Call for a 3-yr PhD Position in Ecology, Phylogeography and Landscape Genetics


Incorporating Phylogeographic infOrmation into niche moDels to improve species re-distribution projections under climAte waRming and habitat fragmentation: the Case of forest-dwelling specIes across European agricultural landscapeS [PODARCIS]


Climate warming and habitat fragmentation are two key components of global change that push species to redistribute or evolve to adapt to the new conditions (Lenoir & Svenning, 2015; Pecl et al., 2017). To hindcast and forecast species redistribution under past and future environmental conditions, respectively, the state-of-the-art is to use species distribution models (SDMs) (Guisan & Zimmermann, 2000). However, traditional SDMs assume that individuals from all populations of a given species respond equally to environmental changes although different populations from the same species may respond differently to environmental changes (Valladares et al., 2014). The most recent scientific literature on SDMs suggests that incorporating intraspecific variation into SDMs leads to less pessimistic redistribution projections (Pearman et al., 2010; Oney et al., 2013). Both phylogeography (Guiller & Madec, 2010; Guiller et al., 2012) and landscape genetics can provide spatially and temporally explicit information on the genetic structure and differences among populations of the same species that could be used to incorporate intraspecific variation into SDMs and thus improve redistribution projections under climate change. This PhD project entitled PODARCIS specifically aims at incorporating intraspecific variation data obtained from a union of phylogeography and landscape genetics (Rissler, 2016) into SDMs. PODARCIS is part of the EU (BiodivERsA) project Woodnet and the regional (Hauts-de-France) project Pegase. Three model species of European temperate forests will be studied throughout the PhD project: the plants Geum urbanum and Oxalis acetosella characterized by different dispersal capacities as well as the tick Ixodes ricinus considered as the main vector of the Lyme Borreliosis in Western Europe and thus implying potential public health hazards. PODARCIS rests on three basic pillars:

  • Phylogeography and historical demography to determine the phylogeographic structure of each species and to disentangle the relative impacts of past versus current climatic changes in shaping the geographic distributions of genealogical lineages;
  • Fundamental ecology to develop SDMs adapted to each genealogical lineage and to compare these lineage-specific SDMs to classical SDMs at different periods (Pleistocene and Anthropocene);
  • Landscape genetics to identify landscape and environmental features that constrain genetic connectivity and thus to account for dispersal and gene flow across the landscape.


Climate change, ecoepidemiology, forest ecosystems, landscape genetics, phylogeography, population genetics, spatial statistics, species distribution modelling


The candidate is expected to have good training in statistics or mathematical modelling and have a strong background in ecology or evolutionary biology (population genetics and phylogeography). Typical PhD candidates will have a master degree in ecology or evolutionary biology. Basic knowledge and interest in ecology and landscape genetics is required. Experience in molecular genetics and GIS knowledge will be further appreciated. Programming skills in Free and Open Source Software (FOSS) such as in the R and GRASS environments will be a clear advantage. Teamwork skills, curiosity, autonomy at work as well as good oral and written communication skills in English will also be valued.


The student will be hosted within the research unit EDYSAN (Ecologie et Dynamique des Systèmes Anthropisés, FRE 3498 CNRS – UPJV, head Prof. Guillaume Decocq), 33 rue Saint Leu, 80000 Amiens, France. EDYSAN is a young, diverse, vibrant and international research community with strong collaborative interdisciplinary ties within and beyond Amiens.


Applications (letter, CV and 2 contacts for references) should be sent to Annie Guiller, Jonathan Lenoir and Guillaume Decocq ( no later than June 15. The selected candidate will have an audition with the Doctoral Department at UPJV (Université de Picardie Jules Verne, Amiens) in the beginning of July and, if successful, will start in September 2017.


