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Volumn 31, Issue 2, 2014, Pages 474-483

A guide for the design of evolve and resequencing studies

Author keywords

adaptation; bioinformatics; evolve resequencing; experimental evolution; next generation sequencing

Indexed keywords

NUCLEOTIDE;

EID: 84893126398     PISSN: 07374038     EISSN: 15371719     Source Type: Journal    
DOI: 10.1093/molbev/mst221     Document Type: Article
Times cited : (111)

References (38)
  • 2
    • 84869131230 scopus 로고    scopus 로고
    • How does adaptation sweep through the genome? Insights from long-term selection experiments
    • Burke MK. 2012. How does adaptation sweep through the genome? Insights from long-term selection experiments. Proc Biol Sci. 279: 5029-5038.
    • (2012) Proc Biol Sci. , vol.279 , pp. 5029-5038
    • Burke, M.K.1
  • 4
    • 84867554607 scopus 로고    scopus 로고
    • What paths do advantageous alleles take during short-term evolutionary change?
    • Burke MK, Long AD. 2012. What paths do advantageous alleles take during short-term evolutionary change? Mol Ecol. 21:4913-4916.
    • (2012) Mol Ecol. , vol.21 , pp. 4913-4916
    • Burke, M.K.1    Long, A.D.2
  • 5
    • 59449107920 scopus 로고    scopus 로고
    • Selective sweep at a quantitative trait locus in the presence of background genetic variation
    • Chevin LM, Hospital F. 2008. Selective sweep at a quantitative trait locus in the presence of background genetic variation. Genetics 180: 1645-1660.
    • (2008) Genetics , vol.180 , pp. 1645-1660
    • Chevin, L.M.1    Hospital, F.2
  • 6
    • 52649157765 scopus 로고    scopus 로고
    • Substantial biases in ultra-short read data sets from high-throughput DNA sequencing
    • Dohm JC, Lottaz C, Borodina T, Himmelbauer H. 2008. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res. 36:e105.
    • (2008) Nucleic Acids Res. , vol.36
    • Dohm, J.C.1    Lottaz, C.2    Borodina, T.3    Himmelbauer, H.4
  • 7
    • 79954469204 scopus 로고    scopus 로고
    • Fastsimcoal: A continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios
    • Excoffier L, Foll M. 2011. fastsimcoal: a continuous-time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios. Bioinformatics 27:1332-1334.
    • (2011) Bioinformatics , vol.27 , pp. 1332-1334
    • Excoffier, L.1    Foll, M.2
  • 9
    • 78751665708 scopus 로고    scopus 로고
    • The next generation of molecular markers from massively parallel sequencing of pooled DNA samples
    • Futschik A, Schlötterer C. 2010. The next generation of molecular markers from massively parallel sequencing of pooled DNA samples. Genetics 186:207-218.
    • (2010) Genetics , vol.186 , pp. 207-218
    • Futschik, A.1    Schlötterer, C.2
  • 12
    • 84955349191 scopus 로고
    • A mathematical theory of natural and artificial selection, part V: Selection and mutation
    • Haldane JBS. 1927. A mathematical theory of natural and artificial selection, part V: selection and mutation. Proceedings of the Cambridge Philosophical Society, Vol. 23. p. 838-844.
    • (1927) Proceedings of the Cambridge Philosophical Society , vol.23 , pp. 838-844
    • Haldane, J.B.S.1
  • 13
    • 0003684449 scopus 로고    scopus 로고
    • The elements of statistical learning: Data mining, inference, and prediction
    • New York: Springer- Verlag
    • Hastie T, Tibshirani R, Friedman J. 2009. The elements of statistical learning: data mining, inference, and prediction. Springer series in statistics. New York: Springer-Verlag.
    • (2009) Springer Series in Statistics
    • Hastie, T.1    Tibshirani, R.2    Friedman, J.3
  • 14
    • 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
  • 15
    • 84866848293 scopus 로고    scopus 로고
    • Epistasis dominates the genetic architecture of Drosophila quantitative traits
    • (25 co-authors).
    • HuangW, Richards S, Carbone MA, et al. (25 co-authors). 2012. Epistasis dominates the genetic architecture of Drosophila quantitative traits. Proc Natl Acad Sci USA. 109:15553-15559.
