A semi-Markov model to assess reliably survival patterns from birth to death in free-ranging populations

Methods in Ecology and Evolution

Volumn 2, Issue 4, 2011, Pages 383-389

  Choquet, Rémi ^a   Viallefont, Anne ^b   Rouan, Lauriane ^c   Gaanoun, Kamel ^a   Gaillard, Jean Michel ^b  

^a CENTRE D ECOLOGIE FONCTIONNELLE ET EVOLUTIVE   (France)

^b UNIVERSITÉ LYON 1   (France)

^c CIRAD   (France)

Author keywords

Continuous function; Cormack Jolly Seber model; Long lived species; Mixture; Nonlinear model; Reduce Additive Weibull; Siler

Indexed keywords

EID: 84867671899     PISSN: None     EISSN: 2041210X     Source Type: Journal    
DOI: 10.1111/j.2041-210X.2011.00088.x     Document Type: Article

References (42)

1. Bebbington, M., Lai, C. & Zitikis, R. (2007a) Modeling human mortality using mixtures of bathtub shaped failure distributions. Journal of Theoretical Biology, 245, 528-538.
2. Bebbington, M., Lai, C.D. & Zitikis, R. (2007b) A flexible weibull extension. Reliability Engineering and System Safety, 92, 719-726.
3. Bennett, P. & Owens, I. (2002) Evolutionary Ecology of Birds. Life Histories, Mating Systems and Extinction. Ecology and Evolution, Oxford University Press, Oxford, UK.
4. Bonduriansky, R., Maklakov, A., Zajitschek, F. & Brooks, R. (2008) Sexual selection, sexual conflict and the evolution of ageing and life span. Functional Ecology, 22, 443-453.
5. Burnham, K. & Anderson, D. (2002) Model Selection and Inference: A Practical Information-Theoretic Approach, 2nd edn. Springer-Verlag, New York.
6. Caughley, G. (1966) Mortality patterns in mammals. Ecology, 47, 906-918.
7. Charmantier, A., Perrins, C., McCleery, R.H. & Sheldon, B.C. (2006) Quantitative genetics of age at reproduction in wild swans: support for antagonistic pleiotropy models of senescence. Proceedings of the National Academy of Sciences of the United States of America, 103, 6587-6592.
8. Choquet, R., Lebreton, J.D., Gimenez, O., Reboulet, A. & Pradel, R. (2009a) U-CARE: utilities for performing goodness of fit tests and manipulating CApture-REcapture data. Ecography, 32, 1071-1074.
9. Choquet, R., Rouan, L. & Pradel, R. (2009b) Program E-SURGE: a software application for fitting multievent models. Modeling Demographic Processes in Marked Populations, Volume 3 of Springer Series: Environmental and Ecological Statistics (eds D.L. Thomson, E.G. Cooch & M.J. Conroy), pp. 845-865. Springer, Dunedin.
10. Clutton-Brock, T.H. & Isvaran, K. (2007) Sex differences in ageing in natural populations of vertebrates. Proceedings of the Royal Society B-Biological Sciences, 274, 3097-3104.
11. Coulson, T., Guinness, F., Pemberton, J. & Clutton-Brock, T. (2004) The demographic consequences of releasing a population of red deer from culling. Ecology, 85, 411-422.
12. Dennis, J. & Schnabel, R. (1983) Numerical Methods for Unconstrained Optimization and Nonlinear Equations. Classics in applied mathematics, SIAM.
13. Descamps, S., Boutin, S., Berteaux, D. & Gaillard, J.M. (2006) Best squirrels trade a long life for an early reproduction. Proceedings of the Royal Society B-Biological Sciences, 273, 2369-2374.
14. Festa-Bianchet, M., Gaillard, J.M. & Cote, S.D. (2003) Variable age structure and apparent density dependence in survival of adult ungulates. Journal of Animal Ecology, 72, 640-649.
15. Gaillard, J.M., Delorme, D., Boutin, J.M., Vanlaere, G., Boisaubert, B. & Pradel, R. (1993a) Roe deer survival patterns - a comparative-analysis of contrasting populations. Journal of Animal Ecology, 62, 778-791.
16. Gaillard, J.M., Delorme, D., Jullien, J.M. & Tatin, D. (1993b) Timing and synchrony of births in roe deer. Journal of Mammalogy, 74, 738-744.
17. Gaillard, J.M., Allaine, D., Pontier, D., Yoccoz, N.G. & Promislow, D.E.L. (1994) Senescence in natural-populations of mammals - a reanalysis. Evolution, 48, 509-516.
18. Gaillard, J.M., Boutin, J.M., Delorme, D., Van Laere, G., Duncan, P. & Lebreton, J.-D. (1997) Early survival in roe deer: causes and consequences of cohort variation in two contrasted populations. Oecologia, 112, 502-513.
19. Gaillard, J.M., Festa-Bianchet, M., Yoccoz, N.G., Loison, A. & Toigo, C. (2000) Temporal variation in fitness components and population dynamics of large herbivores. Annual Review of Ecology and Systematics, 31, 367-393.
20. Gaillard, J.M., Duncan, P., Delorme, D., van Laere, G., Pettorelli, N., Maillard, D. & Renaud, G. (2003) Effects of hurricane Lothar on the population dynamics of european roe deer. Journal of Wildlife Management, 67, 767-773.
