- Data/Project manager (January 2018 - Ongoing)
- Human Genetics and Cognitive Functions (GHFC), Institut Pasteur, Paris, France
- Team leader : Pr. Thomas Bourgeron
- Postdoctoral associate (May 2017 - December 2017)
- Comparative evolution of Astyanax mexicanus and Lucifuga cavefish
- Laboratoire Évolution, Génomes, Comportement et Écologie (EGCE), Gif-sur-Yvette, France
- Advisor: Pr. Didier Casane
- Bioinformatics engineer (November 2016 - May 2017)
- High Throughput Sequencing Platform, Institut de Biologie Intégrative de la Cellule (I2BC), Gif-sur-Yvette, France
- Advisor: Dr. Claude Thermes
- PhD Student (September 2013 - December 2016)
- Tempo and mode of Astyanax mexicanus cavefish evolution
- Laboratoire Évolution, Génomes, Comportement et Écologie (EGCE), Gif-sur-Yvette, France
- Advisor: Pr. Didier Casane
- Teaching assistant, Université Paris Diderot (January 2013-May 2017)
- Second year of bachelor (64h on the period): population genetics, phylogeny, phylogeography, genetic of development
- First year of bachelor (70h on the period): Basic use of a computer (internet, searching information, office software)
- PhD in Population Genomics, Université Paris Saclay (2016)
- Title: Tempo and mode of Astyanax mexicanus cavefish evolution
- Supervisor: Pr. Didier Casane
- Laboratory: Évolution, Génomes, Comportement et Écologie (EGCE), Gif-sur-Yvette, France
- MSc in Bioinformatics, Université Paris Diderot (2013)
- BSc in Life science, Université Paris Diderot (2011)
L. Espinasa, L. Legendre, J. Fumey, M. Blin, S. Rétaux, and M. Espinasa, “A new cave locality for Astyanax cavefish in Sierra de El Abra, Mexico”, Subterranean Biology, vol. 26, p. 39-53, Jul. 2018.
M. Hassan, A. A. Namasivayam, D. DeBlasio, N. Fatima, B. Siranosian, R. G. Parra, B. Cuypers, S. Shome, A. M. Monzon, J. Fumey, and F. Rahman, “Reflections on a journey: a retrospective of the ISCB Student Council symposium series”, BMC Bioinformatics, vol. 19, no. S12, 2018.
J. Fumey, H. Hinaux, C. Noirot, C. Thermes, S. Rétaux, and D. Casane, “Evidence for late Pleistocene origin of Astyanax mexicanus cavefish”, BMC Evolutionary Biology, vol. 18, no. 1, 2018.
J. Fumey and C. Wicker-Thomas, “Mutations at the Darkener of Apricot locus modulate pheromone production and sex behavior in Drosophila melanogaster.”, Journal of insect physiology, vol. 98, p. 182–187, 2017.Abstract: Mutations at the Darkener of Apricot (Doa) locus of Drosophila melanogaster alter sexual differentiation by disrupting sex-specific splicing of doublesex pre-mRNA, a key regulator of sex determination. Here, we study the effect of seven Doa alleles and several trans-heterozygous combinations on pheromones and courtship behavior. The cuticular hydrocarbon (CHC) profile was slightly masculinized in females, with an accumulation of shorter compounds (C23 and C25) and a reduction in longer compounds (C27 and C29). The profile was feminized in males. Female cuticular profiles showed fewer dienes and female pheromones in six alleles and in the trans-heterozygotes and showed more male pheromones (tricosene and pentacosene) in three alleles (DEM, E786 and HD) and in all trans-heterozygotes. Courtship was severely affected in Doa males; in particular, males made fewer copulation attempts and copulated less with both control and Doa females. These results suggest that Doa could modulate pheromone production and sex behavior by altering sexual differentiation in the cuticle and the nervous system.
