Effects of natural and anthropogenic change on habitat use and movement of endangered salt marsh harvest mice.

The northern salt marsh harvest mouse (Reithrodontomys raviventris halicoetes) is an endangered species endemic to the San Francisco Bay Estuary. Using a conservation behavior perspective, we examined how salt marsh harvest mice cope with both natural (daily tidal fluctuations) and anthropogenic (modification of tidal regime) changes in natural tidal wetlands and human-created diked wetlands, and investigated the role of behavioral flexibility in utilizing a human-created environment in the Suisun Marsh. We used radio telemetry to determine refuge use at high tide, space use, and movement rates to investigate possible differences in movement behavior in tidal versus diked wetlands. We found that the vast majority of the time salt marsh harvest mice remain in vegetation above the water during high tides. We also found no difference in space used by mice during high tide as compared to before or after high tide in either tidal or diked wetlands. We found no detectable difference in diurnal or nocturnal movement rates in tidal wetlands. However, we did find that diurnal movement rates for mice in diked wetlands were lower than nocturnal movement rates, especially during the new moon. This change in movement behavior in a relatively novel human-created habitat indicates that behavioral flexibility may facilitate the use of human-created environments by salt marsh harvest mice

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. We analyzed capture data within a SECR modeling framework that allowed us to account for differences in detection and movement between sexes. We compared the full dataset to subsampling scenarios to evaluate how the grid size (area) of the trap design, trap density (spacing), and number of consecutive trapping occasions (duration) influenced density estimates. To validate the subsampling methods, we ran Monte Carlo simulations based on the true parameter estimates for each specific year. We found that reducing the area of the trapping design by more than 36% resulted in the inability of the SECR model to replicate density estimates within the SE of the original density estimates. However, when trapping occasions were reduced from 4 to 3-nights the density estimates were indistinguishable from the full dataset. Furthermore, reducing trap density by 50% also resulted in density estimates comparable to the full dataset and was a substantially better model than reducing the trap area by 50%. Overall, our results indicated that moderate reductions in the number of trapping occasions or trap density could yield similar density estimates when using a SECR approach. This approach allows the optimization of field trapping efforts and designs by reducing field efforts while maintaining the same population estimate compared to the full dataset. Using a SECR approach may help other wildlife programs identify sampling efficiencies without sacrificing data integrity for long term monitoring of population densities

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

The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non-native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non-native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non-native rodents? RERA diet was dominated by two plants, native Salicornia and non-native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co-occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non-native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant

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

Abstract The salt marsh harvest mouse (Reithrodontomys raviventris; RERA) is an endangered species endemic to the coastal wetlands of the San Francisco Estuary, California. RERA are specialized to saline coastal wetlands, and their historical range has been severely impacted by landscape conversion and the introduction of non‐native plant and rodent species. A better understanding of their diet is needed to assess habitat quality, particularly in relation to potential competitors. We investigated three questions using DNA metabarcoding with ITS2 and trnL markers: (1) Do RERA specialize on the native plant, pickleweed (Salicornia pacifica), (2) Do RERA consume non‐native plants, and (3) What is the dietary niche breadth and overlap with three sympatric native and non‐native rodents? RERA diet was dominated by two plants, native Salicornia and non‐native salt bush (Atriplex spp.), but included 48 plant genera. RERA diet breadth was narrowest in fall, when they consumed the highest frequencies of Salicornia and Atriplex, and broadest in spring, when the frequencies of these two plants were lowest. Diet breadth was slightly lower for RERA than for co‐occurring species in pairwise comparisons. All four species consumed similarly high frequencies of wetland plants, but RERA consumed fewer grasses and upland plants, suggesting that it may be less suited to fragmented habitat than sympatric rodents. Diet overlap was lowest between RERA and the native California vole (Microtis californicus). In contrast, RERA diet overlapped substantially with the native western harvest mouse (R. megalotis) and non‐native house mouse (Mus musculus), suggesting potential for competition if these species become sufficiently abundant

Toward Salt Marsh Harvest Mouse Recovery: Research Priorities

[Abstracts are not presented for essays. -The SFEWS Editors.

Minimum convex polygons for salt marsh harvest mice in diked wetlands.

<p>Green polygons represent points occurring more than one hour before high tide. Yellow polygons represent points falling within one hour before or after high tide. Red polygons represent points occurring more than one hour following high tide. Each block represents an individual mouse. Some blocks have all three polygons, while those that lack 6 or more individual points during the before or after time period, only have two polygons.</p

Toward Salt Marsh Harvest Mouse Recovery: Research Priorities

[Abstracts are not presented for essays. -The SFEWS Editors.

Individual locations at Lower Joice Island South Tidal.

<p>Individual salt marsh harvest mouse locations at high tide at Lower Joice Island South Tidal. Each individual is represented by a different color. Each point represents a mouse location within one hour of the high tide. Data Source: California Department of Fish And Game: NAIP 2010 Aerial Imagery. © Katherine Smith</p

Individual locations at Joice Island Tidal.

<p>Individual salt marsh harvest mouse locations at high tide at Joice Island Tidal. Each individual is represented by a different color. Each point represents a mouse location within one hour of the high tide. Data Source: California Department of Fish And Game: NAIP 2010 Aerial Imagery. © Katherine Smith</p

Average movement rates of salt marsh harvest in meters per hour for treatments.

<p>All rates before, during, and after high tides are included in this analysis.</p><p>Average movement rates of salt marsh harvest in meters per hour for treatments.</p