Begun lab publications

2017
Zhao L, Begun DJ. Genomics of parallel adaptation at two timescales in Drosophila. PLoS Genet. 2017;13(10):e1007016. doi: 10.1371/journal.pgen.1007016. PDF
2016

Svetec N, Cridland JM, Zhao L, Begun DJ. The Adaptive Significance of Natural Genetic Variation in the DNA Damage Response of Drosophila melanogaster. PLoS Genet. 2016;12(3):e1005869. doi: 10.1371/journal.pgen.1005869. PDF

Schrider DR, Hahn MW, Begun DJ. Parallel Evolution of Copy-Number Variation across Continents in Drosophila Melanogaster. Mol Biol Evol. 2016. pii: msw014 PDF

Sedghifar A, Saelao P, Begun DJ. Genomic Patterns of Geographic Differentiation in Drosophila simulans. Genetics. 2016;202(3):1229-40. doi: 10.1534/genetics.115.185496. PDF

2015

Zhao L, Wit J, Svetec N, Begun DJ. Parallel Gene Expression Differences between Low and High Latitude Populations of Drosophila melanogaster and D. simulans. PLOS Genet. 2015;11(5): e1005184. doi:10.1371/journal.pgen.1005184 PDF

Svetec N, Zhao L, Saelao P, Chiu JC, Begun DJ. Evidence that natural selection maintains genetic variation for sleep in Drosophila melanogaster. BMC Evol Biol. 2015;15:41. doi:10.1186/s12862-015-0316-2 PDF

2014
Hamm CA, Begun DJ, Vo A, Smith CC, Saelao P, Shaver AO, Jaenike J, Turelli M. Wolbachia do not live by reproductive manipulation alone: infection polymorphism in Drosophila suzukii and D. subpulchrella. Mol Ecol. 2014;23(19):4871-85. doi: 10.1111/mec.12901. PDF
Zhao L, Saelao P, Jones CD, Begun DJ. Origin and spread of de novo genes in Drosophila melanogaster populations. Science. 2014;343(6172):769-72. doi: 10.1126/science.1248286. PDF or Full Text
Reinhardt JA, Kolaczkowski B, Jones CD, Begun DJ, Kern AD. Parallel geographic variation in Drosophila melanogaster. Genetics. 2014;197(1):361-73. doi: 10.1534/genetics.114.161463. PDF
Lee YC, Langley CH, Begun DJ. Differential strengths of positive selection revealed by hitchhiking effects at small physical scales in Drosophila melanogaster. Mol Biol Evol. 2014;31(4):804-16. doi: 10.1093/molbev/mst270. PDF

2013

Reinhardt JA, Wanjiru BM, Brant AT, Saelao P, Begun DJ, Jones CD. De novo ORFs in Drosophila are important to organismal fitness and evolved rapidly from previously non-coding sequences. PLoS Genet. 2013;9(10):e1003860. doi: 10.1371/journal.pgen.1003860. PDF
Chiu JC, Jiang X, Zhao L, Hamm CA, Cridland JM, Saelao P, Hamby KA, Lee EK, Kwok RS, Zhang G, Zalom FG, Walton VM, Begun DJ. Genome of Drosophila suzukii, the spotted wing drosophila. G3 (Bethesda). 2013;3(12):2257-71. doi: 10.1534/g3.113.008185. PDF
Schrider DR, Begun DJ, Hahn MW. Detecting highly differentiated copy-number variants from pooled population sequencing. Pac Symp Biocomput. 2013:344-55. PDF

