메뉴 건너뛰기




Volumn 85, Issue 6, 2010, Pages 359-376

Statistical methods for detecting natural selection from genomic data

Author keywords

Divergence data; Polymorphism data; Recent ongoing natural selection; Recurrent natural selection; Statistical methods

Indexed keywords

CPG OLIGODEOXYNUCLEOTIDE; MESSENGER RNA; MICRORNA; PIWI INTERACTING RNA; SMALL INTERFERING RNA; SMALL NUCLEOLAR RNA; TRANSFER RNA;

EID: 79952938714     PISSN: 13417568     EISSN: 18805779     Source Type: Journal    
DOI: 10.1266/ggs.85.359     Document Type: Review
Times cited : (36)

References (172)
  • 1
    • 65149103048 scopus 로고    scopus 로고
    • Constructing genomic maps of positive selection in humans: Where do we go from here?
    • Akey, J. M. (2009) Constructing genomic maps of positive selection in humans: where do we go from here? Genome Res. 19, 711-722.
    • (2009) Genome Res , vol.19 , pp. 711-722
    • Akey, J.M.1
  • 2
    • 0036911353 scopus 로고    scopus 로고
    • Interrogating a high-density SNP map for signatures of natural selection
    • Akey, J. M., Zhang, G., Zhang, K., Jin, L., and Shriver, M. D. (2002) Interrogating a high-density SNP map for signatures of natural selection. Genome Res. 12, 1805-1814.
    • (2002) Genome Res , vol.12 , pp. 1805-1814
    • Akey, J.M.1    Zhang, G.2    Zhang, K.3    Jin, L.4    Shriver, M.D.5
  • 3
    • 27144491328 scopus 로고    scopus 로고
    • Adaptive evolution of non-coding DNA in Drosophila
    • Andolfatto, P. (2005) Adaptive evolution of non-coding DNA in Drosophila. Nature 437, 1149-1152.
    • (2005) Nature , vol.437 , pp. 1149-1152
    • Andolfatto, P.1
  • 4
    • 34250659350 scopus 로고    scopus 로고
    • More genes underwent positive selection in chimpanzee evolution than in human evolution
    • Bakewell, M. A., Shi, P., and Zhang, J. (2007) More genes underwent positive selection in chimpanzee evolution than in human evolution. Proc. Natl. Acad. Sci. USA 104, 7489-7494.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 7489-7494
    • Bakewell, M.A.1    Shi, P.2    Zhang, J.3
  • 6
    • 19944373422 scopus 로고    scopus 로고
    • Tertiary windowing to detect positive diversifying selection
    • Berglund, A.-C., Wallner, B., Elofsson, A., and Liberles, D. A. (2005) Tertiary windowing to detect positive diversifying selection. J. Mol. Evol. 60, 499-504.
    • (2005) J. Mol. Evol , vol.60 , pp. 499-504
    • Berglund, A.-C.1    Wallner, B.2    Elofsson, A.3    Liberles, D.A.4
  • 7
    • 58849161775 scopus 로고    scopus 로고
    • Hotspots of biased nucleotide substitutions in human genes
    • Berglund, J., Pollard, K. S., and Webster, M. T. (2009) Hotspots of biased nucleotide substitutions in human genes. PLoS Biol. 7, e1000026.
    • (2009) PLoS Biol , vol.7
    • Berglund, J.1    Pollard, K.S.2    Webster, M.T.3
  • 8
    • 28744452463 scopus 로고    scopus 로고
    • Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test
    • Berlin, S., and Smith, N. G.C. (2005) Testing for adaptive evolution of the female reproductive protein ZPC in mammals, birds and fishes reveals problems with the M7-M8 likelihood ratio test. BMC Evol. Biol. 5, 65.
    • (2005) BMC Evol. Biol , vol.5 , pp. 65
    • Berlin, S.1    Smith, N.G.C.2
  • 10
    • 0342383237 scopus 로고
    • Effects of linkage on rates of molecular evolution
    • Birky, C. W. Jr., and Walsh, J. B. (1988) Effects of linkage on rates of molecular evolution. Proc. Natl. Acad. Sci. USA 85, 6414-6418.
    • (1988) Proc. Natl. Acad. Sci. USA , vol.85 , pp. 6414-6418
    • Birky Jr., C.W.1    Walsh, J.B.2
  • 14
    • 0036207384 scopus 로고    scopus 로고
    • Listening to silence and understanding nonsense: Exonic mutations that affect splicing
    • Cartegni, L., Chew, S. L., and Krainer, A. R. (2002) Listening to silence and understanding nonsense: exonic mutations that affect splicing. Nat. Rev. Genet. 3, 285-298.
    • (2002) Nat. Rev. Genet , vol.3 , pp. 285-298
    • Cartegni, L.1    Chew, S.L.2    Krainer, A.R.3
  • 15
    • 31144465926 scopus 로고    scopus 로고
    • Hearing silence: Non-neutral evolution at synonymous sites in mammals
    • Chamary, J. V., Parmley, J. L., and Hurst, L. D. (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat. Rev. Genet. 7, 98-108.
    • (2006) Nat. Rev. Genet , vol.7 , pp. 98-108
    • Chamary, J.V.1    Parmley, J.L.2    Hurst, L.D.3
  • 16
    • 0028222304 scopus 로고
    • 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
  • 17
    • 33745624539 scopus 로고    scopus 로고
    • The rate of adaptive evolution in enteric bacteria
    • Charlesworth, J., and Eyre-Walker, A. (2006) The rate of adaptive evolution in enteric bacteria. Mol. Biol. Evol. 23, 1348-1356.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 1348-1356
    • Charlesworth, J.1    Eyre-Walker, A.2
  • 18
    • 69749122314 scopus 로고    scopus 로고
    • Identification of deleterious mutations within three human genomes
    • Chun, S., and Fay, J. C. (2009) Identification of deleterious mutations within three human genomes. Genome Res. 19, 1553-1561.
    • (2009) Genome Res , vol.19 , pp. 1553-1561
    • Chun, S.1    Fay, J.C.2
  • 19
    • 0025939530 scopus 로고
    • Excess nonsynonymous substitution at shared polymorphic sites among self-incompatibility alleles of Solanaceae
    • Clark, A. G., and Kao, T.-H. (1991) Excess nonsynonymous substitution at shared polymorphic sites among self-incompatibility alleles of Solanaceae. Proc. Natl. Acad. Sci. USA 88, 9823-9827.
