-
1
-
-
0038441327
-
Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation
-
Elena S.F., Lenski R.E. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet 2003, 4:457-469.
-
(2003)
Nat Rev Genet
, vol.4
, pp. 457-469
-
-
Elena, S.F.1
Lenski, R.E.2
-
2
-
-
60149106871
-
The Beagle in a bottle
-
Buckling A., Craig Maclean R., Brockhurst M.A., Colegrave N. The Beagle in a bottle. Nature 2009, 457:824-829.
-
(2009)
Nature
, vol.457
, pp. 824-829
-
-
Buckling, A.1
Craig Maclean, R.2
Brockhurst, M.A.3
Colegrave, N.4
-
3
-
-
84901355368
-
The fates of mutant lineages and the distribution of fitness effects of beneficial mutations in laboratory budding yeast populations
-
Frenkel E.M., Good B.H., Desai M.M. The fates of mutant lineages and the distribution of fitness effects of beneficial mutations in laboratory budding yeast populations. Genetics 2014, 196:1217-1226.
-
(2014)
Genetics
, vol.196
, pp. 1217-1226
-
-
Frenkel, E.M.1
Good, B.H.2
Desai, M.M.3
-
4
-
-
33645076253
-
An equivalence principle for the incorporation of favorable mutations in asexual populations
-
Hegreness M., Shoresh N., Hartl D., Kishony R. An equivalence principle for the incorporation of favorable mutations in asexual populations. Science 2006, 311:1615-1617.
-
(2006)
Science
, vol.311
, pp. 1615-1617
-
-
Hegreness, M.1
Shoresh, N.2
Hartl, D.3
Kishony, R.4
-
5
-
-
84903291815
-
Global epistasis makes adaptation predictable despite sequence-level stochasticity
-
Kryazhimskiy S., Rice D.P., Jerison E.R., Desai M.M. Global epistasis makes adaptation predictable despite sequence-level stochasticity. Science 2014, 344:1519-1522.
-
(2014)
Science
, vol.344
, pp. 1519-1522
-
-
Kryazhimskiy, S.1
Rice, D.P.2
Jerison, E.R.3
Desai, M.M.4
-
6
-
-
45849093668
-
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
-
Blount Z.D., Borland C.Z., Lenski R.E. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proc Natl Acad Sci U S A 2008, 105:7899-7906.
-
(2008)
Proc Natl Acad Sci U S A
, vol.105
, pp. 7899-7906
-
-
Blount, Z.D.1
Borland, C.Z.2
Lenski, R.E.3
-
7
-
-
0028977087
-
Experimental tests of the roles of adaptation, chance, and history in evolution
-
Travisano M., Mongold J., Bennett A., Lenski R. Experimental tests of the roles of adaptation, chance, and history in evolution. Science 1995, 267:87-90.
-
(1995)
Science
, vol.267
, pp. 87-90
-
-
Travisano, M.1
Mongold, J.2
Bennett, A.3
Lenski, R.4
-
8
-
-
0033555421
-
Diminishing returns from mutation supply rate in asexual populations
-
de Visser J.A.G.M., Zeyl C.W., Gerrish P.J., Blanchard J.L., Lenski R.E. Diminishing returns from mutation supply rate in asexual populations. Science 1999, 283:404-406.
-
(1999)
Science
, vol.283
, pp. 404-406
-
-
de Visser, J.A.G.M.1
Zeyl, C.W.2
Gerrish, P.J.3
Blanchard, J.L.4
Lenski, R.E.5
-
9
-
-
33847256353
-
The speed of evolution and maintenance of variation in asexual populations
-
Desai M.M., Fisher D.S., Murray A.W. The speed of evolution and maintenance of variation in asexual populations. Curr Biol 2007, 17:385-394.
-
(2007)
Curr Biol
, vol.17
, pp. 385-394
-
-
Desai, M.M.1
Fisher, D.S.2
Murray, A.W.3
-
10
-
-
56749107039
-
Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae
-
Kao K.C., Sherlock G. Molecular characterization of clonal interference during adaptive evolution in asexual populations of Saccharomyces cerevisiae. Nat Genet 2008, 40:1499-1504.
-
(2008)
Nat Genet
, vol.40
, pp. 1499-1504
-
-
Kao, K.C.1
Sherlock, G.2
-
11
-
-
79960137718
-
Genetic variation and the fate of beneficial mutations in asexual populations
-
Lang G.I., Botstein D., Desai M.M. Genetic variation and the fate of beneficial mutations in asexual populations. Genetics 2011, 188:647-661.
-
(2011)
Genetics
, vol.188
, pp. 647-661
-
-
Lang, G.I.1
Botstein, D.2
Desai, M.M.3
-
12
-
-
84856514801
-
Estimation of the rate and effect of new beneficial mutations in asexual populations
-
Zhang W., Sehgal V., Dinh D.M., Azevedo R.B.R., Cooper T.F., Azencott R. Estimation of the rate and effect of new beneficial mutations in asexual populations. Theor Popul Biol 2012, 81:168-178.
-
(2012)
Theor Popul Biol
, vol.81
, pp. 168-178
-
-
Zhang, W.1
Sehgal, V.2
Dinh, D.M.3
Azevedo, R.B.R.4
Cooper, T.F.5
Azencott, R.6
-
13
-
-
84891475093
-
An ABC method for estimating the rate and distribution of effects of beneficial mutations
-
Moura de Sousa J.A., Campos P.R.A., Gordo I. An ABC method for estimating the rate and distribution of effects of beneficial mutations. Genome Biol Evol 2013, 5:794-806.
