This document presents a monitoring protocol for the Stephens’ kangaroo rat (Dipodomys stephensi, SKR) on Marine Corps Base Camp Pendleton (MCBCP). A two-day scientific workshop was held in 2004 for the purpose of designing this program. The workshop attendees included a four member Scientific Peer Review Panel with expertise in spatial and statistical monitoring design and SKR biology, and additional biologists from several federal, state, and local wildlife agencies. The panel and other members reviewed and discussed SKR life history, conceptual models, monitoring schemes, and detection methods before reaching consensus on the basics of a monitoring program. Protocol specifics were determined by consultation among the USGS, the scientific panel, and MCBCP after the workshop.
There is a large body of evidence to show that SKR populations are both spatially and temporally dynamic. SKR abundance and capture probabilities are highly variable making detection of demographic trends problematic and time intensive. Suitable habitat for SKR may also vary through time and space in relation to disturbance and vegetation succession. This is particularly true on MCBCP, where there is a relatively high level of disturbance from frequent fires and military training activities. In consideration of these and other factors, we designed a relatively simple, multi-tiered, habitat-based, adaptive monitoring program for SKR. This monitoring program will track yearly trends in the total area occupied by SKR on base over a large number of fixed sample plots. It includes measurement of habitat and environmental variables that are hypothesized to affect the probability of occupancy, rate of colonization, and/or rate of extinction over time. Predictors that are found to be significant will be used for habitat-based recommendations for management.
It is unknown whether trends in SKR distribution are directly related to trends in SKR abundance; therefore, the program includes a density index. We considered active burrow counts for use as an index, as they have been shown to correlate and trend with SKR density estimates from live-
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trapping. However, previous monitoring efforts on MCBCP have shown that even in optimum habitat, SKR frequently co-exist with the sympatric Dulzura kangaroo rat (Dipodomys simulans, DKR), and that the proportion of SKR/DKR is both spatially and temporally variable. As a result, we cannot expect a consistent relationship between kangaroo rat burrow co
The Stephens’s kangaroo rat (Dipodomys stephensi; SKR) currently exists only in fragmented populations separated by urban landscapes. The species is listed as threatened by the state of California and endangered by the USFWS. The draft recovery plan for the species (1997) calls for conservation, funding and management within an established reserve system in Riverside and San Diego Counties. Species management plans are in place within some reserves and a translocation program is being established for the species to develop methods to reduce Take due to development (Shier 2009, 2010, 2011, Shier and Swaisgood 2012). Translocation may mitigate habitat fragmentation and restore historical gene flow by relocating animals between reserves or from areas slated for development projects onto reserves. It is not clear whether translocation is required to manage the species range-wide because, to date, the species landscape genetics and phylogeography are not well understood. To develop a successful range-wide long term management plan for the species that conserves extant genetic variation, it is critical to understand the genetic structure, dispersal characteristics and population histories of the fragmented populations in an evolutionary context.
In 2012, the U.S. Geological Survey (USGS) started a small animal connectivity study as part of
Connectivity Monitoring Strategic Plan (CMSP) developed by the San Diego Monitoring and
Management Program (SDMMP). The plan focused on small animals and their use of 8 underpasses
throughout San Diego County. Specialized infrared motion detection cameras were set up at each of the
underpasses and monitored from May 15 to October 1, 2102 and from March 19 to September 23, 2012.
After the first year, concrete structures were set up along the interior wall at 4 of the underpasses to
determine if the addition of structure would enhance the use of wildlife undercrossings by small
vertebrates.
