Pacific Pocket Mouse Monitoring and Research Program

Science Center Objects

Once thought to be extinct, the Pacific pocket mouse (Perognathus longimembris pacificus) was rediscovered in 1993 and is currently found at three population sites along the southern California coast. USGS researchers and their partners developed a comprehensive long-term monitoring plan to assess the status and trends of Pacific pocket mouse and identify important drivers of population dynamics. Initiated in 2012, this research program continues to provide data that enables managers to make informed decisions for management and recovery of this critically endangered species.


The Pacific pocket mouse is one of 19 subspecies of the little pocket mice in the Heteromyid family and weighs an average of only 6 grams (0.04 oz).  They exhibit typical behaviors of heteromyid rodents including sand bathing to keep pelage clean and healthy, collecting seeds in external cheek pouches, and caching of seeds below ground and within burrow systems for sustenance throughout the year. 

Hand holding a tiny mouse between two fingers

Pacific pocket mouse in hand.

(Credit: Cheryl Brehme, USGS Western Ecological Research Center. Public domain.)

The Pacific pocket mouse has historically occupied marine terraces and alluvial plains along the southern California coast and has been typically associated with open patches of sandy soils. They were believed to be extinct in 1972, but were rediscovered in 1993, and federally listed as endangered in 1994. There are currently only three known extant populations, one on Dana Point and the two largest on Marine Corps Base Camp Pendleton. Potential threats and stressors include habitat loss, habitat alteration, fragmentation, predation risks, competition for seed resources, and impacts from vibrations, noise, and artificial lighting.

In 2007, the USGS was contracted to develop a scientifically valid and cost-effective monitoring program for the Pacific pocket mouse on Camp Pendleton to help fulfill stewardship and regulatory requirements for the natural resources on Base. Several pilot studies were carried out by USGS to determine the best sampling methodology to meet program goals and objectives. Studies included live-trapping, canine scent detection, and newly developed track tubes. Following these informative studies, USGS researchers collaborated with a scientific panel to design a relatively simple, multi-scaled, habitat-based, adaptive monitoring program for Pacific pocket mouse on Camp Pendleton. This design allows USGS to track trends and identify predictors of occupancy, colonization, and extinction.

Full monitoring efforts began in 2012. USGS established a number of 100 m x 100 m (1.0 ha) monitoring plots stratified across all population sites on MCBCP. Each plot is multi-scaled, comprised of 64 smaller 12.5 m x 12.5 m (0.0156 ha) subplots (the average size of a core Pacific pocket mouse home range), to allow researchers to explore the dynamics of these populations at different spatial scales as they respond to changes in habitat and disturbance. Within each plot, a subset of 32 subplots are sampled using track tubes.

Research Tools

Track Tubes

Track tube surveys are a simple and passive method of identifying small mammals by their tracks. In pilot studies, passive sampling using track tubes demonstrated the best detection probability, lowest impact to the species and habitat, and was most cost-effective among the sampling methodologies tested.

When small mammals enter the track tube to retrieve bait, they step on an inked pad and leave prints on track paper inside. Biologists are then able to interpret tracks and identify the distinct prints of Pacific pocket mouse and other sympatric rodent species. Data from systematically deployed track tubes can inform researchers about occupancy, colonization, extinction, seasonal activity, as well as co-occurring species.

Mouse pokes its head out of a tube

Pacific pocket mouse exiting track tube 

(Credit: Brittany Ewing, USGS Western Ecological Research Center. Public domain.)

Ruler placed next to a paper with mouse footprint

Width measurement for Pacific pocket mouse forefoot print on track card

(Credit: Tritia Matsuda, Western Ecological Research Center. Public domain.)

Mouse standing at the opening of a metal trap

Pacific pocket mouse in Sherman trap

(Credit: Cheryl Brehme, USGS Western Ecological Research Center. Public domain.)

















Live Trapping

In addition to track tubes, several live-trapping sessions are conducted throughout the monitoring period to provide data on Pacific pocket mouse demography, survivorship among years, as well as onset, timing, and length of reproduction. Live-trapping at a subset of plots within each population site helps to explain varying population dynamics across Pacific pocket mouse habitat and characterize the relationship between habitat variables and reproductive success.

Habitat Suitability Modeling

Habitat covariates hypothesized to be important for Pacific pocket mouse habitat suitability are recorded at each subplot, including topography, soil, vegetation cover, primary food plants, and types of disturbance. These covariates are incorporated into modeling to help assess drivers of Pacific pocket mouse distribution and inform management actions. Additionally, plant phenology data (the timing of flowering and seeding) collected during each trapping session is essential to understanding how these factors may influence Pacific pocket mouse activity and reproduction and can aid in predictions of this species' responses to environmental change.