    • (2012) Proc Natl Acad Sci USA. , vol.109 , pp. 15553-15559
    • Huangw Richards, S.1    Carbone, M.A.2
  • 16
    • 84858419168 scopus 로고    scopus 로고
    • Quantifying selection acting on a complex trait using allele frequency time series data
    • Illingworth CJR, Parts L, Schiffels S, Liti G, Mustonen V. 2012. Quantifying selection acting on a complex trait using allele frequency time series data. Mol Biol Evol. 29:1187-1197.
    • (2012) Mol Biol Evol. , vol.29 , pp. 1187-1197
    • Illingworth, C.J.R.1    Parts, L.2    Schiffels, S.3    Liti, G.4    Mustonen, V.5
  • 17
    • 0035970061 scopus 로고    scopus 로고
    • Fitness effects of advantageous mutations in evolving Escherichia coli populations
    • Imhof M, Schlötterer C. 2001. Fitness effects of advantageous mutations in evolving Escherichia coli populations. Proc Natl Acad Sci USA. 98: 1113-1117.
    • (2001) Proc Natl Acad Sci USA. , vol.98 , pp. 1113-1117
    • Imhof, M.1    Schlötterer, C.2
  • 18
    • 33645394597 scopus 로고    scopus 로고
    • Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria
    • Kassen R, Bataillon T. 2006. Distribution of fitness effects among beneficial mutations before selection in experimental populations of bacteria. Nat Genet. 38:484-8.
    • (2006) Nat Genet. , vol.38 , pp. 484-488
    • Kassen, R.1    Bataillon, T.2
  • 20
    • 0001017871 scopus 로고
    • Solution of a process of random genetic drift with a continuous model
    • Kimura M. 1955. Solution of a process of random genetic drift with a continuous model. Proc Natl Acad Sci USA. 41: 144-150.
    • (1955) Proc Natl Acad Sci USA. , vol.41 , pp. 144-150
    • Kimura, M.1
  • 21
    • 0000800333 scopus 로고
    • On the probability of fixation of mutant genes in a population
    • Kimura M. 1962. On the probability of fixation of mutant genes in a population. Genetics 47:713-719.
    • (1962) Genetics , vol.47 , pp. 713-719
    • Kimura, M.1
  • 23
    • 83355175374 scopus 로고    scopus 로고
    • Popoolation2: Identifying differentiation between populations using sequencing of pooled dna samples (pool-seq)
    • Kofler R, Pandey RV, Schlötterer C. 2011. Popoolation2: identifying differentiation between populations using sequencing of pooled dna samples (pool-seq). Bioinformatics 27:3435-6.
    • (2011) Bioinformatics , vol.27 , pp. 3435-3436
    • Kofler, R.1    Pandey, R.V.2    Schlötterer, C.3
  • 24
    • 0001194272 scopus 로고
    • Average partial association in three-way contingency tables: A review and discussion of alternative tests
    • Landis JR, Heyman ER, Koch GG. 1978. Average partial association in three-way contingency tables: a review and discussion of alternative tests. Int Stat Rev. 46:237-254.
    • (1978) Int Stat Rev. , vol.46 , pp. 237-254
    • Landis, J.R.1    Heyman, E.R.2    Koch, G.G.3
  • 25
    • 0024370623 scopus 로고
    • Analyzing a portion of the ROC curve
    • McClish DK. 1989. Analyzing a portion of the ROC curve. Med Decis Making. 9:190-195.
    • (1989) Med Decis Making. , vol.9 , pp. 190-195
    • McClish, D.K.1
  • 26
    • 80455126001 scopus 로고    scopus 로고
    • Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems
    • Minoche AE, Dohm JC, Himmelbauer H. 2011. Evaluation of genomic high-throughput sequencing data generated on Illumina HiSeq and genome analyzer systems. Genome Biol. 12:R112.
    • (2011) Genome Biol. , vol.12
    • Minoche, A.E.1    Dohm, J.C.2    Himmelbauer, H.3
  • 27
    • 84867574655 scopus 로고    scopus 로고
    • Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles
    • Orozco-terWengel P, Kapun M, Nolte V, Kofler R, Flatt T, Schlötterer C. 2012. Adaptation of Drosophila to a novel laboratory environment reveals temporally heterogeneous trajectories of selected alleles. Mol Ecol. 21:4931-4941.
    • (2012) Mol Ecol. , vol.21 , pp. 4931-4941
    • Orozco-Terwengel, P.1    Kapun, M.2    Nolte, V.3    Kofler, R.4    Flatt, T.5    Schlötterer, C.6