-
(2013)
Genome Biol Evol
, vol.5
, pp. 794-806
-
-
Moura de Sousa, J.A.1
Campos, P.R.A.2
Gordo, I.3
-
14
-
-
84860663163
-
Evolutionary insight from whole-genome sequencing of experimentally evolved microbes
-
Dettman J.R., Rodrigue N., Melnyk A.H., Wong A., Bailey S.F., Kassen R. Evolutionary insight from whole-genome sequencing of experimentally evolved microbes. Mol Ecol 2012, 21:2058-2077.
-
(2012)
Mol Ecol
, vol.21
, pp. 2058-2077
-
-
Dettman, J.R.1
Rodrigue, N.2
Melnyk, A.H.3
Wong, A.4
Bailey, S.F.5
Kassen, R.6
-
15
-
-
79951808135
-
Next-generation sequencing as a tool to study microbial evolution
-
Brockhurst M.A., Colegrave N., Rozen D.E. Next-generation sequencing as a tool to study microbial evolution. Mol Ecol 2011, 20:972-980.
-
(2011)
Mol Ecol
, vol.20
, pp. 972-980
-
-
Brockhurst, M.A.1
Colegrave, N.2
Rozen, D.E.3
-
16
-
-
84957441018
-
The spectrum of adaptive mutations in experimental evolution
-
Lang G.I., Desai M.M. The spectrum of adaptive mutations in experimental evolution. Genomics 2014, 104:412-416.
-
(2014)
Genomics
, vol.104
, pp. 412-416
-
-
Lang, G.I.1
Desai, M.M.2
-
17
-
-
84888001845
-
Genome dynamics during experimental evolution
-
Barrick J.E., Lenski R.E. Genome dynamics during experimental evolution. Nat Rev Genet 2013, 14:827-839.
-
(2013)
Nat Rev Genet
, vol.14
, pp. 827-839
-
-
Barrick, J.E.1
Lenski, R.E.2
-
18
-
-
34548104987
-
Clonal interference is alleviated by high mutation rates in large populations
-
Bollback J.P., Huelsenbeck J.P. Clonal interference is alleviated by high mutation rates in large populations. Mol Biol Evol 2007, 24:1397-1406.
-
(2007)
Mol Biol Evol
, vol.24
, pp. 1397-1406
-
-
Bollback, J.P.1
Huelsenbeck, J.P.2
-
19
-
-
61549106268
-
Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence
-
Bollback J.P., Huelsenbeck J.P. Parallel genetic evolution within and between bacteriophage species of varying degrees of divergence. Genetics 2009, 181:225-234.
-
(2009)
Genetics
, vol.181
, pp. 225-234
-
-
Bollback, J.P.1
Huelsenbeck, J.P.2
-
20
-
-
64049094567
-
Genomewide patterns of substitution in adaptively evolving populations of the RNA bacteriophage MS2
-
Betancourt A.J. Genomewide patterns of substitution in adaptively evolving populations of the RNA bacteriophage MS2. Genetics 2009, 181:1535-1544.
-
(2009)
Genetics
, vol.181
, pp. 1535-1544
-
-
Betancourt, A.J.1
-
21
-
-
0030823001
-
Exceptional convergent evolution in a virus
-
Bull J.J., Badgett M.R., Wichman H.A., Huelsenbeck J.P., Hillis D.M., Gulati A., Ho C., Molineux I.J. Exceptional convergent evolution in a virus. Genetics 1997, 147:1497-1507.
-
(1997)
Genetics
, vol.147
, pp. 1497-1507
-
-
Bull, J.J.1
Badgett, M.R.2
Wichman, H.A.3
Huelsenbeck, J.P.4
Hillis, D.M.5
Gulati, A.6
Ho, C.7
Molineux, I.J.8
-
22
-
-
0033575348
-
Different trajectories of parallel evolution during viral adaptation
-
Wichman H.A., Badgett M.R., Scott L.A., Boulianne C.M., Bull J.J. Different trajectories of parallel evolution during viral adaptation. Science 1999, 285:422-424.
-
(1999)
Science
, vol.285
, pp. 422-424
-
-
Wichman, H.A.1
Badgett, M.R.2
Scott, L.A.3
Boulianne, C.M.4
Bull, J.J.5
-
23
-
-
78951475034
-
Mutational effects and population dynamics during viral adaptation challenge current models
-
Miller C.R., Joyce P., Wichman H.A. Mutational effects and population dynamics during viral adaptation challenge current models. Genetics 2011, 187:185-202.
-
(2011)
Genetics
, vol.187
, pp. 185-202
-
-
Miller, C.R.1
Joyce, P.2
Wichman, H.A.3
-
24
-
-
70350641005
-
Genome evolution and adaptation in a long-term experiment with Escherichia coli
-
Barrick J.E., Yu D.S., Yoon S.H., Jeong H., Oh T.K., Schneider D., Lenski R.E., Kim J.F. Genome evolution and adaptation in a long-term experiment with Escherichia coli. Nature 2009, 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
Lenski, R.E.7
Kim, J.F.8
-
25
-
-
77957746208
-
Genome-wide mutational diversity in an evolving population of Escherichia coli
-
Barrick J.E., Lenski R.E. Genome-wide mutational diversity in an evolving population of Escherichia coli. Cold Spring Harb Symp Quant Biol 2009, 74:119-129.
