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Volumn 9, Issue 12, 2013, Pages

Contributions of Protein-Coding and Regulatory Change to Adaptive Molecular Evolution in Murid Rodents

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; REGULATOR PROTEIN;

EID: 84892714881     PISSN: 15537390     EISSN: 15537404     Source Type: Journal    
DOI: 10.1371/journal.pgen.1003995     Document Type: Article
Times cited : (84)

References (53)
  • 1
    • 7244245762 scopus 로고    scopus 로고
    • Finishing the euchromatic sequence of the human genome
    • International Human Genome Sequencing Consortium
    • International Human Genome Sequencing Consortium (2004) Finishing the euchromatic sequence of the human genome. Nature 431: 931-945.
    • (2004) Nature , vol.431 , pp. 931-945
  • 4
    • 84863585352 scopus 로고    scopus 로고
    • Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome
    • Carnerio M, Albert FW, Melo-Ferreira J, Galtier N, Gayral P, et al. (2012) Evidence for widespread positive and purifying selection across the European rabbit (Oryctolagus cuniculus) genome. Mol Biol Evol 29: 1837-1849.
    • (2012) Mol Biol Evol , vol.29 , pp. 1837-1849
    • Carnerio, M.1    Albert, F.W.2    Melo-Ferreira, J.3    Galtier, N.4    Gayral, P.5
  • 5
    • 80054973803 scopus 로고    scopus 로고
    • A High-resolution map of human evolutionary constraint using 29 mammals
    • Lindblad-Toh K, Garber M, Zuk O, Lin MF, Parker BJ, et al. (2011) A High-resolution map of human evolutionary constraint using 29 mammals. Nature 478: 476-482.
    • (2011) Nature , vol.478 , pp. 476-482
    • Lindblad-Toh, K.1    Garber, M.2    Zuk, O.3    Lin, M.F.4    Parker, B.J.5
  • 6
    • 84865790047 scopus 로고    scopus 로고
    • An integrated encyclopedia of DNA elements in the human genome
    • The ENCODE Project Consortium
    • The ENCODE Project Consortium (2012) An integrated encyclopedia of DNA elements in the human genome. Nature 489: 57-74.
    • (2012) Nature , vol.489 , pp. 57-74
  • 7
    • 84875847924 scopus 로고    scopus 로고
    • Is junk DNA bunk? A critique of ENCODE
    • Doolittle WF, (2013) Is junk DNA bunk? A critique of ENCODE. PNAS 110: 5294-5300.
    • (2013) PNAS , vol.110 , pp. 5294-5300
    • Doolittle, W.F.1
  • 8
    • 84875275808 scopus 로고    scopus 로고
    • On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE
    • Graur D, Zheng Y, Price N, Azevedo RBR, Zufall RA, Elhaik E, (2013) On the immortality of television sets: "function" in the human genome according to the evolution-free gospel of ENCODE. Genome Biol Evol 5: 578-590.
    • (2013) Genome Biol Evol , vol.5 , pp. 578-590
    • Graur, D.1    Zheng, Y.2    Price, N.3    Azevedo, R.B.R.4    Zufall, R.A.5    Elhaik, E.6
  • 9
    • 0016669094 scopus 로고
    • Evolution at two levels in humans and chimpanzees
    • King M-C, Wilson AC, (1975) Evolution at two levels in humans and chimpanzees. Science 188: 107-116.
    • (1975) Science , vol.188 , pp. 107-116
    • King, M.-C.1    Wilson, A.C.2
  • 10
    • 22744439568 scopus 로고    scopus 로고
    • Evolution at two levels: on genes and form
    • Carroll SB, (2005) Evolution at two levels: on genes and form. PLoS Biol 3: 1159.
    • (2005) PLoS Biol , vol.3 , pp. 1159
    • Carroll, S.B.1
  • 11
    • 33847057226 scopus 로고    scopus 로고
    • The evolutionary significance of cis-regulatory mutations
    • Wray GA, (2007) The evolutionary significance of cis-regulatory mutations. Nat Rev Genet 8: 206-216.
