TY - JOUR AU - Maddison, W. P. PY - 1997 DA - 1997// TI - Gene trees in species trees JO - Syst Biol VL - 46 UR - https://doi.org/10.1093/sysbio/46.3.523 DO - 10.1093/sysbio/46.3.523 ID - Maddison1997 ER - TY - JOUR AU - Rokas, A. AU - Williams, B. L. AU - King, N. AU - Carroll, S. B. PY - 2003 DA - 2003// TI - Genome-scale approaches to resolving incongruence in molecular phylogenies JO - Nature VL - 425 UR - https://doi.org/10.1038/nature02053 DO - 10.1038/nature02053 ID - Rokas2003 ER - TY - JOUR AU - Jarvis, E. D. AU - Mirarab, S. AU - Aberer, A. J. AU - Li, B. AU - Houde, P. AU - Li, C. AU - Ho, S. Y. AU - Faircloth, B. C. AU - Nabholz, B. AU - Howard, J. T. PY - 2014 DA - 2014// TI - Whole-genome analyses resolve early branches in the tree of life of modern birds JO - Science VL - 346 UR - https://doi.org/10.1126/science.1253451 DO - 10.1126/science.1253451 ID - Jarvis2014 ER - TY - JOUR AU - Fontaine, M. C. AU - Pease, J. B. AU - Steele, A. AU - Waterhouse, R. M. AU - Neafsey, D. E. AU - Sharakhov, I. V. AU - Jiang, X. AU - Hall, A. B. AU - Catteruccia, F. AU - Kakani, E. PY - 2015 DA - 2015// TI - Mosquito genomics. Extensive introgression in a malaria vector species complex revealed by phylogenomics JO - Science VL - 347 UR - https://doi.org/10.1126/science.1258524 DO - 10.1126/science.1258524 ID - Fontaine2015 ER - TY - JOUR AU - Pease, J. B. AU - Haak, D. C. AU - Hahn, M. W. AU - Moyle, L. C. PY - 2016 DA - 2016// TI - Phylogenomics reveals three sources of adaptive variation during a rapid radiation JO - PLoS Biol VL - 14 UR - https://doi.org/10.1371/journal.pbio.1002379 DO - 10.1371/journal.pbio.1002379 ID - Pease2016 ER - TY - JOUR AU - Guerrero, R. F. AU - Hahn, M. W. PY - 2018 DA - 2018// TI - Quantifying the risk of hemiplasy in phylogenetic inference JO - Proc Natl Acad Sci U S A VL - 115 UR - https://doi.org/10.1073/pnas.1811268115 DO - 10.1073/pnas.1811268115 ID - Guerrero2018 ER - TY - JOUR AU - Gogarten, J. P. AU - Doolittle, W. F. AU - Lawrence, J. G. PY - 2002 DA - 2002// TI - Prokaryotic evolution in light of gene transfer JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004046 DO - 10.1093/oxfordjournals.molbev.a004046 ID - Gogarten2002 ER - TY - JOUR AU - Jain, R. AU - Rivera, M. C. AU - Moore, J. E. AU - Lake, J. A. PY - 2002 DA - 2002// TI - Horizontal gene transfer in microbial genome evolution JO - Theor Popul Biol VL - 61 UR - https://doi.org/10.1006/tpbi.2002.1596 DO - 10.1006/tpbi.2002.1596 ID - Jain2002 ER - TY - JOUR AU - Doolittle, W. F. AU - Papke, R. T. PY - 2006 DA - 2006// TI - Genomics and the bacterial species problem JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-9-116 DO - 10.1186/gb-2006-7-9-116 ID - Doolittle2006 ER - TY - JOUR AU - Wolf, Y. I. AU - Rogozin, I. B. AU - Grishin, N. V. AU - Koonin, E. V. PY - 2002 DA - 2002// TI - Genome trees and the tree of life JO - Trends Genet VL - 18 UR - https://doi.org/10.1016/S0168-9525(02)02744-0 DO - 10.1016/S0168-9525(02)02744-0 ID - Wolf2002 ER - TY - JOUR AU - Lerat, E. AU - Daubin, V. AU - Moran, N. A. PY - 2003 DA - 2003// TI - From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria JO - PLoS Biol VL - 1 UR - https://doi.org/10.1371/journal.pbio.0000019 DO - 10.1371/journal.pbio.0000019 ID - Lerat2003 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 - Bobay, L. M. AU - Ochman, H. PY - 2017 DA - 2017// TI - Biological species are universal across Life's domains JO - Genome Biol Evol VL - 9 UR - https://doi.org/10.1093/gbe/evx026 DO - 10.1093/gbe/evx026 ID - Bobay2017 ER - TY - JOUR AU - Vos, M. AU - Didelot, X. PY - 2009 DA - 2009// TI - A comparison of homologous recombination rates in bacteria and archaea JO - ISME J VL - 3 UR - https://doi.org/10.1038/ismej.2008.93 DO - 10.1038/ismej.2008.93 ID - Vos2009 ER - TY - JOUR AU - Didelot, X. AU - Wilson, D. J. PY - 2015 DA - 2015// TI - ClonalFrameML: efficient inference of recombination in whole bacterial genomes JO - PLoS Comput Biol VL - 11 UR - https://doi.org/10.1371/journal.pcbi.1004041 DO - 10.1371/journal.pcbi.1004041 ID - Didelot2015 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 - Lin, M. AU - Kussell, E. PY - 2019 DA - 2019// TI - Inferring bacterial recombination rates from large-scale sequencing datasets JO - Nat Methods VL - 16 UR - https://doi.org/10.1038/s41592-018-0293-7 DO - 10.1038/s41592-018-0293-7 ID - Lin2019 ER - TY - JOUR AU - Rosen, M. J. AU - Davison, M. AU - Bhaya, D. AU - Fisher, D. S. PY - 2015 DA - 2015// TI - Microbial diversity. Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche JO - Science VL - 348 UR - https://doi.org/10.1126/science.aaa4456 DO - 10.1126/science.aaa4456 ID - Rosen2015 ER - TY - STD TI - Gonzalez-Torres P, Rodriguez-Mateos F, Anton J, Gabaldon T. Impact of homologous recombination on the evolution of prokaryotic core genomes. MBio. 2019;10(1):e02494–18. ID - ref19 ER - TY - JOUR AU - Hudson, R. R. PY - 1983 DA - 1983// TI - Properties of a neutral allele model with intragenic recombination JO - Theor Popul Biol VL - 23 UR - https://doi.org/10.1016/0040-5809(83)90013-8 DO - 10.1016/0040-5809(83)90013-8 ID - Hudson1983 ER - TY - JOUR AU - Milkman, R. AU - Bridges, M. M. PY - 1990 DA - 1990// TI - Molecular evolution of the Escherichia coli chromosome. III. Clonal frames JO - Genetics VL - 126 ID - Milkman1990 ER - TY - JOUR AU - Smith, J. M. AU - Smith, N. H. AU - O'Rourke, M. AU - Spratt, B. G. PY - 1993 DA - 1993// TI - How clonal are bacteria? JO - Proc Natl Acad Sci U S A VL - 90 UR - https://doi.org/10.1073/pnas.90.10.4384 DO - 10.1073/pnas.90.10.4384 ID - Smith1993 ER - TY - JOUR AU - Maynard Smith, J. AU - Smith, N. H. PY - 1998 DA - 1998// TI - Detecting recombination from gene trees JO - Mol Biol Evol VL - 15 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025960 DO - 10.1093/oxfordjournals.molbev.a025960 ID - Maynard Smith1998 ER - TY - JOUR AU - Schierup, M. H. AU - Hein, J. PY - 2000 DA - 2000// TI - Recombination and the molecular clock JO - Mol Biol Evol VL - 17 UR - https://doi.org/10.1093/oxfordjournals.molbev.a026256 DO - 10.1093/oxfordjournals.molbev.a026256 ID - Schierup2000 ER - TY - JOUR AU - Schierup, M. H. AU - Hein, J. PY - 2000 DA - 2000// TI - Consequences of recombination on traditional phylogenetic analysis JO - Genetics VL - 156 ID - Schierup2000 ER - TY - JOUR AU - Worobey, M. PY - 2001 DA - 2001// TI - A novel approach to detecting and measuring recombination: new insights into evolution in viruses, bacteria, and mitochondria JO - Mol Biol Evol VL - 18 UR - https://doi.org/10.1093/oxfordjournals.molbev.a003928 DO - 10.1093/oxfordjournals.molbev.a003928 ID - Worobey2001 ER - TY - JOUR AU - Posada, D. AU - Crandall, K. A. PY - 2002 DA - 2002// TI - The effect of recombination on the accuracy of phylogeny estimation JO - J Mol Evol VL - 54 UR - https://doi.org/10.1007/s00239-001-0034-9 DO - 10.1007/s00239-001-0034-9 ID - Posada2002 ER - TY - JOUR AU - Anisimova, M. AU - Nielsen, R. AU - Yang, Z. PY - 2003 DA - 2003// TI - Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites JO - Genetics