Biological Science Faculty Member
Dr. Darin R. Rokyta
- Office: 4019 King Life Sciences
- Office: (850) 645-8812
- Area: Ecology & Evolution
- Lab: King Life Sciences
- Lab: (850) 645-8817
- Fax: (850) 645-8447
- Mail code: 4295
- E-mail: drokyta@bio.fsu.edu
Professor
Ph.D., University of Idaho, 2006
Graduate Faculty Status
Research and Professional Interests:
My research investigates the molecular and statistical properties of adaptive evolution. The overarching goal of my work is to develop a robust, quantitative model of adaptive evolution at the molecular level and the statistical methology to test the model predictions and assumptions, but the available empirical data are insufficient for evaluating the strengths and weaknesses of current models and guiding future efforts. My research therefore also involves generating empirical data sets using experimental evolution approaches.
Selected Publications:
Holding ML, Trevine VC, Zinenko O, Strickland JL, Rautsaw RM, Mason AJ, Hogan MP, Parkinson CL, Grazziotin FG, Santana SE, Davis MA, Rokyta DR. 2022. Evolutionary allometry and ecological correlates of fang length evolution in vipers. Proceedings of the Royal Society B 289: 20221132.
Myers EA, Stricklan JL, Rautsaw RM, Mason AJ, Schramer TD, Nystrom GS, Hogan MP, Yooseph S, Rokyta DR, Parkinson CL. 2022. De Novo genome assembly highlights the role of lineage-specific gene duplications in the evolution of venom in Fea's Viper (Azemiops feae). Genome Biology and Evolution 14: 1-9.
Harrison CM, Colbert J, Richter CJ, McDonald PJ, Trumbull LM, Ellsworth SA, Hogan MP, Rokyta DR, and Margres MJ. 2022. Using morphological, genetic, and venom analyses to present current and historic evidence of Crotalus horridus×adamanteus hybridization on Jekyll Island, Georgia. Southeastern Naturalist 21:158-174.
Mason AJ, Holding ML, Rautsaw RM, Rokyta DR, Parkinson CL, Gibbs HL. 2022. Venom gene sequence diversity and expression jointly shape diet adaptation in pitvipers. Molecular Biology and Evolution 39: msac082.
Nystrom GS, Fry LG, Ellsworth SA, Rokyta DR. 2022. Contrasting patterns of venom regeneration in a centipede (Scolopendra viridis) and a scorpion (Centruroides hentzi). Toxicon 210:132-140.
Xie B, Dashevsky D, Rokyta DR, Ghezellou P, Fathinia B, Shi Q, Richardson MK, Fry BG. 2022. Dynamic genetic differentiation drives the widespread structural and functional convergent evolution of snake venom proteinaceous toxins. BMC Biology 20:4.
Schramer TD, Rautsaw RM, Bayona Serrano JD, Nystrom GS, West TR, Ortiz-Medina JA, Sabido-Alpuche B, Meneses-MillaÌn M, Borja M, Junqueira de Azevedo ILM, Rokyta DR, Parkinson CL. 2021. An integrative view of the toxic potential of Conophis lineatus (Dipsadidae: Xenodontinae), a medically relevant rear-fanged snake. Toxicon 205:38-52.
Margres MJ, Wray KP, Sanader D, McDonald PJ, Trumbull LM, Patton AH, Rokyta DR. 2021. Varying intensities of introgression obscure incipient venom-associated speciation in the Timber Rattlesnake (Crotalus horridus). Toxins 13:782.
Hogan MP, Whittington AC, Broe MB, Ward MJ, Gibbs HL, Rokyta DR. 2021. The chemosensory repertoire of the eastern diamondback rattlesnake (Crotalus adamanteus) reveals complementary genetics of olfactory and vomeronasal-type receptors. Journal of Molecular Evolution 89:313-328.
