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ELENA Santiago

  • Evolutionary Systems Virology Group, I2SysBio (CSIC-UV), Valencia, Spain
  • Adaptation, Bioinformatics & Computational Biology, Evolutionary Dynamics, Evolutionary Epidemiology, Experimental Evolution, Genome Evolution, Molecular Evolution
  • recommender

Recommendation:  1

Reviews:  0

Educational and work
1990. MSc in Biochemistry (University of Valencia). 1994. Visiting scholar at the Department of Biology, UC San Diego. Supervisor: Prof. Dr. John J. Holland. Topic: effect of population bottlenecks on VSV fitness. 1995. PhD in Molecular and Evolutionary Genetics (University of Valencia). Supervisors: Prof. Dr. Andrés Moya and Prof. Dr. Esteban Domingo. Topics: experimental evolution of VSV; dynamics of adaptation; effect of deleterious mutations; theoretical population genetics and molecular evolution. 1995-1998. Postdoc in the Center for Microbial Ecology, Michigan State University. Supervisor: Prof. Dr. Richard E. Lenski. Topics: experimental evolution of E. coli; punctuated evolution; mechanisms maintaining genetic diversity in microbial populations; deleterious mutations; epistasis and genetic canalization; evolution of antibiotic-resistance gene expression. 1998-2001. Assistant Professor of Genetics. University of Valencia. 2001-2002. Associated Professor of Population Genetics (leave in absence). University of Valencia. 2002. Visiting professor. Department of Microbiology and Molecular Genetics, Michigan State University. Supervisor: Prof. Dr. Richard E. Lenski. Topic: artificial life. 2002-2005. Senior scientist at the Spanish National Research Council (CSIC). Instituto de Biología Molecular y Celular de Plantas (IBMCP), Valencia. 2005-2018. Professor. IBMCP (CSIC-UPV), Valencia. 2018-present. Professor. I2SysBio (CSIC-UV), Valencia. Topics: experimental evolution of plant viruses and viroids; mechanisms of mutational robustness; evolution of virulence; emerging viruses and evolutionary trade-offs; host-parasite interaction; artificial life; theoretical population genetics and molecular evolution. 2008–present. External Professor of the Santa Fe Institute. Santa Fe (NM), USA. Topics: evolution of robustness and evolvability in RNA viruses; artificial life; evolutionary systems biology. 2016. Visiting professor. Department of Biology, UC San Diego. Supervisor: Prof. Dr. Lin Chao. Topic: game theory applications to the analysis of mixed viral infections. June 2005–October 2009. Head of the Stress Biology Department. IBMCP, Valencia. January 2011–February 2014. Head of the Virology Department. IBMCP, Valencia. Published more than 210 peer-reviewed papers and more than 250 contributions to conferences in the fields of Evolutionary Genetics, Virology and Systems Biology. Supervisor of 19 PhD theses. PI for 18 grants (including from EMBO, HFSP, The John Templeton Foundation, and EU FP7) and research contracts with industry. Member of the American Society for the Study of Evolution, European Society of Evolutionary Biologists (ESEB), and Society of Molecular Epidemiology and Evolutionary Genetics of Infections Disease. Member of the ESEB Council (2003-2007, 2011-2019). Past or current Associated Editor of American Naturalist; BMC Evolutionary Biology; Evolution; Frontiers in Microbiology; Infection, Genetics and Evolution; International Journal of Evolutionary Biology; Journal of Evolutionary Biology; Open Genomics Journal; Open Parasitology Journal; Open Virology Journal; PLoS Pathogens (occasional guest editor); Proceedings of the Royal Society B; Virus Evolution (co-editor in chief). Academic member of Faculty of 1000and the Peer Community in Evolutionary Biology. Awarded as EMBO Young Investigator in 2004. Elected EMBO Member in 2011. Hirsch’ h index of 53 (in Google Scholar) , 217 publications, 10516 citations. Research ID: A-4191-2011 Scopus ID: 7006364449 ORCID: 0000-0001-8249-5593

Recommendation:  1

30 Aug 2021
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The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions

