메뉴 건너뛰기




Volumn 170, Issue 3, 2005, Pages 1411-1421

A composite-likelihood approach for detecting directional selection from DNA sequence data

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPOSITE LIKELIHOOD APPROACH; DIRECTED MOLECULAR EVOLUTION; DNA SEQUENCE; GENE IDENTIFICATION; GENETIC MODEL; GENETIC RECOMBINATION; GENETIC SELECTION; NATURAL SELECTION; NEGATIVE SELECTION; PERFORMANCE; POPULATION GROWTH; POSITIVE SELECTION; PRIORITY JOURNAL; SIMULATION; STATISTICAL ANALYSIS; STATISTICAL MODEL; WRIGHT FISHER MODEL;

EID: 23344453718     PISSN: 00166731     EISSN: None     Source Type: Journal    
DOI: 10.1534/genetics.104.035097     Document Type: Article
Times cited : (46)

References (50)
  • 1
    • 0003455528 scopus 로고
    • Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
    • ASHBURNER, M., 1989 Drosophila: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY.
    • (1989) Drosophila: A Laboratory Manual
    • Ashburner, M.1
  • 2
    • 0030819029 scopus 로고    scopus 로고
    • A physical map of human chromosome 7: An integrated YAC contig map with average STS spacing of 79kb
    • BOUFFARD, G. G., J. R. IDOL, V. V. BRADEN, L. M. IYER, A. F. CUNNINGHAM et al., 1997 A physical map of human chromosome 7: an integrated YAC contig map with average STS spacing of 79kb. Genome Res. 7: 673-692.
    • (1997) Genome Res. , vol.7 , pp. 673-692
    • Bouffard, G.G.1    Idol, J.R.2    Braden, V.V.3    Iyer, L.M.4    Cunningham, A.F.5
  • 3
    • 0035691964 scopus 로고    scopus 로고
    • Directional selection and the site-frequency spectrum
    • BUSTAMANTE, C. D., J. WAKELEY, S. 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.3    Hartl, D.L.4
  • 4
    • 0037944231 scopus 로고    scopus 로고
    • Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data
    • BUSTAMANTE, C. D., R. NIELSEN and D. L. HARTL, 2003 Maximum likelihood and Bayesian methods for estimating the distribution of selective effects among classes of mutations using DNA polymorphism data. Theor. Popul. Biol. 63 (2): 91-103.
    • (2003) Theor. Popul. Biol. , vol.63 , Issue.2 , pp. 91-103
    • Bustamante, C.D.1    Nielsen, R.2    Hartl, D.L.3
  • 5
    • 0036263105 scopus 로고    scopus 로고
    • Population, evolutionary and genomic consequences of interference selection
    • COMERON, J. M., and M. KREITMAN, 2002 Population, evolutionary and genomic consequences of interference selection. Genetics 161: 389-410.
    • (2002) Genetics , vol.161 , pp. 389-410
    • Comeron, J.M.1    Kreitman, M.2
  • 6
    • 0016121072 scopus 로고
    • A note on the sampling theory for infinite alleles and infinite sites models
    • EWENS, W. J., 1974 A note on the sampling theory for infinite alleles and infinite sites models. Theor. Popul. Biol. 6: 143-148.
    • (1974) Theor. Popul. Biol. , vol.6 , pp. 143-148
    • Ewens, W.J.1
  • 7
    • 0033911640 scopus 로고    scopus 로고
    • Hitchhiking under positive Darwinian selection
    • FAY, J. C., and C.-I WU, 2000 Hitchhiking under positive Darwinian selection. Genetics 155: 1405-1413.
    • (2000) Genetics , vol.155 , pp. 1405-1413
    • Fay, J.C.1    Wu, C.-I.2
  • 8
    • 0036433716 scopus 로고    scopus 로고
    • Approximate likelihood methods for estimating local recombination rates
    • FEARNHEAD, P., and P. DONNELLY, 2002 Approximate likelihood methods for estimating local recombination rates. J. R. Stat. Soc. Ser. 64: 657-680.
    • (2002) J. R. Stat. Soc. Ser. , vol.64 , pp. 657-680
    • Fearnhead, P.1    Donnelly, P.2
  • 9
    • 0016110957 scopus 로고
    • The evolutionary advantage of recombination
    • FELSENSTEIN, J., 1974 The evolutionary advantage of recombination. Genetics 78: 737-756.
    • (1974) Genetics , vol.78 , pp. 737-756
    • Felsenstein, J.1
  • 10
    • 0027453041 scopus 로고
    • Statistical tests of neutrality of mutations
    • FU, Y.-X., and W.-H. LI, 1993 Statistical tests of neutrality of mutations. Genetics 133: 693-709.
