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:
I am an evolutionary biologist studying the genetics of adaptation across a diverse array of experimental systems. Throughout my career, I have endeavored to integrate fine-scale molecular and genetic details into our understanding of the biases and patterns of evolution. My specific interests lie in understanding why adapting populations take the evolutionary trajectories they do and why or whether adaptation is repeatable or predictable. This pursuit began by developing predictive evolutionary theory and testing these predictions using experimental evolution in bacteriophages. This simple experimental system revealed the importance of genetics in determining the outcomes of adaptive evolution, which propelled me toward similar investigations in more complex systems. To this end, I developed animal venoms as model systems for studying the genetics of adaptation. My work in this area has involved the study of the evolution of venoms of snakes, scorpions, centipedes, and spiders. The evolution of venoms, however, cannot truly be understood without parallel investigation of how those venoms influence the evolution of the animals into which they are injected. My research group therefore also studies the genetics and molecular mechanisms of venom resistance in prey species.
Selected Publications:
Nachtigall PG, Durham AM, Rokyta DR, Junqueira-de-Azevedo ILM. In press. ToxCodAn-Genome: an automated pipeline for toxin-gene annotation in genome assembly of venomous lineages. GigaScience.
Nystrom GS, Ellsworth SA, Ward MJ, Rokyta DR. 2023. Varying modes of selection among toxin families in the venoms of the Giant Desert Hairy Scorpions (Hadrurus). Journal of Molecular Evolution 91:935-962. https://doi.org/10.1007/s00239-023-10148-7
Lane AN, Nash PD, Ellsworth SA, Nystrom GS, Rokyta DR. 2023. The arylsulfatase- and phospholipase-rich venom of the plutoniumid centipede Theatops posticus. Toxicon 233:107231. https://doi.org/10.1016/j.toxicon.2023.107231
Rosales-García RA, Rautsaw RM, Hofmann EP, Grünwald CI, Franz-Chavez H, Ahumada-Carrillo IT, Ramirez-Chaparro R, De la Torre-Loranca MA, Strickland JL, Mason AJ, Holding ML, Borja M, Gamaliel Castaneda-Gaytan G, Myers EA, Sasa M, Rokyta DR, Parkinson CL. 2023. Sequence divergence in venom genes within and between montane pitviper (Viperidae: Crotalinae: Cerrophidion) species is driven by mutation-drift equilibrium. Journal of Molecular Evolution 91:514-535. https://doi.org/10.1007/s00239-023-10115-2
Heptinstall TC, Strickland JL, Rosales-Garcia RA, Rautsaw RM, Simpson CL, Nystrom GS, Ellsworth SA, Hogan MP, Borja M, Fernandes Campos P, Grazziotin FG, Rokyta DR, Junqueira-de-Azevedo ILM, Parkinson CL. 2023. Venom phenotype conservation suggests integrated specialization in a lizard-eating snake. Toxicon 229:107135. https://doi.org/10.1016/j.toxicon.2023.107135
Nystrom GS, Ellsworth SA, Rokyta DR. 2023. The remarkably enzyme-rich venom of the Big Bend Scorpion (Diplocentrus whitei). Toxicon 226:107080. https://doi.org/10.1016/j.toxicon.2023.107080
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. https://doi.org/10.1098/rspb.2022.1132
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. https://doi.org/10.1093/gbe/evac082
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. https://doi.org/10.1656/058.021.0209
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. https://doi.org/10.1093/molbev/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. https://doi.org/10.1016/j.toxicon.2022.02.022
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. https://doi.org/10.1186/s12915-021-01208-9
Schramer TD, Rautsaw RM, Bayona Serrano JD, Nystrom GS, West TR, Ortiz-Medina JA, Sabido-Alpuche B, Meneses-Millán 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. https://doi.org/10.1016/j.toxicon.2021.11.009
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. https://doi.org/10.3390/toxins13110782
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. https://doi.org/10.1007/s00239-021-10007-3
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. https://doi.org/10.1073/pnas.2015579118
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. https://doi.org/10.1093/bib/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. https://doi.org/10.3390/toxins13020124
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. https://doi.org/10.3390/toxins13070501
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. https://doi.org/10.1086/714936
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. https://doi.org/10.1073/pnas.2014634118
Freitas-de-Sousa LA, Nachtigall P, Portes-Junior JA, Holding ML, Nystrom GS, Ellsworth SA, da Costa Guimaráes 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. https://doi.org/10.3390/toxins12120791
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. https://doi.org/10.3390/toxins12100659
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. https://doi.org/10.1111/mec.15517
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. https://doi.org/10.1021/acsptsci.9b00079
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. https://doi.org/10.1186/s12864-020-6545-9
Nystrom GS, Ward MJ, Ellsworth SA, Rokyta DR. 2019. Sex-based venom variation in the eastern bark centipede (Hemiscolopendra marginata). Toxicon 168: 45-58. https://doi.org/10.1016/j.toxicon.2019.08.001
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. https://doi.org/10.1016/j.toxicon.2019.06.021
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. https://doi.org/10.1098/rspb.2019.0810
Sackman AM, Rokyta DR. 2019. No cost of complexity in bacteriophages adapting to a complex environment. Genetics 212(1): 267-276. https://doi.org/10.1534/genetics.119.302029
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. https://doi.org/10.1093/molbev/msy207
