Evolutionary Systems Virology Group

Prof. Santiago F. Elena

CSIC Research Professor

SFI External Professor

Instituto de Biología Molecular y Celular de Plantas

Major in Biology (Biochemistry), Universitat de València, 1990
Ph.D. in Molecular and Evolutionary Genetics,
Universitat de València, 1995

Research Interests:

In general, my scientific interests are related with the evolutionary biology of microbes.  More concretely, this interest is focused in the study, within the framework of Populations Genetics, of the mechanisms that generate and maintain the genetic variability of RNA viruses.  The model systems that we use now for our experiments are the RNA viruses Tobacco etch potyvirus (TEV) and Turnip mosaic potyvirus (TuMV), the para-retrovirus Cauliflower mosaic caulimovirus (CaMV), and the viroids.  I have also been exploring the endless potential of digital organisms as model systems for evolutionary studies.  And finally, to avoid missing the wave of Systems Biology we are now developing in silico and mathematical hierarchical models of the entire viral infectious cycle.


Among the projects that we are currently working on, I would like to highlight the following:

    1. Effect of the accumulation of deleterious mutations in TEV fitness on its natural hosts Nicotiana tabacum.  Characterization of the level of epistasis among deleterious mutations both, within and among genes.
    2. Statistical characterization of the distribution of mutational effects on TEV fitness and virulence on tobacco.  Characterization of the molecular basis of differences in virulence.  Correlation between viral replicative fitness and virulence.  Evolution of virulence under multiple-infections dynamics and vector-mediated transmission.
    3. Characterization of adaptive dynamics of TEV to new hosts (Arabidopsis thaliana and Capsicum annuum).  Host range and evolutionary correlated response to new hosts.  Tradeoffs in simultaneous adaptation to different hosts.  How does the pattern of plant gene expression changes as a consequence of viral adaptation?
    4. Experimental test of the model of clonal interference among beneficial mutations (TEV).  Molecular characterization of beneficial mutations fixed at successive adaptive steps and its effect on the rate of adaptation.
    5. Evolutionary significance of genome segmentation.
    6. Evolution of mechanisms of genetic robustness in highly mutable RNA genomes (TEV).  The role of population size and mutation rate in the evolution of genetic robustness.  Genetic robustness as a correlated response to environmental robustness.  Neutral networks and the evolution of robustness in viroid species.
    7. The suppression of post-transcriptional gene silencing as a viral evolutionary strategy to overcome plant defences.  Characterization of mutational effects on the suppressor protein (HC-Pro) of TEV.  Compensatory evolution of suppression function and genetic architecture of the trait.  Molecular evolution of viral suppressor proteins.
    8. Evolutionary stability of A. thaliana transgenic plants that express amiRNAs targeting TuMV HC-Pro.  Estimation of the likelihood of resistance-breaking by evolving TuMV populations.  Molecular basis of resistance-breaking.  In cooperation with Prof. Nam-Hai Chua (Rockefeller University).
    9. Synergistic interactions among viruses coinfecting the same plant (TuMV and CaMV infecting Brassica rappa). Coevolutionary dynamics.
    10. Molecular evolution and phylogenetic studies of different plant viruses.
    11. Development and systemic analysis of in silico and analytical models of viral gene interaction networks.  Models of cell-to-cell and systemic movement.  Epidemiological models.  In cooperation with Prof. Ricard V. Solé (Universitat Pompeu Fabra).
    12. Optimal mutation rate and the relationship between mutational robustness and evolvability in digital organisms.  In cooperation with Prof. R.E. Lenski and Dr. C. Ofria (Michigan State University).


Selected Publications:

