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Volumn 2, Issue 10, 2006, Pages 1580-1589

Inferring the demographic history and rate of adaptive substitution in Drosophila

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DEMOGRAPHY; DNA POLYMORPHISM; DROSOPHILA; DROSOPHILA MELANOGASTER; GENE MUTATION; GENETIC VARIABILITY; INSECT GENETICS; NONHUMAN; POPULATION GENETICS; SINGLE NUCLEOTIDE POLYMORPHISM; X CHROMOSOME; ADAPTATION; AFRICA; ANIMAL; BIOLOGICAL MODEL; EUROPE; GENETIC SELECTION; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; MUTAGENESIS;

EID: 33750491918     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.0020166     Document Type: Article
Times cited : (249)

References (45)
  • 1
    • 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 WH, Wu CI, Luo CC (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
  • 2
    • 0026428610 scopus 로고
    • Adaptive protein evolution at the Adh locus in Drosophila
    • McDonald JH, 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
  • 3
    • 20444430245 scopus 로고    scopus 로고
    • A scan for positively selected genes in the genomes of humans and chimpanzees
    • DOI: 10.1371/journal.pbio.0030170
    • Nielsen R, Bustamante C, Clark AG, Glanowski S, Sackton TB, et al. (2005) A scan for positively selected genes in the genomes of humans and chimpanzees. PLoS Biol 3: e170. DOI: 10.1371/journal.pbio.0030170
    • (2005) PLoS Biol , vol.3
    • Nielsen, R.1    Bustamante, C.2    Clark, A.G.3    Glanowski, S.4    Sackton, T.B.5
  • 4
    • 0037186564 scopus 로고    scopus 로고
    • Adaptive protein evolution in Drosophila
    • Smith NGC, Eyre-Walker A (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
  • 5
    • 0036961560 scopus 로고    scopus 로고
    • 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
  • 6
    • 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
  • 7
    • 0027453041 scopus 로고
    • Statistical tests of neutrality of mutations
    • Fu YX, Li WH (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
  • 8
    • 0033911640 scopus 로고    scopus 로고
    • Hitchhiking under positive Darwinian selection
    • Fay JC, Wu CI (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
  • 9
    • 0036189827 scopus 로고    scopus 로고
    • Detecting a local signature of genetic hitchhiking along a recombining chromosome
    • Kim Y, 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
  • 10
    • 3843073210 scopus 로고    scopus 로고
    • Linkage disequilibrium as a signature of selective sweeps
    • Kim Y, Nielsen R (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
  • 11
    • 23344438911 scopus 로고    scopus 로고
    • Distinguishing between selective sweeps and demography using DNA polymorphism data
    • Jensen JD, Kim Y, Bauer DuMont V, Aquadro CF, Bustamante CD (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 DuMont, V.3    Aquadro, C.F.4    Bustamante, C.D.5
  • 12
    • 26444508054 scopus 로고    scopus 로고
    • Maximum likelihood methods for detecting recent positive selection and localizing the selected site in the genome
    • Li H, Stephan W (2005) Maximum likelihood methods for detecting recent positive selection and localizing the selected site in the genome. Genetics 171: 377-384.
    • (2005) Genetics , vol.171 , pp. 377-384
    • Li, H.1    Stephan, W.2
  • 14
    • 0036196885 scopus 로고    scopus 로고
    • The signature of positive selection at randomly chosen loci
    • Przeworski M (2002) The signature of positive selection at randomly chosen loci. Genetics 160: 1179-1189.
    • (2002) Genetics , vol.160 , pp. 1179-1189
    • Przeworski, M.1
  • 15
    • 0027374393 scopus 로고
    • African and North American populations of Drosophila melanogaster are very different at the DNA level
    • Begun DJ, Aquadro CF (1993) African and North American populations of Drosophila melanogaster are very different at the DNA level. Nature 365: 548-550.
    • (1993) Nature , vol.365 , pp. 548-550
    • Begun, D.J.1    Aquadro, C.F.2
  • 16
    • 0347065347 scopus 로고    scopus 로고
    • Demography and natural selection have shaped genetic variation in Drosophila melanogaster: A multi-locus approach
    • Glinka S, Ometto L, Mousset S, Stephan W, De Lorenzo D (2003) Demography and natural selection have shaped genetic variation in Drosophila melanogaster: A multi-locus approach. Genetics 165: 1269-1278.
    • (2003) Genetics , vol.165 , pp. 1269-1278