Over the two year period we collected over 3 million of pictures, developed specialized software
and methods for processing images, and documented the following species; Pocket Mouse (Chaetodipus
spp.), Kangaroo Rat (Dipodomys spp.), California Vole (Microtus californicus), Woodrats (Neotoma
spp.), Grey Shrew (Notiosorex crawfordi), Brush Mouse (Peromyscus boylii), California Mouse
(Peromyscus californicus), Deer Mouse (Peromyscus maniculatus), White footed Mouse (Peromyscus
spp.), Domestic Rat (Rattus rattus), Orange Throated Lizard (Cnemidophorus hyperythrus), Western
Whiptail (Cnemidophorus tigris), Western Fence Lizard (Sceloporus occidentalis), Granite Spiny Lizard
(Sceloporus orcutti), Side Blotched, Lizard (Uta stansburia), Red Diamond Rattlesnake (Crotalus
ruber)- outside only, Western Rattlesnake (Crotalus viridis), Bobcat (Lynx rufus), Coyote (Canis
latrans), Grey Fox (Urocyon cinereoargenteus), Mule Deer (Odocoileus hemionus), Greater
Roadrunner (Geococcyx californianus), Opossum (Didelphis marsupialis), Striped Skunk (Mephitis
mephitis), Raccoon (Procyon lotor), Spotted Skunk (Spilogale putorius), Jackrabbit (Lepus
californicus), Rabbit species (Sylvilagus spp.), California Ground Squirrel (Spermophilus beecheyi),
Chipmunk Species (Neotamias merriami).
This is the first study, to our knowledge, to show the use of underpasses by a community of
small vertebrates. Previous studies have lacked the sensitivity to document mice, lizards and snakes.
We have shown that these members of the community can be studied successfully using these passive
methods.
The results of modeling gave evidence to support the short-term effectiveness of the added
structure treatments on small vertebrate use and suggested that these rates changed on the specific side
In 2005, we implemented a new monitoring program for the endangered Stephens’ kangaroo rat (Dipodomys stephensi, SKR) on Marine Corps Base Camp Pendleton (MCBCP). It is a relatively simple, multi-tiered, habitat-based, adaptive monitoring program designed to track yearly trends in the total area occupied by SKR on base. There is a two-phased approach for sampling. The first phase involves a complete search for any potential kangaroo rat sign and measurement of habitat and environmental variables. If any potential sign is observed, two to four days of live-trapping are conducted for the second phase. Live-trapping is necessary to determine if plots are occupied by the Stephens’ kangaroo rat and/or the Dulzura kangaroo rat (D. simulans, DKR). In order to provide continuity with previous monitoring efforts, we also live-trapped 10 SKR grids that were historically monitored biennially from 1996 to 2002.
After five years of the current program, we present a multi-faceted report on SKR monitoring with: 1) Multiyear trend analysis for the past five years (2005 to fall/winter 2009/2010). This includes assessment of factors associated with SKR occupancy, probability of detection, colonization and extinction; and 2) A monitoring program evaluation, optimization, and recommendations for future monitoring. This includes re-evaluation of the sampling area and power analyses of current and proposed alternate sampling scenarios to detect changes in the occupancy of SKR on Base.
Multi-year Trend Analysis:
Overall, the estimated area occupied by SKR in 2009-10 on MCB Camp Pendleton has been relatively stable since 2007-8 (within a single standard error) and is greater than the initial years of monitoring at MCBCP in 2005-6 and 2006-7. Within the high suitability stratum (which defines almost all know SKR habitat), we estimated SKR occupied 118.4 ha (SE=39.1) in 2009-10, in comparison to a high estimate of 147.3 ha (SE=39.1) in 2008 and low estimate of 60.0 ha (SE=24.2) in 2005. We detected no SKR in the medium suitability stratum. In areas occupied by SKR in 2009-10, animal
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densities were higher than all previous years at 30.2 and 47.1 SKR/ha, which is considered “high” for this species (Tetratech and SJM Biological Consultants 1999). The positive trend suggests a continued pattern of high survivorship and colonization of SKR in the high suitability stratum
This was the first year we were able to analyze all of the data in a multi-state framework and established th
In 2005, we implemented a monitoring program for the endangered Stephens’ Kangaroo Rat (Dipodomys stephensi, SKR) on Marine Corps Base Camp Pendleton (MCBCP). It is a relatively simple, multi-tiered, habitat-based, adaptive monitoring program designed to track yearly trends in the total area occupied by SKR on base. We revised the program in 2011 after a five-year review and program evaluation to increase our power to document population changes over time and gain a better understanding of the importance of habitat characteristics, environmental factors, fire and military disturbance in the occupation and persistence of SKR. We focused our sampling and monitoring efforts within the recently revised SKR habitat boundaries totaling 628 hectares. Seventeen percent of our sample effort is for discovery of SKR within potentially suitable habitat outside of these boundaries. There is a two-phased approach for sampling. The first phase involves a complete search for any potential kangaroo rat sign and measurement of habitat and environmental variables. If any potential sign is observed, two to four days of live-trapping are conducted for the second phase. Live-trapping is necessary to determine if plots are occupied by SKR and/or the Dulzura Kangaroo Rat (D. simulans, DKR).
