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Pygmy Rabbits in Peril in the U.S.A.

Lisa Shipley


The decline of pygmy rabbits in the Columbia Basin in Washington State indicate trouble for groups of these animals elsewhere in the U.S. Using the ideas presented here, other organizations can

  • discover what types of diseases and predators afflict the species;
  • gather information about preserving habitat; and
  • learn how to initiate repopulation in threatened areas.

February 2008

Rabbits are not thought of as endangered species.

It is ironic that rabbits are a symbol of fertility throughout the world. Recent estimates suggest that 25% of rabbit species worldwide are declining or endangered. Examples of declining rabbit species include:

An endangered Columbia Basin pygmy rabbit juvenile born at the captive breeding facility at Washington State University, Pullman, Washington, USA. Photo: Tara Davila

  • Brazilian rabbit—Brazil
  • Volcano rabbit— Mexico
  • Amami rabbit—Japan
  • Riverine rabbit—South Africa
  • California brush rabbit—USA
  • Pygmy rabbit—USA
Pygmy rabbits and their sagebrush habitats are in peril.

Until recently, the status of pygmy rabbit populations in the U.S has received little attention. Their range consists of the Great Basin and surrounding intermountain regions, including Montana, Idaho, Wyoming, Utah, Nevada, Northern California, Oregon, and Washington. There is one exception—the Columbia Basin pygmy rabbit. It was extirpated from the wild in Washington by 2004, and this genetically distinct population was listed by the U.S. Fish and Wildlife Service as an endangered distinct population.

Subsequent surveys documented the disappearance of many historic populations in other states in which pygmy rabbits reside—all of which now classify pygmy rabbits as “a species of concern” or “vulnerable.” Although pygmy rabbits are also considered a federal “species at risk,” the U. S. Fish and Wildlife Service declined petitions for listing pygmy rabbits as threatened range wide—citing insufficient evidence and inconsistent survey techniques.

What is so special about pygmy rabbits?

The unique life history and specialized habitat requirements of this species have made conserving and restoring this small rabbit especially challenging.

  • Pygmy rabbits are on average the smallest rabbit, with large individuals weighing about 1 pound.

  • Pygmy rabbits require habitats containing both tall, dense sagebrush and deep soils.

  • Up to 90% of its winter diet and up to 50% of its summer diet consists of sagebrush leaves. Most animals avoid sagebrush because of its toxic chemical defenses.

The Pygmy is the smallest rabbit in North America.
  • In addition to the volcano rabbit of Mexico, pygmy rabbits are the only North American rabbit that dig their own burrows.

  • They dig a series of residential burrows for hiding and thermal cover. They also dig a separate natal burrow in which they place newborn young.

  • Females return to the natal burrow 1-2 times per day to nurse, covering the entrance with soil after each visit. Young emerge from the natal burrow 15 days after birth.

  • Pygmy rabbits mate during chasing sessions, and mating stimulates ovulation, thus they can become pregnant again immediately after giving birth. Pygmy rabbits, therefore, can have up to four litters of 2-7 young between February and July every year.

  • Pygmy rabbits are prey for a host of sagebrush-steppe predators, including coyotes, badgers, weasels, and raptors.

Why are pygmy rabbits at risk or endangered?

Because pygmy rabbits are restricted to sagebrush habitats with deep soils, they have always been rare and patchily distributed across their range. Biologists agree that the main threats to pygmy rabbits across their range are habitat loss and fragmentation caused by:

  • conversion of sagebrush rangeland to agriculture;
  • development, including oil and gas production; and
  • wildfire frequency in some areas.
Their sagebrush habitat is dwindling.

In addition, most remaining pygmy rabbit habitat—throughout its range—is currently grazed by livestock, which may reduce habitat quality for pygmy rabbits. In some areas, wildfires have destroyed remaining pockets of pygmy rabbit habitats. The temperature and frequency of these fires may increase by the invasion of the exotic annual grass, cheatgrass; thus, it is more likely to destroy sagebrush stands. Coyotes—important rabbit predators—have increased in number over the last few decades, presumably because of habitat changes. In addition, diseases like tularemia and sylvatic plague can decimate rabbit populations periodically.

Pygmy rabbits in Washington State, however, have been particularly vulnerable. This population was separated from those in other parts of their range as sagebrush communities receded with climate changes. Analysis of the rabbit’s genome suggests that the divergence of the Washington population occurred between 15,000 and 115,000 years ago. Because of long-term geographic isolation and local habitat fragmentation, the Washington population exhibits significantly lower genetic diversity than the populations in neighboring states.

Low genetic diversity can increase the likelihood of extinction.