-
(2009)
Cold Spring Harb Symp Quant Biol
, vol.74
, pp. 119-129
-
-
Barrick, J.E.1
Lenski, R.E.2
-
26
-
-
84920877236
-
The impact of macroscopic epistasis on long-term evolutionary dynamics
-
Good B.H., Desai M.M. The impact of macroscopic epistasis on long-term evolutionary dynamics. Genetics 2015, 199:177-190.
-
(2015)
Genetics
, vol.199
, pp. 177-190
-
-
Good, B.H.1
Desai, M.M.2
-
27
-
-
84890116570
-
Long-term dynamics of adaptation in asexual populations
-
Wiser M.J., Ribeck N., Lenski R.E. Long-term dynamics of adaptation in asexual populations. Science 2013, 342:1364-1367.
-
(2013)
Science
, vol.342
, pp. 1364-1367
-
-
Wiser, M.J.1
Ribeck, N.2
Lenski, R.E.3
-
28
-
-
79955590028
-
Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape
-
Kvitek D.J., Sherlock G. Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet 2011, 7:e1002056.
-
(2011)
PLoS Genet
, vol.7
, pp. e1002056
-
-
Kvitek, D.J.1
Sherlock, G.2
-
29
-
-
84897389131
-
The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps
-
Barroso-Batista J., Sousa A., Lourenço M., Bergman M.-L., Sobral D., Demengeot J., Xavier K.B., Gordo I. The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps. PLoS Genet 2014, 10:e1004182.
-
(2014)
PLoS Genet
, vol.10
, pp. e1004182
-
-
Barroso-Batista, J.1
Sousa, A.2
Lourenço, M.3
Bergman, M.-L.4
Sobral, D.5
Demengeot, J.6
Xavier, K.B.7
Gordo, I.8
-
30
-
-
84871981698
-
Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load
-
Wielgoss S., Barrick J.E., Tenaillon O., Wiser M.J., Dittmar W.J., Cruveiller S., Chane-Woon-Ming B., Medigue C., Lenski R.E., Schneider D. Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load. Proc Natl Acad Sci U S A 2013, 110:222-227.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. 222-227
-
-
Wielgoss, S.1
Barrick, J.E.2
Tenaillon, O.3
Wiser, M.J.4
Dittmar, W.J.5
Cruveiller, S.6
Chane-Woon-Ming, B.7
Medigue, C.8
Lenski, R.E.9
Schneider, D.10
-
31
-
-
84883132678
-
Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations
-
Lang G.I., Rice D.P., Hickman M.J., Sodergren E., Weinstock G.M., Botstein D., Desai M.M. Pervasive genetic hitchhiking and clonal interference in forty evolving yeast populations. Nature 2013, 500:571-574.
-
(2013)
Nature
, vol.500
, pp. 571-574
-
-
Lang, G.I.1
Rice, D.P.2
Hickman, M.J.3
Sodergren, E.4
Weinstock, G.M.5
Botstein, D.6
Desai, M.M.7
-
32
-
-
84888213196
-
Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment
-
Kvitek D.J., Sherlock G. Whole genome, whole population sequencing reveals that loss of signaling networks is the major adaptive strategy in a constant environment. PLoS Genet 2013, 9:e1003972.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003972
-
-
Kvitek, D.J.1
Sherlock, G.2
-
33
-
-
84931464826
-
Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli
-
Maddamsetti R., Lenski R.E., Barrick J.E. Adaptation, clonal interference, and frequency-dependent interactions in a long-term evolution experiment with Escherichia coli. Genetics 2015.
-
(2015)
Genetics
-
-
Maddamsetti, R.1
Lenski, R.E.2
Barrick, J.E.3
-
34
-
-
84874535714
-
Parallel evolutionary dynamics of adaptive diversification in Escherichia coli
-
Herron M.D., Doebeli M. Parallel evolutionary dynamics of adaptive diversification in Escherichia coli. PLoS Biol 2013, 11:e1001490.
-
(2013)
PLoS Biol
, vol.11
, pp. e1001490
-
-
Herron, M.D.1
Doebeli, M.2
-
35
-
-
84872541144
-
Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections
-
Traverse C.C., Mayo-Smith L.M., Poltak S.R., Cooper V.S. Tangled bank of experimentally evolved Burkholderia biofilms reflects selection during chronic infections. Proc Natl Acad Sci U S A 2013, 110:E250-E259.
-
(2013)
Proc Natl Acad Sci U S A
, vol.110
, pp. E250-E259
-
-
Traverse, C.C.1
Mayo-Smith, L.M.2
Poltak, S.R.3
Cooper, V.S.4
-
36
-
-
77957346489
-
Genome-wide analysis of a long-term evolution experiment with Drosophila
-
Burke M.K., Dunham J.P., Shahrestani P., Thornton K.R., Rose M.R., Long A.D. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 2010, 467:587-590.