    • (1991) Proc. Natl. Acad. Sci. USA , vol.88 , pp. 9823-9827
    • Clark, A.G.1    Kao, T.-H.2
  • 21
    • 0029563023 scopus 로고
    • A method for estimating the numbers of synonymous and nonsynonymous substitutions per site
    • Comeron, J. M. (1995) A method for estimating the numbers of synonymous and nonsynonymous substitutions per site. J. Mol. Evol. 41, 1152-1159.
    • (1995) J. Mol. Evol , vol.41 , pp. 1152-1159
    • Comeron, J.M.1
  • 23
    • 47549097539 scopus 로고    scopus 로고
    • Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution
    • Drummond, D. A., and Wilke, C. O. (2008) Mistranslation-induced protein misfolding as a dominant constraint on coding-sequence evolution. Cell 134, 341-352.
    • (2008) Cell , vol.134 , pp. 341-352
    • Drummond, D.A.1    Wilke, C.O.2
  • 24
    • 59849095985 scopus 로고    scopus 로고
    • Comment on "Human-specific gain of function in a developmental enhancer
    • Duret, L., and Galtier, N. (2009) Comment on "Human-specific gain of function in a developmental enhancer". Science 323, 714c.
    • (2009) Science , vol.323
    • Duret, L.1    Galtier, N.2
  • 25
    • 70349506039 scopus 로고    scopus 로고
    • Detecting loci under selection in a hierarchically structured population
    • Excoffier, L., Hofer, T., and Foll, M. (2009) Detecting loci under selection in a hierarchically structured population. Heredity 103, 285-298.
    • (2009) Heredity , vol.103 , pp. 285-298
    • Excoffier, L.1    Hofer, T.2    Foll, M.3
  • 26
    • 0033911640 scopus 로고    scopus 로고
    • Hitchhiking under positive Darwinian selection
    • Fay, J. C., and Wu, C.-I. (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
  • 27
    • 0034924997 scopus 로고    scopus 로고
    • Positive and negative selection on the human genome
    • Fay, J. C., Wyckoff, G. J., and Wu, C.-I. (2001) Positive and negative selection on the human genome. Genetics 158, 1227-1234.
    • (2001) Genetics , vol.158 , pp. 1227-1234
    • Fay, J.C.1    Wyckoff, G.J.2    Wu, C.-I.3
  • 28
    • 70349953726 scopus 로고    scopus 로고
    • Molecular signatures of adaptive evolution
    • (eds.: M. Pagel, and A. Pomiankowski, Sinauer Associates, Inc., Massachusetts
    • Filipski, A., Prohaska, S., and Kumar, S. (2007) Molecular signatures of adaptive evolution. In: Evolutionary Genomics and Proteomics (eds.: M. Pagel, and A. Pomiankowski), pp. 241-254. Sinauer Associates, Inc., Massachusetts.
    • (2007) Evolutionary Genomics and Proteomics , pp. 241-254
    • Filipski, A.1    Prohaska, S.2    Kumar, S.3
  • 29
    • 0030750055 scopus 로고    scopus 로고
    • Long term trends in the evolution of H(3) HA1 human influenza type A
    • Fitch, W. M., Bush, R. M., Bender, C. A., and Cox, N. J. (1997) Long term trends in the evolution of H(3) HA1 human influenza type A. Proc. Natl. Acad. Sci. USA 94, 7712-7718.
    • (1997) Proc. Natl. Acad. Sci. USA , vol.94 , pp. 7712-7718
    • Fitch, W.M.1    Bush, R.M.2    Bender, C.A.3    Cox, N.J.4
  • 30
    • 77957233773 scopus 로고    scopus 로고
    • The effect of insertions, deletions and alignment errors on the branch-site test of positive selection
    • Fletcher, W., and Yang, Z. (2010) The effect of insertions, deletions and alignment errors on the branch-site test of positive selection. Mol. Biol. Evol. 27, 2257-2267.
    • (2010) Mol. Biol. Evol , vol.27 , pp. 2257-2267
    • Fletcher, W.1    Yang, Z.2
  • 31
    • 58149347836 scopus 로고    scopus 로고
    • A genome-scan method to identify selection loci appropriate for both dominant and codominant markers: A Baysian perspective
    • Foll, M., and Gaggiotti, O. (2008) A genome-scan method to identify selection loci appropriate for both dominant and codominant markers: a Baysian perspective. Genetics 180, 977-993.
    • (2008) Genetics , vol.180 , pp. 977-993
    • Foll, M.1    Gaggiotti, O.2
  • 33
    • 33750997047 scopus 로고    scopus 로고
    • Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods
    • Friedman, R., and Hughes, A. L. (2007) Likelihood-ratio tests for positive selection of human and mouse duplicate genes reveal nonconservative and anomalous properties of widely used methods. Mol. Phylogenet. Evol. 42, 388-393.
    • (2007) Mol. Phylogenet. Evol , vol.42 , pp. 388-393
    • Friedman, R.1    Hughes, A.L.2
  • 34
    • 0027453041 scopus 로고
    • Statistical tests of neutrality of mutations
    • Fu, Y.-X., and Li, W.-H. (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
  • 35
    • 58149328496 scopus 로고    scopus 로고
    • GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates
    • Galtier, N., Duret, L., Glemin, S., and Ranwez, V. (2009) GC-biased gene conversion promotes the fixation of deleterious amino acid changes in primates. Trends Genet. 25, 1-5.
    • (2009) Trends Genet , vol.25 , pp. 1-5
    • Galtier, N.1    Duret, L.2    Glemin, S.3    Ranwez, V.4
  • 36
    • 34250308719 scopus 로고    scopus 로고
    • Extreme individual marker FST values do not imply population-specific selection in humans: The NRG1 example
    • Gardner, M., Williamson, S., Casals, F., Bosch, E., Navarro, A., Calafell, F., Bertranpetit, J., and Comas, D. (2007) Extreme individual marker FST values do not imply population-specific selection in humans: the NRG1 example. Hum. Genet. 121, 759-762.
    • (2007) Hum. Genet , vol.121 , pp. 759-762
    • Gardner, M.1    Williamson, S.2    Casals, F.3    Bosch, E.4    Navarro, A.5    Calafell, F.6    Bertranpetit, J.7    Comas, D.8
  • 37
    • 72649087519 scopus 로고    scopus 로고
    • Measuring the sensitivity of singlelocus "neutrality tests" using a direct perturbation approach
    • Garrigan, D., Lewontin, R., and Wakeley, J. (2010) Measuring the sensitivity of singlelocus "neutrality tests" using a direct perturbation approach. Mol. Biol. Evol. 27, 73-89.
