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Data from: Assessing cetacean populations using integrated population models: an example with Cook Inlet beluga whales

Citation

Jacobson, Eiren et al. (2020), Data from: Assessing cetacean populations using integrated population models: an example with Cook Inlet beluga whales, Dryad, Dataset, https://doi.org/10.5061/dryad.9zw3r229w

Abstract

Effective conservation and management of animal populations requires knowledge of abundance and trends. For many species, these quantities are estimated using systematic visual surveys. Additional individual-level data are available for some species. Integrated population modelling (IPM) offers a mechanism for leveraging these datasets into a single estimation framework. IPMs that incorporate both population- and individual-level data have previously been developed for birds, but have rarely been applied to cetaceans. Here, we explore how IPMs can be used to improve the assessment of cetacean populations. We combined three types of data that are typically available for cetaceans of conservation concern: population-level visual survey data, individual-level capture-recapture data, and data on anthropogenic mortality. We used this IPM to estimate the population dynamics of the Cook Inlet population of beluga whales (CIBW; Delphinapterus leucas) as a case study. Our state-space IPM included a population process model and three observational submodels: 1) a group detection model to describe group size estimates from aerial survey data; 2) a capture-recapture model to describe individual photographic capture-recapture data; and 3) a Poisson regression model to describe historical hunting data. The IPM produces biologically plausible estimates of population trajectories consistent with all three datasets. The estimated population growth rate since 2000 is less than expected for a recovering population. The estimated juvenile/adult survival rate is also low compared to other cetacean populations, indicating that low survival may be impeding recovery. This work demonstrates the value of integrating various data sources to assess cetacean populations and serves as an example of how multiple, imperfect datasets can be combined to improve our understanding of a population of interest. The model framework is applicable to other cetacean populations and to other taxa for which similar data types are available.

Methods

/Data/CIBW_RSideCapHist_McGuire&Stephens.csv contains a matrix of right side capture histories (1 = captured, 0 = not captured) for each individual (rows) and year (columns).  Photographic capture-recapture data were collected by Tamara McGuire. These data are made available here, without restriction, but anyone wishing to use these data is requested to contact tamaracookinletbeluga@gmail.com, who can provide further information on how raw data were processed to provide capture histories.

/Data/CIBW_HuntData_Mahoney&Shelden2000.xlsx contains the minimum documented number of animals killed (MinKilled) for years between 1950 and 1998 as published in Mahoney and Shelden 2000.  Entries which are NA indicate that no data were available for that year. 

/Data/CIBW_Abundance_HobbsEtAl2015.xlsx contains the total group size estimates from Hobbs et al. 2015.

/Data/CIBW_Abundance_BoydEtAl2019.txt contains an array with dimensions [1:1000, 1:8, 1:11] containing 1000 posterior samples of total group size for up to 8 survey days over 11 years, as described in Boyd et al. 2019.

 

Usage Notes

Models/CIBW_IPM_BetaPObs.txt contains the JAGS model specification as presented in Appendix Data S1.  

Scripts/CIBW_01_CalcPObs.R provides the scripts used to calculate the scale and shape parameters of the beta distribution used as a prior for the probability of observing belugas, as described in Appendix S1.

Scripts/CIBW_02_LoadData.R includes code for reading in and formatting data prior to modeling.

Scripts/CIBW_03_RunModel.R runs the Bayesian model using jagsUI and outputs an RData object.

Funding

North Pacific Research Board, Award: 1718