BRAVO Ignacio's profile
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BRAVO Ignacio

  • Laboratory MIVEGEC UMR CNRS IRD UniMontp, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
  • Evolutionary Applications, Evolutionary Epidemiology, Experimental Evolution, Genome Evolution, Molecular Evolution, Other, Phylogenetics / Phylogenomics, Systematics / Taxonomy
  • recommender

Recommendations:  2

Reviews:  0

Educational and work
Academic Career 2015->> Research Director. French National Center for Scientific Research (CNRS), Montpellier, France. 2011-2015 Head of the Infections and Cancer Laboratory. Catalan Institute of Oncology (ICO), Barcelona, Spain. 2008-2011 Ramón y Cajal Research Fellow. Centre for Public Health Research (CSISP). Valencia. Spain. 2007-2008 Junior Professorship. Institute for Evolution and Biodiversity. University Münster, Münster, Germany. 2006. EMBO Short term fellowship (3 months). Laboratory Prof. Dr. Hervé Philippe. Université de Montréal, Canada. 2006-2007 Research Scientist. Laboratory Prof. Dr. Lutz Gissmann, Genome Modifications and Carcinogenesis, German Cancer Research Centre, Heidelberg, Germany. 2002-2006 Postdoctoral researcher. Laboratory Prof. Dr. Ángel Alonso Cell Differentiation, German Cancer Research Centre, Heidelberg, Germany. 1998-2002 PhD in Biology. 2002. Universidad de León, Spain. Selected recent publications Pimenoff V, Mendes de Oliveira C, Bravo IG. Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16. Mol Biol Evol. 2017 Jan;34(1):4-19. doi: 10.1093/molbev/msw214. Nicolás-Párraga S, Gandini C, Pimenoff VN, Alemany L, de Sanjosé S, Bosch FX and Bravo IG*. HPV16 variants distribution in invasive cancers of the cervix, vulva, vagina, penis, and anus. Cancer Med. 2016 Oct;5(10):2909-2919. doi: 10.1002/cam4.870. Mengual-Chuliá B, Bedhomme S, Lafforgue G, Elena SF, Bravo IG. Assessing parallel gene histories in viral genomes. BMC Evol Biol. 2016 Feb 5;16(1):32. doi: 10.1186/s12862-016-0605-4. Félez-Sánchez M, Trösemeier JH, Bedhomme S, González-Bravo MI, Kamp C, Bravo IG. Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses. Genome Biol Evol. 2015 Jul 1;7(8):2117-35. doi: 10.1093/gbe/evv129. Bravo IG and Félez-Sánchez M. “Papillomaviruses: viral evolution, cancer and evolutionary medicine". Evol Med Public Health. 2015 Jan 28;2015(1):32-51. doi: 10.1093/emph/eov003. Garcia-Perez, R, Ibanez C, Godinez JM, Arechiga N, Garin I, Perez-Suarez G, de Paz O, Juste J, Echevarria JE, Bravo IG.
 “Novel papillomaviruses in free-ranging Iberian bats: no virus-host co-evolution, no strict host specificity and hints for recombination”. 
Genome Biol Evol (2014) 6(1):94-104. doi: 10.1093/gbe/evt211 Godínez JM, Nicolás-Párraga S, Pimenoff VN, Mengual-Chuliá B, Muñoz N, Bosch FX, Sánchez GI, McCloskey J, Bravo IG. “Phylogenetically related, clinically different: human papillomaviruses 6 and 11 variants distribution in genital warts and in laryngeal papillomatosis”. Clin Microbiol Infect. (2014) 20(6):O406-13. doi: 10.1111/1469-0691.12420.

Recommendations:  2

13 Dec 2018
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A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps

Recommended by based on reviews by Alejandro Manzano-Marín and 1 anonymous reviewer

