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[Cesab] Bonnes pratiques pour une recherche reproductible en écologie numérique

Le Cesab de la FRB et le GDR EcoStat proposent une formation sur cinq jours intitulée Bonnes pratiques pour une recherche reproductible en écologie numérique. L’objectif de cette formation est de former de jeunes chercheurs / chercheuses aux outils de reproductibilité, de développement logiciel et de gestion de versions (e.g. R, git, markdown, tidyverse) appliqués à la recherche en biodiversité.
Cette formation, dispensée en français, sera ouverte aux jeunes chercheurs / chercheuses évoluant dans le domaine de la biodiversité (doctorant(e)s, post-doctorant(e)s, ingénieur(e)s). Les pré-inscriptions se font en remplissant le formulaire disponible via le lien ci-dessous et se clôtureront le vendredi 8 novembre 2019, à minuit. Le nombre de places étant limité, les inscriptions seront confirmées au plus tard le mercredi 13 novembre 2019.
Le prix de la formation s’élève à 350 € pour la semaine et inclut les repas du midi. Les frais de transport, d’hébergement et les repas du soir sont à la charge des participant(e)s. Les étudiant(e)s appartenant aux laboratoires membres du GDR EcoStat peuvent, solliciter une aide financière de la part du GDR.
Liste des intervenants (par ordre alphabétique) :
  • Nicolas CASAJUS (FRB-Cesab)
  • Stéphane DRAY (CNRS LBBE)
  • Olivier GIMENEZ (CNRS Cefe)
  • Loreleï GUÉRY (IRD Marbec)
  • François GUILHAUMON (IRD Marbec)
  • Nina SCHIETTEKATTE (Criobe)

[FRB-CESAB] First CESAB Workhop

From 2 to 6 December, the FRB’s Center for the Synthesis and Analysis of Biodiversiry (CESAB) and the GDR EcoStat organised a training course entitled Good Practices for Reproducible Research in Digital Ecology.



17 students, engineers and researchers from all over France came to attend this training at CESAB’s premises in Montpellier.


Nicolas CASAJUS (FRB-Cesab), Stéphane DRAY (CNRS LBBE), Olivier GIMENEZ (CNRS Cefe), Loreleï GUÉRY (IRD Marbec), François GUILHAUMON (IRD Marbec), Nina SCHIETTEKATTE (EPHE Criobe) presented the essential tools for reproducible research (git/GitHub, rmarkdown, drake, R packages, etc.). Participants put into practice the knowledge acquired at the beginning of the training through projects in sub-groups. Everyone left satisfied with this experience.


Building on this success, a second edition will be organised in 2020. Subscribe to the newsletter of the FRB and its CESAB to be kept informed.


Formation Cesab décembre 2019

[FRB-CESAB] Challenges and opportunities in large-scale conservation


The working group Pelagic from the Centre for the Synthesis and Analysis of Biodiversity (CESAB) will hold a symposium in Montpellier on Friday the 29th of November 2019. During this symposium a groups of international researchers will present the new challenges associated with monitoring both wildlife and human activities in Protected Area using up to date technologies. 



Organizing Committee:
  • David MOUILLOT (University of Montpellier, FR)
  • Tom LETESSIER (Zoological Society of London, UK)


  • Jessica MEEUWIG (University of Western Australia, AU)
  • Tom LETESSIER (Zoological Society of London, UK)
  • Marc CHAUMONT (University of Nîmes, LIRMM, FR)
  • Ana NUNO (University of Exeter, UK)
  • Rachel JONES (Zoological Society of London, UK)

Analytic report on the use of DSI on genetic resources for food and agriculture

The main findings of the report were therefore:


  • To propose an appellation to replace the term “digital sequence information” with “digital data on genetic resource sequences” or “digital sequence data”;
  • To define a typology following the chronology of the bioinformatics protocol for processing sequencer data outputs: raw data, cleaned data, analysed data;
  • To list the main applications of this digital data.



The report was launched during a seminar that took place on Monday, 8 October, at the House of Oceans in Paris. The seminar was attended by almost 50 people with different backgrounds (representatives of ministries, diplomats, researchers, industrialists, journalists). The seminar’s meeting minutes and the speakers’ presentations are available on the FRB website.

[FRB-CESAB] Two calls open early December 2019

  • Joint call FRB-CESAB / CIEE : launch December 3, 2019

Biodiversity in a time of global change


The Canadian Institute of Ecology and Evolution (CIEE) and the Centre for the Synthesis and Analysis of Biodiversity (CESAB) of the French Foundation for Biodiversity Research (FRB) offer a joint call for working groups that include researchers based primarily in Canada and France, on the topic “Biodiversity in a time of Global Change”.