    • (2010) Mol. Biol. Evol , vol.27 , pp. 73-89
    • Garrigan, D.1    Lewontin, R.2    Wakeley, J.3
  • 38
    • 34247248182 scopus 로고    scopus 로고
    • Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution
    • Gojobori, J., Tang, H., Akey, J. M., and Wu, C.-I. (2007) Adaptive evolution in humans revealed by the negative correlation between the polymorphism and fixation phases of evolution. Proc. Natl. Acad. Sci. USA 104, 3907-3912.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 3907-3912
    • Gojobori, J.1    Tang, H.2    Akey, J.M.3    Wu, C.-I.4
  • 39
    • 0028168856 scopus 로고
    • A codon-based model of nucle-otide substitution for protein-coding DNA sequences
    • Goldman, N., and Yang, Z. (1994) A codon-based model of nucle-otide 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
  • 40
    • 77952385218 scopus 로고    scopus 로고
    • Phylogenomic evidence of adaptive evolution in the ancestry of humans
    • Goodman, M., and Sterner, K. N. (2010) Phylogenomic evidence of adaptive evolution in the ancestry of humans. Proc. Natl. Acad. Sci. USA 107, 8918-8923.
    • (2010) Proc. Natl. Acad. Sci. USA , vol.107 , pp. 8918-8923
    • Goodman, M.1    Sterner, K.N.2
  • 45
    • 39749133684 scopus 로고    scopus 로고
    • Toward a selection theory of molecular evolution
    • Hahn, M. W. (2008) Toward a selection theory of molecular evolution. Evolution 62, 255-265.
    • (2008) Evolution , vol.62 , pp. 255-265
    • Hahn, M.W.1
  • 47
    • 34548346860 scopus 로고    scopus 로고
    • Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
    • Haygood, R., Fedrigo, O., Hanson, B., Yokoyama, K. D., and Wray, G. A. (2007) Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution. Nat. Genet. 39, 1140-1144.
    • (2007) Nat. Genet , vol.39 , pp. 1140-1144
    • Haygood, R.1    Fedrigo, O.2    Hanson, B.3    Yokoyama, K.D.4    Wray, G.A.5
  • 48
  • 49
    • 70349501387 scopus 로고    scopus 로고
    • Who believes in whole-genome scans for selection?
    • Hermisson, J. (2009) Who believes in whole-genome scans for selection? Heredity 103, 283-284.
    • (2009) Heredity , vol.103 , pp. 283-284
    • Hermisson, J.1
  • 50
    • 0013979181 scopus 로고
    • The effect of linkage on limits to artificial selection
    • Hill, W. G., and Robertson, A. (1966) The effect of linkage on limits to artificial selection. Genet. Res. 8, 269-294.
    • (1966) Genet. Res , vol.8 , pp. 269-294
    • Hill, W.G.1    Robertson, A.2
  • 51
    • 0023339852 scopus 로고
    • A test of neutral molecular evolution based on nucleotide data
    • Hudson, R. R., Kreitman, M., and Aguade, M. (1987) A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153-159.
    • (1987) Genetics , vol.116 , pp. 153-159
    • Hudson, R.R.1    Kreitman, M.2    Aguade, M.3
  • 52
    • 0026709389 scopus 로고
    • Estimation of levels of gene flow from DNA sequence data
    • Hudson, R. R., Slatkin, M., and Maddison, W. P. (1992) Estimation of levels of gene flow from DNA sequence data. Genetics 132, 583-589.
    • (1992) Genetics , vol.132 , pp. 583-589
    • Hudson, R.R.1    Slatkin, M.2    Maddison, W.P.3
  • 53
    • 45249106003 scopus 로고    scopus 로고
    • Near neutrality: Leading edge of the neutral theory of molecular evolution
    • Hughes, A. L. (2008a) Near neutrality: leading edge of the neutral theory of molecular evolution. Ann. NY Acad. Sci. 1133, 162-179.
    • (2008) Ann. NY Acad. Sci , vol.1133 , pp. 162-179
    • Hughes, A.L.1
  • 54
    • 51649108111 scopus 로고    scopus 로고
    • The origin of adaptive phenotypes
    • Hughes, A. L. (2008b) The origin of adaptive phenotypes. Proc. Natl. Acad. Sci. USA 105, 13193-13194.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 13193-13194
    • Hughes, A.L.1
  • 55
    • 0023764283 scopus 로고
    • Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
    • Hughes, A. L., and Nei, M. (1988) Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335, 167-170.
    • (1988) Nature , vol.335 , pp. 167-170
    • Hughes, A.L.1    Nei, M.2
  • 56
    • 51649122447 scopus 로고    scopus 로고
    • Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes
    • Hughes, A. L., Friedman, R., Rivailler, P., and French, J. O. (2008) Synonymous and nonsynonymous polymorphisms versus divergences in bacterial genomes. Mol. Biol. Evol. 25, 2199-2209.
    • (2008) Mol. Biol. Evol , vol.25 , pp. 2199-2209
    • Hughes, A.L.1    Friedman, R.2    Rivailler, P.3    French, J.O.4
  • 57
    • 59049102163 scopus 로고    scopus 로고
    • A positive becomes a negative
    • Hurst, L. D. (2009) A positive becomes a negative. Nature 457, 543-544.
    • (2009) Nature , vol.457 , pp. 543-544
    • Hurst, L.D.1
  • 58
    • 0035252561 scopus 로고    scopus 로고
    • Evidence for purifying selection acting on silent sites in BRCA1
    • Hurst, L. D., and Pal, C. (2001) Evidence for purifying selection acting on silent sites in BRCA1. Trends Genet. 17, 62-65.
    • (2001) Trends Genet , vol.17 , pp. 62-65
    • Hurst, L.D.1    Pal, C.2
  • 59
    • 0028906291 scopus 로고
    • New methods for estimating the numbers of synonymous and nonsynonymous substitutions
    • Ina, Y. (1995) New methods for estimating the numbers of synonymous and nonsynonymous substitutions. J. Mol. Evol. 40, 190-226.
    • (1995) J. Mol. Evol , vol.40 , pp. 190-226
    • Ina, Y.1
  • 60
    • 1842636602 scopus 로고    scopus 로고
    • Population subdivision and the Hudson-Kreitman-Aguade test: Testing for deviations from the neutral model in organelle genomes
    • Ingvarsson, P. K. (2004) Population subdivision and the Hudson-Kreitman-Aguade test: testing for deviations from the neutral model in organelle genomes. Genet. Res. 83, 31-39.
    • (2004) Genet. Res , vol.83 , pp. 31-39
    • Ingvarsson, P.K.1
  • 61
    • 0024372736 scopus 로고
    • The "hitchhiking effect" revisited
    • Kaplan, N. L., Hudson, R. R., and Langley, C. H. (1989) The "hitchhiking effect" revisited. Genetics 123, 887-899.