Holding ML, Strickland JL, Rautsaw RM, Hofmann EP, Mason AJ, Hogan MP, Nystrom GS, Ellsworth SA, Colston TJ, Borja M, Grunwald CI, Castaneda G, Jones JM, de Sousa LAF, Margres MJ, Grazziotin FG, Azevedo I, Moura da Silva A, Gibbs HL, Rokyta DR, Parkinson CL. 2021. Phylogenetically diverse diets favor more complex venoms in North American pitvipers. Proceedings of the National Academy of Sciences USA 118:e2015579118.
Nachtigall PG, Rautsaw RM, Ellsworth SA, Mason AJ, Rokyta DR, Parkinson CL, Junqueira-de-Azevedo ILM. 2021. ToxCodAn: a new toxin annotator and guide to venom gland transcriptomics. Briefings in Bioinformatics 22:bbab095.
Dashevsky D, Rokyta DR, Frank N, Nouwens A, Fry BG. 2021. Electric blue: molecular evolution of three-finger toxins in the long-glanded coral snake species Calliophis bivirgatus. Toxins 13:124.
El-Aziz TMA, Xiao Y, Kline J, Gridley H, Heaston A, Linse KD, Ward MJ, Rokyta DR, Stockand JD, Cummins TR, Fornelli L, and Rowe AH. 2021. Identification and characterization of novel proteins from Arizona bark scorpion venom that inhibit Nav1.8, a voltage-gated sodium channel regulator of pain signaling. Toxins 13:501.
Claunch NM, Holding M, Frazier JT, Huff EM, Schonour RB, Vernasco B, Moore IT, Rokyta DR, and Taylor EN. 2021. Experimental manipulation of corticosterone levels does not affect venom composition or functional activity in free-ranging rattlesnakes. Physiological and Biochemical Zoology 94:286-301.
Margres MJ, Rautsaw RM, Strickland JL, Mason AJ, Schramer T, Hofmann EP, Stiers E, Ellsworth SA, Nystrom GS, Hogan MP, Bartlett DA, Colston TJ, Gilbert DM, Rokyta DR, Parkinson CL. 2021. The tiger rattlesnake genome reveals a complex genotype underlying a simple venom phenotype. Proceedings of the National Academy of Sciences USA 118:e2014634118.
Freitas-de-Sousa LA, Nachtigall P, Portes-Junior JA, Holding ML, Nystrom GS, Ellsworth SA, da Costa Guimarães N, Tioyama E, Ortiz F, Rocha da Silva B, Saraiva Kunz T, de Loiola Meirelles Junqueira-de-Azevedo I, Grazziotin FG, Rokyta DR, Moura-da-Silva AM. 2020. Size matters: an evaluation on the molecular basis of ontogenetic modifications in the composition of Bothrops jararacussu snake venom. Toxins 12:791.
Schonour RB, Huff EM, Holding ML, Claunch NM, Ellsworth SA, Hogan MP, Wray KP, McGivern JJ, Margres MJ, Colston TJ, Rokyta DR. 2020. Gradual and discrete ontogenetic shifts in rattlesnake venom composition and assessment of hormonal and ecological correlates. Toxins 12:659.
Ochoa A, Broe M, Lemmon AR, Lemmon EM, Rokyta DR, Gibbs HL. 2020. Drift, selection, and adaptive variation in small populations of a threatened rattlesnake. Molecular Ecology 29:2612-2625.
Chow CY, Chin Y, Walker A, Guo S, Blomster L, Ward M, Herzig V, Rokyta DR, King G. 2020. Venom peptides with dual modulatory activity on the voltage-gated sodium channel Nav1.1 provide novel leads for development of anti-epileptic drugs. ACS Pharmacology and Translational Science 3:119-134.
Mason AJ, Margres MJ, Strickland JL, Rokyta DR, Sasa M, Parkinson CL. 2020. Trait differentiation and modular toxin expression in palm-pitvipers. BMC Genomics 21:147.
Nystrom GS, Ward MJ, Ellsworth SA, Rokyta DR. 2019. Sex-based venom variation in the eastern bark centipede (Hemiscolopendra marginata). Toxicon 168: 45-58.