Two working groups of eight researchers will be funded for two meetings each (the first one in 2020 in Vancouver – Canada; the second one in 2021 in Montpellier – France).


The full proposals should be sent by e-mail before 31/01/2020 and the selection will be made by the 06/03/2020.


  • Joint call FRB-CESAB / CeMEB: launch December 9, 2019

Short term stays for foreign researchers (2-3 months)


The CeMEB LabEx (Mediterranean Environment and Biodiversity Centre) and the Centre for the Synthesis and Analysis of Biodiversity (CESAB) of the French Foundation for Biodiversity Research (FRB) offer financial support for hosting 2 foreign researchers for short stays at the CESAB in Montpellier (from 2 months minimum to 3 months maximum).


The full proposals should be sent by e-mail before 12/03/2020 and the selection will be made by the 15/05/2020.

Call for an ambitious COP 15 Biodiversity and for bridging the Rio conventions

The 15th Conference of the Parties (COP) to the United Nations Convention on Biological Diversity (CBD) will be held in China at the end of 2020. Countries member of the convention will be invited to announce specific commitments to biodiversity conservation.

It would be dramatic if the different states gathered on this occasion could only agree on a lower common denominator in terms of commitments and actions and if the decisions of the COP were not up to the challenge of the collapse of biodiversity.

States must commit to clear, precise, multiple and quantifiable actions, giving priority to the rapid and effective reduction of major pressure factors, while developing large-scale protection actions in order to rapidly safeguard what remains of biodiversity and restore its broad capacity for evolution.

Private stakeholders must also support this approach by working on reducing their sector-specific pressures on biodiversity.

Finally, citizens must be the driving force behind a major change in the way we consume, perceive and use biodiversity.


The two platforms of global scientific expertise, which are considering the future of biodiversity (IPBES) and of climate (IPCC), generally agree on the urgent need to quickly revise unsustainable production processes that aggravate both biodiversity erosion and climate change.


IPBES points out in its global assessment of the state of biodiversity presented in May 2019, that biodiversity is diminishing at an increasing rate, leading to the degradation of soil and ecosystem functioning. As a result, the services that humans receive from biodiversity are also declining rapidly, threatening the future of our societies. The direct drivers behind this degradation of biodiversity are well known and their respective importance has been assessed: land-use change at the expense of poorly humanized ecosystems and biotopes; exploitation, and often overexploitation, of marine and land resources; increasing chemical and physical pollution; climate change; and the multiplication of invasive alien species. All these drivers are aggravating each other and are also reinforced by indirect drivers: human population growth and the full range of socio-economic and political processes that lead to unsustainable consumption of the planet’s resources.

IPBES stresses the multiple negative impacts of intensive agricultural production systems on biodiversity, two excesses of which are now well documented. On the one hand, the excessive use of pesticides and chemical fertilizers; and on the other hand, the increase in the production of plant-based proteins for animal feed which induces long-distance trade and relocates the negative impacts in regions with high biodiversity, such as tropical forests. Projections by 2050 show that without major lifestyle changes, the erosion of biodiversity and the loss of services that humans receive from the living world will continue.


Since the publication of the IPBES Global Assessment, the IPCC has produced a report on the links between climate change and land use, including through agricultural and forestry activities. The key messages of this report are consistent with those found in the IPBES assessment on land degradation and restoration published in 2018. The IPCC report highlights the importance of the contribution of the entire world food system to the production of greenhouse gases and recalls that changes in land cover, use and condition influence regional and global climates. It also recalls that climate change is a source of increased risks to the world food system and biodiversity, risks that will become even greater as food consumption, water needs and the consumption of multiple resources continue to increase. The IPCC calls for actions to adapt to and reduce climate change by highlighting the co-benefits that biodiversity can expect from them. The IPCC therefore calls for a sustainable management of soils and ecosystems as the only way to halt their degradation, maintain their productivity and contribute to the adaptation and the reduction of climate change. The IPCC emphasizes the need to reduce food waste and other waste while also accompanying the change in diets. Finally, the IPCC stresses the need to act quickly and to focus on the short term. It also highlights in its projections the need to increase forest areas.


