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Volumn 10, Issue 7, 2016, Pages 1589-1601

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIUM; COEXISTENCE; ECOTYPE; GENE FLOW; GENETIC ANALYSIS; GENETIC VARIATION; GENOME; LAKE ECOSYSTEM; POLYMORPHISM; SPECIATION (BIOLOGY); SPECIES DIVERSITY;

EID: 84953439697     PISSN: 17517362     EISSN: 17517370     Source Type: Journal    
DOI: 10.1038/ismej.2015.241     Document Type: Article
Times cited : (176)

References (61)
  • 1
    • 84879678051 scopus 로고    scopus 로고
    • Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes
    • Albertsen M, Hugenholtz P, Skarshewski A, Nielsen KL, Tyson GW, Nielsen PH. (2013). Genome sequences of rare, uncultured bacteria obtained by differential coverage binning of multiple metagenomes. Nat Biotechnol 31: 533-538
    • (2013) Nat Biotechnol , vol.31 , pp. 533-538
    • Albertsen, M.1    Hugenholtz, P.2    Skarshewski, A.3    Nielsen, K.L.4    Tyson, G.W.5    Nielsen, P.H.6
  • 3
    • 77957746208 scopus 로고    scopus 로고
    • Genome-wide mutational diversity in an evolving population of Escherichia coli
    • Barrick JE, Lenski RE. (2009). Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb Symp Quant Biol 74: 119-129
    • (2009) Cold Spring Harb Symp Quant Biol , vol.74 , pp. 119-129
    • Barrick, J.E.1    Lenski, R.E.2
  • 4
    • 70350641005 scopus 로고    scopus 로고
    • Genome evolution and adaptation in a long-Term experiment with Escherichia coli
    • Barrick JE, Yu DS, Yoon SH, Jeong H, Oh TK, Schneider D, et al. (2009). Genome evolution and adaptation in a long-Term experiment with Escherichia coli. Nature 461: 1243-1247
    • (2009) Nature , vol.461 , pp. 1243-1247
    • Barrick, J.E.1    Yu, D.S.2    Yoon, S.H.3    Jeong, H.4    Oh, T.K.5    Schneider, D.6
  • 6
    • 78650609210 scopus 로고    scopus 로고
    • Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea
    • Caro-Quintero A, Deng J, Auchtung J, Brettar I, Hofle MG, Klappenbach J, et al. (2011). Unprecedented levels of horizontal gene transfer among spatially co-occurring Shewanella bacteria from the Baltic Sea. ISME J 5: 131-140
    • (2011) ISME J , vol.5 , pp. 131-140
    • Caro-Quintero, A.1    Deng, J.2    Auchtung, J.3    Brettar, I.4    Hofle, M.G.5    Klappenbach, J.6
  • 9
    • 0028173732 scopus 로고
    • The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes
    • Cohan FM. (1994). The effects of rare but promiscuous genetic exchange on evolutionary divergence in prokaryotes. Am Nat 143: 965-986
    • (1994) Am Nat , vol.143 , pp. 965-986
    • Cohan, F.M.1
  • 10
    • 0035527404 scopus 로고    scopus 로고
    • Bacterial species and speciation
    • Cohan FM. (2001). Bacterial species and speciation. Syst Biol 50: 513-524
    • (2001) Syst Biol , vol.50 , pp. 513-524
    • Cohan, F.M.1
  • 11
    • 34247884459 scopus 로고    scopus 로고
    • A systematics for discovering the fundamental units of bacterial diversity
    • Cohan FM, Perry EB. (2007). A systematics for discovering the fundamental units of bacterial diversity. Curr Biol 17: R373-R386
    • (2007) Curr Biol , vol.17 , pp. R373-R386
    • Cohan, F.M.1    Perry, E.B.2
  • 12
    • 34548491646 scopus 로고    scopus 로고
    • Code and context: Prochlorococcus as a model for cross-scale biology
    • Coleman ML, Chisholm SW. (2007). Code and context: Prochlorococcus as a model for cross-scale biology. Trends Microbiol 15: 398-407
    • (2007) Trends Microbiol , vol.15 , pp. 398-407
    • Coleman, M.L.1    Chisholm, S.W.2
  • 13
    • 84896398453 scopus 로고    scopus 로고
    • Explaining microbial genomic diversity in light of evolutionary ecology
    • Cordero OX, Polz MF. (2014). Explaining microbial genomic diversity in light of evolutionary ecology. Nat Rev Microbiol 12: 263-273
    • (2014) Nat Rev Microbiol , vol.12 , pp. 263-273
    • Cordero, O.X.1    Polz, M.F.2
  • 14
