-
1
-
-
33645112661
-
Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations
-
Barrett R D H, MacLean RC, Bell G. 2006. Mutations of intermediate effect are responsible for adaptation in evolving Pseudomonas fluorescens populations. Biol Lett. 2:236-238.
-
(2006)
Biol Lett.
, vol.2
, pp. 236-238
-
-
Barrett, R.D.H.1
MacLean, R.C.2
Bell, G.3
-
2
-
-
77952796777
-
Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects
-
Barrick JE, Kauth MR, Strelioff CC, Lenski RE. 2010. Escherichia coli rpoB mutants have increased evolvability in proportion to their fitness defects. Mol Biol Evol. 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
-
3
-
-
81255211330
-
Cost of adaptation and fitness effects of beneficial mutations in Pseudomonas fluorescens
-
Bataillon T, Zhang T, Kassen R. 2011. Cost of adaptation and fitness effects of beneficial mutations in Pseudomonas fluorescens. Genetics 189:939-949.
-
(2011)
Genetics
, vol.189
, pp. 939-949
-
-
Bataillon, T.1
Zhang, T.2
Kassen, R.3
-
4
-
-
0036964474
-
Approximate Bayesian computation in population genetics
-
Beaumont MA, Zhang W, Balding DJ. 2002. Approximate Bayesian computation in population genetics. Genetics 162:2025-2035.
-
(2002)
Genetics
, vol.162
, pp. 2025-2035
-
-
Beaumont, M.A.1
Zhang, W.2
Balding, D.J.3
-
5
-
-
33751106943
-
Fitness effects of beneficial mutations: The mutational landscape model in experimental evolution
-
Betancourt AJ, Bollback JP. 2006. Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution. Curr Opin Genet Dev. 16:618-623.
-
(2006)
Curr Opin Genet Dev.
, vol.16
, pp. 618-623
-
-
Betancourt, A.J.1
Bollback, J.P.2
-
6
-
-
33746237567
-
Genomic insights into positive selection
-
Biswas S, Akey JM. 2006. Genomic insights into positive selection. Trends Genet. 22:437-446.
-
(2006)
Trends Genet.
, vol.22
, pp. 437-446
-
-
Biswas, S.1
Akey, J.M.2
-
7
-
-
52049123852
-
Estimation of 2Nes from temporal allele frequency data
-
Bollback JP, York TL, Nielsen R. 2008. Estimation of 2Nes from temporal allele frequency data. Genetics 179:497-502.
-
(2008)
Genetics
, vol.179
, pp. 497-502
-
-
Bollback, J.P.1
York, T.L.2
Nielsen, R.3
-
8
-
-
77957346489
-
Genome-wide analysis of a long-term evolution experiment with Drosophila
-
Burke MK, et al. 2010. Genome-wide analysis of a long-term evolution experiment with Drosophila. Nature 467:587-590.
-
(2010)
Nature
, vol.467
, pp. 587-590
-
-
Burke, M.K.1
-
9
-
-
0027305597
-
The effect of deleterious mutations on neutral molecular variation
-
Charlesworth B, Morgan MT, Charlesworth D. 1993. The effect of deleterious mutations on neutral molecular variation. Genetics 134:1289-1303.
-
(1993)
Genetics
, vol.134
, pp. 1289-1303
-
-
Charlesworth, B.1
Morgan, M.T.2
Charlesworth, D.3
-
11
-
-
84861153207
-
ABC: An R package for approximate Bayesian computation (ABC)
-
Csilléry K, François O, Blum M G B. 2012. ABC: an R package for approximate Bayesian computation (ABC). Methods Ecol Evol. 3:475-479.
-
(2012)
Methods Ecol Evol.
, vol.3
, pp. 475-479
-
-
Csilléry, K.1
François, O.2
Blum, M.G.B.3
-
12
-
-
77955146078
-
Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
-
Cutter AD, Choi JY. 2010. Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae. Genome Res. 20:1103-1111.
-
(2010)
Genome Res.
, vol.20
, pp. 1103-1111
-
-
Cutter, A.D.1
Choi, J.Y.2
-
13
-
-
84864089075
-
Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes
-
Denver DR, et al. 2012. Variation in base-substitution mutation in experimental and natural lineages of Caenorhabditis nematodes. Genome Biol Evol. 4:513-522.
-
(2012)
Genome Biol Evol.