    • (2007) Nat Rev Genet , vol.8 , pp. 206-216
    • Wray, G.A.1
  • 12
    • 84859462157 scopus 로고    scopus 로고
    • The genomic basis of adaptive evolution in threespine sticklebacks
    • Jones FC, Grabherr MG, Chan YF, Russell P, Mauceli E, et al. (2012) The genomic basis of adaptive evolution in threespine sticklebacks. Nature 484: 55-61.
    • (2012) Nature , vol.484 , pp. 55-61
    • Jones, F.C.1    Grabherr, M.G.2    Chan, Y.F.3    Russell, P.4    Mauceli, E.5
  • 13
    • 34247855863 scopus 로고    scopus 로고
    • The locus of evolution: evo devo and the genetics of adaptation
    • Hoekstra HE, Coyne JA, (2007) The locus of evolution: evo devo and the genetics of adaptation. Evolution 61: 995-1016.
    • (2007) Evolution , vol.61 , pp. 995-1016
    • Hoekstra, H.E.1    Coyne, J.A.2
  • 14
    • 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
  • 15
    • 70149100044 scopus 로고    scopus 로고
    • Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence
    • Torgerson DG, Boyko AR, Hernandez RD, Indap A, Hu X, et al. (2009) Evolutionary processes acting on candidate cis-regulatory regions in humans inferred from patterns of polymorphism and divergence. PLoS Genet 5: e1000592.
    • (2009) PLoS Genet , vol.5
    • Torgerson, D.G.1    Boyko, A.R.2    Hernandez, R.D.3    Indap, A.4    Hu, X.5
  • 16
    • 79952171635 scopus 로고    scopus 로고
    • Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice
    • Kousathanas A, Oliver F, Halligan DL, Keightley PD, (2011) Positive and negative selection on noncoding DNA close to protein-coding genes in wild house mice. Mol Biol Evol 28: 1183-1191.
    • (2011) Mol Biol Evol , vol.28 , pp. 1183-1191
    • Kousathanas, A.1    Oliver, F.2    Halligan, D.L.3    Keightley, P.D.4
  • 17
    • 80052168287 scopus 로고    scopus 로고
    • Positive and negative selection in murine ultra-conserved noncoding elements
    • Halligan DL, Oliver F, Guthrie J, Stemshorn KC, Harr B, et al. (2011) Positive and negative selection in murine ultra-conserved noncoding elements. Mol Biol Evol 28: 2651-2660.
    • (2011) Mol Biol Evol , vol.28 , pp. 2651-2660
    • Halligan, D.L.1    Oliver, F.2    Guthrie, J.3    Stemshorn, K.C.4    Harr, B.5
  • 18
    • 34249093040 scopus 로고    scopus 로고
    • Reduced X-linked diversity in derived populations of house mice
    • Baines JF, Harr B, (2007) Reduced X-linked diversity in derived populations of house mice. Genetics 175: 1911-1921.
    • (2007) Genetics , vol.175 , pp. 1911-1921
    • Baines, J.F.1    Harr, B.2
  • 19
    • 80051914599 scopus 로고    scopus 로고
    • Three periods of regulatory innovation during vertebrate evolution
    • Lowe CB, Kellis M, Siepel A, Raney BJ, Clamp M, et al. (2011) Three periods of regulatory innovation during vertebrate evolution. Science 333: 1019-1024.
    • (2011) Science , vol.333 , pp. 1019-1024
    • Lowe, C.B.1    Kellis, M.2    Siepel, A.3    Raney, B.J.4    Clamp, M.5
  • 20
    • 84864462544 scopus 로고    scopus 로고
    • A map of the cis-regulatory sequences in the mouse genome
    • Shen Y, Yue F, McCleary DF, Ye Z, Edsall L, et al. (2012) A map of the cis-regulatory sequences in the mouse genome. Nature 488: 116-120.
