Montpellier Scientific Community



Botany and computational plant architecture (AMAP)

Director: Pierre Couteron pierre.couteron@cirad.fr
Research area
The Joint Research Unit Botany and computational plant architecture (AMAP) is a multidisciplinary lab which focuses on the analysis and modelling of structure, development and diversity of plants and vegetation. AMAP specifically develops interface research between applied mathematics/informatics and plant/vegetation sciences. This research encompasses basic science along with methodological and applied topics and deals with cultivated as well as natural plants in temperate, mediterranean and tropical contexts. AMAP applies biomathematics and computational techniques to characterize taxa, explore evolution of functional architecture, plant-plant interactions and dynamics of stands and crops. Diversity of plants and vegetation is a prominent topic which embraces morphological, functional and phylogenetical aspects along with ecological and biogeographic dimensions. Applied informatics is contributing through the design of innovative databases and the conception of software for the collaborative gathering, sharing and use of massive datasets, and for efficient simulations and 3D visualization of structural and functional information at plant, stands and landscape scales. AMAP is carrying out field investigations and supervises reference herbaria and collections (paleobotany) in France (Montpellier) and overseas (IRD herbaria of Cayenne and Nouméa).
Research highlights
  • Botany
  • Paleobotanyand plant evolution
  • Computer-assisted plant identificationand botanical databases
  • Plant architecture and biomechanics
  • Biomathematics and computational biology
  • Structure and dynamics of plant communities, ecosystems and landscapes
Staff profile
Research Org.
Researchers ProfessorsResearch Eng. Techn. &  admin staffPhD
UM2, CIRAD, CNRS, INRA, IRD 38 4 15 19

28
Research teams
The unit is organized into three research groups having a wide variety of disciplines, including botany, ecology, evolution, applied mathematics and informatics.

Team 1 - Diversity of plants and plant communities: Inventorying biodiversity and understanding its variations requires i) classifying species in a coherent way by combining morphological, architectural and biological knowledge with molecular approaches, ii) understanding the determinants of species' distributions and their roles in ecosystems, in order to predict the reaction of the latter to global change as well as to local modifications of the environment. This objective relies on the constitution of increasing numbers of multicriteria and reliable datasets, as well as the development of new methods of exploration, aggregation and analyses of heterogeneous repositories of information.

Team 2 - Architecture, function and evolution of plants: with the aim of understanding and predicting plant growth, plant architecture and evolution, and to identify genetic and environmental factors that affect growth and structure of actual and fossil plants. The main objectives are to: i) develop an understanding of plant architecture using morphological and anatomical traits; ii) identify phenotypic characteristics and genetic controls for structural diversity and phenotypic plasticity; iii) analyse growth and physiological processes for understanding architectural development; iv) model plant growth and integrate biophysical and physiological processes for predicting plant architectural development under cultivated and in variable ecological and climatic conditions.

Team 3 - Organisational dynamics of plant populations and landscapes: We focus on (agro)forests subjected to natural or anthropogenic disturbances in fragmented landscapes or constrained by the physical environment. The main objectives are: i) to understand emergent properties of overall stand dynamics from parsimonious models of local interactions; ii) to assess whether emergent properties allow us to infer broad scale stand characteristics from remote sensing data (inversion problem); iii) to combine structural and functional dynamic modelling for the large-scale prediction of spatio-temporal variations of stand characteristics under various scenarios of environmental forcing; iv) to integrate knowledge on ecological and biophysical processes within a context of ecological engineering applications.
Platforms and other tools

Facilities for Botany and plant systematics: IRD herbaria of Nouméa (NOU) and Cayenne (CAY); University Montpellier 2 herbarium (MPU) and collections of palaeobotany.

Platforms and software packages:

