Julien Dhinaut PhD thesis

montage-tenebrioEvolutionary ecology of immune priming in the mealworm beetle, Tenebrio molitor

Funding: ministry of research

Supervisor: Moret Yannick

Beginning of the thesis: october 2014



Many organisms can improve their immune response as a function of their immunological experience, a phenomenon called immune priming. While the mechanisms through which immune priming is achieved remain unknown, individuals that survived to a given parasite are better protected against subsequent exposures. This immune priming can cross generations (trans-generational immune priming – TGIP), preparing offspring for prevailing parasite environment. Both individual and trans-generational immune priming might be adaptive and may have evolved from repeated challenges by the same pathogens during the host lifetime or across generation. While protection could be cross-reactive, a certain level of specificity may exist in response to the range of pathogens from which immue priming may have evolved. Thus, immune priming and TGIP should be more efficient and less costly with respect to pathogens exposing the host to the greatest probability of re-infection. Moreover, it is now known that insect immune response is genetically variable. To understand the evolution of TGIP and its impact on life history evolution, we need to explore its quantitative genetics. During my thesis, I found that the expression of individual immune priming and TGIP in the mealworm beetle, Tenebrio molitor, is dependent of a range of pathogens that might have been a major selective pressure on the immune system of this insect species. This was done through the characterisation of costs and benefits of the expression of immune priming in response to challenges with a large range of bacterial pathogens. This work also highlighted potential mechanisms through which these immune phenomena could be achieved.

Costs and benefits associated to immune priming and TGIP suggest that Gram-positive bacteria might have been a major selective pressure at the origin of these phenomena in T. molitor. Whether TGIP has genetic basis still required further research.



Tenebrio molitor, trans-generational immune priming, quantitative genetics, immunology



Joël Meunier, université de Tours
Aurélie Tasiemski, université de Lille
Benjamin Gourbal, université de Perpignan
Christine Coustau, CNRS Sophia Agrobiotech
Thierry Rigaud, université de Bourgogne Franche-Comté
Yannick Moret, université de Bourgogne Franche-Comté – supervisor

Florian Raymond PhD thesis

Thumbnail imageWinter time long dry spells in the Mediterranean Basin and associated atmospheric dynamics: actual and future variability (1957-2100)

Supervisors: Pierre Camberlin and Albin Ullmann

Funding: ministerial research allocation

Beginning of the thesis: october 2014



In the context of climate change, as reflected by a dryer Mediterranean basin, this thesis focused on the study of the contemporary and future variability (1957-2100) of the wintertime (September to April) very long dry spells events (called VLDSe) in the Mediterranean basin. An original methodology was developed in this thesis in order to define VLDSe as singular climatic events, characterized by location, duration and spatial extent criteria.

76 VLDSe were detected in the Mediterranean basin on the contemporary period (1957-2013). These events are divided into 4 main geographical patterns: North-East, West, Scattered Localized and South-East. North-East and West configurations are associated with anticyclonic conditions located approximately 1 000 km northwestern to the areas affected by the VLDSe, favoring a clear sky and no precipitations. The Scattered Localized and South-East configurations are special: the first one is characterized as a residual class grouping VLDSe with small spatial extent and distributed throughout the entire basin, and the second one is characterized by seasonal VLDSe which are the continuation of the dry summer observed in the east of the Mediterranean basin.

Euro-Atlantic weather regimes have some control on the VLDSe. The positive phase of the north-atlantic oscillation regime (NAO+) is the only one that is clearly favorable to the development of VLDSe on almost the entire basin. The east-atlantic regime (EA) does not show any control on the VLDSe, and the atlantic ridge (AR) and the negative phase of the northatlantic oscillation (NAO-) regimes are generally detrimental to VLDSe. However, some VLDSe can sometimes be associated with AR, EA and NAO- regimes. This requires these three weather regimes to be associated with slightly higher atmospheric pressure northwest of the areas impacted by the VLDSe, compared to their respective climatology. Long duration of the AR, EA and NAO+ regimes, which are coupled with sustained atmospheric stability, are preferentially associated with VLDSe, in contrast to the short duration. Conversely, the long duration of the NAO- regime, reinforcing the low atmospheric pressure on Europe and the Mediterranean basin, are weakly associated with VLDSe.