    • (1989) Genetics , vol.123 , pp. 887-899
    • Kaplan, N.L.1    Hudson, R.R.2    Langley, C.H.3
  • 62
    • 0344824015 scopus 로고    scopus 로고
    • Functional constraints and frequency of deleterious mutations in non-coding DNA of rodents
    • Keightley, P. D., and Gaffney, D. J. (2003) Functional constraints and frequency of deleterious mutations in non-coding DNA of rodents. Proc. Natl. Acad. Sci. USA 100, 13402-13406.
    • (2003) Proc. Natl. Acad. Sci. USA , vol.100 , pp. 13402-13406
    • Keightley, P.D.1    Gaffney, D.J.2
  • 63
    • 15744388330 scopus 로고    scopus 로고
    • Evidence for widespread degradation of gene control regions in hominid genomes
    • Keightley, P. D., Lercher, M. J., and Eyre-Walker, A. (2005) Evidence for widespread degradation of gene control regions in hominid genomes. PLoS Biol. 3, e42.
    • (2005) PLoS Biol , vol.3
    • Keightley, P.D.1    Lercher, M.J.2    Eyre-Walker, A.3
  • 64
    • 33746693757 scopus 로고    scopus 로고
    • Genomic signatures of positive selection in humans and the limits of outlier approaches
    • Kelley, J. L., Madeoy, J., Calhoun, J. C., Swanson, W., and Akey, J. M. (2006) Genomic signatures of positive selection in humans and the limits of outlier approaches. Genome Res. 16, 980-989.
    • (2006) Genome Res , vol.16 , pp. 980-989
    • Kelley, J.L.1    Madeoy, J.2    Calhoun, J.C.3    Swanson, W.4    Akey, J.M.5
  • 65
    • 0036189827 scopus 로고    scopus 로고
    • Detecting a local signature of genetic hitchhiking along a recombining chromosome
    • Kim, Y., and Stephan, W. (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
  • 67
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura, M. (1968) Evolutionary rate at the molecular level. Nature 217, 624-626.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 68
    • 0017368336 scopus 로고
    • Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution
    • Kimura, M. (1977) Preponderance of synonymous changes as evidence for the neutral theory of molecular evolution. Nature 267, 275-276.
    • (1977) Nature , vol.267 , pp. 275-276
    • Kimura, M.1
  • 70
    • 55849095847 scopus 로고    scopus 로고
    • A practical genome scan for population-specific strong selective sweeps that have reached fixation
    • Kimura, R., Fujimoto, A., Tokunaga, K., and Ohashi, J. (2007) A practical genome scan for population-specific strong selective sweeps that have reached fixation. PLoS ONE 2, e286.
    • (2007) PLoS ONE , vol.2
    • Kimura, R.1    Fujimoto, A.2    Tokunaga, K.3    Ohashi, J.4
  • 71
    • 0027163079 scopus 로고
    • Evolution of hominoid mitochondrial DNA with special reference to the silent substitution rate over the genome
    • Kondo, R., Horai, S., Satta, Y., and Takahata, N. (1993) Evolution of hominoid mitochondrial DNA with special reference to the silent substitution rate over the genome. J. Mol. Evol. 36, 517-531.
    • (1993) J. Mol. Evol , vol.36 , pp. 517-531
    • Kondo, R.1    Horai, S.2    Satta, Y.3    Takahata, N.4
  • 72
    • 17744396121 scopus 로고    scopus 로고
    • Not so different after all: A comparison of methods for detecting amino acid sites under selection
    • Kosakovsky Pond, S. L., and Frost, S. D. (2005) Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol. Biol. Evol. 22, 1208-1222.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 1208-1222
    • Kosakovsky Pond, S.L.1    Frost, S.D.2
  • 73
    • 33750491918 scopus 로고    scopus 로고
    • Inferring the demographic history and rate of adaptive substitution in Drosophila
    • Li, H., and Stephan, W. (2006) Inferring the demographic history and rate of adaptive substitution in Drosophila. PLoS Genet. 2, e166.
    • (2006) PLoS Genet , vol.2
    • Li, H.1    Stephan, W.2
  • 74
    • 0027403961 scopus 로고
    • Unbiased estimation of the rates of synonymous and nonsynonymous substitution
    • Li, W.-H. (1993) Unbiased estimation of the rates of synonymous and nonsynonymous substitution. J. Mol. Evol. 36, 96-99.
    • (1993) J. Mol. Evol , vol.36 , pp. 96-99
    • Li, W.-H.1
  • 75
    • 0022005270 scopus 로고
    • A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes
    • Li, W.-H., Wu, C.-I., and Luo, C.-C. (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol. Biol. Evol. 2, 150-174.
    • (1985) Mol. Biol. Evol , vol.2 , pp. 150-174
    • Li, W.-H.1    Wu, C.-I.2    Luo, C.-C.3
  • 77
    • 67649240664 scopus 로고    scopus 로고
    • Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees
    • Liu, K., Raghavan, S., Nelesen, S., Linder, C. R., and Warnow, T. (2009) Rapid and accurate large-scale coestimation of sequence alignments and phylogenetic trees. Science 324, 1561-1564.
    • (2009) Science , vol.324 , pp. 1561-1564
    • Liu, K.1    Raghavan, S.2    Nelesen, S.3    Linder, C.R.4    Warnow, T.5
  • 78
    • 66049087893 scopus 로고    scopus 로고
    • The difficulty of avoiding false positives in genome scans for natural selection
    • Mallick, S., Gnerre, S., Muller, P., and Reich, D. (2009) The difficulty of avoiding false positives in genome scans for natural selection. Genome Res. 19, 922-933.
    • (2009) Genome Res , vol.19 , pp. 922-933
    • Mallick, S.1    Gnerre, S.2    Muller, P.3    Reich, D.4
  • 79
    • 0037487984 scopus 로고
    • A note on the speed of gene frequency changes in reverse direction in a finite population
    • Maruyama, T., and Kimura, M. (1974) A note on the speed of gene frequency changes in reverse direction in a finite population. Evolution 28, 161-163.
    • (1974) Evolution , vol.28 , pp. 161-163
    • Maruyama, T.1    Kimura, M.2
  • 80
    • 17444412589 scopus 로고    scopus 로고
    • Detecting amino acid sites under positive selection and purifying selection
    • Massingham, T., and Goldman, N. (2005) Detecting amino acid sites under positive selection and purifying selection. Genetics 169, 1753-1762.
