David Begun

David Begun

Position Title

Department of Evolution and Ecology
Center for Population Biology

3350A Storer

Research Interests

Population genetics and molecular evolution

Population genetics and molecular evolution. Drosophila evolutionary genetics.

Grad Group Affiliations

  • Integrative Genetics and Genomics
  • Population Biology

Specialties / Focus

  • Molecular Evolution
  • Population and Quantitative Genetics


  • EVE 10
  • EVE 100 Intro to Evolution
  • PBG 200A Principles of Population Biology


  • The Begun Lab http://begunlab.ucdavis.edu/


  • 1985 BA Biology Brandeis University
  • 1989 MS Zoology Arizona State University
  • 1994 PhD Genetics and Development Cornell University


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.

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.

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.

Levine MT, Begun DJ. (2008) Evidence of spatially varying selection acting on four chromatin-remodeling loci in Drosophila melanogaster. Genetics. 179(1):475-85.

Kern AD, Begun DJ.(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(2):1021-7

Lawniczak MK, Holloway AK, Begun DJ, Jones CD. (2008) Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans, Genome Biol. 9(8):R125.

Turner TL, Levine MT, Eckert ML, Begun DJ. (2008) Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics. 179(1):455-73.

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

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

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.

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

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.

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.

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.

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., 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, 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.

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.

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.

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

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., 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.

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.

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.

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.

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.

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.

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.

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

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

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

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

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 DJ 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.

Clark AG, DJ Begun, and T Prout. (1999) Female x male interactions in Drosophila sperm competition. Science. 283:217-220

Begun DJ. (1997) Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila. Genetics. 145:375-387