Multievent CR worshop | Montpellier, France

Currently listed training opportunities (short courses, workshops, meetings...) -- software neutral.

Multievent CR worshop | Montpellier, France

Postby rplp » Wed Nov 15, 2017 1:51 pm

Upcoming workshop on the analysis of multievent capture-recapture data to be held at CEFE (Center for Evolutionary and Functional Ecology), Montpellier, France, 19-23 March 2018. The registration of participants will be at CEFE the 19 March on evening and will be followed by 3 days of lectures and practical exercises plus 1 day of practical work on the participants' data.

You are hereby cordially invited to take part in the workshop:

MODELLING MULTIEVENT CAPTURE-RECAPTURE DATA
Organized by the Biostatistics and Population Biology team of CEFE, Montpellier (France)

The estimation of population parameters (survival, recruitment, dispersal, and population growth rate) is critical to many areas of fundamental and applied biology. The major source of data for such estimation comes from observations of marked animals. This workshop will deal with recent advances in the analysis of such data. The content is aimed at providing the participants with a solid background in the philosophy, theory and practices for the analysis of data from marked animals, with a specific focus on multievent data and models. Multievent capture-recapture models are a natural generalization of the multisite recapture models. Similarly, individuals are sampled on discrete occasions, at which they may be captured or not. However, contrary to the multisite case, uncertainty in the assessment of state such as breeder, diseased or highly catchable can be incorporated into the analysis. Conceptually, it is not states that are observed but rather something dubbed an "event" (a particular breeding behaviour, a positive blood test or just encounter), which reflects to some extent the underlying state. The presence of imperfect observations and the lack of information on individual quality presently make multievent models an invaluable tool in virtually any area of population biology. Current applications include the study of dispersal, epidemiology, individual heterogeneity, mixture of information... New developments allow the treatment of individual heterogeneity through random effects as well as through mixture models, and the inclusion of individual as well as environmental covariates. For examples of topics that can be addressed in the multievent framework, see the non-exhaustive bibliography below. Depending on the participants’ wishes, one of the following theme will be developed during the workshop:
  • stopover
  • epidemiology
  • site occupancy
Emphasis will be placed on stringent procedures for building and selecting the most appropriate models for the data set at hand, in order to be able to draw reliable biological conclusions.

Format of the workshop will be a combination of lectures and computer lab exercises with the programs E-SURGE and U-CARE. (http://www.cefe.cnrs.fr/fr/recherche/bc/bbp/1045-desc/264-logiciels). U-CARE incorporates goodness-of-fit tests for multistate models, and E-SURGE makes the building of complex models easy based on a language describing the structure of models in a compact and user-friendly way. All lectures and course material will be in English.

It is our hope that participants will bring their own capture-recapture data to work on them during the workshop. To take full advantage of the workshop, it is expected that the participants will have some basic practice of the analysis of CR data.

Teachers: Roger Pradel, Rémi Choquet, Olivier Gimenez, Lucile Marescot, Nina Santostasi, Giacomo Tavecchia.

Participants will have to provide their own laptop computer that is capable of running Windows-based software.

Thank you for disseminating this message to colleagues and students who may not have received it.

