-
2
-
-
0016355478
-
A new look at statistical model identification
-
AKAIKE, H., 1974 A new look at statistical model identification. IEEE Trans. Automat. Control 19: 716-723.
-
(1974)
IEEE Trans. Automat. Control
, vol.19
, pp. 716-723
-
-
Akaike, H.1
-
3
-
-
0029985179
-
Molecular evolution between Drosophila melanogaster and D. simulans: Reduced codon bias, faster rates of amino acid substitution, and large proteins in D. melanogaster
-
AKASHI, H., 1996 Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and large proteins in D. melanogaster. Genetics 144: 1297-1307.
-
(1996)
Genetics
, vol.144
, pp. 1297-1307
-
-
Akashi, H.1
-
4
-
-
0030903283
-
Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila
-
AKASHI, H., and S. W. SCHAEFFER, 1997 Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics 146: 295-307.
-
(1997)
Genetics
, vol.146
, pp. 295-307
-
-
Akashi, H.1
Schaeffer, S.W.2
-
5
-
-
0035107550
-
Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans
-
ANDOLFATTO, P., 2001 Contrasting patterns of X-linked and autosomal nucleotide variation in Drosophila melanogaster and Drosophila simulans. Mol. Biol. Evol. 18: 279-290.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 279-290
-
-
Andolfatto, P.1
-
6
-
-
13944275268
-
Patterns of selection on synonymous and nonsynonymous variatns in Drosophila miranda
-
BARTOLOMÉ, C., X. MASIDE, S. YI, A. L. GRANT and B. CHARLESWORTH, 2005 Patterns of selection on synonymous and nonsynonymous variatns in Drosophila miranda. Genetics 169: 1495-1507.
-
(2005)
Genetics
, vol.169
, pp. 1495-1507
-
-
Bartolomé, C.1
Maside, X.2
Yi, S.3
Grant, A.L.4
Charlesworth, B.5
-
7
-
-
0034938613
-
The frequency distribution of nucleotide variation in Drosophila simulans
-
BEGUN, D. J., 2001 The frequency distribution of nucleotide variation in Drosophila simulans. Mol. Biol. Evol. 18: 1343-1352.
-
(2001)
Mol. Biol. Evol.
, vol.18
, pp. 1343-1352
-
-
Begun, D.J.1
-
8
-
-
0036149744
-
Protein variation in Drosophila simulans, and comparison of genes from centromeric versus noncentromeric regions of chromosome 3
-
BEGUN, D. J., 2002 Protein variation in Drosophila simulans, and comparison of genes from centromeric versus noncentromeric regions of chromosome 3. Mol. Biol. Evol. 19: 201-203.
-
(2002)
Mol. Biol. Evol.
, vol.19
, pp. 201-203
-
-
Begun, D.J.1
-
9
-
-
0034705169
-
Reduced X-linked nucleotide polymorphism in Drosophila simulans
-
USA
-
BEGUN, D. J., and P. WHITLEY, 2000 Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc. Natl. Acad. Sci. USA 97: 5960-5965.
-
(2000)
Proc. Natl. Acad. Sci.
, vol.97
, pp. 5960-5965
-
-
Begun, D.J.1
Whitley, P.2
-
10
-
-
3042544623
-
The genomic rate of adaptive amino acid substitution in Drosophila
-
BIERNE, N., and A. EYRE-WALKER, 2004 The genomic rate of adaptive amino acid substitution in Drosophila. Mol. Biol. Evol. 21: 1350-1360.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1350-1360
-
-
Bierne, N.1
Eyre-Walker, A.2
-
11
-
-
0025941139
-
The selection-mutation-drift theory of synonymous codon usage
-
BULMER, M., 1991 The selection-mutation-drift theory of synonymous codon usage. Genetics 129: 897-907.
-
(1991)
Genetics
, vol.129
, pp. 897-907
-
-
Bulmer, M.1
-
12
-
-
0035691964
-
Directional selection and the site-frequency spectrum
-
BUSTAMANTE, C. D., J. WAKELEY, S. A. SAWYER and D. L. HARTL, 2001 Directional selection and the site-frequency spectrum. Genetics 159: 1779-1788.
