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

Abstract

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 (Reithrodontomys raviventris, 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. The dominant cover was pickleweed (Salicornia pacifica) with 86% mean cover and 37 cm mean height, and bare ground with about 10% mean cover. We tested 38 variants of Bayesian network (BN) models to determine covariates that best account for presence of RERA and of all nine small mammal species. Best models had lowest complexity and highest classification accuracy. Among RERA presence models, three best BN models used covariates of latitude-longitude, distance to paved roads, and habitat patch size, with 0% error of false presence, 20% error of false nonpresence, and 20% overall error. The all-species presence models suggested that within the pickleweed marsh environment, RERA are mostly habitat generalists. Accounting for presence of other species did not improve prediction of RERA. Habitat attributes compared between RERA and the next most frequently captured species, California vole (Microtus californicus), suggested substantial habitat overlap, with RERA habitat being somewhat higher in marsh elevation, greater in percent cover of the dominant plant species, closer to urban areas, further from agricultural areas, and, perhaps most significant, larger in continuous size of marsh patch. Findings will inform conservation management of the marsh environment for RERA by identifying best microhabitat elements, landscape attributes, and adverse interspecific interactions. K E Y W O R D SBayesian network models, California vole, habitat use, Microtus californicus, occupancy, Reithrodontomys raviventris, salt marsh harvest mouse, San Francisco Bay, San Pablo Bay, small mammal assemblage | 663 MARCOT eT Al.

Dietary characterization of the endangered salt marsh harvest mouse and sympatric rodents using DNA metabarcoding

“…Indeed, we note that REME, MUMU, and MICA generally are considered upland species, thus, our characterizations of their diets is specific to the individuals occurring on the upland/marshland edges and likely not reflective of these species as a whole. Habitat fragmentation and small patch size reduce the probability of RERA occurrence (Bias & Morrison, 2006 ; Marcot et al, 2020 ), and occupancy of marsh habitat by REME and MUMU may be dependent upon the degree of habitat fragmentation and penetration of terrestrial grass microhabitats into the marsh (Bias & Morrison, 2006 ; Fisler, 1965 ). Our results support these important management issues, adding to a growing literature suggesting that fragmentation of marsh habitat and the associated increase in edge habitat are potential threats to RERA with respect to competition from upland‐adapted rodents.…”

“…Previous work has indicated both negative (Geissel et al, 1988 ) and positive (Sustaita et al, 2011 ) associations between RERA and MICA habitat use, but their diet interactions remain unknown. Finally, non‐native MUMU commonly co‐occur with RERA throughout the SFE (e.g., Bias & Morrison, 2006 ; Marcot et al, 2020 ). MUMU are highly fecund (Bronson, 1979 ; Pye, 1993 ), opportunistic, and tolerant of a wide range of ecological conditions (Berry, 1981 ).…”

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

“…Mixed vegetation including rabbitsfoot grass ( Polypogon monspeliensis ), fat hen, pickleweed, watergrass (Echinochloa crus-galli ), and alkali bulrush ( Bolboschoenus maritimus ) may provide additional seed resources for foraging SMHM [ 40 ]. Within pickleweed-dominated tidal marshes SMHM appeared to be a habitat generalist and associated positively with larger continuous marsh patch sizes that were not bisected by levees or roads [ 41 ]. Habitat loss, degradation, and fragmentation as well as species interactions, competition, contaminants, disease, and climate related impacts such as sea-level rise, severe drought, and changes in heavy storms, are all challenges to SMHM recovery; however, no single driver of SMHM population densities has been identified and many data gaps remain [ 42 ].…”

Strategic Habitat Conservation for Beach Mice: Estimating Management Scenario Efficiencies

“…Human population density is 3 times higher in coastal areas than inland areas, and coastal erosion and flooding are expected to increase because of sea‐level rise and greater frequency of intense storms (Small and Nicholls 2003, Holgate and Woodworth 2004, Feagin et al 2005, Defeo et al 2009, Arkema et al 2013). These stressors negatively affect coastal wildlife, which are often threatened or endangered species, by increasing mortality and making their habitats rare or unsuitable (i.e., unable to support growth, survival, and reproduction; Defeo et al 2009, Elko et al 2016, Marcot et al 2020). Consequently, linking wildlife to coastal landscape characteristics is important for coastal planners and natural resource managers to prioritize areas and management actions.…”

“…Estimating habitat demand and the efficiency of management scenarios can help managers justify targeted conservation actions designed to mitigate stressors. Bayesian network models have been developed on a wide variety of environmental, ecological, species‐specific, and management issues (McCann et al 2006, Nyberg et al 2006), including evaluations of tidal‐marsh bird densities in the northeastern United States (Wiest et al 2019) and salt marsh harvest mice ( Reithrodontomys raviventris ) in San Francisco Bay, coastal California, USA (Marcot et al 2020).…”