Nestedness and modularity in plant-parasite infection networks

Recommended by based on reviews by Rubén González and 2 anonymous reviewers

In a landmark paper, Flores et al. (2011) showed that the interactions between bacteria and their viruses could be nicely described using a bipartite infection networks.  Two quantitative properties of these networks were of particular interest, namely modularity and nestedness.  Modularity emerges when groups of host species (or genotypes) shared groups of viruses.  Nestedness provided a view of the degree of specialization of both partners: high nestedness suggests that hosts differ in their susceptibility to infection, with some highly susceptible host genotypes selecting for very specialized viruses while strongly resistant host genotypes select for generalist viruses.  Translated to the plant pathology parlance, this extreme case would be equivalent to a gene-for-gene infection model (Flor 1956): new mutations confer hosts with resistance to recently evolved viruses while maintaining resistance to past viruses.  Likewise, virus mutations for expanding host range evolve without losing the ability to infect ancestral host genotypes.  By contrast, a non-nested network would represent a matching-allele infection model (Frank 2000) in which each interacting organism evolves by losing its capacity to resist/infect its ancestral partners, resembling a Red Queen dynamic.  Obviously, the reality is more complex and may lie anywhere between these two extreme situations.

Recently, Valverde et al. (2020) developed a model to explain the emergence of nestedness and modularity in plant-virus infection networks across diverse habitats.  They found that local modularity could coexist with global nestedness and that intraspecific competition was the main driver of the evolution of ecosystems in a continuum between nested-modular and nested networks.  These predictions were tested with field data showing the association between plant host species and different viruses in different agroecosystems (Valverde et al. 2020).  The effect of interspecific competition in the structure of empirical plant host-virus infection networks was also tested by McLeish et al. (2019).  Besides data from agroecosystems, evolution experiments have also shown the pervasive emergence of nestedness during the diversification of independently-evolved lineages of potyviruses in Arabidopsis thaliana genotypes that differ in their susceptibility to infection (Hillung et al. 2014; González et al. 2019; Navarro et al. 2020).

In their study, Moury et al. (2021) have expanded all these previous observations to a diverse set of pathosystems that range from viruses, bacteria, oomycetes, fungi, nematodes to insects.  While modularity was barely seen in only a few of the systems, nestedness was a common trend (observed in ~94% of all systems).  This nestedness, as seen in previous studies and as predicted by theory, emerged as a consequence of the existence of generalist and specialist strains of the parasites that differed in their capacity to infect more or less resistant plant genotypes.

As pointed out by Moury et al. (2021) in their conclusions, the ubiquity of nestedness in plant-parasite infection matrices has strong implications for the evolution and management of infectious diseases.

References

Flor, H. H. (1956). The complementary genic systems in flax and flax rust. In Advances in genetics, 8, 29-54. https://doi.org/10.1016/S0065-2660(08)60498-8

Flores, C. O., Meyer, J. R., Valverde, S., Farr, L., and Weitz, J. S. (2011). Statistical structure of host–phage interactions. Proceedings of the National Academy of Sciences, 108, E288-E297. https://doi.org/10.1073/pnas.1101595108

Frank, S. A. (2000). Specific and non-specific defense against parasitic attack. Journal of Theoretical Biology, 202, 283-304. https://doi.org/10.1006/jtbi.1999.1054

González, R., Butković, A., and Elena, S. F. (2019). Role of host genetic diversity for susceptibility-to-infection in the evolution of virulence of a plant virus. Virus evolution, 5(2), vez024. https://doi.org/10.1093/ve/vez052

Hillung, J., Cuevas, J. M., Valverde, S., and Elena, S. F. (2014). Experimental evolution of an emerging plant virus in host genotypes that differ in their susceptibility to infection. Evolution, 68, 2467-2480. https://doi.org/10.1111/evo.12458

McLeish, M., Sacristán, S., Fraile, A., and García-Arenal, F. (2019). Coinfection organizes epidemiological networks of viruses and hosts and reveals hubs of transmission. Phytopathology, 109, 1003-1010. https://doi.org/10.1094/PHYTO-08-18-0293-R

Moury B, Audergon J-M, Baudracco-Arnas S, Krima SB, Bertrand F, Boissot N, Buisson M, Caffier V, Cantet M, Chanéac S, Constant C, Delmotte F, Dogimont C, Doumayrou J, Fabre F, Fournet S, Grimault V, Jaunet T, Justafré I, Lefebvre V, Losdat D, Marcel TC, Montarry J, Morris CE, Omrani M, Paineau M, Perrot S, Pilet-Nayel M-L and Ruellan Y (2021) The quasi-universality of nestedness in the structure of quantitative plant-parasite interactions. bioRxiv, 2021.03.03.433745, ver. 4 recommended and peer-reviewed by PCI Evolutionary Biology. https://doi.org/10.1101/2021.03.03.433745

