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Volumn 238, Issue 1, 1999, Pages 39-51

Within- and between-species DNA sequence variation and the 'footprint' of natural selection

Author keywords

Adaptive evolution; Molecular evolution; Nearly neutral theory; Neutral theory; Population genetics

Indexed keywords

AMINO ACID; NUCLEOTIDE; PROTEIN;

EID: 0032869219     PISSN: 03781119     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0378-1119(99)00294-2     Document Type: Article
Times cited : (71)

References (59)
  • 1
    • 0028797897 scopus 로고
    • Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA
    • Akashi H. Inferring weak selection from patterns of polymorphism and divergence at "silent" sites in Drosophila DNA. Genetics. 139:1995;1067-1076.
    • (1995) Genetics , vol.139 , pp. 1067-1076
    • Akashi, H.1
  • 2
    • 0029985179 scopus 로고    scopus 로고
    • Molecular evolution between Drosophila melanogaster and D. simulans: Reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster
    • Akashi H. Molecular evolution between Drosophila melanogaster and D. simulans: reduced codon bias, faster rates of amino acid substitution, and larger proteins in D. melanogaster. Genetics. 144:1996;1297-1307.
    • (1996) Genetics , vol.144 , pp. 1297-1307
    • Akashi, H.1
  • 3
    • 0031593202 scopus 로고    scopus 로고
    • Codon bias evolution in Drosophila: Population genetics of mutation-selection-drift
    • Akashi H. Codon bias evolution in Drosophila: population genetics of mutation-selection-drift. Gene. 205:1997;269-278.
    • (1997) Gene , vol.205 , pp. 269-278
    • Akashi, H.1
  • 4
    • 0031303812 scopus 로고    scopus 로고
    • Distinguishing the effects of mutational biases and natural selection on DNA sequence variation
    • letter
    • Akashi H. Distinguishing the effects of mutational biases and natural selection on DNA sequence variation. letter Genetics. 147:1997;1989-1991.
    • (1997) Genetics , vol.147 , pp. 1989-1991
    • Akashi, H.1
  • 5
    • 0032953881 scopus 로고    scopus 로고
    • Inferring the fitness effects of DNA mutations from patterns of polymorphism and divergence: Statistical power to detect directional selection under stationarity and free recombination
    • Akashi H. Inferring the fitness effects of DNA mutations from patterns of polymorphism and divergence: statistical power to detect directional selection under stationarity and free recombination. Genetics. 151:1999;221-238.
    • (1999) Genetics , vol.151 , pp. 221-238
    • Akashi, H.1
  • 6
    • 0031738130 scopus 로고    scopus 로고
    • Translational selection and molecular evolution
    • Akashi H., Eyre-Walker A. Translational selection and molecular evolution. Curr. Opin. Genet. Dev. 8:1998;688-693.
    • (1998) Curr. Opin. Genet. Dev. , vol.8 , pp. 688-693
    • Akashi, H.1    Eyre-Walker, A.2
  • 7
    • 0030903283 scopus 로고    scopus 로고
    • Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila
    • Akashi H., Schaeffer S.W. Natural selection and the frequency distributions of "silent" DNA polymorphism in Drosophila. Genetics. 146:1997;295-307.
    • (1997) Genetics , vol.146 , pp. 295-307
    • Akashi, H.1    Schaeffer, S.W.2
  • 8
    • 0025297285 scopus 로고
    • Codon preferences in free-living microorganisms
    • Andersson S.G.E., Kurland C.G. Codon preferences in free-living microorganisms. Microbiol. Rev. 54:1990;198-210.
    • (1990) Microbiol. Rev. , vol.54 , pp. 198-210
    • Andersson, S.G.E.1    Kurland, C.G.2
  • 9
    • 0028046414 scopus 로고
    • Unraveling selection in the mitochondrial genome of Drosophila
    • Ballard J.W.O., Kreitman M. Unraveling selection in the mitochondrial genome of Drosophila. Genetics. 138:1994;757-772.
    • (1994) Genetics , vol.138 , pp. 757-772
    • Ballard, J.W.O.1    Kreitman, M.2
  • 10
    • 84993842127 scopus 로고
    • Are codon usage patterns in unicellular organisms determined by selection-mutation balance
    • Bulmer M. Are codon usage patterns in unicellular organisms determined by selection-mutation balance. J. Evol. Biol. 1:1988;15-26.
    • (1988) J. Evol. Biol. , vol.1 , pp. 15-26
    • Bulmer, M.1
  • 11
    • 0025941139 scopus 로고
    • The selection-mutation-drift theory of synonymous codon usage
    • Bulmer M. The selection-mutation-drift theory of synonymous codon usage. Genetics. 129:1991;897-907.
