-
1
-
-
21644441587
-
Do orthologous gene phylogenies really support tree-thinking?
-
Bapteste E, Susko E, Leigh J, MacLeod D, Charlebois RL, Doolittle WF (2005) Do orthologous gene phylogenies really support tree-thinking? BMC Evol Biol 5: 33.
-
(2005)
BMC Evol Biol
, vol.5
, pp. 33
-
-
Bapteste, E.1
Susko, E.2
Leigh, J.3
Macleod, D.4
Charlebois, R.L.5
Doolittle, W.F.6
-
2
-
-
70449515444
-
Prokaryotic evolution and the tree of life are two different things
-
Bapteste E, O'Malley MA, Beiko RG, Ereshefsky M, Gogarten JP, Franklin-Hall L, Lapointe FJ, Dupré J, Dagan T, Boucher Y, Martin W (2009) Prokaryotic evolution and the tree of life are two different things. Biol Direct 4: 34.
-
(2009)
Biol Direct
, vol.4
, pp. 34
-
-
Bapteste, E.1
O'Malley, M.A.2
Beiko, R.G.3
Ereshefsky, M.4
Gogarten, J.P.5
Franklin-Hall, L.6
Lapointe, F.J.7
Dupré, J.8
Dagan, T.9
Boucher, Y.10
Martin, W.11
-
3
-
-
0003356711
-
Homeostasis, species, and higher taxa
-
R. Wilson (Ed.), Cambridge: MIT Press
-
Boyd R (1999) Homeostasis, species, and higher taxa. In: Wilson R (ed) Species: new interdisciplinary essays. MIT Press, Cambridge, pp 141-185.
-
(1999)
Species: New Interdisciplinary Essays
, pp. 141-185
-
-
Boyd, R.1
-
4
-
-
77956241816
-
-
Butela K, Lawrence JG (2009) Selection for antigenic diversity in Salmonella. In: Falush D, Robinson A (eds) Bacterial population genetics in infectious disease. Wiley-Blackwell, London (in press).
-
-
-
-
5
-
-
0035527404
-
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
-
7
-
-
0034132468
-
Uprooting the tree of life
-
Doolittle WF (2000) Uprooting the tree of life. Sci Am 282: 90-95.
-
(2000)
Sci Am
, vol.282
, pp. 90-95
-
-
Doolittle, W.F.1
-
8
-
-
33847790997
-
Pattern pluralism and the tree of life hypothesis
-
Doolittle WF, Bapteste E (2007) Pattern pluralism and the tree of life hypothesis. Proc Natl Acad Sci USA 104: 2043-2049.
-
(2007)
Proc Natl Acad Sci USA
, vol.104
, pp. 2043-2049
-
-
Doolittle, W.F.1
Bapteste, E.2
-
9
-
-
0025788069
-
Recombination in Escherichia coli and the definition of biological species
-
Dykhuizen DE, Green L (1991) Recombination in Escherichia coli and the definition of biological species. J Bacteriol 173: 7257-7268.
-
(1991)
J Bacteriol
, vol.173
, pp. 7257-7268
-
-
Dykhuizen, D.E.1
Green, L.2
-
10
-
-
33751207098
-
Mismatch induced speciation in Salmonella: Model and data
-
Falush D, Torpdahl M, Didelot X, Conrad DF, Wilson DJ, Achtman M (2006) Mismatch induced speciation in Salmonella: model and data. Philos Trans R Soc Lond B Biol Sci 361: 2045-2053.
-
(2006)
Philos Trans R Soc Lond B Biol Sci
, vol.361
, pp. 2045-2053
-
-
Falush, D.1
Torpdahl, M.2
Didelot, X.3
Conrad, D.F.4
Wilson, D.J.5
Achtman, M.6
-
11
-
-
0034769889
-
Recombination and the population structures of bacterial pathogens
-
Feil EJ, Spratt BG (2001) Recombination and the population structures of bacterial pathogens. Annu Rev Microbiol 55: 561-590.
-
(2001)
Annu Rev Microbiol
, vol.55
, pp. 561-590
-
-
Feil, E.J.1
Spratt, B.G.2
-
12
-
-
0035793056
-
Recombination within natural populations of pathogenic bacteria: Short-term empirical estimates and long-term phylogenetic consequences
-
Feil EJ, Holmes EC, Bessen DE, Chan MS, Day NP, Enright MC, Goldstein R, Hood DW, Kalia A, Moore CE, Zhou J, Spratt BG (2001) Recombination within natural populations of pathogenic bacteria: short-term empirical estimates and long-term phylogenetic consequences. Proc Natl Acad Sci USA 98: 182-187.