    • (1993) Genetics , vol.133 , pp. 693-709
    • Fu, Y.-X.1    Li, W.-H.2
  • 11
    • 0034086970 scopus 로고    scopus 로고
    • Detecting bottlenecks and selective sweeps from DNA sequence polymorphism
    • GALTIER, N., F. DEPAULIS and H. N. BARTON, 2000 Detecting bottlenecks and selective sweeps from DNA sequence polymorphism. Genetics 155: 981-987.
    • (2000) Genetics , vol.155 , pp. 981-987
    • Galtier, N.1    Depaulis, F.2    Barton, H.N.3
  • 12
    • 0030498194 scopus 로고    scopus 로고
    • Ancestral inference from samples of DNA sequences with recombination
    • GRIFFITHS, R., and P. MARJORAM, 1996 Ancestral inference from samples of DNA sequences with recombination. J. Comp. Biol. 3: 479-502.
    • (1996) J. Comp. Biol. , vol.3 , pp. 479-502
    • Griffiths, R.1    Marjoram, P.2
  • 13
    • 0027978722 scopus 로고
    • Selection intensity for codon bias
    • HARTL, D. L., E. N. MORIYAMA and S. A. SAWYER, 1994 Selection intensity for codon bias. Genetics 138: 227-234.
    • (1994) Genetics , vol.138 , pp. 227-234
    • Hartl, D.L.1    Moriyama, E.N.2    Sawyer, S.A.3
  • 14
    • 0031035812 scopus 로고    scopus 로고
    • A coalescent estimator of the population recombination rate
    • HEY, J., and J. WAKELEY, 1997 A coalescent estimator of the population recombination rate. Genetics 145: 833-846.
    • (1997) Genetics , vol.145 , pp. 833-846
    • Hey, J.1    Wakeley, J.2
  • 15
    • 0013979181 scopus 로고
    • The effect of linkage on the limits to artificial selection
    • HILL, W. G., and A. ROBERTSON, 1966 The effect of linkage on the limits to artificial selection. Genet. Res. 8: 269-294.
    • (1966) Genet. Res. , vol.8 , pp. 269-294
    • Hill, W.G.1    Robertson, A.2
  • 16
    • 0023612034 scopus 로고
    • Estimating the recombination parameter of a finite population model without selection
    • HUDSON, R. R., 1987 Estimating the recombination parameter of a finite population model without selection. Genet. Res. 50: 245-250.
    • (1987) Genet. Res. , vol.50 , pp. 245-250
    • Hudson, R.R.1
  • 18
    • 0035692320 scopus 로고    scopus 로고
    • Two-locus sampling distributions and their application
    • HUDSON, R. R., 2001 Two-locus sampling distributions and their application. Genetics 159: 1805-1817.
    • (2001) Genetics , vol.159 , pp. 1805-1817
    • Hudson, R.R.1
  • 19
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model
    • HUDSON, R. R., 2002 Generating samples under a Wright-Fisher neutral model. Bioinformatics 18: 337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 20
    • 0022211482 scopus 로고
    • Statistical properties of the number of recombination events in the history of a sample of DNA sequences
    • HUDSON, R. R., and N. L. KAPLAN, 1985 Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111: 147-164.
    • (1985) Genetics , vol.111 , pp. 147-164
    • Hudson, R.R.1    Kaplan, N.L.2
  • 21
    • 3242714766 scopus 로고    scopus 로고
    • Pattern of polymorphism after strong artificial selection in a domestication event
    • INNAN, H., and Y. KIM, 2004 Pattern of polymorphism after strong artificial selection in a domestication event. Proc. Natl. Acad. Sci. USA 101 (29): 10667-10672.
    • (2004) Proc. Natl. Acad. Sci. USA , vol.101 , Issue.29 , pp. 10667-10672
    • Innan, H.1    Kim, Y.2
  • 22
    • 23344438911 scopus 로고    scopus 로고
    • Distinguishing between selective sweeps and demography using DNA polymorphism data
    • JENSEN, J. D., Y. KIM, V. BAUER-DUMONTH, C. F. AQUADRO and C. D. BUSTAMANTE, 2005 Distinguishing between selective sweeps and demography using DNA polymorphism data. Genetics 170: 1401-1410.
