Appendix C. Detailed description of habitat classifications listed in Fig. 1 caption.

Detailed description of habitat classifications listed in Fig. 1 caption

Appendix D. Plot of data and fitted estimates of site-specific abundance for goliath grouper and mutton snapper.

Plot of data and fitted estimates of site-specific abundance for goliath grouper and mutton snapper

Appendix B. Description of the generalized linear mixed model (GLMM) presented for comparison with the demographic model.

Description of the generalized linear mixed model (GLMM) presented for comparison with the demographic model

Appendix A. Description of the site-structured demographic model.

Description of the site-structured demographic model

Supplement 1. Code necessary for replicating the simulation analysis included in this study.

<h2>File List</h2><div> <p><a href="Sim_test--for_supplements.R">Sim_test--for_supplements.R</a> (MD5: 2efc9a4718adb22d7c0d346a44176211)</p> <p><a href="Fn_models--for_supplements.R">Fn_models--for_supplements.R</a> (MD5: 5052b921baa24149ea4e24533b3ef630)</p> </div><h2>Description</h2><div> <p>Sim_test--for_supplements.R – File containing R script used to run simulation experiment comparing the estimation performance of the demographic (Dail-Madsen) and generalized-linear mixed models (GLMM).</p> <p>Fn_models--for_supplements.R – File containing R functions used by "Sim_test--for_supplements.R" file, which is called by "Sim_test--for_supplements.R" to source them into local memory. These functions include (1) the function for writing .bug files that define the model structure for each candidate model; (2) the function generating initial values for each function; (3) and a function for parallelizing JAGS code.</p> </div

Appendix E. Relationship between the total length of focal predators and their stable-isotope values.

Relationship between the total length of focal predators and their stable-isotope values

Appendix D. Predictions of the reliance of focal predators on source habitats derived using Bayesian isotope mixing models parameterized with different fractionation values.

Predictions of the reliance of focal predators on source habitats derived using Bayesian isotope mixing models parameterized with different fractionation values

Supplement 1. JAGS code used in the stable-isotope mixing model.

<h2>File List</h2><p> <a href="Jags_mixing.txt">Jags_mixing.txt</a> (md5: 902a881891bc516447495be936e73e43) </p><h2>Description</h2><p> Jags_mixing.txt contains code designed for JAGS (compatible with WinBUGS and OpenBUGS) for implementing the stable isotope mixing model described in this report. This code outlines the details of prior specification and model parameterization. </p

Appendix B. Description of the stable-isotope values of lower trophic level organisms and resident predatory fish collected from lagoon, forereef, and pelagic habitats.

Description of the stable-isotope values of lower trophic level organisms and resident predatory fish collected from lagoon, forereef, and pelagic habitats

Using Stable Isotope Analysis to Understand the Migration and Trophic Ecology of Northeastern Pacific White Sharks (<em>Carcharodon carcharias</em>)

<div><p>The white shark (<em>Carcharodon carcharias</em>) is a wide-ranging apex predator in the northeastern Pacific (NEP). Electronic tagging has demonstrated that white sharks exhibit a regular migratory pattern, occurring at coastal sites during the late summer, autumn and early winter and moving offshore to oceanic habitats during the remainder of the year, although the purpose of these migrations remains unclear. The purpose of this study was to use stable isotope analysis (SIA) to provide insight into the trophic ecology and migratory behaviors of white sharks in the NEP. Between 2006 and 2009, 53 white sharks were biopsied in central California to obtain dermal and muscle tissues, which were analyzed for stable isotope values of carbon (δ¹³C) and nitrogen (δ¹⁵N). We developed a mixing model that directly incorporates movement data and tissue incorporation (turnover) rates to better estimate the relative importance of different focal areas to white shark diet and elucidate their migratory behavior. Mixing model results for muscle showed a relatively equal dietary contribution from coastal and offshore regions, indicating that white sharks forage in both areas. However, model results indicated that sharks foraged at a higher relative rate in coastal habitats. There was a negative relationship between shark length and muscle δ¹³C and δ¹⁵N values, which may indicate ontogenetic changes in habitat use related to onset of maturity. The isotopic composition of dermal tissue was consistent with a more rapid incorporation rate than muscle and may represent more recent foraging. Low offshore consumption rates suggest that it is unlikely that foraging is the primary purpose of the offshore migrations. These results demonstrate how SIA can provide insight into the trophic ecology and migratory behavior of marine predators, especially when coupled with electronic tagging data.</p> </div