Begun, D. J. and C. F. Aquadro, 1991  Molecular population genetics of the distal portion of the X chromosome in Drosophila: evidence for genetic hitchhiking of the yellow-achaete region. Genetics 129: 1147-1158.

Begun, D. J  and C. F. Aquadro, 1992  Levels of naturally occurring DNA polymorphism correlate with recombination rate in D. melanogaster. Nature 356: 519-520.

Begun, D. J.  and C. F. Aquadro, 1993  African and North American populations of Drosophila melanogaster  are very different at the DNA level. Nature 365: 548-550.

Begun, D. J. and C. F. Aquadro, 1994  Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of Drosophila: selection and geographic differentiation.  Genetics 136: 155-171.

Begun, D. J., S. N. Boyer, and C. F. Aquadro, 1994 cut locus variation in natural populations of Drosophila. Mol. Biol. Evol. 11: 806-809.

Wu, C.I., H. Hollocher, D. J. Begun, C. F. Aquadro, Y. Xu and M.-L. Wu., 1995  Sexual isolation in Drosophila melanogaster: a possible case of incipient speciation.  Proc. Natl. Acad. Sci. USA 92: 2519-2533.

Begun, D. J. and C. F. Aquadro, 1995 Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. Genetics 140: 1019-1032.

Begun, D. J. and C. F. Aquadro, 1995  Evolution at the tip and base of the X chromosome in an African population of Drosophila melanogaster.  Mol. Biol. Evol. 12(3): 382-390.

Begun, D. J., 1996 Population genetics of silent and replacement variation in Drosophila simulans and D. melanogaster: X/autosome differences? Mol. Biol. Evol. 13: 1405-1407.

Begun, D. J., 1997  Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila. Genetics 145: 375-387.

Turelli, M. and D. J. Begun, 1997 Haldane’s rule and X-chromosome size in Drosophila. Genetics 147: 1799-1815.

Clark, A. G. and D. J. Begun, 1998  Female genotypes affect sperm displacement in Drosophila.  Genetics 149: 1487-1493.

Clark, A. G., D. J. Begun, and T. Prout, 1999  Female x male interactions in Drosophila sperm competition.  Science 283: 217-220.

Begun, D. J., A. J. Betancourt, C. H. Langley, and W. Stephan, 1999 Is the Fast/Slow allozyme variation at the Adh locus of D. melanogaster an ancient balanced polymorphism?  Mol. Biol. Evol. 16: 1816-1819.

Begun, D. J. and P. Whitley, 2000  Adaptive evolution of RELISH, a Drosophila NF-kB/IkB protein.  Genetics 154: 2131-1238.

Begun, D. J. and P. Whitley, 2000 Genetics of a-amanitin resistance in a natural population of Drosophila melanogaster. Heredity 85:184-190

Begun, D. J. and P. Whitley, 2000 Reduced X-linked nucleotide polymorphism in Drosophila simulans.  Proc. Natl. Acad. Sci. (USA) 97 (11): 5960-5965.

Begun, D. J., P. Whitley, B. Todd, H. Waldrip-Diehl, and A. G. Clark, 2000 Molecular population genetics of male accessory gland proteins in Drosophila. Genetics 156: 1879-1888.

Begun, D. J., 2001 The frequency distribution of nucleotide variation in Drosophila simulans. Mol. Biol. Evol. 18: 1343-1352.

Begun, D. J., 2002  Protein variation in Drosophila simulans, and comparison of genes from centromeric vs. non-centromeric regions of chromosome 3.  Mol. Biol Evol. 19: 201-203.

Begun, D. J. and P. Whitley, 2002 Molecular population genetics of Xdh and the evolution of base composition in Drosophila. Genetics 162:1725-1735.

Kern, A. D., C. D. Jones and D. J. Begun, 2002 Genomic effects of nucleotide substitutions in Drosophila simulans. Genetics 162:1753-1761.

Schlenke. T.A. and D. J. Begun,  2003, Natural selection drives Drosophila immune system evolution.  Genetics 164:1471-1480

Schlenke, T. A. and D. J. Begun, 2004,  Strong selective sweep associated with a transposon insertion in Drosophila simulans, Proc. Natl. Acad. Sci. USA 101: 1626-1631.

Kern, A. D., C. D. Jones, and D. J. Begun, 2004 Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics 167:725-735.

Holloway, A. K. and D. J. Begun, 2004, Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila, Mol. Biol. Evol. 21:1625-1628.

Lawniczak, M. K. N. and D. J. Begun, 2004, A genome-wide analysis of courting and mating responses in Drosophila melanogaster females. Genome, 47(5):900-910.