    • (2005) Genetics , vol.170 , pp. 1401-1410
    • Jensen, J.D.1    Kim, Y.2    Bauer-Dumonth, V.3    Aquadro, C.F.4    Bustamante, C.D.5
  • 24
    • 3843073210 scopus 로고    scopus 로고
    • Linkage disequilibrium as a signature of selective sweeps
    • KIM, Y., and R. NIELSEN, 2004 Linkage disequilibrium as a signature of selective sweeps. Genetics 167: 1513-1524.
    • (2004) Genetics , vol.167 , pp. 1513-1524
    • Kim, Y.1    Nielsen, R.2
  • 25
    • 0036189827 scopus 로고    scopus 로고
    • Detecting a local signature of genetic hitchhiking along a recombining chromosome
    • KIM, Y., and W. STEPHAN, 2002 Detecting a local signature of genetic hitchhiking along a recombining chromosome. Genetics 160: 765-777.
    • (2002) Genetics , vol.160 , pp. 765-777
    • Kim, Y.1    Stephan, W.2
  • 26
    • 0030877679 scopus 로고    scopus 로고
    • Ancestral processes with selection
    • KRONE, S. M., and C. NEUHAUSER, 1997 Ancestral processes with selection. Theor. Popul. Biol. 51: 210-237.
    • (1997) Theor. Popul. Biol. , vol.51 , pp. 210-237
    • Krone, S.M.1    Neuhauser, C.2
  • 29
    • 0347361674 scopus 로고    scopus 로고
    • Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data
    • LI, N., and M. STEPHENS, 2003 Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165: 2213-2233.
    • (2003) Genetics , vol.165 , pp. 2213-2233
    • Li, N.1    Stephens, M.2
  • 30
    • 0036199914 scopus 로고    scopus 로고
    • A coalescent-based method for detecting and estimating recombination from gene sequences
    • MCVEAN, G., P. AWADALLA and P. FEARNHEAD, 2002 A coalescent-based method for detecting and estimating recombination from gene sequences. Genetics 160: 1231-1241.
    • (2002) Genetics , vol.160 , pp. 1231-1241
    • Mcvean, G.1    Awadalla, P.2    Fearnhead, P.3
  • 31
    • 2142773942 scopus 로고    scopus 로고
    • The fine-scale structure of recombination rate variation in the human genome
    • MCVEAN, G., S. R. MYERS, S. HUNT, P. DELOUKAS, D. R. BENTLEY et al., 2004 The fine-scale structure of recombination rate variation in the human genome. Science 304 (5670): 581-584.
    • (2004) Science , vol.304 , Issue.5670 , pp. 581-584
    • Mcvean, G.1    Myers, S.R.2    Hunt, S.3    Deloukas, P.4    Bentley, D.R.5
  • 32
    • 14444286943 scopus 로고    scopus 로고
    • X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content
    • NAGARAJA, R., S. MACMILLAN, J. KERE, C. JONES, S. GRIFFIN et al., 1997 X chromosome map at 75-kb STS resolution, revealing extremes of recombination and GC content. Genome Res. 7: 210-222.
    • (1997) Genome Res. , vol.7 , pp. 210-222
    • Nagaraja, R.1    Macmillan, S.2    Kere, J.3    Jones, C.4    Griffin, S.5
  • 33
    • 0031014102 scopus 로고    scopus 로고
    • The genealogy of samples in models with selection
    • NEUHAUSER, C., and S. M. KRONE, 1997 The genealogy of samples in models with selection. Genetics 145: 519-534.
    • (1997) Genetics , vol.145 , pp. 519-534
    • Neuhauser, C.1    Krone, S.M.2
  • 34
    • 0034809334 scopus 로고    scopus 로고
    • Statistical tests of selective neutrality in the age of genomics
    • NIELSEN, R., 2001 Statistical tests of selective neutrality in the age of genomics. Heredity 86: 641-647.
    • (2001) Heredity , vol.86 , pp. 641-647
    • Nielsen, R.1
  • 35
    • 0000111927 scopus 로고
    • Inbreeding in artificial selection programmes
    • ROBERTSON, A., 1961 Inbreeding in artificial selection programmes. Genet. Res. 2: 189-194.
    • (1961) Genet. Res. , vol.2 , pp. 189-194
    • Robertson, A.1
  • 36
    • 0026460082 scopus 로고
    • 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
  • 37
    • 0347380978 scopus 로고    scopus 로고
    • 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
  • 38
    • 0035227780 scopus 로고    scopus 로고
    • Simulation of 'hitch-hiking' genealogies
    • SLADE, P. F., 2001 Simulation of 'hitch-hiking' genealogies. J. Math. Biol. 42 (1): 41-70.