  • Pl@ntNet's web platform and tools for interactive plant identification and collaborative aggregation of data on plants featuring : Pl@ntNote (handling local datbases on plants), IDAO (computer-aided plant identification), Pl@ntNet-ID, a web tool for automated identification using content-based image retrieving
  • Xplo, and AMAPsim : software for plant architecture exploration, simulation, visualisation at different scales, for botanists, agronomists and educational purposes
  • CAPSIS, an open source software platform for forest growth/dynamics models. . ... and various other software about plant visualisation, landscape modelling, image segmentation and analysis at different scales from microscope to satellite, simulation of light interception and lidar backcscattering on 3D virtual plants.
Most important international partnerships
AMAP has a wide network of academic, scientific, technological and commercial partnerships in Europe, North America, Argentina, China, Cameroon, India, and Vietnam, with scientists in permanent positions in the latter three countries.
Facts and figures
Publications in international ranking journals
2009: 55
2008: 63
2007: 37
2006: 35
2005: 42
Representative publications
1. Meyer-Berthaud B., Decombeix A.-L. 2007. A tree without leaves. Nature, 446(7138): 861-862.
2. Gratiot N., Anthony E.J., Gardel A., Gaucherel C., Proisy C., Wells J.T. 2008. Significant contribution of the 18.6 year tidal cycle to regional coastal changes. Nature Geoscience, 1(3): 169-172.
3. Gaume L., Forterre Y. 2007. A viscoelastic deadly fluid in carnivorous pitcher plants. Plos One, 2(11) [on line http://dx.doi.org/10.1371/journal.pone.0001185]
4. Barthélémy D., Caraglio Y. 2007. Plant architecture: a dynamic, multilevel and comprehensive approach of plant form, structure and ontogeny. Annals of Botany, 99(3): 375-407. [Invited paper]
5. Barbier, N., Couteron, P., Proisy, C., Malhi, Y., 2010. The variation of apparent crown size and canopy heterogeneity across lowland Amazonian forests. Global Ecology and Biogeography, 19 (1) : 72-84.
6. Bonhomme, V., Pelloux-Prayer, H., Jousselin, E., Forterre, Y., Labat, J.-J., & Gaume, L., 2011. Slippery or sticky? Functional diversity in the trapping strategy of Nepenthes carnivorous plants. New Phytologist, published online DOI: 10.1111/j.1469-8137.2011.03696.x.
7. Decombeix, A.-L., Meyer-Berthaud, B., Galtier, J., 2011. Transitional changes in arborescent lignophytes at the Devonian/Carboniferous boundary. Journal of the Geological Society, 168 (2) : 547-557.
8. Deng, Q. Q., Zhang, X. P., Gang, Y., Jaeger, M., 2010. Multiresolution Foliage for Forest Rendering. Computer Animation and Virtual Worlds, 20 (1) : 1-23.
9. Fourcaud, T., Zhang, X. P., Stokes, A., Lambers, H., Koerner, C., 2008. Plant growth modelling and applications: the increasing importance of plant architecture in growth models. Annals of Botany, 101 (8) : 1053-1063.
10. Gaucherel, C., Griffon, S., Houet, T., Misson, L., 2010. Combining process-based models for future biomass assessment at landscape scale. Landscape Ecology, 25 (2) : 201-215.
11. Isnard S., Rowe N. 2008. Mechanical role of the leaf sheath in rattans. New Phytologist, 177(3): 643-652. 12. Isnard, S., Cobb, A. R., Holbrook, N. M., Zwieniecki, M., Dumais, J., 2009. Tensioning the helix: a mechanism for force generation in twining plants. Proceedings of the Royal Society of London. B- Biological Sciences, 276 (1667) : 2643-2650.
13. Kang, M. Z., Cournède, P. H., de Reffye, P., Auclair, D., 2008. Analytical study of a stochastic plant growth model: application to the GreenLab model. Mathematics and Computers in Simulation, 78 (1) : 57-75.
14. Munoz F., Couteron P., Ramesh B.R. 2008. Beta-diversity in spatially-implicit neutral models: a new way to assess species migration. American Naturalist, 172(1): 116-127.
15. Pélissier R., Couteron P. 2007. An operational, additive framework for diversity partitioning and beta-diversity analysis. Journal of Ecology, 95(2): 294-300.
16. Pillon, Y., Munzinger, J., Amir, H., Lebrun, M., 2010. Ultramafic soils and species sorting in the flora of New Caledonia. Journal of Ecology, 98 (5) : 1108-1116.
17. Stokes, A., Sotir, R. B., Chen, W., Ghestem, M., 2010. Soil bio- and eco-engineering in China: past experience and future priorities. Ecological Engineering, 36 (3) : 247-257.
Total annual budget
(in Euros) 2008 2009 2010
Total annual contract 4 389 000 5 751 000 6 419 000
External contracts 546 000 1 065 000 1 212 000
ANR 123 000 96 000 52 000
EU 70 000 216 000 283 000
Private sector 101 000 32 000 172 000
Others 252 000 721 000 705 000