Kern, A. D. and D. J. Begun, 2005, Patterns of polymorphism and divergence from non-coding sequences of Drosophila melanogaster and D. simulans: Evidence for non-equilibrium processes. Mol. Biol. Evol. 22:51-62

Wagstaff, B. J. and D. J. Begun, 2005, Comparative genomics of accessory gland protein genes in Drosophila melanogaster and D. pseudoobscura. Mol. Biol. Evol. 22:818-832.

Schlenke, T. A. and D. J. Begun, 2005, Linkage disequilibrium and recent selection in three potential pattern recognition receptor loci in Drosophila simulans, Genetics 169:2013-2022.

Jones, C. D., A. W. Custer and D. J. Begun, 2005, Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche. Genetics 170:207-219.

Begun, D. J. and H. A. Lindfors, 2005, Rapid evolution of genomic Acp complement in the melanogaster subgroup of Drosophila, Mol. Biol. Evol. 22:2010-2021.

Jones, C. D. and D. J. Begun, 2005, Parallel evolution of chimeric fusion genes, Proc. Natl. Acad. Sci. (USA) 102:11373-11378.

Wagstaff, B. J. and D. J. Begun, 2005, Molecular population genetics of accessory gland protein genes and testis-expressed genes in Drosophila mojavensis and D. arizonae. Genetics 171:1083-1101.

Lawniczak, M. K. N. and D. J. Begun, 2005, A QTL analysis of female variation contributing to refractoriness and sperm competition in Drosophila melanogaster. Genetical Research 86:107-114.

Begun, D. J., H. A. Lindfors, M. E. Thompson and A. K. Holloway, 2006, Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics 172:1675-1681.

Levine, M. T., C. D. Jones, A. D. Kern, H. A. Lindfors and D. J. Begun, 2006, Novel genes derived from non-coding DNA in Drosophila melanogaster are frequently X-linked and show testis-biased expression. Proc. Natl. Acad. Sci (USA) 103:9935-9939.

Begun, D. J., H. A. Lindfors, A. D. Kern, C. D. Jones, 2007, Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics 176:1131-1137.

Levine, M. T. and D. J. Begun, 2007, Comparative population genetics of the immunity gene, Relish: Is adaptive evolution idiosyncratic? PLoS ONE: May 16;2;e442.

Lawniczak, M. K. N. and D. J. Begun, 2007, Molecular population genetics of female-expressed mating induced serine proteases in Drosophila melanogaster.  Mol. Biol. Evol. 24(9):1944-1951.

Wagstaff, B. J., A. K. Holloway, and D. J. Begun, 2007, Adaptive evolution of recently duplicated accessory gland protein genes in desert Drosophila. Genetics 177: 1023-1030.

Holloway, A. K., M. K. N. Lawniczak, J. G. Mezey, D. J. Begun and C. D. Jones, 2007, Adaptive gene expression divergence inferred from population genomics. PLoS Genetics 3(10):e187.

Holloway, A. K. and D. J. Begun, 2007, Population genomic analysis of protein domain evolution in Drosophila simulans, PLoS ONE 2(10): e1113.

Begun, D. J., A. K. Holloway, K. Stevens, et al., 2007, Population genomics: whole genome analysis of polymorphism and divergence in Drosophila simulans.  PLoS Biology 5(11): e310.

Drosophila 12 Genomes Consortium, 2007, Evolution of genes and genomes on the Drosophila phylogeny. Nature 450:203-218.

Levine, M. T., A. K. Holloway, U. Arshad and D. J. Begun, 2007, Pervasive and largely lineage-specific adaptive protein evolution in the dosage compensation complex of Drosophila melanogaster, Genetics 177:1959-1962

Turner, T. L., M. T. Levine, M. L. Eckert, and D. J. Begun, 2008, Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics 179:455-473.

Levine, M. T. and D. J. Begun, 2008, Evidence of spatially varying selection acting on four chromatin remodeling genes in Drosophila melanogaster. Genetics 179:475-485.

Kern, A. D. and D. J. Begun, 2008, Recurrent deletion and gene presence/absence polymorphism: telomere dynamics dominate evolution at the tip of 3L in Drosophila melanogaster and D. simulans, Genetics 179:1021-1027.

Holloway, A., K., D. J. Begun, A. Siepal, and K. S. Pollard, 2008, Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster.  Genome Research, 18(10)1592-1601.

Lawniczak, M. K., A. K. Holloway, D. J. Begun, and C. D. Jones, 2008, Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biology 9(8):R25.

Levine, M. T., M. L. Eckert, and D. J. Begun, 2011, Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from eastern Australia. Molec. Biol. Evol. 28:249-256.

Kolaczkowski, B., A. D. Kern, A. K. Holloway and D. J. Begun, 2011, Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics 187:245-260.