21. Gaillard, J.M., Viallefont, A., Loison, A. & Festa-Bianchet, M. (2004) Assessing senescence patterns in populations of large mammals. Animal Biodiversity and Conservation, 27, 47-58.
22. Gimenez, O., Covas, R., Brown, C., Anderson, M., Brown, M. & Lenormand, T. (2006) Nonparametric estimation of natural selection on a quantitative trait using mark-recapture data. Evolution, 60, 460-466.
23. Gimenez, O., Viallefont, A., Charmantier, A., Pradel, R., Cam, E., Brown, C.R., Anderson, M.D., Brown, M.B., Covas, R. & Gaillard, J.M. (2008) The risk of flawed inference in evolutionary studies when detectability is less than one. American Naturalist, 172, 441-448.
24. Guédon, Y. (1999) Computational methods for discrete hidden semi-Markov chains. Applied Stochastic Models in Business and Industry, 15, 195-224.
25. Guédon, Y. (2004) Hidden hybrid Markov/semi-Markov chains. Computational Statistics and Data Analysis, 49, 663-688.
26. Hamel, S., Gaillard, J.M., Festa-Bianchet, M. & Cote, S.D. (2009) Individual quality, early-life conditions, and reproductive success in contrasted populations of large herbivores. Ecology, 90, 1981-1995.
27. Heligman, L. & Pollard, J. (1980) The age pattern of mortality. Journal of the Institute of Actuaries, 107, 47-77.
28. Jones, O.R., Gaillard, J.M., Tuljapurkar, S., Alho, J.S., Armitage, K.B., Becker, P.H., Bize, P., Brommer, J., Charmantier, A., Charpentier, M., Clutton-Brock, T., Dobson, F.S., Festa-Bianchet, M., Gustafsson, L., Jensen, H., Jones, C.G., Lillandt, B.G., McCleery, R., Merila, J., Neuhaus, P., Nicoll, M.A.C., Norris, K., Oli, M.K., Pemberton, J., Pietiainen, H., Ringsby, T.H., Roulin, A., Saether, B.E., Setchell, J.M., Sheldon, B.C., Thompson, P.M., Weimerskirch, H., Wickings, E.J. & Coulson, T. (2008) Senescence rates are determined by ranking on the fast-slow life-history continuum. Ecology Letters, 11, 664-673.
29. Lebreton, J.-D., Burnham, K., Clobert, J. & Anderson, D. (1992) Modeling survival and testing biological hypotheses using marked animals: a unified approach with case studies. Ecological Monographs, 62, 67-118.
30. Lescroel, A., Dugger, K.M., Ballard, G. & Ainley, D.G. (2009) Effects of individual quality, reproductive success and environmental variability on survival of a long-lived seabird. Journal of Animal Ecology, 78, 798-806.
31. Loison, A., Festa-Bianchet, M., Gaillard, J.M., Jorgenson, J.T. & Jullien, J.M. (1999) Age-specific survival in five populations of ungulates: evidence of senescence. Ecology, 80, 2539-2554.
32. Menkens, G.E. & Boyce, M.S. (1993) Comments on the use of time-specific and cohort life-tables. Ecology, 74, 2164-2168.
33. Nichols, J.D., Brownie, C., Hines, J.E., Pollock, K.H. & Hestbeck, J.B. (1993) The estimation of exchanges among populations or subpopulations. Marked Individuals in the Study of Bird Population (eds J.-D. Lebreton & P.M. North), pp. 265-279. Birkhauser Verlag, Basel, Switzerland.
34. Nussey, D., Coulson, T., Festa-Bianchet, M. & Gaillard, J.M. (2008) Measuring senescence in wild animal populations: towards a longitudinal approach. Functional Ecology, 22, 393-406.
35. Péron, G., Crochet, P.A., Choquet, R., Pradel, R., Lebreton, J.D. & Gimenez, O. (2010a) Capture-recapture models with heterogeneity to study survival senescence in the wild. Oikos, 119, 524-532.
36. Péron, G., Gimenez, O., Charmantier, A., Gaillard, J.M. & Crochet, P.A. (2010b) Age at the onset of senescence in birds and mammals is predicted by early-life performance. Proceedings of the Royal Society B-Biological Sciences, 277, 2849-2856.
37. Pradel, R. (2005) Multievent: an extension of multistate capture-recapture models to uncertain states. Biometrics, 61, 442-447.
38. Pradel, R., Hines, J., Lebreton, J.-D. & Nichols, J. (1997) Capture-recapture survival models taking account of transients. Biometrics, 53, 60-72.
39. Ricklefs, R.E. & Cadena, C.D. (2007) Lifespan is unrelated to investment in reproduction in populations of mammals and birds in captivity. Ecology Letters, 10, 867-872. DOI: 10.1007/513253-010-0031-9.
40. Siler, W. (1979) Competing-risk model for animal mortality. Ecology, 60, 750-757.
41. Viallefont, A. (2011) Capture-recapture smooth estimation of age-specific survival probabilities in animal populations. Journal of Agricultural Biological and Environmental Statistics
42. Xie, M. & Lai, C.D. (1996) Reliability analysis using an additive weibull model with bathtub-shaped failure rate function. Reliability Engineering and System Safety, 52, 87-93.