All reprints are intended only for personal use.


  • Sackman AM, Rokyta DR. In press. Mutation-driven parallel evolution during viral adaptation. Molecular Biology and EvolutionLink

  • Margres MJ, Wray KP, Hassinger ATB, Ward MJ, McGivern JJ, Lemmon EM, Lemmon AR, Rokyta DR. In press. Quantity, not quality: rapid adaptation in a polygenic trait proceeded exclusively through expression differentiation. Molecular Biology and EvolutionLink

  • Rokyta DR, Margres MJ, Ward MJ, Sánchez EE. 2017. The genetics of venom ontogeny in the eastern diamondback rattlesnake (Crotalus adamanteus). PeerJ 5: e3249. PDF

  • Rokyta DR, Ward MJ. 2017. Venom-gland transcriptomics and venom proteomics of the black-back scorpion (Hadrurus spadix) reveal detectability challenges and an unexplored realm of animal toxin diversity. Toxicon 128: 23-37. PDF

  • Margres MJ, Bigelow AT, Lemmon EM, Lemmon AR, Rokyta DR. 2017. Selection to increase epression, not sequence diversity, precedes gene family origin and expansion in rattlesnake venom. Genetics 206: 1569-1580. PDF


  • Pearson VM, Caudle SB, Rokyta DR. 2016. Viral recombination blurs taxonomic lines: examination of single-stranded DNA viruses in a wastewater treatment plant. PeerJ 4: e2585. PDF

  • Margres MJ, Walls R, Suntravat M, Lucena S, Sánchez EE, Rokyta DR. 2016. Functional characterizations of venom phenotypes in the eastern diamondback rattlesnake (Crotalus adamanteus) and evidence for expression-driven divergence in toxic activities among populations. Toxicon 119: 28–38. PDF

  • McGee LW, Sackman A, Morrison AJ, Pierce J, Anisman J, Rokyta DR. 2016. Synergistic pleiotropy overrides the costs of complexity in viral adaptation. Genetics 202:285–295. PDF

  • Margres MJ, Wray KP, Seavy M, McGivern JJ, Herrera ND, Rokyta DR. 2016. Expression differentiation is constrained to low-expression proteins over ecological timescales. Genetics 202: 273–283. PDF


  • Sackman AM, Reed D, Rokyta DR. 2015. Intergenic incompatibilities reduce fitness in hybrids of extremely closely related bacteriophages. PeerJ 3: e1320. PDF

  • Rokyta DR, Margres MJ, Calvin K. 2015. Post-transcriptional mechanisms contribute little to phenotypic variation in snake venoms. G3: Genes|Genomes|Genetics 5: 2375–2382. PDF

  • Wray KP, Ward M, Rokyta DR. 2015. The establishment of the exotic centipede Rhysida longipes longipes (Newport, 1845; Scolopendramorpha: Scolopendridae: Otostigminae) in south Florida. Florida Entomologist 98: 979–980. PDF

  • Margres MJ, Wray KP, Seavy M, McGivern JJ, Sanader D, Rokyta DR. 2015. Phenotypic integration in the feeding system of the eastern diamondback rattlesnake (Crotalus adamanteus). Molecular Ecology 24: 3405–3420. PDF

  • Rokyta DR, Wray KP, McGivern JJ, Margres MJ. 2015. The transcriptomic and proteomic basis for the evolution of a novel venom phenotype within the Timber Rattlesnake (Crotalus horridus). Toxicon 98: 34–48. PDF

  • Wray KP, Margres MJ, Seavy M, Rokyta DR. 2015. Early significant ontogenetic changes in snake venoms. Toxicon 96: 74–81. PDF

  • Margres MJ, McGivern JJ, Seavy M, Wray KP, Facente J, Rokyta DR. 2015. Contrasting modes and tempos of venom expression evolution in two snake species. Genetics 199: 165–176. PDF


  • McGivern JJ, Wray KP, Margres MJ, Couch ME, Mackessy SP, Rokyta DR. 2014. RNA-seq and high-definition mass spectrometry reveal the complex and divergent venoms of two rear-fanged colubrid snakes. BMC Genomics 15: 1061. PDF

  • McGee LW, Aitchison EW, Caudle SB, Morrison AJ, Zheng L, Yang W, Rokyta DR. 2014. Payoffs, not tradeoffs, in the adaptation of a virus to ostensibly conflicting selective pressures. PLOS Genetics 10: e1004611. PDF

