Interview of Sonia Kefi

Sonia Kefi is a theoretical ecologist at CNRS, at the Institut des Sciences de l’Evolution de Montpellier, France. In December 2015, Sonia and two of her PhD students visited CES to work on a collaborative project with Vishwesha Guttal’s team. During her visit, Sonia also gave a talk about her work on building comprehensive ecological networks that include both trophic and non-trophic interactions (link to a paper based on this work). After her talk, I spoke to Sonia about the making of this study and her other research interests.

Interview conducted on 8 December 2015 in CES seminar hall.


HS: What brings you to India and CES?

SK: I have known Vishwesha [Guttal] since my PhD days. We met at a conference when we were both still PhD students. We were working on very similar topics, he in the US and I in the Netherlands. We have kept in touch since then. Recently, there was an opportunity to apply for an IFCAM (Indo-French Centre for Applied Mathematics) grant for a joint research project. The grant finances, for 3 years, one trip per year for each of the team members to visit the institute of the collaborator. We applied for the grant and got it. It is a great opportunity for us to start working together and for our students to be able to meet.


HS: Is this grant for work on a specific project?

SK: Yes. We are working on indicators of ecosystem degradation. From our earlier work, we have identified very broad indicators that signal whether an ecosystem is on the way to degradation or not – what people have called ‘early-warning signals’. Until now, these indicators have been studied in quite simple models, where, in particular, the external perturbation is usually completely homogenous in space. However, there are a number of cases in nature where the external pressure is clearly not homogenous. We started thinking about this because my former postdoc, Florian Schneider, was working on grazing, and he wanted to improve the realism with which grazing was introduced in those models in the context of the CASCADE project. We realised that grazers don’t eat the plants randomly, especially when the vegetation cover is fragmented. Rather, there is a higher grazer-induced mortality at the edges of the vegetation patches than in the middle because of ‘associative protection’. So, Florian started modelling the grazers’ pressure in a spatially explicit way, and he showed that this affected the behaviour of the indicators. Following up with those results, the first objective of the IFCAM project is to investigate the behaviour of the indicators of ecosystems degradation in a number of ecological models where the stress is spatially explicit – a mussel bed model, where waves are the perturbation, a forest gap model where the wind is the perturbation, a predator-prey model, where predation is the pressure, and Florian’s grazing model.


HS: I will come back to your other research interests later, but I first want to talk about the work you presented at CES yesterday. In that talk you said that most of the work on ecological networks so far has focussed on one single interaction at a time, i.e. food, mutualistic interactions like plant-pollinators and plant dispersers, and host-parasite interactions. You make the point that non-trophic interactions, especially positive ones, haven’t received as much attention in network approaches to understanding ecological communities. Why do you think this is the case? Is it because of the difficulty of identifying them in the field or have there been analytical challenges?

SK: It is probably a combination of all of that. For long, there was a bias in studying negative interactions – particularly predator-prey and competitive interactions. To some extent that makes sense, but it is also based on a certain conception of nature, the idea that those processes are the ones that structure ecological communities, the ones that we need to understand. In addition, like you say, a lot of non-trophic interactions are non-trivial to measure. Trophic interactions can often be observed – an individual eats or does not eat other individuals – but a lot of non-trophic interactions are not directly observable and require experiments. On the more theoretical side, people have built simple models (small communities) incorporating trophic and non-trophic interactions, but complex networks are often built on a single interaction type.


HS: Is this study a first of its kind – a unipartite network which includes trophic and, positive and negative, non-trophic interactions? Are there any other examples of that?

SK: Very recently, a paper from Sander, Wootton and Allesina used a similar dataset from Tatoosh Island, although this network seems to have fewer non-trophic interactions. The other work that is along the same lines is the paper from Michael Pocock (Jane Memmott’s group), published in Science in 2012. It’s based on a different approach merging several bipartite networks (plant-pollinator, plant- disperser, host-parasite, plant-herbivore and so on). For a unipartite network, I think that the Chilean web is quite unique for now, but such data sets are probably going to become more frequent in ecology.


HS: And what made this possible for you is the availability of this huge dataset from Chile, right?

