Natural Selection and the Frequency Distributions of ``Silent'' DNA Polymorphism in Drosophila

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				P. R. Haddrill, D. Bachtrog, and P. Andolfatto Positive and Negative Selection on Noncoding DNA in Drosophila simulans Mol. Biol. Evol., September 1, 2008; 25(9): 1825 - 1834. [Abstract] [Full Text] [PDF]

				R. Egea, S. Casillas, and A. Barbadilla Standard and generalized McDonald-Kreitman test: a website to detect selection by comparing different classes of DNA sites Nucleic Acids Res., July 1, 2008; 36(suppl_2): W157 - W162. [Abstract] [Full Text] [PDF]

				A. Llopart and J. M. Comeron Recurrent Events of Positive Selection in Independent Drosophila Lineages at the Spermatogenesis Gene roughex Genetics, June 1, 2008; 179(2): 1009 - 1020. [Abstract] [Full Text] [PDF]

				D. Bachtrog Evidence for Male-Driven Evolution in Drosophila Mol. Biol. Evol., April 1, 2008; 25(4): 617 - 619. [Abstract] [Full Text] [PDF]

				V. Nolte and C. Schlotterer African Drosophila melanogaster and D. simulans Populations Have Similar Levels of Sequence Variability, Suggesting Comparable Effective Population Sizes Genetics, January 1, 2008; 178(1): 405 - 412. [Abstract] [Full Text] [PDF]

				P. Andolfatto Hitchhiking effects of recurrent beneficial amino acid substitutions in the Drosophila melanogaster genome Genome Res., December 1, 2007; 17(12): 1755 - 1762. [Abstract] [Full Text] [PDF]

				N. D. Singh, V. L. Bauer DuMont, M. J. Hubisz, R. Nielsen, and C. F. Aquadro Patterns of Mutation and Selection at Synonymous Sites in Drosophila Mol. Biol. Evol., December 1, 2007; 24(12): 2687 - 2697. [Abstract] [Full Text] [PDF]

				J. D. Jensen, V. L. Bauer DuMont, A. B. Ashmore, A. Gutierrez, and C. F. Aquadro Patterns of Sequence Variability and Divergence at the diminutive Gene Region of Drosophila melanogaster: Complex Patterns Suggest an Ancestral Selective Sweep Genetics, October 1, 2007; 177(2): 1071 - 1085. [Abstract] [Full Text] [PDF]

				R. D. Hernandez, S. H. Williamson, and C. D. Bustamante Context Dependence, Ancestral Misidentification, and Spurious Signatures of Natural Selection Mol. Biol. Evol., August 1, 2007; 24(8): 1792 - 1800. [Abstract] [Full Text] [PDF]

				D. Bachtrog and P. Andolfatto Selection, Recombination and Demographic History in Drosophila miranda Genetics, December 1, 2006; 174(4): 2045 - 2059. [Abstract] [Full Text] [PDF]

				C. Bartolome and B. Charlesworth Evolution of Amino-Acid Sequences and Codon Usage on the Drosophila miranda Neo-Sex Chromosomes Genetics, December 1, 2006; 174(4): 2033 - 2044. [Abstract] [Full Text] [PDF]

				J. J. Welch Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila Genetics, June 1, 2006; 173(2): 821 - 837. [Abstract] [Full Text] [PDF]

				J. M. Comeron Weak selection and recent mutational changes influence polymorphic synonymous mutations in humans PNAS, May 2, 2006; 103(18): 6940 - 6945. [Abstract] [Full Text] [PDF]

				H. Akashi, W.-Y. Ko, S. Piao, A. John, P. Goel, C.-F. Lin, and A. P. Vitins Molecular Evolution in the Drosophila melanogaster Species Subgroup: Frequent Parameter Fluctuations on the Timescale of Molecular Divergence Genetics, March 1, 2006; 172(3): 1711 - 1726. [Abstract] [Full Text] [PDF]

				L. Loewe, B. Charlesworth, C. Bartolome, and V. Noel Estimating Selection on Nonsynonymous Mutations Genetics, February 1, 2006; 172(2): 1079 - 1092. [Abstract] [Full Text] [PDF]

