Sonia Kéfi

CNRS research director

Chair of the departmentCHANGE

External Professor atSFI

Email:sonia.kefi (at)

I am a researcher at theCNRSbased in theBioDICée teamat the Institut des Sciences de l’Evolution de Montpellier (ISEM), France.

In an era of global change, my research aims at understanding how ecosystems persist and change under pressures from changing climate and land use. What makes ecosystems resilient to changes and what makes them fragile?

I combine mathematical modeling and data analysis to investigate the role of ecological interactions (in particular facilitation) in stabilizing and destabilizing ecosystems, but also to develop indicators of resilience that could warn us of approaching ecosystem shifts.


In ecological communities, interactions between species form complex networks that mediate their response to perturbations. So far, ecological network studies have typically focused on one (or a few) interaction types at a time, but data and models of webs including different interaction types simultaneously have recently become available. How and when does the diversity of interactions matter for the dynamics and resilience of ecological systems? My recent research aims at analyzing ecological networks including different types of interactions. Moving beyond unidimensional analyses of ecological networks may contribute to improving our understanding and predictive capacity of the way ecological systems respond to disturbances.

Play with the Chilean web multiplex clusters(by V. Miele)

Learn more about theANR project ECONET(2019-2022)

Some publications:Mieleet al.2019.PLoS Computational Biology.Pilosof, al.2017.Nature in Ecology and Evolution.Kéfi, S., V. Mieleet al.2016.PLOS Biology.Kéfi, S. et al. 2015.Ecology.
Kéfi, S. et al. 2012.Ecology Letters.

With the current global change, it is becoming increasingly important for us to be able to anticipate shifts in ecological communities. Shifts are often responsible for large, long-lasting changes and can result in dramatic ecological and economic consequences. Are there early warning signs that an ecosystem is loosing resilience?

Generic indicators, that can be quantified on the temporal and spatial dynamics of ecosystems, have been identified in the literature. In addition, for terrestrial ecosystems, it has been hypothesized that vegetation patchiness could be used as a signature of imminent transitions in ecosystems. Using both field data and modelling approaches,I investigate when and where these indicators can be quantified and when their predictions in terms of ecosystem degradation are reliable, with a current focus on arid ecosystems.

Arid and semi-arid ecosystems, which cover about 40% of the Earth’s terrestrial surface, are expected to be among the ecosystems most sensitive to environmental changes. There are growing concerns that climatic changes may lead to increased desertification, impacting approximately 25% of the world’s population. I am developing models of the vegetation dynamics in arid ecosystems aiming at better understanding the functioning of arid ecosystems and their response to changes in external conditions, such as grazing pressure or climate change.

Learn more about theEuropean project CASCADE(2011-2017)

R-package on spatial early warning signals(by A. Génin)

Seeherefor general information about early warning signals (with V. Dakos)

Some publications:Génin, A. et al. 2020Biological Conservation. Génin, al.2018.Methods in Ecology and Evolution. Kéfi, S. and P. Couteron. 2018.Ecological indicators.Berdugo, al.2017.Nature in Ecology and Evolution.Schneider, F.D. and S. Kéfi. 2016.Theoretical Ecology.Kéfi, al.2014.PLoS ONE.Kéfi, al.2013.Oikos.Kéfi, al.2011.Ecology Letters.Kéfi, al.2007.Theoretical Population Biology.Kéfi, S. et al. 2007.Nature.

In harsh environments, individuals can modify their habitat and make it more hospitable for themselves and/or others by relieving the environmental stress. Although evidence on the importance of such positive interactions is accumulating in a wide range of ecosystems, they are largely ignored by current models in ecology. Including positive interactions into ecological theory may be key to understanding population and community processes in physically stressful habitats. Studies already showed that positive interactions in the form of habitat amelioration can have profound effects on the spatial distribution of organisms, on their abundance, and on ecosystem resilience. I am interested in the role of positive interactions for the functioning of ecological communities.

Furthermore, despite their potential importance for community resilience, little is known about the role of positive interactions embedded in complex networks in stabilizing or destabilizing communities. The aim of a current project is to study the functional role of positive interactions in ecological networks. How do positive interactions affect the functioning of ecological communities, as well as the response of these communities to changing external conditions ?

