The effects of human-caused mortality, such as fisheries bycatch, of endangered, threatened and protected (ETP) species of marine mammals can be evaluated using population model-based stock assessments. The information available to conduct such assessments is often very limited. Available data might include fragmented time-series of abundance estimates, incomplete data on bycatch for the fisheries that interact with ETP species (often few years and low observer coverage), and perhaps some data on scale and trends in fishing effort. Such data are challenging to use as the basis for stock assessments, which generally assume that estimates of removals (bycatch, in our context) through time are available for at least the most recent decade or two. This paper describes a stock assessment method for use with sparse observer data on bycatch mortality, applied within the context of a Bayesian estimation framework. The method produces estimates, with associated measures of precision, of population size and historical time-series of bycatch mortality that are consistent with the observer and abundance data. It provides a rigorous way to account for the uncertainty arising from animals that are caught but released alive and then die subsequent to release, given a post-release mortality rate prior. Observer data from industrial and artisanal purse seine and trawl fisheries and survey data for South American sea lions (Otaria byronia) and South American fur seals (Arctocephalus australis) off Chile are used to illustrate the method.

Motivated by the need to estimate the abundance of marine mammal populations to inform conservation assessments, especially relating to fishery bycatch, this paper provides background on abundance estimation and reviews the various methods available for pinnipeds, cetaceans and sirenians. We first give an “entry-level” introduction to abundance estimation, including fundamental concepts and the importance of recognizing sources of bias and obtaining a measure of precision. Each of the primary methods available to estimate abundance of marine mammals is then described, including data collection and analysis, common challenges in implementation, and the assumptions made, violation of which can lead to bias. The main method for estimating pinniped abundance is extrapolation of counts of animals (pups or all-ages) on land or ice to the whole population. Cetacean and sirenian abundance is primarily estimated from transect surveys conducted from ships, small boats or aircraft. If individuals of a species can be recognized from natural markings, mark-recapture analysis of photo-identification data can be used to estimate the number of animals using the study area. Throughout, we cite example studies that illustrate the methods described. To estimate the abundance of a marine mammal population, key issues include: defining the population to be estimated, considering candidate methods based on strengths and weaknesses in relation to a range of logistical and practical issues, being aware of the resources required to collect and analyze the data, and understanding the assumptions made. We conclude with a discussion of some practical issues, given the various challenges that arise during implementation.