[1] | Wichman HA, Badgett MR, Scott LA, Boulianne CM, Bull JJ (1999) Different trajectories of parallel evolution during viral adaptation. Science 285: 422–424.
|
[2] | Cooper TF, Rozen DE, Lenski RE (2003) Parallel changes in gene expression after 20,000 generations of evolution in . Proc Natl Acad Sci U S A 100: 1072–1077.
|
[3] | Elena SF, Lenski RE (2003) Evolution experiments with microorganisms: The dynamics and genetic bases of adaptation. Nat Rev Genet 4: 457–469.
|
[4] | Zeyl C (2004) Capturing the adaptive mutation in yeast. Res Microbiol 155: 217–223.
|
[5] | Crozat E, Philippe N, Lenski RE, Geiselmann J, Schneider D (2005) Long-term experimental evolution in Escherichia coli XII. DNA topology as a key target of selection. Genetics 169: 523–532.
|
[6] | Notley-McRobb L, Ferenci T (1999) Adaptive mgl-regulatory mutations and genetic diversity evolving in glucose-limited populations. Environ Microbiol 1: 33–43.
|
[7] | Dekel E, Alon U (2005) Optimality and evolutionary tuning of the expression level of a protein. Nature 436: 588–592.
|
[8] | Adams J, Puskas-Rozsa S, Simlar J, Wilke CM (1992) Adaptation and major chromosomal changes in populations of . Curr Genet 22: 13–19.
|
[9] | Schneider D, Lenski RE (2004) Dynamics of insertion sequence elements during experimental evolution of bacteria. Res Microbiol 155: 319–327.
|
[10] | Blanc VM, Adams J (2003) Evolution in Saccharomyces cerevisiae Identification of mutations increasing fitness in laboratory populations. Genetics 165: 975–983.
|
[11] | Lenski RE, Winkworth CL, Riley MA (2003) Rates of DNA sequence evolution in experimental populations of during 20,000 generations. J Mol Evol 56: 498–508.
|
[12] | Honisch C, Raghunathan A, Cantor CR, Palsson BO, van den Boom D (2004) High-throughput mutation detection underlying adaptive evolution of -K12. Genome Res 14: 2495–2502.
|
[13] | Shendure J, Porreca GJ, Reppas NB, Lin X, McCutcheon JP, et al. (2005) Accurate multiplex polony sequencing of an evolved bacterial genome. Science 309: 1728–1732.
|
[14] | Ferea TL, Botstein D, Brown PO, Rosenzweig RF (1999) Systematic changes in gene expression patterns following adaptive evolution in yeast. Proc Natl Acad Sci U S A 96: 9721–9726.
|
[15] | Dunham MJ, Badrane H, Ferea T, Adams J, Brown PO, et al. (2002) Characteristic genome rearrangements in experimental evolution of . Proc Natl Acad Sci U S A 99: 16144–16149.
|
[16] | Albertson RC, Streelman JT, Kocher TD (2003) Directional selection has shaped the oral jaws of Lake Malawi cichlid fishes. Proc Natl Acad Sci U S A 100: 5252–5257.
|
[17] | Shapiro MD, Marks ME, Peichel CL, Blackman BK, Nereng KS, et al. (2004) Genetic and developmental basis of evolutionary pelvic reduction in threespine sticklebacks. Nature 428: 717–723.
|
[18] | Lenski RE (1988) Experimental studies of pleiotropy and epistasis in I. Variation in competitive fitness among mutants resistant to virus T4. Evolution 42: 425–432.
|
[19] | Steinmetz LM, Davis RW (2004) Maximizing the potential of functional genomics. Nat Rev Genet 5: 190–201.
|
[20] | Lander ES, Botstein D (1989) Mapping mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics 121: 185–199.
|
[21] | Doerge RW (2002) Mapping and analysis of quantitative trait loci in experimental populations. Nat Rev Genet 3: 43–52.