-
(2001)
Proc Natl Acad Sci USA
, vol.98
, pp. 182-187
-
-
Feil, E.J.1
Holmes, E.C.2
Bessen, D.E.3
Chan, M.S.4
Day, N.P.5
Enright, M.C.6
Goldstein, R.7
Hood, D.W.8
Kalia, A.9
Moore, C.E.10
Zhou, J.11
Spratt, B.G.12
-
13
-
-
33846625056
-
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
-
14
-
-
23944437942
-
Re-evaluating prokaryotic species
-
Gevers D, Cohan FM, Lawrence JG, Spratt BG, Coenye T, Feil EJ, Stackebrandt E, van de Peer Y, Vandamme P, Thompson FL, Swings J (2005) Re-evaluating prokaryotic species. Nat Rev Microbiol 3: 733-739.
-
(2005)
Nat Rev Microbiol
, vol.3
, pp. 733-739
-
-
Gevers, D.1
Cohan, F.M.2
Lawrence, J.G.3
Spratt, B.G.4
Coenye, T.5
Feil, E.J.6
Stackebrandt, E.7
van de Peer, Y.8
Vandamme, P.9
Thompson, F.L.10
Swings, J.11
-
16
-
-
0346882653
-
The distribution and genetic structure of Escherichia coli in Australian vertebrates: Host and geographic effects
-
Gordon DM, Cowling A (2003) The distribution and genetic structure of Escherichia coli in Australian vertebrates: host and geographic effects. Microbiology 149: 3575-3586.
-
(2003)
Microbiology
, vol.149
, pp. 3575-3586
-
-
Gordon, D.M.1
Cowling, A.2
-
17
-
-
0031436694
-
Recombination and clonality in natural populations of Escherichia coli
-
Guttman DS (1997) Recombination and clonality in natural populations of Escherichia coli. Trends Ecol Evol 12: 16-22.
-
(1997)
Trends Ecol Evol
, vol.12
, pp. 16-22
-
-
Guttman, D.S.1
-
18
-
-
0028605344
-
Clonal divergence in Escherichia coli as a result of recombination, not mutation
-
Guttman DS, Dykhuizen DE (1994a) Clonal divergence in Escherichia coli as a result of recombination, not mutation. Science 266: 1380-1383.
-
(1994)
Science
, vol.266
, pp. 1380-1383
-
-
Guttman, D.S.1
Dykhuizen, D.E.2
-
19
-
-
0028030110
-
Detecting selective sweeps in naturally occurring Escherichia coli
-
Guttman DS, Dykhuizen DE (1994b) 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
-
20
-
-
22144486947
-
Fuzzy species among recombinogenic bacteria
-
Hanage WP, Fraser C, Spratt BG (2005) Fuzzy species among recombinogenic bacteria. BMC Biol 3: 6.
-
(2005)
BMC Biol
, vol.3
, pp. 6
-
-
Hanage, W.P.1
Fraser, C.2
Spratt, B.G.3
-
21
-
-
30744470609
-
Application of phylogenetic networks in evolutionary studies
-
Huson DH, Bryant D (2006) Application of phylogenetic networks in evolutionary studies. Mol Biol Evol 23: 254-267.
-
(2006)
Mol Biol Evol
, vol.23
, pp. 254-267
-
-
Huson, D.H.1
Bryant, D.2
-
22
-
-
70149100417
-
A statistical approach for distinguishing hybridization and incomplete lineage sorting
-
Joly S, McLenachan PA, Lockhart PJ (2009) A statistical approach for distinguishing hybridization and incomplete lineage sorting. Am Nat 174: E54-E70.
-
(2009)
Am Nat
, vol.174
-
-
Joly, S.1
McLenachan, P.A.2
Lockhart, P.J.3
-
23
-
-
70449503880
-
The fundamental units, processes and patterns of evolution, and the tree of life conundrum
-
Koonin EV, Wolf YI (2009) The fundamental units, processes and patterns of evolution, and the tree of life conundrum. Biol Direct 4: 33.
-
(2009)
Biol Direct
, vol.4
, pp. 33
-
-
Koonin, E.V.1
Wolf, Y.I.2
-
24
-
-
0036209592
-
Strains of Escherichia coli O157:H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms
-
Kudva IT, Evans PS, Perna NT, Barrett TJ, Ausubel FM, Blattner FR, Calderwood SB (2002a) Strains of Escherichia coli O157: H7 differ primarily by insertions or deletions, not single-nucleotide polymorphisms. J Bacteriol 184: 1873-1879.