    • 0033860832 scopus 로고    scopus 로고
    • RpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity
    • Dahllof I, Baillie H, Kjelleberg S. (2000). rpoB-based microbial community analysis avoids limitations inherent in 16S rRNA gene intraspecies heterogeneity. Appl Environ Microbiol 66: 3376-3380
    • (2000) Appl Environ Microbiol , vol.66 , pp. 3376-3380
    • Dahllof, I.1    Baillie, H.2    Kjelleberg, S.3
  • 16
    • 84860160394 scopus 로고    scopus 로고
    • In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids
    • Denef VJ, Banfield JF. (2012). In situ evolutionary rate measurements show ecological success of recently emerged bacterial hybrids. Science 336: 462-466
    • (2012) Science , vol.336 , pp. 462-466
    • Denef, V.J.1    Banfield, J.F.2
  • 17
    • 79955483667 scopus 로고    scopus 로고
    • A framework for variation discovery and genotyping using next-generation DNA sequencing data
    • DePristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, et al. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 43: 491-498
    • (2011) Nat Genet , vol.43 , pp. 491-498
    • DePristo, M.A.1    Banks, E.2    Poplin, R.3    Garimella, K.V.4    Maguire, J.R.5    Hartl, C.6
  • 18
    • 84861847839 scopus 로고    scopus 로고
    • Population genomics: How bacterial species form and why they don?t exist
    • Doolittle WF. (2012). Population genomics: how bacterial species form and why they don?t exist. Curr Biol 22: R451-R453
    • (2012) Curr Biol , vol.22 , pp. R451-R453
    • Doolittle, W.F.1
  • 19
    • 0029610851 scopus 로고
    • The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species
    • Eisen JA. (1995). The RecA protein as a model molecule for molecular systematic studies of bacteria: comparison of trees of RecAs and 16S rRNAs from the same species. J Mol Evol 41: 1105-1123
    • (1995) J Mol Evol , vol.41 , pp. 1105-1123
    • Eisen, J.A.1
  • 20
    • 0035909914 scopus 로고    scopus 로고
    • Recombination and mutation during longterm gastric colonization by Helicobacter pylori: Estimates of clock rates, recombination size, and minimal age
    • Falush D, Kraft C, Taylor NS, Correa P, Fox JG, Achtman M, et al. (2001). Recombination and mutation during longterm gastric colonization by Helicobacter pylori: estimates of clock rates, recombination size, and minimal age. Proc Natl Acad Sci USA 98: 15056-15061
    • (2001) Proc Natl Acad Sci USA , vol.98 , pp. 15056-15061
    • Falush, D.1    Kraft, C.2    Taylor, N.S.3    Correa, P.4    Fox, J.G.5    Achtman, M.6
  • 21
    • 33846625056 scopus 로고    scopus 로고
    • Recombination and the nature of bacterial speciation
    • Fraser C, Hanage WP, Spratt BG. (2007). Recombination and the nature of bacterial speciation. Science 315: 476-480
    • (2007) Science , vol.315 , pp. 476-480
    • Fraser, C.1    Hanage, W.P.2    Spratt, B.G.3
  • 22
    • 59849086092 scopus 로고    scopus 로고
    • The bacterial species challenge: Making sense of genetic and ecological diversity
    • Fraser C, Alm EJ, Polz MF, Spratt BG, Hanage WP. (2009). The bacterial species challenge: making sense of genetic and ecological diversity. Science 323: 741-746
    • (2009) Science , vol.323 , pp. 741-746
    • Fraser, C.1    Alm, E.J.2    Polz, M.F.3    Spratt, B.G.4    Hanage, W.P.5
  • 23
    • 0028030110 scopus 로고
    • Detecting selective sweeps in naturally occurring Escherichia coli
    • Guttman DS, Dykhuizen DE. (1994). Detecting selective sweeps in naturally occurring Escherichia coli. Genetics 138: 993-1003
    • (1994) Genetics , vol.138 , pp. 993-1003
    • Guttman, D.S.1    Dykhuizen, D.E.2
  • 24
    • 84874535714 scopus 로고    scopus 로고
    • Parallel evolutionary dynamics of adaptive diversification in Escherichia coli
    • Herron MD, Doebeli M. (2013). Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PLos Biol 11: e1001490
    • (2013) PLos Biol , vol.11 , pp. e1001490