, vol.4
, pp. 513-522
-
-
Denver, D.R.1
-
14
-
-
33847256353
-
The speed of evolution and maintenance of variation in asexual populations
-
Desai MM, Fisher DS, Murray AW. 2007. The speed of evolution and maintenance of variation in asexual populations. Curr Biol. 17:385-394.
-
(2007)
Curr Biol.
, vol.17
, pp. 385-394
-
-
Desai, M.M.1
Fisher, D.S.2
Murray, A.W.3
-
17
-
-
0038441327
-
Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation
-
Elena SF, Lenski RE. 2003. Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat Rev Genet. 4:457-469.
-
(2003)
Nat Rev Genet.
, vol.4
, pp. 457-469
-
-
Elena, S.F.1
Lenski, R.E.2
-
18
-
-
77649215825
-
Human and non-human primate genomes share hotspots of positive selection
-
Enard D, Depaulis F, Roest Crollius H. 2010. Human and non-human primate genomes share hotspots of positive selection. PLoS Genet. 6:e1000840.
-
(2010)
PLoS Genet.
, vol.6
-
-
Enard, D.1
Depaulis, F.2
Roest Crollius, H.3
-
19
-
-
79960845135
-
Fitness recovery and compensatory evolution in natural mutant lines of C elegans
-
Estes S, Phillips PC, Denver DR. 2011. Fitness recovery and compensatory evolution in natural mutant lines of C. elegans. Evolution 65:2335-2344.
-
(2011)
Evolution
, vol.65
, pp. 2335-2344
-
-
Estes, S.1
Phillips, P.C.2
Denver, D.R.3
-
20
-
-
34447546660
-
The distribution of fitness effects of new mutations
-
Eyre-Walker A, Keightley PD. 2007. The distribution of fitness effects of new mutations. Nat Rev Genet. 8:610-618.
-
(2007)
Nat Rev Genet.
, vol.8
, pp. 610-618
-
-
Eyre-Walker, A.1
Keightley, P.D.2
-
22
-
-
2542583245
-
The fate of competing beneficial mutations in an asexual population
-
Gerrish PJ, Lenski RE. 1998. The fate of competing beneficial mutations in an asexual population. Genetica 102-103:127-144.
-
(1998)
Genetica
, vol.102-103
, pp. 127-144
-
-
Gerrish, P.J.1
Lenski, R.E.2
-
23
-
-
84859448396
-
Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations
-
Good BH, et al. 2012. Distribution of fixed beneficial mutations and the rate of adaptation in asexual populations. Proc Natl Acad Sci U S A. 109:4950-4955.
-
(2012)
Proc Natl Acad Sci U S A
, vol.109
, pp. 4950-4955
-
-
Good, B.H.1
-
25
-
-
76749155514
-
A composite of multiple signals distinguishes causal variants in regions of positive selection
-
Grossman SR, et al. 2010. A composite of multiple signals distinguishes causal variants in regions of positive selection. Science 327:883-886.
-
(2010)
Science
, vol.327
, pp. 883-886
-
-
Grossman, S.R.1
-
26
-
-
84874069538
-
Identifying recent adaptations in large-scale genomic data
-
Grossman SR, et al. 2013. Identifying recent adaptations in large-scale genomic data. Cell 152:703-713.
-
(2013)
Cell
, vol.152
, pp. 703-713
-
-
Grossman, S.R.1
-
27
-
-
55349135251
-
Detecting the genetic signature of natural selection in human populations: Models, methods, and data
-
Hancock AM, Di Rienzo A. 2008. Detecting the genetic signature of natural selection in human populations: models, methods, and data. Annu Rev Anthropol. 37:197-217.
-
(2008)
Annu Rev Anthropol.
, vol.37
, pp. 197-217
-
-
Hancock, A.M.1
Di Rienzo, A.2
-
28
-
-
33645076253
-
An equivalence principle for the incorporation of favorable mutations in asexual populations
-
Hegreness M, Shoresh N, Hartl D, Kishony R. 2006. An equivalence principle for the incorporation of favorable mutations in asexual populations. Science 311:1615-1617.
-
(2006)
Science
, vol.311
, pp. 1615-1617
-
-
Hegreness, M.1
Shoresh, N.2
Hartl, D.3
Kishony, R.4
-
29
-
-
79956357160
-
From the cover: Experimental illumination of a fitness landscape
-
Hietpas RT, Jensen JD, Bolon D N A. 2011. From the cover: experimental illumination of a fitness landscape. Proc Natl Acad Sci U S A. 108:7896-7901.
