Evolutionary Systems Virology Group
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.
the projects that we are currently working on, I would like to highlight the
- 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.
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
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
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.
significance of genome segmentation.
- 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
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
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
interactions among viruses coinfecting the same plant (TuMV and CaMV
infecting Brassica rappa). Coevolutionary
evolution and phylogenetic studies of different plant viruses.
and systemic analysis of in silico
and analytical models of viral gene interaction networks. Models of cell-to-cell and systemic
models. In cooperation with Prof. Ricard V. Solé
(Universitat Pompeu Fabra).
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
- 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:
- 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:
- 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
- Elena, S.F. and Lenski, R.E. (2003). Evolution experiments
with microorganisms: the dynamics and genetic bases of adaptation. Nat. Rev. Genet. 4:
- Elena, S.F. and Sanjuán, R. (2003). Climb every mountain? Science 302:
- 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:
- Martin, G., Elena, S.F. and Lenormand, T.
(2007). Distribution of epistasis in microbes fit predictions from a
fitness landscape model. Nat. Genet.
- 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
- 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.
And the most recently published…
At the present, I am member of the Editorial Board of:
|I was elected EMBO Member in 2011.
this link for a complete
description of my CV.
Prof. Santiago F.
Biología Molecular y Celular de Plantas
Campus UPV, CPI 8E
Fausto Elio s/n
Last modified: June 25th,
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