Researcher and Lecturer at the French Museum of natural History, UMR 7204 CNRS-UPMC, 61 rue Buffon, 75005 Paris, France
Research associate, Mathematical Ecology Research Group, Department of Zoology, University of Oxford, UK, http://merg.zoo.ox.ac.uk/
Associate editor, BMC Ecology
pavoine AT mnhn.fr
Feb 2008 - Feb 2009 Marie Curie Fellow, Mathematical Ecology Research Group, Department of Zoology, University of Oxford, South Parks Road, OX1 3PS, UK
PhD : « Statistical methods for measuring biodiversity » University Claude Bernard Lyon I, France, December 2005
I studied mathematics, population and community ecology at the University of Lyon I, France, and obtained my PhD in statistical ecology at the University of Lyon I in December 2005. I moved to the Museum of Natural History as a researcher and lecturer in Paris, France, in October 2005 and obtained a permanent position in June 2006. I spent one year as a Marie Curie fellow at the University of Oxford, UK, (from January 2008 to February 2009) and became research associate in January 2011.
30 septembre 2011
I am particularly interested in developing and studying new mathematical approaches to analyse biodiversity, population and community assembly.
Measurement and analysis of biodiversity : patterns and processes
A myriad of indices (mathematical functions) of biodiversity have been developed. Even the definition of biodiversity is so general that each discipline develops its own rules, definitions and indices. Working on the measure of biodiversity requires thus efficient communications and exchanges among disciplines, including mathematics and biology. In my research, I try to merge disciplines to analyse and measure biodiversity consistently, taking account of temporal, evolutionary or spatial scales. In this framework, I am particularly interested in indices that include measures of abundances and differences among organisms (based on genetics, phylogeny, life history, behaviour, physiology, etc). These researches are made in the contexts of Conservation Biology and Ecology. They also have consequences for any disciplines interested in measuring an aspect of diversity, and they are cited for instance in Genetics, Medicine, Microbiology and also Computer science, Physics, Economics.
Among all aspects of biodiversity, acoustic diversity is particularly under-explored. A classical approach to assess biodiversity richness is to determine the number of species present. However, inventorying all species in a place might be invasive and costly. In contrast, acoustic approaches might be non-invasive, while producing lots of data. Part of the animal biodiversity produces sounds. These sounds can be recorded by field-based sensors. The recorded acoustic data can be used to estimate a level of local acoustic richness. Multiplying the recordings in many places at many times would enable the comparison of levels of biodiversity in space and time. We are particularly interested in developing measures of the complexity and diversity of the sounds recorded (bio-sounds) without species identifications.
Ecology and Community dynamics
The process of community assembly involves ecological, evolutionary and stochastic processes. They structure the functional (trait) and phylogenetic diversities of communities in space and time. Biodiversity partitioning based on explanatory factors and factorial analyses are two key approaches to analyse how communities assemble. Partitioning biodiversity is for instance finding the contribution of a factor to the diversity of a community or to the differences among communities. Factorial analyses are in essence mathematical, geometric, multivariate methods. Under certain conditions, they enable a description of biodiversity at different scales, for instance of the differences among species and communities in terms of genes, traits or phylogenies. My research interest in this field concerns the developments of partitioning and factorial methods to identify traits and clades involved in ecological mechanisms including environmental filtering and limiting similarity.
One aspect of diversity which is increasingly used in conservation biology is phylogenetic diversity. It is expected that phylogenetic diversity reflects diversity of characters, even characters still unidentified. Measures have been developed to provide an overall assessment of the phylogenetic diversity of a set of species and its future. Another point of view focuses on the contribution of each species to the phylogenetic diversity, leading to the notion of originality of a species. A species is original, from a phylogenetic point of view, if it belongs to a lineage with little or no sibling species. A typical example of such species is the platypus Ornithorhynchus anatinus in mammals. I am particularly interested in analyzing the human-driven threats that may impact the future of phylogenetic diversity and originality of different taxa including mammals.
