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Three population monitoring methods were evaluated in support of a trap/vaccinate/release program for controlling a bat variant of rabies virus in skunks (Mephitis mephitis) in Flagstaff, Arizona (USA). Skunks were the primary species targeted for population monitoring during the program, but feral cats were also monitored as they represented an abundant secondary vector species capable of rabies transmission. Skunks were vaccinated and released, except for a subset tested for rabies. All captured cats were placed in the local animal shelter. Spotlight surveys essentially did not detect skunks, and were not able to detect reductions in the cat population. Catch-per-unit-effort marginally tracked population trends, but a passive track index adapted for an urban setting was most sensitive for detecting changes in skunk and cat populations. Mark-recapture population estimates could not be validly calculated from the data on captures and recaptures due to multiple violations of analytical assumptions.