* = corresponding author
Vande Zande, P., M.S. Hill, and J. Wittkopp (2022) Pleiotropic effects of trans-regulatory mutations on fitness and gene expression. Science, 377, 105-109. PDF
Krieger, G., O. Lupo, J. Wittkopp, N. Barkai (2022) Evolution of transcription factor binding through sequence variations and turnover of binding sites. Genome Research, 32, 1099-1111. PDF
Duveau, F*., P. Vande Zande, B.P.H. Metzger, C. Diaz, E. Walker, Tryban, M. Siddiq, B. Yang, and P.J. Wittkopp* (2021). Mutational sources of trans-regulatory variation affecting gene expression in S. cerevisiae, eLife, 10, e67806. PDF
Massey, J.H, Li, J., Stern, D.L., J. Wittkopp*. (2021) Distinct genetic architectures underlie divergent body, leg, and wing pigmentation between Drosophila elegans and D. gunungcola. Heredity, 127,467-474. PDF
Hill, M.S., P. Vande Zande, and J. Wittkopp*. (2021) Molecular and evolutionary processes generating variation in gene expression. Nature Reviews Genetics, 22, 203–215. PDF
Massey, J.H., Li, J., and J. Wittkopp (2020) A method using CO2 anesthesia to collect embryos for microinjection in non-model Drosophila. Drosophila Information Service 103,75-77.
Sramkoski, L.L, N. McLaughlin, A.M. Cooley, D.C. Yuan, A. John, and P.J. Wittkopp* (2020) Genetic architecture of a body colour cline in Drosophila americana, Molecular Ecology, 29, 2840-2854. PDF
Lamb, A. M., Z. Wang, P. Simmer, H. Chung, and P.J. Wittkopp* (2020) ebony affects pigmentation divergence and cuticular hydrocarbons in Drosophila americana and D. novamexicana. Frontiers in Ecology and Evolution, 8, 184. Full text
Massey, J.H., Rice, G.R., Firdaus, A., Chen, C.‐Y., Yeh, S.‐D., Stern, D.L. and Wittkopp, P.J. (2020), Co‐evolving wing spots and mating displays are genetically separable traits in Drosophila. Evolution. Accepted Author Manuscript. doi:10.1111/evo.13990 PDF
Massey, J.H, D. Chung, I. Siwanowicz, D.L. Stern*, P.J. Wittkopp* (2019) The yellow gene influences Drosophila male mating success through sex comb melanization. eLife. 2019 Oct 15;8. PDF
Metzger, B.P.H., and P.J. Wittkopp* (2019) Compensatory trans-regulatory alleles minimizing variation in TDH3 expression are common within Saccharomyces cerevisiae. Evol Lett. 2019 Aug 29;3(5):448-461 PDF
Hodgins-Davis, A., F. Duveau, E. Walker, P.J. Wittkopp* (2019) Empirical measures of mutational effects define neutral models of regulatory evolution in Saccharomyces cerevisiae. Proceedings of the National Academy of Sciences, Proc Natl Acad Sci U S A. 2019 Oct 15;116(42):21085-21093 PDF
Massey J.H., N. Akiyama, T. Bien, K. Dreisewerd, P.J. Wittkopp*, J.Y. Yew*, A. Takahashi* (2019) Pleiotropic effects of ebony and tan on pigmentation and cuticular hydrocarbon composition in Drosophila melanogaster. Frontiers in Physiology, 10, 518. PDF
Kalay, G., J. Lachowiec, U. Rosas, M.R. Dome, and P.J. Wittkopp. 2019 Redundant and Cryptic Enhancer Activities of the Drosophila yellow Gene, Genetics, PDF
Duveau, F., A. Hodgins-Davis, B.P.H. Metzger, B. Yang, S. Tryban, E.A. Walker, P. Lybrook, and P.J. Wittkopp. 2018 Fitness effects of altering gene expression noise in Saccharomyces cerevisiae, eLife, PDF
Duveau, F., D.C. Yuan, B.P.H. Metzger, A. Hodgins-Davis, and P.J. Wittkopp. 2017 Effects of mutation and selection on plasticity of a promoter activity in Saccharomyces cerevisiae, PNAS, PDF
Duveau, F., W. Toubiana, and P.J. Wittkopp. 2017 Fitness effects of cis-regulatory variants in the Saccharomyces cerevisiae TDH3 promoter, Molecular Biology and Evolution, PDF
Metzger, B.P.H., P. J. Wittkopp, and J.D. Coolon*. Evolutionary dynamics of regulatory changes underlying gene expression divergence among Saccharomyces species, Genome Biology and Evolution, PDF
Yang, B. and P. J. Wittkopp*. 2017 Structure of the transcriptional regulatory network correlates with regulatory divergence in Drosophila. Molecular Biology and Evolution, in press. PDF
