8 Life history
WORK IN PROGRESS
See https://www.oxfordbibliographies.com/display/document/obo-9780199830060/obo-9780199830060-0016.xml and https://en.wikipedia.org/wiki/Life_history_theory for a definition. I think that all case studies below fall in the LH category. I might consider moving the disease ecology case study in the main Sites and states chapter. See however https://onlinelibrary.wiley.com/doi/epdf/10.1111/ele.13681 for a link between disease ecology and life history theory.
8.1 Access to reproduction
Pradel et al. (1997)
Transition matrix:
\[\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix} \hspace{-1.2em} \begin{matrix} z_t=J & z_t=1yNB & z_t=2yNB & z_t=B & z_t=D \\ \hdashline 0 & \phi_1 (1-\alpha_1) & 0 & \phi_1 \alpha_1 & 1 - \phi_1\\ 0 & 0 & \phi_2 (1-\alpha_2) & \phi_2 \alpha_2 & 1 - \phi_2\\ 0 & 0 & 0 & \phi_3 & 1 - \phi_3\\ 0 & 0 & 0 & \phi_B & 1 - \phi_B\\ 0 & 0 & 0 & 0 & 1 \end{matrix} \hspace{-0.2em} \begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t-1} = J \\ z_{t-1} = 1yNB \\ z_{t-1} = 2yNB \\ z_{t-1} = B \\ z_{t-1} = D \end{matrix} \end{matrix}\]
First-year and second-year individuals breed with probabilities \(\alpha_1\) and \(\alpha_2\). Then, everybody breeds from age 3.
Observation matrix:
\[\begin{matrix} & \\ \mathbf{\Omega} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\12 \end{matrix} } \right . \end{matrix} \hspace{-1.2em} \begin{matrix} y_t = 1 & y_t = 2 & y_t = 3 & y_t = 4\\ \hdashline 1 & 0 & 0 & 0\\ 1 - p_1 & p_1 & 0 & 0\\ 1 - p_2 & 0 & p_2 & 0\\ 1 - p_3 & 0 & 0 & p_3\\ 1 & 0 & 0 & 0 \end{matrix} \hspace{-0.2em} \begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \\ 12 \\12 \end{matrix} } \right ) \begin{matrix} z_t = J \\ z_t = 1yNB \\ z_t = 2yNB \\ z_t = B \\ z_t = D \end{matrix} \end{matrix}\]
Juveniles are never detected.
8.2 Tradeoffs
Morano et al. (2013), Shefferson et al. (2003), and Cruz-Flores et al. (n.d.)
Case study with simulations as in Oikos paper, see Figure 1 and Table 2. Would be a nice example of the use of simulations. Another example could the statistical power analyses.
8.3 Breeding dynamics
Pradel, Choquet, and Béchet (2012), Desprez et al. (2011), Desprez et al. (2013), and Pacoureau et al. (2019)
8.4 Using data on dead recoveries
8.4.2 Combination of live captures and dead recoveries
Combine live recapture w/ dead recoveries by Lebreton, Almeras, and Pradel (1999).
Transition matrix
\[\begin{matrix} & \\ \mathbf{\Gamma} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right . \end{matrix} \hspace{-1.2em} \begin{matrix} z_t=A & z_t=JD & z_t=D \\ \hdashline s & 1-s & 0\\ 0 & 0 & 1\\ 0 & 0 & 1 \end{matrix} \hspace{-0.2em} \begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t-1}=\text{alive} \\ z_{t-1}=\text{just dead} \\ z_{t-1}=\text{dead for good} \end{matrix} \end{matrix}\]
Observation matrix
\[\begin{matrix} & \\ \mathbf{\Omega} = \left ( \vphantom{ \begin{matrix} 12 \\ 12 \\ 12\end{matrix} } \right . \end{matrix} \hspace{-1.2em} \begin{matrix} y_t=1 & y_t=2 & y_t=3 \\ \hdashline 1 - p & 0 & p\\ 1 - r & r & 0\\ 1 & 0 & 0 \end{matrix} \hspace{-0.2em} \begin{matrix} & \\ \left . \vphantom{ \begin{matrix} 12 \\ 12 \\ 12 \end{matrix} } \right ) \begin{matrix} z_{t}=A \\ z_{t}=JD \\ z_{t}=D \end{matrix} \end{matrix}\]
8.5 Stopover duration
Guérin et al. (2017) for a comparison of method, would be great to reproduce all analyses.
8.6 Actuarial senescence
Choquet et al. (2011), Péron et al. (2016) and Marzolin, Charmantier, and Gimenez (2011).
8.7 Uncertainty in age
E.g. Gervasi et al. (2017).
8.8 Uncertainty in age and size
E.g. Gowan et al. (2021).