2012

Pool JE, Corbett-Detig RB, Sugino RP, Stevens KA, Cardeno CM, Crepeau MW, Duchen P, Emerson JJ, Saelao P, Begun DJ, Langley CH. Population Genomics of sub-saharan Drosophila melanogaster: African diversity and non-African admixture. PLoS Genet. 2012;8(12):e1003080. doi: 10.1371/journal.pgen.1003080. PDF
Poh YP, Ting CT, Fu HW, Langley CH, Begun DJ. Population genomic analysis of base composition evolution in Drosophila melanogaster. Genome Biol Evol. 2012;4(12):1245-55. doi: 10.1093/gbe/evs097. PDF
Langley CH, Stevens K, Cardeno C, Lee YC, Schrider DR, Pool JE, Langley SA, Suarez C, Corbett-Detig RB, Kolaczkowski B, Fang S, Nista PM, Holloway AK, Kern AD, Dewey CN, Song YS, Hahn MW, Begun DJ. Genomic variation in natural populations of Drosophila melanogaster. Genetics. 2012;192(2):533-98. doi: 10.1534/genetics.112.142018. PDF

2011

Kolaczkowski B, Kern AD, Holloway AK, Begun DJ. Genomic differentiation between temperate and tropical Australian populations of Drosophila melanogaster. Genetics. 2011;187(1):245-60. doi: 10.1534/genetics.110.123059. PDF
Levine MT, Eckert ML, Begun DJ. Whole-genome expression plasticity across tropical and temperate Drosophila melanogaster populations from Eastern Australia. Mol Biol Evol. 2011;28(1):249-56. doi: 10.1093/molbev/msq197. PDF

2006-2010

Lawniczak MK, Holloway AK, Begun DJ, Jones CD. Genomic analysis of the relationship between gene expression variation and DNA polymorphism in Drosophila simulans. Genome Biol. 2008;9(8):R125. doi: 10.1186/gb-2008-9-8-r125. PDF
Holloway AK, Begun DJ, Siepel A, Pollard KS. Accelerated sequence divergence of conserved genomic elements in Drosophila melanogaster. Genome Res. 2008;18(10):1592-601. doi: 10.1101/gr.077131.108. PDF
Kern AD, Begun DJ. Recurrent deletion and gene presence/absence polymorphism: telomere dynamics dominate evolution at the tip of 3L in Drosophila melanogaster and D. simulans. Genetics. 2008;179(2):1021-7. doi: 10.1534/genetics.107.078345. PDF
Turner TL, Levine MT, Eckert ML, Begun DJ. Genomic analysis of adaptive differentiation in Drosophila melanogaster. Genetics. 2008;179(1):455-73. PDF
Levine MT, Begun DJ. Evidence of spatially varying selection acting on four chromatin-remodeling loci in Drosophila melanogaster. Genetics. 2008;179(1):475-85. doi: 10.1534/genetics.107.085423. PDF
Levine MT, Holloway AK, Arshad U, Begun DJ. Pervasive and largely lineage-specific adaptive protein evolution in the dosage compensation complex of Drosophila melanogaster. Genetics. 2007;177(3):1959-62. PDF
Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, Hahn MW, Nista PM, Jones CD, Kern AD, Dewey CN, Pachter L, Myers E, Langley CH. Population genomics: whole-genome analysis of polymorphism and divergence in Drosophila simulans. PLoS Biol. 2007;5(11):e310. PDF
Holloway AK, Begun DJ. Rampant adaptive evolution in regions of proteins with unknown function in Drosophila simulans. PLoS One. 2007;2(10):e1113. PDF
Holloway AK, Lawniczak MK, Mezey JG, Begun DJ, Jones CD. Adaptive gene expression divergence inferred from population genomics. PLoS Genet. 2007;3(10):2007-13. PDF
Wagstaff BJ, Begun DJ. Adaptive evolution of recently duplicated accessory gland protein genes in desert Drosophila. Genetics. 2007;177(2):1023-30. PDF
Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny. Nature. 2007;450(7167):203-18. PDF
Lawniczak MK, Begun DJ. Molecular population genetics of female-expressed mating-induced serine proteases in Drosophila melanogaster. Mol Biol Evol. 2007;24(9):1944-51. PDF
Levine MT, Begun DJ. Comparative population genetics of the immunity gene, Relish: is adaptive evolution idiosyncratic? PLoS One. 2007;2(5):e442. PDF
Begun DJ, Lindfors HA, Kern AD, Jones CD. Evidence for de novo evolution of testis-expressed genes in the Drosophila yakuba/Drosophila erecta clade. Genetics. 2007;176(2):1131-7. PDF
Levine MT, Jones CD, Kern AD, Lindfors HA, Begun DJ. Novel genes derived from noncoding DNA in Drosophila melanogaster are frequently X-linked and exhibit testis-biased expression. Proc Natl Acad Sci U S A. 2006;103(26):9935-9. PDF
Begun DJ, Lindfors HA, Thompson ME, Holloway AK. Recently evolved genes identified from Drosophila yakuba and D. erecta accessory gland expressed sequence tags. Genetics. 2006;172(3):1675-81. PDF