2 février 2013
Biodiversity Institute, Oxford, U.K., March 31, 2011 ; CBGP, Montpellier, France, March 21, 2011 ; ECOBIO (Ecosystems, Biodiversity, Evolution), University of Rennes, France, October 8 2010 ; Mathematical modelling and Biodiversity, MNHN-Polytechnique-Veolia Environnement, Paris, France, November 30, 2009 ; Seminars of Applied Statistics, Agropolis, Montpellier, France, May 4, 2009 ; Department of Zoology, University of Oxford, U.K., January 22, 2009 ; MNHN, Paris, France, November 18, 2005 ; Department of Biometry, INRA, Avignon, France, January 17, 2005 ; Biological station, Tour du Valat, Arles, France, November 8, 2004, Seminar in biostatistics, Lyon Sud Hospital, France, October 23, 2003.
Invited talks in national and international conferences :
- Pavoine S. La mesure idéale de biodiversité existe-elle ? Journée biodiversité et bioinformatique. Réunion satellite du congrès national de bioinformatique JOBIM. 16 septembre 2014.
- Pavoine, S. Partitioning and visualizing biodiversity : when species dissimilarity matters. Invited plenary talk. Exploratory Conference on the Mathematics of Biodiversity. July 2-6, 2012.
- Pavoine, S., M. Love and M. B. Bonsall. Which phylogenetic diversity are we losing ? a temporal partitioning of phylogenetic diversity reveals rockfish diversity loss in the Southern California Bight. Invited Symposium. 12th European Ecological Federation Congress. Avila, Spain, September 24-29, 2011.
- Pavoine, S., O. Hardy, P. Couteron and F. Munoz. Caractériser la diversité phylogénétique des communautés : hypothèses et mesures. Phylocom - un colloque sur la phylogénie des communautés. Invited conference. Montpellier, France, 3-4 mai 2010.
- Pavoine, S. Measuring phylogenetic diversity and originality with the quadratic entropy, Invited Symposium on Phylogenetic diversity. In : Evolution2007, Christchurch, New-Zealand, June 2007.
- Dufour, A. B. et S. Pavoine. Comment étudier la typologie des différences entre populations humaines et zones géographiques ou la double analyse en coordonnées principales. XIIème colloque de la société de biométrie humaine, MNHN, Paris, 16-18 novembre 2005.
- Pavoine, S. and R. Pélissier. Phylogenetic diversity and typology of communities : connections between diversity, originality, ordination and spatial analysis. Workshop on Phylogenies and community ecology, Station CNRS de Moulis, France 7-9 novembre 2005.
7 août 2014
- Dray, S., Choler, P., Dolédec, S., Peres-Neto, P.R., Thuiller, W., Pavoine, S. & ter Braak, C. (2014) Combining the fourth-corner and the RLQ methods for assessing trait responses to environmental variation. Ecology. 95:14-21.
- Dray, S., Pavoine, S., Aguirre de Cárcer, D. Considering external information to improve the phylogenetic comparison of microbial communities : a new approach based on constrained Double Principal Coordinates Analysis (cDPCoA). Molecular Ecology Resources. Accepted.
- Lellouch, L., Pavoine, S., Jiguet F., Glotin, H., Sueur, J. (2014) Monitoring temporal changes of bird communities with dissimilarity acoustic indices. Methods in Ecology & Evolution. 5:495-505.
- Pavoine, S., Baguette, M., Stevens, V.M., Leibold M.A., Turlure C. & Bonsall, M.B. Life-history traits, but not phylogeny, drive compositional patterns in a butterfly metacommunity. Ecology. Early view.
- Pavoine, S., Izsak, J. (2014) New biodiversity measure that includes consistent interspecific and intraspecific components. Methods in Ecology and Evolution. 5:165-172.
- Pavoine, S., Ricotta, C. (2014) Functional and phylogenetic similarities among communities. Methods in Ecology & Evolution. 5:666-675.
- Prinzing, A., d’Haese, C., Pavoine, S. & Ponge, J.-F. (2014) Species living in harsh environments have low clade rank and are localised on former Laurasian continents - the case of Willemia (Collembola). Journal of Biogeography. 41:353-365.