  • Guiller & Madec (2010). Historical biogeography of the land snail Cornu aspersum: a new scenario inferred from haplotype distribution in the Western Mediterranean Basin. BMC Evolutionary Biology, 10: 18
  • Guiller et al. (2012) Tracing the invasion of the Mediterranean land snail Cornu aspersum aspersum becoming an agricultural and garden pest in areas recently introduced. PLoS ONE, 7: e49674
  • Guisan & Zimmermann (2000) Predictive habitat distribution models in ecology. Ecological Modelling, 135: 147–186
  • Lenoir & Svenning (2015). Climate-related range shifts – a global multidimensional synthesis and new research directions. Ecography, 38: 15–28
  • Oney et al. (2013). Intraspecific variation buffers projected climate change impacts on Pinus contorta. Ecology and Evolution, 3: 437–449
  • Pearman et al. (2010). Within-taxon niche structure: niche conservatism, divergence and predicted effects of climate change. Ecography, 33: 990–1003
  • Pecl et al. (2017). Biodiversity redistribution under climate change: Impacts on ecosystems and human well-being. Science, 355: eaai9214
  • Rissler (2016). Union of phylogeography and landscape genetics. PNAS, 113: 8079–8086
  • Valladares et al. (2014). The effects of phenotypic plasticity and local adaptation on forecasts of species range shifts under climate change. Ecology Letters, 17: 1351–1364



The Climatic Debt Explained

I guess some of you may wonder: what the hell is the climatic debt? Well, in ecology, this term is used to refer to communities of living organisms being in a state of disequilibrium with climate (cf. the equilibrium between community composition and climatic conditions has been disrupted). This is best illustrated by time-lagged response of living organisms to climate change. The inertia of long-lived organisms such as trees or perennial plants after a climate-forcing event makes forest ecosystems particularly prone to the climatic debt.

In a recent paper led by Romain Bertrand, we found that the magnitude of the disequilibrium with climate, aka climatic debt, in understory plant communities across the French forests (see map) increases with the severity of baseline temperature conditions, the exposure to climate warming and species thermal tolerance.


I’m really proud to write these few lines, not only because this is an important result (sorry I might be biased here) but mostly because it is always inspiring, rewarding and cool to work with a good buddy on a fun topic. Romain and I discussed this idea of “explaining the climatic debt” a very long time ago. It all started in 2011, few days after Romain’s original work on the assessment of the climatic debt in french forests’ understory plant communities was published. Well, we were not smart enough to use the fancy “climatic debt” at that time but reported it as “biotic responses lagging behind climate change” instead. Anyway, the thing is that we received a thorough (and inspiring) commentary from Pieter De Frenne and his colleagues arguing that the climatic debt we found in understory plant communities of temperate deciduous forests could be the result of changes in forest management practices. The reasoning behind this argument being that the abandonment of coppicing (a traditional sylvicultural practice in Europe: see picture below) and the subsequent natural succession towards mature close forests may provide microclimatic conditions that buffer understory plant communities against macroclimate warming. This is indeed a very important hypothesis and you can learn more on the potential importance of microclimate as a moderator of plant responses to macroclimate warming by reading the excellent paper written by Pieter De Frenne and his team. Although neither their commentary nor our reply was published, this was a fruitful discussion that has generated new and exiting findings.

The seminal analyses that we provided five years ago in our reply to the commentary just involved the respective impacts of macroclimate warming and changes in understory light conditions on the magnitude of the climatic debt and demonstrated that changes in understory light conditions had a minor impact on the climatic debt, as it is also the case in the now published paper. It would have been a shame to stop there given the efforts made to provide a convincing reply (we might have been too much convincing on this). So, we elaborated a list of the potential drivers involved in the climatic debt that we observed in understory forest plant communities. In that respect, Romain went far beyond our initial list and provided a very comprehensive (23 explanatory variables) analysis of the potential determinants of the climatic debt not only involving environmental (i.e. baseline conditions and exposure to environmental changes) and anthropogenic (e.g. sylvicultural practices, land-use changes, habitat fragmentation) constraints but also plant traits and characteristics involved in persistence (e.g. species’ life span and thermal tolerance) and migration (e.g. species’ dispersal limitation) mechanisms.

