S F Elena

Summary

Country: Spain

Publications

  1. pmc Genotypic but not phenotypic historical contingency revealed by viral experimental evolution
    Stephanie Bedhomme
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022, Valencia, Spain
    BMC Evol Biol 13:46. 2013
  2. pmc Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein
    Beata Hasiów-Jaroszewska
    Institute of Plant Protection National Research Institute, ul Wł Węgorka 20, 60 318 Poznan, Poland
    Virol J 8:318. 2011
  3. pmc Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus
    Patricia Agudelo-Romero
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022 Valencia, Spain
    Virol J 5:92. 2008
  4. pmc Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
    Javier Carrera
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Ingeniero Fausto Elio s n, 46022 Valencia, Spain
    Genome Biol 10:R96. 2009
  5. pmc Robust dynamical pattern formation from a multifunctional minimal genetic circuit
    Guillermo Rodrigo
    Synth Bio Group, Epigenomics Project, Genopole Université Evry Val d Essonne CNRS UPS3201, 91034 Evry Cedex, France
    BMC Syst Biol 4:48. 2010
  6. pmc Analysis of epistatic interactions and fitness landscapes using a new geometric approach
    Niko Beerenwinkel
    Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
    BMC Evol Biol 7:60. 2007
  7. ncbi request reprint Effects of population size and mutation rate on the evolution of mutational robustness
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, 46022 Valencia, Spain
    Evolution 61:666-74. 2007
  8. pmc The effect of genetic robustness on evolvability in digital organisms
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, Valencia, Spain
    BMC Evol Biol 8:284. 2008
  9. ncbi request reprint Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation rates
    Santiago F Elena
    Inst for Molecular and Cellular Plant Biology, CSIC UPV, Valencia, Spain
    Int Microbiol 8:271-8. 2005
  10. pmc Mechanisms of genetic robustness in RNA viruses
    Santiago F Elena
    Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Avenida de los Naranjos s n, 46022 Valencia, Spain
    EMBO Rep 7:168-73. 2006

Collaborators

Detail Information

Publications70

  1. pmc Genotypic but not phenotypic historical contingency revealed by viral experimental evolution
    Stephanie Bedhomme
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022, Valencia, Spain
    BMC Evol Biol 13:46. 2013
    ..We thereafter evaluated the degree of adaptation to the new host as well as to the original ones and characterized the consensus sequence of each lineage...
  2. pmc Tridimensional model structure and patterns of molecular evolution of Pepino mosaic virus TGBp3 protein
    Beata Hasiów-Jaroszewska
    Institute of Plant Protection National Research Institute, ul Wł Węgorka 20, 60 318 Poznan, Poland
    Virol J 8:318. 2011
    ..However, little is known about the mechanisms and pattern of PepMV molecular evolution and about the role of individual proteins in host-pathogen interactions...
  3. pmc Changes in the gene expression profile of Arabidopsis thaliana after infection with Tobacco etch virus
    Patricia Agudelo-Romero
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022 Valencia, Spain
    Virol J 5:92. 2008
    ..Gene expression profiles were monitored in whole plants 21 days post-inoculation (dpi). Microarrays contained 26,173 protein-coding genes and 87 miRNAs...
  4. pmc Reverse-engineering the Arabidopsis thaliana transcriptional network under changing environmental conditions
    Javier Carrera
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Ingeniero Fausto Elio s n, 46022 Valencia, Spain
    Genome Biol 10:R96. 2009
    ....
  5. pmc Robust dynamical pattern formation from a multifunctional minimal genetic circuit
    Guillermo Rodrigo
    Synth Bio Group, Epigenomics Project, Genopole Université Evry Val d Essonne CNRS UPS3201, 91034 Evry Cedex, France
    BMC Syst Biol 4:48. 2010
    ....
  6. pmc Analysis of epistatic interactions and fitness landscapes using a new geometric approach
    Niko Beerenwinkel
    Program for Evolutionary Dynamics, Harvard University, Cambridge, MA 02138, USA
    BMC Evol Biol 7:60. 2007
    ..In this paper, we propose and employ a new mathematical approach that allows a more complete description of multi-way interactions and provides new insights into the structure of fitness landscapes...
  7. ncbi request reprint Effects of population size and mutation rate on the evolution of mutational robustness
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, 46022 Valencia, Spain
    Evolution 61:666-74. 2007
    ..These results are independent of whether genomes were constrained to their original length or allowed to change in size...