The workshop organizers
Roger Pradel, Rémi Choquet, Olivier Gimenez

To apply, go to http://multievent.sciencesconf.org/

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Dispersal:
Doligez et al (2012) Estimation and comparison of heritability and parent–offspring resemblance in dispersal probability from capture–recapture data using different methods: the Collared Flycatcher as a case study. J Ornithol (2012) 152 (Suppl 2):S539–S554
Gillingham MAF, Cézilly F, Wattier R, Béchet A (2013) Evidence for an Association between Post-Fledging Dispersal and Microsatellite Multilocus Heterozygosity in a Large Population of Greater Flamingos. PLoS ONE 8(11): e81118.
Doxa A et al (2013) Inferring dispersal dynamics from local population demographic modelling: the case of the slender-billed gull in France. Animal Conservation 16 684–693.
Fernández-Chacón, A., M. Genovart, R. Pradel, G. Tavecchia, A. Bertolero, J. Piccardo, M. G. Forero, I. Afán, J. Muntaner, and D. Oro. 2013. When to stay, when to disperse and where to go: survival and dispersal patterns in a spatially structured seabird population. Ecography 36(10):1117–1126.
Gourlay-Larour, M.-L., R. Pradel, M. Guillemain, J.-S. Guitton, M. L’Hostis, H. Santin-Janin, and A. Caizergues. 2014. Movement patterns in a partial migrant: A multi-event capture-recapture approach. PLoS ONE 9(5):e96478.
Lagrange, P., R. Pradel, M. Bélisle, and O. Gimenez. 2014. Estimating dispersal among numerous sites using capture-recapture data. Ecology 95(8):2316–2323.
Hardouin et al (2014) Meteorological conditions influence short-term survival and dispersal in a reinforced bird population. Journal of Applied Ecology 2014, 51, 1494–1503
Souchay, G., G. Gauthier, J. Lefebvre, and R. Pradel. 2015. Absence of difference in survival between two distant breeding sites of greater snow geese. Journal of Wildlife Management 79(4):570–578.
Barthold et al (2016) Dead or gone? Bayesian inference on mortality for the dispersing sex. Ecology and Evolution 6(14): 4910-4923
Tournier et al. (2017) Manipulating waterbody hydroperiod affects movement behaviour and occupancy dynamics in an amphibian. Freshwater Biology. 2017;62:1768–1782.
Cayuela, H., Pradel, R., Joly, P., & Besnard, A. (2017). Analyzing movement behavior and dynamic space-use strategies among habitats using multi-event capture–recapture modeling. Methods in Ecology and Evolution 2017, 8, 1124–1132
Acker et al (2017) Insights on dispersal and recruitment paradigms: sex‑and age‑dependent variations in a nomadic breeder. Oecologia DOI 10.1007/s00442-017-3972-7
Lagrange et al 2017. Assessment of individual and conspecific reproductive success as determinants of breeding dispersal of female tree swallows: A capture–recapture approach. Ecology and Evolution. 7:7334–7346
Avril A, Letty J, Pradel R, Léonard Y, Santin-Janin H, Pontier D (2012). A multi-event model to study stage-dependence dispersal in radio-collared hares: when hunting promotes costly transience. Ecology 93:1305-1316.
Balkız Ö, Béchet A, Rouan L, Choquet R, Germain C, Aguilar Amat J, Rendón-Martos M, Baccetti N, Nissardi S, Özesmi U, Pradel R (2010) Experience-dependent natal philopatry of breeding Greater flamingos. Journal of Animal Ecology 79:1045-1056.
Devillard, S. and Y. Bray (2009). Assessing the effect on survival of natal dispersal using multistate capture-recapture models. Ecology 90(10): 2902-2912.
Doxa A, Besnard A, Bechet A, Pin C, Lebreton JD, Sadoul N (2013) Inferring dispersal dynamics from local population demographic modelling: the case of the slender-billed gull in France. Animal Conservation 16:684-693
Gauthier G, Milot E, Weimerskirch H (2012). Estimating dispersal, recruitment and survival in a biennially breeding species, the Wandering Albatross. Journal of Ornithology 152:S457-S467. 10.1007/s10336-010-0541-9

Epidemiology:
Lachish S, Bonsall MB, Lawson B, Cunningham AA, Sheldon BC (2012) Individual and Population-Level Impacts of an Emerging Poxvirus Disease in a Wild Population of Great Tits. PLoS ONE 7(11): e48545
Choquet et al (2013) Estimating transitions between states using measurements with imperfect detection: application to serological data. Ecology, 94(10), 2013, pp. 2160–2165
Santoro et al 2014. Multi-event capture–recapture modeling of host–pathogen dynamics among European rabbit populations exposed to myxoma and Rabbit Hemorrhagic Disease Viruses: common and heterogeneous patterns. Veterinary Research, 45:39
Buzdugan et al (2017) Inference of the infection status of individuals using longitudinal testing data from cryptic populations: Towards a probabilistic approach to diagnosis. SCIENTIFIC RepoRts 7: 1111
Chambert T, Staszewski V, Lobato E, Choquet R, Carrie C, McCoy KD, Tveraa T, Boulinier T (2012). Exposure of black-legged kittiwakes to Lyme disease spirochetes: dynamics of the immune status of adult hosts and effects on their survival. Journal of Animal Ecology 81:986-995. 10.1111/j.1365-2656.2012.01979.x
Conn, P. B. and E. G. Cooch (2009). Multistate capture-recapture analysis under imperfect state observation: an application to disease models. Journal of Applied Ecology 46(2): 486-492.
Cooch EG, Conn PB, Ellner SP, Dobson AP, Pollock KH (2009). Disease dynamics in wild populations: modeling and estimation: a review. Journal of Ornithology 152:S485-S509. 10.1007/s10336-010-0636-3
Lachish S, Knowles SCL, Alves R, Wood MJ, Sheldon BC (2011). Infection dynamics of endemic malaria in a wild bird population: parasite species-dependent drivers of spatial and temporal variation in transmission rates. Journal of Animal Ecology 80:1207-1216. 10.1111/j.1365-2656.2011.01893.x