- Ricotta, C., Bacaro G., Pavoine, S. A cautionary note on some phylogenetic dissimilarity measures. Journal of Plant Ecology. Accepted.
- Rodriguez, A., Gasc, A., Pavoine, S., Grandcolas, P., Gaucher, P. & Sueur, J. Temporal and spatial dynamics of animal sound within a neotropical forest. (2014) Ecological Informatics. 21:133-143.
- Sueur, J., Farina, A., Gasc, A., Pieretti, N. & Pavoine, S. (2014) Acoustic indices for biodiversity assessment and landscape ecology. Acta Acustica. 100:772-781.
- Clavel, J. Poulet, N., Porcher, E., Blanchet, S., Grenouillet, G., Pavoine, S., Biton, A., Seon-Massin, N., Argillier, C., Daufresne, M., Teillac-Deschamp, P., Julliard, R. (2013) A new freshwater biodiversity indicator based on fish community assemblages. PloS One. 8:e80968.
- Gasc, A., Sueur, J., Jiguet, F., Devictor, V., Grandcolas, P., Burrow, C., Depraetere, M. & Pavoine, S. (2013) Assessing biodiversity with sound : do acoustic diversity indices reflect phylogenetic and functional diversities of bird communities ? Ecological Indicators. 25:279-287.
- Gasc, A., Sueur, J., Pavoine, S., Pellens, R. & Grandcolas, P. (2013) Biodiversity sampling using a global acoustic approach : contrasting sites with microendemics in New Caledonia. PloS One. 8(5):e65311.
- Mason, N., deBello, F., Mouillot, D., Pavoine, S. & Dray, S. (2013) A guide for using functional diversity indices to reveal changes in assembly processes along ecological gradients. Journal of Vegetation Science. Special Feature : Functional Diversity. 24:794-806.
- Mason, N. & Pavoine, S. (2013) Does trait conservatism guarantee that indicators of phylogenetic community structure will reveal niche-based assembly processes along stress gradients ? Journal of Vegetation Science. Special Feature : Functional Diversity. 24:820-833.
- Ozinga W., Colles A., Bartish I., Hennion F., Hennekens S., Pavoine S., Poschlod P., Hermant M., Schaminée J., Prinzing A. (2013) Specialists leave fewer descendants within a region than generalists. Global Ecology and Biogeography. 22:213-222.
- Pavoine S., Blondel J., Dufour A.-B., Gasc A., Bonsall M.B. (2013) A new technique for analysing interacting factors affecting biodiversity patterns : crossed-DPCoA. PloS One 8:e54530.
- Pavoine, S., Gasc, A., Bonsall, M.B., Mason, N.W.H. (2013) Correlations between phylogenetic and functional diversity : mathematical artefacts or true ecological and evolutionary processes ? Journal of Vegetation Science. Special Feature : Functional Diversity. 24:781-793.
- Pavoine S. & Ricotta C. (2013) Testing for phylogenetic signal in biological traits : the ubiquity of cross-product statistics. Evolution. 67:828-840.
- Depraetere M., Pavoine S., Jiguet F., Gasc A., Duvail S. & Sueur J. (2012) Monitoring animal diversity using acoustic indices : implementation in a temperate woodland. Ecological Indicators. 13:46-54.
- Hardy O. & Pavoine S. (2012) Assessing phylogenetic signal with measurement error : a comparison of Mantel tests, Blomberg et al.’s K and phylogenetic distograms. Evolution. 66, 2614–2621.
- Izsak J. & Pavoine S. (2012) Links between the species abundance distribution and the shape of the corresponding rank abundance curve. Ecological Indicators. 14:1-6.
- Jono C.M.A. & Pavoine S. (2012) Threat diversity will erode mammalian phylogenetic diversity in the near future. PloS One. 7:e46235.
