Statistical Demography (Fernando Colchero)

Description

• Bayesian inference methods for demography: We developed the Bayesian Survival Trajectory Analysis framework to make inference on age-specific survival when individual times of birth are missing. The approach is formalized in the R package BaSTA (Colchero et al. 2012, Colchero & Clark 2012, Colchero et al. 2021). Similarly, we are currently extending our demographic toolkit to Bayesian Fertility Trajectory Analysis (BaFTA) for inference on age-specific fertility using models developed in other disciplines.

• Comparative biodemography: We use the methods developed in our group to explore the evolution of life-history strategies. For instance, we are analyzing one of the largest datasets on individual longevity from captive animals to explore the evolution of sex differences in longevity among mammals and birds. We are also studying the effect of hormonal and surgical contraception on longevity among mammals. 

• Evolution of Ageing: We are interested in understanding the evolutionary and proximal mechanisms that determine ageing patterns among primates and other groups.

Colchero, F. (Under review) Inference on age-specific fertility in ecology and evolution. Learning from other disciplines and improving the state of the art.

da Silva, R., D.A. Conde, A. Baudisch, F. Colchero (2022) Slow and negligible senescence among testudines challenge evolutionary theories of senescence. Science 376 (6600): 1466-1470

Vincze, O., F. Colchero, J.-F. Lemaître, D.A. Conde, S. Pavard, M. Bieuville, J.A. Teare, A.O. Urrutia, B. Ujvari, F. Thomas, M. Giraudeau (2022) Cancer risk across mammals. Nature 601(7892):263-267

Colchero, F., J.M. Aburto, E.A. Archie, C. Boesch, T. Breuer, F.A. Campos, A. Collins, D.A. Conde, M. Cords, C. Crockford, M.E. Thompson, L.M. Fedigan, C. Fichtel, M. Groenenberg, C. Hobaiter, P.M. Kappeler, R.R. Lawler, R.J. Lewis, Z.P. Machanda, M.L. Manguette, M.N. Muller, Craig Packer, R.J. Parnell, S. Perry, A.E. Pusey, M.M. Robbins, R.M. Seyfarth, J.B. Silk, J. Staerk, T.S. Stoinski, E.J. Stokes, K.B. Strier, S.C. Strum, J. Tung, F. Villavicencio, R.M. Wittig, R.W. Wrangham, K. Züberbuhler, J.W. Vaupel, S.C. Alberts (2021) The long lives of primates and the "invariant rate of aging" hypothesis. Nature Communications 12:3666

Colchero, F., W. Eckardt, T. Stoinski (2021) Evidence of demographic buffering in an endangered great ape: social buffering on immature survival and the role of refined sex-age-classes on population fitness. Journal of Animal Ecology 90(7):1701-1713

Lemaître, J.-F., V. Ronget, M. Tidière, D. Allainé, V. Berger, A. Cohas, F. Colchero, D.A. Conde, A. Liker, G. Marais, A. Scheuerlein, T. Székely, J.-M. Gaillard (2020) Sex differences in longevity and aging rates across wild mammals. PNAS 117(15):8546-8553

Colchero, F. and B.Y. Kiyakoglu (2020) Beyond the proportional frailty model: Bayesian estimation of individual heterogeneity in mortality parameters. Biometrical Journal 62(1):124-135

Staerk, J., D.A. Conde, V. Ronget, J.-F. Lemaître, J-M. Gaillard and F. Colchero (2019) Performance of generation time approximations for extinction risk assessments. Journal of Applied Ecology 56(6): 1436-1446

Colchero, F., O.R. Jones, D.A. Conde, D. Hodgson, F. Zajitschek, B.R. Schmidt, A.F. Malo, S.C. Alberts, P.H. Becker, S. Bouwhuis, A.M. Bronikowski, K.M. De Vleeschouwer, R.J. Delahay, S. Dummermuth, E. Fernández-Duque, J. Frisenvæatnge, M. Hesselsøe, S. Larson, J.-F. Lemaître, J. McDonald, D.A.W. Miller, C. O'Donnell, C. Packer, B.E. Raboy, C.J. Reading, E. Wapstra, H. Weimerskirch, G.M. While, A. Baudisch, T. Flatt, T. Coulson and J.-M. Gaillard (2019) The diversity of population responses to environmental change. Ecology Letters 22(2): 342-353

Colchero, F., R. Rau, O.R. Jones, J. Barthold, D.A. Conde, A. Lenart, L. Nemeth, A. Scheuerlein, J. Schoeley, C. Torres, V. Zarulli, J. Altmann, D.K. Brockman, A.M. Bronikowski, L.M. Fedigan, A. Pusey, T.S. Stoinski, K.B. Strier, A. Baudisch, S.C. Alberts and J.W. Vaupel (2016) The emergence of longevous populations. PNAS 113 (48): E7681-E7690

Barthold, J., A. Loveridge, D. W. Macdonald, C. Packer, F. Colchero (2016) Bayesian estimates of male and female African lion mortality for future use in population management. Journal of Applied Ecology 53: 295-304

Colchero, F. and R. Schaible (2014) Mortality as a bivariate function of age and size in indeterminate growers. Ecosphere 5(12): 161

Colchero, F., O.R. Jones and M. Rebke (2012) BaSTA: an R package for Bayesian estimation of age-specific survival from incomplete mark-recapture/recovery data with covariates. Methods in Ecology and Evolution 3: 466-470

Colchero, F. and James S. Clark (2012) Bayesian inference on age-specific survival for censored and truncated data. Journal of Animal Ecology 81: 139-149

We develop R packages for demographic and comparative analyses:

• BaSTA: Bayesian Survival Trajectory Analysis. Inference on age-specific fertility for capture-mark-recapture data with truncated and censored records and for which times of birth and/or death might be missing for some individuals.
•  paramDemo: parametric functions for age-specific survival and fertility. The package includes functions to calculate product limit estimators.
• CreateRproj: Functions to create an R project directory or an R package directory, allowing to start an Rstudio project and a Git repository.
• BayesPGLS: Functions to carry out Bayesian phylogenetic least squares.