    • (2005) Genetics , vol.169 , pp. 1753-1762
    • Massingham, T.1    Goldman, N.2
  • 81
    • 0016220238 scopus 로고
    • The hitch-hiking effect of a favourable gene
    • Maynard Smith, J., and 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, S.J.1    Haigh, J.2
  • 82
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • McDonald, J. H., and Kreitman, M. (1991) Adaptive protein 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
  • 83
    • 0002134284 scopus 로고
    • Old age and natural death
    • Medawar, P. B. (1946) Old age and natural death. Mod. Quart. 2, 30-49.
    • (1946) Mod. Quart , vol.2 , pp. 30-49
    • Medawar, P.B.1
  • 85
    • 0019134329 scopus 로고
    • Molecular evolution of mRNA: A method for estimating evolutionary rates of synonymous and amino-acid substitutions from homologous nucleotide sequences and its application
    • Miyata, T., and Yasunaga, T. (1980) Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino-acid substitutions from homologous nucleotide sequences and its application. J. Mol. Evol. 16, 23-36.
    • (1980) J. Mol. Evol , vol.16 , pp. 23-36
    • Miyata, T.1    Yasunaga, T.2
  • 86
    • 0030054305 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates
    • Muse, S. V. (1996) Estimating synonymous and nonsynonymous substitution rates. Mol. Biol. Evol. 13, 105-114.
    • (1996) Mol. Biol. Evol , vol.13 , pp. 105-114
    • Muse, S.V.1
  • 87
    • 0028024626 scopus 로고
    • A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome
    • Muse, S. V., and Gaut, B. S. (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol. Biol. Evol. 11, 715-724.
    • (1994) Mol. Biol. Evol , vol.11 , pp. 715-724
    • Muse, S.V.1    Gaut, B.S.2
  • 88
    • 70349566593 scopus 로고
    • Diabetes mellitus: A "thrifty" genotype rendered detrimental by "progress
    • Neel, J. V. (1962) Diabetes mellitus: a "thrifty" genotype rendered detrimental by "progress"? Am. J. Hum. Genet. 14, 353-362.
    • (1962) Am. J. Hum. Genet , vol.14 , pp. 353-362
    • Neel, J.V.1
  • 89
    • 0022507362 scopus 로고
    • Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions
    • Nei, M., and Gojobori, T. (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol. Biol. Evol. 3, 418-426.
    • (1986) Mol. Biol. Evol , vol.3 , pp. 418-426
    • Nei, M.1    Gojobori, T.2
  • 91
    • 0005814023 scopus 로고
    • Mathematical model for studying genetic variation in terms of restriction endonucleases
    • Nei, M., and Li, W.-H. (1979) Mathematical model for studying genetic variation in terms of restriction endonucleases. Proc. Natl. Acad. Sci. USA 76, 5269-5273.
    • (1979) Proc. Natl. Acad. Sci. USA , vol.76 , pp. 5269-5273
    • Nei, M.1    Li, W.-H.2
  • 92
    • 0017050740 scopus 로고
    • Effects of random fluctuation of selection intensity on genetic variability in a finite population
    • Nei, M., and Yokoyama, S. (1976) Effects of random fluctuation of selection intensity on genetic variability in a finite population. Jpn. J. Genet. 51, 355-369.
    • (1976) Jpn. J. Genet , vol.51 , pp. 355-369
    • Nei, M.1    Yokoyama, S.2
  • 93
    • 77957959525 scopus 로고    scopus 로고
    • The neutral theory of molecular evolution in the genomic era
    • Nei, M., Suzuki, Y., and Nozawa, M. (2010) The neutral theory of molecular evolution in the genomic era. Annu. Rev. Genomics Hum. Genet. 11, 265-289.
    • (2010) Annu. Rev. Genomics Hum. Genet , vol.11 , pp. 265-289
    • Nei, M.1    Suzuki, Y.2    Nozawa, M.3
  • 94
    • 0035026704 scopus 로고    scopus 로고
    • Predicting deleterious amino acid substitutions
    • Ng, P., and Henikoff, S. (2001) Predicting deleterious amino acid substitutions. Genome Res. 11, 863-874.
    • (2001) Genome Res , vol.11 , pp. 863-874
    • Ng, P.1    Henikoff, S.2
  • 95
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen, R., and Yang, Z. (1998) Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics 148, 929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 99
    • 66149086564 scopus 로고    scopus 로고
    • Reliabilities of identifying positive selection by the branch-site and the site prediction methods
    • Nozawa, M., Suzuki, Y., and Nei, M. (2009a) Reliabilities of identifying positive selection by the branch-site and the site prediction methods. Proc. Natl. Acad. Sci. USA 106, 6700-6705.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 6700-6705
    • Nozawa, M.1    Suzuki, Y.2    Nei, M.3
  • 100
    • 70349308387 scopus 로고    scopus 로고
    • Response to Yang et al.: Problems with Bayesian methods of detecting positive selection at the DNA sequence level
    • Nozawa, M., Suzuki, Y., and Nei, M. (2009b) Response to Yang et al.: problems with Bayesian methods of detecting positive selection at the DNA sequence level. Proc. Natl. Acad. Sci. USA 106, E96.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106
    • Nozawa, M.1    Suzuki, Y.2    Nei, M.3
  • 101
    • 0027318192 scopus 로고
    • Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size
    • Ohta, T. (1993) Amino acid substitution at the Adh locus of Drosophila is facilitated by small population size. Proc. Natl. Acad. Sci. USA 90, 4548-4551.
    • (1993) Proc. Natl. Acad. Sci. USA , vol.90 , pp. 4548-4551
    • Ohta, T.1
  • 102
    • 0037058932 scopus 로고    scopus 로고
    • Near-neutrality in evolution of genes and gene regulation
    • Ohta, T. (2002) Near-neutrality in evolution of genes and gene regulation. Proc. Natl. Acad. Sci. USA 99, 16134-16137.
    • (2002) Proc. Natl. Acad. Sci. USA , vol.99 , pp. 16134-16137
    • Ohta, T.1
  • 103
    • 0015162354 scopus 로고
    • On the constancy of the evolutionary rate of cistrons
    • Ohta, T., and Kimura, M. (1971) On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1, 18-25.
    • (1971) J. Mol. Evol , vol.1 , pp. 18-25
    • Ohta, T.1    Kimura, M.2
  • 104
    • 0027533924 scopus 로고
    • Evolution of the Zf x and Zf y genes: Rates and interdependence between the genes
    • Pamilo, P., and Bianchi, O. (1993) Evolution of the Zf x and Zf y genes: rates and interdependence between the genes. Mol. Biol. Evol. 10, 271-281.