Woman looks down at a dog sitting in the grass

Conservation Canine alerts his handler that Pacific pocket mouse scent has been detected.

(Credit: Cheryl Brehme, USGS Western Ecological Research Center. Public domain.)

Canine Scent Detection 

Dogs from the Center for Conservation Biology, University of Washington have been successfully trained to identify the scent of Pacific pocket mouse scat. Although this method is not as suitable for annual monitoring, canines can cover large areas over a fairly short time frame. Canine scent detection has been shown to be most efficient and effective for discovery surveys for the Pacific pocket mice. Use of this detection tool prior to implementation of our monitoring program identified areas with pocket mice that were previously unknown and expanded the known occupied population area by several hundred hectares. 

Genetic Fingerprinting

In collaboration with Dr. Amy Vandergast (USGS), genetic fingerprinting techniques have been used to further explore the Pacific pocket mouse diet. Genetic analysis of scat can also identify plant species most suitable for habitat management, restoration, and for the selection of receiver sites for establishing new Pacific pocket mouse populations.



Response to Non-Native Grasses, Drought, and Wildfire

Data from the sampling program combined with a spatial occupancy modeling approach have enabled researchers to track trends in Pacific pocket mouse abundance and distribution across Camp Pendleton and identify predictors of mouse presence within and across populations. Models have demonstrated that forbs (annual plants), rather than soil type, are a major driver of mouse occupancy. The data also indicate that there is a negative association between Pacific pocket mouse and non-native grasses. Multi-year models have consistently shown a strong link between recent fire and mouse occupancy, colonization, and extinction at one population site on Camp Pendleton. Fire maintains open habitat required by Pacific pocket mouse by clearing non-native grasses and promoting forb growth. The data suggest that fire plays a positive role in maintaining suitable habitat and prescribed burns are expected to enhance habitat and allow for population expansion. Camp Pendleton is currently using prescribed fire and habitat management to support Pacific pocket mouse populations on the Base.

USGS research has documented responses of Pacific pocket mouse populations and their habitat to prolonged drought, severe drought years, and wildfire. In 2018, southern California experienced a severe drought when plant phenology surveys showed that most forbs died before producing seed. In the same year, there was no evidence of Pacific pocket mouse reproduction. This suggests that the availability of food resources was too limited to support energy and nutrient demands of reproduction and establishes indirect evidence of a link between climate, forb phenology and population dynamics.

Set of three figures showing PPM occupancy vs fire (neg), vs non-native grass cover (neg), and forb cover (pos)

Probability of PPM occupancy in relation to years since last fire, probability of PPM occupancy in relation to non-native grass cover, and probability of PPM occupancy in relation to Forb cover.

(Credit: Cheryl Brehme, USGS Western Ecological Research Center. Public domain.)

Diet Research

Recent genetic analysis of Pacific pocket mouse scat on Camp Pendleton has revealed that their diet varies across populations, years and seasons and that, regardless of available seed resources, they tend to select for a wide variety of forb seeds. Resource selection analyses have also shown that they consume little grass seed, even though it is highly available in their habitat. As grass seeds are not a preferred seed in their diet and high non-native grass cover reduces open areas for foraging and dust bathing, these results further help to explain occupancy modeling relationships that indicate Pacific pocket mice are negatively associated with non-native grasses.

Habitat Management at Dana Point

In coordination with the Center for Natural Lands Management (CNLM) and the City of Dana Point conducted vegetation management to remove woody debris and open shrub canopy cover to promote forb growth in late 2019 and early 2020. Later in 2020, USGS and CNLM sampled Pacific pocket mouse on Dana Point using track tubes and live-trapping to assess the impacts of vegetation management on the mice. Habitat surveys in the spring of 2020 recorded  high amounts forb cover after vegetation management. Follow up track tube monitoring and live-trapping documented a significant increase in the population at this site. Modeling results confirmed the most significant predictors of the distribution of Pacific pocket mice  at Dana Point were recent habitat management and associated increased forb cover. 