Within the SKR Monitoring Area in Fall/Winter 2017/18, SKR occupied an estimated 231 ha which was an insignificant 6.6% decrease in comparison to 2016/17. Long term results indicate the amount of habitat occupied by SKR steadily increased from a low estimate of only 60 ha in 2005 to 248 ha in 2016/17, a four-fold increase, and has remained relatively stable for the past 7 years. SKR density estimates in occupied areas (11 SKR/0.25 ha) were also high in relation to historic values (1-10 SKR/0.25 ha) and have been stable and/or increasing for the past 6 years.
SKR have often been associated with open forb- dominated areas and have historically been shown to respond positively to habitat disturbance. Occupancy models showed that open ground was a significant predictor of all parameters of SKR dynamics (occupancy, colonization, extinction). The greatest probability of SKR occupancy was with between 40 to 80% open ground. Additionally, forb
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cover > 40%, more compact soils and flat slopes were also top predictors of SKR occupancy. Forbs are the primary seed resource for SKR, while firmer soils may increase seed foraging efficiency for SKR and better support their burrow structures from disturb
In 2005, we implemented a new monitoring program for the endangered Stephens’ kangaroo rat (Dipodomys stephensi) on Marine Corps Base Camp Pendleton (MCBCP). It is a relatively simple, multi-tiered, habitat-based, adaptive monitoring program designed to track yearly trends in the total area occupied by SKR on base. There is a two-phased approach for sampling. The first phase involves a complete search for any potential kangaroo rat sign and measurement of habitat and environmental variables. If any potential sign is observed, two to four days of live-trapping are conducted for the second phase. Live-trapping is necessary to determine if plots are occupied by the Stephens’ kangaroo rat and/or the Dulzura kangaroo rat (D. simulans). In order to provide continuity with previous monitoring efforts, we also live-trapped 10 SKR grids that were historically monitored biennially from 1996 to 2002.
Overall, the estimates of SKR occupancy in 2006 on MCB Camp Pendleton were similar to the previous year. Within the high suitability stratum, we estimated SKR occupied 70.8 ha (SE=29.7) in 2006 compared to 60.0 ha (SE=24.2) in 2005. At the spatial scale of 50x50m grids, occupied habitat is approximately 20% of that expected and reported before the onset of this program. In areas occupied by SKR, density was estimated at 5.5 SKR/ha (SE=2.3), which is considered “medium” for this species (O’Farrell and Uptain 1987) or “low” (Tetratech and SJM Biological Consultants 1999) and were comparable to 2005 estimates of 4 to 7 SKR/ha in occupied habitat. At this time, we are not finding support for SKR existing at multiple densities across habitats, but in similar densities in a patchy framework, often co-occurring with DKR. We are also finding that DKR are much more prevalent in the pre-identified SKR habitat (or high suitability stratum) than are SKR. These results continue to indicate that SKR are likely much rarer on MCB Camp Pendleton than previously thought, greatly increasing the importance of active management for this species.
In the high suitability stratum, our estimates of proportion of area occupied (PAO) over the past two years have been less than 0.10 (or 10%). At this low level, we have very little power to model habitat suitability and have low precision for our occupancy estimates. These are of utmost importance
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to MCBCP for assessing the status and trends of SKR as well as understanding the importance of habitat, environmental, and disturbance variables