-
(2010)
Nature
, vol.467
, pp. 587-590
-
-
Burke, M.K.1
Dunham, J.P.2
Shahrestani, P.3
Thornton, K.R.4
Rose, M.R.5
Long, A.D.6
-
37
-
-
79953735688
-
Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster
-
Turner T.L., Stewart A.D., Fields A.T., Rice W.R., Tarone A.M. Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet 2011, 7:e1001336.
-
(2011)
PLoS Genet
, vol.7
, pp. e1001336
-
-
Turner, T.L.1
Stewart, A.D.2
Fields, A.T.3
Rice, W.R.4
Tarone, A.M.5
-
38
-
-
79952291784
-
Experimental selection of hypoxia-tolerant Drosophila melanogaster
-
Zhou D., Udpa N., Gersten M., Visk D.W., Bashir A., Xue J., Frazer K.A., Posakony J.W., Subramaniam S., Bafna V., et al. Experimental selection of hypoxia-tolerant Drosophila melanogaster. Proc Natl Acad Sci U S A 2011, 108:2349-2354.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 2349-2354
-
-
Zhou, D.1
Udpa, N.2
Gersten, M.3
Visk, D.W.4
Bashir, A.5
Xue, J.6
Frazer, K.A.7
Posakony, J.W.8
Subramaniam, S.9
Bafna, V.10
-
39
-
-
84925014763
-
Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae
-
Burke M.K., Liti G., Long A.D. Standing genetic variation drives repeatable experimental evolution in outcrossing populations of Saccharomyces cerevisiae. Mol Biol Evol 2014, 31:3228-3239.
-
(2014)
Mol Biol Evol
, vol.31
, pp. 3228-3239
-
-
Burke, M.K.1
Liti, G.2
Long, A.D.3
-
40
-
-
84874466788
-
Statistical questions in experimental evolution
-
Desai M.M. Statistical questions in experimental evolution. J Stat Mech Theory Exp 2013, 2013:P01003.
-
(2013)
J Stat Mech Theory Exp
, vol.2013
, pp. P01003
-
-
Desai, M.M.1
-
41
-
-
33645666942
-
Darwinian evolution can follow only very few mutational paths to fitter proteins
-
Weinreich D.M., Delaney N.F., Depristo M.A., Hartl D.L. Darwinian evolution can follow only very few mutational paths to fitter proteins. Science 2006, 312:111-114.
-
(2006)
Science
, vol.312
, pp. 111-114
-
-
Weinreich, D.M.1
Delaney, N.F.2
Depristo, M.A.3
Hartl, D.L.4
-
43
-
-
84922384542
-
A systematic survey of an intragenic epistatic landscape
-
Bank C., Hietpas R.T., Jensen J.D., Bolon D.N.A. A systematic survey of an intragenic epistatic landscape. Mol Biol Evol 2015, 32:229-238.
-
(2015)
Mol Biol Evol
, vol.32
, pp. 229-238
-
-
Bank, C.1
Hietpas, R.T.2
Jensen, J.D.3
Bolon, D.N.A.4
-
44
-
-
84856258903
-
The molecular diversity of adaptive convergence
-
Tenaillon O., Rodriguez-Verdugo A., Gaut R.L., McDonald P., Bennett A.F., Long A.D., Gaut B.S. The molecular diversity of adaptive convergence. Science 2012, 335:457-461.
-
(2012)
Science
, vol.335
, pp. 457-461
-
-
Tenaillon, O.1
Rodriguez-Verdugo, A.2
Gaut, R.L.3
McDonald, P.4
Bennett, A.F.5
Long, A.D.6
Gaut, B.S.7
-
45
-
-
84906309036
-
Different tradeoffs result from alternate genetic adaptations to a common environment
-
Rodríguez-Verdugo A., Carrillo-Cisneros D., González-González A., Gaut B.S., Bennett A.F. Different tradeoffs result from alternate genetic adaptations to a common environment. Proc Natl Acad Sci U S A 2014, 111:12121-12126.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 12121-12126
-
-
Rodríguez-Verdugo, A.1
Carrillo-Cisneros, D.2
González-González, A.3
Gaut, B.S.4
Bennett, A.F.5
-
46
-
-
84896845939
-
The predictability of molecular evolution during functional innovation
-
Blank D., Wolf L., Ackermann M., Silander O.K. The predictability of molecular evolution during functional innovation. Proc Natl Acad Sci U S A 2014, 111:3044-3049.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 3044-3049
-
-
Blank, D.1
Wolf, L.2
Ackermann, M.3
Silander, O.K.4
-
47
-
-
84922862545
-
The genomic landscape of compensatory evolution
-
Szamecz B., Boross G., Kalapis D., Kovács K., Fekete G., Farkas Z., Lázár V., Hrtyan M., Kemmeren P., Groot Koerkamp M.J.A., et al. The genomic landscape of compensatory evolution. PLoS Biol 2014, 12:e1001935.
-
(2014)
PLoS Biol
, vol.12
, pp. e1001935
-
-
Szamecz, B.1
Boross, G.2
Kalapis, D.3
Kovács, K.4
Fekete, G.5
Farkas, Z.6
Lázár, V.7
Hrtyan, M.8
Kemmeren, P.9
Groot Koerkamp, M.J.A.10
-
48
-
-
84923532949
-
The rule of declining adaptability in microbial evolution experiments
-
Couce A., Tenaillon O.A. The rule of declining adaptability in microbial evolution experiments. Front Genet 2015, 6:99.