Some publications:Danet, al. 2020.Theoretical Ecology. Danet, al.2018.Journal of vegetation science.Zélé, al.2018.Nature communications.

Danet, al.2017.Ecology and Evolution.
Kéfi, al.2016.Functional Ecology.
Kéfi, al.2007.Theoretical Population Biology.

Current post-docs and Ph.D.s

Selected publications

Kéfi, S., C. Saade, E. L. Berlow, J. S. Cabral, E. A. Fronhofer. 2022. Scaling up our understanding of tipping points. Philosophical transactions of the Royal Society B. 377: 1857.

Pilosof, S., Porter M.A., Pascual M.,Kéfi S.2017. The multilayer nature of ecological networks.Nature in Ecology and Evolution. 1:0101

Kéfi*, S., V. Miele*, E.A. Wieters, S.A. Navarrete, E.L. Berlow. 2016. How structured is the entangled bank? The surprisingly simple organization of multiplex ecological networks leads to increased persistence and resilience.PLOS Biology. DOI:10.1371/journal.pbio.100252*These authors contributed equally to the study

Kéfi, S., E. Berlow, E. Wieters, S. Navarrete, O. Petchey, S. Wood, A. Boit, L. Joppa, K. Lafferty, R. Williams, N. Martinez, B. Menge, C. Blanchette, A. Iles, U. Brose. 2012. More than a meal… Integrating non-feeding interactions into food webs.Ecology Letters. 15(4):291-300

Kéfi, S., V. Guttal, W.A. Brock, S.R. Carpenter, A.M. Ellison, V. Livina, D.A. Seekell, M. Scheffer, E.H. van Nes, V. Dakos. 2014. Early Warning signals of ecological transitions: Methods for spatial patterns.PLoS ONE. 9(3):2097

Kéfi, S., M. Rietkerk, M. van Baalen, M. Loreau. 2007. Local facilitation, bistability and transitions in arid ecosystems.Theoretical Population Biology. 71(3):267-400

Kéfi, S., M. Rietkerk, C. L. Alados, Y. Pueyo, A. ElAich, V. Papanastasis, P. C. de Ruiter. 2007. Spatial vegetation patterns and imminent desertification in Mediterranean arid ecosystems.Nature. 449(7159):213-217 Access the recommendation on F1000

All publications

Kéfi, S., C. Saade, E. L. Berlow, J. S. Cabral, E. A. Fronhofer. 2022. Scaling up our understanding of tipping points. Philosophical transactions of the Royal Society B. 377: 1857.

Dakos, V., andKéfi S. 2022. Ecological Resilience: What to Measure and How.Environmental Research Letters17:

Saade, C.,S Kéfi, C. Gougat-Barbera, B. Rosenbaum, E.A. Fronhofer. 2022. Spatial autocorrelation of local patch extinctions drives recovery dynamics in metacommunities.Proceedings of the Royal Society B289(1972), 20220543.

Rigal, S., Devictor V., Gaüzère P.,Kéfi S., Forsman JT, Kajanus MH, Mönkkönen M, Dakos V. 2022. Biotic homogenisation in bird communities leads to large-scale changes in species associations.Oikos00:1–14.doi:10.1111/oik.08756

A Vasques, M Baudena, VR Vallejo,S Kéfi, S Bautista, VM Santana, MJ Baeza, P. Maia, J.J. Keizer, M. Rietkerk.  2022. Post-fire Regeneration Traits of Understorey Shrub Species Modulate Successional Responses to High Severity Fire in Mediterranean Pine Forests.Ecosystems, 1-15.

Houngnandan, F.,S. Kéfi, T. Bockel, J. Deter. 2022. The joint influence of environmental and anthropogenic factors on the invasion of two alien caulerpae in northwestern Mediterranean. Biological Invasions 24 (2), 449-462.

Génin, A., T. Dutoit, A. Danet, A. le Priol,S. Kéfi.
Grazing and the vanishing complexity of plant association networks in grasslands.
Oikos. 130(4): 541-552.

Blog poston this paper

Danet, A., F.D. Schneider, F. Anthelme,S. Kéfi.
Indirect facilitation drives species composition and stability in drylands.
Theoretical Ecology. 14:189-203.

