Sampling stochasticity leads to overestimation of extinction risk in population viability analysis

Which method should be used for estimating extinction risk? We present four separate estimates of extinction risk for the threatened pine lily (Lilium catesbaei Walter), based on two methods of estimating abundance (direct abundance counts and Jolly-Seber abundance estimates) and two methods of estimating extinction risk (direct simulation of the stochastic exponential growth (SEG) model, and the diffusion approximation). We compare the accuracy of these four combinations with a simulated data set where simulated-true population abundance and extinction risk is known. The Jolly-Seber method of abundance estimation in combination with direct estimation of extinction risk is the least biased combination of the four methods tested. We conclude that Jolly-Seber (or other mark-recapture) estimates should be used in combination with direct simulation of the SEG, when sampling error is expected. For the pine lily, we conclude that risk of extinction is low in the population studied.