Few studies have evaluated the optimal sampling design for tracking small mammal population trend... more 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 validat...
Journal of Geophysical Research: Biogeosciences, 2022
Disturbances are a key component of ecological processes in coastal ecosystems. Investigating fac... more Disturbances are a key component of ecological processes in coastal ecosystems. Investigating factors that affect tidal marsh accretion and elevation change is important, largely due to accelerating sea‐level rise and the ecological and economic value of wetlands. Sediment accumulation rates, elevation change, and flooding were examined at five marshes along a riverine‐tidal gradient in the northern San Francisco Bay‐Delta, California, USA during an Atmospheric River storm event in 2017 using Surface Elevation Tables (SETs), feldspar marker horizons (MH), and continuous water‐level sensors. Our results showed that localized marsh flooding increased during the storm event, but not evenly across sites. Marsh surface elevation increased the most at the tidal freshwater marsh site in response to the storms, with an average surface elevation gain of 45.6 ± 13.1 mm, and the least at a tidal saline marsh with an average surface elevation gain of 4.0 ± 1.2 mm. A marsh located on the large embayment did not exhibit an immediate response to the storm but had a surface elevation gain of 21.5 ± 13.7 mm 6 months after the storm. During the storm period, marsh distance to the bay was the strongest predictor of elevation change, followed by SET‐MH elevations. Conversely, during non‐storm periods, SET‐MH elevation was a relatively strong predictor of elevation change. Atmospheric Rivers appear to be a major factor affecting short‐term spatial and temporal variability in flooding and sedimentation rates in tidal marsh systems. Incorporating information about storms into monitoring could increase our understanding of how episodic storms can impact marshes.
These datasets provide information on total plant cover, Normalized Difference Vegetation Index, ... more These datasets provide information on total plant cover, Normalized Difference Vegetation Index, and Antioch Dunes evening primrose (Oenothera deltoides subsp. howellii) abundance within grids across the subspecies' extant range in California. These data support the following publication: Jones, S.F., Kennedy, A., Freeman, C.M. et al. Intensity of grass invasion negatively correlated with population density and age structure of an endangered dune plant across its range. Biol Invasions (2021). https://doi.org/10.1007/s10530-021-02516-5
Invasive species are a global threat to ecosystem biodiversity and function; non-native grass inv... more Invasive species are a global threat to ecosystem biodiversity and function; non-native grass invasion has been particularly problematic in sparsely vegetated ecosystems such as open dunes. Native plant population responses to invasion, however, are infrequently translated to landscape scales, limiting the effectiveness of these data for addressing conservation issues. We quantified population density, total population size, and age class distribution of the federally-endangered plant species Antioch Dunes evening primrose (Oenothera deltoides subsp. howellii), at sites along a non-native grass invasion gradient in California, USA. We then scaled relationships between invasion and plant density across the species’ range using spatial models and remote sensing data. Adult and juvenile O. deltoides subsp. howellii densities were more than 10 times higher in non-invaded areas (grids with 10% total plant cover) when compared to highly-invaded areas (grids with 80% total plant cover). Th...
Robust assessments of ecosystem stability are critical for informing conservation and management ... more Robust assessments of ecosystem stability are critical for informing conservation and management decisions. Tidal marsh ecosystems provide vital services, yet are globally threatened by anthropogenic alterations to physical and biological processes. A variety of monitoring and modeling approaches have been undertaken to determine which tidal marshes are likely to persist into the future. Here, we conduct the most robust comparison of marsh metrics to date, building on two foundational studies that had previously and independently developed metrics for marsh condition. We characterized pairs of marshes with contrasting trajectories of marsh cover across six regions of the United States, using a combination of remote-sensing and field-based metrics. We also quantified decadal trends in marsh conversion to mudflat/open water at these twelve marshes. Our results suggest that metrics quantifying the distribution of vegetation across an elevational gradient represent the best indicators o...
A comprehensive field and modeling study indicates vulnerability of tidal wetlands to sea-level r... more A comprehensive field and modeling study indicates vulnerability of tidal wetlands to sea-level rise on the U.S. Pacific coast.