Thompson, P.L.,S. Kéfi, Y.R. Zelnik, L.E. Dee, S. Wang, C. de Mazancourt, M. Loreau, A. Gonzalez.
Scaling up biodiversity–ecosystem functioning relationships: the role of environmental heterogeneity in space and time.
Proceedings of the Royal Society B.288(1946).

Maestre, F., B. Benito, M. Berdugo, L. Concostrina-Zubiri, M. Delgado-Baquerizo, D. Eldridge, E. Guirado, N. Gross,S. Kéfi, Y. Le Bagousse-Pinguet,  R. Ochoa Hueso, S. Soliveres.
Biogeography of global drylands.
New Phytologist. 231(2): 540-558. doi:10.1111/nph.17395.

Battiston, F., E. Amico, A. Barrat, G. Bianconi, G. Ferraz de Arruda, B. Franceschiello, I. Iacopini,S. Kéfi, V. Latora, Y. Moreno, M. M. Murray, T. P. Peixoto, F. Vaccarino, G. Petri. 2021.
Higher-order interactions in complex networks: an opportunity for new physics.
Nature Physics. 17:1093.

Lurgi, M., N. Galiana, B.R. Broitman,S. Kéfi, E.A. Wieters, S.A. Navarrete. 2021
Geographical variation of multiplex ecological networks in marine intertidal communities
Bulletin of the Ecological Society of America 102 (1), 1-7

Génin, A., S. Lee, E.L. Berlow, S. Ostoja,S. Kéfi.
Mapping hotspots of potential ecosystem fragility using commonly available spatial data.
Biological Conservation. 241: 108388.

Kéfi, S.
Ecological Networks: from structure to dynamics.
Chapter 10 in: Theoretical ecology: Concepts and applications. Oxford University Press.

Houngnandan, F.,S. Kéfi, J. Deter.
Identifying key-conservation areas for Posidonia oceanica seagrass beds.
Biological Conservation. 246: 108546.

Gonzalez, A., R.M. Germain, D.S. Srivastava, E. Filotas, L.E. Dee, D. Gravel, M.I. O’Connor, P.L. Thompson, J. Cowles, F. Isbell, S. Wang,S. Kéfi, J. Montoya, Y. Zelnik, M Loreau.
Scaling-up biodiversity-ecosystem functioning research.
Ecology Letters. 23(4): 757-776.

Arnoldi, J.-F., S. Coq,S. Kéfi, S. Ibanez.
Positive plant-soil feedbacks trigger tannin evolution by niche construction: a spatial stoichiometric model.Journal of Ecology. 108(1): 378-391.

Lurgi, M., N. Galiana, B. Broitman,S. Kéfi, E. Wieters, S. Navarrete.
Geographical variation of multiplex ecological networks in marine intertidal communities.
Ecology. 101(11): e03165.
Related articlein the Bulletin of the ESA

van den Elsen, E., L. Stringer, C. de Ita, R. Hessel,S. Kéfi, F.D. Schneider, S. Bautista, A. Garcia Mayor, M. Baudena, M. Rietkerk, A. Valdecantos, V. Ramon Vallejo, N. Geeson, J. Brandt, L. Fleskens, L. Hemerik, P. Panagos, S. Valente, J. Jacob Keizer, G. Schwilch, M. Jucker Riva, D. Sietz, M.A. Christoforou, D.G. Hadjimitsis, C. Papoutsa, G. Quaranta, R. Salvia, I. Tsanis, I.N. Daliakopoulos, H. Claringbould, P.C. De Ruiter.
Advances in understanding and managing catastrophic shifts in Mediterranean ecosystems.
Frontiers in Ecology and Evolution.

Drake, J.M., S.M. O’Regan, V. Dakos, S. Kéfi, P. Rohani.
Alternative stable states, tipping points, and early warning signals of ecological transitions.
Chapter 15 in: Theoretical ecology: Concepts and applications. Oxford University Press.

Dominguez-Garcia, V., V. Dakos,S. Kéfi.
Unveiling dimensions of stability in complex ecological networks.
PNAS. 116(51): 25714-25720.