Ellsworth SA, Nystrom GS, Hogan MP, Ward MJ, Rokyta DR. 2019. Convergent recruitment of adamalysin-like metalloproteases in the red bark centipede (Scolopocryptops sexspinosus). Toxicon 168: 1-15.
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.
Sackman AM, Rokyta DR. 2019. No cost of complexity in bacteriophages adapting to a complex environment. Genetics 212(1): 267-276.
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.
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.
Strickland JL, Smith CF, Mason AJ, Schield DR, Borja M, Castañeda-GaytaÌn G, Spencer CL, Smith LL, TraÌpaga A, Bouzid MM, Campillo-GarciÌa 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.
Hofmann EP, Rautsaw RM, Strickland JL, Holding ML, Hogan MP, Mason AJ, Rokyta DR, Parkinson CL. 2018. 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.
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.
Dashevsky D, Debono J, Rokyta DR, Nouwens A, Josh P, Fry BG. 2018. Three-finger toxin diversification in the venoms of cat-eye snakes (Colubridae: Boiga). Journal of Molecular Evolution 86(8): 531-545.
Ward MJ, Rokyta DR. 2018. Venom-gland transcriptomics and venom proteomics of the giant Florida blue centipede, Scolopendra viridis. Toxicon 152: 121-136.
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.
Calvete JJ, Casewell NR, HernaÌndez-GuzmaÌn U, Quesada-Bernat S, Sanz L, Rokyta DR, Storey D, Albulescu L-O, Wüster W, Smith CF, Schuett GW, Booth W. 2018. Venom complexity in a pitviper produced by facultative parthenogenesis. Scientific Reports 8: 11539.
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.
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.
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.
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(4): 887-898.
Sackman AM, Rokyta DR. 2018. Additive phenotypes underlie epistasis of fitness effects. Genetics 208(1): 339-348.
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.
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.
Sackman AM, Rokyta DR. 2017. Mutation-driven parallel evolution during viral adaptation. Molecular Biology and Evolution 34: 3243-3253.
Margres MJ, Bigelow AT, Lemmon EM, Lemmon AR, Rokyta DR. 2017. Selection to increase expression, not sequence diversity, precedes gene family origin and expansion in rattlesnake venom. Genetics 206: 1569-1580.
Rokyta DR, Margres MJ, Ward MJ, SaÌnchez EE. 2017. The genetics of venom ontogeny in the eastern diamondback rattlesnake (Crotalus adamanteus). PeerJ 5: e3249.
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.
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.
Margres MJ, Walls R, Suntravat M, Lucena S, SaÌnchez 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.
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.
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.
Sackman AM, Reed D, Rokyta DR. 2015. Intergenic incompatibilities reduce fitness in hybrids of extremely closely related bacteriophages. PeerJ 3: e1320.
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.
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.
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.
Rokyta D. R., K. P. Wray, J. J McGivern, and M. J. Margres. 2015. The transcriptomic and proteomic basis for the evolution of a novel venom phenotype within the Timber Rattlesnake (Crotalus horridus). Toxicon 98:34-48.
Wray K. P., M. J. Margres, M. Seavy, and D. R. Rokyta. 2015. Early significant ontogenetic changes in snake venoms. Toxicon 96:74-81.
Margres M. J., J. J. McGivern, M. Seavy, K. P. Wray, J. Facente, and D. R. Rokyta. 2015. Contrasting modes and tempos of venom expression evolution in two snake species. Genetics 199:165-176.
McGivern J. J., K. P. Wray, M. J. Margres, M. E. Couch, S. P. Mackessy, and D. R. Rokyta. 2014. RNA-seq and high-definition mass spectrometry reveal the complex and divergent venoms of two rear-fanged colubrid snakes. BMC Genomics 15:1061.
McGee, L. W., E. W. Aitchison, S. B. Caudle, A. J. Morrison, L. Zheng, W. Yang, and D. R. Rokyta. 2014. Payoffs, not tradeoffs, in the adaptation of a virus to ostensibly conflicting selective pressures. PLoS Genetics 10:e1004611.