				J. M. Comeron and T. B. Guthrie Intragenic Hill-Robertson Interference Influences Selection Intensity on Synonymous Mutations in Drosophila Mol. Biol. Evol., December 1, 2005; 22(12): 2519 - 2530. [Abstract] [Full Text] [PDF]

				M. Nei Selectionism and Neutralism in Molecular Evolution Mol. Biol. Evol., December 1, 2005; 22(12): 2318 - 2342. [Abstract] [Full Text] [PDF]

				D. Bachtrog Sex chromosome evolution: Molecular aspects of Y-chromosome degeneration in Drosophila Genome Res., October 1, 2005; 15(10): 1393 - 1401. [Abstract] [Full Text] [PDF]

				N. D. Singh, J. C. Davis, and D. A. Petrov X-Linked Genes Evolve Higher Codon Bias in Drosophila and Caenorhabditis Genetics, September 1, 2005; 171(1): 145 - 155. [Abstract] [Full Text] [PDF]

				S. H. Williamson, R. Hernandez, A. Fledel-Alon, L. Zhu, R. Nielsen, and C. D. Bustamante Simultaneous inference of selection and population growth from patterns of variation in the human genome PNAS, May 31, 2005; 102(22): 7882 - 7887. [Abstract] [Full Text] [PDF]

				C. Bartolome, X. Maside, S. Yi, A. L. Grant, and B. Charlesworth Patterns of Selection on Synonymous and Nonsynonymous Variants in Drosophila miranda Genetics, March 1, 2005; 169(3): 1495 - 1507. [Abstract] [Full Text] [PDF]

				H. Qin, W. B. Wu, J. M. Comeron, M. Kreitman, and W.-H. Li Intragenic Spatial Patterns of Codon Usage Bias in Prokaryotic and Eukaryotic Genomes Genetics, December 1, 2004; 168(4): 2245 - 2260. [Abstract] [Full Text] [PDF]

				N. Bierne and A. Eyre-Walker The Genomic Rate of Adaptive Amino Acid Substitution in Drosophila Mol. Biol. Evol., July 1, 2004; 21(7): 1350 - 1360. [Abstract] [Full Text] [PDF]

				V. B. DuMont, J. C. Fay, P. P. Calabrese, and C. F. Aquadro DNA Variability and Divergence at the Notch Locus in Drosophila melanogaster and D. simulans: A Case of Accelerated Synonymous Site Divergence Genetics, May 1, 2004; 167(1): 171 - 185. [Abstract] [Full Text] [PDF]

				Y. Kim Effect of Strong Directional Selection on Weakly Selected Mutations at Linked Sites: Implication for Synonymous Codon Usage Mol. Biol. Evol., February 1, 2004; 21(2): 286 - 294. [Abstract] [Full Text] [PDF]

				D. Bachtrog Protein Evolution and Codon Usage Bias on the Neo-Sex Chromosomes of Drosophila miranda Genetics, November 1, 2003; 165(3): 1221 - 1232. [Abstract] [Full Text] [PDF]

				J. A. Perez, A. Munte, J. Rozas, C. Segarra, and M. Aguade Nucleotide Polymorphism in the RpII215 Gene Region of the Insular Species Drosophila guanche: Reduced Efficacy of Weak Selection on Synonymous Variation Mol. Biol. Evol., November 1, 2003; 20(11): 1867 - 1875. [Abstract] [Full Text] [PDF]

				M. T. Webster, N. G. C. Smith, and H. Ellegren Compositional Evolution of Noncoding DNA in the Human and Chimpanzee Genomes Mol. Biol. Evol., February 1, 2003; 20(2): 278 - 286. [Abstract] [Full Text] [PDF]

				D. J. Begun and P. Whitley Molecular Population Genetics of Xdh and the Evolution of Base Composition in Drosophila Genetics, December 1, 2002; 162(4): 1725 - 1735. [Abstract] [Full Text] [PDF]