|
[22] | Winzeler EA, Richards DR, Conway AR, Goldstein AL, Kalman S, et al. (1998) Direct allelic variation scanning of the yeast genome. Science 281: 1194–1197.
|
[23] | Winzeler EA, Castillo-Davis CI, Oshiro G, Liang D, Richards DR, et al. (2003) Genetic diversity in yeast assessed with whole-genome oligonucleotide arrays. Genetics 163: 79–89.
|
[24] | Steinmetz LM, Sinha H, Richards DR, Spiegelman JI, Oefner PJ, et al. (2002) Dissecting the architecture of a quantitative trait locus in yeast. Nature 416: 326–330.
|
[25] | Deutschbauer AM, Davis RW (2005) Quantitative trait loci mapped to single-nucleotide resolution in yeast. Nat Genet 37: 1333–1340.
|
[26] | Darvasi A, Soller M (1994) Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics 138: 1365–1373.
|
[27] | Sham P, Bader JS, Craig I, O'Donovan M, Owen M (2002) DNA Pooling: A tool for large-scale association studies. Nat Rev Genet 3: 862–871.
|
[28] | Pareek CS, Pareek RS, Walawski K (2002) Novel linkage mapping approach using DNA pooling in human and animal genetics. I. Detection of complex disease loci. J Appl Genet 43: 175–192.
|
[29] | Norton N, Williams NM, O'Donovan MC, Owen MJ (2004) DNA pooling as a tool for large-scale association studies in complex traits. Ann Med 36: 146–152.
|
[30] | Meaburn E, Butcher LM, Schalkwyk LC, Plomin R (2006) Genotyping pooled DNA using 100K SNP microarrays: A step towards genomewide association scans. Nucleic Acids Res 34: e27.
|
[31] | Michelmore RW, Paran I, Kesseli RV (1991) Identification of markers linked to disease-resistance genes by bulked segregant analysis: a rapid method to detect markers in specific genomic regions by using segregating populations. Proc Natl Acad Sci U S A 88: 9828–9832.
|
[32] | Churchill GA, Giovannoni JJ, Tanksley SD (1993) Pooled-sampling makes high-resolution mapping practical with DNA markers. Proc Natl Acad Sci U S A 90: 16–20.
|
[33] | Borevitz JO, Liang D, Plouffe D, Chang HS, Zhu T, et al. (2003) Large-scale identification of single-feature polymorphisms in complex genomes. Genome Res 13: 513–523.
|
[34] | Wolyn DJ, Borevitz JO, Loudet O, Schwartz C, Maloof J, et al. (2004) Light-response quantitative trait loci identified with composite interval and eXtreme array mapping in . Genetics 167: 907–917.
|
[35] | Pareek CS, Pareek RS, Walawski K (2002) Novel linkage mapping approach using DNA pooling in human and animal genetics. II. Detection of quantitative traits loci in dairy cattle. J Appl Genet 43: 309–318.
|
[36] | Taylor BA, Wnek C, Schroeder D, Phillips SJ (2001) Multiple obesity QTLs identified in an intercross between the NZO (New Zealand obese) and the SM (small) mouse strains. Mamm Genome 12: 95–103.
|
[37] | Leu JY, Murray AW (2006) Experimental evolution of mating discrimination in budding yeast. Curr Biol 16: 280–286.
|
[38] | Bhat PJ, Murthy TV (2001) Transcriptional control of the GAL/MEL regulon of yeast Saccharomyces cerevisiae Mechanism of galactose-mediated signal transduction. Mol Microbiol 40: 1059–1066.
|
[39] | Peng G, Hopper JE (2002) Gene activation by interaction of an inhibitor with a cytoplasmic signaling protein. Proc Natl Acad Sci U S A 99: 8548–8553.
|
[40] | Melcher K (2005) Mutational hypersensitivity of a gene regulatory protein: Gal80p. Genetics 171: 469–476.
