Margot Bernardi PhD thesis

Primates hearing: between form, function, ecology and behavior

Funding: doctoral grant 'Paris sciences et lettres'

Supervisors: Sophie Montuire & Sébastien Couette

Thesis beginned in octobre 2015



The morphology of the basi-cranial elements and especially the ear structures shape have been essentially studied for taxonomic and phylogenetic purposes. Since the development of new acquisition techniques such as micro-computed tomography (µCT), new morphological data are available. Thus, interest in the inner and middle ear morphology is growing for many mammals groups. Ear plays an important role in hearing system and balance but most studies focus on balance and locomotion. Hearing is one of the central functions in survival and reproduction of mammals. Hearing sensitivity is variable among primate’s species, suggesting an adaptive selection on this function related to socio-ecological parameters. The order Primates is the third most diverse order (number of species) of mammals, but also one whose life history traits, lifestyles, behaviors and social interactions are the more diverse. The objective of this project is to quantify and understand the morphological variations of the auditory system in the Primate group. It will be discussed under four main headings:
- Maturation of the morphology of the ear during growth,
- Morphology of the ear and vocalizations,
- Morphology of the ear and socio-ecological parameters,
- Morphology of the ear and paleo-ecological and paleo-environmental assumptions in the fossil species.



primate, ear, morphology, hearing, vocalizations, paleo-ecology

Chloé Laubu PhD thesis

Thumbnail imageInfluence of social context and personality on the decision rules in mate choice

Funding: Ministry or research

Supervisor: François-Xavier Dechaume-Moncharmont

Beginning of the thesis: october 2015



Coming soon...



decision rules - heuristics - scramble competition - mate choice - personality - cognitive style - speed-accuracy trade-off - sexual selection

Paul Perron PhD thesis

Reservoirs architecture control by tectonic and lithosphere heterogeneities in intracratonic Paleozoic basins

Funding: ENGIE

uB supervisors: Michel Guiraud and Emmanuelle Vennin

ENGIE supervisor: Eric Portier, Isabelle Moretti

UPMC supervisor: Laetitia le Pouhriet

beginning of the thesis: november 2015



Paleozoic intracratonic basins (of Gondwana especially) are characterized by a slow subsidence, large wavelength of a few 100’s km, regular rejuvenation of paleohighs not easily related to global geodynamic cycles. Frequent regional unconformities, and subtle and complex facies portioning (architecture) make reservoir prediction complicated. Petroleum systems associated to these basins are among the most prolific, either as conventional plays, or as more challenging plays, such as stratigraphic traps and shales gas (oil).

Main features of these intracratonic basins are not well characterized and are still debated. The objectives of this project is therefore to adress the following questions:
Which are the driving mechanisms of these slow subsidence rate basins?
How can we characterize crustal and lithospheric deformations, and associated stress? What is the nature of the apparently permanent lithospheric & rheologogical heterogeneities through 100 millions years?
What are the control & trigger of the regular uplifts through time of inherited paleohighs and of the extensive & coeval unconformities / hiatuses?
Which are the controlling factors of the sedimentary record, the reservoir architecture and facies distribution – conventional as well as shale?



intracratonic basin, Paleozoic , heritage , heterogeneity, lithosphere

Adrien Quiles PhD thesis

Evolutionary history of microsporidia and amphipods symbioses: feminization and co-phylogeny

Funding: ANR CytoSexDet

Supervisors: Thierry Rigaud and Rémi Wattier

Beginning of the thesis: october 2016



Micropsoridia are a phylum of endosymbiotic eukaryotic microorganisms who realize their life cycle by infesting the cytoplasm of their hosts. This is a phylogenetically highly diverse phylum. Microsporidia were detected in many invertebrates and vertebrates species. Two transmissions strategies were observed, including either horizontal transmission (TH), from individual to individual within the host species or vertical transmission (TV), from the mother to its progeny. The first objective of this thesis is to explore the co-evolutionary history between microsporidia and is host for two species groups within the genus Gammarus (G. balcanicus and G. roeseli) for which the evolutionary history was recently resolved (Mamos et al 2016 ; Grabowski et al submitted). The second objective of this thesis is to focus on species Gammarus roeseli, for which the presence of three microspories, Nosema granulosis, Dictyocoela muelleri and D. roselum was demonstrated (Haine et al 2004). The TV, the feminization and the impact on the fitness of the host were clearly highlighted for N. granulosis (Haine et al 2007). The feminization character and the TV for the other two microsporidia are suspected and will be explored.