    • Herron, M.D.1    Doebeli, M.2
  • 25
    • 44449178480 scopus 로고    scopus 로고
    • Resource partitioning and sympatric differentiation among closely related bacterioplankton
    • Hunt DE, David LA, Gevers D, Preheim SP, Alm EJ, Polz MF. (2008). Resource partitioning and sympatric differentiation among closely related bacterioplankton. Science 320: 1081-1085
    • (2008) Science , vol.320 , pp. 1081-1085
    • Hunt, D.E.1    David, L.A.2    Gevers, D.3    Preheim, S.P.4    Alm, E.J.5    Polz, M.F.6
  • 27
    • 33645216333 scopus 로고    scopus 로고
    • Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients
    • Johnson ZI, Zinser ER, Coe A, McNulty NP, Woodward EMS, Chisholm SW. (2006). Niche partitioning among Prochlorococcus ecotypes along ocean-scale environmental gradients. Science 311: 1737-1740
    • (2006) Science , vol.311 , pp. 1737-1740
    • Johnson, Z.I.1    Zinser, E.R.2    Coe, A.3    McNulty, N.P.4    Woodward, E.M.S.5    Chisholm, S.W.6
  • 28
    • 84940387197 scopus 로고    scopus 로고
    • MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
    • Kang DD, Froula J, Egan R, Wang Z. (2015). MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities. PeerJ 3: e1165
    • (2015) PeerJ , vol.3 , pp. e1165
    • Kang, D.D.1    Froula, J.2    Egan, R.3    Wang, Z.4
  • 29
    • 14044262978 scopus 로고    scopus 로고
    • Genomic insights that advance the species definition for prokaryotes
    • Konstantinidis KT, Tiedje JM. (2005). Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102: 2567-2572
    • (2005) Proc Natl Acad Sci USA , vol.102 , pp. 2567-2572
    • Konstantinidis, K.T.1    Tiedje, J.M.2
  • 30
    • 53849115701 scopus 로고    scopus 로고
    • Genomic patterns of recombination, clonal divergence and environment in marine microbial populations
    • Konstantinidis KT, DeLong EF. (2008). Genomic patterns of recombination, clonal divergence and environment in marine microbial populations. ISME J 2: 1052-1065
    • (2008) ISME J , vol.2 , pp. 1052-1065
    • Konstantinidis, K.T.1    DeLong, E.F.2
  • 31
    • 84867339877 scopus 로고    scopus 로고
    • Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by wholegenome sequencing
    • Lee H, Popodi E, Tang HX, Foster PL. (2012). Rate and molecular spectrum of spontaneous mutations in the bacterium Escherichia coli as determined by wholegenome sequencing. Proc Natl Acad Sci USA 109: E2774-E2783
    • (2012) Proc Natl Acad Sci USA , vol.109 , pp. E2774-E2783
    • Lee, H.1    Popodi, E.2    Tang, H.X.3    Foster, P.L.4
  • 32
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler transform
    • Li H, Durbin R. (2009). Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25: 1754-1760
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 33
    • 84942887758 scopus 로고    scopus 로고
    • SOAPdenovo2: An empirically improved memoryefficient short-read de novo assembler
    • Luo R, Liu B, Xie Y, Li Z, Huang W, Yuan J, et al. (2012). SOAPdenovo2: an empirically improved memoryefficient short-read de novo assembler. Gigascience 1: 18
    • (2012) Gigascience , vol.1 , pp. 18
    • Luo, R.1    Liu, B.2    Xie, Y.3    Li, Z.4    Huang, W.5    Yuan, J.6
  • 34
    • 80054913451 scopus 로고    scopus 로고
    • FLASH: Fast length adjustment of short reads to improve genome assemblies
    • Magoc T, Salzberg SL. (2011). FLASH: fast length adjustment of short reads to improve genome assemblies. Bioinformatics 27: 2957-2963
    • (2011) Bioinformatics , vol.27 , pp. 2957-2963
    • Magoc, T.1    Salzberg, S.L.2
  • 35
    • 84861930803 scopus 로고    scopus 로고
    • The multiplicity of divergence mechanisms in a single evolving population
    • Maharjan RP, Ferenci T, Reeves PR, Li Y, Liu B, Wang L. (2012). The multiplicity of divergence mechanisms in a single evolving population. Gene Biol 13: R41
    • (2012) Gene Biol , vol.13 , pp. R41