|
[41] | Nogi Y, Fukasawa T (1989) Functional domains of a negative regulatory protein, GAL80, of . Mol Cell Biol 9: 3009–3017.
|
[42] | Darvasi A, Pisante-Shalom A (2002) Complexities in the genetic dissection of quantitative trait loci. Trends Genet 18: 489–491.
|
[43] | Abiola O, Angel JM, Avner P, Bachmanov AA, Belknap JK, et al. (2003) The nature and identification of quantitative trait loci: A community's view. Nat Rev Genet 4: 911–916.
|
[44] | Dekkers JCM (2000) Quantitative trait locus mapping based on selective DNA pooling. J Anim Breed Genet 117: 1–16.
|
[45] | Jawaid A, Bader JS, Purcell S, Cherny SS, Sham P (2002) Optimal selection strategies for QTL mapping using pooled DNA samples. Eur J Hum Genet 10: 125–132.
|
[46] | Kim S, Zhao K, Jiang R, Molitor J, Borevitz J, et al. (2006) Association mapping with single-feature polymorphisms. Genetics. In press.
|
[47] | Gresham D, Ruderfer DM, Pratt SC, Schacherer J, Dunham MJ, et al. (2006) Genome-wide detection of polymorphisms at nucleotide resolution with a single DNA microarray. Science 311: 1932–1936.
|
[48] | Protas ME, Hersey C, Kochanek D, Zhou Y, Wilkens H, et al. (2006) Genetic analysis of cavefish reveals molecular convergence in the evolution of albinism. Nat Genet 38: 107–111.
|
[49] | Colosimo PF, Peichel CL, Nereng K, Blackman BK, Shapiro MD, et al. (2004) The genetic architecture of parallel armor plate reduction in threespine sticklebacks. PLoS Biol 2: e109. doi: 10.1371/journal.pbio.0020109.
|
[50] | Salmeron JM, Leuther KK, Johnston SA (1990) GAL4 mutations that separate the transcriptional activation and GAL80-interactive functions of the yeast GAL4 protein. Genetics 125: 21–27.
|
[51] | Blank TE, Woods MP, Lebo CM, Xin P, Hopper JE (1997) Novel Gal3 proteins showing altered Gal80p binding cause constitutive transcription of Gal4p-activated genes in . Mol Cell Biol 17: 2566–2575.
|
[52] | Slate J (2005) Quantitative trait locus mapping in natural populations: Progress, caveats and future directions. Mol Ecol 14: 363–379.
|
[53] | Cao L, Alani E, Kleckner N (1990) A pathway for generation and processing of double-strand breaks during meiotic recombination in . Cell 61: 1089–1101.
|
[54] | Gu Z, David L, Petrov D, Jones T, Davis RW, et al. (2005) Elevated evolutionary rates in the laboratory strain of . Proc Natl Acad Sci U S A 102: 1092–1097.
|
[55] | Ito H, Fukuda Y, Murata K, Kimura A (1983) Transformation of intact yeast cells treated with alkali cations. J Bacteriol 153: 163–168.
|
[56] | Guthrie C, Fink GR (2004) Guide to yeast genetics and molecular and cell biology. San Diego: Academic Press. 933 p.
|
[57] | Lipshutz RJ, Fodor SP, Gingeras TR, Lockhart DJ (1999) High density synthetic oligonucleotide arrays. Nat Genet 21: 20–24.
|
[58] | Zar JH (1999) Biostatistical analysis. New Jersey: Prentice-Hall, Inc. 663 p.
|
[59] | Churchill GA, Doerge RW (1994) Empirical threshold values for quantitative trait mapping. Genetics 138: 963–971.
|
[60] | Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673–4680.
|
[61] | Li C, Wong WH (2001) Model-based analysis of oligonucleotide arrays: Expression index computation and outlier detection. Proc Natl Acad Sci U S A 98: 31–36.
|