AU - Petrov, D. A. PY - 2010 DA - 2010// TI - Evidence that mutation is universally biased towards AT in bacteria JO - PLoS Genet VL - 6 UR - https://doi.org/10.1371/journal.pgen.1001115 DO - 10.1371/journal.pgen.1001115 ID - Hershberg2010 ER - TY - JOUR AU - Agashe, D. AU - Shankar, N. PY - 2014 DA - 2014// TI - The evolution of bacterial DNA base composition JO - J Exp Zool B Mol Dev Evol VL - 322 UR - https://doi.org/10.1002/jez.b.22565 DO - 10.1002/jez.b.22565 ID - Agashe2014 ER - TY - JOUR AU - Lynch, M. AU - Ackerman, M. S. AU - Gout, J. F. AU - Long, H. AU - Sung, W. AU - Thomas, W. K. AU - Foster, P. L. PY - 2016 DA - 2016// TI - Genetic drift, selection and the evolution of the mutation rate JO - Nat Rev Genet VL - 17 UR - https://doi.org/10.1038/nrg.2016.104 DO - 10.1038/nrg.2016.104 ID - Lynch2016 ER - TY - JOUR AU - Giovannoni, S. J. AU - Tripp, H. J. AU - Givan, S. AU - Podar, M. AU - Vergin, K. L. AU - Baptista, D. AU - Bibbs, L. AU - Eads, J. AU - Richardson, T. H. AU - Noordewier, M. PY - 2005 DA - 2005// TI - Genome streamlining in a cosmopolitan oceanic bacterium JO - Science VL - 309 UR - https://doi.org/10.1126/science.1114057 DO - 10.1126/science.1114057 ID - Giovannoni2005 ER - TY - JOUR AU - Kettler, G. C. AU - Martiny, A. C. AU - Huang, K. AU - Zucker, J. AU - Coleman, M. L. AU - Rodrigue, S. AU - Chen, F. AU - Lapidus, A. AU - Ferriera, S. AU - Johnson, J. PY - 2007 DA - 2007// TI - Patterns and implications of gene gain and loss in the evolution of Prochlorococcus JO - PLoS Genet VL - 3 UR - https://doi.org/10.1371/journal.pgen.0030231 DO - 10.1371/journal.pgen.0030231 ID - Kettler2007 ER - TY - JOUR AU - Bohlin, J. AU - Eldholm, V. AU - Pettersson, J. H. AU - Brynildsrud, O. AU - Snipen, L. PY - 2017 DA - 2017// TI - The nucleotide composition of microbial genomes indicates differential patterns of selection on core and accessory genomes JO - BMC Genomics VL - 18 UR - https://doi.org/10.1186/s12864-017-3543-7 DO - 10.1186/s12864-017-3543-7 ID - Bohlin2017 ER - TY - JOUR AU - Castillo-Ramirez, S. AU - Harris, S. R. AU - Holden, M. T. AU - He, M. AU - Parkhill, J. AU - Bentley, S. D. AU - Feil, E. J. PY - 2011 DA - 2011// TI - The impact of recombination on dN/dS within recently emerged bacterial clones JO - PLoS Pathog VL - 7 UR - https://doi.org/10.1371/journal.ppat.1002129 DO - 10.1371/journal.ppat.1002129 ID - Castillo-Ramirez2011 ER - TY - JOUR AU - Touchon, M. AU - Hoede, C. AU - Tenaillon, O. AU - Barbe, V. AU - Baeriswyl, S. AU - Bidet, P. AU - Bingen, E. AU - Bonacorsi, S. AU - Bouchier, C. AU - Bouvet, O. PY - 2009 DA - 2009// TI - Organised genome dynamics in the Escherichia coli species results in highly diverse adaptive paths JO - PLoS Genet VL - 5 UR - https://doi.org/10.1371/journal.pgen.1000344 DO - 10.1371/journal.pgen.1000344 ID - Touchon2009 ER - TY - JOUR AU - Croucher, N. J. AU - Page, A. J. AU - Connor, T. R. AU - Delaney, A. J. AU - Keane, J. A. AU - Bentley, S. D. AU - Parkhill, J. AU - Harris, S. R. PY - 2015 DA - 2015// TI - Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins JO - Nucleic Acids Res VL - 43 UR - https://doi.org/10.1093/nar/gku1196 DO - 10.1093/nar/gku1196 ID - Croucher2015 ER - TY - JOUR AU - Willenbrock, H. AU - Friis, C. AU - Juncker, A. S. AU - Ussery, D. W. PY - 2006 DA - 2006// TI - An environmental signature for 323 microbial genomes based on