    • (1991) Genetics , vol.129 , pp. 897-907
    • Bulmer, M.1
  • 12
    • 12044252488 scopus 로고
    • Compositional bias, character-state bias, and character-state reconstruction using parsimony
    • Collins T.M., Wimberger P.H., Naylor G.J.P. Compositional bias, character-state bias, and character-state reconstruction using parsimony. Syst. Biol. 43:1994;482-496.
    • (1994) Syst. Biol. , vol.43 , pp. 482-496
    • Collins, T.M.1    Wimberger, P.H.2    Naylor, G.J.P.3
  • 13
    • 0027304241 scopus 로고
    • Evidence for adaptive evolution of the G6pd gene in the Drosophila melanogaster and Drosophila simulans lineages
    • Eanes W.F., Kirchner M., Yoon J. Evidence for adaptive evolution of the G6pd gene in the Drosophila melanogaster and Drosophila simulans lineages. Proc. Natl. Acad. Sci. USA. 90:1993;7475-7479.
    • (1993) Proc. Natl. Acad. Sci. USA. , vol.90 , pp. 7475-7479
    • Eanes, W.F.1    Kirchner, M.2    Yoon, J.3
  • 14
    • 0030007094 scopus 로고    scopus 로고
    • Large-scale search for genes on which positive selection may operate
    • Endo T., Ikeo K., Gojobori T. Large-scale search for genes on which positive selection may operate. Mol. Biol. Evol. 13:1996;685-690.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 685-690
    • Endo, T.1    Ikeo, K.2    Gojobori, T.3
  • 15
    • 0031303811 scopus 로고    scopus 로고
    • Differentiating between selection and mutational bias
    • letter
    • Eyre-Walker A. Differentiating between selection and mutational bias. letter Genetics. 147:1997;1983-1987.
    • (1997) Genetics , vol.147 , pp. 1983-1987
    • Eyre-Walker, A.1
  • 16
    • 0032434101 scopus 로고    scopus 로고
    • Problems with parsimony in sequences of biased base composition
    • Eyre-Walker A. Problems with parsimony in sequences of biased base composition. J. Mol. Evol. 47:1998;686-690.
    • (1998) J. Mol. Evol. , vol.47 , pp. 686-690
    • Eyre-Walker, A.1
  • 17
    • 0002690901 scopus 로고
    • On the evolution of base composition of DNA
    • Freese E. On the evolution of base composition of DNA. J. Theor. Biol. 3:1962;82-101.
    • (1962) J. Theor. Biol. , vol.3 , pp. 82-101
    • Freese, E.1
  • 18
    • 0028010308 scopus 로고
    • Using phylogenies to test hypotheses of adaptation: A critique of some current proposals
    • Frumhoff P.C., Reeve H.K. Using phylogenies to test hypotheses of adaptation: a critique of some current proposals. Evolution. 48:1994;172-180.
    • (1994) Evolution , vol.48 , pp. 172-180
    • Frumhoff, P.C.1    Reeve, H.K.2
  • 20
    • 0022446440 scopus 로고
    • Sequence evolution within populations under multiple types of mutation
    • Golding G.B., Aquadro C.F., Langley C.H. Sequence evolution within populations under multiple types of mutation. Proc. Natl. Acad. Sci. USA. 83:1986;427-431.
    • (1986) Proc. Natl. Acad. Sci. USA. , vol.83 , pp. 427-431
    • Golding, G.B.1    Aquadro, C.F.2    Langley, C.H.3
  • 21
    • 0027978722 scopus 로고
    • Selection intensity for codon bias
    • Hartl D.L., Moriyama E.N., Sawyer S. Selection intensity for codon bias. Genetics. 138:1994;227-234.
    • (1994) Genetics , vol.138 , pp. 227-234
    • Hartl, D.L.1    Moriyama, E.N.2    Sawyer, S.3
  • 22
    • 0027214053 scopus 로고
    • Levels of DNA polymorphism and divergence yield important insights into evolutionary processes
    • comment
    • Hudson R.R. Levels of DNA polymorphism and divergence yield important insights into evolutionary processes. comment Proc. Natl. Acad. Sci. USA. 90:1993;7425-7426.
    • (1993) Proc. Natl. Acad. Sci. USA. , vol.90 , pp. 7425-7426
    • Hudson, R.R.1
  • 23
    • 0023764283 scopus 로고
    • Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection
    • Hughes A.L., Nei M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature. 335:1988;167-170.