-
(2002)
J Bacteriol
, vol.184
, pp. 1873-1879
-
-
Kudva, I.T.1
Evans, P.S.2
Perna, N.T.3
Barrett, T.J.4
Ausubel, F.M.5
Blattner, F.R.6
Calderwood, S.B.7
-
25
-
-
0036206173
-
Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157:H7 strain typing
-
Kudva IT, Evans PS, Perna NT, Barrett TJ, DeCastro GJ, Ausubel FM, Blattner FR, Calderwood SB (2002b) Polymorphic amplified typing sequences provide a novel approach to Escherichia coli O157: H7 strain typing. J Clin Microbiol 40: 1152-1159.
-
(2002)
J Clin Microbiol
, vol.40
, pp. 1152-1159
-
-
Kudva, I.T.1
Evans, P.S.2
Perna, N.T.3
Barrett, T.J.4
Decastro, G.J.5
Ausubel, F.M.6
Blattner, F.R.7
Calderwood, S.B.8
-
26
-
-
0036598066
-
Gene transfer in bacteria: Speciation without species?
-
Lawrence JG (2002) Gene transfer in bacteria: speciation without species? Theor Popul Biol 61: 449-460.
-
(2002)
Theor Popul Biol
, vol.61
, pp. 449-460
-
-
Lawrence, J.G.1
-
27
-
-
65549114090
-
The interplay of homologous recombination and horizontal gene transfer in bacterial speciation
-
Lawrence JG, Retchless AC (2009) The interplay of homologous recombination and horizontal gene transfer in bacterial speciation. Methods Mol Biol 532: 29-53.
-
(2009)
Methods Mol Biol
, vol.532
, pp. 29-53
-
-
Lawrence, J.G.1
Retchless, A.C.2
-
28
-
-
84918041379
-
Gene recombination and linked segregations in Escherichia coli
-
Lederberg J (1947) Gene recombination and linked segregations in Escherichia coli. Genetics 32: 505-525.
-
(1947)
Genetics
, vol.32
, pp. 505-525
-
-
Lederberg, J.1
-
29
-
-
51149212256
-
Gene recombination in Escherichia coli
-
Lederberg J, Tatum EL (1946) Gene recombination in Escherichia coli. Nature 158: 558.
-
(1946)
Nature
, vol.158
, pp. 558
-
-
Lederberg, J.1
Tatum, E.L.2
-
30
-
-
0019619751
-
Periodic selection, infectious gene exchange and the genetic structure of E. coli populations
-
Levin BR (1981) Periodic selection, infectious gene exchange and the genetic structure of E. coli populations. Genetics 99: 1-23.
-
(1981)
Genetics
, vol.99
, pp. 1-23
-
-
Levin, B.R.1
-
33
-
-
0002175468
-
Change of genetic environment and evolution
-
J. S. Huxley, A. C. Hardy, and E. B. Ford (Eds.), London: Allen and Unwin
-
Mayr E (1954) Change of genetic environment and evolution. In: Huxley JS, Hardy AC, Ford EB (eds) Evolution as a process. Allen and Unwin, London, pp 156-180.
-
(1954)
Evolution as a Process
, pp. 156-180
-
-
Mayr, E.1
-
35
-
-
0027337721
-
The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: The relationship between the ompT and kcpA loci
-
Nakata N, Tobe T, Fukuda I, Suzuki T, Komatsu K, Yoshikawa M, Sasakawa C (1993) The absence of a surface protease, OmpT, determines the intercellular spreading ability of Shigella: the relationship between the ompT and kcpA loci. Mol Microbiol 9: 459-468.
-
(1993)
Mol Microbiol
, vol.9
, pp. 459-468
-
-
Nakata, N.1
Tobe, T.2
Fukuda, I.3
Suzuki, T.4
Komatsu, K.5
Yoshikawa, M.6
Sasakawa, C.7
-
36
-
-
0023514080
-
Evolution in bacteria: Evidence for a universal substitution rate in cellular genomes
-
Ochman H, Wilson AC (1988) Evolution in bacteria: evidence for a universal substitution rate in cellular genomes. J Mol Evol 26: 74-86.
-
(1988)
J Mol Evol
, vol.26
, pp. 74-86
-
-
Ochman, H.1
Wilson, A.C.2
-
37
-
-
0034682335
-
Lateral gene transfer and the nature of bacterial innovation
-
Ochman H, Lawrence JG, Groisman E (2000) Lateral gene transfer and the nature of bacterial innovation. Nature 405: 299-304.