Future Studies

Continued research into the short and long term drivers of Pacific pocket mouse population dynamics will further inform management actions to support the military mission on Camp Pendleton and to benefit species recovery across all population sites. Future research may include:

  • Formal analysis of the relationship between Pacific pocket mouse occupancy and density
  • Community resource selection and species competition modeling
  • Assessment of Argentine ant and native fire ant occurrence and potential impact to Pacific pocket mouse
  • Pacific pocket mouse telemetry to examine home ranges and movements in different habitats

USGS Pacific Pocket Mouse Monitoring and Research Team 

Cheryl Brehme, Devin Adsit-Morris, Tristan Edgarian, Brittany Ewing, Jennifer Kingston, Wendy Bear, Denise Clark, Tritia Matsuda, Jeremy Sebes, James Molden, Jenna Levy, Maxwell Newton, Samuel O’dell, Chase Stafford, Alexandra Sumarli 



  • Brehme, C.S., Matsuda, T.A., Adsit-Morris, D.T., Clark, D.R., Burlaza, M.A.T., Sebes, J.B., and Fisher, R.N., 2019, Track tube construction and field protocol for small mammal surveys with emphasis on the endangered Pacific pocket mouse (Perognathus longimembris pacificus): U.S. Geological Survey Techniques and Methods, book 2, chap. A15, 18 p., plus appendix,
  • Iwanowicz, D.D., Vandergast, A.G., Cornman, R.S., Adams, C.R., Kohn, J.R., Fisher, R.N. and Brehme, C.S., 2016. Metabarcoding of fecal samples to determine herbivore diets: A case study of the endangered Pacific pocket mouse. PloS one, 11(11), p.e0165366. 

Selected Reports

  • Brehme, C.S., D.T. Adsit-Morris, T.K. Edgarian and R.N. Fisher. 2021. Marine Corps Base, Camp Pendleton Pacific Pocket Mouse Monitoring Results for 2019 with Trend Analysis from 2012 to 2019. Draft Cooperator report prepared for Environmental Security Department, Marine Corps Base, Camp Pendleton. 53p. 

  • Brehme, C.S., D.T. Adsit-Morris, J.A. Tracey, T.K. Edgarian and R.N. Fisher. 2017. Marine Corps Base, Camp Pendleton Pacific Pocket Mouse Monitoring Results for 2016: 5-year Trend Analysis and Monitoring Program Evaluation. MCB, Camp Pendleton. Prepared for Environmental Security Department, Marine Corps Base, Camp Pendleton. 66p. 

  • Brehme, C.S, J. Sebes, T. Matsuda, D. Clark, and R.N. Fisher. 2014.  MCBCP Pacific Pocket Mouse Monitoring Results for 2013 and Multi-year Trend Analysis from 2012 to 2013. Prepared for AC/S Environmental Security, Marine Corps Base, Camp Pendleton. 69p. 

  • Brehme, C.S., T.A. Matsuda, L.R. Albert, B.H. Smith, and R.N. Fisher. 2012. Pacific Pocket Mouse Studies 2010, MCB, Camp Pendleton; Discovery and Population Mapping-- with additional studies for scent effects on detectability and surveys for the Argentine ant at North and South San Mateo. Marine Corps Base, Camp Pendleton. Prepared for AC/S Environmental Security, Marine Corps Base, Camp Pendleton. 40p.  

  • Brehme, C.S, Albert, L.R., Matsuda, T., Booth, R.N., and R.N. Fisher. 2010. Pacific Pocket Mouse Sampling Methodology Study, Marine Corps Base, Camp Pendleton. Data Summary prepared for AC/S Environmental Security, Marine Corps Base, Camp Pendleton. 47p. 

  • Brehme, C.S. and R.N. Fisher. 2009. 2008 Survey Results for the Pacific Pocket Mouse: North and South San Mateo, Marine Corps Base, Camp Pendleton; with additional analyses to inform long-term monitoring design. Prepared for AC/S Environmental Security, Marine Corps Base, Camp Pendleton. 40p. 

Selected Presentations

  • Brehme, CS. 2015. The Use of Canine Scent Detection, Tracking Tubes, Dynamic Occupancy Modeling and Genetic Analysis of Scat to Better Understand and Inform Recovery of the Pacific Pocket Mouse. Presentation to San Diego Association of Governments: Monitoring and Management Meeting, San Diego, CA, February 25, 2015  

  • Brehme, C. S, Alberts, L.R., Matsuda, T.M., Booth, R., and R. N. Fisher. 2011. On the road to a monitoring program:  Pilot studies and evaluation of live-traps, tracking tubes, and canines to detect the endangered Pacific Pocket mouse. Annual Conference: The Wildlife Society Western Section. Riverside, CA.  February 8-11, 2011 


Marine Corps Base Camp Pendleton

US Fish and Wildlife Service

Center for Natural Lands Management

City of Dana Point

Conservation Canines (University of Washington)

California Department of Fish and Wildlife

San Diego State University

San Diego Zoo Wildlife Alliance Beckman Center for Conservation Research