Genetic intimacy of filamentous viruses and endoparasitoid wasps

Viruses establish intimate relationships with the cells they infect. The virocell is a novel entity, different from the original host cell and beyond the mere combination of viral and cellular genetic material. In these close encounters, viral and cellular genomes often hybridise, combine, recombine, merge and excise. Such chemical promiscuity leaves genomics scars that can be passed on to descent, in the form of deletions or duplications and, importantly, insertions and back and forth exchange of genetic material between viruses and their hosts.
In this preprint [1], Di Giovanni and coworkers report the identification of 13 genes present in the extant genomes of members of the Leptopilina wasp genus, bearing sound signatures of having been horizontally acquired from an ancestral virus. Importantly the authors identify Leptopilina boulardi filamentous virus (LbFV) as an extant relative of the ancestral virus that served as donor for the thirteen horizontally transferred genes. While pinpointing genes with a likely possible viral origin in eukaryotic genomes is only relatively rare, identifying an extant viral lineage related to the ancestral virus that continues to infect an extant relative of the ancestral host is remarkable. But the amazing evolutionary history of the Leptopilina hosts and these filamentous viruses goes beyond this shared genes. These wasps are endoparasitoids of Drosophila larvae, the female wasp laying the eggs inside the larvae and simultaneously injecting venom that hinders the immune response. The composition of the venoms is complex, varies between wasp species and also between individuals within a species, but a central component of all these venoms are spiked structures that vary in morphology, symmetry and size, often referred to as virus-like particles (VLPs).
In this preprint, the authors convincingly show that the expression pattern in the Leptopilina wasps of the thirteen genes identified to have been horizontally acquired from the LbFV ancestor coincides with that of the production of VLPs in the female wasp venom gland. Based on this spatio-temporal match, the authors propose that these VLPs have a viral origin. The data presented in this preprint will undoubtedly stimulate further research on the composition, function, origin, evolution and diversity of these VLP structures, which are highly debated (see for instance [2] and [3]).

References

[1] Di Giovanni, D., Lepetit, D., Boulesteix, M., Ravallec, M., & Varaldi, J. (2018). A behavior-manipulating virus relative as a source of adaptive genes for parasitoid wasps. bioRxiv, 342758, ver. 5 peer-reviewed and recommended by PCI Evol Biol. doi: 10.1101/342758
[2] Poirié, M., Colinet, D., & Gatti, J. L. (2014). Insights into function and evolution of parasitoid wasp venoms. Current Opinion in Insect Science, 6, 52-60. doi: 10.1016/j.cois.2014.10.004
[3] Heavner, M. E., Ramroop, J., Gueguen, G., Ramrattan, G., Dolios, G., Scarpati, M., ... & Govind, S. (2017). Novel organelles with elements of bacterial and eukaryotic secretion systems weaponize parasites of Drosophila. Current Biology, 27(18), 2869-2877. doi: 10.1016/j.cub.2017.08.019

07 Jul 2017
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Negative frequency-dependent selection is frequently confounding

Recommended by based on reviews by David Baltrus and 2 anonymous reviewers

Unmasking the delusive appearance of negative frequency-dependent selection

Explaining the processes that maintain polymorphisms in a population has been a fundamental line of research in evolutionary biology. One of the main mechanisms identified that preserves genetic diversity is negative frequency-dependent selection (NFDS), which constitutes a powerful framework for interpreting the presence of persistent polymorphisms. Nevertheless, a number of patterns that are often explained by invoking NFDS may also be compatible with, and possibly more easily explained by, different processes.
In the present manuscript [1], Brisson acknowledges first that genuine NFDS has been instrumental for our understanding on the dynamics that perpetuate polymorphisms, and that the power and importance of NFDS cannot be disregarded. Second, the author aims at identifying certain of the processes that may result in maintenance of genetic diversity, and whose outcome may be mistaken for NFDS, namely directional selection in changing environments, density-dependent fitness, multiple niche selection and community diversity. The author claims that systematic resort to NFDS as explanatory device may have lead to its application to systems where it does not apply or that do not fulfil the basic assumptions of NFDS. The author struggles in the text to provide with a precise, verbal definition of NFDS, and the exchanges with the reviewers during the recommendation process show that agreeing on such a verbal definition of NFDS is not trivial. Probably a profound mathematical formulation of the varying value of a genotype’s fitness relative to other competing ones as a function of their frequency (developing further the synthesis by Heino [2]) may still be wanting. Indeed, the text is intended for a broad audience of evolutionary biologists with operational mathematical knowledge and interest in models, rather than for modellers or biomathematicians. Nevertheless, the manuscript is rich in references to original literature, elaborates on interesting lines of thought and discussion and will hopefully trigger novel experimental and formal research to clarify the role of NFDS and to discern between alternative mechanisms that may render similar patterns of maintenance of genetic diversity.