-
(2015)
Front Genet
, vol.6
, pp. 99
-
-
Couce, A.1
Tenaillon, O.A.2
-
49
-
-
34247349509
-
Understanding the evolutionary fate of finite populations: the dynamics of mutational effects
-
Silander O.K., Tenaillon O., Chao L. Understanding the evolutionary fate of finite populations: the dynamics of mutational effects. PLoS Biol 2007, 5:e94.
-
(2007)
PLoS Biol
, vol.5
, pp. e94
-
-
Silander, O.K.1
Tenaillon, O.2
Chao, L.3
-
50
-
-
84890874862
-
Rates of fitness decline and rebound suggest pervasive epistasis
-
Perfeito L., Sousa A., Bataillon T., Gordo I. Rates of fitness decline and rebound suggest pervasive epistasis. Evolution 2014, 68:150-162.
-
(2014)
Evolution
, vol.68
, pp. 150-162
-
-
Perfeito, L.1
Sousa, A.2
Bataillon, T.3
Gordo, I.4
-
51
-
-
77952796777
-
Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects
-
Barrick J.E., Kauth M.R., Strelioff C.C., Lenski R.E. Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol 2010, 27:1338-1347.
-
(2010)
Mol Biol Evol
, vol.27
, pp. 1338-1347
-
-
Barrick, J.E.1
Kauth, M.R.2
Strelioff, C.C.3
Lenski, R.E.4
-
52
-
-
79957958115
-
Diminishing returns epistasis among beneficial mutations decelerates adaptation
-
Chou H.H., Chiu H.C., Delaney N.F., Segre D., Marx C.J. Diminishing returns epistasis among beneficial mutations decelerates adaptation. Science 2011, 332:1190-1192.
-
(2011)
Science
, vol.332
, pp. 1190-1192
-
-
Chou, H.H.1
Chiu, H.C.2
Delaney, N.F.3
Segre, D.4
Marx, C.J.5
-
53
-
-
79957948242
-
Negative epistasis between beneficial mutations in an evolving bacterial population
-
Khan A.I., Dinh D.M., Schneider D., Lenski R.E., Cooper T.F. Negative epistasis between beneficial mutations in an evolving bacterial population. Science 2011, 332:1193-1196.
-
(2011)
Science
, vol.332
, pp. 1193-1196
-
-
Khan, A.I.1
Dinh, D.M.2
Schneider, D.3
Lenski, R.E.4
Cooper, T.F.5
-
54
-
-
84866944595
-
Genomic analysis of a key innovation in an experimental Escherichia coli population
-
Blount Z.D., Barrick J.E., Davidson C.J., Lenski R.E. Genomic analysis of a key innovation in an experimental Escherichia coli population. Nature 2012, 489:513-518.
-
(2012)
Nature
, vol.489
, pp. 513-518
-
-
Blount, Z.D.1
Barrick, J.E.2
Davidson, C.J.3
Lenski, R.E.4
-
55
-
-
84893827275
-
Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli
-
Quandt E.M., Deatherage D.E., Ellington A.D., Georgiou G., Barrick J.E. Recursive genomewide recombination and sequencing reveals a key refinement step in the evolution of a metabolic innovation in Escherichia coli. Proc Natl Acad Sci U S A 2014, 111:2217-2222.
-
(2014)
Proc Natl Acad Sci U S A
, vol.111
, pp. 2217-2222
-
-
Quandt, E.M.1
Deatherage, D.E.2
Ellington, A.D.3
Georgiou, G.4
Barrick, J.E.5
-
56
-
-
84897086957
-
Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli
-
Plucain J., Hindré T., Le Gac M., Tenaillon O., Cruveiller S., Médigue C., Leiby N., Harcombe W.R., Marx C.J., Lenski R.E., et al. Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli. Science 2014, 343:1366-1369.
-
(2014)
Science
, vol.343
, pp. 1366-1369
-
-
Plucain, J.1
Hindré, T.2
Le Gac, M.3
Tenaillon, O.4
Cruveiller, S.5
Médigue, C.6
Leiby, N.7
Harcombe, W.R.8
Marx, C.J.9
Lenski, R.E.10
-
57
-
-
84896702264
-
Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1
-
Carroll S.M., Lee M.-C., Marx C.J. Sign epistasis limits evolutionary trade-offs at the confluence of single- and multi-carbon metabolism in Methylobacterium extorquens AM1. Evolution 2014, 68:760-771.
-
(2014)
Evolution
, vol.68
, pp. 760-771
-
-
Carroll, S.M.1
Lee, M.-C.2
Marx, C.J.3
-
58
-
-
84879630282
-
Environmental dependence of genetic constraint
-
de Vos M.G.J., Poelwijk F.J., Battich N., Ndika J.D.T., Tans S.J. Environmental dependence of genetic constraint. PLoS Genet 2013, 9:e1003580.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003580
-
-
de Vos, M.G.J.1
Poelwijk, F.J.2
Battich, N.3
Ndika, J.D.T.4
Tans, S.J.5
-
59
-
-
84923250136
-
Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq
-
Deatherage D.E., Traverse C.C., Wolf L.N., Barrick J.E. Detecting rare structural variation in evolving microbial populations from new sequence junctions using breseq. Front Genet 2015, 5:468.