    • (1988) Nature , vol.335 , pp. 167-170
    • Hughes, A.L.1    Nei, M.2
  • 24
    • 0021958933 scopus 로고
    • Codon usage and tRNA content in unicellular and multicellular organisms
    • Ikemura T. Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2:1985;13-34.
    • (1985) Mol. Biol. Evol. , vol.2 , pp. 13-34
    • Ikemura, T.1
  • 25
    • 0028854940 scopus 로고
    • Nucleotide variation at the hypervariable esterase 6 isozyme locus of Drosophila simulans
    • Karotam J., Boyce T.M., Oakeshott J.G. Nucleotide variation at the hypervariable esterase 6 isozyme locus of Drosophila simulans. Mol. Biol. Evol. 12:1995;113-122.
    • (1995) Mol. Biol. Evol. , vol.12 , pp. 113-122
    • Karotam, J.1    Boyce, T.M.2    Oakeshott, J.G.3
  • 26
    • 0000800333 scopus 로고
    • On the probability of fixation of mutant genes in a population
    • Kimura M. On the probability of fixation of mutant genes in a population. Genetics. 47:1962;713-719.
    • (1962) Genetics , vol.47 , pp. 713-719
    • Kimura, M.1
  • 27
    • 0014421064 scopus 로고
    • Evolutionary rate at the molecular level
    • Kimura M. Evolutionary rate at the molecular level. Nature. 217:1968;624-626.
    • (1968) Nature , vol.217 , pp. 624-626
    • Kimura, M.1
  • 29
    • 0014680905 scopus 로고
    • Non-Darwinian evolution
    • King J.L., Jukes T.H. Non-Darwinian evolution. Science. 164:1969;788-798.
    • (1969) Science , vol.164 , pp. 788-798
    • King, J.L.1    Jukes, T.H.2
  • 30
    • 0031931071 scopus 로고    scopus 로고
    • The role of gene conversion in determining sequence variation and divergence in the Est-5 gene family in Drosophila pseudoobscura
    • King L.M. The role of gene conversion in determining sequence variation and divergence in the Est-5 gene family in Drosophila pseudoobscura. Genetics. 148:1998;305-315.
    • (1998) Genetics , vol.148 , pp. 305-315
    • King, L.M.1
  • 31
    • 0023064998 scopus 로고
    • Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons
    • Li W.-H. Models of nearly neutral mutations with particular implications for nonrandom usage of synonymous codons. J. Mol. Evol. 24:1987;337-345.
    • (1987) J. Mol. Evol. , vol.24 , pp. 337-345
    • Li, W.-H.1
  • 32
    • 0003421005 scopus 로고    scopus 로고
    • Massachusetts: Sinauer Associates
    • Li W.-H. Molecular Evolution. 1996;Sinauer Associates, Massachusetts.
    • (1996) Molecular Evolution
    • Li, W.-H.1
  • 33
    • 0027905006 scopus 로고
    • Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila
    • Long M., Langley C.H. Natural selection and the origin of jingwei, a chimeric processed functional gene in Drosophila. Science. 260:1993;91-95.
    • (1993) Science , vol.260 , pp. 91-95
    • Long, M.1    Langley, C.H.2
  • 34
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • McDonald J.H., Kreitman M. Adaptive protein evolution at the Adh locus in Drosophila. Nature. 351:1991;652-654.
    • (1991) Nature , vol.351 , pp. 652-654
    • McDonald, J.H.1    Kreitman, M.2
  • 35
    • 0027153966 scopus 로고
    • Codon usage bias and base composition of nuclear genes in Drosophila
    • Moriyama E.N., Hartl D.L. Codon usage bias and base composition of nuclear genes in Drosophila. Genetics. 134:1993;847-858.
    • (1993) Genetics , vol.134 , pp. 847-858
    • Moriyama, E.N.1    Hartl, D.L.2
  • 36
    • 0028279173 scopus 로고
    • Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice
    • Nachman M.W., Boyer S.N., Aquadro C.F. Nonneutral evolution at the mitochondrial NADH dehydrogenase subunit 3 gene in mice. Proc. Natl. Acad. Sci. USA. 91:1994;6364-6368.
    • (1994) Proc. Natl. Acad. Sci. USA. , vol.91 , pp. 6364-6368
    • Nachman, M.W.1    Boyer, S.N.2    Aquadro, C.F.3
  • 37
    • 0030011347 scopus 로고    scopus 로고
    • Nonneutral mitochondrial DNA variation in humans and chimpanzees
    • Nachman M.W., Brown W.M., Stoneking M., Aquadro C.F. Nonneutral mitochondrial DNA variation in humans and chimpanzees. Genetics. 142:1996;953-963.
