Assessing small-mammal trapping design using spatially explicit capture recapture (SECR) modeling on long-term monitoring data.

Few studies have evaluated the optimal sampling design for tracking small mammal population trends, especially for rare or difficult to detect species. Spatially explicit capture-recapture (SECR) models present an advancement over non-spatial models by accounting for individual movement when estimating density. The salt marsh harvest mouse (SMHM; Reithrodontomys raviventris) is a federal and California state listed endangered species endemic to the San Francisco Bay-Delta estuary, California, USA; where a population in a subembayment has been continually monitored over an 18-year period using mark-recapture methods.

Habitat of the endangered salt marsh harvest mouse () in San Francisco Bay.

Understanding habitat associations is vital for conservation of at-risk marsh-endemic wildlife species, particularly those under threat from sea level rise. We modeled environmental and habitat associations of the marsh-endemic, Federally endangered salt marsh harvest mouse (, RERA) and co-occurrence with eight associated small mammal species from annual trap data, 1998-2014, in six estuarine marshes in North San Francisco Bay, California. Covariates included microhabitat metrics of elevation and vegetation species and cover; and landscape metrics of latitude-longitude, distance to anthropogenic features, and habitat patch size.