    • (2012) Nature , vol.488 , pp. 116-120
    • Shen, Y.1    Yue, F.2    McCleary, D.F.3    Ye, Z.4    Edsall, L.5
  • 21
    • 23744458086 scopus 로고    scopus 로고
    • Evolutionarily conserved elements in vertebrate, insect,worm, and yeast genomes
    • Siepel A, Bejerano G, Pedersen JS, Hinrichs AS, Hou M, et al. (2005) Evolutionarily conserved elements in vertebrate, insect,worm, and yeast genomes. Genome Res 15: 1034-1050.
    • (2005) Genome Res , vol.15 , pp. 1034-1050
    • Siepel, A.1    Bejerano, G.2    Pedersen, J.S.3    Hinrichs, A.S.4    Hou, M.5
  • 22
    • 59449103500 scopus 로고    scopus 로고
    • Controlling type-I error of the McDonald-Kreitman test in genome wide scans for selection on noncoding DNA
    • Andolfatto P, (2008) Controlling type-I error of the McDonald-Kreitman test in genome wide scans for selection on noncoding DNA. Genetics 180: 1767-71.
    • (2008) Genetics , vol.180 , pp. 1767-1771
    • Andolfatto, P.1
  • 23
    • 31144465926 scopus 로고    scopus 로고
    • Hearing silence: non-neutral evolution at synonymous sites in mammals
    • Chamary JV, Parmley JL, Hurst LD, (2006) Hearing silence: non-neutral evolution at synonymous sites in mammals. Nature Reviews Genetics 7: 98-108.
    • (2006) Nature Reviews Genetics , vol.7 , pp. 98-108
    • Chamary, J.V.1    Parmley, J.L.2    Hurst, L.D.3
  • 24
    • 84888623468 scopus 로고    scopus 로고
    • Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates
    • doi:10.1093/molbev/mst128
    • Doherty A, McInerney JO, (2013) Translational selection frequently overcomes genetic drift in shaping synonymous codon usage patterns in vertebrates. Mol Biol Evol 30: 2263-2267 doi:10.1093/molbev/mst128.
    • (2013) Mol Biol Evol , vol.30 , pp. 2263-2267
    • Doherty, A.1    McInerney, J.O.2
  • 25
    • 72649102150 scopus 로고    scopus 로고
    • Distribution of selectively constrained sites and the deleterious mutation rate in the hominid and murid genomes
    • Eo{double acute}ry L, Halligan DL, Keightley PD, (2010) Distribution of selectively constrained sites and the deleterious mutation rate in the hominid and murid genomes. Mol Biol Evol 27: 177-192.
    • (2010) Mol Biol Evol , vol.27 , pp. 177-192
    • Eory, L.1    Halligan, D.L.2    Keightley, P.D.3
  • 26
    • 33645798112 scopus 로고    scopus 로고
    • Genome-wide identification of human functional DNA using a neutral indel model
    • Lunter G, Ponting CP, Hein J, (2006) Genome-wide identification of human functional DNA using a neutral indel model. PLoS Comput Biol 2: e5.
    • (2006) PLoS Comput Biol , vol.2
    • Lunter, G.1    Ponting, C.P.2    Hein, J.3
  • 27
    • 37449015848 scopus 로고    scopus 로고
    • Nucleotide variation in wild and inbred mice
    • Salcedo T, Geraldes A, Nachman MW, (2007) Nucleotide variation in wild and inbred mice. Genetics 177: 2277-2291.
    • (2007) Genetics , vol.177 , pp. 2277-2291
    • Salcedo, T.1    Geraldes, A.2    Nachman, M.W.3
  • 28
    • 37249042614 scopus 로고    scopus 로고
    • Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies
    • Keightley PD, Eyre-Walker A, (2007) Joint inference of the distribution of fitness effects of deleterious mutations and population demography based on nucleotide polymorphism frequencies. Genetics 177: 2251-2261.