Individual heterogeneity:
Fletcher et al (2012) Bias in estimation of adult survival and asymptotic population growth rate caused by undetected capture heterogeneity. Methods in Ecology and Evolution 2012, 3, 206-216
Caniglia et al (2012) An improved procedure to estimate wolf abundance using non-invasive genetic sampling and capture–recapture mixture models. Conserv Genet (2012) 13:53–64
Chevallier et al (2013) Use of mixture models to characterize site quality in philopatric animals: a case study with Bonelli's eagle. Animal Conservation 16 (2013) 198–206
Doxa A et al (2013) Inferring dispersal dynamics from local population demographic modelling: the case of the slender-billed gull in France. Animal Conservation 16 684–693.
Bonnet et al (2013) How the common vole copes with modern farming: Insights from a capture–mark–recapture experiment. Agriculture, Ecosystems and Environment 177 (2013) 21-27
Abadi F, Botha A, Altwegg R (2013) Revisiting the Effect of Capture Heterogeneity on Survival Estimates in Capture-Mark-Recapture Studies: Does It Matter? PLoS ONE 8(4): e62636
Lindberg et al (2013) Individual heterogeneity in black brant survival and recruitment with implications for harvest dynamics. Ecology and Evolution 2013; 3(12): 4045-4056
Barbraud C, Tuck GN, Thomson R, Delord K, Weimerskirch H (2013) Fisheries Bycatch as an Inadvertent Human-Induced Evolutionary Mechanism. PLoSONE 8(4): e60353
Guillemain, M., R. Pradel, O. Devineau, G. Simon, and M. Gauthier-Clerc. 2014. Demographic heterogeneity among individuals can explain the discrepancy between capture-mark-recapture and waterfowl count results. Condor 116(3):293–302.
Gourlay-Larour, M.-L., R. Pradel, M. Guillemain, J.-S. Guitton, M. L’Hostis, H. Santin-Janin, and A. Caizergues. 2014. Movement patterns in a partial migrant: A multi-event capture-recapture approach. PLoS ONE 9(5):e96478.
Schmaltz et al (2015) Apparent annual survival of staging ruffs during a period of population decline: insights from sex and site-use related differences. Popul Ecol (2015) 57:613–624
Gervasi V et al (2016) Sharing data improves monitoring of trans-boundary populations: the case of wolverines in central Scandinavia. Wildlife Biology, 22(3):95-106
Fay et al (2016) Variation in the age of first reproduction: different strategies or individual quality? Ecology, 97(7), 2016, pp. 1842–1851
Guéry et al. 2017. Hidden survival heterogeneity of three Common eider populations in response to climate fluctuations. Journal of Animal Ecology 2017, 86, 683–693.
Gimenez O, Cam E, Gaillard J-M (2017) Individual heterogeneity and capture–recapture models: what, why and how? Oikos 000: 001–021, 2017
Jenouvrier S, Aubry LM, Barbraud C, Weimerskirch H, Caswell H. Interacting effects of unobserved heterogeneity and individual stochasticity in the life-history of the Southern fulmar. J Anim Ecol. 2017;00:1–11.
Péron, G., J.-M. Gaillard, C. Barbraud, C. Bonenfant, A. Charmantier, R. Choquet, T. Coulson, V. Grosbois, A. Loison, G. Marzolin, N. Owen-Smith, D. Pardo, F. Plard, R. Pradel, C. Toigo, and O. Gimenez. 2016. Evidence of reduced individual heterogeneity in adult survival of long-lived species. Evolution 70(12):2909–2914.
Cam E, Gimenez O, Alpizar-Jara R, Aubry LM, Authier M, Cooch EG, Koons DN, Link WA, Monnat J-Y, Nichols JD, Rotella JJ, Royle JA, Pradel R (2013). Looking for a needle in a haystack: inference about individual fitness components in a heterogeneous population. Oikos. 122: 739-753.
Crespin, L., R. Choquet, et al. (2008). "Is heterogeneity of catchability in capture-recapture studies a mere sampling artifact or a biologically relevant feature of the population?" Population Ecology 50(3): 247-256.
Cubaynes S, Lavergne C, Marboutin E, Gimenez O (2012). Assessing individual heterogeneity using model selection criteria: how many mixture components in capture-recapture models? Methods in Ecology and Evolution 3:564-573. 10.1111/j.2041-210X.2011.00175.x
Cubaynes, S., R. Pradel, et al. (2010). "Importance of Accounting for Detection Heterogeneity When Estimating Abundance: the Case of French Wolves." Conservation Biology 24(2): 621-626.
Fletcher D, Lebreton JD, Marescot L, Schaub M, Gimenez O, Dawson S, Slooten E (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. 10.1111/j.2041-210X.2011.00137.x
Gimenez, O. and R. Choquet (2010). "Individual heterogeneity in studies on marked animals using numerical integration: capture-recapture mixed models." Ecology 91(4): 951-957.
Gourlay Larour M-L, Pradel R, Guillemain M, Santin-Janin H, L'Hostis M, Caizergues A (2013) Individual turnover in Common Pochards wintering in western France. Journal of Wildlife Management: 77(3): 477-485.
Marescot L, Pradel R, Duchamp C, Cubaynes S, Marboutin E, Choquet R, Miquel C, Gimenez O (2011) Capture-recapture population growth rate as a robust tool against detection heterogeneity for population management. Ecological Applications 21:2898-2907.
Marzolin G, Charmantier A, Gimenez O (2011). Frailty in state-space models: application to actuarial senescence in the Dipper. Ecology 92:562-567. 10.1890/10-0306.1
Oliver LJ, Morgan BJT, Durant SM, Pettorelli N (2011). Individual heterogeneity in recapture probability and survival estimates in cheetah. Ecological Modelling 222:776-784. 10.1016/j.ecolmodel.2010.11.021
Peron, G., P. A. Crochet, et al. (2010). "Capture-recapture models with heterogeneity to study survival senescence in the wild." Oikos 119(3): 524-532.
Peron, G., J. D. Lebreton, et al. (2010). "Breeding dispersal in black-headed gull: the value of familiarity in a contrasted environment." Journal of Animal Ecology 79(2): 317-326.
Pradel R, Choquet R, Lima MA, Merritt JF, Crespin L (2010) Estimating population growth rate from capture-recapture data in presence of capture heterogeneity. Journal of Agricultural, Biological and Environmental Statistics 15:248-258. 10.1007/s13253-009-0008-8
Veran, S., O. Gimenez, et al. (2007). "Quantifying the impact of longline fisheries on adult survival in the black-footed albatross." Journal of Applied Ecology 44(5): 942-952.