    • (1996) Genetics , vol.142 , pp. 953-963
    • Nachman, M.W.1    Brown, W.M.2    Stoneking, M.3    Aquadro, C.F.4
  • 38
    • 0031972161 scopus 로고    scopus 로고
    • Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene
    • Nielsen R., Yang Z. Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene. Genetics. 148:1998;929-936.
    • (1998) Genetics , vol.148 , pp. 929-936
    • Nielsen, R.1    Yang, Z.2
  • 39
    • 0015722319 scopus 로고
    • Slightly deleterious mutant substitutions in evolution
    • Ohta T. Slightly deleterious mutant substitutions in evolution. Nature. 246:1973;96-98.
    • (1973) Nature , vol.246 , pp. 96-98
    • Ohta, T.1
  • 40
    • 0027020232 scopus 로고
    • The nearly neutral theory of molecular evolution
    • Ohta T. The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23:1992;263-286.
    • (1992) Annu. Rev. Ecol. Syst. , vol.23 , pp. 263-286
    • Ohta, T.1
  • 41
    • 0015162354 scopus 로고
    • On the constancy of the evolutionary rate of cistrons
    • Ohta T., Kimura M. On the constancy of the evolutionary rate of cistrons. J. Mol. Evol. 1:1971;18-25.
    • (1971) J. Mol. Evol. , vol.1 , pp. 18-25
    • Ohta, T.1    Kimura, M.2
  • 42
    • 0024722501 scopus 로고
    • Errors and alternatives in reading the universal genetic code
    • Parker J. Errors and alternatives in reading the universal genetic code. Microbiol. Rev. 53:1989;273-298.
    • (1989) Microbiol. Rev. , vol.53 , pp. 273-298
    • Parker, J.1
  • 43
    • 0027942996 scopus 로고
    • Neutral and nonneutral evolution of Drosophila mitochondrial DNA
    • Rand D.M., Dorfsman M., Kann L.M. Neutral and nonneutral evolution of Drosophila mitochondrial DNA. Genetics. 138:1994;741-756.
    • (1994) Genetics , vol.138 , pp. 741-756
    • Rand, D.M.1    Dorfsman, M.2    Kann, L.M.3
  • 44
    • 0026460082 scopus 로고
    • Population genetics of polymorphism and divergence
    • Sawyer S.A., Hartl D.L. Population genetics of polymorphism and divergence. Genetics. 132:1992;1161-1176.
    • (1992) Genetics , vol.132 , pp. 1161-1176
    • Sawyer, S.A.1    Hartl, D.L.2
  • 45
    • 0023413802 scopus 로고
    • Confidence interval for the number of selectively neutral amino acid polymorphisms
    • Sawyer S.A., Dykhuizen D.E., Hartl D.L. Confidence interval for the number of selectively neutral amino acid polymorphisms. Proc. Natl. Acad. Sci. USA. 84:1987;6225-6228.
    • (1987) Proc. Natl. Acad. Sci. USA. , vol.84 , pp. 6225-6228
    • Sawyer, S.A.1    Dykhuizen, D.E.2    Hartl, D.L.3
  • 46
    • 0031417707 scopus 로고    scopus 로고
    • Likelihood of ancestral states in adaptive radiation
    • Schluter D., Price T., Mooers A.O., Ludwig D. Likelihood of ancestral states in adaptive radiation. Evolution. 51:1997;1699-1711.
    • (1997) Evolution , vol.51 , pp. 1699-1711
    • Schluter, D.1    Price, T.2    Mooers, A.O.3    Ludwig, D.4
  • 47
    • 0022856787 scopus 로고
    • An evolutionary perspective on synonymous codon usage in unicellular organisms
    • Sharp P.M., Li W.-H. An evolutionary perspective on synonymous codon usage in unicellular organisms. J. Mol. Evol. 24:1986;28-38.
    • (1986) J. Mol. Evol. , vol.24 , pp. 28-38
    • Sharp, P.M.1    Li, W.-H.2
  • 49
    • 0027787871 scopus 로고
    • The crystal structure of lysin, a fertilization protein
    • Shaw A., McRee D.E., Vacquier V.D., Stout C.D. The crystal structure of lysin, a fertilization protein. Science. 262:1993;1864-1867.
