Population genetics and molecular evolution

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.