SK: Yes, intertidal communities have been studied very well from the point of view on non-trophic interactions for decades, and also in an experimental way.


HS: You mean this particular intertidal community or in general?

SK: There is a long tradition of natural history and manipulative experiments in intertidal communities in general. Sergio Navarrete and Evie Wieters have done immense work in that area, but many others as well such as the teams of Robert Paine, Mark Bertness or Bruce Menge for example. I am not sure about why this tradition is there in intertidal communities. Maybe because some non-trophic interactions are particularly obvious there – e.g. refuge provisioning, competition for space, recruitment facilitation. This is why those communities are such a great opportunity to incorporate all that knowledge in a network context along with trophic interactions.


HS: I would like to talk a little more on how this collaboration came about – between you and the team in Chile. Can you tell us about the history of this project?

SK: My PhD focussed on drylands – I was working on models of vegetation dynamics. The idea was to investigate how catastrophic shifts emerge in these ecosystems. Toward the end of my PhD, it seemed natural to wonder what would happen if plants were not treated as one whole component (as classically done in models of dryland vegetation dynamics) but instead as individual species with different characteristics. The question is then how taking this plant diversity into account affects the ecosystem dynamics, its resilience and the behaviour of the indicators. This was how I started thinking about food webs and networks and how I became familiar with the body of ecological theory looking at species diversity and coexistence. I applied for a postdoc with Ulrich Brose in Germany who is a specialist of food web dynamics. My postdoc project was about studying resilience of complex ecological networks with different interactions types between species. I realised quickly that I had no idea where to introduce non-trophic links in such complex networks. The possibilities were immense. I had no idea even how frequent those interactions were. Around that time, Eric Berlow and Carol Blanchette organized a workshop in California with Sergio Navarrete, Evie Wieters, Bruce Menge, Lucas Joppa, Spencer Wood and others. I went to that workshop and that’s where the idea of building the Chilean web came up.


HS: Let’s go over the list of authors on the paper – can you tell me how each one contributed to this study?

SK: Eric Berlow organised the workshop, together with Carol Blanchette back in 2009. Eric, Sergio Navarrete, Evie Wieters and Spencer Wood are intertidal communities experts. Sergio and Evie assembled the core of the dataset. Most of the analyses were done with Lucas Joppa, Ulrich Brose and Eric.


HS: Over what period of time was the data that went into the paper collected?

SK: They did not collect field data specifically for that paper but they used their own expert knowledge of years of observation and experimentation along the central coast of Chile. They also dug into the rich literature about these communities to compile the data set. Sergio and Evie started working on the data set at the workshop in 2009, and I think that we had a first version of the ecological network in 2010.


HS: Was Ecology the first place you submitted this paper to?

SK: No, we initially submitted a much larger manuscript to Ecology Letters, in late 2010 or early 2011. That manuscript was an Ideas and Perspectives paper with the Chilean network analysis included as an illustration. But the editor felt that it was too much for one paper and asked us so to publish either the Ideas and Perspectives bit or the network. So we ended up publishing the Ideas and Perspective part in Ecology Letters in 2012. We then felt that we needed to do more analysis on the Chilean network if we wanted to publish it as an independent paper since the first version was really just presenting the dataset and some simple statistics. So, once the Ecology Letters paper was out of the way, we focused on the additional analysis. We eventually decided to submit to Ecology instead of Ecology Letters again.


HS: How long did it take from idea to publication? When did the workshop happen?

SK: The workshop took place in 2009, the Ecology Letters paper came out in 2012 and the Ecology paper in 2015.


HS: Did the authors meet as a group often?

SK: The first meeting was at the workshop in Yosemite in 2009. After that, from 2011, I have been going to Chile once a year to meet with Sergio, Evie and Eric. But, basically, most of our discussions were over email.


HS: You write in the paper that complex ecological networks are “works-in-progress” because the information on the links between species is constantly being updated. You have made available online the dataset you used for this project and invited people to contribute new information on the links. That, to my knowledge, is somewhat unique – keeping the dataset used in the paper ‘alive’. Tell us more about that.