Although the two climate models ALADIN52 and LMDZ4-NEMOMED8 differ in several respects, they agree in that VLDSe should be longer by 2100, especially in the RCP8.5 trajectory. A multi-model analysis with 12 CMIP5 simulations shows that wintertime sea-level pressure tends to increase in the Atlantic Ocean, off the French coast and in the central the Mediterranean basin for the RCP8.5 trajectory. Conversely, the frequency and duration of the 4 weather regimes do not show significant trends until the end of the 21st century.

Finally, a study is carried out to assess the impact of VLDSe on agricultural production in Spain. The number of VLDSe days has a larger impacts on the yields of barley, wheat and oats (winter species and cultivated through rainfed agriculture) than the simple ratio of dry days or seasonal rainfall amounts in Spain. A two-season case study, based on seasons with comparable rainfall amounts, shows that in addition to yields, a VLDSe causes a significant decrease in soil moisture and in the Ebro River flow.


Key words

Mediterranean Basin, winter droughts, atmospheric conditions, climate change, agro-environmental impacts


Steering committee

- Sylvain Bigot (UJF, LTHE, Grenoble)
- Philippe Drobinski (École pPolytechnique, LMD, Paris)
- Nicolas Martin (UNS, Espace, Nice)



Martin Beniston, université de Genève – reviewer
Vincent Moron, université d'Aix-Marseille – reviewer
Philippe Drobinski, CNRS/École polytechnique – examiner
Sylvain Bigot, université Grenoble-Alpes – examiner
Yves Tramblay, IRD/HydroSciences Montpellier  – examiner
Pierre Camberlin, université de Bourgogne-Franche Comté – supervisor de thèse
Albin Ullmann, université de Bourgogne-Franche Comté – co-supervisor)

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

Gwénaël Caravaca PhD thesis

Thumbnail imageDepositional environments and bioconstructions in the Early Triassic of western USA

funding: Agence nationale de la recherche ("After" project)

supervisors: Arnaud Brayard and Christophe Thomazo

beginning of the thesis: octobre 2014



The Sonoma Foreland Basin (SFB, western USA) presents an excellent fossil and sedimentary record of the Early Triassic (~252-248 Ma), a critical period in the biotic recovery in the aftermath of the end-Permian amss extinction. Whilst the understanding of the paleogeographical framework of this basin is of prime importance in reconstructing then ecosystems, this latter is still poorly constrained up to now.

An original integrative study has therefore been done to characterize the controlling factors and the spatio-temporal evolution of the depositional settings present in the SFB. For that, a multi-scale and multidisciplinary approach was performed, using sedimentological, paleontological, geochemical, structural and geodynamical data.

Thumbnail imageIntegration of this diverse data allows to get a better understanding of the paleogeography of the SFB, which appears to be composed by two distinct sub-basins rather than one whole basin as previsouly thought. Also, this work hightlights multi-scale controlling factors (acting from local- to basin-scale) over the 4D evolution of the depositional settings, which in turn acts over the geobiological evolution of the basin.



Early Triassic, post-crisis recovery, Sonoma Foreland Basin, western USA, paleoenvironmental reconstructions, palinspastic reconstructions, structural evolution



A. Brayard, université de Bourgogne - supervisor
C. Thomazo, université de Bourgogne - supervisor
S. Bourquin, université de Rennes 1 - abstracter
F. Boulvain, université de Liège (Belgique) - abstracter
E. Vennin, université de Bourgogne - examiner
G. Escarguel, université Claude Bernard Lyon1 - examiner
M. Guiraud, université de Bourgogne - invited