    • Maharjan, R.P.1    Ferenci, T.2    Reeves, P.R.3    Li, Y.4    Liu, B.5    Wang, L.6
  • 36
    • 0344931878 scopus 로고    scopus 로고
    • Adapt globally, act locally: The effect of selective sweeps on bacterial sequence diversity
    • Majewski J, Cohan FM. (1999). Adapt globally, act locally: the effect of selective sweeps on bacterial sequence diversity. Genetics 152: 1459-1474
    • (1999) Genetics , vol.152 , pp. 1459-1474
    • Majewski, J.1    Cohan, F.M.2
  • 39
    • 77956295988 scopus 로고    scopus 로고
    • The genome analysis toolkit: A mapreduce framework for analyzing next-generation DNA sequencing data
    • McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res 20: 1297-1303
    • (2010) Genome Res , vol.20 , pp. 1297-1303
    • McKenna, A.1    Hanna, M.2    Banks, E.3    Sivachenko, A.4    Cibulskis, K.5    Kernytsky, A.6
  • 40
    • 84885911072 scopus 로고    scopus 로고
    • Population genomics of rapid adaptation by soft selective sweeps
    • Messer PW, Petrov DA. (2013). Population genomics of rapid adaptation by soft selective sweeps. Trends Ecol Evol 28: 659-669
    • (2013) Trends Ecol Evol , vol.28 , pp. 659-669
    • Messer, P.W.1    Petrov, D.A.2
  • 41
    • 0032950018 scopus 로고    scopus 로고
    • Photophysiology of the marine cyanobacterium Prochlorococcus: Ecotypic differences among cultured isolates
    • Moore LR, Chisholm SW. (1999). Photophysiology of the marine cyanobacterium Prochlorococcus: ecotypic differences among cultured isolates. Limnol Oceanogr 44: 628-638
    • (1999) Limnol Oceanogr , vol.44 , pp. 628-638
    • Moore, L.R.1    Chisholm, S.W.2
  • 42
    • 80052753042 scopus 로고    scopus 로고
    • Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem
    • Oh S, Caro-Quintero A, Tsementzi D, DeLeon-Rodriguez N, Luo CW, Poretsky R, et al. (2011). Metagenomic insights into the evolution, function, and complexity of the planktonic microbial community of Lake Lanier, a temperate freshwater ecosystem. Appl Environ Microbiol 77: 6000-6011
    • (2011) Appl Environ Microbiol , vol.77 , pp. 6000-6011
    • Oh, S.1    Caro-Quintero, A.2    Tsementzi, D.3    DeLeon-Rodriguez, N.4    Luo, C.W.5    Poretsky, R.6
  • 43
    • 84937040910 scopus 로고    scopus 로고
    • CheckM: Assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
    • Parks DH, Imelfort M, Skennerton CT, Hugenholtz P, Tyson GW. (2015). CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res 25: 1043-1055
    • (2015) Genome Res , vol.25 , pp. 1043-1055
    • Parks, D.H.1    Imelfort, M.2    Skennerton, C.T.3    Hugenholtz, P.4    Tyson, G.W.5
  • 44
    • 84880863425 scopus 로고    scopus 로고
    • Metastats: An improved statistical method for analysis of metagenomic data
    • Paulson JN, Pop M, Bravo HC. (2011). Metastats: an improved statistical method for analysis of metagenomic data. Genome Biol 12: P17
    • (2011) Genome Biol , vol.12 , pp. P17
    • Paulson, J.N.1    Pop, M.2    Bravo, H.C.3
  • 46
    • 0042878464 scopus 로고    scopus 로고
    • Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation
    • Rocap G, Larimer FW, Lamerdin J, Malfatti S, Chain P, Ahlgren NA, et al. (2003). Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation. Nature 424: 1042-1047
    • (2003) Nature , vol.424 , pp. 1042-1047
    • Rocap, G.1    Larimer, F.W.2    Lamerdin, J.3    Malfatti, S.4    Chain, P.5    Ahlgren, N.A.6
  • 48
    • 84930626863 scopus 로고    scopus 로고
    • Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche
    • Rosen MJ, Davison M, Bhaya D, Fisher DS. (2015). Fine-scale diversity and extensive recombination in a quasisexual bacterial population occupying a broad niche. Science 348: 1019-1023
    • (2015) Science , vol.348 , pp. 1019-1023
    • Rosen, M.J.1    Davison, M.2    Bhaya, D.3    Fisher, D.S.4
  • 50
    • 84899979623 scopus 로고    scopus 로고
    • Ordering microbial diversity into ecologically and genetically cohesive units