Mixture of information, Trap-dependency, Radio failure, Tag loss:
Fletcher et al (2012) Bias in estimation of adult survival and asymptotic population growth rate caused by undetected capture heterogeneity. Methods in Ecology and Evolution 2012, 3, 206-216
Tavecchia G, Adrover J, Muñoz Navarro A, Pradel R (2012) Modelling mortality causes in longitudinal data in the presence of tag loss: application to raptor poisoning and electrocution. Journal of Applied Ecology 49:297-305.
Pradel R, Sanz-Aguilar A (2012) Modeling Trap-Awareness and Related Phenomena in Capture-Recapture Studies. PLOS One 7:e32666.
Kendall et al 2013. Combinin g dead recovery, auxiliary observations and robust design data to estimate demographic parameters from marked individuals. Methods in Ecology and Evolution 2013, 4, 828–835
Souchay, G., G. Gauthier, and R. Pradel. 2014. To breed or not: A novel approach to estimate breeding propensity and potential trade-offs in an Arctic-nesting species. Ecology 95(10):2745–2756.
Mihoub et al (2014) Comparing the effects of release methods on survival of the Eurasian black vulture Aegypius monachus reintroduced in France. Oryx, 48(1), 106–115
Reisinger RR, Oosthuizen WC, Péron G, Cory Toussaint D, Andrews RD, et al. (2014) Satellite Tagging and Biopsy Sampling of Killer Whales at Subantarctic Marion Island: Effectiveness, Immediate Reactions and Long-Term Responses. PLoS ONE 9(11): e111835
Souchay, G., G. Gauthier, J. Lefebvre, and R. Pradel. 2015. Absence of difference in survival between two distant breeding sites of greater snow geese. Journal of Wildlife Management 79(4):570–578.
Ruette et al (2015) Comparative survival pattern of the syntopic pine and stone martens in a trapped rural area in France. Journal of Zoology 295 (2015) 214–222
Sanz‑Aguilar et al 2015. Age‑dependent survival of island vs. mainland populations of two avian scavengers: delving into migration costs. Oecologia 179:405–414
Chapple et al. (2016) A novel application of multi-event modeling to estimate class segregation in a highly migratory oceanic vertebrate. Ecology, 97(12), 2016, pp. 3494–3502
Payo-Payo, A., M. Genovart, A. Bertolero, R. Pradel, and D. Oro. 2016. Consecutive cohort effects driven by density-dependence and climate influence early-life survival in a long-lived bird. Proceedings of the Royal Society B: Biological Sciences 283(1829):20153042.
Genovart et al. (2016) Demography of the critically endangered Balearic shearwater: the impact of fisheries and time to extinction. Journal of Applied Ecology 2016, 53, 1158–1168
Hernandez et al (2017) Environmental conditions, age, and senescence differentially influence survival and reproduction in the Storm Petrel. J Ornithol 158:113–123
Matovic et al (2017) Disentangling the effects of predation and oceanographic fluctuations in the mortality of two allopatric seabird populations. Popul Ecol 59:225–238
Tosoni et al (2017) Assessment of key reproductive traits in the Apennine brown bear population. Ursus 28(1):105–116
Pacoureau et al. (2017) Early-life density-dependence effects on growth and survival in subantarctic fur seals. Popul Ecol (2017) 59:139–155
Duriez, O., S. A. Saether, et al. (2009). "Estimating survival and movements using both live and dead recoveries: a case study of oystercatchers confronted with habitat change." Journal of Applied Ecology 46(1): 144-153.
Gauthier, G. and J. D. Lebreton (2008). "Analysis of band-recovery data in a multistate capture-recapture framework." Canadian Journal of Statistics-Revue Canadienne De Statistique 36(1): 59-73.
Hardouin LA, Nevoux M, Robert A, Gimenez O, Lacroix F, Hingrat Y (2012). Determinants and costs of natal dispersal in a lekking species. Oikos 121:804-812. 10.1111/j.1600-0706.2012.20313.x
Juillet C, Choquet R, Gauthier G, Pradel R (2011) A capture-recapture model with double-marking, live and dead encounters, and heterogeneity of reporting due to auxiliary mark loss. Journal of Agricultural, Biological and Environmental Statistics 16:88-104.
Péron G, Ferrand Y, Choquet R, Pradel R, Gossmann F, Bastat C, Guénézan M, Bauthian I, Julliard R, Gimenez O (2012) Spatial heterogeneity in mortality and its impact on the population dynamics of Eurasian woodcocks. Population Ecology 54:305-312. 10.1007/s10144-012-0309-6
Sanz-Aguilar A, Tavecchia G, Genovart M, Igual JM, Oro D, Rouan L, Pradel R (2011) Studying the reproductive skipping behavior in long-lived birds by adding nest-inspection to individual-based data. Ecological Applications 21:555-564.
Recruitment and breeding probability:
Melin et al (2012) Age-specific recruitment and natality of California sea lions at San Miguel Island, California. MARINE MAMMAL SCIENCE, 28(4): 751–776
Reichert et al (2012) Extreme weather and experience influence reproduction in an endangered bird. Ecology, 93(12), 2012, pp. 2580–2589
Barbraud & Weimerskirch (2012) Estimating survival and reproduction in a quasi-biennially breeding seabird with uncertain and unobservable states. J Ornithol (2012) 152 (Suppl 2):S605–S615
Desprez et al (2013) Known unknowns in an imperfect world: incorporating uncertainty in recruitment estimates using multi-event capture–recapture models. Ecology and Evolution 2013; 3(14): 4658-4668
Desprez M, Harcourt R, Hindell MA, Cubaynes S, Gimenez O, McMahon CR. 2014 Age-specific cost of first reproduction in female southern elephant seals. Biol. Lett. 10: 20140264.
Soldatini C, Albores-Barajas YV, Massa B, Gimenez O (2014) Climate Driven Life Histories: The Case of the Mediterranean Storm Petrel. PLoS ONE 9(4): e94526.
Goutte et al (2014) Demographic consequences of heavy metals and persistent organic pollutants in a vulnerable long-lived bird, the wandering albatross. Proc. R. Soc. B 281 : 20133313
Goutte et al (2014) Demographic responses to mercury exposure in two closely related Antarctic top predators. Ecology, 95(4), 1075–1086