codon adaptation indices JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-12-r114 DO - 10.1186/gb-2006-7-12-r114 ID - Willenbrock2006 ER - TY - JOUR AU - Bobay, L. M. AU - Ochman, H. PY - 2017 DA - 2017// TI - Impact of recombination on the base composition of Bacteria and archaea JO - Mol Biol Evol VL - 34 UR - https://doi.org/10.1093/molbev/msx189 DO - 10.1093/molbev/msx189 ID - Bobay2017 ER - TY - JOUR AU - Rocha, E. P. AU - Feil, E. J. PY - 2010 DA - 2010// TI - Mutational patterns cannot explain genome composition: are there any neutral sites in the genomes of bacteria? JO - PLoS Genet VL - 6 UR - https://doi.org/10.1371/journal.pgen.1001104 DO - 10.1371/journal.pgen.1001104 ID - Rocha2010 ER - TY - JOUR AU - Seward, E. A. AU - Kelly, S. PY - 2016 DA - 2016// TI - Dietary nitrogen alters codon bias and genome composition in parasitic microorganisms JO - Genome Biol VL - 17 UR - https://doi.org/10.1186/s13059-016-1087-9 DO - 10.1186/s13059-016-1087-9 ID - Seward2016 ER - TY - JOUR AU - Reva, O. N. AU - Tummler, B. PY - 2004 DA - 2004// TI - Global features of sequences of bacterial chromosomes, plasmids and phages revealed by analysis of oligonucleotide usage patterns JO - BMC bioinformatics [computer file] VL - 5 UR - https://doi.org/10.1186/1471-2105-5-90 DO - 10.1186/1471-2105-5-90 ID - Reva2004 ER - TY - JOUR AU - Chen, W. H. AU - Lu, G. AU - Bork, P. AU - Hu, S. AU - Lercher, M. J. PY - 2016 DA - 2016// TI - Energy efficiency trade-offs drive nucleotide usage in transcribed regions JO - Nat Commun VL - 7 UR - https://doi.org/10.1038/ncomms11334 DO - 10.1038/ncomms11334 ID - Chen2016 ER - TY - JOUR AU - Long, H. AU - Sung, W. AU - Kucukyildirim, S. AU - Williams, E. AU - Miller, S. F. AU - Guo, W. AU - Patterson, C. AU - Gregory, C. AU - Strauss, C. AU - Stone, C. PY - 2018 DA - 2018// TI - Evolutionary determinants of genome-wide nucleotide composition JO - Nat Ecol Evol VL - 2 UR - https://doi.org/10.1038/s41559-017-0425-y DO - 10.1038/s41559-017-0425-y ID - Long2018 ER - TY - JOUR AU - Treangen, T. J. AU - Ondov, B. D. AU - Koren, S. AU - Phillippy, A. M. PY - 2014 DA - 2014// TI - The harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes JO - Genome Biol VL - 15 UR - https://doi.org/10.1186/s13059-014-0524-x DO - 10.1186/s13059-014-0524-x ID - Treangen2014 ER - TY - JOUR AU - Gouy, M. AU - Guindon, S. AU - Gascuel, O. PY - 2010 DA - 2010// TI - SeaView version 4: a multiplatform graphical user interface for sequence alignment and phylogenetic tree building JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msp259 DO - 10.1093/molbev/msp259 ID - Gouy2010 ER - TY - JOUR AU - Elson, D. AU - Chargaff, E. PY - 1954 DA - 1954// TI - Regularities in the composition of pentose nucleic acids JO - Nature VL - 173 UR - https://doi.org/10.1038/1731037a0 DO - 10.1038/1731037a0 ID - Elson1954 ER - TY - STD TI - Pinheiro J, Bates D, DebRoy S, Sarkar D. R Core Team (2014) nlme: linear and nonlinear mixed effects models. R package version 3.1–117. 2014. See http://CRAN.R-project.org/package=nlme. UR - http://cran.r-project.org/package=nlme ID - ref29 ER - TY - STD TI - Team RDC: R: A language and environment for statistical computing. R Foundation for Statistical Computing. In., vol. 2.14; 2011. ID - ref30 ER - TY - STD TI - Wickham H: ggplot2: elegant graphics for data analysis: Springer; 2016. ID - ref31 ER -