    • Shapiro BJ, Polz MF. (2014). Ordering microbial diversity into ecologically and genetically cohesive units. Trends Microbiol 22: 235-247
    • (2014) Trends Microbiol , vol.22 , pp. 235-247
    • Shapiro, B.J.1    Polz, M.F.2
  • 51
    • 84871956840 scopus 로고    scopus 로고
    • Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization
    • Sharon I, Morowitz MJ, Thomas BC, Costello EK, Relman DA, Banfield JF. (2013). Time series community genomics analysis reveals rapid shifts in bacterial species, strains, and phage during infant gut colonization. Genome Res 23: 111-120
    • (2013) Genome Res , vol.23 , pp. 111-120
    • Sharon, I.1    Morowitz, M.J.2    Thomas, B.C.3    Costello, E.K.4    Relman, D.A.5    Banfield, J.F.6
  • 52
    • 48349103531 scopus 로고    scopus 로고
    • Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation
    • Simmons SL, Dibartolo G, Denef VJ, Goltsman DS, Thelen MP, Banfield JF. (2008). Population genomic analysis of strain variation in Leptospirillum group II bacteria involved in acid mine drainage formation. PLos Biol 6: e177
    • (2008) PLos Biol , vol.6 , pp. e177
    • Simmons, S.L.1    Dibartolo, G.2    Denef, V.J.3    Goltsman, D.S.4    Thelen, M.P.5    Banfield, J.F.6
  • 54
    • 84899553363 scopus 로고    scopus 로고
    • RAxML version 8: A tool for phylogenetic analysis and post-Analysis of large phylogenies
    • Stamatakis A. (2014). RAxML version 8: a tool for phylogenetic analysis and post-Analysis of large phylogenies. Bioinformatics 30: 1312-1313
    • (2014) Bioinformatics , vol.30 , pp. 1312-1313
    • Stamatakis, A.1
  • 55
    • 0031402617 scopus 로고    scopus 로고
    • A theoretical approach to structuring mechanisms in the pelagic food web
    • Thingstad TF. (1998). A theoretical approach to structuring mechanisms in the pelagic food web. Hydrobiologia 363: 59-72
    • (1998) Hydrobiologia , vol.363 , pp. 59-72
    • Thingstad, T.F.1
  • 56
    • 0033826796 scopus 로고    scopus 로고
    • Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems
    • Thingstad TF. (2000). Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Limnol Oceanogr 45: 1320-1328
    • (2000) Limnol Oceanogr , vol.45 , pp. 1320-1328
    • Thingstad, T.F.1
  • 57
    • 0041289720 scopus 로고
    • Species and the variety as ecological units
    • Turesson G. (1922). Species and the variety as ecological units. Hereditas 3: 100-113
    • (1922) Hereditas , vol.3 , pp. 100-113
    • Turesson, G.1
  • 58
    • 1542377296 scopus 로고    scopus 로고
    • Community structure and metabolism through reconstruction of microbial genomes from the environment
    • Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, et al. (2004). Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 428: 37-43
    • (2004) Nature , vol.428 , pp. 37-43
    • Tyson, G.W.1    Chapman, J.2    Hugenholtz, P.3    Allen, E.E.4    Ram, R.J.5    Richardson, P.M.6
  • 59
    • 8444238946 scopus 로고    scopus 로고
    • Evolution of the RNA polymerase B? Subunit gene (rpoB?) in Halobacteriales: A complementary molecular marker to the SSU rRNA gene
    • Walsh DA, Bapteste E, Kamekura M, Doolittle WF. (2004). Evolution of the RNA polymerase B? subunit gene (rpoB?) in Halobacteriales: a complementary molecular marker to the SSU rRNA gene. Mol Biol Evol 21: 2340-2351
    • (2004) Mol Biol Evol , vol.21 , pp. 2340-2351
    • Walsh, D.A.1    Bapteste, E.2    Kamekura, M.3    Doolittle, W.F.4
  • 60
    • 27844577665 scopus 로고    scopus 로고
    • Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus
    • Whitaker RJ, Grogan DW, Taylor JW. (2005). Recombination shapes the natural population structure of the hyperthermophilic archaeon Sulfolobus islandicus. Mol Biol Evol 22: 2354-2361
    • (2005) Mol Biol Evol , vol.22 , pp. 2354-2361
    • Whitaker, R.J.1    Grogan, D.W.2    Taylor, J.W.3


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