symbiosis, microsporidia, amphipods, phylogeny, hosts, parasites

Corentin Iltis PhD thesis

Insect senescence: interactions between survival, reproduction and immunity

Funding: ANR

Supervisors:  Jérôme Moreau, Philippe Louâpre and Denis Thiéry

Beginning of the thesis: october 2016



In  most  animals,  ageing  is  associated  with  a  decline  of  several  physiological functions  including  immunity  and  reproduction.  Because  immunity  and  reproduction  are  costly traits, their relative value is likely to change across an organism’s lifespan. In particular, levels of investment into  immune  defence  an  individual  should  achieve  to  itself  or  its progeny  as  function  its  age  and  its reproductive   effort   are   still   unknown.   This  project   aims   to   study   the   relationships   between reproduction,   immunity and   senescence   in   the   insect   model Tenebrio   molitor (Coleoptera, Tenebrionidae),  for  which  it  is  relatively  easy  to  manipulate  and  quantify  the investment  into reproductive effort and immunity across its lifespan. We are particularly interested in examining effects of  age-dependent  investments  into  reproduction  and immunity  on  patterns  of  senescence  (immunity, reproduction and survival). In addition, we would like to study the consequences of trans-generational immune priming (TGIP) on patterns of senescence in the offspring (in terms of immunity, reproduction and survival).



evolution, TTGI, aging, Tenebrio molitor

Adeline Roche PhD thesis

Intrinsec and extrinsec controlling factors of microbialites

Fellowship: contrat doctoral, université de Bourgogne Franche-Comté

Supervisor: Emmanuelle Vennin

beginned in october 2016



Microbial-mediated mineralization is considered as one of the main natural processes controlling CO2 levels in the atmosphere and a major structural and ecological player in the modern and in the past ecosystems. The result of this process is the formation of microbial deposits. Microbialites (organo-sedimentary structure predominantly accreted by sediment trapping, binding, and/or in situ precipitation as a result of the growth and metabolic activity of microorganisms) are found throughout the geological record and are the first bio-signatures of the early Earth and in the search for extra-terrestrial life potential. The oldest preserved fossil stromatolites in the geological record are about 3.4 billion years old and have been found in Australia and Canada. In modern natural systems, biological carbonates precipitation occurs in different forms, fabrics and in different environments (saline lagoons, hypersaline, alkaline lakes, freshwater rivers and lakes). The study of mechanisms of microbialite formation at different scales (km until nm) is critical for interpretation and understanding their origin and evolution. This multi-scale approach concern: (1) macro-scale (tectonics, climate); (2) meso-scale (hydrothermal circulation, water chemistry); (3) micro-scale (microbial - mineral interaction, mineralogy/morphology). Two fieldworks are chosen: modern (Great Salt Lake, USA) and ancient (Oligo-Miocene basin of Limagnes, France) microbialites. The results can help to answer important questions about i) carbonate formations in past (geological context) and present time (biogeochemical cycle and context of CO2 storage); ii) preservation in the fossil record of mineralization processes.



microbialites, microbial mats, mineralization, preservation

Marc Knapou PhD thesis

Thumbnail imageExtreme rainfall in the southern coastal belt of West Africa

funding: Excellence Eiffel scholarship

supervisors: Pierre Camberlin and Expédit Vissin

beginning of the thesis: september 2016



The emission of greenhouse gaze will continue despite the agreement of climate initialised at Paris in december 2015 and earth’s temperature will increase during this century. According to the IPCC, in a context of climate warming, water cycle could be intensified causing drought and heavy rainfall episodes. For exemple, the heavy rainfall whom caused flooding and mud casting in Colombia (1st april 2017) has been induced by el-Nino phenomeno.

In West Africa, origins of heavy rainfall are unknown. More, the Atlantic ocean role in occurrence of heavy rainfall remains little studied.

The most biggest towns of West Africa are localised all along the southern coastal area, inducing a high human concentration in this region of west Africa. So, people of this coastal region are exposed to damages caused by heavy rainfall.

This study will allow to well understand the spatial and time scale distribution and origins of occurrence of heavy rainfall. From these replies, warning system will be help Benin, Togo, Ghana and Côte d’Ivoire autorities to take good decisions for a better adaptation to heavy rainfall.



heavy rainfall, southern coast, West Africa

Comity members

Pierre Camberlin, Expédit Vissin, Pascal Roucou, Hervé Giordani, Théo Vischel et Etienne Houngninou

Sébastien Zito PhD thesis

Climate change impacts on phytosanitary risk evolution in north-eastern France vineyards: observations and modeling


co-funded by BIVB (Bureau Interprofessionnel des Vins de Bourgogne) and CIVC (Comité Interprofessionnel des Vins de Champagne)