Navarro, R., Ambros, S., Martinez, F., Wu, B., Carrasco, J. L., and Elena, S. F. (2020). Defects in plant immunity modulate the rates and patterns of RNA virus evolution. bioRxiv. doi: https://doi.org/10.1101/2020.10.13.337402

Valverde, S., Vidiella, B., Montañez, R., Fraile, A., Sacristán, S., and García-Arenal, F. (2020). Coexistence of nestedness and modularity in host–pathogen infection networks. Nature ecology & evolution, 4, 568-577. https://doi.org/10.1038/s41559-020-1130-9

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ELENA Santiago

  • Evolutionary Systems Virology Group, I2SysBio (CSIC-UV), Valencia, Spain
  • Adaptation, Bioinformatics & Computational Biology, Evolutionary Dynamics, Evolutionary Epidemiology, Experimental Evolution, Genome Evolution, Molecular Evolution
  • recommender

Recommendation:  1

Reviews:  0

Educational and work
1990. MSc in Biochemistry (University of Valencia). 1994. Visiting scholar at the Department of Biology, UC San Diego. Supervisor: Prof. Dr. John J. Holland. Topic: effect of population bottlenecks on VSV fitness. 1995. PhD in Molecular and Evolutionary Genetics (University of Valencia). Supervisors: Prof. Dr. Andrés Moya and Prof. Dr. Esteban Domingo. Topics: experimental evolution of VSV; dynamics of adaptation; effect of deleterious mutations; theoretical population genetics and molecular evolution. 1995-1998. Postdoc in the Center for Microbial Ecology, Michigan State University. Supervisor: Prof. Dr. Richard E. Lenski. Topics: experimental evolution of E. coli; punctuated evolution; mechanisms maintaining genetic diversity in microbial populations; deleterious mutations; epistasis and genetic canalization; evolution of antibiotic-resistance gene expression. 1998-2001. Assistant Professor of Genetics. University of Valencia. 2001-2002. Associated Professor of Population Genetics (leave in absence). University of Valencia. 2002. Visiting professor. Department of Microbiology and Molecular Genetics, Michigan State University. Supervisor: Prof. Dr. Richard E. Lenski. Topic: artificial life. 2002-2005. Senior scientist at the Spanish National Research Council (CSIC). Instituto de Biología Molecular y Celular de Plantas (IBMCP), Valencia. 2005-2018. Professor. IBMCP (CSIC-UPV), Valencia. 2018-present. Professor. I2SysBio (CSIC-UV), Valencia. Topics: experimental evolution of plant viruses and viroids; mechanisms of mutational robustness; evolution of virulence; emerging viruses and evolutionary trade-offs; host-parasite interaction; artificial life; theoretical population genetics and molecular evolution. 2008–present. External Professor of the Santa Fe Institute. Santa Fe (NM), USA. Topics: evolution of robustness and evolvability in RNA viruses; artificial life; evolutionary systems biology. 2016. Visiting professor. Department of Biology, UC San Diego. Supervisor: Prof. Dr. Lin Chao. Topic: game theory applications to the analysis of mixed viral infections. June 2005–October 2009. Head of the Stress Biology Department. IBMCP, Valencia. January 2011–February 2014. Head of the Virology Department. IBMCP, Valencia. Published more than 210 peer-reviewed papers and more than 250 contributions to conferences in the fields of Evolutionary Genetics, Virology and Systems Biology. Supervisor of 19 PhD theses. PI for 18 grants (including from EMBO, HFSP, The John Templeton Foundation, and EU FP7) and research contracts with industry. Member of the American Society for the Study of Evolution, European Society of Evolutionary Biologists (ESEB), and Society of Molecular Epidemiology and Evolutionary Genetics of Infections Disease. Member of the ESEB Council (2003-2007, 2011-2019). Past or current Associated Editor of American Naturalist; BMC Evolutionary Biology; Evolution; Frontiers in Microbiology; Infection, Genetics and Evolution; International Journal of Evolutionary Biology; Journal of Evolutionary Biology; Open Genomics Journal; Open Parasitology Journal; Open Virology Journal; PLoS Pathogens (occasional guest editor); Proceedings of the Royal Society B; Virus Evolution (co-editor in chief). Academic member of Faculty of 1000and the Peer Community in Evolutionary Biology. Awarded as EMBO Young Investigator in 2004. Elected EMBO Member in 2011. Hirsch’ h index of 53 (in Google Scholar) , 217 publications, 10516 citations. Research ID: A-4191-2011 Scopus ID: 7006364449 ORCID: 0000-0001-8249-5593