    • (2007) Genetics , vol.177 , pp. 2251-2261
    • Keightley, P.D.1    Eyre-Walker, A.2
  • 29
    • 33745347447 scopus 로고    scopus 로고
    • The distribution of fitness of new deleterious amino acid mutations in humans
    • Eyre-Walker A, Woolfit M, Phelps T, (2006) The distribution of fitness of new deleterious amino acid mutations in humans. Genetics 173: 891-900.
    • (2006) Genetics , vol.173 , pp. 891-900
    • Eyre-Walker, A.1    Woolfit, M.2    Phelps, T.3
  • 31
    • 84876350995 scopus 로고    scopus 로고
    • Comparing models for inferring the distribution of fitness effects of new mutations
    • Kousathanas A, Keightley PD, (2013) Comparing models for inferring the distribution of fitness effects of new mutations. Genetics 193: 1197-1208.
    • (2013) Genetics , vol.193 , pp. 1197-1208
    • Kousathanas, A.1    Keightley, P.D.2
  • 32
    • 68949202924 scopus 로고    scopus 로고
    • Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change
    • Eyre-Walker A, Keightley PD, (2009) Estimating the rate of adaptive molecular evolution in the presence of slightly deleterious mutations and population size change. Mol Biol Evol 26: 2097-2108.
    • (2009) Mol Biol Evol , vol.26 , pp. 2097-2108
    • Eyre-Walker, A.1    Keightley, P.D.2
  • 33
    • 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
  • 34
    • 84878147503 scopus 로고    scopus 로고
    • Frequent adaptation and the McDonald-Kreitman test
    • Messer PW, Petrov DA, (2013) Frequent adaptation and the McDonald-Kreitman test. Proc Natl Acad Sci., USA 110: 8615-8620.
    • (2013) Proc Natl Acad Sci., USA , vol.110 , pp. 8615-8620
    • Messer, P.W.1    Petrov, D.A.2
  • 35
    • 79952263624 scopus 로고    scopus 로고
    • Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans
    • Sattath S, Elyashiv E, Kolodny O, Rinott Y, Sella G, (2011) Pervasive adaptive protein evolution apparent in diversity patterns around amino acid substitutions in Drosophila simulans. PLoS Genetics 7: e1001302.
    • (2011) PLoS Genetics , vol.7
    • Sattath, S.1    Elyashiv, E.2    Kolodny, O.3    Rinott, Y.4    Sella, G.5
  • 37
    • 0027235978 scopus 로고
    • Analysis of a genetic hitchhiking model and its application to DNA polymorphism data from Drosophila melanogaster
    • Wiehe THE, Stephan W, (1993) Analysis of a genetic hitchhiking model and its application to DNA polymorphism data from Drosophila melanogaster. Mol Biol Evol 10: 842-854.
    • (1993) Mol Biol Evol , vol.10 , pp. 842-854
    • Wiehe, T.H.E.1    Stephan, W.2
  • 38
    • 59249100200 scopus 로고    scopus 로고
    • Pervasive hitchhiking at coding and regulatory sites in humans
    • Cai JJ, Macpherson MJ, Sella G, Petrov DA, (2009) Pervasive hitchhiking at coding and regulatory sites in humans. PLoS Genet 5: e1000336.
    • (2009) PLoS Genet , vol.5
    • Cai, J.J.1    Macpherson, M.J.2    Sella, G.3    Petrov, D.A.4
  • 39
    • 67149096366 scopus 로고    scopus 로고
    • Widespread genomic signatures of natural selection in hominid evolution
    • McVicker G, Gordon D, Davis C, Green P, (2009) Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet 5: e1000471.
    • (2009) PLoS Genet , vol.5
    • McVicker, G.1    Gordon, D.2    Davis, C.3    Green, P.4
  • 40
    • 0029962309 scopus 로고    scopus 로고
    • The effect of recombination on background selection
    • Nordborg M, Charlesworth B, Charlesworth D, (1996) The effect of recombination on background selection. Genet Res 67: 159-174.