J. Fumey, H. Hinaux, C. Noirot, S. Rétaux, and D. Casane, “Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish”, bioRxiv, p. 094748, 2016.Abstract: Background: Cavefish populations belonging to the Mexican tetra species Astyanax mexicanus are outstanding models to study the tempo and mode of adaptation to a radical environmental change. They share similar phenotypic changes such as blindness and depigmentation that are the result of independent and convergent evolution. In particular they allow to examine whether their evolution involved the fixation of standing genetic variation and/or de novo mutations. Cavefish populations are currently assigned to two main groups, the so-called "old" and "new" lineages, which would have populated several caves independently and at different times. However, we do not have yet accurate estimations of the time frames of evolution of these populations. Results: First, we reanalyzed published mitochondrial DNA and microsatellite polymorphism and we found that these data do not unambiguously support an ancient origin of the old lineage. Second, we identified a large number of single-nucleotide polymorphisms (SNPs) in transcript sequences of two pools of embryos (Pool-seq) belonging to the "old" Pachón cave population and a surface population of Texas. Based on the summary statistics that could be computed with these data, we developed a method in order to 1) detect a recently isolated small population and 2) estimate its age. This approach is based on the detection of a transient increase of the neutral substitution rate in such a population. Indeed Pachón cave population showed more neutral substitutions than the surface population, which could be a signature of its recent origin. Third, when we applied this method to estimate the age of the Pachón cave population which is considered one of the oldest and most isolated cavefish populations we found that it has been isolated less than 30,000 years, that is during the Late Pleistocene. Conclusions: Although it is often assumed that Pachón cavefish population has a very ancient origin, within the range of the late Miocene to the middle Pleistocene, a recent origin of this population is well supported by our analyses of DNA polymorphism as well as by other sources of evidence. It suggests that the many phenotypic changes observed in these cavefish would have mainly involved the fixation of genetic variants present in surface fish populations and within a short period of time.
D. Casane, J. Fumey, and P. Laurenti, “L'apophénie d'ENCODE ou Pangloss examine le génome humain.”, Médecine sciences : M/S, vol. 31, no. 6-7, p. 680–686, 2015.Abstract: In September 2012, a batch of more than 30 articles presenting the results of the ENCODE (Encyclopaedia of DNA Elements) project was released. Many of these articles appeared in Nature and Science, the two most prestigious interdisciplinary scientific journals. Since that time, hundreds of other articles dedicated to the further analyses of the Encode data have been published. The time of hundreds of scientists and hundreds of millions of dollars were not invested in vain since this project had led to an apparent paradigm shift: contrary to the classical view, 80% of the human genome is not junk DNA, but is functional. This hypothesis has been criticized by evolutionary biologists, sometimes eagerly, and detailed refutations have been published in specialized journals with impact factors far below those that published the main contribution of the Encode project to our understanding of genome architecture. In 2014, the Encode consortium released a new batch of articles that neither suggested that 80% of the genome is functional nor commented on the disappearance of their 2012 scientific breakthrough. Unfortunately, by that time many biologists had accepted the idea that 80% of the genome is functional, or at least, that this idea is a valid alternative to the long held evolutionary genetic view that it is not. In order to understand the dynamics of the genome, it is necessary to re-examine the basics of evolutionary genetics because, not only are they well established, they also will allow us to avoid the pitfall of a panglossian interpretation of Encode. Actually, the architecture of the genome and its dynamics are the product of trade-offs between various evolutionary forces, and many structural features are not related to functional properties. In other words, evolution does not produce the best of all worlds, not even the best of all possible worlds, but only one possible world.
