StrandCet: R package for estimating natural and non-natural mortality-at-age of cetaceans from age-structured strandings.

Camilo Saavedra

doi:10.7717/peerj.5768

Abstract

Mortality is one of the most important parameters for the study of population dynamics. One of the main sources of information to calculate the mortality of cetaceans arises from the observed age-structure of stranded animals. A method based on an adaptation of a Heligman-Pollard model is proposed. A freely accessible package of functions (strandCet) has been created to apply this method in the statistical software R. Total, natural, and anthropogenic mortality-at-age is estimated using only data of stranded cetaceans whose age is known. Bayesian melding estimation with Incremental Mixture Importance Sampling is used for fitting this model. This characteristic, which accounts for uncertainty, further eases the estimation of credible intervals. The package also includes functions to perform life tables, Siler mortality models to calculate total mortality-at-age and Leslie matrices to derive population projections. Estimated mortalities can be tested under different scenarios. Population parameters as population growth, net production or generation time can be derived from population projections. The strandCet R package provides a new analytical framework to assess mortality in cetacean populations and to explore the consequences of management decisions using only stranding-derived data.

Highlights

Cetaceans are protected by several international agreements and legislation (e.g., Agreement on the Conservation of Small Cetaceans of the Baltic, North East Atlantic, Irish and North Seas—ASCOBANS; the “Habitats” Directive—European Council, 1992; European Parliament, 2008) and effective management is needed to ensure their conservation
Modeling population dynamics provides a useful tool to assess the consequences of human activities and the impact on cetacean populations, and as such can support conservation management decisions
It is necessary to know the total mortality-at-age, and what fraction of it is due to natural processes and what fraction to anthropogenic processes, for example, fishery bycatch, which represents a significant threat to many cetacean species in the European Atlantic and other parts of the world (Northridge, 1991; Read, Drinker & Northridge, 2006; Young & Iudicello, 2007; Reeves, McClellan & Werner, 2013; Dolman et al, 2017; Peltier et al, 2016)

Summary

INTRODUCTION

Cetaceans are protected by several international agreements and legislation (e.g., Agreement on the Conservation of Small Cetaceans of the Baltic, North East Atlantic, Irish and North Seas—ASCOBANS; the “Habitats” Directive—European Council, 1992; European Parliament, 2008) and effective management is needed to ensure their conservation. Secchi & Fletcher (2004) proposed an extension of the Siler model, later improved using reproductive data and adapted to a Bayesian framework by Moore & Read (2008) This method uses age-structured strandings and bycatch to study cetacean demography in a mixture model that allows the study of natural mortality. The HP follows a similar pattern as the Siler model but includes more flexibility to model an extra mortality component A set of functions have been written and compiled in a R package called strandCet (Saavedra, 2018) to assess mortality in cetacean populations and explore the consequences of management decisions using only stranding-derived data

MATERIALS AND METHODS

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DISCUSSION

CONCLUSIONS