    • Glinka, S.1    Ometto, L.2    Mousset, S.3    Stephan, W.4    De Lorenzo, D.5
  • 17
    • 22344444998 scopus 로고    scopus 로고
    • Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations
    • Haddrill PR, Thornton KR, Charlesworth B, Andolfatto P (2005) Multilocus patterns of nucleotide variability and the demographic and selection history of Drosophila melanogaster populations. Genome Res 15: 790-799.
    • (2005) Genome Res , vol.15 , pp. 790-799
    • Haddrill, P.R.1    Thornton, K.R.2    Charlesworth, B.3    Andolfatto, P.4
  • 18
    • 24744465216 scopus 로고    scopus 로고
    • Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation
    • Ometto L, Glinka S, De Lorenzo D, Stephan W (2005) Inferring the effects of demography and selection on Drosophila melanogaster populations from a chromosome-wide scan of DNA variation. Mol Biol Evol 22: 2119-2130.
    • (2005) Mol Biol Evol , vol.22 , pp. 2119-2130
    • Ometto, L.1    Glinka, S.2    De Lorenzo, D.3    Stephan, W.4
  • 19
    • 0033965571 scopus 로고    scopus 로고
    • Estimation of population parameters and recombination rates from single nucleotide polymorphisms
    • Nielsen R (2000) Estimation of population parameters and recombination rates from single nucleotide polymorphisms. Genetics 154: 931-942.
    • (2000) Genetics , vol.154 , pp. 931-942
    • Nielsen, R.1
  • 20
    • 0031018637 scopus 로고    scopus 로고
    • Estimating ancestral population parameters
    • Wakeley J, Hey J (1997) Estimating ancestral population parameters. Genetics 145: 847-855.
    • (1997) Genetics , vol.145 , pp. 847-855
    • Wakeley, J.1    Hey, J.2
  • 21
    • 0033178244 scopus 로고    scopus 로고
    • Paleo-demography of the Drosophila melanogaster subgroup: Application of the maximum likelihood method
    • Li YJ, Satta Y, Takahata N (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
  • 22
    • 0030821992 scopus 로고    scopus 로고
    • Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection
    • Fu YX (1997) Statistical tests of neutrality of mutations against population growth, hitchhiking and background selection. Genetics 147: 915-925.
    • (1997) Genetics , vol.147 , pp. 915-925
    • Fu, Y.X.1
  • 23
    • 0031827528 scopus 로고    scopus 로고
    • Inference of population history using a likelihood approach
    • Weiss G, von Haeseler A (1998) Inference of population history using a likelihood approach. Genetics 149: 1539-1546.
    • (1998) Genetics , vol.149 , pp. 1539-1546
    • Weiss, G.1    Von Haeseler, A.2
  • 24
    • 33644763127 scopus 로고    scopus 로고
    • Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster
    • Thornton KR, Andolfatto P (2006) Approximate Bayesian inference reveals evidence for a recent, severe bottleneck in a Netherlands population of Drosophila melanogaster. Genetics 172: 1607-1619.
    • (2006) Genetics , vol.172 , pp. 1607-1619
    • Thornton, K.R.1    Andolfatto, P.2
  • 25
    • 0032894285 scopus 로고    scopus 로고
    • Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila
    • Comeron JM, Kreitman M, Aguadé M (1999) Natural selection on synonymous sites is correlated with gene length and recombination in Drosophila. Genetics 151: 239-249.
    • (1999) Genetics , vol.151 , pp. 239-249
    • Comeron, J.M.1    Kreitman, M.2    Aguadé, M.3
  • 26
    • 0027011221 scopus 로고
    • Global changes during the last 3 million years: Climatic controls and biotic responses
    • Webb T III, Bartlein PJ (1992) Global changes during the last 3 million years: Climatic controls and biotic responses. Annu Rev Ecol Syst 23: 141-173.
    • (1992) Annu Rev Ecol Syst , vol.23 , pp. 141-173
    • Webb III, T.1    Bartlein, P.J.2
  • 27
    • 2542466234 scopus 로고    scopus 로고
    • Holocene vegetation change and the mammal faunas of South America and Africa
    • De Vivo M, Carmignotto AP (2004) Holocene vegetation change and the mammal faunas of South America and Africa. J Biogeogr 31: 943-957.
    • (2004) J Biogeogr , vol.31 , pp. 943-957
    • De Vivo, M.1    Carmignotto, A.P.2
  • 28
    • 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
  • 29
    • 33744815615 scopus 로고    scopus 로고
    • How reliable are empirical genomic scans for selective sweeps?
    • Teshima KM, Coop G, 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
  • 30
    • 0016220238 scopus 로고
    • The hitch-hiking effect of a favourable gene
    • Maynard Smith J, Haigh J (1974) The hitch-hiking effect of a favourable gene. Genet Res 23: 23-35.