In addition, the Conference of the Parties to the Convention to Combat Desertification (UNCCD), the third of the Rio Conventions, was held in India in September 2019, calling for a halt to land degradation and for its restoration to preserve ecosystem functioning and services, and to enhance food security. In the New Delhi Declaration calling for investment in land conservation and for unlocking all opportunities for action, COP Desertification underlines the importance of taking into account land management solutions against global warming and for biodiversity conservation.


Finally, the New York Declaration on Forests initiative, initiated in 2014 by major research institutions, think-tanks and NGOs, noting the continuing deforestation, particularly of tropical rainforests, solemnly called for the protection and restoration of the world’s forests to preserve their biodiversity and carbon sequestration capacity, thus joining the COPs in their call for governments to engage in systemic change.


In all cases, the findings of these bodies relay the warnings made by scientists over a long period of time, and their recommendations have been acknowledged or endorsed by a majority of countries around the world. Therefore governments cannot say that the warning has not been given and that the urgency of the necessary actions in favor of biodiversity has not been highlighted. Some countries quickly made commitments, such as France which announced a significant increase in the area of national protected areas, a major initiative, but which only partially meets the needs for essential actions, particularly in the short term.


However, significant differences of opinion persist when it comes to strategies and options to restore biodiversity or to mitigate climate change.


This is the case, for example, of the inclusion of the large development of energy crop areas in the IPCC scenarios, which, on a large scale, would have a major negative impact on biodiversity – and to which IPBES drew the attention of decision-makers. The same applies to the development of BECCS (Bioenergy with Carbon Capture and Storage) energy technologies or the development of intensive afforestation strategies. It is on these topics that exchanges between climate and biodiversity experts on one hand and between the various international strategic and political coordination mechanisms (UN conventions and agencies) on the other hand should be the most significant. It is crucial to recall that the fight against climate change is not an end in itself, but an urgent and indispensable means to enable the living, human and non-human, to continue their pathways of life and evolution. The fight against climate change cannot therefore be implemented by worsening the biodiversity situation. More than ever, FRB’s slogan, “biodiversity and climate, same fight”, remains clearly relevant.


Beyond COP 15 Biodiversity, COP Desertification or the forthcoming COP Climate, the Conferences of the Parties of the three Rio Conventions must move forward together. It raises the question of the necessary global coordination of actions that are likely to put the planet on a pathway ensuring both the future of human populations and of all living beings on mainland, islands and in the seas, without simple, caricatural solutions and while respecting freedoms and cultural differences.

Facing global challenges, it is no longer possible to continue to think in silos: climate on one hand, biodiversity or desertification on the other, and to allow solutions to emerge that will be poor compromises, not allowing all the major global challenges to be addressed simultaneously and with the same level of priority.


Several alternatives are possible to make solutions recommended by international bodies relevant to all the major challenges we are facing:


  • Merge the three Rio Conventions into a single Environment Convention that would address all environmental issues under the United Nations Environment Programme, UNEP. This would make possible to consider jointly and in full synergy the challenges of climate, land desertification and biodiversity, and to provide decision-makers with suggestions for commitments and actions that would not favor the solution of one problem at the expense of others. It would also provide a stronger direct link to an updated version of the UN Sustainable Development Goals, which could then be called the Goals for a Sustainable Planet. The scientific and technological subsidiary bodies (SBSTA and SBSTTA) of the conventions would also merge. Simultaneously, it should be decided whether or not to institutionalize the relationships between the scientific expertise platforms, IPCC and IPBES, and to ensure that the merger of the three conventions, by creating a very large structure that is difficult to manage in practice, does not break their current internal dynamics.
  • Maintain the three existing COPs and establish, under UNEP, a coordinating umbrella structure to harmonize and make the decisions of the COPs more coherent and reliable. This could be a simple structure combining the secretariats of the conventions and the heads of the associated scientific expertise structures. As in the previous option, international platforms of scientific expertise would be invited to collaborate much more effectively than at present. Such an umbrella structure must be operated with a strong need for reactivity.
  • Establish a new way of operating between the Conventions so that they rely on the work of all dedicated scientific and technological support bodies (SBSTA and SBSTTA) and international scientific expertise platforms, in particular IPCC and IPBES. This option would require institutionalizing an independent platform of scientific expertise on desertification, such as the Global Soil Partnership, currently under FAO.
  • Formally and rapidly establish operational collaboration between all scientific and technical support bodies and scientific expertise platforms such as the IPCC and IPBES so that no report from one or the other is published without having benefited from the validation of the other expert groups. This may involve the publication of joint reports or an assessment of the recommendations made to the states, with a systematic exclusion of solutions that would undermine the challenges of fighting climate change, biodiversity erosion or desertification. The latter option would be the easiest to implement and the conventions would be able to work from a base of expertise that is not necessarily common, but whose recommendations have been aligned as much as possible.