-
(2001)
Genetics
, vol.159
, pp. 1779-1788
-
-
Bustamante, C.D.1
Wakeley, J.2
Sawyer, S.A.3
Hartl, D.L.4
-
13
-
-
0037041421
-
The cost of inbreeding in Arabidopsis
-
BUSTAMANTE, C. D., R. NIELSEN, S. A. SAWYER, K. M. OLSEN, M. D. PURUGGANAN et al., 2002 The cost of inbreeding in Arabidopsis. Nature 416: 531-534.
-
(2002)
Nature
, vol.416
, pp. 531-534
-
-
Bustamante, C.D.1
Nielsen, R.2
Sawyer, S.A.3
Olsen, K.M.4
Purugganan, M.D.5
-
14
-
-
0028222304
-
The effect of background selection against deleterious mutations on weakly selected, linked variants
-
CHARLESWORTH, B., 1994 The effect of background selection against deleterious mutations on weakly selected, linked variants. Genet. Res. 63: 213-227.
-
(1994)
Genet. Res.
, vol.63
, pp. 213-227
-
-
Charlesworth, B.1
-
15
-
-
0028863202
-
The pattern of neutral molecular variation under the background selection model
-
CHARLESWORTH, D., B. CHARLESWORTH and M. T. MORGAN, 1995 The pattern of neutral molecular variation under the background selection model. Genetics 141: 1619-1632.
-
(1995)
Genetics
, vol.141
, pp. 1619-1632
-
-
Charlesworth, D.1
Charlesworth, B.2
Morgan, M.T.3
-
17
-
-
0036961560
-
Changing effective population size and the McDonald-Kreitman test
-
EYRE-WALKER, A., 2002 Changing effective population size and the McDonald-Kreitman test. Genetics 162: 2017-2024.
-
(2002)
Genetics
, vol.162
, pp. 2017-2024
-
-
Eyre-Walker, A.1
-
18
-
-
0034924997
-
Positive and negative selection on the human genome
-
FAY, J. C., G. J. WYCOFF and C.-I. WU, 2001 Positive and negative selection on the human genome. Genetics 158: 1227-1234.
-
(2001)
Genetics
, vol.158
, pp. 1227-1234
-
-
Fay, J.C.1
Wycoff, G.J.2
Wu, C.-I.3
-
19
-
-
0037186608
-
Testing the neutral theory of molecular evolution with genomic data from Drosophila
-
FAY, J. C., G. J. WYCOFF and C.-I. WU, 2002 Testing the neutral theory of molecular evolution with genomic data from Drosophila. Nature 415: 1024-1026.
-
(2002)
Nature
, vol.415
, pp. 1024-1026
-
-
Fay, J.C.1
Wycoff, G.J.2
Wu, C.-I.3
-
20
-
-
0037864375
-
-
Network Theory, Bristol, UK
-
GALASSI, M., J. DAVIES, J. THEILER, B. GOUGH, G. JUNGMAN et al., 2004 GNU Scientific Library Reference Manual: Ed. 1.6, for GSL Version 1.6. Network Theory, Bristol, UK.
-
(2004)
GNU Scientific Library Reference Manual: Ed. 1.6, for GSL Version 1.6
-
-
Galassi, M.1
Davies, J.2
Theiler, J.3
Gough, B.4
Jungman, G.5
-
21
-
-
0003533590
-
The Causes of Molecular Evolution
-
Oxford University Press, Oxford
-
GILLESPIE, J. H., 1991 The Causes of Molecular Evolution (Oxford Series in Ecology and Evolution). Oxford University Press, Oxford.
-
(1991)
Oxford Series in Ecology and Evolution
-
-
Gillespie, J.H.1
-
22
-
-
0028943546
-
On Ohta's hypothesis: Most amino acid substitutions are deleterious
-
GILLESPIE, J. H., 1995 On Ohta's hypothesis: most amino acid substitutions are deleterious. J. Mol. Evol. 40: 64-69.
-
(1995)
J. Mol. Evol.
, vol.40
, pp. 64-69
-
-
Gillespie, J.H.1
-
23
-
-
0035678847
-
Is the population size of a species relevant to its evolution?
-
GILLESPIE, J. H., 2001 Is the population size of a species relevant to its evolution? Evolution 55: 2161-2169.