    • (1996) Genet Res , vol.67 , pp. 159-174
    • Nordborg, M.1    Charlesworth, B.2    Charlesworth, D.3
  • 41
    • 0027305597 scopus 로고
    • The effect of deleterious mutations on neutral molecular variation
    • Charlesworth B, Morgan MT, Charlesworth D, (1993) The effect of deleterious mutations on neutral molecular variation. Genetics 134: 1289-1303.
    • (1993) Genetics , vol.134 , pp. 1289-1303
    • Charlesworth, B.1    Morgan, M.T.2    Charlesworth, D.3
  • 43
    • 77951600170 scopus 로고    scopus 로고
    • What can we learn about the distribution of fitness effects of new mutations from DNA sequence data?
    • Keightley PD, Eyre-Walker A, (2010) What can we learn about the distribution of fitness effects of new mutations from DNA sequence data? Phil Trans R Soc B 365: 1187-1193.
    • (2010) Phil Trans R Soc B , vol.365 , pp. 1187-1193
    • Keightley, P.D.1    Eyre-Walker, A.2
  • 44
    • 84866775366 scopus 로고    scopus 로고
    • Evidence of abundant purifying selection in humans for recently-acquired regulatory functions
    • Ward LD, Kellis M, (2012) Evidence of abundant purifying selection in humans for recently-acquired regulatory functions. Science 337: 1675-1678.
    • (2012) Science , vol.337 , pp. 1675-1678
    • Ward, L.D.1    Kellis, M.2
  • 45
    • 28644440530 scopus 로고    scopus 로고
    • The signature of selection on standing genetic variation
    • Przeworski M, Coop G, Wall JD, (2005) The signature of 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
  • 46
    • 84868152411 scopus 로고    scopus 로고
    • Distinguishing between selective sweeps from standing variation and from a de novo mutation
    • Peter BM, Huerta-Sanchez E, Nielsen R, (2012) Distinguishing between selective sweeps from standing variation and from a de novo mutation. PLoS Genet 8: e1003011.
    • (2012) PLoS Genet , vol.8
    • Peter, B.M.1    Huerta-Sanchez, E.2    Nielsen, R.3
  • 47
    • 0034118493 scopus 로고    scopus 로고
    • Inference of population structure using multilocus genotype data
    • Pritchard JK, Stephens M, Donnelly PJ, (2000) Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
    • (2000) Genetics , vol.155 , pp. 945-959
    • Pritchard, J.K.1    Stephens, M.2    Donnelly, P.J.3
  • 49
    • 80051532482 scopus 로고    scopus 로고
    • Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans
    • Keightley PD, Halligan DL, (2011) Inference of site frequency spectra from high-throughput sequence data: quantification of selection on nonsynonymous and synonymous sites in humans. Genetics 188: 931-940.
    • (2011) Genetics , vol.188 , pp. 931-940
    • Keightley, P.D.1    Halligan, D.L.2
  • 50
    • 67649884743 scopus 로고    scopus 로고
    • Fast and accurate short read alignment with Burrows-Wheeler Transform
    • Li H, Durbin R, (2009) Fast and accurate short read alignment with Burrows-Wheeler Transform. Bioinformatics 25: 1754-1760.
    • (2009) Bioinformatics , vol.25 , pp. 1754-1760
    • Li, H.1    Durbin, R.2
  • 51
    • 0019296687 scopus 로고
    • A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences
    • Kimura M, (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16: 111-120.
    • (1980) Journal of Molecular Evolution , vol.16 , pp. 111-120
    • Kimura, M.1
  • 52
    • 84862672172 scopus 로고    scopus 로고
    • Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small
    • Keightley PD, Eyre-Walker A, (2012) Estimating the rate of adaptive molecular evolution when the evolutionary divergence between species is small. Journal of Molecular Evolution 74: 61-68.
    • (2012) Journal of Molecular Evolution , vol.74 , pp. 61-68
    • Keightley, P.D.1    Eyre-Walker, A.2


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