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

Romain Jattiot PhD thesis

The Smithian (Early Triassic) ammonoid diversification-extinction cycle

Funding: Swiss National Science Fondation

Supervisors: Arnaud Brayard (laboratoire Biogéosciences) and Hugo Bucher

Beginned in september 2013



The Permian-Triassic (PT) boundary mass extinction (~252 Ma) is known as the largest biodiversity crisis in the history of life, with a loss of about 80-90% of marine species. This event led to the replacement of typical Palaeozoic marine faunas by taxa typical of Modern faunas. Nevertheless, some nekto-pelagic organisms such as ammonoids rapidly recovered during the Early Triassic compared to many other marine organisms. Ammonoids reached taxonomic richness levels much higher than during the Permian in the early-middle Smithian, i.e., only ~1 myr after the PT crisis. Then, the late Smithian witnessed the most severe intra-Triassic crisis affecting the nekton. This late Smithian event turns out to be of equal or larger magnitude than that of the PT boundary mass extinction. Thus, the Smithian is a crucial time interval recording the first global, major ammonoid diversification-extinction cycle after the PT boundary mass extinction. Although Smithian ammonoids have received a steadily increasing attention from the earth science community in the last decade, in-depth investigations on Smithian ammonoid taxonomy, biostratigraphy and biogeography are still of paramount importance in the frame of studies on the Early Triassic biotic recovery. This dissertation particularly focuses on material from Timor Island and from the western USA basin, both areas being recognized as including an exceptional record of Smithian ammonoids.

As a first step towards an all-encompassing understanding of the Smithian ammonoid diversification- extinction cycle, we reinvestigate in the first part of this dissertation the late Smithian ammonoid extinction and its emblematic taxon: Anasibirites Mojsisovics. The number of valid species that should be included in this genus is a highly relevant question when analysing this extinction at the highest possible taxonomic resolution. Taking intraspecific and ontogenetic variations into account, our revised taxonomy of Anasibirites leads to a substantial amendment of the magnitude of this late Smithian event. Accordingly, the severity of this extinction is likely greater than previously assumed.

The second part of this dissertation is devoted to Smithian ammonoids from Palomino Ridge, Nevada. This section was initially discovered in 1967 by Norm Silberling, but its stratigraphic succession and associated faunas have never been described till now. More than a thousand ammonoid specimens were collected with a detailed bedrock stratigraphic control, leading to a monographic work on their taxonomy and systematics. One new genus (Palominoceras) and one new species (Pseudosageceras bullatum) are described. We also provide the first quantitative Smithian ammonoid biochronological scheme for the western USA basin, using the Unitary Associations method.

In the third part of this dissertation, the biogeography of Smithian ammonoids is investigated quantitatively within the western USA basin, i.e., at a regional scale finer than all Early Triassic ammonoid biogeographical studies achieved so far. Previous studies identified a subdivision between the northern part and the southern part of this basin in terms of thickness and dominant lithologies of the sedimentary record, as well as subsidence rates. This N/S subdivision is also qualitatively perceptible in the distribution of ammonoid faunas within the basin, but it remained to be quantitatively analysed based on a large dataset covering the entire basin and as many depositional environments as possible. Potential parameters controlling the distribution and abundance of ammonoids at this mesoscale are discussed.

Finally, in a fourth part, a tremendous collection of Smithian ammonoids from Timor Island was examined. This region has long been recognized for yielding extraordinarily well-preserved Early Triassic ammonoids. The considerable amount of specimens, treated into a comprehensive monograph, made it possible to thoroughly revise their taxonomy, with a special emphasis on ontogeny and covariation between shell shape and ornamentation. Based on the unprecedented assessment of intraspecific variation for many species, their synonymy is discussed in details whenever possible. One new genus (Roopnarinites) and five new species (Paraspidites bicarinatus, Flemingites lidakensis, Subflemingites bihatiense, Baidites obesus and Churkites warei) are also described. These results have a direct impact on the accuracy of diversity counts at the species level, which is important for potential future broad-scale diversity analyses. This material also provides highly valuable data for comprehensive biogeographical and phylogenetic studies hopefully to come.



Ammonoids, Early Triassic biotic recovery, paleobiogeography, taxonomy, Smithian, western USA basin, Timor



M. Arnaud Brayard, Director
M. Hugo Bucher, Co-director
M. Emmanuel Fara, Examiner
M. Marcelo Sanchez, Examiner
M. Neil Landman, Reviewer
M. Dieter Korn, Reviewer

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)