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David Begun

Professor
djbegun@ucdavis.edu


Evolution and Ecology

Office
3350A Storer




Degrees:

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

Research Contribution to Society:

We study basic mechanisms of evolution from a genetic perspective

Research Interests:

Population genetics and molecular evolution
Population genetics and molecular evolution. Drosophila evolutionary genetics.


CBS Graduate Group Affiliations:

Genetics  
Population Biology   Chair

Specialties / Focus:

Genetics

Publications:

Last updated 8/23/2011
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
 


Laboratory Personnel:

The Begun Lab
http://www.eve.ucdavis.edu/djbegun/




Teaching Interests:

Undergraduate: Evolution Graduate: Molecular Evolution, Population Genetics

Courses:

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