Few studies have evaluated the optimal sampling design for tracking small mammal population trend... more 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 validat...
Journal of Geophysical Research: Biogeosciences, 2022
Disturbances are a key component of ecological processes in coastal ecosystems. Investigating fac... more Disturbances are a key component of ecological processes in coastal ecosystems. Investigating factors that affect tidal marsh accretion and elevation change is important, largely due to accelerating sea‐level rise and the ecological and economic value of wetlands. Sediment accumulation rates, elevation change, and flooding were examined at five marshes along a riverine‐tidal gradient in the northern San Francisco Bay‐Delta, California, USA during an Atmospheric River storm event in 2017 using Surface Elevation Tables (SETs), feldspar marker horizons (MH), and continuous water‐level sensors. Our results showed that localized marsh flooding increased during the storm event, but not evenly across sites. Marsh surface elevation increased the most at the tidal freshwater marsh site in response to the storms, with an average surface elevation gain of 45.6 ± 13.1 mm, and the least at a tidal saline marsh with an average surface elevation gain of 4.0 ± 1.2 mm. A marsh located on the large embayment did not exhibit an immediate response to the storm but had a surface elevation gain of 21.5 ± 13.7 mm 6 months after the storm. During the storm period, marsh distance to the bay was the strongest predictor of elevation change, followed by SET‐MH elevations. Conversely, during non‐storm periods, SET‐MH elevation was a relatively strong predictor of elevation change. Atmospheric Rivers appear to be a major factor affecting short‐term spatial and temporal variability in flooding and sedimentation rates in tidal marsh systems. Incorporating information about storms into monitoring could increase our understanding of how episodic storms can impact marshes.
These datasets provide information on total plant cover, Normalized Difference Vegetation Index, ... more These datasets provide information on total plant cover, Normalized Difference Vegetation Index, and Antioch Dunes evening primrose (Oenothera deltoides subsp. howellii) abundance within grids across the subspecies' extant range in California. These data support the following publication: Jones, S.F., Kennedy, A., Freeman, C.M. et al. Intensity of grass invasion negatively correlated with population density and age structure of an endangered dune plant across its range. Biol Invasions (2021). https://doi.org/10.1007/s10530-021-02516-5
Invasive species are a global threat to ecosystem biodiversity and function; non-native grass inv... more Invasive species are a global threat to ecosystem biodiversity and function; non-native grass invasion has been particularly problematic in sparsely vegetated ecosystems such as open dunes. Native plant population responses to invasion, however, are infrequently translated to landscape scales, limiting the effectiveness of these data for addressing conservation issues. We quantified population density, total population size, and age class distribution of the federally-endangered plant species Antioch Dunes evening primrose (Oenothera deltoides subsp. howellii), at sites along a non-native grass invasion gradient in California, USA. We then scaled relationships between invasion and plant density across the species’ range using spatial models and remote sensing data. Adult and juvenile O. deltoides subsp. howellii densities were more than 10 times higher in non-invaded areas (grids with 10% total plant cover) when compared to highly-invaded areas (grids with 80% total plant cover). Th...
Robust assessments of ecosystem stability are critical for informing conservation and management ... more Robust assessments of ecosystem stability are critical for informing conservation and management decisions. Tidal marsh ecosystems provide vital services, yet are globally threatened by anthropogenic alterations to physical and biological processes. A variety of monitoring and modeling approaches have been undertaken to determine which tidal marshes are likely to persist into the future. Here, we conduct the most robust comparison of marsh metrics to date, building on two foundational studies that had previously and independently developed metrics for marsh condition. We characterized pairs of marshes with contrasting trajectories of marsh cover across six regions of the United States, using a combination of remote-sensing and field-based metrics. We also quantified decadal trends in marsh conversion to mudflat/open water at these twelve marshes. Our results suggest that metrics quantifying the distribution of vegetation across an elevational gradient represent the best indicators o...
A comprehensive field and modeling study indicates vulnerability of tidal wetlands to sea-level r... more A comprehensive field and modeling study indicates vulnerability of tidal wetlands to sea-level rise on the U.S. Pacific coast.
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Papers by Chase Freeman