Although we expected climate-change exposure to be an important determinant (plants are more likely to lag behind climate change in locations where the magnitude of the change is the highest), we were very surprised to find that both baseline temperature conditions and species’ intrinsic ability to tolerate water and thermal stresses outweigh the impact of climate-change exposure. Warmer baseline conditions (cf. lowland forests at low latitudes) contribute to a high climatic debt and yet these ecosystems are usually given less priority than cold ecosystems (e.g. mountains) in conservation biology. Similarly, species’ persistence mechanisms as a response to climate change have been neglected so far due to the strong emphasis on migration mechanisms involved in climate-driven range shifts that are particularly pronounced along the elevation gradient where short distances between isotherms allow plants to move upslope. And yet, both lowland ecosystems and persistence mechanisms are very important to consider, especially so for forest plant which dispersal abilities are very limited. Consequently and importantly, persistence mechanisms outweigh migration mechanisms in explaining the climatic debt in forest ecosystems. We also note that lowland ecosystems and warm climates in general are richer in stress-tolerant plants, which could be a reason why warmer climates are more likely to harbour plant communities lagging behind climate change.


Carpet of flowering bluebells (Hyacinthoides non-scripts) in a coppice dominated by beech (Fagus slvatica) and hornbeam (Carpinus betulus) (Vadencourt Wood, 80560 Contay, France). Due to its wide climatic-niche breadth and its affinity for moist and buffered microhabitats, bluebells likely contribute to increase the climatic debt in the understory (Photo: J. Lenoir).

Unfortunately, plants can only tolerate a limited amount of change in temperature conditions and future climate change projections suggest temperature increases that may go far beyond the thermal tolerance of plants, thus initiating local extirpation events with potential cascading effects for living organisms relying on these habitat-forming species.

PhD Opportunity on Biodiversity in Heterogeneous Environments under Contemporary Climate Change

WANTED: excellent candidates for a PhD position on “Biodiversity in heterogeneous environments“. Department of Biology at NTNU in Trondheim (Norway) can fund two PhD positions among 14 different topics. Together with Irja Ida Ratikainen (Behaviour and Evolution) and Bente Jessen Graae (Ecology), we would like to find an excellent and highly motivated candidate for going into the competition of the projects funded by the Department of Biology. Our project aims to test theories on how landscape topography with all its microclimatic variation affects species capacity to adapt or disperse in response to climate change. The approaches to study this topic will involve fieldwork, theoretical and/or macroecological methods. If this sounds interesting to you, please read more about the project here and here and then take contact with one of us before 22nd of January using the below email adresses:

Irja Ida Ratikainen:
Jonathan Lenoir:
Bente Jessen Graae:


The Niche Concept under Contemporary Climate Change

I’m proud to announce the forthcoming PhD defense of Safaa Wasof who did her PhD under my supervision at Jules Verne University of Picardie (UPJV) within the research unit “Ecologie et dynamique des systèmes anthropisés” (Edysan, FRE3498 CNRS-UPJV). Safaa’s PhD defense is scheduled on Friday 27 November at 9H00 am at the Faculty of Pharmacy (Pôle Santé Saint Charles, 1 Rue des Louvels, 80037 Amiens Cedex, France). If you are somewhere around at that time, you are welcome to join. Please find below a short summary written by Safaa. You can also read more on Safaa’s work by downloading her papers on (i) “Disjunct populations of European vascular plant species keep the same climatic niches” and (ii) “Ecological niche shifts of understorey plants along a latitudinal gradient of temperate forests in north-western Europe“, both published in Global Ecology and Biogeography.