To complicate matters, the existing population in Washington (already low) has declined in diversity, over the last 50 years, which may have reduced the fitness, thus survival and reproduction, of this small and isolated group of pygmy rabbits. Burrow surveys and other records indicate a continuously declining population during the last 20 years. Habitat loss and fragmentation was also accelerated in this state when dams on the Columbia River provided irrigation that allowed land in these arid regions to be converted to agriculture.

What can be done for the Columbia Basin pygmy rabbits?

Landowners are hesitant to allow endangered species on their property.

To date, efforts at conserving pygmy rabbits have focused on acquiring information about their distribution, abundance, and life history.

In Washington, management efforts by a number of agencies have included acquiring and restoring potential habitat for the endangered Columbia Basin pygmy rabbit—a slow and expensive task. Because some pygmy rabbit habitat is contained within private lands, agencies have attempted to work with local ranchers and farmers to develop mutually beneficial resource management plans and Safe Harbor agreements. Many private landowners are wary of having endangered species on their land and mistrust state and federal natural resource agencies, however, so this work has been sensitive and arduous. As a parallel course of action, and perhaps the last chance for saving the Columbia Basin pygmy rabbit4, Washington Department of Fish and Wildlife initiated a program in 2001 for captive breeding and restoration of pygmy rabbits, which is now a key component of the Federal Recovery Plan for the Columbia Basin pygmy rabbit.

  • The last 16 Columbia Basin pygmy rabbits were trapped from their last remaining population at Sagebrush Flats in central Washington.

  • Animals were transported to captive breeding facilities at Washington State University in Pullman, Oregon Zoo in Portland, and Northwest Trek Animal Park near Pullayup, Washington.

  • The genetic profile of all rabbits was ascertained by sequencing DNA from a skin biopsy.

The ongoing captive breeding program takes into account the pygmy rabbit’s special needs:

  • Animals are housed individually because they exhibit aggression in breeding pens. The pens are designed to allow for at least 2 feet of soil for building burrows;

  • Pens contain artificial nestboxes and burrows, and are connected with breeding tunnels with doors;

Pygmies are nurtured for breeding.
  • Pygmy rabbits are fed commercial and custom rabbit pellets consisting of grains, alfalfa, grass hay, vitamins, and minerals. Each breeding facility grows fresh grasses and greens, and rabbits are provided with greenhouse-grown or wild-cut sagebrush;

  • To allow mating to occur, a door connecting adjacent pens holding a male and female rabbit is left open for 3-4 days; and

  • At each pairing, mates are selected to maximize genetic diversity of the offspring.

What are the challenges of boosting pygmy populations?

Restoring an extirpated population using captive breeding poses three management challenges:

  • maximizing pygmy rabbit reproduction;
  • minimizing mortality of the animal in captivity; and
  • developing techniques to reintroduce them into the wild successfully.

Maximizing reproduction

Pygmy rabbits can have up to four litters a year!

Breeding success was very low during the first few years of the captive breeding program. Only about half of the female Columbia Basin pygmy rabbits became pregnant and half of the males sired young during the breeding season. Less that 18% of pairings resulted in pregnancies. In contrast—all pygmy rabbits from populations in Idaho, which are not considered endangered—became pregnant or sired young, and 60% of pairings were successful. Litter sizes and kit survival, however, were similar. Three main strategies were attempted to increase pregnancy rates of Columbia Basin pygmy rabbits:

  • increase the nutritional quality of the breeding diet;
  • intercross Columbia Basin pygmy rabbits with pygmy rabbits from Idaho; and
  • mate rabbits right after parturition.

At first, many of the animals were relatively thin, with lower body masses than those caught from the wild, so the protein and digestibility of the breeding diets were increased and the fiber content was decreased. During the 2 years following the diet change, the average weight of adult males and females increased 5%, and their kits increased 15%. At the same time, pregnancy rates of Columbia Basin rabbits increased to 28% of pairings, and litter sizes increased to five kits.

Columbia Basin rabbits have low genetic diversity.

Differences in pregnancy rate between Columbia Basin and Idaho pygmy rabbits, and the extremely low genetic diversity of the Columbia Basin rabbits, suggested that inbreeding depression might have played an important role in low pregnancy rates. Therefore, our second strategy was to begin a process of genetic rescue, where the Columbia Basin pygmy rabbits were intercrossed with Idaho rabbits, aiming for creating and maintaining a captive and release population of greater than 75% Columbia Basin genes. Intercrossing required maintaining a balance between preserving the unique genetic profile of the Columbia Basin pygmy rabbit, while increasing the genetic diversity overall. Rabbits from the two populations mated readily, and the intercross rabbits had higher pregnancy and siring rates; thus, they produced more kits per adult than the pure Columbia Basin pygmy rabbits.