Andrade López, J. M., Lanno, S. M., Auerbach, J. M., Moskowitz, E. C., Sligar, L. A., Wittkopp, P. J., and J. D. Coolon*. 2016. Genetic basis of octanoic acid resistance in Drosophila sechellia: functional analysis of a fine-mapped region. Molecular Ecology, in press. PDF
Massey, J., Wittkopp, P.J. 2016. The genetic basis of pigmentation differences within and between Drosophila species. Curr Top Dev Biol. 2016; 119: 27–61. PDF
Wittkopp, P.J. 2016. Voices: Big Questions in Evolution. Cell 166, 528-29. Invited opinion PDF
Kalay, G., R. Lusk, M. Dome, K. Hens, B. Deplancke and P.J. Wittkopp*. 2016. Potential direct regulators of the Drosophila yellow gene identified by yeast one-hybrid and RNAi screens. G3: Genes, Genomics, Genetics 13, 3419-343. PDF
Lamb, A.M., Walker, E.A., and Wittkopp PJ.* 2016. Tools and strategies for scarless allele replacement in Drosophila using CRISPR/Cas9. Fly. PDF
John, A.V., Sramkoski L.L., Walker E.A., Cooley A.M., and Wittkopp PJ.* 2016. Sensitivity of allelic divergence to genomic position: Lessons from the Drosophila tan gene. G3: Genes, Genomics, Genetics. PDF
Metzger BPH, Duveau F, Yuan D, Tryban S, Yang B, Wittkopp PJ.* 2016. Contrasting frequencies and effects of cis- and trans- regulatory mutations affecting gene expression. Molecular biology and Evolution PDF
Moczek AP, Sears, KE, Stollewerk A, Wittkopp PJ, Diggle P, Dworkin I, Ledon-Rettig C, Matus DQ, Roth S, Abouheif E, Brown FD, Chiu C, Cohen CS, De Tomaso AW, Gilbert SF, Hall B, Love A, Lyons DC, Sanger T, Smith J, Specht C, Vallejo-Marin M, Extavour CG 2015. The significance and scope of evolutionary developmental biology: a vision for the 21st century. Evolution & Development PDF
Coolon, J.D*, K.R. Stevenson, C.J. McManus, B.R. Graveley, and P.J. Wittkopp*. (2015) Molecular mechanisms and evolutionary processes contributing to accelerated divergence of gene expression on the Drosophila X chromosome. Molecular Biology and Evolution. PDF
Metzger,B.P.H.1, D.C. Yuan1, J.D. Gruber, F. Duveau and P.J. Wittkopp*. (2015) Selection on noise constrains variation in a eukaryotic promoter. Nature. PDF 1 These authors contributed equally to this work.
Duveau, F*., B.P.H. Metzger, J.D. Gruber, K. Mack, N. Sood, T. Brooks and P.J. Wittkopp*. (2014) Mapping small effect mutations in Saccharomyces cerevisiae: impacts of experimental design and mutational properties. G3: Genes, Genomics, Genetics. July Vol. 4. No. 7 1205-1216 PDF
Coolon, J.D., C.J., McManus, K. Stevenson, B.R. Graveley, and P.J. Wittkopp*. (2014) Tempo and mode of regulatory evolution in Drosophila. Genome Research 24: 797-808 PDF Genome sequences, chain files, and custom scripts used in this work are available as supplemental resources from the Genome Research website.
McManus, C.J.*, J.D. Coolon, J. Eipper-Mains, P.J. Wittkopp, and B.R. Graveley* (2014) Evolution of Splicing Regulatory Networks in Drosophila. Genome Research, 24: 786-796 PDF Genome sequences for D. melanogaster, D. simulans, and D. sechellia used in this work can be downloaded here. For details, see readme file included with the download.
He, B.Z.*, M.Z. Ludwig, D.A. Dickerson, L. Barse, B. Arun, S-Y. Park, N.A. Tamarina, S.B. Selleck, P.J. Wittkopp, G.I. Bell, and M. Kreitman* (2013) Effect of Natural Genetic Variation on Phenotype in a Drosophila Model of Diabetes-Associated Misfolded Human Proinsulin. Genetics. 196, 557-67 PDF
Meiklejohn, C. D*., Coolon, J., D. L. Hartl, and P. J. Wittkopp. (2013) The roles of cis- and trans-regulation in the evolution of regulatory incompatibilities and sexually dimorphic gene expression. Genome Research, 24, 84-9. PDF
Coolon, J.D.*, W. Webb, and P.J. Wittkopp. (2013) Sex-specific effects of cis-regulatory variants in Drosophila melanogaster. Genetics, 195, 1419-22. PDF
Stevenson, K., J.D. Coolon, and P.J., Wittkopp. (2013) Sources of bias in measures of allele-specific expression derived from RNA-seq data aligned to a single reference genome. BMC Genomics, 14: 536. PDF Highly accessed Selected by Faculty of 1000 Scripts used in this work can be downloaded here and instructions for using them here.