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. https://doi.org/10.1007/s00239-018-9882-4
Strickland JL, Smith CF, Mason AJ, Schield DR, Borja M, Castañeda-Gaytán G, Spencer CL, Smith LL, Trápaga A, Bouzid MM, Campillo-García 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. https://doi.org/10.1038/s41598-018-35810-9
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. https://doi.org/10.1038/s41598-018-33943-5
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. https://doi.org/10.1111/jeb.13347
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. https://doi.org/10.1007/s00239-018-9864-6
Ward MJ, Rokyta DR. 2018. Venom-gland transcriptomics and venom proteomics of the giant Florida blue centipede, Scolopendra viridis. Toxicon 152: 121-136. https://doi.org/10.1016/j.toxicon.2018.07.030
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. https://doi.org/10.1016/j.toxicon.2018.07.026
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. https://doi.org/10.1038/s41598-018-29791-y
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. https://doi.org/10.3390/toxins10060249
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. https://doi.org/10.1016/j.jprot.2018.03.032
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. https://doi.org/10.3390/toxins10040135
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. https://doi.org/10.1093/molbev/msx334
Sackman AM, Rokyta DR. 2018. Additive phenotypes underlie epistasis of fitness effects. Genetics 208(1): 339-348. https://doi.org/10.1534/genetics.117.300451
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. https://doi.org/10.1016/j.toxicon.2017.12.042
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. https://doi.org/10.1093/molbev/msx231
Sackman AM, Rokyta DR. 2017. Mutation-driven parallel evolution during viral adaptation. Molecular Biology and Evolution 34: 3243-3253. https://doi.org/10.1093/molbev/msx257
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. https://doi.org/10.1534/genetics.117.202655
Rokyta DR, Margres MJ, Ward MJ, SaÌnchez EE. 2017. The genetics of venom ontogeny in the eastern diamondback rattlesnake (Crotalus adamanteus). PeerJ 5: e3249. https://doi.org/10.7717/peerj.3249
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. https://doi.org/10.1016/j.toxicon.2017.01.014
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. https://doi.org/10.7717/peerj.2585
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. https://doi.org/10.1016/j.toxicon.2016.05.005
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. https://doi.org/10.1534/genetics.115.181628
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. https://doi.org/10.1534/genetics.115.180547
Sackman AM, Reed D, Rokyta DR. 2015. Intergenic incompatibilities reduce fitness in hybrids of extremely closely related bacteriophages. PeerJ 3: e1320. https://doi.org/10.7717/peerj.1320
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. https://doi.org/10.1534/g3.115.020578
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. https://doi.org/10.1653/024.098.0329
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. https://doi.org/10.1111/mec.13240
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. https://doi.org/10.1016/j.toxicon.2015.02.015
Wray K. P., M. J. Margres, M. Seavy, and D. R. Rokyta. 2015. Early significant ontogenetic changes in snake venoms. Toxicon 96:74-81. https://doi.org/10.1016/j.toxicon.2015.01.010
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. https://doi.org/10.1534/genetics.114.172437
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. https://doi.org/10.1186/1471-2164-15-1061
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. https://doi.org/10.1371/journal.pgen.1004611
Caudle, S. B., C. R. Miller, and D. R. Rokyta. 2014. Environment determines epistatic patterns for a ssDNA virus. Genetics 196:267-279. https://doi.org/10.1534/genetics.113.158154
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. https://doi.org/10.1016/j.jprot.2013.11.001
Sackman, A. M. and D. R. Rokyta. 2013. The adaptive potential of hybridization demonstrated with bacteriophages. Journal of Molecular Evolution 77:221-230. https://doi.org/10.1007/s00239-013-9586-8
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. https://doi.org/10.1186/1471-2164-14-531
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. https://doi.org/10.1186/1471-2164-14-394
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. https://doi.org/10.1371/journal.pone.0043864
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. https://doi.org/10.1186/1471-2164-13-312
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. https://doi.org/10.1371/journal.pgen.1002075
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. https://doi.org/10.1016/j.toxicon.2011.01.008
Rokyta, D. R., and H. A. Wichman. 2009. Genic incompatibilities in two hybrid bacteriophages. Molecular Biology and Evolution 26:2831-2839. https://doi.org/10.1093/molbev/msp199
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. https://doi.org/10.1007/s00239-009-9267-9
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. https://doi.org/10.1534/genetics.108.088716
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. https://doi.org/10.1007/s00239-008-9153-x
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. https://doi.org/10.1534/genetics.106.068585
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. https://doi.org/10.1016/j.jtbi.2006.06.008
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. https://doi.org/10.1128/JB.188.3.1134-1142.2006
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. https://doi.org/10.1038/ng1535
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. https://doi.org/10.1007/s00239-003-2470-1
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. https://doi.org/10.1093/oxfordjournals.molbev.a004076