-
(2000)
Nature
, vol.405
, pp. 299-304
-
-
Ochman, H.1
Lawrence, J.G.2
Groisman, E.3
-
38
-
-
70449568272
-
Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli
-
Ogura Y, Ooka T, Iguchi A, Toh H, Asadulghani M, Oshima K, Kodama T, Abe H, Nakayama K, Kurokawa K, Tobe T, Hattori M, Hayashi T (2009) Comparative genomics reveal the mechanism of the parallel evolution of O157 and non-O157 enterohemorrhagic Escherichia coli. Proc Natl Acad Sci USA 106: 17939-17944.
-
(2009)
Proc Natl Acad Sci USA
, vol.106
, pp. 17939-17944
-
-
Ogura, Y.1
Ooka, T.2
Iguchi, A.3
Toh, H.4
Asadulghani, M.5
Oshima, K.6
Kodama, T.7
Abe, H.8
Nakayama, K.9
Kurokawa, K.10
Tobe, T.11
Hattori, M.12
Hayashi, T.13
-
39
-
-
0023822631
-
Relationships between gene trees and species trees
-
Pamilo P, Nei M (1988) Relationships between gene trees and species trees. Mol Biol Evol 5: 568-583.
-
(1988)
Mol Biol Evol
, vol.5
, pp. 568-583
-
-
Pamilo, P.1
Nei, M.2
-
40
-
-
34548246020
-
Temporal fragmentation of speciation in bacteria
-
Retchless AC, Lawrence JG (2007) Temporal fragmentation of speciation in bacteria. Science 317: 1093-1096.
-
(2007)
Science
, vol.317
, pp. 1093-1096
-
-
Retchless, A.C.1
Lawrence, J.G.2
-
41
-
-
0028355860
-
Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster
-
Stevenson G, Neal B, Liu D, Hobbs M, Packer NH, Batley M, Redmond JW, Lindquist L, Reeves P (1994) Structure of the O antigen of Escherichia coli K-12 and the sequence of its rfb gene cluster. J Bacteriol 176: 4144-4156.
-
(1994)
J Bacteriol
, vol.176
, pp. 4144-4156
-
-
Stevenson, G.1
Neal, B.2
Liu, D.3
Hobbs, M.4
Packer, N.H.5
Batley, M.6
Redmond, J.W.7
Lindquist, L.8
Reeves, P.9
-
42
-
-
0002983450
-
The meaning of species and speciation: A genetic perspective
-
D. Otte and J. A. Endler (Eds.), Sunderland: Sinauer Associates
-
Templeton AR (1989) The meaning of species and speciation: a genetic perspective. In: Otte D, Endler JA (eds) Speciation and its consequences. Sinauer Associates, Sunderland, pp 3-27.
-
(1989)
Speciation and Its Consequences
, pp. 3-27
-
-
Templeton, A.R.1
-
43
-
-
0000314099
-
Ecological species, multispecies, and oaks
-
van Valen L (1976) Ecological species, multispecies, and oaks. Taxon 25: 223-239.
-
(1976)
Taxon
, vol.25
, pp. 223-239
-
-
van Valen, L.1
-
44
-
-
0030924545
-
Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in Enterobacteria
-
Vulic M, Dionisio F, Taddei F, Radman M (1997) Molecular keys to speciation: DNA polymorphism and the control of genetic exchange in Enterobacteria. Proc Natl Acad Sci USA 94: 9763-9767.
-
(1997)
Proc Natl Acad Sci USA
, vol.94
, pp. 9763-9767
-
-
Vulic, M.1
Dionisio, F.2
Taddei, F.3
Radman, M.4
-
45
-
-
0033594973
-
Mutation, recombination, and incipient speciation of bacteria in the laboratory
-
Vulic M, Lenski RE, Radman M (1999) Mutation, recombination, and incipient speciation of bacteria in the laboratory. Proc Natl Acad Sci USA 96: 7348-7351.
-
(1999)
Proc Natl Acad Sci USA
, vol.96
, pp. 7348-7351
-
-
Vulic, M.1
Lenski, R.E.2
Radman, M.3
-
46
-
-
34547702305
-
Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches
-
Walk ST, Alm EW, Calhoun LM, Mladonicky JM, Whittam TS (2007) Genetic diversity and population structure of Escherichia coli isolated from freshwater beaches. Environ Microbiol 9: 2274-2288.