Caudle, S. B., C. R. Miller, and D. R. Rokyta. 2014. Environment determines epistatic patterns for a ssDNA virus. Genetics 196:267-279.
Margres, M. J., J. J. McGivern, K. P. Wray, M. Seavy, K. Calvin, and D. R. Rokyta. 2014. Linking the transcriptome and proteome to characterize the venom of the eastern diamondback rattlesnake (Crotalus adamanteus). Journal of Proteomics 96C:145-158.
Sackman, A. M. and D. R. Rokyta. 2013. The adaptive potential of hybridization demonstrated with bacteriophages. Journal of Molecular Evolution 77:221-230.
Margres, M. J., K. Aronow, J. Loyacano, and D. R. Rokyta. 2013. The venom-gland transcritome of the eastern coral snake (Micrurus fulvius) reveals high venom complexity in the intragenomic evolution of venoms. BMC Genomics 14:531.
Rokyta, D. R., K. P. Wray, and M. J. Margres. 2013. The genesis of an exceptionally lethal venom in the timber rattlesnake (Crotalus horridus) revealed through comparative venom-gland transcriptomics. BMC Genomics 14:394.
Pearson, V. M., C. R. Miller, and D. R. Rokyta. 2012. The consistency of beneficial fitness effects of mutations across diverse genetic backgrounds. PLoS One 7:e43864.
Rokyta, D. R., A. R. Lemmon, M. J. Margres, and K. Aronow. 2012. The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus). BMC Genomics 13:312.
Rokyta, D. R., P. Joyce, S. B. Caudle, C. Miller, C. J. Beisel, and H. A. Wichman. 2011. Epistasis between benecial mutations and the phenotype-to-fitness map for a ssDNA virus. PLoS Genetics 7:e1002075.
Rokyta, D. R., K. P. Wray, A. R. Lemmon, E. C. Moriarty Lemmon, and S. B. Caudle. 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.
Rokyta, D. R., and H. A. Wichman. 2009. Genic incompatibilities in two hybrid bacteriophages. Molecular Biology and Evolution 26:2831-2839.
Rokyta, D. R., Z. Abdo, and H. A. Wichman. 2009. The genetics of adaptation for eight microvirid bacteriophages. Journal of Molecular Evolution 69:229-239.
Joyce, P., D. R. Rokyta, C. J. Beisel, and H. A. Orr. 2008. A general extreme value theory model for the adaptation of DNA sequences under strong selection and weak mutation. Genetics 180:1627-1643.
Rokyta, D. R., C. J. Beisel, P. Joyce, M. T. Ferris, C. L. Burch, and H. A. Wichman. 2008. Beneficial fitness effects are not exponential for two viruses. Journal of Molecular Evolution 67:368-376.
Beisel, C. J., D. R. Rokyta, H. A. Wichman, and P. Joyce. 2007. Testing the extreme value domain of attraction for distributions of beneficial fitness effects. Genetics 176:2441-2449.
Rokyta, D. R., C. J. Beisel, and P. Joyce. 2006. Properties of adaptive walks on uncorrelated landscapes under strong selection and weak mutation. Journal of Theoretical Biology 243:114120.
Rokyta, D. R., C. L. Burch, S. B. Caudle, and H. A. Wichman. 2006. Horizontal gene transfer and the evolution of microvirid coliphage genomes. Journal of Bacteriology 188:11341142 (featured on the cover).
Rokyta, D. R., P. Joyce, S. B. Caudle, and H. A. Wichman. 2005. An empirical test of the mutational landscape model of adaptation using a single-stranded DNA virus. Nature Genetics 37: 441444 (featured in News and Views).
Bull, J. J., M. R. Badgett, D. Rokyta, and I. J. Molineux. 2003. Experimental evolution yields hundreds of mutations in a functional viral genome. Journal of Molecular Evolution 57:241248.
Rokyta, D., M. R. Badgett, I. J. Molineux, and J. J. Bull. 2002. Experimental genomic evolution: extensive compensation for loss of DNA ligase activity in a virus. Molecular Biology and Evolution 19:230238.