Light detection and ranging (lidar) has emerged as a valuable tool for examining the fine-scale characteristics of vegetation. However, lidar is rarely used to examine coastal wetland vegetation or the habitat selection of small mammals. Extensive anthropogenic modification has threatened the endemic species in the estuarine wetlands of the California coast, such as the endangered salt marsh harvest mouse (Reithrodontomys raviventris; SMHM). A better understanding of SMHM habitat selection could help managers better protect this species. We assessed the ability of airborne topographic lidar imagery in measuring the vegetation structure of SMHM habitats in a coastal wetland with a narrow range of vegetation heights. We also aimed to better understand the role of vegetation structure in habitat selection at different spatial scales. Habitat selection was modeled from data compiled from 15 small mammal trapping grids collected in the highly urbanized San Francisco Estuary in California, USA. Analyses were conducted at three spatial scales: microhabitat (25 m²), mesohabitat (2,025 m²), and macrohabitat (~10,000 m²). A suite of structural covariates was derived from raw lidar data to examine vegetation complexity. We found that adding structural covariates to conventional habitat selection variables significantly improved our models. At the microhabitat scale in managed wetlands, SMHM preferred areas with denser and shorter vegetation, and selected for proximity to levees and taller vegetation in tidal wetlands. At the mesohabitat scale, SMHM were associated with a lower percentage of bare ground and with pickleweed (Salicornia pacifica) presence. All covariates were insignificant at the macrohabitat scale. Our results suggest that SMHM preferentially selected microhabitats with access to tidal refugia and mesohabitats with consistent food sources. Our findings showed that lidar can contribute to improving our understanding of habitat selection of wildlife in coastal wetlands and help to guide future conservation of an endangered species.

The majority of historical tidal wetlands in the San Francisco Estuary have been substantially anthropogenically impacted which makes these areas difficult to restore to tidal action once they are no longer in use, or difficult to manage even when water control infrastructure remains. One such property is Lower Coyote Creek Reach 1A, a mitigation area managed by Santa Clara Valley Water District (Valley Water). This area consists of diked, managed marsh, a shorebird pond, and adjacent uplands, with unmuted tidal marsh directly adjacent to the mitigation area. The diked marsh has been managed for the endangered salt marsh harvest mouse (SMHM) for decades, though SMHM have never thrived there. Following a SMHM survey in 2020, Valley Water biologists worked with WRA, Inc. biologists to develop updated management strategies. Between 2020-2023, Valley Water increased tidal action to the marsh by flooding the diked marsh for a one-week period once a month at peak tidal cycle, a significant change from the previous management strategy of flooding 2-3 times per year. Subsequently, in 2023, the mean pickleweed cover increased, captures of house mouse and rats decreased by 70%, and captures of Western harvest mouse and SMHM increased by 20% and 100% respectively.

The state and federally endangered salt marsh harvest mouse (SMHM) was first described 115 years ago, and despite having a relatively restricted and delineated range (San Francisco Estuary) a comprehensive "census" of the species had never been attempted. In 2019 a group of researchers applied successfully to the National Fish and Wildlife Foundation for funding to plan and implement the first ever Rangewide Survey for SMHM. The planning process was supported by both an analysis of potential habitat value throughout the Estuary based on historical trapping data, and the recent development of methods for assessing occupancy via fecal DNA. Sampling areas were selected systematically across the species range, and location and scheduling balanced staff availability, safety and accessibility, king tides, and other considerations. In all, 60 sites were selected for live trapping and 25 for fecal DNA sampling. Over 60 biologists and volunteers working across 9,000 trap nights processed 1,930 rodent captures, resulting in 651 individual SMHM captured at all but seven of the live-trapping sites. SMHM were also detected at 14 of the fecal DNA sampling locations. These results will inform ongoing analyses, and guide future conservation decisions and habitat management efforts, in support of SMHM recovery.

Although tidal marsh restoration is occurring on an almost ongoing basis within the San Francisco Estuary, there has been relatively little monitoring of wildlife composition before, during, and after these projects. Monitoring efforts are imperative to understanding the effects of habitat enhancement efforts on the population dynamics and densities of wildlife, which can be especially important when it comes to special-status species. During the initial planning phases of a potential wetland enhancement project, Marin County partnered with WRA, Inc. to plan and implement a preliminary small mammal study, with a focus on the endangered salt marsh harvest mouse (Reithrodontomys raviventris; SMHM). The study area, McInnis Marsh, is a well connected, moderately sized marsh consisting of diked and tidal wetlands. Monitoring has occurred each spring and fall between 2020 and 2023 and across those years precipitation has been highly variable. Results were somewhat unexpected, often with much higher captures of SMHM in the ostensibly low quality diked wetlands, dominated by invasive plants, than the pickleweed-dominated tidal wetlands. There were also shifts in patterns of SMHM captures in response to variable precipitation. These results have provided valuable insights and influenced the planning process, demonstrating the value of comprehensive pre-project monitoring.

The salt marsh harvest mouse (Reithrodontomys raviventris, SMHM) is an endangered species, endemic to the wetlands of the San Francisco Bay Area. Habitat loss and fragmentation are some of the largest threats to the species, and these threats can be exacerbated by other factors such as sea level rise. In smaller, fragmented habitats with little high tide escape cover SMHM are more vulnerable to climatic events such as winter flooding. After heavy rains during the winter of 2022-2023, we wanted to evaluate the effects on SMHM populations at sites throughout their range. To do this, we re-trapped a subset of sites that were part of the SMHM range wide survey in summer 2022 and sites in Suisun Marsh that are part of long-term monitoring efforts. At all sites but one SMHM captures were lower than the previous year, and we found a significant decrease in catch per unit effort. This study highlights the importance of long-term monitoring efforts and regular monitoring of SMHM populations especially as the frequency of stochastic events like seasonal flooding increases. Regular monitoring will help managers gain a more accurate understanding of the status of SMHM, guiding future conservation and management.