SK: The idea came because Sergio and Evie felt that, although they were putting together all the information they were aware of, they were likely to have missed some. There are also many ongoing experiments, so that knowledge about these communities is constantly building over time. That was the motivation for the online live database. Eric funded a company that specializes in network visualisation and has develop a cloud-based software called Mappr. It provides a really nice interface where one can click on the nodes and see information about the species and pictures as well as submit new information regarding the nodes or the links.


HS: Have people already started contributing to the database?

SK: Only people we know, so far.


HS: Is the Mappr software also available to other researchers working on ecological networks?

SK: They intent to make it available for academics.


HS: Can you give us a simple step-by-step breakup of the process of going from data in the field to the final published network?

SK: Before even thinking of the data, there was enormous discussion about what type of information we needed in what format. There was then discussions with experts, going through the literature and gathering everything that’s known about every pairwise interaction of species in the dataset. There was a lot of work in making the dataset “clean” categorising every interaction as “certain” or “uncertain”. For example, maybe we found only one paper on a particular pairwise interaction which means that there is a question mark over that particular pair. Then, once the dataset was ready, there was the question of the analyses. We decided to focus on three ‘layers’ – the trophic interactions on the one hand, the non-trophic interactions on the other hand, and within non-trophic interactions whether the interactions were positive or negative. So, we split the network into three networks that we thought were most relevant for the analysis and later for incorporation into ecological theory. When we started doing statistics on the network, we went back to the field experts, to get a feel of whether the patterns emerging made sense, whether they corresponded to their intuition based on field experience. Little by little, we identified some mistakes – species that were misidentified or interactions that were mislabelled – and corrected them.


HS: What are the main take-homes from this study?

SK: It was surprising that all those non-trophic interactions were a lot more frequent than we had assumed. In the Chilean web, there are actually more than two times more non-trophic than trophic interactions. Moreover, they are structured – their structure is not random relative to the trophic interactions. So, we need to start investigating whether they matter for community dynamics and resilience and how. Can we identify key interactions and key structures in these networks that matter for the functioning of ecological systems? Collecting this kind of information is very time consuming, so the message is not that we should all start collecting all those different types of interactions everywhere, but rather that we should start investigating the possible consequences of the presence of this variety of interactions and their interplay. Mathematical models might help addressing those questions, especially now that some data sets start being available that can help constrain the structure of the modelled interactions networks.


HS: You say that modularity and nestedness are important characteristics of a network from the point of view of stability. Can you tell us why?

SK: There has been quite a lot of work on mutualistic networks that have shown that certain types of structures, like nestedness – for example, that more specialist pollinators tend to pollinate a subset of plant species pollinated by generalists – stabilize mutualistic networks, i.e. it makes them less vulnerable to breakdown when species are lost. For antagonistic networks, especially food webs, researchers have shown that a modular structure, where you have groups of species that are more connected with each other than with the rest of the web – is very stabilizing. The idea is that perturbations tend to remain within the modules or compartments. That’s why in our network we wanted to know whether we observe such structures, especially whether the trophic network is more modular than expected and whether the facilitative network is more nested than expected. We found some evidence of both modularity and nestedness in the Chilean web.


HS: In general, what would you say are the implications of this study for our understanding of how complex systems respond to external changes?

SK: We really need to go on with the next step, which is modelling such complex networks. This work has given us some hints about how to model such complex systems – where to put the non-trophic interactions, how abundant they are compared to trophic interactions etc. Based on this, we can integrate non-trophic interactions in a more realistic way into food web models and examine how they affect the stability of ecological networks to external perturbations. Right now I am unable to say more, except that we are in the process of building such models.


HS: Stepping away from this piece of work, I find a common theme underlies all the different research projects you lead – trying to understand how resilient ecological systems are to change. Is that coincidental or a conscious choice?

SK: Ecological resilience was my initial interest and probably one of the reasons why I went to ecology, particularly theoretical ecology. As a student, I was fascinated by work on the non-linear behaviour of ecosystems. I really liked mathematics and I thought that theoretical ecology would be such a nice combination of interesting mathematical questions with possible concrete applications. My original interest was trying to understand emergent phenomena and responses of complex systems to perturbations – what determines the ability of a system to absorb a perturbation and to come back to an initial state or not.


