ANR project ‘Jeunes Chercheur(e)s’
January 2009 – December 2011
Olivier Gimenez (PI), Rémi Choquet, Roger Pradel, Jean-Dominique Lebreton
PhD students: Sarah Cubaynes, Mathieu Buoro, Lucile Marescot, Guillaume Péron
Master students: Marlène Gamelon, Marine Desprez, Julien Papaïx
People hired thanks to ANR funding: Elena Papadatou (post-doc), Sabrina Servanty (post-doc), Erica Nogué (software engineer)
Integrating individual, temporal and spatial heterogeneity in population dynamics
Animal population dynamics studies variation of population size and structure in time and space. Associated models allow addressing important questions in conservation biology, ecology and evolutionary biology. However, in natural conditions, it is difficult to estimate demographic parameters that are required to calibrate these models because of the practical impossibility in the field to detect exhaustively all the individuals of a population at any time. Capture-recapture (CR) models allow estimating demographic parameters while accounting for imperfect detectability (detection probability < 1). Despite their advantages, these models rely on the strong assumption of homogeneity in the parameters, which comes with the risk of statistical bias and flawed biological inference. In our project, we have extended standard CR models to incorporate different sources of heterogeneity. These methodological developments have been motivated with case studies in population biology and have been implemented in a computer software with a large diffusion towards biologists.
Capture-recapture mixed models
To ensure the adoption of our new framework, we have built up relevant statistical models, implemented reliable and fast numerical algorithms and developed a user-friendly and free of charge computer program available on the Internet. These new tools have allowed the estimation of the French wolf population size, the suggestion of management strategies for wild boar management, the quantification of evolutionary trade-offs in the Atlantic salmon, the evidence of the influence of experience in kittiwakes, the description of senescence patterns in black-headed gulls, the quantification of hunting pressure in the Eurasian woodcock, the study of the effect of climate on breeding of red-footed albatross, the disentangling of environmental vs. genetic factors on survival of blue tits, and the estimation of inter-population and inter-specific differences in survival of several bats species.
This project provides a formal framework to biologists in order to take heterogeneity into account in population dynamics through, among others, the availability of a computer program. These results have been obtained thanks to the collaborative work of a team made of researchers, engineers, Master students, PhD students and post-docs funded by ANR and working at the interface of biostatistics and population biology.
The project has led to the publication of 30 papers in international peer-reviewed journals both on the i) methodological aspects dealing with models, algorithms and software developed within the duration of the project ii) biological aspects about the results obtained in conservation biology, population ecology and evolutionary biology.
The project Capture-Recapture Mixed Models is a fundamental research project led by Olivier Gimenez. The project started in January 2009 and last for 36 months. It was funded by ANR with a budget of 190000€ for a total cost of approximately 1200000€.
- Choquet, R., A. Sanz-Aguilar, B. Doligez, E. Nogué, R. Pradel, L. Gustafsson and O. Gimenez (2013). Estimating demographic parameters from capture-recapture data with dependence among individuals within clusters. Methods in Ecology and Evolution. 4: 474–482.
- de Villemereuil, P., Gimenez, O., Doligez, B. (2012). Comparing parent-offspring regression with Frequentist and Bayesian animal models to estimate heritability in wild populations: a simulation study for Gaussian and binary traits. Methods in Ecology and Evolution. 4: 260-275
- Gimenez, O., Lebreton, J.-D., Gaillard, J.-M., Choquet, R. and R. Pradel (2012). Estimating demographic parameters using hidden process dynamic models. Theoretical Population Biology. 82: 307-316
- Buoro, M., E. Prévost, O. Gimenez (2012). Digging through model complexity: using hierarchical models to uncover evolutionary processes in the wild. Journal of Evolutionary Biology. 25: 2077-2090
- Lebreton, J.-D., R. Choquet andO. Gimenez (2012). Simple estimation and test procedures in capture-mark-recapture mixed models. Biometrics. 68:494-503
- Cubaynes, S., C. Lavergne, E. Marboutin, and O. Gimenez (2012). Assessing individual heterogeneity using model selection criteria: How many mixture components in capture-recapture models? Methods in Ecology and Evolution. 3: 564-573
- Péron, G., Y. Ferrand, F. Gossmann, C. Bastat, M. Guenezan and O. Gimenez (2012). Spatial heterogeneity in mortality and its impact on the population dynamics of Eurasian woodcocks. Population Ecology. 54: 305-312