  8. pmc The effect of genetic robustness on evolvability in digital organisms
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, Valencia, Spain
    BMC Evol Biol 8:284. 2008
    ..However, several issues related to robustness remain poorly understood, such as its implications for evolvability (the ability to produce adaptive evolutionary innovations)...
  9. ncbi request reprint Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation rates
    Santiago F Elena
    Inst for Molecular and Cellular Plant Biology, CSIC UPV, Valencia, Spain
    Int Microbiol 8:271-8. 2005
    ..coli B, and an estimate of 200 generations per year, it was estimated that B and K-12 diverged several hundred thousand years ago, while O157:H7 split off from their common ancestor about 1.5-2 million years ago...
  10. pmc Mechanisms of genetic robustness in RNA viruses
    Santiago F Elena
    Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Avenida de los Naranjos s n, 46022 Valencia, Spain
    EMBO Rep 7:168-73. 2006
    ..Finally, we discuss the possibility that viruses might exploit cellular buffering mechanisms for their own benefit, producing a sort of extrinsic robustness...
  11. doi request reprint Experimental evolution of plant RNA viruses
    S F Elena
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, Valencia, Spain
    Heredity (Edinb) 100:478-83. 2008
    ....
  12. pmc Adaptive value of high mutation rates of RNA viruses: separating causes from consequences
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Avenida de los Naranjos s n, 46022 Valencia, Spain
    J Virol 79:11555-8. 2005
  13. ncbi request reprint RNA viruses as complex adaptive systems
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, 46022 Valencia, Spain
    Biosystems 81:31-41. 2005
    ....
  14. pmc Environmental stress and the effects of mutation
    Santiago F Elena
    Instituto de Biología Molecular y Celular de Plantas CSIC, Campus UPV, Avenida de los Naranjos s n, 46022 Valencia, Spain
    J Biol 2:12. 2003
    ..Recent results suggest that the effects of deleterious mutations can, instead, sometimes be ameliorated in stressful environments...
  15. ncbi request reprint Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas, 46022 Valencia, Spain
    Nat Rev Genet 4:457-69. 2003
    ....
  16. doi request reprint Simple genomes, complex interactions: epistasis in RNA virus
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Ingeniero Fausto Elio s n, 46022 Valencia, Spain
    Chaos 20:026106. 2010
    ..However, the magnitude of this effect is larger if replication occurs geometrically than if it proceeds linearly...
  17. doi request reprint A systems biology approach to the evolution of plant-virus interactions
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, Ingeniero Fausto Elio s n, 46022 Valencia, Spain
    Curr Opin Plant Biol 14:372-7. 2011
    ..Here, we review studies identifying host genes regulated by viruses and discuss how these genes integrate in host regulatory and interaction networks, with a particular focus on the physical properties of these networks...
  18. doi request reprint The causes of epistasis in genetic networks
    Javier Macia
    Complex Systems Laboratory, ICREA Universitat Pompeu Fabra, 08003 Barcelona, Spain
    Evolution 66:586-96. 2012
    ....
  19. doi request reprint The evolutionary genetics of emerging plant RNA viruses
    Santiago F Elena
    Instituto de Biologia Molecular, Consejo Superior de Investigaciones Cientificas, Valencia, Spain
    Mol Plant Microbe Interact 24:287-93. 2011
    ....
  20. ncbi request reprint Evolution. Climb every mountain?
    Santiago F Elena
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022 Valencia, Spain
    Science 302:2074-5. 2003
  21. ncbi request reprint In silico predicted robustness of viroid RNA secondary structures. II. Interaction between mutation pairs
    Rafael Sanjuan
    Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Valencia, Spain
    Mol Biol Evol 23:2123-30. 2006
    ..In good agreement with our previous finding of an evolutionary trend toward increased robustness, we now found a trend toward reduced antagonistic epistasis...
  22. pmc Magnitude and sign epistasis among deleterious mutations in a positive-sense plant RNA virus
    J Lalic
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Valencia, Spain
    Heredity (Edinb) 109:71-7. 2012
    ..Overall, our results are in good agreement to those previously reported for other viruses and further consolidate the view that positive epistasis is the norm for small and compact genomes that lack genetic robustness...