-
(2015)
Front Genet
, vol.5
, pp. 468
-
-
Deatherage, D.E.1
Traverse, C.C.2
Wolf, L.N.3
Barrick, J.E.4
-
60
-
-
84908439725
-
Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli
-
e01377-14
-
Raeside C., Gaffé J., Deatherage D.E., Tenaillon O., Briska A.M., Ptashkin R.N., Cruveiller S., Médigue C., Lenski R.E., Barrick J.E., et al. Large chromosomal rearrangements during a long-term evolution experiment with Escherichia coli. mBio 2014, 5:e01377-14.
-
(2014)
mBio
, vol.5
-
-
Raeside, C.1
Gaffé, J.2
Deatherage, D.E.3
Tenaillon, O.4
Briska, A.M.5
Ptashkin, R.N.6
Cruveiller, S.7
Médigue, C.8
Lenski, R.E.9
Barrick, J.E.10
-
61
-
-
84961287763
-
Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution
-
Renda B.A., Dasgupta A., Leon D., Barrick J.E. Genome instability mediates the loss of key traits by Acinetobacter baylyi ADP1 during laboratory evolution. J Bacteriol 2015, 197:872-881.
-
(2015)
J Bacteriol
, vol.197
, pp. 872-881
-
-
Renda, B.A.1
Dasgupta, A.2
Leon, D.3
Barrick, J.E.4
-
62
-
-
84923257096
-
Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq
-
Barrick J.E., Colburn G., Deatherage D.E., Traverse C.C., Strand M.D., Borges J.J., Knoester D.B., Reba A., Meyer A.G. Identifying structural variation in haploid microbial genomes from short-read resequencing data using breseq. BMC Genomics 2014, 15:1039.
-
(2014)
BMC Genomics
, vol.15
, pp. 1039
-
-
Barrick, J.E.1
Colburn, G.2
Deatherage, D.E.3
Traverse, C.C.4
Strand, M.D.5
Borges, J.J.6
Knoester, D.B.7
Reba, A.8
Meyer, A.G.9
-
63
-
-
0020640576
-
Frequency of fixation of adaptive mutations is higher in evolving diploid than haploid yeast populations
-
Paquin C., Adams J. Frequency of fixation of adaptive mutations is higher in evolving diploid than haploid yeast populations. Nature 1983, 302:495-500.
-
(1983)
Nature
, vol.302
, pp. 495-500
-
-
Paquin, C.1
Adams, J.2
-
64
-
-
40949087238
-
Ploidy reduction in Saccharomyces cerevisiae
-
Gerstein A.C., McBride R.M., Otto S.P. Ploidy reduction in Saccharomyces cerevisiae. Biol Lett 2008, 4:91-94.
-
(2008)
Biol Lett
, vol.4
, pp. 91-94
-
-
Gerstein, A.C.1
McBride, R.M.2
Otto, S.P.3
-
65
-
-
69249203618
-
Ploidy and the causes of genomic evolution
-
Gerstein A.C., Otto S.P. Ploidy and the causes of genomic evolution. J Hered 2009, 100:571-581.
-
(2009)
J Hered
, vol.100
, pp. 571-581
-
-
Gerstein, A.C.1
Otto, S.P.2
-
66
-
-
83055173235
-
Cryptic fitness advantage: diploids invade haploid populations despite lacking any apparent advantage as measured by standard fitness assays
-
Gerstein A.C., Otto S.P. Cryptic fitness advantage: diploids invade haploid populations despite lacking any apparent advantage as measured by standard fitness assays. PLoS ONE 2011, 6:e26599.
-
(2011)
PLoS ONE
, vol.6
, pp. e26599
-
-
Gerstein, A.C.1
Otto, S.P.2
-
67
-
-
79951764712
-
Haploids adapt faster than diploids across a range of environments
-
Gerstein A.C., Cleathero L.A., Mandegar M.A., Otto S.P. Haploids adapt faster than diploids across a range of environments. J Evol Biol 2011, 24:531-540.
-
(2011)
J Evol Biol
, vol.24
, pp. 531-540
-
-
Gerstein, A.C.1
Cleathero, L.A.2
Mandegar, M.A.3
Otto, S.P.4
-
68
-
-
84925009217
-
Polyploidy can drive rapid adaptation in yeast
-
Selmecki A.M., Maruvka Y.E., Richmond P.A., Guillet M., Shoresh N., Sorenson A.L., De S., Kishony R., Michor F., Dowell R., et al. Polyploidy can drive rapid adaptation in yeast. Nature 2015, 519:349-352.
-
(2015)
Nature
, vol.519
, pp. 349-352
-
-
Selmecki, A.M.1
Maruvka, Y.E.2
Richmond, P.A.3
Guillet, M.4
Shoresh, N.5
Sorenson, A.L.6
De, S.7
Kishony, R.8
Michor, F.9
Dowell, R.10
-
69
-
-
84871375832
-
Chromosomal duplication is a transient evolutionary solution to stress
-
Yona A.H., Manor Y.S., Herbst R.H., Romano G.H., Mitchell A., Kupiec M., Pilpel Y., Dahan O. Chromosomal duplication is a transient evolutionary solution to stress. Proc Natl Acad Sci U S A 2012, 109:21010-21015.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 21010-21015
-
-
Yona, A.H.1
Manor, Y.S.2
Herbst, R.H.3
Romano, G.H.4
Mitchell, A.5
Kupiec, M.6
Pilpel, Y.7
Dahan, O.8
-
70
-
-
0037058930
-
Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae
-
Dunham M.J., Badrane H., Ferea T., Adams J., Brown P.O., Rosenzweig F., Botstein D. Characteristic genome rearrangements in experimental evolution of Saccharomyces cerevisiae. Proc Natl Acad Sci U S A 2002, 99:16144-16149.
