Estimating population abundance using counts from an auxiliary population

We develop a new method for estimating population abundance for notoriously difficult to count populations. This is made possible using an easy to count auxiliary population with a known link to the target population under the framework of a layered hidden Markov model. We apply the new methods to estimate the breeding population of an Ancient Murrelet seabird colony, using Ancient Murrelet chicks as an auxiliary population. We compare our results to those of the established survey methodology from the Canadian Wildlife Service (CWS), which similarly shows a decrease in population over 1995 to 2006. Our methods improve upon the CWS survey methods by allowing density differences across sampling sites, and by allowing estimates to be made between CWS survey years.