References

[1] Brisson D. 2017. Negative frequency-dependent selection is frequently confounding. bioRxiv 113324, ver. 3 of 20th June 2017. doi: 10.1101/113324

[2] Heino M, Metz JAJ and Kaitala V. 1998. The enigma of frequency-dependent selection. Trends in Ecology & Evolution 13: 367-370. doi: 1016/S0169-5347(98)01380-9

avatar

BRAVO Ignacio

  • Laboratory MIVEGEC UMR CNRS IRD UniMontp, Centre National de la Recherche Scientifique (CNRS), Montpellier, France
  • Evolutionary Applications, Evolutionary Epidemiology, Experimental Evolution, Genome Evolution, Molecular Evolution, Other, Phylogenetics / Phylogenomics, Systematics / Taxonomy
  • recommender

Recommendations:  2

Reviews:  0

Educational and work
Academic Career 2015->> Research Director. French National Center for Scientific Research (CNRS), Montpellier, France. 2011-2015 Head of the Infections and Cancer Laboratory. Catalan Institute of Oncology (ICO), Barcelona, Spain. 2008-2011 Ramón y Cajal Research Fellow. Centre for Public Health Research (CSISP). Valencia. Spain. 2007-2008 Junior Professorship. Institute for Evolution and Biodiversity. University Münster, Münster, Germany. 2006. EMBO Short term fellowship (3 months). Laboratory Prof. Dr. Hervé Philippe. Université de Montréal, Canada. 2006-2007 Research Scientist. Laboratory Prof. Dr. Lutz Gissmann, Genome Modifications and Carcinogenesis, German Cancer Research Centre, Heidelberg, Germany. 2002-2006 Postdoctoral researcher. Laboratory Prof. Dr. Ángel Alonso Cell Differentiation, German Cancer Research Centre, Heidelberg, Germany. 1998-2002 PhD in Biology. 2002. Universidad de León, Spain. Selected recent publications Pimenoff V, Mendes de Oliveira C, Bravo IG. Transmission between Archaic and Modern Human Ancestors during the Evolution of the Oncogenic Human Papillomavirus 16. Mol Biol Evol. 2017 Jan;34(1):4-19. doi: 10.1093/molbev/msw214. Nicolás-Párraga S, Gandini C, Pimenoff VN, Alemany L, de Sanjosé S, Bosch FX and Bravo IG*. HPV16 variants distribution in invasive cancers of the cervix, vulva, vagina, penis, and anus. Cancer Med. 2016 Oct;5(10):2909-2919. doi: 10.1002/cam4.870. Mengual-Chuliá B, Bedhomme S, Lafforgue G, Elena SF, Bravo IG. Assessing parallel gene histories in viral genomes. BMC Evol Biol. 2016 Feb 5;16(1):32. doi: 10.1186/s12862-016-0605-4. Félez-Sánchez M, Trösemeier JH, Bedhomme S, González-Bravo MI, Kamp C, Bravo IG. Cancer, Warts, or Asymptomatic Infections: Clinical Presentation Matches Codon Usage Preferences in Human Papillomaviruses. Genome Biol Evol. 2015 Jul 1;7(8):2117-35. doi: 10.1093/gbe/evv129. Bravo IG and Félez-Sánchez M. “Papillomaviruses: viral evolution, cancer and evolutionary medicine". Evol Med Public Health. 2015 Jan 28;2015(1):32-51. doi: 10.1093/emph/eov003. Garcia-Perez, R, Ibanez C, Godinez JM, Arechiga N, Garin I, Perez-Suarez G, de Paz O, Juste J, Echevarria JE, Bravo IG.
 “Novel papillomaviruses in free-ranging Iberian bats: no virus-host co-evolution, no strict host specificity and hints for recombination”. 
Genome Biol Evol (2014) 6(1):94-104. doi: 10.1093/gbe/evt211 Godínez JM, Nicolás-Párraga S, Pimenoff VN, Mengual-Chuliá B, Muñoz N, Bosch FX, Sánchez GI, McCloskey J, Bravo IG. “Phylogenetically related, clinically different: human papillomaviruses 6 and 11 variants distribution in genital warts and in laryngeal papillomatosis”. Clin Microbiol Infect. (2014) 20(6):O406-13. doi: 10.1111/1469-0691.12420.