-
(2002)
Proc Natl Acad Sci U S A
, vol.99
, pp. 16144-16149
-
-
Dunham, M.J.1
Badrane, H.2
Ferea, T.3
Adams, J.4
Brown, P.O.5
Rosenzweig, F.6
Botstein, D.7
-
71
-
-
84897008356
-
The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection
-
Payen C., Di Rienzi S.C., Ong G.T., Pogachar J.L., Sanchez J.C., Sunshine A.B., Raghuraman M.K., Brewer B.J., Dunham M.J. The dynamics of diverse segmental amplifications in populations of Saccharomyces cerevisiae adapting to strong selection. G3 2014, 4:399-409.
-
(2014)
G3
, vol.4
, pp. 399-409
-
-
Payen, C.1
Di Rienzi, S.C.2
Ong, G.T.3
Pogachar, J.L.4
Sanchez, J.C.5
Sunshine, A.B.6
Raghuraman, M.K.7
Brewer, B.J.8
Dunham, M.J.9
-
72
-
-
84930668371
-
The fitness consequences of aneuploidy are driven by condition-dependent gene effects
-
Sunshine A.B., Payen C., Ong G.T., Liachko I., Tan K.M., Dunham M.J. The fitness consequences of aneuploidy are driven by condition-dependent gene effects. PLoS Biol 2015, 13:e1002155.
-
(2015)
PLoS Biol
, vol.13
, pp. e1002155
-
-
Sunshine, A.B.1
Payen, C.2
Ong, G.T.3
Liachko, I.4
Tan, K.M.5
Dunham, M.J.6
-
73
-
-
58149166731
-
The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast
-
Gresham D., Desai M.M., Tucker C.M., Jenq H.T., Pai D.A., Ward A., DeSevo C.G., Botstein D., Dunham M.J. The repertoire and dynamics of evolutionary adaptations to controlled nutrient-limited environments in yeast. PLoS Genet 2008, 4:e1000303.
-
(2008)
PLoS Genet
, vol.4
, pp. e1000303
-
-
Gresham, D.1
Desai, M.M.2
Tucker, C.M.3
Jenq, H.T.4
Pai, D.A.5
Ward, A.6
DeSevo, C.G.7
Botstein, D.8
Dunham, M.J.9
-
74
-
-
84893817979
-
Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments
-
Hong J., Gresham D. Molecular specificity, convergence and constraint shape adaptive evolution in nutrient-poor environments. PLoS Genet 2014, 10:e1004041.
-
(2014)
PLoS Genet
, vol.10
, pp. e1004041
-
-
Hong, J.1
Gresham, D.2
-
75
-
-
84875989311
-
Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression
-
Dunn B., Paulish T., Stanbery A., Piotrowski J., Koniges G., Kroll E., Louis E.J., Liti G., Sherlock G., Rosenzweig F. Recurrent rearrangement during adaptive evolution in an interspecific yeast hybrid suggests a model for rapid introgression. PLoS Genet 2013, 9:e1003366.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003366
-
-
Dunn, B.1
Paulish, T.2
Stanbery, A.3
Piotrowski, J.4
Koniges, G.5
Kroll, E.6
Louis, E.J.7
Liti, G.8
Sherlock, G.9
Rosenzweig, F.10
-
76
-
-
84863668598
-
Repeated, selection-driven genome reduction of accessory genes in experimental populations
-
Lee M.-C., Marx C.J. Repeated, selection-driven genome reduction of accessory genes in experimental populations. PLoS Genet 2012, 8:e1002651.
-
(2012)
PLoS Genet
, vol.8
, pp. e1002651
-
-
Lee, M.-C.1
Marx, C.J.2
-
77
-
-
84891351800
-
Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures
-
Lieberman T.D., Flett K.B., Yelin I., Martin T.R., McAdam A.J., Priebe G.P., Kishony R. Genetic variation of a bacterial pathogen within individuals with cystic fibrosis provides a record of selective pressures. Nat Genet 2014, 46:82-87.
-
(2014)
Nat Genet
, vol.46
, pp. 82-87
-
-
Lieberman, T.D.1
Flett, K.B.2
Yelin, I.3
Martin, T.R.4
McAdam, A.J.5
Priebe, G.P.6
Kishony, R.7
-
78
-
-
0032474853
-
Adaptive radiation in a heterogeneous environment
-
Rainey P.B., Travisano M. Adaptive radiation in a heterogeneous environment. Nature 1998, 394:69-72.
-
(1998)
Nature
, vol.394
, pp. 69-72
-
-
Rainey, P.B.1
Travisano, M.2
-
79
-
-
0034104460
-
Long-term experimental evolution in Escherichia coli. VIII. Dynamics of a balanced polymorphism
-
Rozen D.E., Lenski R.E. Long-term experimental evolution in Escherichia coli. VIII. Dynamics of a balanced polymorphism. Am Nat 2000, 155:24-35.