  23. ncbi request reprint A real-time RT-PCR assay for quantifying the fitness of tobacco etch virus in competition experiments
    P Carrasco
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Avenida de los Naranjos s n, 46022 Valencia, Spain
    J Virol Methods 139:181-8. 2007
    ..Reproducibility was assessed by running multiple competition experiments for the same genotype. Sensitivity was assessed by comparing the results of competition experiments against TEV-PC1 of 24 single-nucleotide substitutions mutants...
  24. pmc Mixed infections of Pepino mosaic virus strains modulate the evolutionary dynamics of this emergent virus
    P Gomez
    Centro de Edafologia y Biologia Aplicada del Segura, Consejo Superior de Investigaciones Cientificas, 30100 Espinardo, Murcia, Spain
    J Virol 83:12378-87. 2009
    ..Thus, mixed infections appear to be contributing to shaping the genetic structure and dynamics of PepMV populations...
  25. pmc Epistasis correlates to genomic complexity
    Rafael Sanjuan
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022 Valencia, Spain
    Proc Natl Acad Sci U S A 103:14402-5. 2006
    ..We propose that antagonistic epistasis might be a property of compact genomes with few nonpleiotropic biological functions, whereas in complex genomes, synergism might emerge from mutational robustness...
  26. pmc Adaptation of tobacco etch potyvirus to a susceptible ecotype of Arabidopsis thaliana capacitates it for systemic infection of resistant ecotypes
    Jasna Lalić
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022 Valencia, Spain
    Philos Trans R Soc Lond B Biol Sci 365:1997-2007. 2010
    ..Second, the concept of resistance genes may only be valid for a well-defined viral genotype but not for polymorphic viral populations...
  27. pmc Viroids: an Ariadne's thread into the RNA labyrinth
    José Antonio Daròs
    Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Universidad Politecnica de Valencia, Avenida de los Naranjos s n, 46022 Valencia, Spain
    EMBO Rep 7:593-8. 2006
    ..Viroids elicit RNA-silencing phenomena, which might mediate some of their biological properties, including pathogenesis. As some viroids behave as catalytic RNAs, they are regarded as remnants of the RNA world...
  28. doi request reprint Network design meets in silico evolutionary biology
    Guillermo Rodrigo
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas Universidad Politecnica de Valencia, 46022 Valencia, Spain
    Biochimie 92:746-52. 2010
    ..Finally, we briefly discuss the modular designability of gene regulatory networks and its potential application in biotechnology...
  29. ncbi request reprint In silico predicted robustness of viroids RNA secondary structures. I. The effect of single mutations
    Rafael Sanjuan
    Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Avenida de los Naranjos s n, Valencia, Spain
    Mol Biol Evol 23:1427-36. 2006
    ..We also show that genomic redundancy can contribute to the robustness of these simple RNA genomes...
  30. pmc Structural discrimination of robustness in transcriptional feedforward loops for pattern formation
    Guillermo Rodrigo
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas Universidad Politecnica de Valencia, Valencia, Spain
    PLoS ONE 6:e16904. 2011
    ..Finally, we discussed the evolution of incoherent regulations in terms of multifunctionality and robustness...
  31. ncbi request reprint Evolutionary relationships among members of the Bromoviridae deduced from whole proteome analysis
    F M Codoñer
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Valencia, Spain
    Arch Virol 151:299-307. 2006
    ....
  32. ncbi request reprint Evolution of RNA virus in spatially structured heterogeneous environments
    J M Cuevas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Departament de Genetica, Universitat de Valencia, Valencia, Spain
    J Evol Biol 16:456-66. 2003
    ..The performance in a given tissue was negatively correlated with its distance to the tissue hosting the population. This correlation decreased with migration rate...
  33. ncbi request reprint Low genetic variability in the coat and movement proteins of American plum line pattern virus isolates from different geographic origins
    M C Herranz
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Valencia, Spain
    Arch Virol 153:367-73. 2008
    ..The MP and CP of APLPV possess most of the functional motifs described for other members of the genus Ilarvirus...
  34. ncbi request reprint Transmission bottlenecks and the evolution of fitness in rapidly evolving RNA viruses
    S F Elena
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de València Apartat 2085, 46071, Valencia, Spain
    Infect Genet Evol 1:41-8. 2001
    ..In addition, high levels of viral fitness in horizontally transmitted populations were explained by competition among viral variants...
