Offer title : PhD thesis (M/W) in ecology (H/F)
Reference : UMR5175-CYRVIO-007
Number of position : 1
Type of Contract : PhD Student contract / Thesis offer
Contract Period : 36 months
Start date of the thesis : 1 October 2023
Proportion of work : Full time
Remuneration : 2 135,00 € gross monthly
Section(s) CN : Biodiversity, evolution and biological adaptations: from macromolecules to communities

Title: Role of intraspecific diversity and functional rarity in regulating the functioning of natural and cultivated ecosystems

Key words : biodiversity, genetic diversity, intraspecific variability, biotic interactions, functional trait, conservation, agroecology

Description of the thesis: The aim of this thesis is to recast biodiversity-ecosystem functioning relationships by: (i) testing their robustness when intraspecific rather than interspecific diversity is manipulated, (ii) testing the role of functionally rare species or genotypes in regulating ecosystem functioning, (iii) providing a predictive framework by extending an existing theoretical development. The balance between these different objectives will depend on the interests of the person recruited. Similarly, we will adjust experimental tests on wild and/or cultivated species following the same logic.

Background : The regulation of ecosystem functioning by biodiversity is probably one of the most studied issues in ecology over the last 30 years [1]. The stakes are indeed huge. Firstly, for biodiversity: demonstrating the role played by biodiversity in regulating ecosystem functioning is a powerful argument in favor of biodiversity conservation for decision-makers.

Secondly, for ecosystems: understanding the regulatory role played by biodiversity enables us to understand and predict the effects of the biodiversity crisis on natural ecosystems, to better restore degraded ecosystems, and to propose innovative Nature-based solutions for the agrosystems of the future.

Despite decades of research, there is a striking lack of consensus in the literature on the role of biodiversity in driving ecosystem functions. There are many reasons for this, of which we will mention just two here. The first reason is a strong bias towards interspecific analyses. However, interspecific comparisons hold several limitations, including a difficulty to identify the underlying mechanisms. Genetic and phenotypic differences between species reflect a variety of evolutionary and ecological processes, which can have antagonistic effects on ecosystem functions.

Conversely, although it has been suggested that intraspecific (genetic) diversity can have a positive effect on ecosystem functioning [2], empirical demonstrations of these links remain limited. However, such a demonstration could have major implications for crop diversification through the use of “varietal mixtures” in the context of the agroecological transition of agriculture [3,4].

The second reason is the main focus of this research on the role played by the diversity of i) species (specific richness in particular) or ii) functions (e.g. functional diversity), at the expense of more detailed analyses that would make it possible to identify the potentially key role played by particular species. However, not all species within an ecosystem play the same role.

Few works suggest that a small number of “key” species perform most of the biotic regulation of ecosystem functioning [5–8]. If these results are confirmed, they will have major implications for biodiversity research and conservation. This would provide more objective elements to help prioritize the conservation of certain species over others. Furthermore, in agroecology, no publication to date has explored the role of “key” genotypes for the functioning of agroecosystems, even though the identification of “assembly rules” to maximize a set of ecosystem services is one of the main challenges of the agroecological transition.

Until now, it has been difficult to identify singular species within ecosystems and quantify their role within them. In 2017, Violle and colleagues proposed a conceptual framework to characterize the rarity of a species within an ecosystem not only in terms of its distribution, but also by the unique functions it carries, thus defining the concept of functional rarity [9]. Functional ecology has long established a list of functional traits likely to account for these functions [10]. Thus, a functionally rare species (or genotype) will be characterized by a set of trait values distinct from other species (or genotypes) within an ecosystem.

Today, a major question is whether these functionally rare species (or genotypes) contribute disproportionately to ecosystem functioning. If this were the case, it would redirect an entire field of research towards analyzing the role of species (or genotypes) rather than that of biodiversity as a whole. It would also contribute to a paradigm shift in conservation biology, which today focuses on population dynamics rather than on the functions carried out by individuals.


We propose to quantify the role of intraspecific diversity and functional rarity in regulating ecosystem functioning in plants. We will combine experimental and theoretical approaches. Depending on the candidate’s interests and preferred experimental models (wild and/or cultivated species), we will discuss the implications of the results obtained within the framework of conservation biology and/or agroecology.

The first step will be to synthesize existing work on the role of intraspecific diversity in regulating ecosystem functioning, in both wild and cultivated species. Pioneering work [2] suggested a predominant role for intraspecific diversity (genetic in particular), but no synthesis has been produced so far. In particular, we will examine the mechanisms that are directly modulated by intraspecific diversity (e.g. kin recognition).

From an experimental point of view, we will be focusing on intraspecific tests to explore the mechanisms involved. Arabidopsis thaliana is a model of choice, as we have a large collection of fully sequenced genotypes at our disposal. We will be able to experimentally assemble different genotypes in order to test different facets of intraspecific diversity (number of genotypes, genetic distances, phenotypic distances) on the regulation of the productivity of these assemblages and their stability over time.

Past work within our group has enabled us to identify functionally rare genotypes. We will set experimental designs to specifically test their role. We will unravel the mechanisms associated with the presence of these unique genotypes by studying their role in regulating biotic interactions, to test, for example, their ability to escape competition from others.

We will be flexible in terms of experimental models, depending on the candidate’s areas of interest. For instance, we can extend these experimental tests to other species of the Brassicaceae family in order to: (i) quantify the relative importance of intra- vs. interspecific diversity in regulating ecosystem functioning, (ii) identify “assembly rules” for agronomic mixtures that are less dependent on inputs, (iii) test theoretical expectations on the intraspecific diversity – interspecific diversity relationship [11].