  • 28
    • 79956073707 scopus 로고    scopus 로고
    • Revealing the genetic structure of a trait by sequencing a population under selection
    • (14 co-authors)
    • Parts L, Cubillos FA, Warringer J, et al. (14 co-authors). 2011. Revealing the genetic structure of a trait by sequencing a population under selection. Genome Res. 21:1131-8.
    • (2011) Genome Res. , vol.21 , pp. 1131-1138
    • Parts, L.1    Cubillos, F.A.2    Warringer, J.3
  • 29
    • 28644440530 scopus 로고    scopus 로고
    • The signature of positive selection on standing genetic variation
    • Przeworski M, Coop G, Wall JD. 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
  • 30
    • 84863304598 scopus 로고    scopus 로고
    • R Core Team Vienna (Austria): R Foundation for Statistical Computing
    • R Core Team. 2012. R: a language and environment for statistical computing. Vienna (Austria): R Foundation for Statistical Computing.
    • (2012) R: A Language and Environment for Statistical Computing
  • 31
    • 84868134353 scopus 로고    scopus 로고
    • Genomic basis of aging and life-history evolution in Drosophila melanogaster
    • Remolina SC, Chang PL, Leips J, Nuzhdin SV, Hughes KA. 2012. Genomic basis of aging and life-history evolution in Drosophila melanogaster. Evolution 66:3390-3403.
    • (2012) Evolution , vol.66 , pp. 3390-3403
    • Remolina, S.C.1    Chang, P.L.2    Leips, J.3    Nuzhdin, S.V.4    Hughes, K.A.5
  • 32
    • 0021549310 scopus 로고
    • Artificial selection on a fitness-component in Drosophila melanogaster
    • Rose MR. 1984. Artificial selection on a fitness-component in Drosophila melanogaster. Evolution 38:516-526.
    • (1984) Evolution , vol.38 , pp. 516-526
    • Rose, M.R.1
  • 33
    • 79955931968 scopus 로고    scopus 로고
    • New experiments for an undivided genetics
    • Rose MR, Mueller LD, Burke MK. 2011. New experiments for an undivided genetics. Genetics 188:1-10.
    • (2011) Genetics , vol.188 , pp. 1-10
    • Rose, M.R.1    Mueller, L.D.2    Burke, M.K.3
  • 35
    • 0024385165 scopus 로고
    • On the statistical analysis of ROC curves
    • Thompson ML, Zucchini W. 1989. On the statistical analysis of ROC curves. Stat Med. 8:1277-1290.
    • (1989) Stat Med. , vol.8 , pp. 1277-1290
    • Thompson, M.L.1    Zucchini, W.2
  • 36
    • 84893147360 scopus 로고    scopus 로고
    • Massive habitatspecific genomic response in D melanogaster populations during experimental evolution in hot and cold environments
    • Forthcoming Advance Access published October 22, 2013 doi: 10.1093/molbev/mst205
    • Tobler R, Franssen SU, Kofler R, Orozco-terWengel P, Nolte V, Hermisson J, Schlötterer C. Forthcoming 2013. Massive habitatspecific genomic response in D. melanogaster populations during experimental evolution in hot and cold environments. Mol Biol Evol. Advance Access published October 22, 2013, doi: 10.1093/molbev/mst205.
    • (2013) Mol Biol Evol.
    • Tobler, R.1    Franssen, S.U.2    Kofler, R.3    Orozco-Terwengel, P.4    Nolte, V.5    Hermisson, J.6    Schlötterer, C.7
  • 37
    • 84862564386 scopus 로고    scopus 로고
    • Investigating natural variation in Drosophila courtship song by the evolve & resequence approach
    • Turner TL, Miller PM. 2012. Investigating natural variation in Drosophila courtship song by the evolve & resequence approach. Genetics 191: 633-642.
    • (2012) Genetics , vol.191 , pp. 633-642
    • Turner, T.L.1    Miller, P.M.2
  • 38
    • 79953735688 scopus 로고    scopus 로고
    • Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster
    • Turner TL, Stewart AD, Fields AT, Rice WR, Tarone AM. 2011. Population-based resequencing of experimentally evolved populations reveals the genetic basis of body size variation in Drosophila melanogaster. PLoS Genet. 7:e1001336.
    • (2011) PLoS Genet. , vol.7
    • Turner, T.L.1    Stewart, A.D.2    Fields, A.T.3    Rice, W.R.4    Tarone, A.M.5


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.