-
(2011)
Proc Natl Acad Sci U S A
, vol.108
, pp. 7896-7901
-
-
Hietpas, R.T.1
Jensen, J.D.2
Bolon, D.N.A.3
-
30
-
-
81255146514
-
Distinguishing driver and passenger mutations in an evolutionary history categorized by interference
-
Illingworth CJ, Mustonen V. 2011. Distinguishing driver and passenger mutations in an evolutionary history categorized by interference. Genetics 189:989-1000.
-
(2011)
Genetics
, vol.189
, pp. 989-1000
-
-
Illingworth, C.J.1
Mustonen, V.2
-
31
-
-
84859086320
-
A method to infer positive selection from marker dynamics in an asexual population
-
Illingworth CJ, Mustonen V. 2012. A method to infer positive selection from marker dynamics in an asexual population. Bioinformatics 28:831-837.
-
(2012)
Bioinformatics
, vol.28
, pp. 831-837
-
-
Illingworth, C.J.1
Mustonen, V.2
-
32
-
-
0035970061
-
Fitness effects of advantageous mutations in evolving Escherichia coli populations
-
Imhof M, Schlotterer C. 2001. Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci U S A. 98:1113-1117.
-
(2001)
Proc Natl Acad Sci U S A
, vol.98
, pp. 1113-1117
-
-
Imhof, M.1
Schlotterer, C.2
-
33
-
-
52949128377
-
An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila
-
Jensen JD, Thornton KR, Andolfatto P. 2008. An approximate Bayesian estimator suggests strong, recurrent selective sweeps in Drosophila. PLoS Genet. 4:e1000198.
-
(2008)
PLoS Genet.
, vol.4
-
-
Jensen, J.D.1
Thornton, K.R.2
Andolfatto, P.3
-
35
-
-
33645394597
-
Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria
-
Kassen R, Bataillon T. 2006. Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria. Nat Genet. 38:484-488.
-
(2006)
Nat Genet.
, vol.38
, pp. 484-488
-
-
Kassen, R.1
Bataillon, T.2
-
36
-
-
0031769320
-
Inference of genome-wide mutation rates and distributions of mutation effects for fitness traits: A simulation study
-
Keightley PD. 1998. Inference of genome-wide mutation rates and distributions of mutation effects for fitness traits: a simulation study. Genetics 150:1283-1293.
-
(1998)
Genetics
, vol.150
, pp. 1283-1293
-
-
Keightley, P.D.1
-
37
-
-
77951600170
-
What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?
-
Keightley PD, Eyre-Walker A. 2010. What can we learn about the distribution of fitness effects of new mutations from DNA sequence data? Philos Trans R Soc Lond B Biol Sci. 365:1187-1193.
-
(2010)
Philos Trans R Soc Lond B Biol Sci.
, vol.365
, pp. 1187-1193
-
-
Keightley, P.D.1
Eyre-Walker, A.2
-
38
-
-
0029931416
-
Estimate of the genomic mutation rate deleterious to overall fitness in E coli
-
Kibota TT, Lynch M. 1996. Estimate of the genomic mutation rate deleterious to overall fitness in E. coli. Nature 381:694-696.
-
(1996)
Nature
, vol.381
, pp. 694-696
-
-
Kibota, T.T.1
Lynch, M.2
-
39
-
-
0016087667
-
On some principles governing molecular evolution
-
Kimura M, Ohta T. 1974. On some principles governing molecular evolution. Proc Natl Acad Sci U S A. 71:2848-2852.
-
(1974)
Proc Natl Acad Sci U S A
, vol.71
, pp. 2848-2852
-
-
Kimura, M.1
Ohta, T.2
-
40
-
-
79955590028
-
Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape
-
Kvitek DJ, Sherlock G. 2011. Reciprocal sign epistasis between frequently experimentally evolved adaptive mutations causes a rugged fitness landscape. PLoS Genet. 7:e1002056.
-
(2011)
PLoS Genet.
, vol.7
-
-
Kvitek, D.J.1
Sherlock, G.2
-
41
-
-
79960137718
-
Genetic variation and the fate of beneficial mutations in asexual populations
-
Lang GI, Botstein D, Desai MM. 2011. Genetic variation and the fate of beneficial mutations in asexual populations. Genetics 188:647-661.
-
(2011)
Genetics
, vol.188
, pp. 647-661
-
-
Lang, G.I.1
Botstein, D.2
Desai, M.M.3
-
42
-
-
36348968947
-
The evolution of contact-dependent inhibition in non-growing populations of Escherichia coli
-
Lemonnier M, et al. 2008. The evolution of contact-dependent inhibition in non-growing populations of Escherichia coli. Proc Biol Sci. 275:3-10.