    • (1974) Genet Res , vol.23 , pp. 23-35
    • Maynard Smith, J.1    Haigh, J.2
  • 32
    • 7344226732 scopus 로고
    • The effect of strongly selected substitutions on neutral polymorphism: Analytical results based on diffusion theory
    • Stephan W, Wiehe THE, Lenz MW (1992) The effect of strongly selected substitutions on neutral polymorphism: Analytical results based on diffusion theory. Theor Popul Biol 41: 237-254.
    • (1992) Theor Popul Biol , vol.41 , pp. 237-254
    • Stephan, W.1    Wiehe, T.H.E.2    Lenz, M.W.3
  • 33
    • 0031673084 scopus 로고    scopus 로고
    • The effect of hitchhiking on neutral genealogies
    • Barton NH (1998) The effect of hitchhiking on neutral genealogies. Genet Res 72: 123-133.
    • (1998) Genet Res , vol.72 , pp. 123-133
    • Barton, N.H.1
  • 34
    • 3242714766 scopus 로고    scopus 로고
    • Pattern of polymorphism after strong artificial selection in a domestication event
    • Innan H, Kim Y (2004) Pattern of polymorphism after strong artificial selection in a domestication event. Proc Natl Acad Sci U S A 101: 10667-10672.
    • (2004) Proc Natl Acad Sci U S A , vol.101 , pp. 10667-10672
    • Innan, H.1    Kim, Y.2
  • 35
    • 18844439645 scopus 로고    scopus 로고
    • Soft sweeps: Molecular population genetics of adaptation from standing genetic variation
    • Hermisson J, Pennings PS (2005) Soft sweeps: Molecular population genetics of adaptation from standing genetic variation. Genetics 169: 2335-2352.
    • (2005) Genetics , vol.169 , pp. 2335-2352
    • Hermisson, J.1    Pennings, P.S.2
  • 36
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences
    • Kimura M (1980) A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16: 111-120.
    • (1980) J Mol Evol , vol.16 , pp. 111-120
    • Kimura, M.1
  • 37
    • 0031876602 scopus 로고    scopus 로고
    • Correlation between the substitution rate and rate variation among sites in protein evolution
    • Zhang J, Gu X (1998) Correlation between the substitution rate and rate variation among sites in protein evolution. Genetics 149: 1615-1625.
    • (1998) Genetics , vol.149 , pp. 1615-1625
    • Zhang, J.1    Gu, X.2
  • 38
    • 0037354718 scopus 로고    scopus 로고
    • Neutrality tests using DNA polymorphism from multiple samples
    • Li H, Zhang Y, Zhang YP, Fu YX (2003) Neutrality tests using DNA polymorphism from multiple samples. Genetics 163: 1147-1151.
    • (2003) Genetics , vol.163 , pp. 1147-1151
    • Li, H.1    Zhang, Y.2    Zhang, Y.P.3    Fu, Y.X.4
  • 39
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • Futuyma D, Antonovics J, editors. New York: Oxford University Press
    • Hudson RR (1990) Gene genealogies and the coalescent process. In: Futuyma D, Antonovics J, editors. Oxford surveys in evolutionary biology. Volume 7. New York: Oxford University Press. pp. 1-44.
    • (1990) Oxford Surveys in Evolutionary Biology , vol.7 , pp. 1-44
    • Hudson, R.R.1
  • 40
    • 0001936734 scopus 로고    scopus 로고
    • Coalescent theory and its applications in population genetics
    • Halloran E, editor. New York: Springer-Verlag
    • Li WH, Fu YX (1998) Coalescent theory and its applications in population genetics. In: Halloran E, editor. Statistics in genetics. New York: Springer-Verlag.
    • (1998) Statistics in Genetics
    • Li, W.H.1    Fu, Y.X.2
  • 41
    • 0033150745 scopus 로고    scopus 로고
    • Recombination as a point process along sequences
    • Wiuf C, Hein J (1999) Recombination as a point process along sequences. Theoret Popul Biol 55: 248-259.
    • (1999) Theoret Popul Biol , vol.55 , pp. 248-259
    • Wiuf, C.1    Hein, J.2
  • 42
  • 44
    • 0027099659 scopus 로고
    • Estimating effective population size from samples of sequences: A bootstrap Monte Carlo integration method
    • Felsenstein J (1992) Estimating effective population size from samples of sequences: A bootstrap Monte Carlo integration method. Genet Res 60: 209-220.
    • (1992) Genet Res , vol.60 , pp. 209-220
    • Felsenstein, J.1
  • 45
    • 0029027992 scopus 로고
    • Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling
    • Kuhner MK, Yamato J, Felsenstein J (1995) Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. Genetics 140: 1421-1430.
    • (1995) Genetics , vol.140 , pp. 1421-1430
    • Kuhner, M.K.1    Yamato, J.2    Felsenstein, J.3


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