Intro
Professional
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At work

As you maybe do not know, the French government and president, which are in general working hard at making my country going back to the Middle-Age, are also planning to weaken French research as much as they can. Several villainous laws have thus been voted that progressively come into force. Most French researchers vigorously fight for the survival of their activity and passion: please support us by making some noise about it around you, wherever you are.

Me

I am the guy on the photo right here.
Date of birth: May 5th 1981
Place of birth: Montauban, France
Present address: UMR CNRS 5023, HBES team / Université Claude Bernard Lyon 1 / Bât. Darwin C, 43 bd du 11 novembre 1918 / F-69622 Villeurbanne Cedex / France
Email address: sebastien.calvignac@univ-lyon1.fr
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My formation

My academic formation was mainly focused on virology and immunology. Following, I began fundamental research with a first training in immunology during which I worked on the immunomodulative properties of the Core protein of HCV in the lab of Bernard Pipy in Toulouse, France.

At this point, I nearly made a topic u-turn since I started working in the paleogenetics lab of Catherine Hänni in Lyon, France. As a child, I was fascinated with paleontology. Since then I always kept on reading books about evolution. I learned the existence of Catherine's lab by chance and thought it was a unique occasion to do something really different while fulfilling my young years dream.

I first performed another research training, mainly working on ancient brown bears. Then, I went on by doing a PhD thesis whose central focus was still on extinct populations of brown bears (more particularly those from North Africa and Middle-East). Our results clearly showed that these recently extinct populations accounted for a significant part of the whole species genetic diversity. In our mind, this, together with results obtained by others on Ursus arctos phylogeographic pattern modifications through time, shows that very recent events (maybe human induced fragmentation of the habitat) rather than older climatic events (e.g. the Last Glacial Maximum) explain most of the structure of the genetic diversity found in present-day brown bears. 

In the mean time, I also had the opportunity to work on a topic I introduced in the lab: paleoretrovirology. We managed to prove that retroviruses can still be amplified from bone material aged a hundred years, which is of course of interest if we really intend to better understand the early twentieth century transspecies transmission of SIV to humans, that ultimately resulted in the AIDS pandemic.

I took part to other projects including increasing the resolution of Ursid or extinct lemur phylogenies.

I passed my PhD on November 15th 2007.
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My interests and objectives now

While much of my previous research has been based on the use of neutral genetic markers (that allow properly inferring phylogenies), the project I am now concentrating on is clearly focused on adaptive evolution.

In the group of Pierre Marmonier (HBES team, Université Claude Bernard Lyon 1, France), Christophe Douady (who is my research supervisor) is notably investigating the emblematic question of the genomic consequences of subterranean life, dealing with the case of some Crustaceans belonging to the genus Proasellus. Of course, one would expect that conditions such as those encountered by subterranean organisms drive some kind of genomic response (which does not necessarily imply that this response will tend to improve their fitness). This would be particularly true for parts of the genome controlling functions that seem to be useless underground, such as vision. Clearly, genes involved in the maintainance of this sense are expected to show important drift, due to the relaxation of environmental constraints. An important effort of sequencing is presently ongoing in the lab, focusing on a major candidate: the opsin gene. I am involved in that "genomic" part of the project, trying to acquire new sequences. Besides I am also trying to set up the conditions of experiments (other than PCRs) that would help to extend our understanding of the real consequences of the genomic variations we observe.

A mid-term objective is to obtain a position in either a French university or research organism.

My publications

Here is the list of the published works I have been involved in. When useful, articles are accompanied by suggestions of background readings.

Terme, J.M., Calvignac, S., Duc Dodon, M., Gazzolo, L. , Jordan, A. 2009. E box motifs as mediators of proviral latency of human retroviruses. Retrovirology, 6: 81.
Background: Terme et al. 2008

Calvignac, S., Hughes, S. and Hänni, C. 2009. Genetic diversity of endangered brown bear (Ursus arctos) populations at the crossroads of Europe, Asia and Africa. Diversity and Distributions, 15: 742-750.
Background: Miller et al. 2006, Calvignac et al. 2008
An interesting comparison can be made with the case of Ursus arctos sister species, Ursus spelaeus. See the article by Knapp et al. 2009.

Calvignac, S. 2009. Mito-communications. MTDNA, accepted.

Calvignac, S. 2008. [Climatic events and geographical patterns of the genetic diversity]. French. Médecine/Sciences, 24 (8): 686-8.
Background: Leonard et al. 2000, Barnes et al. 2002, Valdiosera et al. 2007

Calvignac, S. 2008. [Alternative methods for the study of simian retroviral genetic diversity]. French. Médecine/Sciences, 24 (6): 577-8.
Background: Van Heuverswyn et al. 2006, Keele et al. 2006, Calvignac et al. 2008

Orlando, L., Calvignac, S., Schnebelen, C., Douady, C.J., Godfrey, L.R. and Hänni, C. 2008. DNA from extinct giant lemurs links archaeolemurids to extant indriids. BMC Evolutionary Biology, 8:121.
Background: Karanth et al. 2005, Horvath et al. 2008

Calvignac, S., Terme, J.M., Hensley, S., Jalinot, P., Greenwood, A. and Hänni, C. 2008. Ancient DNA identification of early 20th century Simian T-Cell Leukemia Virus Type 1 (STLV-1). Molecular Biology and Evolution, 25 (6): 1093-98.
Background: Li et al. 1999, Sonoda et al. 2000, Gessain et al. 2000, Vandamme et al. 2000, Coulthart et al. 2006

Calvignac, S., Hughes, S., Tougard, C., Michaux, J., Thévenot, M., Philippe, M., Hamdine, W. and Hänni, C. 2008. Ancient DNA evidence for the loss of a highly divergent brown bear clade during historical times. Molecular Ecology, 17 (8): 1962-70.
Background: Leonard et al. 2000; Barnes et al. 2002; Hofreiter et al. 2004; Miller et al. 2006; Valdiosera et al. 2007

Pagès, M., Calvignac, S., Klein, C., Paris M., Hughes S. and Hänni, C. 2008. Combined analysis of fourteen nuclear genes refines the Ursidae phylogeny. Molecular Phylogenetics and Evolution, 47 (1): 73-83.
Background: Waits et al. 1998; Yu et al. 2004; Yu et al. 2007

Orlando, L., Pagès, M., Calvignac, S., Hughes, S. and Hänni, C. 2007. Does the 43bp sequence from an 800,000 year old Cretan dwarf elephantid really rewrite the textbook on mammoths ? Biology Letters, 3 (1): 57-59.
Background: Poulakakis et al. 2006; Binladen et al. 2007

You can download most of these articles as well as my detailed CV and my PhD thesis manuscript by going to the Downloads section that appears in the menu.


dimanche 20 septembre 2009