Wittkopp, P.J.* (2013) “Evolution of Gene Expression” in The Princeton Guide to Evolution (Editor-in-chief, Jonathan Losos; Second editor, Hopi Hoekstra). PDF Invited book chapter
Wittkopp, P.J. (2013) Population Genetics and a Study of Speciation using Next-Generation Sequencing: An Educational Primer for Use with “Patterns of Transcriptome Divergence in the Male Accessory Gland of Two Closely Related Species of Field Crickets”. Genetics 193, 671-675. PDF Invited primer
Coolon, J.D. and P.J. Wittkopp*. (2013) “cis– and trans-regulation in interspecific Drosophila hybrids” in Polyploid and Hybrid Genomics, Wiley-Blackwell Publishing. Editors: Z. Jeffrey Chen and Jim Birchler. PDF Invited book chapter
Coolon, J.D.*, K. Stevenson, C.J., McManus, B. Graveley, and P.J. Wittkopp. (2012) Genomic imprinting absent in Drosophila melanogaster adult females, Cell Reports 2,69-75. PDF
Cooley, A.M.*, L. Shefner, W.N. McLaughlin, E.E. Stewart, and P.J. Wittkopp. (2012) The ontogeny of color: Developmental origins of divergent pigmentation in Drosophila americana and D. novamexicana. Evolution and Development 14, 317-325. PDF Cover Article
Gruber, J.D., K. Vogel, G. Kalay, and P.J. Wittkopp*. (2012) Contrasting Properties of Gene-specific Regulatory, Coding, and Copy Number Mutations in Saccharomyces cerevisiae: Frequency, Effects and Dominance. PLoS Genetics, 8, e1002497. PDF Selected by Faculty of 1000
Wittkopp, P.J.*, and G. Kalay. (2012) cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence. Nature Review Genetics, 13, 59-69. PDF Invited book chapter
Wittkopp, P.J.* (2011) Using pyrosequencing to measure allele-specific mRNA abundance and infer the effects of cis– and trans-regulatory differences. Methods Mol Biol. 772, 297-317. PDF Invited book chapter
Kalay, G. and P.J. Wittkopp (2011). Nomadic enhancers: tissue-specific cis-regulatory elements of yellow have divergent genomic positions among Drosophila species. PLoS Genetics 6, e1001222 PDF
Wittkopp, P.J., G. Smith-Winberry, L.L. Arnold, E. M. Thompson, A. M. Cooley, D. Yuan, Q. Song, and B.F. McAllister (2010). Local adaptation for body color inDrosophila americana. Heredity 106, 592-602. PDF
Wittkopp, P.J. (2010). Variable transcription factor binding: a mechanism of evolutionary change. PLoS Biology, 8, e1000342. PDF
McManus, C.J., J.D. Coolon, M. Duff, J. Eiper-Mains, B.R. Graveley, and P.J. Wittkopp (2010). Regulatory divergence in Drosophila revealed by mRNA-Seq. Genome Research, 20, 816-825. PDF Selected by Faculty of 1000
Fontanillas, P., C.R. Landry, P.J. Wittkopp, C. Russ, J.D. Gruber, C. Nusbaum, and D.L. Hartl. (2010) Key considerations for measuring allelic expression on a genomic scale using high-throughput sequencing. Molecular Ecology, 19 (Suppl. 1), 212–227. PDF Next Generation Molecular Ecology special issue Editorial
Wittkopp, P.J., E.E. Stewart, A.H. Neidert, B.K. Haerum, L.L. Arnold, E. M. Thompson, G. Smith-Winberry, and L. Shefner (2009). Intraspecific polymorphism to interspecific divergence: genetics of pigmentation in Drosophila. Science 326, 540-544. PDF
Wittkopp, P.J. and P. Beldade (2009). Development and evolution of insect pigmentation: genetic mechanisms and the potential consequences of pleiotropy.Seminars in Cell and Developmental Biology 20, 65-71. PDF Invited review, Pigment Cell Development special issue
Wittkopp, P.J., B.K. Haerum, and A.G. Clark (2008). Independent effects of cis– and trans-regulatory variants on gene expression in D. melanogaster. Genetics 178, 1831-5. PDF
Wittkopp, P.J., B.K. Haerum, and A. Clark (2008) Genetic basis of regulatory variation within and between Drosophila species, Nature Genetics, 40, 346-50. PDF