This experimental work could also be complemented by the analysis of databases available in our group, in order to test these hypotheses along major environmental gradients on a global scale. From a theoretical point of view, we will collectively advance on a theoretical development initiated several years ago around the rapprochement of evolutionary biology and functional ecology.

This work, which has led to the foundations of a new theory (“Trait Driver Theory”) [12], suggests similar mechanisms between natural selection on a population and the effect of the environment on an entire ecosystem. This work will be carried out in collaboration with an internationally renowned laboratory at the University of Arizona in Tucson, USA (Brian Enquist’s lab).

We have scheduled two international workshops to work on this topic, and visits to Tucson are also planned. The thesis work is also part of an international working group (the “FREE” group) on functional rarity coordinated by Cyrille Violle and Lucie Mahaut. The group meets once a year at CESAB’s premises in Montpellier, in a supportive working environment, The PhD student will participate to these meetings and take an active part in this collective work.

This is a unique opportunity to enhance a PhD in an international context, and to build a network for the post-PhD career. Expected results:

The results obtained throughout the PhD project are expected to make a major contribution both to the burgeoning body of research on the study of biodiversity-ecosystem functioning relationships, and to functional ecology and conservation biology more generally.

The meta-analysis will provide an unprecedented synthesis of work on intraspecific diversity in both wild and cultivated ecosystems. Highlighting the possible role of functionally rare genotypes or species in ecosystem functioning, beyond biodiversity as a whole, will open up a new research program and provide a renewed perspective on conservation biology.

Functional ecology is still lacking theory [13], we expect that our findings will contribute building such a theory. The person recruited will participate in the work of the international FREE group, which will enable him or her to be involved in worldwide analyses of functional rarity across taxa, according to his/her areas of interest.

Work Context This PhD project is funded by the prestigious CNRS-PRIME80 program. It will be supervised by: Cyrille Violle (HDR, CNRS senior researcher, CEFE laboratory), François Vasseur (CNRS senior researcher, CEFE laboratory), Lucie Mahaut (post-doctoral researcher, CEFE laboratory) and Brian Enquist (Professor, University of Arizona).

The four supervisors have strong, complementary expertise in the various disciplines required for this thesis: functional ecology and biogeography (C. Violle), evolutionary biology and genetics (F. Vasseur), community ecology and the biodiversity-ecosystem functioning relationship (L. Mahaut), theoretical ecology and macroecology (B. Enquist). The PhD student will carry out his or her research at CEFE within the ECOPAR team headed by Cyrille Violle.

Weekly meetings will be organized with their supervisors. Most experiments will be carried out at CEFE (greenhouses, experimental field). As with any French PhD project, a steering committee (“comité de thèse”) will be organized each year. The international scope of this thesis project is very strong, as it is part of an international dynamics that the supervisors are contributing to develop. Firstly, the thesis is funded by researchers from both CEFE and the University of Arizona.

Visits to the University of Arizona are planned throughout the PhD project, both to work with Brian Enquist and his group, and to take part in international workshops. Secondly, the PhD project is fully in line with the objectives of the FRB-CESAB FREE international group on functional rarity. The person recruited will be fully integrated into the group, which is a unique opportunity for a PhD student. The FREE group meets once a year in Montpellier.

Additional Information: This PhD project is funded by the CNRS-PRIME80 program.

Cited references :
1. Hooper, D.U. et al. (2005) Effects of biodiversity on ecosystem functioning: a consensus of current knowledge. Ecological Monographs 75, 3–35
2. Hughes, A.R. et al. (2008) Ecological consequences of genetic diversity. Ecology Letters 11, 609–623
3. Gaba, S. et al. (2018) Ecology for sustainable and multifunctional agriculture. In Sustainable Agriculture Reviews 28: Ecology for Agriculture (Gaba, S. et al., eds), pp. 1–46, Springer International Publishing
4. Barot, S. et al. (2017) Designing mixtures of varieties for multifunctional agriculture with the help of ecology. A review. Agronomy for Sustainable Development 37, 13
5. Delalandre, L. et al. (2022) Functionally distinct tree species support long-term productivity in extreme environments. Proceedings of the Royal Society B: Biological Sciences 289, 20211694
6. Brun, P. et al. (2022) Plant community impact on productivity: Trait diversity or key(stone) species effects? Ecology Letters 25, 913–925
7. Mahaut, L. et al. (2020) Multiple facets of diversity effects on plant productivity: Species richness, functional diversity, species identity and intraspecific competition. Functional Ecology 34, 287–298
8. Maire, E. et al. (2018) Community-wide scan identifies fish species associated with coral reef services across the Indo-Pacific. Proceedings of the Royal Society B: Biological Sciences 285, 20181167
9. Violle, C. et al. (2017) Functional Rarity: The Ecology of Outliers. Trends in Ecology & Evolution 32, 356–367
10. Garnier, E. et al. (2016) Plant Functional Diversity: Organism traits, community structure, and ecosystem properties, Oxford University Press
11. Lamy, T. et al. (2017) The contribution of species–genetic diversity correlations to the understanding of community assembly rules. Oikos 126, 759–771
12. Enquist, B.J. et al. (2015) Scaling from traits to ecosystems: developing a general Trait Driver Theory via integrating trait-based and metabolic scaling theories. In Advances in Ecological Research 52, pp. 249–318, Elsevier
13. Enquist, B.J. (2010) Wanted: a general and predictive theory for trait-based plant ecology. BioScience 60, 854–855


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