Ecological niche under climate change: conservatism and role in the biodiversity-ecosystem functioning relationship

Abstract: The scientific literature has shown a revival of interest in the concept of the ecological niche for the recent decades. This interest was largely promoted by the increasing use of species distribution models (SDMs) to inform conservation and management strategies in relation to climate change. In this thesis, I studied and used the concept of the ecological niche to answer two research questions which are heavily debated in ecology: the niche conservatism hypothesis and the relationship between biodiversity and ecosystem functioning. The first part of my work provides the first large-scale (i.e. Europe) assessment of the niche conservatism hypothesis between distinct populations of the same species and for a large number of vascular plant species (389 species) in their native geographical range. Main results from this work suggest that niche conservatism of vascular plant species is a widespread phenomenon. However, we also found that regional differences in niche width and optimum are common suggesting that other processes including adaptive responses are at play. Hence, while we conclude positively on the legitimacy of SDMs for predicting future species distributions, our results nevertheless show the importance of considering regional variations in the key parameters of species’ realized niche (cf. niche width and optimum) as well as the key mechanisms governing them (e.g. local adaptation), in order to accurately predict how these regional subtleties within the ecological space translate into the geographical space. In the second part of my thesis, I incorporated the concept of the ecological niche into the relationship between biodiversity and the net production of aboveground biomass in understory plant communities of temperate deciduous forests in Northern France. For this purpose, we first built a new set of diversity indices capturing the idea of ecological-niche diversity and then used it as an alternative or a complementary facet of biodiversity to test its relative importance for standing biomass in comparison with other facets of biodiversity that are more commonly used in ecology (cf. taxonomic and functional diversity). Among other things, results from this work highlight the importance of considering the ecological niche of species (sensu Hutchison) as an alternative and complementary facet of biodiversity having an important impact on ecosystem functioning, particularly the net production of aboveground biomass within the forest herb layer. These new findings suggesting a strong niche conservatism and supporting the idea to use the concept of the ecological niche as a facet of biodiversity will improve our understanding and our predictions of the effect of climate change on biodiversity and therefore on ecosystem functioning.

Keywords: community ecology, ecological niche, climate change, niche conservatism, biodiversity, vascular plants, forest.

Supervisors: Dr. Jonathan Lenoir & Prof. Guillaume Decocq, UR “Ecologie et dynamique des systèmes anthropisés” (Edysan, FRE 3498 CNRS), Jules Verne University of Picardie.

Exam committee: Prof. Antoine Guisan, Department of Ecology & Evolution, University of Lausanne; Prof. Martin Diekmann, Institute of Ecology, University of Bremen; Prof. Jean-Claude Gégout, UR “Laboratoire d’étude des resources forêts bois” (UMR 1092 LERFoB), AgroParisTech-ENGREF.

Importance du Concept de Niche Ecologique en Contexte de Changement Climatique

Je suis fier d’annoncer que Safaa Wasof, étudiante en thèse à l’Université de Picardie Jules Verne (UPJV) dans l’unité de recherche “Ecologie et dynamise des systèmes anthropisés” (Edysan, FRE3498 CNRS-UPJV), soutiendra sa thèse publiquement le 27 Novembre prochain, à 9H00, en salle des thèses de la Faculté de pharmacie (Pôle Santé Saint Charles : 1 rue des Louvels, 80037 Amiens Cedex 1). Si vous êtes de passage dans les environs vous êtes la/le bienvenu(e). Ce fût un réel plaisir pour moi de travailler aux côtés de Safaa durant ces quatre dernières années (Octobre 2011 – Octobre 2015) et de co-encadrer son travail de thèse dont vous trouverez un résumé écrit par Safaa ci-dessous. Vous trouverez également plus d’informations sur les travaux de Safaa en lisant ses articles intitulés (i) “Disjunct populations of European vascular plant species keep the same climatic niches” et (ii) “Ecological niche shifts of understorey plants along a latitudinal gradient of temperate forests in north-western Europe“, tout deux publiés dans la revue Global Ecology and Biogeography.