2001-2005

Lawniczak MK, Begun DJ. A QTL analysis of female variation contributing to refractoriness and sperm competition in Drosophila melanogaster. Genet Res. 2005;86(2):107-14. PDF
Wagstaff BJ, Begun DJ. Molecular population genetics of accessory gland protein genes and testis-expressed genes in Drosophila mojavensis and D. arizonae. Genetics. 2005;171(3):1083-101. PDF
Jones CD, Begun DJ. Parallel evolution of chimeric fusion genes. Proc Natl Acad Sci U S A. 2005;102(32):11373-8. PDF
Begun DJ, Lindfors HA. Rapid evolution of genomic Acp complement in the melanogaster subgroup of Drosophila. Mol Biol Evol. 2005;22(10):2010-21. PDF
Jones CD, Custer AW, Begun DJ. Origin and evolution of a chimeric fusion gene in Drosophila subobscura, D. madeirensis and D. guanche. Genetics. 2005;170(1):207-19. PDF
Hahn MW, Mezey JG, Begun DJ, Gillespie JH, Kern AD, Langley CH, Moyle LC. Evolutionary genomics: codon bias and selection on single genomes. Nature. 2005;433(7023):E5-6; PDF
Schlenke TA, Begun DJ. Linkage disequilibrium and recent selection at three immunity receptor loci in Drosophila simulans. Genetics. 2005;169(4):2013-22. PDF
Wagstaff BJ, Begun DJ. Comparative genomics of accessory gland protein genes in Drosophila melanogaster and D. pseudoobscura. Mol Biol Evol. 2005;22(4):818-32. PDF
Lawniczak MK, Begun DJ. A genome-wide analysis of courting and mating responses in Drosophila melanogaster females. Genome. 2004;47(5):900-10. PDF
Kern AD, Begun DJ. Patterns of polymorphism and divergence from noncoding sequences of Drosophila melanogaster and D. simulans: evidence for nonequilibrium processes. Mol Biol Evol. 2005;22(1):51-62. PDF
Kern AD, Jones CD, Begun DJ. Molecular population genetics of male accessory gland proteins in the Drosophila simulans complex. Genetics. 2004;167(2):725-35. PDF
Holloway AK, Begun DJ. Molecular evolution and population genetics of duplicated accessory gland protein genes in Drosophila. Mol Biol Evol. 2004;21(9):1625-8. PDF
Schlenke TA, Begun DJ. Strong selective sweep associated with a transposon insertion in Drosophila simulans. Proc Natl Acad Sci U S A. 2004;101(6):1626-31. PDF
Schlenke TA, Begun DJ. Natural selection drives Drosophila immune system evolution. Genetics. 2003;164(4):1471-80. PDF
Kern AD, Jones CD, Begun DJ. Genomic effects of nucleotide substitutions in Drosophila simulans. Genetics. 2002;162(4):1753-61. PDF
Begun DJ, Whitley P. Molecular population genetics of Xdh and the evolution of base composition in Drosophila. Genetics. 2002;162(4):1725-35. PDF
Begun DJ. Protein variation in Drosophila simulans, and comparison of genes from centromeric versus noncentromeric regions of chromosome 3. Mol Biol Evol. 2002;19(2):201-3. PDF
Begun DJ. The frequency distribution of nucleotide variation in Drosophila simulans. Mol Biol Evol. 2001;18(7):1343-52. PDF