- Mouquet N., Devictor V., Meynard C.N., Munoz F., Bersier L.-F., Chave J., Couteron P., Dalecky A., Fontaine C., Gravel D., Hardy O.J., Jabot F., Lavergne S., Leibold M.S., Mouillot D., Münkemüller T., Pavoine S., Prinzing A., Rodrigues A.S.L., Rohr R.P., Thébault E. & Thuiller W. (2012) Ecophylogenetics : advances and perspectives. Biological reviews. 87:769-785.
- Pavoine S. (2012) Clarifying and developing the analyses of biodiversity : towards a generalization of current approaches. Methods in Ecology and Evolution. 3:509-518.
- Politi Bertoncini A., Machon N., Pavoine S. & Muratet A. (2012) Local gardening practices shape urban lawn floristic communities. Landscape and Urban Planning. 105:53-61.
- Ricotta C., Pavoine S., Bacaro G., Acosta, A. (2012) Functional rarefaction for species abundance data. Methods in Ecology and Evolution. 3, 519-525.
- Rolland J., Cadotte M., Davies J., Devictor V., Lavergne S., Mouquet N., Pavoine S., Rodrigues A., Thuiller W., Turcati L., Winter M., Zupan L., Jabot F. & Morlon H. (2012) Using phylogenies in conservation : new perspectives. Biology Letters. 8:692-694.
- Sueur J., Gasc A., Grandcolas P., Pavoine S. (2012) Global estimation of animal diversity using automatic acoustic sensors. In : Sensors for ecology - Towards integrated knowledge of ecosystems (J.-F. Le Galliard, J.-M. Guarini and F. Gaill eds.). pp. 99-117. CNRS. Paris.
- Izsak J. & Pavoine S. (2011) New concentration measures as kinds of the quadratic entropy. Ecological Indicators. 11:540-544.
- Kerbiriou C., Bargain B., Leviol I. & Pavoine S. (2011) Diet and fuelling of the globally threatened aquatic warbler Acrocephalus paludicola at autumn migration stopover as compared with two congeners. Animal Conservation. 14:261–270.
- Pavoine S. & Bonsall M. (2011) Measuring biodiversity to explain community assembly : a unified approach. Biological Reviews. 86:792-812.
- Pavoine S., Vela E., Gachet S., de Bélair G. & Bonsall M.B. (2011) Linking patterns in phylogeny, traits, abiotic variables and
space : a novel approach to linking environmental filtering
and plant community assembly. Journal of Ecology. 99:165-175.
- Baraloto C., Marcon E., Morneau F., Pavoine S. & Roggy J.-C. (2010) Integrating functional diversity into tropical forest plantation designs to study ecosystem processes. Annals of Forest Science. 67:303.
- Jombart T., Pavoine S., Devillard S. & Pontier D. (2010) Putting phylogeny into the analysis of biological traits : a methodological approach. Journal of Theoretical Biology. 264:693–701.
- Pavoine S., Baguette M. & Bonsall M.B. (2010) Decomposition of trait diversity among the nodes of a phylogenetic tree. Ecological Monographs. 80:485-507.
- Sarthou C., Larpin D., Fonty E., Pavoine S. & Ponge J.-F. (2010)
Stability of plant communities along a tropical inselberg ecotone in French Guiana (South America). Flora. 205:682-694.
- Stevens V., Pavoine S. & Baguette M. (2010) Variation within and between closely related species uncovers high intra-specific variability in dispersal. PloS ONE. 5:e11123.
- Valet J., Daniel H., Beaujouan V., Rozé F. & Pavoine S. (2010) Using biological traits to assess how urbanization filters plant species of small woodlands. Applied Vegetation Science. 13:412-424.
- Duyck P.-F., Pavoine S., Tixier P., Chabrier C. & Quénéhervé P. (2009) Host range as an axis of niche partitioning in the plant-feeding nematode community of banana agroecosystems. Soil Biology & Biochemistry. 41:1139-1145.
- Pavoine S. & Bonsall M.B. (2009) Biological diversity : distinct distributions can lead to the maximization of Rao’s quadratic entropy. Theoretical Population Biology. 75:153-163.