H. Hinaux, M. Blin, J. Fumey, L. Legendre, A. Heuzé, D. Casane, and S. Rétaux, “Lens defects in Astyanax mexicanus Cavefish: evolution of crystallins and a role for alphaA-crystallin.”, Developmental Neurobiology, vol. 75, no. 5, p. 505–521, 2015.Abstract: The fish Astyanax mexicanus presents, within the same species, populations of river-dwelling surface fish (SF) and blind cave-living fish. In cavefish (CF), the eyes develop almost normally during embryogenesis. But 40 h after fertilization, the lens enters apoptosis, triggering the progressive degeneration of the entire eye. Before apoptosis, the CF lens expresses early differentiation factors correctly. Here, we searched for possible late differentiation defects that would be causal in CF lens degeneration. We reasoned that crystallins, the major lens structural proteins, could be defective or misregulated. We surveyed the CF and SF transcriptomes and uncovered 14 Astyanax crystallins from the beta, gamma, lambda, mu, and zeta families. These proteins are less polymorphic and accumulate more fixed mutations, some at highly conserved positions, in CF than in SF, suggesting relaxed selection at these loci in CF. In situ hybridizations and qPCR show that crybb1c, crybgx, crygm5 are expressed at much lower levels or are not expressed in the CF lens. For the best crystallin candidates, we tested a potential causal role in CF lens apoptosis. Crybgx, crybb1c (not expressed in CF from very early on), and cryaa (previously shown to be faintly expressed in CF) failed to induce any defect when knocked-down in zebrafish embryos. However, the anti-apoptotic cryaa protected lens cells from apoptosis when reexpressed by transgenesis in CF, suggesting a cell-autonomous effect of cryaa on lens cell survival. Altogether, these data suggest that crystallin sequence evolution and expression defects may contribute to the loss of eyes in CF. © 2014 Wiley Periodicals, Inc.
- Tempo and mode of Astyanax mexicanus cavefish evolution: a population genomic reappraisal, Benelux Bioinformatics Conference 2015 Student Symposium, Antwerp (Belgium), November 2015
- Evidence of Late Pleistocene origin of Astyanax mexicanus cavefish, Astyanax International Meeting (AIM) 2015, Santiago de Queretaro (Mexico), October 2015
- Tempo and mode of Astyanax mexicanus cavefish evolution: a population genomic reappraisal, ETEE2015, Gif-sur-Yvette (France), September 2015
- Tempo and mode of Astyanax mexicanus cavefish evolution: a population genomic reappraisal, HTS-ADEFACE Symposium, Gif-sur-Yvette (France), April 2015
- Evo-devo of Astyanax mexicanus cavefish: a new time frame and its consequence on the underlying evolutionary mechanisms, Petit Pois Déridé 2014, Orsay (France), August 2014
- Tempo and mode of Astyanax mexicanus cavefish evolution: a population genomic reappraisal, IDEEV Day, Gif-sur-Yvette (France), October 2015
- Tempo and mode of Astyanax mexicanus cavefish evolution: a population genomic reappraisal, JOBIM 2015, Clermont-Ferrand (France), July 2015
- Tempo and mode of Astyanax mexicanus cavefish evolution: a population genomic reappraisal, SMBEBA 2015, Montpellier (France), May 2015
- Evo-devo of Astyanax mexicanus cavefish: a new time frame and its consequence on the underlying evolutionary mechanisms, European Conference on Computational Biology (ECCB) 2014, Strasbourg (France), September 2014
Grants & awards
- IDEEV Travel fellowships to go to AIM2015, Queretaro (Mexico) (October 2015)
- IDDEV Travel fellowships to go to ECCB2014, Strasbourg (France) (September 2014)
- RSG France - JeBiF (Association of France’s Young Bioinformatician)
- President from December 2014 to July 2017
- Board member since December 2014
- SFBI (French Society for Computational Biology)
- Board member since July 2015
- ISCB (International Society for Computational Biology)
- ESEB (European Society for Evolutionary Biology
- Chair, ISCB Student Council Symposium 2017, July 2017, Prague (Czech Republic)
- Chair, 3rd BeNeLuxFra Student Symposium, July 2017, Lille (France)
- Co-chair, 2nd BeNeLuxFra Student Symposium, November 2016, Belval (Luxembourg)
- Chair, JeBiF Workshop @ JOBIM 2016, July 2016, Lyon (France)
- Co-chair, BeNeLux Bioinformatics Conference Student Symposium, December 2015, Antwerp (Belgium)
- Chair, JeBiF Workshop @ JOBIM 2015, July 2015, Clermont-Ferrand (France)