HS: Can you tell us how you got into ecology – are you a mathematician by training?

SK: No. There is this undergraduate option in France in which I had one-third biology, one-third physics and one-third maths for two years (so-called ‘classes préparatoires’). I then passed a national exam and went into an engineering school – Agro Paris Tech – where you basically pick what you want to study (in the broad field of engineering and life sciences). It’s more oriented toward life sciences but with a lot of math and computer science. In the last year of that school, I did a master in ecology at Ecole Normale Supérieure, Paris.


HS: At the undergrad. level did you already know you wanted to do ecology?

SK: When I finished high school I really wanted to do maths but I had a hard time projecting what I would do for a job if I studied pure maths. I wanted to work on questions that might have an application not too far off into the future. This is how I discovered theoretical ecology, and I thought this is what I want to do – use maths to model ecosystems.


HS: You said that you were interested in maths but wanted to do something that had an application. Is conservation and management of natural resources always at the back of your mind when you choose your research projects?

 SK: There is a double motivation. I am very interested in the fundamental understanding of these complex systems. My belief is that if we understand those mechanisms well enough, we have a chance of creating tools that might be useful for their management. The degradation indicators I am now working on have to be further developed before that can be used for management – we are still at an early stage, trying to figure out in which cases they are expected to work and how robust they are. My hope is that whenever we are more confident about the degradation indicators, they can be picked up by managers and be actually used in the field. This is one of the objectives of the European project CASCADE, which I am part of.


HS: I wanted to ask you about the early-warning signals toolbox you have developed – is that aimed mainly at managers?

SK: As it is now, the early-warning signals toolbox is more for scientists. Since we need more validation of these indicators, the idea was that the toolbox can help researchers quantify the indicators on data from different kinds of ecosystems. It would be great if it could eventually be used by managers, but there is still some work to do on our side before that – we are still in a testing phase.


HS: Have you always been a theoretical/analytical ecologist or have you also done fieldwork?

SK: My PhD was very much theoretically oriented but I was also collaborating with the team of Inma Alados (IPE-CSIC) in Spain, thanks to which I spent some time in the field during my PhD. Yolanda Pueyo, an ecologist specialized in drylands, was a postdoc in the same team as me in the Netherlands and a former student of Inma Alados. During my PhD, I went about once a year to Spain and I used to join Yolanda in the field. It wasn’t for studies that I was the leader on, but it was very interesting to go and see the ecosystems that I was modelling. Now, two of my PhD students carry out field work. Alexandre Genin does fieldwork in the ‘Réserve Naturelle des Coussouls de Crau’, which is a natural reserve in the South of France, not too far from Montpellier and Alain Danet does fieldwork in Spain, close to Alicante.

HS: From your publication list, I notice that you are involved in many projects other than the ones you lead. You are part of quite a few global multi-author papers with authors from different parts of the world. Can you tell us how you got involved in those?

SK: Most of the time, these multi-author papers are the results of workshops. For example, a couple of years ago, Martin Scheffer invited a group of people to spend a week in the Netherlands to specifically work on a project with Chi Xu, a colleague who was visiting him at the time. It was a very nice experience to work with that group of people, and two papers came out of that workshop last year. Another example is the Ideas and Perspective paper on non-trophic interactions which I mentioned earlier, which started with the workshop in Yosemite. Multi-author papers can be very exiting but they can also be very time consuming. It is great to travel and meet people, but as my career advances what I really lack is time to think. Time has become more fragmented and I struggle to find the time to focus on the core of my research interests.


HS: The core of your research is networks and critical transitions?

SK: I would say resilience of complex systems more generally. There are two ways in which I approach it – 1. through the glasses of drylands – these are the ecosystems that I have studied the most and they have interesting dynamical properties; 2. with network approaches, which provide great sets of tools to approach complex systems.


HS: Since you talked about narrowing down your interests and focussing on fewer things, I want to ask you about the transition from being a researcher to being the head of a research group – something that happened fairly recently to you. What were the main challenges in making that transition?