Costantini D, Goutte A, Barbraud C, Faivre B, Sorci G, Weimerskirch H, et al. (2015) Demographic Responses to Oxidative Stress and Inflammation in the Wandering Albatross ( Diomedea exulans). PLoS ONE 10(8): e0133967.
Paquet et al (2015) Antagonistic effect of helpers on breeding male and female survival in a cooperatively breeding bird. Journal of Animal Ecology 2015, 84, 1354–1362
Fay et al (2015) Population density and climate shape early-life survival and recruitment in a long-lived pelagic seabird. Journal of Animal Ecology 2015, 84, 1423–1433
Goutte et al (2015) Survival rate and breeding outputs in a high Arctic seabird exposed to legacy persistent organic pollutants and mercury. Environmental Pollution 200 (2015) 1-9
Sanz-Aguilar et al (2015) Action on multiple fronts, illegal poisoning and wind farm planning, is required to reverse the decline of the Egyptian vulture in southern Spain. Biological Conservation 187 (2015) 10–18
Fay R, Barbraud C, Delord K, Weimerskirch H. 2016 Paternal but not maternal age influences early-life performance of offspring in a long-lived seabird. Proc. R. Soc. B 283 : 20152318.
Sanz-Aguilar_et_al-2016. Estimating recruitment and survival in partially monitored populations. Journal of Applied Ecology 2016, 53, 73–82
Genovart et al. (2016) Demography of the critically endangered Balearic shearwater: the impact of fisheries and time to extinction. Journal of Applied Ecology 2016, 53, 1158–1168
Fay R, Barbraud C, Delord K, Weimerskirch H (2017) Contrasting effects of climate and population density over time and life stages in a long-lived seabird. Functional Ecology, 31, 1275–1284
Desprez M, Pradel R, Cam E, Monnat J-Y, Gimenez O (2011) Now you see him, now you don't: experience, not age, is related to reproduction in kittiwakes. Proceedings of the Royal Society of London Series B-Biological Sciences 278:3060-3066.
Hernández-Matías, A., J. Real, et al. (2010). "Determinants of territorial recruitment in Bonelli’s eagle (Aquila fasciata) populations." Auk 127(1): 173-184.
Juillet C, Choquet R, Gauthier G, Lefebvre J, Pradel R (2012) Carry-over effects of spring hunt and climate on recruitment to the natal colony in a migratory species. Journal of Applied Ecology: 49: 1237-1246. 10.1111/j.1365-2664.2012.02199.x
Lescroel, A., K. M. Dugger, et al. (2009). "Effects of individual quality, reproductive success and environmental variability on survival of a long-lived seabird." Journal of Animal Ecology 78(4): 798-806.
Lorentzen E, Choquet R, Steen H (2012). Modelling state uncertainty with photo series data for the estimation of breeding success in a cliff-nesting seabird. Journal of Ornithology 152:S477-S483. 10.1007/s10336-011-0723-0
Millon, A., S. J. Petty, et al. (2010). "Pulsed resources affect the timing of first breeding and lifetime reproductive success of tawny owls." Journal of Animal Ecology 79(2): 426-435.
Pradel R, Choquet R, Béchet A (2012) Breeding experience might be a major determinant of breeding probability in long-lived species: the case of the greater flamingo. PLOS One 7(12): e51016.
Reed, E. T., G. Gauthier, et al. (2005). "Effects of neck bands on reproduction and survival of female greater snow geese." Journal of Wildlife Management 69(1): 91-100.
Sanz-Aguilar, A., G. Tavecchia, et al. (2008). "The cost of reproduction and experience-dependent vital rates in a small petrel." Ecology 89(11): 3195–3203.
Schmaltz L, Cezilly F, Bechet A (2011). Using multistate recapture modelling to assess age-specific bottlenecks in breeding success: a case study in the greater flamingo Phoenicopterus roseus. Journal of Avian Biology 42:178-186. 10.1111/j.1600-048X.2010.05112.x
Tavecchia, G., R. Pradel, et al. (2007). "Density-dependent parameters and demographic equilibrium in open populations." Oikos 116(9): 1481-92.
Causes of mortality:
Etterson (2013) Hidden Markov models for estimating animal mortality from anthropogenic hazards. Ecological Applications, 23(8), 2013, pp. 1915–1925
Hardouin et al (2015) Survival and movement of translocated houbara bustards in a mixed conservation area. Animal Conservation 18 (2015) 461–470
Ruette et al (2015) Comparative survival pattern of the syntopic pine and stone martens in a trapped rural area in France. Journal of Zoology 295 (2015) 214–222
Hernández-Matías, A., J. Real, F. Parés, and R. Pradel. 2015. Electrocution threatens the viability of populations of the endangered Bonelli’s eagle (Aquila fasciata) in Southern Europe. Biological Conservation 191:110–116.
Fernández-Chacón A et al (2015) Demographic effects of full vs. partial protection from harvesting: inference from an empirical before–after control-impact study on Atlantic cod. Journal of Applied Ecology 2015, 52, 1206–1215
Gervasi V et al (2016) Sharing data improves monitoring of trans-boundary populations: the case of wolverines in central Scandinavia. Wildlife Biology, 22(3):95-106
Fernández-Chacón A et al (2017) Causes of mortality in depleted populations of Atlantic cod estimated from multi-event modelling of mark–recapture and recovery data. Journal Canadien des sciences halieutiques et aquatiques, 2017, 74(1): 116-126
Kleiven AR, Fernandez-Chacon A, Nordahl J-H, Moland E, Espeland SH, Knutsen H, et al. (2016) Harvest Pressure on Coastal Atlantic Cod (Gadus morhua) from Recreational Fishing Relative to Commercial Fishing Assessed from Tag-Recovery Data. PLoS ONE11(3): e0149595
Genovart M, Doak DF, Igual J-M, Sponza S, Kralj J, Oro D (2017) Varying demographic impacts of different fisheries on three Mediterranean seabird species. Glob Change Biol. 23: 3012–3029.
Schaub, M. and R. Pradel (2004). "Assessing the relative importance of different sources of mortality from recoveries of marked animals." Ecology 85(4): 930-8.
Tavecchia G, Adrover J, Muñoz Navarro A, Pradel R (2012) Modelling mortality causes in longitudinal data in the presence of tag loss: application to raptor poisoning and electrocution. Journal of Applied Ecology 49:297-305.
Sex, age, species uncertainty:
Santoro S, Green AJ, Figuerola J (2013) Environmental Instability as a Motor for Dispersal: A Case Study from a Growing Population of Glossy Ibis. PLoS ONE 8(12): e8298