-
(2001)
Evolution
, vol.55
, pp. 2161-2169
-
-
Gillespie, J.H.1
-
24
-
-
0028168856
-
A codon based model of nucleotide substitution for protein-coding DNA sequences
-
GOLDMAN, N., and Z. YANG, 1994 A codon based model of nucleotide substitution for protein-coding DNA sequences. Mol. Biol. Evol. 11: 725-736.
-
(1994)
Mol. Biol. Evol.
, vol.11
, pp. 725-736
-
-
Goldman, N.1
Yang, Z.2
-
25
-
-
1642392109
-
Effect of breeding structure on population genetic parameters in Drosophila
-
GRAVOT, E., M. HUET and M. VEUILLE, 2004 Effect of breeding structure on population genetic parameters in Drosophila. Genetics 166: 779-788.
-
(2004)
Genetics
, vol.166
, pp. 779-788
-
-
Gravot, E.1
Huet, M.2
Veuille, M.3
-
26
-
-
0032848722
-
Population structure among African and derived populations of Drosophila simulans: Evidence for ancient subdivision and recent admixture
-
HAMBLIN, M. T., and M. VEUILLE, 1999 Population structure among African and derived populations of Drosophila simulans: evidence for ancient subdivision and recent admixture. Genetics 153: 305-317.
-
(1999)
Genetics
, vol.153
, pp. 305-317
-
-
Hamblin, M.T.1
Veuille, M.2
-
27
-
-
31444442779
-
Molecular clocks: When times are a-changin'
-
HO, S. Y. W., and G. LARSON, 2006 Molecular clocks: when times are a-changin'. Trends Ecol. Evol. 22: 79-83.
-
(2006)
Trends Ecol. Evol.
, vol.22
, pp. 79-83
-
-
Ho, S.Y.W.1
Larson, G.2
-
28
-
-
0037379673
-
Phylogenetic estimation: Traditional and Bayesian approaches
-
HOLDER, M., and P. O. LEWIS, 2003 Phylogenetic estimation: traditional and Bayesian approaches. Nat. Rev. Genet. 4: 275-284.
-
(2003)
Nat. Rev. Genet.
, vol.4
, pp. 275-284
-
-
Holder, M.1
Lewis, P.O.2
-
29
-
-
70349119250
-
Regression and time series model selection in small samples
-
HURVICH, C. M., and C.-L. TSAI, 1989 Regression and time series model selection in small samples. Biometrika 76: 297-307.
-
(1989)
Biometrika
, vol.76
, pp. 297-307
-
-
Hurvich, C.M.1
Tsai, C.-L.2
-
31
-
-
3142695506
-
Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex
-
KERN, A. D., C. D. JONES and D. J. BEGUN, 2004 Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics 167: 725-735.
-
(2004)
Genetics
, vol.167
, pp. 725-735
-
-
Kern, A.D.1
Jones, C.D.2
Begun, D.J.3
-
32
-
-
0000896629
-
Some problems of stochastic processes in genetics
-
KIMURA, M., 1957 Some problems of stochastic processes in genetics. Ann. Math. Stat. 28: 882-901.
-
(1957)
Ann. Math. Stat.
, vol.28
, pp. 882-901
-
-
Kimura, M.1
-
33
-
-
0037069428
-
Dobzhansky-Muller incompatibilities in protein evolution
-
USA
-
KONDRASHOV, A., S. SUNYAEV and F. KONDRASHOV, 2002 Dobzhansky-Muller incompatibilities in protein evolution. Proc. Natl. Acad. Sci. USA 99: 14878-14883.
-
(2002)
Proc. Natl. Acad. Sci.
, vol.99
, pp. 14878-14883
-
-
Kondrashov, A.1
Sunyaev, S.2
Kondrashov, F.3
-
34
-
-
0029200909
-
Molecular evidence for natural selection
-
KREITMAN, M., and H. AKASHI, 1995 Molecular evidence for natural selection. Annu. Rev. Ecol. Syst. 26: 403-422.
-
(1995)
Annu. Rev. Ecol. Syst.