  • Elena, S.F., Dopazo, J., Diener, T.O., Flores, R., and Moya, A. (1991). Phylogeny of viroids, viroid-like satellite RNAs ant the viroid-like domain of Human Hepatitis Delta Virus. Proc. Natl. Acad. Sci. USA 88: 5631-5634.
  • Clarke, D.K., Duarte, E.A., Elena, S.F., Moya, A., Domingo, E., and Holland, J.J. (1994). The Red Queen reigns in the kingdom of RNA viruses. Proc. Natl. Acad. Sci. USA 91: 4821-4824.
  • Novella, I.S., Duarte, E.A., Elena, S.F., Moya, A., Domingo, E., and Holland, J.J. (1995). Exponential increases of RNA virus fitness during repeated transmission. Proc. Natl. Acad. Sci. USA 92: 5841-5844.
  • Elena, S.F., Cooper, V.S., and Lenski, R.E. (1996). Punctuated evolution caused by selection of rare beneficial mutations. Science 272: 1802-1804.
  • Elena, S.F., Cooper, V.S., and Lenski, R.E. (1996). Mechanisms of punctuated evolution? Reply. Science 274: 1749-1750.
  • Elena, S.F. and Lenski, R.E. (1997). Test of Synergistic Interactions between deleterious mutations in bacteria. Nature 390: 395-398.
  • Miralles, R., Gerrish, P.J., Moya, A., and Elena, S.F. (1999). Clonal interference and the evolution of RNA viruses. Science 285: 1745-1747.
  • Moya, A., Elena, S.F., Bracho, A., Miralles, R., and Barrio, E. (2000). The evolution of RNA viruses: a population genetic view. Proc. Natl. Acad. Sci. USA 97: 6967-6973.
  • Fares, M.A., Ruiz-González, M.X., Moya, A., Elena, S.F., and Barrio, E. (2002). Endosymbiotic bacteria: GroEL buffers against deleterious mutations. Nature 417: 398.
  • Elena, S.F. and Lenski, R.E. (2003). Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4: 457-469.
  • Elena, S.F. and Sanjuán, R. (2003). Climb every mountain? Science 302: 2074-2075.
  • Sanjuán, R., Moya, A., and Elena, S.F. (2004). The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus. Proc. Natl. Acad. Sci. USA 101: 8396-8401.
  • Sanjuán, R., Moya, A., and Elena, S.F. (2004). The contribution of epistasis to the architecture of fitness in an RNA virus. Proc. Natl. Acad. Sci. USA. 101: 15376-15379.
  • Sanjuán, R. and Elena, S.F. (2006). Epistasis correlates to genomic complexity. Proc. Natl. Acad. Sci. USA 103: 14402-14405.
  •  de Visser, J.A.G.M. and Elena, S.F. (2007). The evolution of sex: empirical insights into the roles of epistasis and drift. Nat. Rev. Genet. 8: 139-149.
  • Martin, G., Elena, S.F. and Lenormand, T. (2007). Distribution of epistasis in microbes fit predictions from a fitness landscape model. Nat. Genet. 33: 555-560.
  • Elena, S.F. and Sanjuán, R. (2007). Virus evolution: insights from an experimental approach. Annu. Rev. Ecol. Evol. Syst. 38: 27-52.
  • Gago, S., Elena, S.F., Flores, R. and Sanjuán, R. (2009). Extremely high mutation rate of a hammerhead viroid. Science 323: 1308.
  • Carrera, J., Elena, S.F. and Jaramillo, A. (2012). Computational design of genomic transcriptional networks with adaptation to varying environments. Proc. Natl. Acad. Sci. USA 109: 15277-15282.
  • Flores, R., Gago-Zachert, S., Serra, P., Sanjuán, R. and Elena, S.F. (2014). Viroids: survivors from RNA world? Annu. Rev. Microbiol. 68: 395-414.
  • Zwart, M.P., Elena, S.F. (2015). Matters of size: genetic bottlenecks in virus infection and their potential impact on evolution. Annu. Rev. Virol. 2: 161-179.


And the most recently published…

  • Folch-Fortuny, A., Bosque, G., Picó, J., Ferrer, A., Elena, S.F. (2016). Fusion of genomic, proteomic and phenotypic data: the case of potyviruses. Mol. BioSyst. 12: 253-261.

At the present, I am member of the Editorial Board of:


BMC Evol Biol




I was elected EMBO Member in 2011.


I’m also an external professor at The Santa Fe Institute (New Mexico, USA), a great place for doing multidisciplinary science.



Follow this link for a complete description of my CV.

Contact Information:

Prof. Santiago F. Elena

Instituto de Biología Molecular y Celular de Plantas (CSIC-UPV)

Campus UPV, CPI 8E lab 2.04

CL. Ingeniero Fausto Elio s/n

46022 València



Phone: +34 963 877 895

FAX: +34 963 877 859


           Last modified: November 11st, 2015

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