Santoro et al. 2016. Immigration enhances fast growth of a newly established source population. Ecology, 97(4), 2016, pp. 1048–1057
Cayuela, H., D. Arsovski, E. Bonnaire, R. Duguet, P. Joly, and A. Besnard. 2016. The impact of severe drought on survival, fecundity and population persistence in an endangered amphibian. Ecosphere 7(2):e01246.
Cayuela et al (2016) Demographic responses to weather fluctuations are context dependent in a long-lived amphibian. Global Change Biology (2016) 22, 2676–2687
Cayuela et al (2016) Contrasting patterns of environmental fluctuation contribute to divergent life histories among amphibian populations. Ecology, 97(4), 2016, pp. 980–991
Cayuela et al (2017) Life history tactics shape amphibians’ demographic responses to the North Atlantic Oscillation. Glob Change Biol. 23:4620–4638.
Gervasi V (2017). Estimating survival in the Apennine brown bear accounting for uncertainty in age classification. Popul Ecol (2017) 59:119–130.
Genovart M, Pradel R, Oro D (2012) Exploiting uncertain ecological fieldwork data with multi-event capture-recapture modelling: an example with bird sex assignment. Journal of Animal Ecology 81:970-977. 10.1111/j.1365-2656.2012.01991.x
Hardouin LA, Nevoux M, Robert A, Gimenez O, Lacroix F, Hingrat Y (2012). Determinants and costs of natal dispersal in a lekking species. Oikos 121:804-812. 10.1111/j.1600-0706.2012.20313.x
Pradel, R., L. Maurin-Bernier, et al. (2008). "Estimation of sex-specific survival with uncertainty in sex assessment." Canadian Journal of Statistics-Revue Canadienne De Statistique 36(1): 29-42.
Runge, J. P., J. E. Hines, et al. (2007). "Estimating species-specific survival and movement when species identification is uncertain." Ecology 88(2): 282-288.
Stopover duration:
Choquet, R., Y. Guédon, A. Besnard, M. Guillemain, and R. Pradel. 2013. Estimating stop over duration in the presence of trap-effects. Ecological Modelling 250:111–118.
Guérin etal (2017) Advances in methods for estimating stopover duration for migratory species using capture–recapture data. Ecological Applications, 27(5), 1594–1604
Choquet R, Guédon Y, Besnard A, Guillemain M, Pradel R (2013) Estimating Stop over Duration in presence of trap-effects. Ecological Modelling 250: 111-118.
Rivalan, P., R. Pradel, et al. (2006). "Estimating clutch frequency in the sea turtle Dermochelys coriacea using stopover duration." Marine Ecology-Progress Series 317: 285-295.
Verkuil, Y. I., J. J. Wijmenga, et al. (2010). "Spring migration of Ruffs Philomachus pugnax in Fryslan: estimates of staging duration using resighting data." Ardea 98(1): 21-33.
Trade-offs:
Souchay, G., G. Gauthier, and R. Pradel. 2014. To breed or not: A novel approach to estimate breeding propensity and potential trade-offs in an Arctic-nesting species. Ecology 95(10):2745–2756.
Robert A, Bolton M, Jiguet F, Bried J. 2015 The survival–reproduction association becomes stronger when conditions are good. Proc. R. Soc. B 282 : 20151529.
Sanz-Aguilar, A. et al. (2017) Sex- and age-dependent patterns of survival and breeding success in a long-lived endangered avian scavenger. Sci. Rep. 7, 40204; doi: 10.1038/srep40204
Rivalan, P., A.-C. Prévot-Julliard, et al. (2005). "Trade-off between current reproductive effort and delay to next reproduction in the leatherback sea turtle." Oecologia 145(4): 564-74.
Schaub, M. and J. von Hirschheydt (2009). "Effect of current reproduction on apparent survival, breeding dispersal, and future reproduction in barn swallows assessed by multistate capture-recapture models." Journal of Animal Ecology 78(3): 625-635.
Memory models:
Cole, D. J., B. J. T. Morgan, R. S. McCrea, R. Pradel, O. Gimenez, and R. Choquet. 2014. Does your species have memory? Analyzing capture-recapture data with memory models. Ecology and Evolution 4(11):2124–2133.
Rouan, L., R. Choquet, et al. (2009). "A General Framework for Modeling Memory in Capture-Recapture Data." Journal of Agricultural Biological and Environmental Statistics 14(3): 338-355.
Migration:
Genovart M, Sanz-Aguilar A, Fernandez-Chacon A, Igual JM, Pradel R, Forero MG, Oro D (2013) Contrasting effects of climatic variability on the demography of a trans-equatorial migratory seabird. Journal of Animal Ecology 82: 121-130.
Lok T, Overdijk O, Piersma T. (2015). The cost of migration: spoonbills suffer higher mortality during trans-Saharan spring migrations only. Biol. Lett. 11: 20140944
Lok T, Overdijk O, Piersma T. (2013). Migration Tendency Delays Distributional Response to Differential Survival Prospects along a Flyway. The american Naturalist 181(4): 520-531
Sanz-Aguilar A, Béchet A, Germain C, Johnson AR, Pradel R (2012) To leave or not to leave: survival tradeoffs between different migratory strategies in the Greater Flamingo. Journal of Animal Ecology. 10.1111/j.1365-2656.2012.01997.x
Robust design:
Kendall et al 2013. Combinin g dead recovery, auxiliary observations and robust design data to estimate demographic parameters from marked individuals. Methods in Ecology and Evolution 2013, 4, 828–835
Cayuela et al (2015) Slow life history and rapid extreme flood: demographic mechanisms and their consequences on population viability in a threatened amphibian. Freshwater Biology (2015) 60, 2349–2361
Cayuela et al (2016) Demographic responses to weather fluctuations are context dependent in a long-lived amphibian. Global Change Biology (2016) 22, 2676–2687
Cayuela et al (2016) Contrasting patterns of environmental fluctuation contribute to divergent life histories among amphibian populations. Ecology, 97(4), 2016, pp. 980–991
Richard et al (2017) From gestation to weaning: Combining robust design and multi- event models unveils cost of lactation in a large herbivore. J Anim Ecol. 86:1497–1509
Kendall WL, White GC, Hines JE, Langtimm CA, Yoshizaki J (2012). Estimating parameters of hidden Markov models based on marked individuals: use of robust design data. Ecology 93:913-920.