La niche écologique en contexte de changement climatique : conservatisme et rôle dans la relation biodiversité-fonctionnement de l’écosystème

Résumé : Ces dernières décennies le concept de niche écologique a connu un véritable regain d’intérêt dans la littérature scientifique. Cet intérêt a été largement promu par l’utilisation croissante des modèles de distribution d’espèces (SDMs) pour informer sur les défis de conservation et de gestion liés aux changements globaux. Dans cette thèse, j’ai étudié et utilisé ce concept de niche écologique pour répondre à deux questions de recherches faisant l’objet d’importants débats en écologie : le conservatisme de la niche écologique et la relation entre biodiversité et fonctionnement de l’écosystème. Le premier volet de mes travaux a ainsi fournit une première estimation globale de l’hypothèse de conservation de la niche entre des populations distinctes de la même espèce et ce chez un grand nombre d’espèces vasculaires (389 espèces) dans leur aire géographique d’indigénat. Cette partie a permis de mettre en évidence que le conservatisme de la niche climatique réalisée est un phénomène répandu. Toutefois, des différences régionales dans les paramètres synthétiques de la niche (cf. l’amplitude et l’optimum de la niche) étaient fréquentes laissant la possibilité d’une adaptation locale potentielle des populations végétales au sein de chaque région. Ces résultats renforcent la légitimité des SDMs, mais ils montrent néanmoins l’importance de considérer les variations régionales de l’amplitude et de l’optimum de la niche réalisée des espèces, ainsi que les mécanismes clés qui les régissent (comme l’adaptation locale), dans les prédictions des SDMs quand il s’agit de traduire ces subtilités régionales dans l’espace géographique. Dans le deuxième volet de ma thèse, je me suis ensuite intéressée à utiliser le concept de niche écologique au service de l’étude de la relation entre biodiversité et un aspect particulier du fonctionnement des écosystèmes : la production nette de biomasse aérienne au sein de la strate herbacée forestière. Nous avons pour cela développé et intégré, pour la première fois, la notion de diversité des niches écologiques comme facette alternative ou complémentaire de la biodiversité et avons comparé son importance vis-à-vis des autres facettes de la biodiversité utilisées plus communément en écologie (cf. diversité taxonomique et fonctionnelle). Entre autres choses, cette partie a permis de démontrer l’importance de considérer la niche écologique des espèces (sensu Hutchison) en tant que facette de la biodiversité ayant un rôle important dans le fonctionnement de l’écosystème, plus particulièrement la production nette de biomasse aérienne des communautés végétales du sous-bois forestier. Dans un contexte de changement climatique, évaluer et étudier les conséquences éventuelles d’un degré élevé de conservatisme de la niche vis-à-vis des conditions climatiques sur la distribution des espèces et donc sur la biodiversité, ainsi que de comprendre la relation entre biodiversité et le fonctionnement de l’écosystème sont deux étapes incontournables pour améliorer notre compréhension ainsi que nos prédictions de l’effet du changement climatique sur la biodiversité et donc sur le fonctionnement des écosystèmes.

Mots-clés : biomasse, biodiversité, changement climatique, conservation de la niche, écologie des communautés, écologie fonctionnelle, écologie végétale, écosystème forestier, niche écologique, plantes vasculaires, productivité.

Encadrants : Dr. Jonathan Lenoir & Prof. Guillaume Decocq, UR “Ecologie et dynamique des systèmes anthropisés” (Edysan, FRE 3498 CNRS), Université de Picardie Jules Verne.

Membres du jury : Prof. Antoine Guisan, Department of Ecology & Evolution, University of Lausanne; Prof. Martin Diekmann, Institute of Ecology, University of Bremen; Prof. Jean-Claude Gégout, UR “Laboratoire d’étude des resources forêts bois” (UMR 1092 LERFoB), AgroParisTech-ENGREF.