In any case, it is becoming urgent to promote strong scientific consensus that can form the basis of ambitious international decisions going beyond sectoral visions and political divisions affecting our future and the future of all life forms.

[CESAB] The project FAIR_Data hosted by CESAB

The CESAB of the FRB is an internationally renowned research structure whose objective is to implement innovative work to synthesize and analyse existing data sets in the field of biodiversity.

CESAB now offers researchers the opportunity to meet and make progress on their projects combining data synthesis and biodiversity. Today, it is inaugurating a new collaboration with the FAIR project by hosting a meeting.

The growing need to make research data ” Findable, Accessible, Interoperable and Reusable” (hence the principles of FAIR data) has led to the creation of a think tank within the Montpellier academic community. The objective of this group is to apply the principles of FAIR data and to develop procedures for their implementation in different disciplinary fields: biodiversity/ecology, agronomy, engineering sciences, human and social sciences. It was set up in spring 2019 at the initiative of LabEx CeMEB, NUMEV, Agro and the DigitAg convergence institute.

The Reflection Group is meeting today for the second time with the objective of designing a data management plan and identifying the relevant terminology resources (metadata, controlled vocabularies) to produce “FAIR” data sets.



Principal Investigator :



Participants :

Cédric BOURRASSET – ATOS ; Sophie BOUTIN – Université de Montpellier ; Marie-Christine CORMIER SALEM – AGROPOLIS ; Olivier GIMENEZ – CNRS ; François GREGOIRE – ATOS ; Mylène JONQUET – LIRMM ; Carole KERDELHUE – INRA ; Anne LAURENT – Université Montpellier ; Emmanuel LE CLEZIO – Université Montpellier ; Nicolas MOUQUET – CNRS-FRB ; Loïc MAISONNASSE – ATOS ; Antoine OLGIATI – ATOS ; Andrea PARMEGGIANI – Université Montpellier  ; Pierre PERE – IRSTEA ; Pascal PONCELET – LIRMM ; Lionel TORRES – Université Montpellier ; Olivier TORRES – UPV.


Le réchauffement climatique, un bouleversement pour les écosystèmes et les scientifiques

Le changement climatique n’est pas un état problématique passager, mais bien une situation pérenne qu’il va falloir considérer dans sa globalité. Il nécessite une adaptation importante des écosystèmes et de ceux qui les étudient. Sous nos latitudes tempérées, ces changements prennent une signification particulière en modifiant la longueur relative des saisons. Or, l’arrivée du printemps rythme le cycle annuel de toute la biodiversité. La remontée printanière des températures s’accompagne d’une reprise explosive de la végétation. Les jeunes feuilles fournissent une nourriture de qualité pour une multitude d’invertébrés herbivores, aux premiers rangs desquels, les chenilles de papillons. Eux-mêmes sont alors consommés par des carnivores. Ce formidable accroissement de la biomasse va, en particulier, permettre aux prédateurs de se reproduire. Ce phénomène est cependant éphémère : les jeunes pousses tendres se chargent rapidement de tanin et deviennent indigestes. On assiste ainsi à un pic d’abondance de nourriture et chaque niveau de la chaîne alimentaire tente de se synchroniser sur le pic dont il dépend.

Biodiversity within the “Environment” theme of the 7th framework programme (2007-2010)

At the European level, biodiversity research projects can be funded through a range of tools, including the seventh framework programme for research and development (FP7) in which the “Environment” theme is recognized as a major source of funding. Indeed, the European Commission provides important funding support for a range of research projects encompassing several sub-activities, including biodiversity, as part of this FP7 “Environment” theme.



Biodiversity, a cross-disciplinary topic, not identified as such in the FP7 “Environment” theme


Within the FP7, biodiversity appears in various sub-activities: “Pressures on environment & climate”, “Marine environments”, “Sustainable management of resources”…, but there is not a unique and delimited entry point for funding biodiversity research. Consequently, assessing the results of FP7 funding for the research community working on biodiversity and associated issues is complex.

To overcome this difficulty, the FRB conducted the present study – downloadable from the resources below – based on the results of the projects submitted to the FP7. The main goal of the study is to assess the importance of biodiversity among the FP7 “Environment” theme, through the sub-activities identified. Temporal trends of funding are also assessed for the 2007-2010 period, and the relative performances of the participating countries are compared.