Senescence:
Koons et al (2014) Methods for studying cause-specific senescence in the wild. Methods in Ecology and Evolution 2014, 5, 924–933
Berger V et al (2016) Age-specific survival in the socially monogamous alpine marmot (Marmota marmota): evidence of senescence. Journal of Mammalogy, 97(3):992–1000
Fay R, Barbraud C, Delord K, Weimerskirch H (2017) From early life to senescence: individual heterogeneity in a long-lived seabird. Ecological Monographs, 0(0), 2017, pp. 1–14
Choquet R, Viallefont A, Rouan L, Gaanoun K, Gaillard JM (2011). A semi-Markov model to assess reliably survival patterns from birth to death in free-ranging populations. Methods in Ecology and Evolution 2:383-389. 10.1111/j.2041-210X.2011.00088.x
Marzolin G, Charmantier A, Gimenez O (2011). Frailty in state-space models: application to actuarial senescence in the Dipper. Ecology 92:562-567. 10.1890/10-0306.1
Peron G, Crochet PA, Choquet R, Pradel R, Lebreton JD, Gimenez O (2010). Capture-recapture models with heterogeneity to study survival senescence in the wild. Oikos 119:524-532. 10.1111/j.1600-1706.2009.17882.x

Site occupancy:
MacKenzie et al (2012) Investigating the population dynamics of California spotted owls without marked individuals. J Ornithol (2012) 152 (Suppl 2):S597–S604
Cayuela et al 2013. Multi-event models reveal the absence of interaction between an invasive frog and a native endangered amphibian. Biol Invasions (2013) 15:2001–2012
Gimenez, O., L. Blanc, A. Besnard, R. Pradel, P. F. Doherty, E. Marboutin, and R. Choquet. 2014. Fitting occupancy models with E-SURGE: Hidden Markov modelling of presence-absence data. Methods in Ecology and Evolution 5(6):592–597.
Mosher BA (2017). Inferential biases linked to unobservable states in complex occupancy models. Ecography 40: 001–008.