  35. doi request reprint The pleiotropic cost of host-specialization in Tobacco etch potyvirus
    Patricia Agudelo-Romero
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Valencia, Spain
    Infect Genet Evol 8:806-14. 2008
    ..Genomic consensus sequences were obtained for each lineage at the end time point. The potential relevance for the evolution of virulence and virus fitness of the characterized mutations is discussed...
  36. doi request reprint Error threshold in RNA quasispecies models with complementation
    Josep Sardanyés
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Ingeniero Fausto Elio s n, 46022 Valencia, Spain
    J Theor Biol 265:278-86. 2010
    ..We have also found that the region in the parameter space (mu,gamma) in which the master sequence survives is reduced when DIPs are introduced into the system...
  37. doi request reprint Extremely high mutation rate of a hammerhead viroid
    Selma Gago
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas Universidad Politecnica de Valencia, 46022 Valencia, Spain
    Science 323:1308. 2009
    ..Our results suggest that the emergence of replication fidelity was critical for the evolution of complexity in the early history of life...
  38. pmc Virus adaptation by manipulation of host's gene expression
    Patricia Agudelo-Romero
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Valencia, Spain
    PLoS ONE 3:e2397. 2008
    ..A major difference is that genes involved in stress and pathogen response are not activated upon infection with the evolved virus, suggesting that selection has favored viral strategies to escape from host defenses...
  39. pmc The rate and spectrum of spontaneous mutations in a plant RNA virus
    Nicolas Tromas
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Cientificas Universidad Politecnica de Valencia, 46022 Valencia, Spain
    Genetics 185:983-9. 2010
    ..Our estimates are in the same biological ballpark that previous values reported for plant RNA viruses. This finding gives further support to the idea that plant RNA viruses may have lower mutation rates than their animal counterparts...
  40. pmc Insights into the selective pressures restricting Pelargonium flower break virus genome variability: Evidence for host adaptation
    Patricia Rico
    Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Campus Universidad Politécnica de Valencia, Avenida de los Naranjos s n, 46022 Valencia, Spain
    J Virol 80:8124-32. 2006
    ..Globally, the results indicate that the selective pressures exerted by the host play a critical role in shaping PFBV populations and that these populations are likely being selected for at both protein and RNA levels...
  41. pmc Fitness declines in Tobacco etch virus upon serial bottleneck transfers
    Francisca de la Iglesia
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022 Valencia, Spain
    J Virol 81:4941-7. 2007
    ..Temporal fitness fluctuations were not explained by random noise but reflected more complex underlying processes related to emergence and self-organization phenomena...
  42. doi request reprint The promiscuous evolutionary history of the family Bromoviridae
    Francisco M Codoñer
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, Valencia, Spain
    J Gen Virol 89:1739-47. 2008
    ..Finally, a phylogenetic network was constructed reflecting these genetic exchanges. The network confirmed the taxonomic status of the different genera within the family, despite the phylogenetic noise introduced by genetic exchange...
  43. ncbi request reprint A sliding window-based method to detect selective constraints in protein-coding genes and its application to RNA viruses
    Mario A Fares
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Valencia, Spain
    J Mol Evol 55:509-21. 2002
    ..The application of the method to different human immunodeficiency virus type 1 and to foot-and-mouth disease virus genes confirms the action of positive selection on previously described regions as well as on new regions...
  44. pmc Distribution of fitness and virulence effects caused by single-nucleotide substitutions in Tobacco Etch virus
    Purificación Carrasco
    Instituto de Biología Molecular y Celular de Plantas CSIC UPV, Avenida de los Naranjos s n, 46022 Valencia, Spain
    J Virol 81:12979-84. 2007
    ..4% increases. Interestingly, the only mutations showing a significant effect on virulence were hypervirulent. Competitive fitness and virulence were uncorrelated traits...
  45. ncbi request reprint Molecular evolution of the plant virus family Bromoviridae based on RNA3-encoded proteins
    Francisco M Codoñer
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, Avenida de los Naranjos s n, Valencia 46022, Spain
    J Mol Evol 61:697-705. 2005
    ..The implications of these results for the taxonomy of this important family of plant viruses are discussed...
  46. pmc Adaptive covariation between the coat and movement proteins of prunus necrotic ringspot virus
    Francisco M Codoñer
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022 Valencia, Spain
    J Virol 80:5833-40. 2006
    ..Finally, we discuss these findings in the light of what is already known about the implication of certain sites and domains in structure and protein-protein and RNA-protein interactions...