- Pavoine S., Love M. & Bonsall M.B. (2009) Hierarchical partitioning of evolutionary and ecological patterns in the organization of phylogenetically-structured species assemblages : application to rockfish (genus : Sebastes) in the Southern California Bight. Ecology Letters. 12:898-908.
- Pavoine S., Vallet J., Dufour A.-B., Gachet S. & Daniel H. (2009) On the challenge of treating various types of variables : application for improving the measurement of functional diversity. Oikos. 118:391-402.
- Rambaud M., Combroux I., Haury J., Moret J., Machon N., Zavodna M. & Pavoine S. (2009) Relationships between channelization structures, environmental characteristics, and plant communities, among four French streams of the Seine-Normandy’s catchment. Journal of the North American Benthological Society. 28:596-610.
- Rambaud M., Pavoine S., Machon N., Moret J. & Combroux I. (2009) Does channelization modify spatial and temporal organization of macrophyte communities and their physical habitat ? Fundamental and Applied Limnology. 174:159-172.
- Duyck P.-F., David P., Pavoine S. & Quilici S. (2008) Can host-range allow niche differentiation of invasive polyphagous fruit flies (Diptera : Tephritidae) in La Réunion ? Ecological Entomology 33:1-14.
- Pavoine S., Ollier S., Pontier D. & Chessel D. (2008) Testing for phylogenetic signal in phenotypic traits : new matrices of phylogenetic proximities. Theoretical Population Biology 73:79-91.
- Sueur J., Pavoine S., Hamerlynck O. & Duvail S. (2008) Rapid acoustic survey for biodiversity appraisal. PloS ONE 3:e4065.
- Pavoine S. & Bailly X. (2007) New analysis for consistency among markers in the study of genetic diversity : development and application to the description of bacterial diversity. BMC Evolutionary Biology 7:e156.
- Pavoine, S., Blondel J., Baguette M. & Chessel D. (2007) A new technique for ordering asymmetrical three-dimensional data sets in ecology. Ecology 88:512-523.
- Dufour A. B., Pavoine S. & Chessel D. (2006) Exemple de démarche biométrique : une étude de la variabilité génétique humaine par la double analyse en coordonnées principales. Revue de la Société de Biométrie Humaine "Biométrie humaine et anthropologie”. Tome 23, n°1-2.
- Pavoine, S. (2006) Dissimilarity coefficient. In : Encyclopedia of Measurement and Statistics (ed.N. J. Salkind). Sage Publications.
- Pavoine S. & Dolédec S. (2005) The apportionment of quadratic entropy : a useful alternative for partitioning diversity in ecological data. Environmental and Ecological Statistics 12:125-138.
- Pavoine S., Ollier S. & Dufour A.B. (2005) Is the originality of a species measurable ? Ecology letters 8:579-586.
- Pavoine S., Ollier S. & Pontier D. (2005) Measuring diversity from dissimilarities with Rao’s quadratic entropy : are any dissimilarity indices suitable ? Theoretical Population Biology 67:231-239.
- Pavoine S., Dufour A.B. & Chessel D. (2004) From dissimilarities among species to dissimilarities among communities : a double principal coordinate analysis. Journal of Theoretical Biology 228:523-537.
7 août 2014
I am contributor of the ade4 package in R : Analyses of Ecological data, Exploratory and Euclidean methods in Environmental sciences.
The R scripts for papers « Pavoine S. et al. (2009) Oikos. 118:391-402 » and « Pavoine S. et al. (2005) Ecology letters 8:579-586 » are now part of the ade4 package ; updates can be obtained by downloading the most recent version of the package at
Other updates of the R scripts associated with my papers can be found here :
- An updated version of Appendix S4 for « Pavoine, S., Ricotta, C. (2014) Methods in Ecology & Evolution. 5:666-675 » is available here :
- Appendix S4
- An updated version of R scripts associated with « Pavoine S., Baguette M. & Bonsall M.B. (2010) Ecological Monographs. 80:485-507. » can be found here :
- Supp File A
7 août 2014