  • Caudle SB, Miller CR, Rokyta DR. 2014. Environment determines epistatic patterns for a ssDNA virus. Genetics 196: 267–279. PDF

  • Margres MJ, McGivern JJ, Wray KP, Seavy M, Calvin K, Rokyta DR. 2014. Linking the transcriptome and proteome to characterize the venom of the eastern diamondback rattlesnake (Crotalus adamanteus). Journal of Proteomics 96C: 145–158. PDF


  • Sackman AM, Rokyta DR. 2013. The adaptive potential of hybridization demonstrated with bacteriophages. Journal of Molecular Evolution 77: 221–230. PDF

  • Margres MJ, Aronow K, Loyacano J, Rokyta DR. 2013. The venom-gland transcriptome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms. BMC Genomics 14: 531. PDF

  • Rokyta DR, Wray KP, Margres MJ. 2013. The genesis of an exceptionally lethal venom in the timber rattlesnake (Crotalus horridus) revealed through comparative venom-gland transcriptomics. BMC Genomics 14: 394. PDF


  • Castoe TA, Braun EL, Bronikowski AM, Cox CL, Davis Rabosky AR, de Koning APJ, Dobry J, Fujita MK, Giorgianni MW, Hargreaves A, Henkel CV, Mackessy SP, O’Meally D, Rokyta DR, Secor SM, Streicher JW, Wray KP, Yokoyama KD, Pollock DD. 2012. Meeting report from the first snake genomics and integrative biology meeting. Standards in Genomic Sciences 7: 1. PDF

  • Pearson VM, Miller CR, Rokyta DR. 2012. The consistency of beneficial fitness effects of mutations across diverse genetic backgrounds. PLOS One 7: e43864. PDF

  • Rokyta DR, Lemmon AR, Margres MJ, Aronow K. 2012. The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus). BMC Genomics 13: 312. PDF

Before 2012

  • Rokyta DR, Joyce P, Caudle SB, Miller C, Beisel CJ, Wichman HA. 2011. Epistasis between beneficial mutations and the phenotype-to-fitness map for a ssDNA virus. PLOS Genetics 7: e1002075. PDF

  • Rokyta DR, Wray KP, Lemmon AR, Moriarty Lemmon EC, Caudle SB. 2011. A high-throughput venom-gland transcriptome for the eastern diamondback rattlesnake (Crotalus adamanteus) and evidence for pervasive positive selection across toxin classes. Toxicon 57: 657–671. PDF

  • Rokyta DR, Wichman HA. 2009. Genic incompatibilities in two hybrid bacteriophages. Molecular Biology and Evolution 26: 2831–2839. PDF

  • Rokyta DR, Abdo Z, Wichman HA. 2009. The genetics of adaptation for eight microvirid bacteriophages. Journal of Molecular Evolution 69: 229–239. PDF

  • Joyce P, Rokyta DR, Beisel CJ, Orr HA. 2008. A general extreme value theory model for the adaptation of DNA sequences under strong selection and weak mutation. Genetics 180: 1627–1643. PDF

  • Rokyta DR, Beisel CJ, Joyce P, Ferris MT, Burch CL, Wichman HA. 2008. Beneficial fitness effects are not exponential for two viruses. Journal of Molecular Evolution 67: 368–376. PDF

  • Beisel CJ, Rokyta DR, Wichman HA, Joyce P. 2007. Testing the extreme value domain of attraction for distributions of beneficial fitness effects. Genetics 176: 2441–2449. PDF

  • Rokyta DR, Beisel CJ, Joyce P. 2006. Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation. Journal of Theoretical Biology 243: 114–120. PDF

  • Rokyta DR, Burch CL, Caudle SB, Wichman HA. 2006. Horizontal gene transfer and the evolution of microvirid coliphage genomes. Journal of Bacteriology 188: 1134–1142. PDF

  • Rokyta DR, Joyce P, Caudle SB, Wichman HA. 2005. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nature Genetics 37: 441–444. PDF

  • Bull JJ, Badgett MR, Rokyta D, Molineux IJ. 2003. Experimental evolution yields hundreds of mutations in a functional viral genome. Journal of Molecular Evolution 57: 241–248. PDF

  • Rokyta D, Badgett MR, Molineux IJ, Bull JJ. 2002. Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus. Molecular Biology and Evolution 19: 230–238. PDF