  47. doi request reprint Application of game theory to the interaction between plant viruses during mixed infections
    Susana Martin
    Instituto de Biología Molecular y Celular de Plantas CSIC UPV, 46022 Valencia, Spain
    J Gen Virol 90:2815-20. 2009
    ..However, the infectivity of each virus was not affected by the presence of the other, and no symptom synergism was observed...
  48. pmc Upper-limit mutation rate estimation for a plant RNA virus
    Rafael Sanjuan
    Instituto de Biologia Molecular y Celular de Plantas, CSIC UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s n, 46022 Valencia, Spain
    Biol Lett 5:394-6. 2009
    ....
  49. doi request reprint Compensatory molecular evolution of HC-Pro, an RNA-silencing suppressor from a plant RNA virus
    Clara Torres-Barceló
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Ingeniero Fausto Elio s n, Valencia, Spain
    Mol Biol Evol 27:543-51. 2010
    ..Negative epistatic effects among beneficial mutations as well as decompensatory epistasis also play an important role during compensatory evolution of RNA-silencing suppression...
  50. pmc The fittest versus the flattest: experimental confirmation of the quasispecies effect with subviral pathogens
    Francisco M Codoñer
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas Universitat Politècnica de València, Valencia, Spain
    PLoS Pathog 2:e136. 2006
    ..In contrast, the slow-growth species was able to outcompete the fast species when the mutation rate was increased. These experimental results were supported by an in silico model of competing viroid quasispecies...
  51. pmc From hypo- to hypersuppression: effect of amino acid substitutions on the RNA-silencing suppressor activity of the Tobacco etch potyvirus HC-Pro
    Clara Torres-Barceló
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, 46022 Valencia, Spain
    Genetics 180:1039-49. 2008
    ....
  52. pmc Tempo and mode of plant RNA virus escape from RNA interference-mediated resistance
    Guillaume Lafforgue
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas Universitat Politecnica deValencia, Valencia, Spain
    J Virol 85:9686-95. 2011
    ..Together, our results contribute to the rational management of amiR-based antiviral resistance in plants...
  53. doi request reprint HC-Pro hypo- and hypersuppressor mutants: differences in viral siRNA accumulation in vivo and siRNA binding activity in vitro
    Clara Torres-Barceló
    Instituto de Biologia Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas UPV, Ingeniero Fausto Elio s n, 46022, Valencia, Spain
    Arch Virol 155:251-4. 2010
    ..As a consequence of lower viral accumulation, plants infected with virus bearing a hyposuppressor allele also accumulate less virus-derived siRNA...
  54. pmc Parasites and mutational load: an experimental test of a pluralistic theory for the evolution of sex
    Tim F Cooper
    Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, USA
    Proc Biol Sci 272:311-7. 2005
    ..These results suggest that, on average, deleterious mutations act multiplicatively with each other but in synergy with infection in determining fitness...
  55. pmc The distribution of fitness effects caused by single-nucleotide substitutions in an RNA virus
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
    Proc Natl Acad Sci U S A 101:8396-401. 2004
    ..The proportion of beneficial mutations was unexpectedly high. Beneficial effects followed a gamma distribution, with expected fitness increases of 1% for random mutations and 5% for preobserved mutations...
  56. ncbi request reprint Perspective: Evolution and detection of genetic robustness
    J Arjan G M de Visser
    Department of Genetics, Wageningen University, Arboretumlaan 4, 6703 BD Wageningen, The Netherlands
    Evolution 57:1959-72. 2003
    ....
  57. ncbi request reprint Restrictions to RNA virus adaptation: an experimental approach
    Santiago F Elena
    Departament de Genetica, Universitat de Valencia, Edifici d lnstituts d Investigació, Spain
    Antonie Van Leeuwenhoek 81:135-42. 2002
    ..Finally, and as another factor imposing a limit to their speed of adaptation, I review results showing that clonal interference also plays an important role during viral evolution...
  58. ncbi request reprint Coinfection and superinfection in RNA virus populations: a selection-mutation model
    Joan Saldaña
    Departament d Informàtica i Matemàtica Aplicada, Campus Montilivi, Universitat de Girona, Spain
    Math Biosci 183:135-60. 2003
    ....