Other changes to the breeding protocol have also helped increase reproduction. Originally, females were re-mated only after their first litter had weaned over a month after mating in an effort to protect newborn kits. We learned that re-breeding females right after giving birth—when the first litter was in the natal burrow—was safe and has doubled the number of possible litters per female within the breeding season.

Minimizing mortality

Ensuring reproduction is one challenge of a captive breeding program—minimizing mortality is the other critical aspect. Most of the deaths of adults and kits in the captive breeding facilities have been caused by common, ubiquitous disease agents—such as mycobacteriosis in adults and coccidiosis in young.

Disease can plague captive rabbits.
  • Mycobacteriosis: Most deaths of adult pygmy rabbits in captivity have been caused by mycobacteriosis (Avian tuberculosis),5 a disease caused by Mycobacterium avium, which causes granulomas in the lungs and other tissues. M. avium is ubiquitous in the environment; the disease is not normally associated with healthy wildlife. Immune response challenges indicated that pygmy rabbits have an unusually high sensitivity to M. avium. Veterinarians at the captive breeding facilities prescribe an intensive antibiotic regime for any animal with the symptoms of mycobacteriosis. This regime has proved to prolong the life of some pygmy rabbits, but does not cure M. avium).

  • Coccidiosis: On the other hand, the most commonly identified source of kit mortality is coccidiosis—an intestinal disease caused by the coccidea parasite. Like M. avium, coccidea is common in the environment, and it affects the young of most domestic animals. The majority of deaths from coccidiosis in pygmy rabbits occur within one week of emergence from the natal burrow. Captive populations are frequently monitored for coccidea and treated continuously with a series of coccidiostats provided in the water and given orally. Unfortunately, both coccidiosis and mycobacteriosis are exacerbated by housing rabbits on soil, which cannot be sanitized. However, attempts to raise young pygmy rabbits in enclosures without soil were unsuccessful. Therefore, the captive breeding program must maintain a difficult balance between ensuring reproduction and minimizing mortality.

Successful reintroduction techniques

By 2006, the combined captive population of pygmy rabbits had reached 100 animals. Clearly, the ultimate goal of any captive breeding program is reintroducing captive-reared animals into native habitats to restore a stable population. To determine what procedures would maximize survival of released rabbits we conducted two tests of release techniques, consisting of four separate releases of 62 pygmy rabbits fitted with radio-collars.

  • Three releases totaling 42 captive-reared Idaho rabbits back into Idaho habitats August, September, and February 2003-2004.

  • One release of 20 captive-reared 75% or greater Columbia Basin pygmy rabbits back into Washington in March 2007.

A pygmy rabbit hops out of its artificial burrow during a pilot reintroduction experiment conducted by Washington State University designed to develop methods suitable for restoring extirpated populations. Photo: Rodney Sayler, Washington State University

Pygmy rabbits—in all the releases—experienced high mortality, primarily from predation, initially. In the Washington release, many animals, especially males, dispersed great distances quickly, often into unsuitable habitat outside the state-owned reserve. Some rabbits survived to reproduce during the breeding season, however.

Although each experimental release will encounter its own challenges, the following would provide the best opportunity for a successful reintroduction. To maintain sustainable, wild populations, researchers should:

Releasing captive rabbits requires special care.
  • transition release animals onto a mostly natural diet of sagebrush, grass, and greens, while in captivity;

  • avoid releasing males with pregnant females during breeding season, as this may encourage the animals to disperse too widely looking for mates, increasing their risk of starvation or predation;

  • release at least 30 pygmy rabbits for up to 10 years, annually;

Rabbits dig their own burrows soon after release.
  • provide large areas of contiguous habitat;

  • offer artificial burrows at release sites, which may serve to protect rabbits and discourage them from dispersing;

Predator barriers may reduce mortalities.
  • stop soft-release caging, as it may serve as a predator trap—confining rabbits with small predators like weasels;

  • utilize targeted predator control (including translocation, hazing, and lethal methods)—in release areas where predator risk is high, immediately before and after a release may be necessary—to allow pygmy rabbits to be accustomed to their new habitat before facing predation risks; and

  • time the release to avoid regional raptor migrations—this is critical.


The Columbia Basin program may give pygmies a fighting chance.