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Kéfi, S., V. Dominguez-Garcia, I. Donohue, C. Fontaine, E. Thébault, V. Dakos.
Advancing our understanding of ecological stability.
Ecology Letters.22(9): 1349-1356.

Kéfi, S.
Multiple Stable States and Catastrophic Shifts in Ecosystems.
In:Oxford Bibliographies in Ecology. Ed. David Gibson. New York: Oxford University Press. DOI: 10.1093/obo/9780199830060-0219

Miele, V., C. Guill, R. Ramos-Jiliberto,S. Kéfi.
Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model.
PLoS Computational Biology. 15(8): e1007269.bioRxiv.

Mayor, A.G., S. Bautista, F. Rodriguez,S. Kéfi.
Connectivity-mediated ecohydrological feedbacks and regime shifts in drylands.
Ecosystems. 22(7):1497-1511.

Gaüzere, P., G. Doulcier, V. Devictor,S. Kéfi.
A framework for estimating species-specific contributions to community indicators.
Ecological Indicators. 99: 74-82.

Berdugo, M., F.T. Maestre,S. Kéfi, N. Gross, Y. Le Bagousse-Pinguet, S. Soliveres.
Aridity preferences alter the relative importance of abiotic and biotic drivers on plant species abundance in global drylands.
Journal of Ecology. 107(1): 190-202.

Berdugo, M., S. Soliveres,S. Kéfi, F.T. Maestre.
The interplay between facilitation and habitat type drives spatial vegetation patterns in global drylands.
Ecography. 42(4): 755-767.bioRxiv.

Rebolledo, R., S.A. Navarrete,S. Kéfi, S. Rojas, P.A. Marquet.
An Open-System Approach to Complex Biological Networks.
SIAM Journal on Applied Mathematics. 79(2): 619-640.

Hutchinson, M.C., B. Bramon Mora, S. Pilosof, A.K. Barner,S. Kéfi, E. Thébault, P. Jordano, D.B. Stouffer.
Seeing the forest for the trees: Putting multilayer networks to work for community ecology.
Functional Ecology.3(2): 206-2017.

Brose, U., P. Archambault, A.D. Barnes, L.-F. Bersier, T. Boy, J. Canning-Clode,et al.
Predator traits determine food-web architecture across ecosystems.
Nature in Ecology andEvolution.3: 919-927.

Kéfi, S., P. Couteron.
Spatiotemporal patterns as early warnings of possible catastrophic shifts in stressed ecological systems.
Ecological Indicators. 94(1): 491-493.

Génin, A., S. Majumder, S. Sankaran, A. Danet, V. Guttal, F.D. Schneider,S. Kéfi.
Monitoring ecosystem degradation using spatial data and the R package spatialwarnings.
Methods in Ecology and Evolution. 9(10): 2067-2075.

spatialwarnings R package
github repositoty

Danet, A., F. Anthelme, N. Gross, S. Kéfi.
Effects of indirect facilitation on functional diversity, dominance and niche differentiation in tropical alpine communities.
Journal of vegetation science. 29(5): 835-846.

Génin, A., S. Majumder, S. Sankaran, F.D. Schneider, A. Danet, M. Berdugo, V. Guttal,S. Kéfi.
Spatially heterogeneous stressors can alter the performance of indicators of regime shifts.
Ecological Indicators. 94(1): 520-533.

Zélé, F., S. Magalhães,S. Kéfi, A.B. Duncan.
Ecology and evolution of facilitation among symbionts: causes and consequences.
Nature communications. 9 (1): 4869.

Sankaran, S., S. Majumder,S.Kéfi, V. Guttal.
Implications of being discrete and spatial for detecting early warning signals of regime shifts.
Ecological Indicators. 94(1): 503-511.

Kadowaki⁠, K., S. Nishijima⁠,S. Kéfi⁠, K.O. Kameda⁠, T. Sasaki⁠.
Merging community assembly into the regime-shift approach for informing ecological restoration.
Ecological Indicators. 85: 991-998.

Maris, V., P. Huneman, A. Coreau,S. Kéfi, R. Pradel, V. Devictor.
Prediction in ecology: promises, obstacles and clarifications.
Oikos,127(2): 171-183.

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