    • (1993) Mol. Biol. Evol , vol.10 , pp. 271-281
    • Pamilo, P.1    Bianchi, O.2
  • 105
    • 77952800173 scopus 로고    scopus 로고
    • On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila
    • Parsch, J., Novozhilov, S., Saminadin-Peter, S. S., Wong, K. M., and Andolfatto, P. (2010) On the utility of short intron sequences as a reference for the detection of positive and negative selection in Drosophila. Mol. Biol. Evol. 27, 1226-1234.
    • (2010) Mol. Biol. Evol , vol.27 , pp. 1226-1234
    • Parsch, J.1    Novozhilov, S.2    Saminadin-Peter, S.S.3    Wong, K.M.4    Andolfatto, P.5
  • 108
    • 33750737061 scopus 로고    scopus 로고
    • Accelerated evolution of conserved noncoding sequences in humans
    • Prabhakar, S., Noonan, J. P., Paabo, S., and Rubin, E. M. (2006) Accelerated evolution of conserved noncoding sequences in humans. Science 314, 786.
    • (2006) Science , vol.314 , pp. 786
    • Prabhakar, S.1    Noonan, J.P.2    Paabo, S.3    Rubin, E.M.4
  • 110
    • 28644440530 scopus 로고    scopus 로고
    • The signature of positive selection on standing genetic variation
    • Przeworski, M., Coop, G., and Wall, J. D. (2005) The signature of positive selection on standing genetic variation. Evolution 59, 2312-2323.
    • (2005) Evolution , vol.59 , pp. 2312-2323
    • Przeworski, M.1    Coop, G.2    Wall, J.D.3
  • 116
    • 0026460082 scopus 로고
    • Population genetics of polymorphism and divergence
    • Sawyer, S. A., and Hartl, D. L. (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
  • 117
    • 0347380978 scopus 로고    scopus 로고
    • Bayesian analysis suggests that most amino acid replacements in Drosophila are driven by positive selection
    • Sawyer, S. A., Kulathinal, R. J., Bustamante, C. D., and Hartl, D. L. (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
  • 118
    • 34249848425 scopus 로고    scopus 로고
    • Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila
    • Sawyer, S. A., Parsch, J., Zhang, Z., and Hartl, D. L. (2007) Prevalence of positive selection among nearly neutral amino acid replacements in Drosophila. Proc. Natl. Acad. Sci. USA 104, 6504-6510.
    • (2007) Proc. Natl. Acad. Sci. USA , vol.104 , pp. 6504-6510
    • Sawyer, S.A.1    Parsch, J.2    Zhang, Z.3    Hartl, D.L.4
  • 119
    • 72149107901 scopus 로고    scopus 로고
    • Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment
    • Schneider, A., Souvorov, A., Sabath, N., Landan, G., Gonnet, G. H., and Graur, D. (2009) Estimates of positive Darwinian selection are inflated by errors in sequencing, annotation, and alignment. Genome Biol. Evol. 1, 114-118.
    • (2009) Genome Biol. Evol , vol.1 , pp. 114-118
    • Schneider, A.1    Souvorov, A.2    Sabath, N.3    Landan, G.4    Gonnet, G.H.5    Graur, D.6
  • 122
    • 50649104620 scopus 로고    scopus 로고
    • Pervasive positive selection on duplicated and nond-uplicated vertebrate protein coding genes
    • Studer, R. A., Penel, S., Duret, L., and Robinson-Rechavi, M. (2008) Pervasive positive selection on duplicated and nond-uplicated vertebrate protein coding genes. Genome Res. 18, 1393-1402.
    • (2008) Genome Res , vol.18 , pp. 1393-1402
    • Studer, R.A.1    Penel, S.2    Duret, L.3    Robinson-Rechavi, M.4
  • 123
    • 0038781903 scopus 로고    scopus 로고
    • Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes
    • Subramanian, S., and Kumar, S. (2003) Neutral substitutions occur at a faster rate in exons than in noncoding DNA in primate genomes. Genome Res. 13, 838-844.
    • (2003) Genome Res , vol.13 , pp. 838-844
    • Subramanian, S.1    Kumar, S.2
  • 124
    • 33750959091 scopus 로고    scopus 로고
    • Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates
    • Subramanian, S., and Kumar, S. (2006) Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Mol. Biol. Evol. 23, 2283-2287.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 2283-2287
    • Subramanian, S.1    Kumar, S.2
  • 126
    • 1542395680 scopus 로고    scopus 로고
    • Negative selection on neutralization epitopes of poliovirus surface proteins: Implications for prediction of candidate epitopes for immunization
    • Suzuki, Y. (2004a) Negative selection on neutralization epitopes of poliovirus surface proteins: implications for prediction of candidate epitopes for immunization. Gene 328, 127-133.
    • (2004) Gene , vol.328 , pp. 127-133
    • Suzuki, Y.1
  • 127
    • 3042725369 scopus 로고    scopus 로고
    • New methods for detecting positive selection at single amino acid sites
    • Suzuki, Y. (2004b) New methods for detecting positive selection at single amino acid sites. J. Mol. Evol. 59, 11-19.
    • (2004) J. Mol. Evol , vol.59 , pp. 11-19
    • Suzuki, Y.1
  • 128
    • 8444220853 scopus 로고    scopus 로고
    • Three-dimensional window analysis for detecting positive selection at structural regions of proteins
    • Suzuki, Y. (2004c) Three-dimensional window analysis for detecting positive selection at structural regions of proteins. Mol. Biol. Evol. 21, 2352-2359.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 2352-2359
    • Suzuki, Y.1
  • 129
    • 33646268795 scopus 로고    scopus 로고
    • Ancient positive selection on CD155 as a possible cause for susceptibility to poliovirus infection in simians
    • Suzuki, Y. (2006a) Ancient positive selection on CD155 as a possible cause for susceptibility to poliovirus infection in simians. Gene 373, 16-22.
    • (2006) Gene , vol.373 , pp. 16-22
    • Suzuki, Y.1
  • 130
    • 33748789595 scopus 로고    scopus 로고
    • Natural selection on the influenza virus genome
    • Suzuki, Y. (2006b) Natural selection on the influenza virus genome. Mol. Biol. Evol. 23, 1902-1911.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 1902-1911
    • Suzuki, Y.1
  • 131
    • 31844450495 scopus 로고    scopus 로고
    • Statistical properties of the methods for detecting positively selected amino acid sites
    • Suzuki, Y. (2006c) Statistical properties of the methods for detecting positively selected amino acid sites. Gene 365, 125-129.