- Cubaynes, S, C. Doutrelant, A. Grégoire, P. Perret, B. Faivre, and O. Gimenez (2012). Testing hypotheses in evolutionary ecology with imperfect detection: Structural equation modeling of mark-recapture data. Ecology. 93: 248-255
- Choquet, R. andO. Gimenez (2012). Towards built-in capture-recapture mixed models in program E-SURGE. Journal of Ornithology.152: 625-639
- Marescot, L., O. Gimenez, C. Duchamp, E. Marboutin and G. Chapron (2012). Reducing matrix population models with application to social animal species. Ecological Modelling. 232: 91-96
- Papadatou, E., R. Pradel, M. Schaub, D. Dolch, H. Geiger, C. Ibañez, G. Kerth, A. Popa-Lisseanu, W. Schorcht, J. Teubner and O. Gimenez (2012). Comparing survival among species with imperfect detection using multilevel analysis of mark-recapture data: a case study on bats. Ecography. 35: 153-161
- Caniglia, R., E. Fabbri, S. Cubaynes, O. Gimenez, J.-D. Lebreton and E. Randi (2012). An improved procedure to estimate wolf abundance using non-invasive genetic sampling and capture-recapture mixture models. Conservation Genetics. 13: 53-64
- Fletcher, D., Lebreton, J.-D., Marescot, L., Schaub, M., Gimenez, O., Slooten, E. and S. Dawson (2012). Bias in estimation of adult survival and asymptotic population growth rate caused by undetected capture heterogeneity. Methods in Ecology and Evolution. 3: 206-216
- Buoro, M., O. Gimenez and E. Prévost (2011). Assessing adaptive phenotypic plasticity by means of conditional strategies from empirical data: The latent environmental threshold model. Evolution. 66:996-1009
- Gamelon, M., A. Besnard, J.-M. Gaillard, S. Servanty, E. Baubet, S. Brandt and O. Gimenez (2011). High hunting pressure selects for earlier birth data: Wild boar as a case study. Evolution. 65:3100-3112
- Marescot, L., Pradel, R., Duchamp, C. Cubaynes, S., Marboutin, E., Choquet, R. Miquel, C. and O. Gimenez (2011). Capture-recapture population growth rate as a robust tool against detection heterogeneity for population management. Ecological Applications. 21:2898-2907
- Péron, G., Y. Ferrand, F. Gossmann, C. Bastat, M. Guenezan and O. Gimenez (2011). Escape migration decisions in Eurasian Woodcocks: insights from survival analyses using large-scale recovery data. Behavioral Ecology and Sociobiology. 65:1949-1955
- Charmantier*, A., M. Buoro*, O. Gimenez and H. Weimerskirch (2011). Heritability of short-scale natal dispersal in a large-scale foraging bird, the wandering albatross. Journal of Evolutionary Biology. 24:1487-1496. *These authors contributed equally to the work.
- Desprez, M. R. Pradel, E. Cam, J.-Y. Monnat and O. Gimenez (2011). Now you see him, now you don’t: Experience, not age, is related to reproduction in Kittiwakes. Proceedings of the Royal Society B: Biological Sciences. 278: 3060-3066
- Péron, G., Y. Ferrand, F. Gossmann, C. Bastat, M. Guenezan and O. Gimenez (2011). Nonparametric spatial regression of survival probability: visualization of population sinks in Eurasian Woodcock. Ecology. 92:1672-1679
- Servanty, S., J.-M. Gaillard, Ronchi, F., Focardi, S., Baubet E. & O. Gimenez (2011). Influence of harvesting pressure on demographic tactics: implications for wildlife management. Journal of Applied Ecology 48: 835–843
- Marzolin, G., A. Charmantier and O. Gimenez (2011). Frailty in state-space models: application to actuarial senescence in the dipper. Ecology. 92:562-567.
- Cubaynes, S., P. F. Doherty Jr, E. A. Schreiber, R. W. Schreiber and O. Gimenez (2011). To breed or not to breed: seabirds response to extreme climatic events. Biology Letters 7: 303-306.
- Papadatou, E.Ibáñez, C., Pradel, R. Juste, J. and O. Gimenez (2011). Assessing survival in a multi-population system: a case study on bat populations. Oecologia 165:925-933.
- Papaïx, J., S. Cubaynes, M. Buoro, A. Charmantier, P. Perret and O. Gimenez (2010). Combining capture–recapture data and pedigree information to assess heritability of demographic parameters in the wild. Journal of Evolutionary Biology 23: 2176-2184.
- Servanty, S., R. Choquet, E. Baubet, S. Brandt, J.-M. Gaillard, M. Schaub, C. Toïgo, J.-D. Lebreton, M. Buoro and O. Gimenez (2010). Assessing whether mortality is additive using marked animals: a Bayesian state-space modeling approach. Ecology. 91: 1916–1923.
- Buoro, M., Prévost, E. and O. Gimenez (2010). Investigating evolutionary trade-offs in wild populations of Atlantic salmon (Salmo salar): incorporating detection probabilities and individual heterogeneity. Evolution 64: 2629-2642.
- Gimenez, O. and R. Choquet(2010). Incorporating individual heterogeneity in studies on marked animals using numerical integration: capture-recapture mixed models Ecology. 91: 951-957.
- Péron, G., Crochet, P.A.C., Choquet, R., Pradel, R., Lebreton, J.-D. and O. Gimenez. (2010). Capture-recapture models with heterogeneity to study survival senescence in the wild. Oïkos 119: 524-532.
- Cubaynes, S. Pradel, R. Choquet, R.Duchamp, C. Gaillard, J.-M., Lebreton, J.-D., Marboutin, E., Miquel, C., Reboulet, A.-M., Poillot, C., Taberlet, P. and O. Gimenez. (2010). Importance of accounting for detection heterogeneity when estimating abundance: the case of French wolves. Conservation Biology 24:621-626.