  59. ncbi request reprint Natural selection and the organ-specific differentiation of HIV-1 V3 hypervariable region
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, 46071 Valencia, Spain
    Evolution 58:1185-94. 2004
    ..In contrast, positive selection does not seem to be the mechanism responsible for the evolution of patient-specific sequences...
  60. pmc Molecular basis of adaptive convergence in experimental populations of RNA viruses
    José M Cuevas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, Spain
    Genetics 162:533-42. 2002
    ..Keeping in mind statistical uncertainties, these estimates suggest that along with several beneficial mutations of major effect, many other mutations got fixed as part of a group of epistatic mutations...
  61. ncbi request reprint Mode of selection and experimental evolution of antiviral drugs resistance in vesicular stomatitis virus
    José M Cuevas
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
    Infect Genet Evol 5:55-65. 2005
    ..Evolution in presence of sub-inhibitory concentrations of antivirals compensated for the reduction in fitness in presence of antiviral therapy...
  62. pmc Epistasis and the adaptability of an RNA virus
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, 46071 Valencia, Spain
    Genetics 170:1001-8. 2005
    ..Finally, for genotypes carrying two deleterious mutations, we found evidence of a negative correlation between the epistastic effect and the rate of compensatory evolution...
  63. ncbi request reprint Simple quasispecies models for the survival-of-the-flattest effect: The role of space
    Josep Sardanyés
    Complex Systems Lab ICREA UPF, Barcelona Biomedical Research Park PRBB GRIB, Dr Aiguader 88, 08003 Barcelona, Spain
    J Theor Biol 250:560-8. 2008
    ..Furthermore, it is shown that space, which involves a lower critical mutation rate, broadens the conditions at which the survival-of-the-flattest may occur...
  64. ncbi request reprint Distributions of epistasis in microbes fit predictions from a fitness landscape model
    Guillaume Martin
    Centre d écologie fonctionnelle et évolutive Centre National de la Recherche Scientifique UMR 5175, 1919 Route de Mende, 34293 Montpellier, France
    Nat Genet 39:555-60. 2007
    ..This model may offer a simple and widely applicable alternative to complex metabolic network models, in particular for making evolutionary predictions...
  65. pmc Natural selection fails to optimize mutation rates for long-term adaptation on rugged fitness landscapes
    Jeff Clune
    Department of Computer Science and Engineering, Michigan State University, East Lansing, Michigan, United States of America
    PLoS Comput Biol 4:e1000187. 2008
    ..This finding has important implications for applied evolutionary research in both biological and computational realms...
  66. ncbi request reprint The evolution of sex: empirical insights into the roles of epistasis and drift
    J Arjan G M de Visser
    Laboratory of Genetics, Wageningen University, 6703 BD Wageningen, The Netherlands
    Nat Rev Genet 8:139-49. 2007
    ....
  67. doi request reprint Genetic diversity of the movement and coat protein genes of South American isolates of Prunus necrotic ringspot virus
    Nicola Fiore
    Facultad de Ciencias Agronómicas, Universidad de Chile, Avenida Santa Rosa, 11315 Santiago, Chile
    Arch Virol 153:909-19. 2008
    ..The study of the distribution of synonymous and nonsynonymous changes along both open reading frames revealed that most amino acid sites are under the effect of negative purifying selection...
  68. ncbi request reprint r- and K-selection in experimental populations of vesicular stomatitis virus
    Antonio V Borderia
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Departament de Genetica, Universitat de Valencia, 46071 Valencia, Spain
    Infect Genet Evol 2:137-43. 2002
    ..Similarly, viral populations evolved at high density showed reduced fitness at low density. Finally, we compare our results with those obtained for other RNA viruses...
  69. ncbi request reprint Endosymbiotic bacteria: groEL buffers against deleterious mutations
    Mario A Fares
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva and Departament de Genètica, Universitat de Valencia, PO Box 22085, 46071 Valencia, Spain
    Nature 417:398. 2002
  70. pmc The contribution of epistasis to the architecture of fitness in an RNA virus
    Rafael Sanjuan
    Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de Valencia, P O Box 22085, 46071 Valencia, Spain
    Proc Natl Acad Sci U S A 101:15376-9. 2004
    ..In this case, all significant interactions were antagonistic. Our results show that the architecture of the fitness depends on complex interactions among genome components...