, vol.26
, pp. 403-422
-
-
Kreitman, M.1
Akashi, H.2
-
35
-
-
8744255562
-
AIC and BIC: Comparisons of assumptions and performance
-
KUHA, J., 2004 AIC and BIC: comparisons of assumptions and performance. Sociol. Methods Res. 33: 188-229.
-
(2004)
Sociol. Methods Res.
, vol.33
, pp. 188-229
-
-
Kuha, J.1
-
36
-
-
0000792280
-
Historical biogeography of the Drosophila melanogaster species subgroup
-
LACHAISE, D., M.-L. CARIOU, J. R. DAVID, F. LEMEUNIER, L. TSACAS et al., 1988 Historical biogeography of the Drosophila melanogaster species subgroup. Evol. Biol. 22: 159-225.
-
(1988)
Evol. Biol.
, vol.22
, pp. 159-225
-
-
Lachaise, D.1
Cariou, M.-L.2
David, J.R.3
Lemeunier, F.4
Tsacas, L.5
-
37
-
-
0033178244
-
Paleo-demography of the Drosophila melanogaster subgroup: Application of the maximum likelihood method
-
LI, Y. J., Y. SATTA and N. TAKAHATA, 1999 Paleo-demography of the Drosophila melanogaster subgroup: application of the maximum likelihood method. Genes Genet. Syst. 74: 117-127.
-
(1999)
Genes Genet. Syst.
, vol.74
, pp. 117-127
-
-
Li, Y.J.1
Satta, Y.2
Takahata, N.3
-
39
-
-
0026428610
-
Adaptive evolution at the Adh locus in Drosophila
-
MCDONALD, J. H., and M. KREITMAN, 1991 Adaptive evolution at the Adh locus in Drosophila. Nature 351: 652-654.
-
(1991)
Nature
, vol.351
, pp. 652-654
-
-
McDonald, J.H.1
Kreitman, M.2
-
40
-
-
0035157374
-
Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila
-
MCVEAN, G., and J. VIEIRA, 2001 Inferring parameters of mutation, selection and demography from patterns of synonymous site evolution in Drosophila. Genetics 157: 245-257.
-
(2001)
Genetics
, vol.157
, pp. 245-257
-
-
McVean, G.1
Vieira, J.2
-
41
-
-
0027020232
-
The nearly neutral theory of molecular evolution
-
OHTA, T., 1992 The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23: 263-286.
-
(1992)
Annu. Rev. Ecol. Syst.
, vol.23
, pp. 263-286
-
-
Ohta, T.1
-
42
-
-
0041836283
-
Estimating the distribution of fitness effects from DNA sequence data: Implications for the molecular clock
-
USA
-
PIGANEAU, G., and A. EYRE-WALKER, 2003 Estimating the distribution of fitness effects from DNA sequence data: implications for the molecular clock. Proc. Natl. Acad. Sci. USA 100: 10335-10340.
-
(2003)
Proc. Natl. Acad. Sci.
, vol.100
, pp. 10335-10340
-
-
Piganeau, G.1
Eyre-Walker, A.2
-
43
-
-
0035527410
-
Selecting the best fit model of nucleotide substitution
-
POSADA, D., and K. A. CRANDALL, 2001 Selecting the best fit model of nucleotide substitution. Syst. Biol. 50: 580-601.
-
(2001)
Syst. Biol.
, vol.50
, pp. 580-601
-
-
Posada, D.1
Crandall, K.A.2
-
44
-
-
0026460082
-
Population genetics of polymorphism and divergence
-
SAWYER, S. A., and D. L. HARTL, 1992 Population genetics of polymorphism and divergence. Genetics 132: 1161-1176.
-
(1992)
Genetics
, vol.132
, pp. 1161-1176
-
-
Sawyer, S.A.1
Hartl, D.L.2
-
45
-
-
0347380978
-
Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection
-
SAWYER, S. A., R. J. KULATHINAL, C. D. BUSTAMANTE and D. L. HARTL, 2003 Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection. J. Mol. Evol. 57: S154-S164.