Plant dormancy:
Fréville, H., R. Choquet, R. Pradel, and P.-O. Cheptou. 2013. Inferring seed bank from hidden Markov models: new insights into metapopulation dynamics in plants. Journal of Ecology 101(6):1572–1580.
Behavior, Sociality:
Culina, A., S. Lachish, R. Pradel, R. Choquet, and B. C. Sheldon. 2013. A multievent approach to estimating pair fidelity and heterogeneity in state transitions. Ecology and Evolution 3(13):4326–4338.
Reisinger RR, Oosthuizen WC, Péron G, Cory Toussaint D, Andrews RD, et al. (2014) Satellite Tagging and Biopsy Sampling of Killer Whales at Subantarctic Marion Island: Effectiveness, Immediate Reactions and Long-Term Responses. PLoS ONE 9(11): e111835
Culina et al (2015) Evidence of a link between survival and pair fi delity across multiple tit populations. Journal of Avian Biology 46: 507–515
Dupont, P., R. Pradel, S. Lardy, D. Allainé, and A. Cohas. 2015. Litter sex composition influences dominance status of Alpine marmots (Marmota marmota). Oecologia 179(3):753–763.
Sanz-Aguilar, A., R. Jovani, C. J. Melián, R. Pradel, and J. L. Tella. 2015. Multi-event capture-recapture analysis reveals individual foraging specialization in a generalist species. Ecology 96(6):1650–1660.
Bonnet X et al. (2016). A prison effect in a wild population: a scarcity of females induces homosexual behaviors in males. Behavioral Ecology, Volume 27, Issue 4, 1 January 2016, Pages 1206–1215.

Indirect information:
Culina, A., S. Lachish, R. Pradel, R. Choquet, and B. C. Sheldon. 2013. A multievent approach to estimating pair fidelity and heterogeneity in state transitions. Ecology and Evolution 3(13):4326–4338.
Genovart, M., A. Sanz-Aguilar, A. Fernández-Chacón, J. M. Igual, R. Pradel, M. G. Forero, and D. Oro. 2013. Contrasting effects of climatic variability on the demography of a trans-equatorial migratory seabird. Journal of Animal Ecology 82(1):121–130.
Culina et al (2015) Evidence of a link between survival and pair fi delity across multiple tit populations. Journal of Avian Biology 46: 507–515
Berger V et al (2016) Age-specific survival in the socially monogamous alpine marmot (Marmota marmota): evidence of senescence. Journal of Mammalogy, 97(3):992–1000.
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