    • (2006) Gene , vol.365 , pp. 125-129
    • Suzuki, Y.1
  • 132
    • 54249105361 scopus 로고    scopus 로고
    • False-positive results obtained from the branch-site test of positive selection
    • Suzuki, Y. (2008a) False-positive results obtained from the branch-site test of positive selection. Genes. Genet. Syst. 83, 331-338.
    • (2008) Genes. Genet. Syst , vol.83 , pp. 331-338
    • Suzuki, Y.1
  • 133
    • 79952925248 scopus 로고    scopus 로고
    • Phylogenetic window analysis for detecting chronological changes in natural selection
    • Suzuki, Y. (2008b) Phylogenetic window analysis for detecting chronological changes in natural selection. Open Evol. J. 2, 13-30.
    • (2008) Open Evol. J , vol.2 , pp. 13-30
    • Suzuki, Y.1
  • 134
    • 0032849322 scopus 로고    scopus 로고
    • A method for detecting positive selection at single amino acid sites
    • Suzuki, Y., and Gojobori, T. (1999) A method for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 16, 1315-1328.
    • (1999) Mol. Biol. Evol , vol.16 , pp. 1315-1328
    • Suzuki, Y.1    Gojobori, T.2
  • 135
    • 0035802435 scopus 로고    scopus 로고
    • Positively selected amino acid sites in the entire coding region of hepatitis C virus subtype 1b
    • Suzuki, Y., and Gojobori, T. (2001) Positively selected amino acid sites in the entire coding region of hepatitis C virus subtype 1b. Gene 276, 83-87.
    • (2001) Gene , vol.276 , pp. 83-87
    • Suzuki, Y.1    Gojobori, T.2
  • 137
    • 0035215112 scopus 로고    scopus 로고
    • Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites
    • Suzuki, Y., and Nei, M. (2001) Reliabilities of parsimony-based and likelihood-based methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 18, 2179-2185.
    • (2001) Mol. Biol. Evol , vol.18 , pp. 2179-2185
    • Suzuki, Y.1    Nei, M.2
  • 138
    • 0036855372 scopus 로고    scopus 로고
    • Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites
    • Suzuki, Y., and Nei, M. (2002) Simulation study of the reliability and robustness of the statistical methods for detecting positive selection at single amino acid sites. Mol. Biol. Evol. 19, 1865-1869.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 1865-1869
    • Suzuki, Y.1    Nei, M.2
  • 139
    • 1942533483 scopus 로고    scopus 로고
    • False positive selection identified by ML-based methods: Examples from the Sig1 gene of diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus
    • Suzuki, Y., and Nei, M. (2004) False positive selection identified by ML-based methods: examples from the Sig1 gene of diatom Thalassiosira weissflogii and the tax gene of a human T-cell lymphotropic virus. Mol. Biol. Evol. 21, 914-921.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 914-921
    • Suzuki, Y.1    Nei, M.2
  • 140
    • 70349916085 scopus 로고    scopus 로고
    • Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level
    • Suzuki, Y., Gojobori, T., and Kumar, S. (2009) Methods for incorporating the hypermutability of CpG dinucleotides in detecting natural selection operating at the amino acid sequence level. Mol. Biol. Evol. 26, 2275-2284.
    • (2009) Mol. Biol. Evol , vol.26 , pp. 2275-2284
    • Suzuki, Y.1    Gojobori, T.2    Kumar, S.3
  • 141
    • 0021066244 scopus 로고
    • Evolutionary relationship of DNA sequences in finite populations
    • Tajima, F. (1983) Evolutionary relationship of DNA sequences in finite populations. Genetics 105, 437-460.
    • (1983) Genetics , vol.105 , pp. 437-460
    • Tajima, F.1
  • 142
    • 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
  • 143
    • 1242352089 scopus 로고    scopus 로고
    • Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks
    • Tamura, K., Subramanian, S., and Kumar, S. (2004) Temporal patterns of fruit fly (Drosophila) evolution revealed by mutation clocks. Mol. Biol. Evol. 21, 36-44.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 36-44
    • Tamura, K.1    Subramanian, S.2    Kumar, S.3
  • 144
    • 34547110828 scopus 로고    scopus 로고
    • A new approach for using genome scans to detect recent positive selection in the human genome
    • Tang, K., Thornton, K. R., and Stoneking, M. (2007) A new approach for using genome scans to detect recent positive selection in the human genome. PLoS Biol. 5, e171.
    • (2007) PLoS Biol , vol.5
    • Tang, K.1    Thornton, K.R.2    Stoneking, M.3
  • 146
    • 33744815615 scopus 로고    scopus 로고
    • How reliable are empirical genomic scans for selective sweeps?
    • Teshima, K. M., Coop, G., and Przeworski, M. (2006) How reliable are empirical genomic scans for selective sweeps? Genome Res. 16, 702-712.
    • (2006) Genome Res , vol.16 , pp. 702-712
    • Teshima, K.M.1    Coop, G.2    Przeworski, M.3
  • 147
    • 24344500211 scopus 로고    scopus 로고
    • Initial sequence of the chimpanzee genome and comparison with the human genome
    • The Chimpanzee Sequencing and Analysis Consortium
    • The Chimpanzee Sequencing and Analysis Consortium. (2005) Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437, 69-87.
    • (2005) Nature , vol.437 , pp. 69-87
  • 148
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • The International HapMap Consotrium
    • The International HapMap Consotrium. (2005) A haplotype map of the human genome. Nature 437, 1299-1320.
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 152
    • 30444460720 scopus 로고    scopus 로고
    • Global landscape of recent inferred Darwinian selection for Homo sapiens
    • Wang, E. T., Kodama, G., Baldi, P., and Moyzis, R. K. (2006) Global landscape of recent inferred Darwinian selection for Homo sapiens. Proc. Natl. Acad. Sci. USA 103, 135-140.
    • (2006) Proc. Natl. Acad. Sci. USA , vol.103 , pp. 135-140
    • Wang, E.T.1    Kodama, G.2    Baldi, P.3    Moyzis, R.K.4
  • 155
    • 38549135938 scopus 로고    scopus 로고
    • Alignment uncertainty and genomic analysis
    • Wong, K. M., Suchard, M. A., and Huelsenbeck, J. P. (2008) Alignment uncertainty and genomic analysis. Science 319, 473-476.
    • (2008) Science , vol.319 , pp. 473-476
    • Wong, K.M.1    Suchard, M.A.2    Huelsenbeck, J.P.3
  • 156
    • 3142739466 scopus 로고    scopus 로고
    • Detecting selection in noncoding regions of nucleotide sequences
    • Wong, W. S. W., and Nielsen, R. (2004) Detecting selection in noncoding regions of nucleotide sequences. Genetics 167, 949-958.