    • (2001) J. Math. Biol. , vol.42 , Issue.1 , pp. 41-70
    • Slade, P.F.1
  • 39
    • 0025951996 scopus 로고
    • Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations
    • SLATKIN, M., and R. R. HUDSON, 1991 Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations. Genetics 129: 555-562.
    • (1991) Genetics , vol.129 , pp. 555-562
    • Slatkin, M.1    Hudson, R.R.2
  • 40
    • 0024313579 scopus 로고
    • Statistical method for testing the neutral mutation hypothesis by DNA polymorphism
    • TAJIMA, F., 1989 Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123: 585-595.
    • (1989) Genetics , vol.123 , pp. 585-595
    • Tajima, F.1
  • 41
    • 0030068317 scopus 로고    scopus 로고
    • Differences in crossover frequency and distribution among three sibling species of Drosophila
    • TRUE, J. R., J. M. MERCER and C. C. LAURIE, 1996 Differences in crossover frequency and distribution among three sibling species of Drosophila. Genetics 142: 507-523.
    • (1996) Genetics , vol.142 , pp. 507-523
    • True, J.R.1    Mercer, J.M.2    Laurie, C.C.3
  • 42
    • 0030954044 scopus 로고    scopus 로고
    • Using the variance of pairwise differences to estimate the recombination rate
    • WAKELEY, J., 1997 Using the variance of pairwise differences to estimate the recombination rate. Genet. Res. 69: 45-48.
    • (1997) Genet. Res. , vol.69 , pp. 45-48
    • Wakeley, J.1
  • 43
    • 0035714381 scopus 로고    scopus 로고
    • The coalescent in an island model with variation among denies
    • WAKELEY, J., 2001 The coalescent in an island model with variation among denies. Theor. Popul. Biol. 59: 133-144.
    • (2001) Theor. Popul. Biol. , vol.59 , pp. 133-144
    • Wakeley, J.1
  • 44
    • 0037277985 scopus 로고    scopus 로고
    • Polymorphism and divergence for island-model species
    • WAKELEY, J., 2003 Polymorphism and divergence for island-model species. Genetics 163: 411-420.
    • (2003) Genetics , vol.163 , pp. 411-420
    • Wakeley, J.1
  • 45
    • 0033955443 scopus 로고    scopus 로고
    • A comparison of estimators of the population recombination rate
    • WALL, J. D., 2000 A comparison of estimators of the population recombination rate. Mol. Biol. Evol. 17: 156-163.
    • (2000) Mol. Biol. Evol. , vol.17 , pp. 156-163
    • Wall, J.D.1
  • 46
    • 3843126537 scopus 로고    scopus 로고
    • Estimating recombination rates using three-site likelihoods
    • WALL, J. D., 2004 Estimating recombination rates using three-site likelihoods. Genetics 167: 1461-1473.
    • (2004) Genetics , vol.167 , pp. 1461-1473
    • Wall, J.D.1
  • 47
    • 0016491430 scopus 로고
    • On the number of segregating sites in genetic models without recombination
    • WATTERSON, G. A., 1975 On the number of segregating sites in genetic models without recombination. Theor. Popul. Biol. 7: 256-276.
    • (1975) Theor. Popul. Biol. , vol.7 , pp. 256-276
    • Watterson, G.A.1
  • 48
    • 0041571679 scopus 로고    scopus 로고
    • Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression
    • WILLIAMSON, S., 2003 Adaptation in the env gene of HIV-1 and evolutionary theories of disease progression. Biol. Evol. Mol. Biol. Evol. 20: 1318-1325.
    • (2003) Biol. Evol. Mol. Biol. Evol. , vol.20 , pp. 1318-1325
    • Williamson, S.1
  • 49
    • 5144231907 scopus 로고    scopus 로고
    • Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance
    • WILLIAMSON, S., A. F. ALON and C. D. BUSTAMANTE, 2004 Population genetics of polymorphism and divergence for diploid selection models with arbitrary dominance. Genetics 168: 463-475.
    • (2004) Genetics , vol.168 , pp. 463-475
    • Williamson, S.1    Alon, A.F.2    Bustamante, C.D.3
  • 50
    • 20344380699 scopus 로고    scopus 로고
    • Simultaneous inference of selection and population growth from patterns of variation in the human genome
    • WILLIAMSON, S., R. HERNANDEZ, A. F. ALON, L. ZHU, R. NIELSEN et al., 2005 Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl. Acad. Sci. USA 102 (22): 7882-7887.
    • (2005) Proc. Natl. Acad. Sci. USA , vol.102 , Issue.22 , pp. 7882-7887
    • Williamson, S.1    Hernandez, R.2    Alon, A.F.3    Zhu, L.4    Nielsen, R.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.