-
(2008)
Proc Biol Sci.
, vol.275
, pp. 3-10
-
-
Lemonnier, M.1
-
43
-
-
78149293610
-
Mutational robustness of ribosomal protein genes
-
Lind PA, Berg OG, Andersson DI. 2010. Mutational robustness of ribosomal protein genes. Science 330:825-827.
-
(2010)
Science
, vol.330
, pp. 825-827
-
-
Lind, P.A.1
Berg, O.G.2
Andersson, D.I.3
-
44
-
-
62149084484
-
The distribution of fitness effects of beneficial mutations in Pseudomonas aeruginosa
-
MacLean RC, Buckling A. 2009. The distribution of fitness effects of beneficial mutations in Pseudomonas aeruginosa. PLoS Genet. 5:e1000406.
-
(2009)
PLoS Genet.
, vol.5
-
-
MacLean, R.C.1
Buckling, A.2
-
45
-
-
84867176367
-
Estimating allele age and selection coefficient from time-serial data
-
Malaspinas AS, Malaspinas O, Evans SN, Slatkin M. 2012. Estimating allele age and selection coefficient from time-serial data. Genetics 192:599-607.
-
(2012)
Genetics
, vol.192
, pp. 599-607
-
-
Malaspinas, A.S.1
Malaspinas, O.2
Evans, S.N.3
Slatkin, M.4
-
46
-
-
33846886349
-
The fitness effect of mutations across environments: A survey in light of fitness landscape models
-
Martin G, Lenormand T. 2006. The fitness effect of mutations across environments: a survey in light of fitness landscape models. Evolution 60:2413-2427.
-
(2006)
Evolution
, vol.60
, pp. 2413-2427
-
-
Martin, G.1
Lenormand, T.2
-
47
-
-
84876432800
-
Estimating selection coefficients in spatially structured populations from time series data of allele frequencies
-
Mathieson I, McVean G. 2013. Estimating selection coefficients in spatially structured populations from time series data of allele frequencies. Genetics 193:973-984.
-
(2013)
Genetics
, vol.193
, pp. 973-984
-
-
Mathieson, I.1
McVean, G.2
-
48
-
-
0016220238
-
The hitch-hiking effect of a favourable gene
-
Maynard-Smith J, Haigh J. 1974. The hitch-hiking effect of a favourable gene. Genet Res. 23:23-35.
-
(1974)
Genet Res.
, vol.23
, pp. 23-35
-
-
Maynard-Smith, J.1
Haigh, J.2
-
49
-
-
79551470995
-
The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens
-
Mcdonald MJ, Cooper TF, Beaumont H J E, Rainey PB. 2011. The distribution of fitness effects of new beneficial mutations in Pseudomonas fluorescens. Biol Lett. 7:98-100.
-
(2011)
Biol Lett.
, vol.7
, pp. 98-100
-
-
Mcdonald, M.J.1
Cooper, T.F.2
Beaumont, H.J.E.3
Rainey, P.B.4
-
50
-
-
29444452921
-
Molecular signatures of natural selection
-
Nielsen R. 2005. Molecular signatures of natural selection. Annu Rev Genet. 39:197-218.
-
(2005)
Annu Rev Genet.
, vol.39
, pp. 197-218
-
-
Nielsen, R.1
-
51
-
-
84867574655
-
Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles
-
Orozcoter Wengel P, et al. 2012. Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol. 21:4931-4941.
-
(2012)
Mol Ecol.
, vol.21
, pp. 4931-4941
-
-
Orozcoter Wengel, P.1
-
52
-
-
77951584625
-
The population genetics of beneficial mutations
-
Orr HA. 2010. The population genetics of beneficial mutations. Philos Trans R Soc Lond B Biol Sci. 365:1195-1201.
-
(2010)
Philos Trans R Soc Lond B Biol Sci.
, vol.365
, pp. 1195-1201
-
-
Orr, H.A.1
-
53
-
-
34547924819
-
Adaptive mutations in bacteria: High rate and small effects
-
Perfeito L, Fernandes L, Mota C, Gordo I. 2007. Adaptive mutations in bacteria: high rate and small effects. Science 317:813-815.