-
(2007)
Environ Microbiol
, vol.9
, pp. 2274-2288
-
-
Walk, S.T.1
Alm, E.W.2
Calhoun, L.M.3
Mladonicky, J.M.4
Whittam, T.S.5
-
47
-
-
70349944351
-
Cryptic lineages of the genus Escherichia
-
Walk ST, Alm EW, Gordon DM, Ram JL, Toranzos GA, Tiedje JM, Whittam TS (2009) Cryptic lineages of the genus Escherichia. Appl Environ Microbiol 75: 6534-6544.
-
(2009)
Appl Environ Microbiol
, vol.75
, pp. 6534-6544
-
-
Walk, S.T.1
Alm, E.W.2
Gordon, D.M.3
Ram, J.L.4
Toranzos, G.A.5
Tiedje, J.M.6
Whittam, T.S.7
-
48
-
-
0037168538
-
Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli
-
Welch RA, Burland V, Plunkett G 3rd, Redford P, Roesch P, Rasko D, Buckles EL, Liou SR, Boutin A, Hackett J, Stroud D, Mayhew GF, Rose DJ, Zhou S, Schwartz DC, Perna NT, Mobley HL, Donnenberg MS, Blattner FR (2002) Extensive mosaic structure revealed by the complete genome sequence of uropathogenic Escherichia coli. Proc Natl Acad Sci USA 99: 17020-17024.
-
(2002)
Proc Natl Acad Sci USA
, vol.99
, pp. 17020-17024
-
-
Welch, R.A.1
Burland, V.2
Plunkett 3rd, G.3
Redford, P.4
Roesch, P.5
Rasko, D.6
Buckles, E.L.7
Liou, S.R.8
Boutin, A.9
Hackett, J.10
Stroud, D.11
Mayhew, G.F.12
Rose, D.J.13
Zhou, S.14
Schwartz, D.C.15
Perna, N.T.16
Mobley, H.L.17
Donnenberg, M.S.18
Blattner, F.R.19
-
49
-
-
0242627658
-
A molecular phylogeny of enteric bacteria and implications for a bacterial species concept
-
Wertz JE, Goldstone C, Gordon DM, Riley MA (2003) A molecular phylogeny of enteric bacteria and implications for a bacterial species concept. J Evol Biol 16: 1236-1248.
-
(2003)
J Evol Biol
, vol.16
, pp. 1236-1248
-
-
Wertz, J.E.1
Goldstone, C.2
Gordon, D.M.3
Riley, M.A.4
-
50
-
-
34250732800
-
Differential Salmonella survival against communities of intestinal amoebae
-
Wildschutte H, Lawrence JG (2007) Differential Salmonella survival against communities of intestinal amoebae. Microbiology 153: 1781-1789.
-
(2007)
Microbiology
, vol.153
, pp. 1781-1789
-
-
Wildschutte, H.1
Lawrence, J.G.2
-
51
-
-
3242695831
-
Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella
-
Wildschutte H, Wolfe DM, Tamewitz A, Lawrence JG (2004) Protozoan predation, diversifying selection, and the evolution of antigenic diversity in Salmonella. Proc Natl Acad Sci USA 101: 10644-10649.
-
(2004)
Proc Natl Acad Sci USA
, vol.101
, pp. 10644-10649
-
-
Wildschutte, H.1
Wolfe, D.M.2
Tamewitz, A.3
Lawrence, J.G.4
-
52
-
-
84959755121
-
The evolutionary species concept reconsidered
-
Wiley EO (1978) The evolutionary species concept reconsidered. Syst Zool 27: 17-26.
-
(1978)
Syst Zool
, vol.27
, pp. 17-26
-
-
Wiley, E.O.1
-
53
-
-
0027250349
-
Variation of the rfb gene clusters in Salmonella enterica
-
Xiang SH, Haase AM, Reeves PR (1993) Variation of the rfb gene clusters in Salmonella enterica. J Bacteriol 175: 4877-4884.
-
(1993)
J Bacteriol
, vol.175
, pp. 4877-4884
-
-
Xiang, S.H.1
Haase, A.M.2
Reeves, P.R.3
-
54
-
-
0029038657
-
The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust
-
Zawadzki P, Roberts MS, Cohan FM (1995) The log-linear relationship between sexual isolation and sequence divergence in Bacillus transformation is robust. Genetics 140: 917-932.
-
(1995)
Genetics
, vol.140
, pp. 917-932
-
-
Zawadzki, P.1
Roberts, M.S.2
Cohan, F.M.3
|