    • (2004) Genetics , vol.167 , pp. 949-958
    • Wong, W.S.W.1    Nielsen, R.2
  • 157
    • 8544225780 scopus 로고    scopus 로고
    • Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites
    • Wong, W. S. W., Yang, Z., Goldman, N., and Nielsen, R. (2004) Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites. Genetics 168, 1041-1051.
    • (2004) Genetics , vol.168 , pp. 1041-1051
    • Wong, W.S.W.1    Yang, Z.2    Goldman, N.3    Nielsen, R.4
  • 158
    • 0000929750 scopus 로고
    • Systems of mating. I. The biometric relations between parent and offspring
    • Wright, S. (1921) Systems of mating. I. The biometric relations between parent and offspring. Genetics 6, 111-123.
    • (1921) Genetics , vol.6 , pp. 111-123
    • Wright, S.1
  • 159
    • 8544246487 scopus 로고    scopus 로고
    • The HKA test revisited: A maximum-likelihood-ratio test of the standard neutral model
    • Wright, S. I., and Charlesworth, B. (2004) The HKA test revisited: a maximum-likelihood-ratio test of the standard neutral model. Genetics 168, 1071-1076.
    • (2004) Genetics , vol.168 , pp. 1071-1076
    • Wright, S.I.1    Charlesworth, B.2
  • 160
    • 0031897964 scopus 로고    scopus 로고
    • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution
    • Yang, Z. (1998) Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution. Mol. Biol. Evol. 15, 568-573.
    • (1998) Mol. Biol. Evol , vol.15 , pp. 568-573
    • Yang, Z.1
  • 161
    • 0031960185 scopus 로고    scopus 로고
    • Synonymous and nonsynony-mous rate variation in nuclear genes of mammals
    • Yang, Z., and Nielsen, R. (1998) Synonymous and nonsynony-mous 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
  • 162
    • 0033979433 scopus 로고    scopus 로고
    • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models
    • Yang, Z., and Nielsen, R. (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol. Biol. Evol. 17, 32-43.
    • (2000) Mol. Biol. Evol , vol.17 , pp. 32-43
    • Yang, Z.1    Nielsen, R.2
  • 163
    • 0036270185 scopus 로고    scopus 로고
    • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages
    • Yang, Z., and Nielsen, R. (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol. Biol. Evol. 19, 908-917.
    • (2002) Mol. Biol. Evol , vol.19 , pp. 908-917
    • Yang, Z.1    Nielsen, R.2
  • 164
    • 39749161509 scopus 로고    scopus 로고
    • Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage
    • Yang, Z., and Nielsen, R. (2008) Mutation-selection models of codon substitution and their use to estimate selective strengths on codon usage. Mol. Biol. Evol. 25, 568-579.
    • (2008) Mol. Biol. Evol , vol.25 , pp. 568-579
    • Yang, Z.1    Nielsen, R.2
  • 165
    • 0034097381 scopus 로고    scopus 로고
    • Codon-substitution models for heterogeneous selection pressure at amino acid sites
    • Yang, Z., Nielsen, R., Goldman, N., and Pedersen, A.M.K. (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155, 431-449.
    • (2000) Genetics , vol.155 , pp. 431-449
    • Yang, Z.1    Nielsen, R.2    Goldman, N.3    Pedersen, A.M.K.4
  • 166
    • 51649122492 scopus 로고    scopus 로고
    • Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates
    • Yokoyama, S., Tada, T., Zhang, H., and Britt, L. (2008) Elucidation of phenotypic adaptations: molecular analyses of dim-light vision proteins in vertebrates. Proc. Natl. Acad. Sci. USA 105, 13480-13485.
    • (2008) Proc. Natl. Acad. Sci. USA , vol.105 , pp. 13480-13485
    • Yokoyama, S.1    Tada, T.2    Zhang, H.3    Britt, L.4
  • 167
    • 3042637218 scopus 로고    scopus 로고
    • Frequent false detection of positive selection by the likelihood method with branch-site models
    • Zhang, J. (2004) Frequent false detection of positive selection by the likelihood method with branch-site models. Mol. Biol. Evol. 21, 1332-1339.
    • (2004) Mol. Biol. Evol , vol.21 , pp. 1332-1339
    • Zhang, J.1
  • 168
    • 0031306932 scopus 로고    scopus 로고
    • Small-sample tests of episodic adaptive evolution: A case study of primate lysozymes
    • Zhang, J., Kumar, S., and Nei, M. (1997) Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes. Mol. Biol. Evol. 14, 1335-1338.
    • (1997) Mol. Biol. Evol , vol.14 , pp. 1335-1338
    • Zhang, J.1    Kumar, S.2    Nei, M.3
  • 169
    • 27844439855 scopus 로고    scopus 로고
    • Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level
    • Zhang, J., Nielsen, R., and Yang, Z. (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol. Biol. Evol. 22, 2472-2479.
    • (2005) Mol. Biol. Evol , vol.22 , pp. 2472-2479
    • Zhang, J.1    Nielsen, R.2    Yang, Z.3
  • 170
    • 0032584099 scopus 로고    scopus 로고
    • Positive Darwinian selection after gene duplication in primate ribonuclease genes
    • Zhang, J., Rosenberg, H. F., and Nei, M. (1998) Positive Darwinian selection after gene duplication in primate ribonuclease genes. Proc. Natl. Acad. Sci. USA 95, 3708-3713.
    • (1998) Proc. Natl. Acad. Sci. USA , vol.95 , pp. 3708-3713
    • Zhang, J.1    Rosenberg, H.F.2    Nei, M.3
  • 171
    • 77954988795 scopus 로고    scopus 로고
    • Detecting positive and purifying selection at synonymous sites in yeast and worm
    • Zhou, T., Gu, W., and Wilke, C. O. (2010) Detecting positive and purifying selection at synonymous sites in yeast and worm. Mol. Biol. Evol. 27, 1912-1922.
    • (2010) Mol. Biol. Evol , vol.27 , pp. 1912-1922
    • Zhou, T.1    Gu, W.2    Wilke, C.O.3
  • 172
    • 75849154706 scopus 로고    scopus 로고
    • Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates
    • Zhuang, H., Chien, M.-S., and Matsunami, H. (2009) Dynamic functional evolution of an odorant receptor for sex-steroid-derived odors in primates. Proc. Natl. Acad. Sci. USA 106, 21247-21251.
    • (2009) Proc. Natl. Acad. Sci. USA , vol.106 , pp. 21247-21251
    • Zhuang, H.1    Chien, M.-S.2    Matsunami, H.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.