-
(2007)
Science
, vol.317
, pp. 813-815
-
-
Perfeito, L.1
Fernandes, L.2
Mota, C.3
Gordo, I.4
-
54
-
-
54349092997
-
Beneficial fitness effects are not exponential for two viruses
-
Rokyta DR, et al. 2008. Beneficial fitness effects are not exponential for two viruses. J Mol Evol. 67:368-376.
-
(2008)
J Mol Evol.
, vol.67
, pp. 368-376
-
-
Rokyta, D.R.1
-
55
-
-
0037172667
-
Fitness effects of fixed beneficial mutations in microbial populations
-
Rozen DE, De Visser J A G M, Gerrish PJ. 2002. Fitness effects of fixed beneficial mutations in microbial populations. Curr Biol. 12:1040-1045.
-
(2002)
Curr Biol.
, vol.12
, pp. 1040-1045
-
-
Rozen, D.E.1
De Visser, J.A.G.M.2
Gerrish, P.J.3
-
56
-
-
2942565781
-
The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
-
Sanjuán R, Moya A, Elena SF. 2004. The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc Natl Acad Sci U S A. 101:8396-8401.
-
(2004)
Proc Natl Acad Sci U S A
, vol.101
, pp. 8396-8401
-
-
Sanjuán, R.1
Moya, A.2
Elena, S.F.3
-
57
-
-
34249848425
-
Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila
-
Sawyer SA, Parsch J, Zhang Z, Hartl DL. 2007. Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc Natl Acad Sci U S A. 104:6504-6510.
-
(2007)
Proc Natl Acad Sci U S A
, vol.104
, pp. 6504-6510
-
-
Sawyer, S.A.1
Parsch, J.2
Zhang, Z.3
Hartl, D.L.4
-
58
-
-
83455176994
-
A method for inferring the rate of occurrence and fitness effects of advantageous mutations
-
Schneider A, Charlesworth B, Eyre-Walker A, Keightley PD. 2011. A method for inferring the rate of occurrence and fitness effects of advantageous mutations. Genetics 189:1427-1437.
-
(2011)
Genetics
, vol.189
, pp. 1427-1437
-
-
Schneider, A.1
Charlesworth, B.2
Eyre-Walker, A.3
Keightley, P.D.4
-
60
-
-
84875947121
-
On detecting selective sweeps using single genomes
-
Sinha P, et al. 2011. On detecting selective sweeps using single genomes. Front Genet. 2:1-5.
-
(2011)
Front Genet.
, vol.2
, pp. 1-5
-
-
Sinha, P.1
-
61
-
-
84862840054
-
Cost of antibiotic resistance and the geometry of adaptation
-
Sousa A, Magalhães S, Gordo I. 2012. Cost of antibiotic resistance and the geometry of adaptation. Mol Biol Evol. 29:1417-1428.
-
(2012)
Mol Biol Evol.
, vol.29
, pp. 1417-1428
-
-
Sousa, A.1
Magalhães, S.2
Gordo, I.3
-
62
-
-
80052341903
-
Frequent beneficial mutations during singlecolony serial transfer of Streptococcus pneumoniae
-
Stevens KE, Sebert ME. 2011. Frequent beneficial mutations during singlecolony serial transfer of Streptococcus pneumoniae. PLoS Genet. 7:e1002232.
-
(2011)
PLoS Genet.
, vol.7
-
-
Stevens, K.E.1
Sebert, M.E.2
-
64
-
-
77951595254
-
Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli
-
Trindade S, Perfeito L, Gordo I. 2010. Rate and effects of spontaneous mutations that affect fitness in mutator Escherichia coli. Philos Trans R Soc Lond B Biol Sci. 365:1177-1186.
-
(2010)
Philos Trans R Soc Lond B Biol Sci.
, vol.365
, pp. 1177-1186
-
-
Trindade, S.1
Perfeito, L.2
Gordo, I.3
-
65
-
-
79952793415
-
Second-order selection for evolvability in a large Escherichia coli population
-
Woods RJ, et al. 2011. Second-order selection for evolvability in a large Escherichia coli population. Science 331:1433-1436.
-
(2011)
Science
, vol.331
, pp. 1433-1436
-
-
Woods, R.J.1
-
66
-
-
84856514801
-
Estimation of the rate and effect of new beneficial mutations in asexual populations
-
Zhang W, et al. 2012. Estimation of the rate and effect of new beneficial mutations in asexual populations. Theor Popul Biol. 81:168-178.
-
(2012)
Theor Popul Biol.
, vol.81
, pp. 168-178
-
-
Zhang, W.1
|