-
(2003)
J. Mol. Evol.
, vol.57
-
-
Sawyer, S.A.1
Kulathinal, R.J.2
Bustamante, C.D.3
Hartl, D.L.4
-
46
-
-
3042692452
-
Patterns of microsatellite variability among X chromosomes and autosomes indicate a high frequency of beneficial mutations in non-African D. simulans
-
SCHÖFL, G., and C. SCHLÖTTERER, 2004 Patterns of microsatellite variability among X chromosomes and autosomes indicate a high frequency of beneficial mutations in non-African D. simulans. Mol. Biol. Evol. 21: 1384-1390.
-
(2004)
Mol. Biol. Evol.
, vol.21
, pp. 1384-1390
-
-
Schöfl, G.1
Schlötterer, C.2
-
47
-
-
85027186089
-
Selection of the order of an autoregressive model by Akaike's information criterion
-
SHIBATA, R., 1976 Selection of the order of an autoregressive model by Akaike's information criterion. Biometrika 63: 117-126.
-
(1976)
Biometrika
, vol.63
, pp. 117-126
-
-
Shibata, R.1
-
48
-
-
0037186564
-
Adaptive protein evolution in Drosophila
-
SMITH, N. G. C., and A. EYRE-WALKER, 2002 Adaptive protein evolution in Drosophila. Nature 415: 1022-1024.
-
(2002)
Nature
, vol.415
, pp. 1022-1024
-
-
Smith, N.G.C.1
Eyre-Walker, A.2
-
50
-
-
0013272874
-
Pre-speciation coalescence and the effective size of ancestral populations
-
edited by M. SLATKIN and M. VEUILLE. Oxford University Press, Oxford
-
TAKAHATA, N., and Y. SATTA, 2002 Pre-speciation coalescence and the effective size of ancestral populations, pp. 52-71 in Modern Developments in Theoretical Population Genetics, the Legacy of Gustave Malecot, edited by M. SLATKIN and M. VEUILLE. Oxford University Press, Oxford.
-
(2002)
Modern Developments in Theoretical Population Genetics, the Legacy of Gustave Malecot
, pp. 52-71
-
-
Takahata, N.1
Satta, Y.2
-
51
-
-
0036743513
-
Testing models of selection and demography in Drosophila simulans
-
WALL, J. D., P. ANDOLFATTO and M. PRZEWORSKI, 2002 Testing models of selection and demography in Drosophila simulans. Genetics 162: 203-216.
-
(2002)
Genetics
, vol.162
, pp. 203-216
-
-
Wall, J.D.1
Andolfatto, P.2
Przeworski, M.3
-
52
-
-
20344380699
-
Simultaneous inference of selection and population growth from patterns of variation in the human genome
-
USA
-
WILLIAMSON, S. H., R. HERNANDEZ, A. FLEDEL-ALON, R. NIELSEN and C. D. BUSTAMANTE, 2005 Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl. Acad. Sci. USA 102: 7882-7887.
-
(2005)
Proc. Natl. Acad. Sci.
, vol.102
, pp. 7882-7887
-
-
Williamson, S.H.1
Hernandez, R.2
Fledel-Alon, A.3
Nielsen, R.4
Bustamante, C.D.5
-
53
-
-
0028064845
-
Maximum likelihood estimation from DNA sequences with variable rates over sites: Approximate methods
-
YANG, Z., 1994 Maximum likelihood estimation from DNA sequences with variable rates over sites: approximate methods. J. Mol. Evol. 39: 306-314.
-
(1994)
J. Mol. Evol.
, vol.39
, pp. 306-314
-
-
Yang, Z.1
-
54
-
-
0031960185
-
Synonymous and nonsynonymous rate variation in nuclear genes of mammals
-
YANG, Z., and R. NIELSEN, 1998 Synonymous and nonsynonymous rate variation in nuclear genes of mammals. J. Mol. Evol. 46: 409-418.
-
(1998)
J. Mol. Evol.
, vol.46
, pp. 409-418
-
-
Yang, Z.1
Nielsen, R.2
-
55
-
-
23344453718
-
A composite likelihood approach for detecting directional selection from DNA sequence data
-
ZHU, L., and C. D. BUSTAMANTE, 2005 A composite likelihood approach for detecting directional selection from DNA sequence data. Genetics 170: 1411-1421.
-
(2005)
Genetics
, vol.170
, pp. 1411-1421
-
-
Zhu, L.1
Bustamante, C.D.2
|