SK: For me the main challenge, more than at the start of my research group, was when I got the position at CNRS in 2011. When I started the new position, I realized that I now had to do many things that I would never have imagined could take up so much of my time. For me that really was the challenge – how to manage my time and, in particular, how to find a good balance between administration and science. Of course, I also supervise and mentor students, which is a great responsibility. But I have had some experience with that right from the first year of my PhD. I have learned a lot with the flow, and I try to discuss as much as possible with the students asking them what works and what doesn’t. In the team, we have regular meetings, where, besides science, we also discuss about what needs improvement. It is very important to me to try to promote a good atmosphere in the group. I am constantly trying to maintain an environment that is both stimulating and also where team members feel supported. I guess that I use a lot of my own experience, but then one also has a tendency of projecting oneself in the students, when, of course, everyone is different and everyone took a different path and has different tastes, skills and expertise. At the beginning, it’s actually very tough to give students the opportunity to develop themselves without interfering. You want to be able to supervise and give advice and you also want them not to go too far off from your own expertise because then you cannot supervise them properly anymore. At the same time, you also want to give them the opportunity of finding out what they are really interested in – what makes them really excited about science. It’s a tough balance. The other challenge is the funding – looking for funding and managing the funding.


HS: Do you enjoy these additional responsibilities that come with being the head of a research group, or do you just put up with it?

SK: I enjoy the supervising a lot. I also enjoy managing the team, trying to promote a stimulating scientific environment. Of course, that involves a number of administrative tasks that are not the reason why I went into science in the first place, but that are necessary if I want to provide a good working environment for the member of the team. What I really enjoy the most is the science itself.


HS: You are now at a stage where you do most of your research through your students. Do you miss being hands-on with the research?

SK: It is important to me to save some time to keep at least one project that is mine, for which I am the one doing the bulk of the research. I guess that this might change with time, but I would not feel as confident in supervising students if I would not be actively involved in the research myself.


HS: You also said that you find yourself with less and less time to think – do you make a conscious effort to find that time?

SK: I haven’t really found the perfect way of doing it, but I try to reserve entire half days, where I don’t have any meetings.


HS: Do you also read and write during this time, or is it meant only for thinking about your research?

SK: It can be reading, writing, coding, putting ideas on paper, but a time when I am not interrupted. I find it difficult to make good progress on my research if I have only small chunks of time. It also takes me lot of time getting back into it every time. So reserving larger chunks of time – at least three-four hours at a stretch – is important for me to keep making progress in my research projects.


HS: You are also involved in a project on the epistemology of ecology. Can you tell us a little more about that?

SK: We created the team BioDICée at the University of Montpellier a bit more than a year ago with Vincent Devictor and Julie Deter. Vincent is an ecologist working at the CNRS who is also doing a PhD in philosophy; he is the one involved in projects on the epistemology of ecology with some of his students. In the team, those topics percolate through reading papers and discussions. This helps us reflect on the concepts we study (stability, resilience, ecological community) but also on the process of doing research itself. I enjoy those discussions very much and also find them important for the way I do science.


HS: If you had to pick a favourite among the pieces of work you have done which would it be?

SK: My 2007 Nature paper was the culmination of a very exciting time during my PhD. I was working on a model of dryland ecosystems that I developed during my master’s – which was published in Theoretical Population Biology in 2007. I was reading literature on power laws and found the topic fascinating. I started studying the distribution of vegetation patch sizes in my model to see if such heavy-tail distributions were observed and under which conditions. I could compare the model outcomes with field data from my collaborators in Spain. Putting theory and data together and seeing the matching was such a nice scientific experience.


HS: Can you name a few other ecologists whose work you really like and a few papers you have enjoyed reading?

SK: The 2001 paper of Marten Scheffer was an eye opener as a student. The article of Rietkerk et al. (2004) was the foundation of my PhD work. Review papers like those of Bertness and Callaway (1994) and Bruno et al. (2003) have been very inspiring. Robert May’s papers (May 1972, May 1977) remain references that I keep reading and studying again.


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