Supervisors: Yves Richard and Benjamin Bois





climatic change, wine growing, grapewine diseaeses, modelisation

Antoine Perrin PhD thesis

Thumbnail imageHabitats anthropization and host-parasite interactions

Funding: école doctorale ES

Supervisors: Bruno Faivre and Stéphane Garnier

Thesis beginned in octobre 2017



Habitat fragmentation is a major threat to biodiversity, as it is responsible for populations and species declines. Despite a large body of literature focusing on the impact of fragmentation on species abundance and diversity, changes in ecological and evolutionary processes due to these two global changes remain poorly understood. This project aims to assess the effects of forest fragmentation on host-parasite interactions, with a special focus on the role of genetic diversity in host populations, and using several Caribbean bird species and avian malaria as a biological system. This project relies on a large collection of samples and data already available. Levels of hosts' infection (prevalence, parasite load, parasite diversity) assessed by molecular methods will be compared between forests more or less fragmented. In order to explore mechanisms responsible for the effect of fragmentation on the outcome of host-parasite interactions, a landscape genetic approach will be used to assess landscape connectivity and its influence on the genetic diversity of host populations. In addition, physiological costs of habitat alteration will be estimated by comparing birds' condition and immunocompetence between large/small and isolated/connected forests fragments.



habitat fragmentation, avian malaria, Caribbean, genetic diversity


Comity members

Karen McCoy, IRD Montpellier

Morgane Oudot PhD thesis

Biomineralization in cephalopods (Mollusca): molecular process and evolution


Supervisors: Frédéric Marin and Pascal Neige

Beginning of the thesis: october 2017



Cephalopods are an important class of molluscs, from which only a part of the living representatives possess a calcified shell (internal or external). The macro-evolutionary history of this clade suggests a general tendency to a shell reduction (to its complete disappearance) and shell internalization, from conserved basal forms to the most derived ones. Although phylogenetic relationships between living shell-bearing cephalopods are rather well established, molecular mechanisms of shell formation are almost entirely unknown. For example, one does not know whether the most derived cephalopods use the same ‘molecular toolbox’ as basal forms, for constructing their shell. To answer this puzzling question, this project proposes to explore the shell biomineralization of living cephalopods (nautilus, paper nautilus, cuttlefish, ram’s horn squid) by using a biochemical and proteomic approach on the calcifying shell matrix. In parallel, a structural work, based on techniques of solid-state physics (SEM, Raman spectroscopy, FT-IR, EBSD) will be performed, considering the phylogenetic context. The viability of the project is guaranteed by the combined expertise of the two project holders: cephalopod evolution and integrated analysis of evolutionary patterns (P. Neige), and carbonated biomineralization and molecular characterization of calcifying matrices (F. Marin).



biomineralization, cephalopods, evolution

Comity members

Antonio Checa (University of Granada) and Isabelle Rouget (Pierre and Marie Curie University, Paris 6)

Marion Fayard PhD thesis

Anxiety and parasitism in an aquatic invertebrate: evolutive and mechanistic approaches

Funding: French ministry of research

Supervisor: Marie-Jeanne Perrot-Minnot ; cosupervisor: Frank Cézilly

Beginned in october 2017



The need to address the existence of emotions in invertebrates such as anxiety, as well as their evolutionary significance, has been recently stressed. In addition, parasites have been evoked as modulators of anxiety in vertebrates. The aim of this research project is precisely to establish the physiological basis and adaptive consequences of anxiety in the freshwater crustacean Gammarus fossarum, as well as the role of manipulative parasites in modulating anxiety. We will first establish whether infection syndrome is comparable to a ‘syndrome of anxiety’, using phenotypic engineering. We will then address the role of the serotonergic pathway in modulating anxiety. Ultimately, we should shed light upon both the adaptive function of anxiety in gammarids, and the evolution of parasitic manipulation through the modulation of such emotional state.



Gammarus fossarum, acanthocephalan parasites, syndrome of anxiety, physiology, serotonergic, adaptive consequences

Alexandre Bauer PhD thesis

Parasitic manipulation in a multi-host context

Supervisor: Thierry Rigaud

Beginned in november 201X



Multi-host parasites may use host species differing in abundance and susceptibility to infection. These various hosts will contribute unequally to the transmission and the fitness of the parasites. The "key hosts" are those contributing significantly more to the completion of the parasite life cycle. Three non-exclusive criteria can be used to identify a key host contributing disproportionately to parasite transmission: high abundance, high exposure / susceptibility to infection, and/or large number of infective stages produced per infected individual.

Complex life-cycle parasites are, by definition, multi-host parasites because they require at least two successive host species to achieve their development. However, may also use several different host species at any stage of their cycle. Many parasites with a complex life cycle have developed the ability to manipulate several aspects of the phenotype of their intermediate hosts, including behaviour, thus increasing the probability of transmission to their definitive hosts. For these parasites, host susceptibility to manipulation should be included in the definition of a "key host" species because of its involvement in parasite transmission.