1995-2000

Begun DJ, Whitley P, Todd BL, Waldrip-Dail HM, Clark AG. Molecular population genetics of male accessory gland proteins in Drosophila. Genetics. 2000;156(4):1879-88. PDF
Begun DJ, Whitley P. Genetics of alpha-amanitin resistance in a natural population of Drosophila melanogaster. Heredity. 2000;85:184-90. PDF
Begun DJ, Whitley P. Reduced X-linked nucleotide polymorphism in Drosophila simulans. Proc Natl Acad Sci U S A. 2000;97(11):5960-5. PDF
Begun DJ, Whitley P. Adaptive evolution of relish, a Drosophila NF-kappaB/IkappaB protein. Genetics. 2000;154(3):1231-8. PDF
Begun DJ, Betancourt AJ, Langley CH, Stephan W. Is the fast/slow allozyme variation at the Adh locus of Drosophila melanogaster an ancient balanced polymorphism? Mol Biol Evol. 1999;16(12):1816-9. PDF
Clark AG, Begun DJ, Prout T. Female x male interactions in Drosophila sperm competition. Science. 1999;283(5399):217-20. PDF
Clark AG, Begun DJ. Female genotypes affect sperm displacement in Drosophila. Genetics. 1998;149(3):1487-93. PDF
Turelli M, Begun DJ. Haldane’s rule and X-chromosome size in Drosophila. Genetics. 1997;147(4):1799-815. PDF
Begun DJ. Origin and evolution of a new gene descended from alcohol dehydrogenase in Drosophila. Genetics. 1997;145(2):375-82. PDF
Begun DJ. Population genetics of silent and replacement variation in Drosophila simulans and D. melanogaster: X/autosome differences? Mol Biol Evol. 1996;13(10):1405-7. PDF

1991-1995

Begun DJ, Aquadro CF. Molecular variation at the vermilion locus in geographically diverse populations of Drosophila melanogaster and D. simulans. Genetics. 1995;140(3):1019-32. PDF
Jones TR, Routman EJ, Begun DJ, Collins JP. Ancestry of an isolated subspecies of salamander, Ambystoma tigrinum stebbinsi Lowe: the evolutionary significance of hybridization. Mol Phylogenet Evol. 1995;4(2):194-202. PDF
Begun DJ, Aquadro CF. Evolution at the tip and base of the X chromosome in an African population of Drosophila melanogaster. Mol Biol Evol. 1995;12(3):382-90. PDF
Wu CI, Hollocher H, Begun DJ, Aquadro CF, Xu Y, Wu ML. Sexual isolation in Drosophila melanogaster: a possible case of incipient speciation. Proc Natl Acad Sci U S A. 1995;92(7):2519-23. PDF
Begun DJ, Boyer SN, Aquadro CF. Cut locus variation in natural populations of Drosophila. Mol Biol Evol. 1994;11(5):806-9. PDF
Begun DJ, Aquadro CF. Evolutionary inferences from DNA variation at the 6-phosphogluconate dehydrogenase locus in natural populations of drosophila: selection and geographic differentiation. Genetics. 1994;136(1):155-71. PDF
Begun DJ, Aquadro CF. African and North American populations of Drosophila melanogaster are very different at the DNA level. Nature. 1993;365(6446):548-50. PDF
Begun DJ, Collins JP. Biochemical plasticity in the Arizona tiger salamander (Ambystoma tigrinum nebulosum). J Hered. 1992;83(3):224-7. PDF
Begun DJ, Aquadro CF. Levels of naturally occurring DNA polymorphism correlate with recombination rates in D. melanogaster. Nature. 1992;356(6369):519-20. PDF
Begun DJ, Aquadro CF. Molecular population genetics of the distal portion of the X chromosome in Drosophila: evidence for genetic hitchhiking of the yellow-achaete region. Genetics. 1991;129(4):1147-58. PDF