In conclusion, captive breeding and releasing rabbits with at least 75% of their genes from the original Columbia Basin population has become a key component of the draft recovery plan for Columbia Basin pygmy rabbits prepared by the U.S. Fish and Wildlife Service. The plan outlines actions aimed at removing or abating threats to prevent extinction and re-establishing and protecting the appropriate number and distribution of free-ranging subpopulations that could withstand foreseeable threats. Although recovering the Columbia Basin pygmy rabbit has been a steep and ongoing challenge, federal and state wildlife agencies, private conservation groups, university researchers, and captive breeding facilities involved in the project for over a decade are committed to saving this unique and endangered population. Acquiring and preserving habitat, acquiring knowledge about biology and ecology and disease, adaptive management within captive breeding and release, are all critical aspects of meeting this challenge. Lessons learned from this struggle to save Columbia Basin pygmy rabbits may help prevent similar extirpation in other parts of the pygmy rabbit’s range.

Lisa Shipley, Ph.D., is a wildlife ecologist and Associate Professor in the Department of Natural Resource Sciences at Washington State University. Her research focuses on foraging behavior, nutrition, and habitat requirements of wildlife. She directs the pygmy rabbit captive breeding program at Washington State University and is a member of the USFWS Recovery Team for pygmy rabbits.

Pygmy Rabbits in Peril in the U.S.A.

Washington State Pygmy Plan

For a look at the complete Washington State Pygmy Recovery Plan, visit

Pygmy Rabbit Information

An overview from the Washington Dept. of Fish and Wildlife.

What can I do?

There are multiple non-profit and government environmental organizations that can help you learn more and get involved. Including: Biodiversity Conservation Alliance (BCA) located in Laramie, WY:

Idaho National Laboratory NERP

Designated as a National Environmental Research Park (NERP) in 1975—due to demand from local citizens, scientists, and Congress—this property is designated as protected land for preservation purposes, as well as to serve as a biological research site. For more details see

U.S. Fish and Wildlife, Environmental Conservation Online System (ecos)

Notes and References
1. wiki 2007. (accessed December 10, 2007)
2. U.S. Fish and Wildlife Service. Species Profile, Pygmy rabbits. 2007. (accessed December 10, 2007).
3. Definition Sagebrush Steppe. 2007. (accessed December 10, 2007).
4. For more about the details of the Columbia Basin problem specifically, see:
5. For details and abstract, see the USDA website,

  • » Elias, B. A., L. A. Shipley, R. D. Sayler, and R. S. Lamson. 2006. Mating behavior and parental care in captive pygmy rabbits. Journal of Mammalogy 87: 921–928.
  • » Federal Register. March 5, 2003. Endangered and threatened wildlife and plants; final rule to list the Columbia Basin distinct population segment of the pygmy rabbit (Brachylagus idahoensis) as endangered. Federal Register 68: 10,388–10,409.
  • » Federal Register. May 20, 2005. Endangered and threatened wildlife and plants: 90-day finding on petition to list the pygmy rabbit as threatened and endangered. Federal Register 70: 29,253–29,265.
  • » Gahr, M. L. 1993. Natural history, burrow habitat use, and home range of the pygmy rabbit of Sagebrush Flats, Washington. M.S. thesis, University of Washington, Seattle, Washington.
  • » Hays, D. 2001. 2001 Addendum: Washington state recovery plan for the pygmy rabbit. Washington Department of Fish and Wildlife Olympia, Washington. 24pp.
  • » Hays, D., and K. Warheit. 2004. Columbia Basin pygmy rabbit captive breeding and genetic management plan. Washington Department of Fish and Wildlife. Olympia, Washington. 29pp.
  • » McAllister, K. R. 1995. Washington state recovery plan for the pygmy rabbit. Wildlife Management Program, Washington Department of Fish and Wildlife, Olympia, WA.
  • » Rachlow, J. L., D. M. Sanchez, and W. A. Estes-Zump. 2005. Natal burrows and nests of free-ranging pygmy rabbits (Brachylagus idahoensis). Western North American Naturalist 65: 136–139.
  • » Shipley, L.. A., T. B. Davila, N. J. Thines, and B. A. Elias. 2006. Nutritional requirements and diet choices of the pygmy rabbit (Brachylagus idahoensis): A sagebrush specialist. Journal of Chemical Ecology 32: 2455–2474.
  • » Thines N. J., L. A. Shipley, and R. D. Sayler. 2004. Effects of cattle grazing on ecology and habitat of Columbia Basin pygmy rabbits (Brachylagus idahoensis). Biological Conservation 119: 525–534.
  • » U.S. Fish and Wildlife Service. 2007. Draft recovery plan for the Columbia Basin distinct population segment of the pygmy rabbit (Brachylagus idahoensis). Portland, Oregon. 118. pp, (accessed 1/10/08; updated 6/29/10).


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