    • (1993) Science , vol.262 , pp. 1864-1867
    • Shaw, A.1    McRee, D.E.2    Vacquier, V.D.3    Stout, C.D.4
  • 50
    • 0024116811 scopus 로고
    • "silent" sites in Drosophila genes are not neutral: Evidence of selection among synonymous codons
    • Shields D.C., Sharp P.M., Higgins D.G., Wright F. "Silent" sites in Drosophila genes are not neutral: evidence of selection among synonymous codons. Mol. Biol. Evol. 5:1988;704-716.
    • (1988) Mol. Biol. Evol. , vol.5 , pp. 704-716
    • Shields, D.C.1    Sharp, P.M.2    Higgins, D.G.3    Wright, F.4
  • 51
    • 3643052747 scopus 로고
    • On the genetic basis of variation and heterogeneity of DNA base composition
    • Sueoka N. On the genetic basis of variation and heterogeneity of DNA base composition. Proc. Natl. Acad. Sci. USA. 48:1962;582-592.
    • (1962) Proc. Natl. Acad. Sci. USA. , vol.48 , pp. 582-592
    • Sueoka, N.1
  • 52
    • 0023991945 scopus 로고
    • Directional mutation pressure and neutral molecular evolution
    • Sueoka N. Directional mutation pressure and neutral molecular evolution. Proc. Natl. Acad. Sci. USA. 85:1988;2653-2657.
    • (1988) Proc. Natl. Acad. Sci. USA. , vol.85 , pp. 2653-2657
    • Sueoka, N.1
  • 53
    • 0029909631 scopus 로고    scopus 로고
    • Contingency tests of neutrality using intra/interspecific gene trees: The rejection of neutrality for the evolution of the mitochondrial cytochroms oxidase II gene in the Hominoid primates
    • Templeton A.R. Contingency tests of neutrality using intra/interspecific gene trees: the rejection of neutrality for the evolution of the mitochondrial cytochroms oxidase II gene in the Hominoid primates. Genetics. 144:1996;1263-1270.
    • (1996) Genetics , vol.144 , pp. 1263-1270
    • Templeton, A.R.1
  • 54
    • 0027640330 scopus 로고
    • Abalone sperm lysin: Unusual model of evolution of a gamete recognition protein
    • Vacquier V.D., Lee Y.-H. Abalone sperm lysin: unusual model of evolution of a gamete recognition protein. Zygote. 1:1993;181-196.
    • (1993) Zygote , vol.1 , pp. 181-196
    • Vacquier, V.D.1    Lee, Y.-H.2
  • 55
    • 0030034586 scopus 로고    scopus 로고
    • Molecular population genetics of ref(2)P, a locus which confers viral resistance in Drosophila
    • Wayne M.L., Contamine D., Kreitman M. Molecular population genetics of ref(2)P, a locus which confers viral resistance in Drosophila. Mol. Biol. Evol. 13:1996;191-199.
    • (1996) Mol. Biol. Evol. , vol.13 , pp. 191-199
    • Wayne, M.L.1    Contamine, D.2    Kreitman, M.3
  • 56
    • 0031908203 scopus 로고    scopus 로고
    • Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees
    • Wise C.A., Sraml M., Easteal S. Departure from neutrality at the mitochondrial NADH dehydrogenase subunit 2 gene in humans, but not in chimpanzees. Genetics. 148:1998;409-421.
    • (1998) Genetics , vol.148 , pp. 409-421
    • Wise, C.A.1    Sraml, M.2    Easteal, S.3
  • 57
    • 0028820333 scopus 로고
    • A new method of inference of ancestral nucleotide and amino acid sequences
    • Yang Z., Kumar S., Nei M. A new method of inference of ancestral nucleotide and amino acid sequences. Genetics. 141:1995;1641-1650.
    • (1995) Genetics , vol.141 , pp. 1641-1650
    • Yang, Z.1    Kumar, S.2    Nei, M.3
  • 58
    • 0031468444 scopus 로고    scopus 로고
    • Molecular genetic basis of adaptive selection: Examples from color vision in vertebrates
    • Yokoyama S. Molecular genetic basis of adaptive selection: examples from color vision in vertebrates. Annu. Rev. Genet. 31:1997;315-336.
    • (1997) Annu. Rev. Genet. , vol.31 , pp. 315-336
    • Yokoyama, S.1
  • 59
    • 0031025677 scopus 로고    scopus 로고
    • Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods
    • Zhang J., Nei M. Accuracies of ancestral amino acid sequences inferred by the parsimony, likelihood, and distance methods. J. Mol. Evol. 44:1997;S139-S146.
    • (1997) J. Mol. Evol. , vol.44
    • Zhang, J.1    Nei, M.2


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