Several species of acanthocephalan manipulative parasites use Gammarus species as intermediate hosts. It has recently been shown that many cryptic species of Gammarus pulex or fossarum live in sympatry in the rivers of eastern France, bringing a new vision of the spectrum of intermediate hosts that acanthocephalans can use, and their relative contribution.

The first objective of the thesis is to carry out in two rivers a temporal monitoring of the relative frequencies of the different cryptic species of Gammarus. The aim is to know whether these frequencies are stable over time (allowing simultaneous use of all host resources by parasites), or whether they vary over time (allowing sequential use of hosts by parasites). The second objective of the thesis is to estimate the susceptibility to infection of the different cryptic species, and then their sensitivity to behavioural manipulation, by carrying out experimental infections in the laboratory.



multi-host parasites, specificity, cryptic diversity

Salomé Fabri-Ruiz PhD thesis

Thumbnail imageEcoregionalization of the Southern Ocean. Modelling Echinoids distribution with a focus on Kerguelen Islands

Funding: French ministry of research

Supervisors: Thomas Saucède (université de Bourgogne) and Bruno Danis (université libre de Bruxelles)

Beginned in october 2015



Biogeographic studies of the oceans are currently conducted according to two approaches: (1) comparative analysis of the composition and distribution of marine communities, and (2) ecoregionalisation, which define ecoregions for conservation purposes that is, biogeographic entities that differ in their biotic and abiotic characteristics. In the case of the Southern Ocean, recognized ecoregions are primarily based on oceanographic parameter analysis, with analysis of marine communities being qualitatively addressed.

Objectives of the PhD:
(1) Improve existing species distribution models to better constrain their biological realism.
(2) By combining distribution models, propose an ecoregionalisation of the Southern Ocean for echinoids faunas.
(3) Based on the available climate change scenarios, build risk maps for echoinoids assemblages. This last part will particularly focus on Kerguelen Islands, which host a large biodiversity considered particularly vulnerable to the expected changes.

Jorune Sakalauskaite PhD thesis

Proteomic approaches for archaeology and cultural heritage: characterising fossil proteins preserved in biominerals (mollusc shells)

Funding: Torino university

Supervisors: Frédéric Marin (UBFC) & Beatrice Demarchi (Unito)

Beginned in November 2017



The growing interest of biominerals and the processes underlying their formation have influenced numerous research studies in the last decades, enabling to study our geological environment, evolution and biodiversity. Proteomic approaches have become the base of in-depth studies of biominerals in these organisms, since the complex shell matrix entrapped into the biomineralized carbonate skeleton can reveal many functions and give precious insights into evolutionary processes. Even though biomineral studies gained such great attention in the last decades, too few studies have been conducted on mollusc shell proteins, considering that there are 85,000 recognized living species of highly diverse molluscs: there is a clear gap in the knowledge of the "biomolecular toolkits" of biomineralisation among these organisms. Research on intracrystalline proteins trapped within the calcite crystals has shown that protein sequences can be preserved deep in time enabling the access to hundreds-of-thousand-years old protein structures that can reveal paleobiogeochemical information and help to answer important environmental and archaeological questions.

Mollusc shells found in archaeological sites are the direct evidence of how humans exploited their environment in the past - they represent one of the most widespread and iconic raw materials used in prehistory to make jewelry. The use of certain species and the ornaments' typology can be used as a proxy for reconstructing patterns of cultural diversity, cohesiveness of local communities and changes in past societies. However, taxonomic identification of shell ornaments among prehistoric artefacts remains challenging. Working the material (e.g. polishing) and/or degradation during burial may have disguised or altered diagnostic morphological features which hampers the building of large datasets of securely-identified ornaments

My research project exploits novel technological advances in biomolecular archaeology (paleoproteomics or "ZooMS", stable isotope geochemistry) and spectroscopic techniques (for microstructural and morphological studies) to focus on the identification of shells that have been notably important for European prehistory such as Spondylidae, Unionoidae, Nassariidae and many others from Upper Palaeolithic, Mesolithic and Neolithic sites. Using  the most recent techniques in proteomics and biomolecular research, an in-depth study of the occluded shell matrix proteins will be carried out. This will give a deeper insight on mollusc shell biominerals to aid the study of conserved biomolecular toolkit responsible for biomineralization processes as well as helping to untangle the complex patterns of human mobility and use of landscape against a changing environmental backdrop during the Pleistocene and the Holocene, revealing possible routes for the exchange of materials and ideas.


Thesis advisory panel

Emmanuel Fara & Matthew Collins