VL - 164 ID - Anisimova2003 ER - TY - JOUR AU - Awadalla, P. PY - 2003 DA - 2003// TI - The evolutionary genomics of pathogen recombination JO - Nat Rev Genet VL - 4 UR - https://doi.org/10.1038/nrg964 DO - 10.1038/nrg964 ID - Awadalla2003 ER - TY - JOUR AU - Wilson, D. J. AU - McVean, G. PY - 2006 DA - 2006// TI - Estimating diversifying selection and functional constraint in the presence of recombination JO - Genetics VL - 172 UR - https://doi.org/10.1534/genetics.105.044917 DO - 10.1534/genetics.105.044917 ID - Wilson2006 ER - TY - JOUR AU - Kubatko, L. S. AU - Degnan, J. H. PY - 2007 DA - 2007// TI - Inconsistency of phylogenetic estimates from concatenated data under coalescence JO - Syst Biol VL - 56 UR - https://doi.org/10.1080/10635150601146041 DO - 10.1080/10635150601146041 ID - Kubatko2007 ER - TY - JOUR AU - Rannala, B. AU - Yang, Z. PY - 2008 DA - 2008// TI - Phylogenetic inference using whole genomes JO - Annu Rev Genomics Hum Genet VL - 9 UR - https://doi.org/10.1146/annurev.genom.9.081307.164407 DO - 10.1146/annurev.genom.9.081307.164407 ID - Rannala2008 ER - TY - JOUR AU - Hedge, J. AU - Wilson, D. J. PY - 2014 DA - 2014// TI - Bacterial phylogenetic reconstruction from whole genomes is robust to recombination but demographic inference is not JO - mBio VL - 5 UR - https://doi.org/10.1128/mBio.02158-14 DO - 10.1128/mBio.02158-14 ID - Hedge2014 ER - TY - JOUR AU - Ahrenfeldt, J. AU - Skaarup, C. AU - Hasman, H. AU - Pedersen, A. G. AU - Aarestrup, F. M. AU - Lund, O. PY - 2017 DA - 2017// TI - Bacterial whole genome-based phylogeny: construction of a new benchmarking dataset and assessment of some existing methods JO - BMC Genomics VL - 18 UR - https://doi.org/10.1186/s12864-016-3407-6 DO - 10.1186/s12864-016-3407-6 ID - Ahrenfeldt2017 ER - TY - STD TI - Sakoparnig T, Field C, van Nimwegen E. Whole genome phylogenies reflect long-tailed distributions of recombination rates in many bacterial species. bioRxiv. 2019; https://doi.org/10.1101/601914. ID - ref35 ER - TY - JOUR AU - Mostowy, R. AU - Croucher, N. J. AU - Andam, C. P. AU - Corander, J. AU - Hanage, W. P. AU - Marttinen, P. PY - 2017 DA - 2017// TI - Efficient inference of recent and ancestral recombination within bacterial populations JO - Mol Biol Evol VL - 34 UR - https://doi.org/10.1093/molbev/msx066 DO - 10.1093/molbev/msx066 ID - Mostowy2017 ER - TY - JOUR AU - Lai, Y. P. AU - Ioerger, T. R. PY - 2018 DA - 2018// TI - A statistical method to identify recombination in bacterial genomes based on SNP incompatibility JO - BMC Bioinformatics VL - 19 UR - https://doi.org/10.1186/s12859-018-2456-z DO - 10.1186/s12859-018-2456-z ID - Lai2018 ER - TY - JOUR AU - Bobay, L. M. AU - Ochman, H. PY - 2018 DA - 2018// TI - Factors driving effective population size and pan-genome evolution in bacteria JO - BMC Evol Biol VL - 18 UR - https://doi.org/10.1186/s12862-018-1272-4 DO - 10.1186/s12862-018-1272-4 ID - Bobay2018 ER - TY - JOUR AU - Shapiro, B. J. AU - Friedman, J. AU - Cordero, O. X. AU - Preheim, S. P. AU - Timberlake, S. C. AU - Szabo, G. AU - Polz, M. F. AU - Alm, E. J. PY - 2012 DA - 2012// TI - Population genomics of early events in the ecological differentiation of bacteria JO - Science VL - 336 UR - https://doi.org/10.1126/science.1218198 DO - 10.1126/science.1218198 ID - Shapiro2012 ER - TY - JOUR AU - Bobay, L. M. PY - 2020 DA - 2020// TI - CoreSimul: a forward-in-time simulator of genome evolution for prokaryotes modeling homologous recombination JO - BMC Bioinformatics VL - 21 UR - https://doi.org/10.1186/s12859-020-03619-x DO - 10.1186/s12859-020-03619-x ID - Bobay2020 ER - TY - JOUR AU - Didelot, X. AU - Maiden, M. C. PY - 2010 DA - 2010// TI - Impact of recombination on bacterial evolution JO - Trends Microbiol VL - 18 UR - https://doi.org/10.1016/j.tim.2010.04.002 DO - 10.1016/j.tim.2010.04.002 ID - Didelot2010 ER - TY - JOUR AU - Balbi, K. J. AU - Rocha, E. P. AU - Feil, E. J. PY - 2009 DA - 2009// TI - The temporal dynamics of slightly deleterious mutations in Escherichia coli and Shigella spp JO - Mol Biol Evol VL - 26 UR - https://doi.org/10.1093/molbev/msn252 DO - 10.1093/molbev/msn252 ID - Balbi2009 ER - TY - JOUR AU - Bobay, L. M. AU - Traverse, C. C. AU - Ochman, H. PY - 2015 DA - 2015// TI - Impermanence of bacterial clones JO - Proc Natl Acad Sci U S A VL - 112 UR - https://doi.org/10.1073/pnas.1501724112 DO - 10.1073/pnas.1501724112 ID - Bobay2015 ER - TY - JOUR AU - Shapiro, B. J. PY - 2014 DA - 2014// TI - Signatures of natural selection and ecological differentiation in microbial genomes JO - Adv Exp Med Biol VL - 781 UR - https://doi.org/10.1007/978-94-007-7347-9_17 DO - 10.1007/978-94-007-7347-9_17 ID - Shapiro2014 ER - TY - JOUR AU - Stamatakis, A. PY - 2014 DA - 2014// TI - RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies JO - Bioinformatics VL - 30 UR - https://doi.org/10.1093/bioinformatics/btu033 DO - 10.1093/bioinformatics/btu033 ID - Stamatakis2014 ER - TY - JOUR AU - Tavare, S. PY - 1986 DA - 1986// TI - Some probabilistic and statistical problems in the analysis of DNA sequences JO - Lect Math Life Sci VL - 17 ID - Tavare1986 ER - TY - JOUR AU - Gascuel, O. PY - 1997 DA - 1997// TI - BIONJ: an improved version of the NJ algorithm based on a simple model of sequence data JO - Mol Biol Evol VL - 14 UR - https://doi.org/10.1093/oxfordjournals.molbev.a025808 DO - 10.1093/oxfordjournals.molbev.a025808 ID - Gascuel1997 ER - TY - JOUR AU - Mau, B. AU - Glasner, J. D. AU - Darling, A. E. AU - Perna, N. T. PY - 2006 DA - 2006// TI - Genome-wide detection and analysis of homologous recombination among sequenced strains of Escherichia coli JO - Genome Biol VL - 7 UR - https://doi.org/10.1186/gb-2006-7-5-r44 DO - 10.1186/gb-2006-7-5-r44 ID - Mau2006 ER - TY - JOUR AU - Didelot, X. AU - Meric, G. AU - Falush, D. AU - Darling, A. E. PY - 2012 DA - 2012// TI - Impact of homologous and non-homologous recombination in the genomic evolution of Escherichia coli JO - BMC Genomics VL - 13 UR - https://doi.org/10.1186/1471-2164-13-256 DO - 10.1186/1471-2164-13-256 ID - Didelot2012 ER - TY - JOUR AU - Everitt, R. G. AU - Didelot, X. AU - Batty, E. M. AU - Miller, R. R. AU - Knox, K. AU - Young, B. C. AU - Bowden, R. AU - Auton, A. AU - Votintseva, A. AU - Larner-Svensson, H. PY - 2014 DA - 2014// TI - Mobile elements drive recombination hotspots in the core genome of staphylococcus aureus JO - Nat Commun VL - 5 UR - https://doi.org/10.1038/ncomms4956 DO - 10.1038/ncomms4956 ID - Everitt2014 ER - TY - JOUR AU - Dettman, J. R. AU - Rodrigue, N. AU - Kassen, R. PY - 2014 DA - 2014// TI - Genome-wide patterns of recombination in the opportunistic human pathogen Pseudomonas aeruginosa JO - Genome Biol Evol VL - 7 UR - https://doi.org/10.1093/gbe/evu260 DO - 10.1093/gbe/evu260 ID - Dettman2014 ER - TY - JOUR AU - Didelot, X. AU - Falush, D. PY - 2007 DA - 2007// TI - Inference of bacterial microevolution using multilocus sequence data JO - Genetics VL - 175 UR - https://doi.org/10.1534/genetics.106.063305 DO - 10.1534/genetics.106.063305 ID - Didelot2007 ER -