Wittkopp, P.J. (2007) Evolutionary Genetics: How flies get naked. Current Biology17, R881-R883. PDF Dispatch for McGregor et al 2007
Kohn, M.H. and P.J. Wittkopp (2007) Annotating ebony on the fly. Molecular Ecology16, 2831-3. PDF News and Views for Pool and Aquadro 2007
Davis, G.K., D. Srinivasan, P.J. Wittkopp, and D.L. Stern (2007) The function and regulation of Ultrabithorax in the legs of Drosophila melanogaster. Developmental Biology 308, 621-631. PDF
Wittkopp, P.J. (2007) Variable gene expression in eukaryotes: a network perspective. J. Experimental Biology 210 , 1567-1575. PDF Invited Review, Post-genomic Comparative Physiology Special Issue
Fay, J. and P.J. Wittkopp (2007) Evaluating the role of natural selection in the evolution of gene regulation. Heredity, May 23 Epub ahead of print. PDF Invited Review, Ecological and Evolutionary Functional Genomics Special Issue
Wittkopp, P.J., B.K. Haerum, and A. Clark (2006) Parent-of-origin effects on mRNA expression in Drosophila melanogaster not caused by genomic imprinting. Genetics 173, 1817-1821. PDF
Wittkopp, P.J. (2006) Evolution of cis-regulatory sequence and function in diptera.Heredity 97, 139-147. PDF Invited Review, Evo-Devo Special Issue
Landry, C.R, P.J. Wittkopp, C. Taubes, J.M. Ranz, A.G. Clark, and D.L. Hartl (2005). Compensatory cis-trans regulation and dysregulation of gene expression in hybrids between species. Genetics, 171, 1813-1822 PDF
Wittkopp, P.J. (2005) Genomic sources of regulatory variation in cis and in trans.Cellular and Molecular Life Sciences 62 , 1779-83. PDF Invited,”Visions & Reflections”
Gompel*, N, B. Prud’homme*, P.J. Wittkopp, V.A. Kassner, and S.B. Carroll (2005) Chance caught on the wing: cis-regulatory evolution and the origin of pigment patterns in Drosophila. Nature 433, 481-487. (*=co-first authors) PDF News &Views
Wittkopp, P.J., B.K. Haerum, and A.G. Clark (2004) Evolutionary divergence of cis and trans gene regulation. Nature, 430, 85-88. PDF
Wittkopp, P.J., S.B. Carroll, and A. Kopp (2003) Evolution in Black and White: Genetic control of pigment patterns in Drosophila. Trends in Genetics, 19, 495-504. PDF
Wittkopp, P.J.*, B.L. Williams*, J.E. Selegue, and S.B. Carroll (2003) Drosophilapigmentation evolution: divergent genotypes underlying convergent phenotypes.Proc Natl Acad Sci U.S.A., 100, 1808-1813 (* = co-first authors) PDF
Drapeau, M.D.*, A. Radovic*, P.J. Wittkopp, and A. Long (2003) A gene necessary for normal male courtship, yellow, acts downstream of fruitless in the Drosophila melanogaster larval brain. J. of Neurobiology, 55, 53-72. (*=co-first authors) PDF
Wittkopp, P.J., K. Vaccaro and S.B. Carroll (2002) Evolution of yellow gene regulation and pigmentation patterns in Drosophila. Current Biology, 12, 1547-1556. PDF
Radovic, A, P.J. Wittkopp, A.D. Long, and M.D. Drapeau (2002) Immunohistochemical colocalization of Yellow and male-specific Fruitless in Drosophila melanogaster neuroblasts. Biochemical and Biophysical Research Communications, 293, 1262-1264. PDF
Wittkopp*, P.J., J.R. True*, and S.B. Carroll (2002) Reciprocal functions of the Drosophila Yellow and Ebony proteins in the development and evolution of pigment patterns. Development, 129, 1849-1858. (*=co-first authors) PDF
Halder* G. H., P. J. Polaczyk*, M.E. Kraus, A. Hudson, J. Kim, A. Laughon, and S.B. Carroll (1998) The Vestigial and Scalloped proteins act together to directly regulate wing-specific gene expression in response to signaling proteins. Genes & Development, 12:3900-3909. (* = co-first authors) PDF
Polaczyk, P.J., R. Gasparini, and G. Gibson (1998) Naturally occurring genetic variation affects Drosophila photoreceptor determination. Development, Genes & Evolution207, 462-470. PDF
