Publications

All reprints are intended only for personal use.

2019

  • Nystrom GS, Ward MJ, Ellsworth SA, Rokyta DR. In press. Sex-based venom variation in the eastern bark centipede (Hemiscolopendra marginata). Toxicon.

  • Ellsworth SA, Nystrom GS, Hogan MP, Ward MJ, Rokyta DR. In press. Convergent recruitment of adamalysin-like metalloproteases in the red bark centipede (Scolopocryptops sexspinosus). Toxicon.

  • Rautsaw RM, Hofmann EP, Margres MJ, Holding ML, Strickland JL, Mason AJ, Rokyta DR, Parkinson CL. 2019. Intraspecific sequence and gene expression variation contribute little to venom diversity in Sidewinder Rattlesnakes (Crotalus cerastes). Proceedings of the Royal Society B: Biological Sciences 286:20190810. PDF

  • Sackman AM, Rokyta DR. 2019. No cost of complexity in bacteriophages adapting to a complex environment. Genetics 212(1): 267–276. PDF

  • Margres MJ, Patton A, Wray KP, Hassinger ATB, Ward MJ, Lemmon EM, Lemmon AR, Rokyta DR. 2019. Tipping the scales: the migration-selection balance leans toward selection in snake venoms. Molecular Biology and Evolution 36(2): 271–282. PDF

  • Whittington AC, Rokyta DR. 2019. Biophysical spandrels form a hot-spot for kosmotropic mutations in bacteriophage thermal adaptation. Journal of Molecular Evolution 87(1): 27–36. PDF

2018

  • Strickland JL, Smith CF, Mason AJ, Schield DR, Borja M, Castañeda-Gaytan G, Spencer CL, Smith LL, Trapaga A, Bouzid MM, Campillo-Garcia G, Flores-Villela OA, Antonio-Rangel D, Mackessy SP, Castoe TA, Rokyta DR, and Parkinson CL. 2018. Evidence for divergent patterns of local selection driving venom variation in Mojave Rattlesnakes (Crotalus scutulatus). Scientific Reports 8: 17622. PDF

  • Hofmann EP, Rautsaw RM, Strickland JL, Holding ML, Hogan MP, Mason AJ, Rokyta DR, Parkinson CL. In press. Comparative venom-gland transcriptomics and venom proteomics of four Sidewinder Rattlesnake lineages (Crotalus cerastes) reveal little differential expression despite individual variation. Scientific Reports 8: 15534. PDF

  • Dashevsky D, Debono J, Rokyta DR, Nouwens A, Josh P, Fry BG. In press. Three-finger toxin diversification in the venoms of cat-eye snakes (Colubridae: Boiga). Journal of Molecular Evolution 86(8): 531-545. PDF

  • Holding ML, Margres MJ, Rokyta DR, Gibbs HL. 2018. Local prey community composition and genetic distance predict venom divergence among populations of the northern Pacific rattlesnake (Crotalus oreganus). Journal of Evolutionary Biology 31(10): 1513-1528. PDF

  • Ward MJ, Rokyta DR. 2018. Venom-gland transcriptomics and venom proteomics of the giant Florida blue centipede, Scolopendra viridis. Toxicon 152: 121–136. PDF

  • Ward MJ, Ellsworth SA, Hogan MP, Nystrom GS, Martinez P, Budheo A, Zelaya R, Perez A, Powell B, He H, Rokyta DR. 2018. Female-biased population divergence in the venom of the Hentz striped scorpion (Centruroides hentzi). Toxicon 152: 137–149. PDF

  • Calvete JJ, Casewell NR, Hernandez-Guzman U, Quesada-Bernat S, Sanz L, Rokyta DR, Storey D, Albulescu L-O, Wuster W, Smith CF, Schuett GW, Booth W. 2018. Venom complexity in a pitviper produced by facultative parthenogenesis. Scientific Reports 8: 11539. PDF

  • Holding ML, Margres MJ, Mason AJ, Parkinson CL, Rokyta DR. 2018. Evaluating the performance of de novo assembly methods for venom-gland transcriptomics. Toxins 10(6): 249. PDF

  • Amazonas D, Portes-Junior J, Nishiyama-Jr M, Nicolau C, Chalkidis H, Mourão R, Rokyta DR, Valente R, Junqueira-de-Azevedo I, Moura-da-Silva AM. 2018. Molecular mechanisms underlying intraspecific variation in snake venom. Journal of Proteomics 181: 60–72. PDF

  • Strickland JL, Mason AJ, Rokyta DR, Parkinson CL. 2018. Phenotypic variation in Mojave Rattlesnake (Crotalus scutulatus) venom is driven by four toxin families. Toxins 10(4): 135. PDF

  • Ward MJ, Ellsworth SA, Nystrom GS. 2018. A global accounting of medically significant scorpions: Epidemiology, major toxins, and comparative resources in harmless counterparts. Toxicon 151: 137–155. Link

  • Sackman AM, Rokyta DR. 2018. Additive phenotypes underlie epistasis of fitness effects. Genetics 208: 339–348. PDF

  • Whittington AC, Mason AJ, Rokyta DR. 2018. A single mutation unlocks cascading exaptations in the origin of a potent pitviper neurotoxin. Molecular Biology and Evolution 35: 887–898. PDF

  • Ward MJ, Ellsworth SA, Rokyta DR. 2018. Venom-gland transcriptomics and venom proteomics of the Hentz striped scorpion (Centruroides hentzi; Buthidae) reveal high toxin diversity in a harmless member of a lethal family. Toxicon 142: 14–29. PDF

2017

  • Sackman AM, McGee LW, Morrison AJ, Pierce J, Anisman J, Hamilton H, Sanderbeck S, Newman C, Rokyta DR. 2017. Mutation-driven parallel evolution during viral adaptation. Molecular Biology and Evolution 34: 3243–3253. PDF

  • Margres MJ, Wray KP, Hassinger ATB, Ward MJ, McGivern JJ, Lemmon EM, Lemmon AR, Rokyta DR. 2017. Quantity, not quality: rapid adaptation in a polygenic trait proceeded exclusively through expression differentiation. Molecular Biology and Evolution 34: 3099–3110. PDF

  • 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

2016

  • 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

2015

  • 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

2014

  • 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

2013

  • 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

2012

  • 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