-
(2000)
Am Nat
, vol.155
, pp. 24-35
-
-
Rozen, D.E.1
Lenski, R.E.2
-
80
-
-
1642388599
-
Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli
-
Friesen M.L., Saxer G., Travisano M., Doebeli M. Experimental evidence for sympatric ecological diversification due to frequency-dependent competition in Escherichia coli. Evolution 2004, 58:245-260.
-
(2004)
Evolution
, vol.58
, pp. 245-260
-
-
Friesen, M.L.1
Saxer, G.2
Travisano, M.3
Doebeli, M.4
-
81
-
-
28544452146
-
Adaptive radiation in microbial microcosms
-
MacLean R.C. Adaptive radiation in microbial microcosms. J Evol Biol 2005, 18:1376-1386.
-
(2005)
J Evol Biol
, vol.18
, pp. 1376-1386
-
-
MacLean, R.C.1
-
82
-
-
0023376305
-
Evolution of Escherichia coli during growth in a constant environment
-
Helling R.B., Vargas C.N., Adams J. Evolution of Escherichia coli during growth in a constant environment. Genetics 1987, 116:349-358.
-
(1987)
Genetics
, vol.116
, pp. 349-358
-
-
Helling, R.B.1
Vargas, C.N.2
Adams, J.3
-
83
-
-
57549104704
-
Death and cannibalism in a seasonal environment facilitate bacterial coexistence
-
Rozen D.E., Philippe N., Arjan de Visser J., Lenski R.E., Schneider D. Death and cannibalism in a seasonal environment facilitate bacterial coexistence. Ecol Lett 2009, 12:34-44.
-
(2009)
Ecol Lett
, vol.12
, pp. 34-44
-
-
Rozen, D.E.1
Philippe, N.2
Arjan de Visser, J.3
Lenski, R.E.4
Schneider, D.5
-
84
-
-
0028094645
-
Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli
-
Rosenzweig R.F., Sharp R., Treves D.S., Adams J. Microbial evolution in a simple unstructured environment: genetic differentiation in Escherichia coli. Genetics 1994, 137:903-917.
-
(1994)
Genetics
, vol.137
, pp. 903-917
-
-
Rosenzweig, R.F.1
Sharp, R.2
Treves, D.S.3
Adams, J.4
-
85
-
-
84862196246
-
Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli
-
Le Gac M., Plucain J., Hindré T., Lenski R.E., Schneider D. Ecological and evolutionary dynamics of coexisting lineages during a long-term experiment with Escherichia coli. Proc Natl Acad Sci U S A 2012, 109:9487-9492.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 9487-9492
-
-
Le Gac, M.1
Plucain, J.2
Hindré, T.3
Lenski, R.E.4
Schneider, D.5
-
86
-
-
84924664063
-
Quantitative evolutionary dynamics using high-resolution lineage tracking
-
Levy S.F., Blundell J.R., Venkataram S., Petrov D.A., Fisher D.S., Sherlock G. Quantitative evolutionary dynamics using high-resolution lineage tracking. Nature 2015, 519:181-186.
-
(2015)
Nature
, vol.519
, pp. 181-186
-
-
Levy, S.F.1
Blundell, J.R.2
Venkataram, S.3
Petrov, D.A.4
Fisher, D.S.5
Sherlock, G.6
-
87
-
-
84941668361
-
The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe
-
Farlow A., Long H., Arnoux S., Sung W., Doak T.G., Nordborg M., Lynch M. The spontaneous mutation rate in the fission yeast Schizosaccharomyces pombe. Genetics 2015.
-
(2015)
Genetics
-
-
Farlow, A.1
Long, H.2
Arnoux, S.3
Sung, W.4
Doak, T.G.5
Nordborg, M.6
Lynch, M.7
-
88
-
-
84937043154
-
The rate and molecular spectrum of spontaneous mutations in the GC-rich multichromosome genome of Burkholderia cenocepacia
-
Dillon M.M., Sung W., Lynch M., Cooper V.S. The rate and molecular spectrum of spontaneous mutations in the GC-rich multichromosome genome of Burkholderia cenocepacia. Genetics 2015, 200:935-946.
-
(2015)
Genetics
, vol.200
, pp. 935-946
-
-
Dillon, M.M.1
Sung, W.2
Lynch, M.3
Cooper, V.S.4
-
89
-
-
84878611860
-
Experimental evolution reveals genome-wide spectrum and dynamics of mutations in the rice blast fungus, Magnaporthe oryzae
-
Jeon J., Choi J., Lee G.-W., Dean R.A., Lee Y.-H. Experimental evolution reveals genome-wide spectrum and dynamics of mutations in the rice blast fungus, Magnaporthe oryzae. PLoS ONE 2013, 8:e65416.
-
(2013)
PLoS ONE
, vol.8
, pp. e65416
-
-
Jeon, J.1
Choi, J.2
Lee, G.-W.3
Dean, R.A.4
Lee, Y.-H.5
-
90
-
-
84876838057
-
Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology
-
Carroll S.M., Marx C.J. Evolution after introduction of a novel metabolic pathway consistently leads to restoration of wild-type physiology. PLoS Genet 2013, 9:e1003427.
-
(2013)
PLoS Genet
, vol.9
, pp. e1003427
-
-
Carroll, S.M.1
Marx, C.J.2
|