Big Data on a Little Pocket Mouse

Small Populations Spell Big Trouble

Weighing about as much as five paper clips, the smallest mouse in North America is the endangered Pacific pocket mouse (PPM). It historically occupied a stretch of sandy soil habitat along the coast of Southern California before large scale development reduced and fragmented its habitat.

Once thought to be extinct, PPM was rediscovered in 1993 and quickly listed under the U.S. Endangered Species Act. Three small remnant populations of PPM remain today in Southern California, each surrounded by an isolating urban landscape. 

Continued population declines and ongoing encroachment prompted the establishment of a captive breeding program at the San Diego Zoo Institute for Conservation Research in 2012 to prevent the extinction of PPM. The immediate goal of the breeding program was to increase population size and preserve the existing genetic diversity so that PPM could be reintroduced back into areas of their historic range.

Happily, five generations of captive breeding saw growth and a steady increase in genetic diversity of PPM individuals. 

Despite the success of the program in bolstering numbers and diversity of PPM, the extremely small sizes of the wild populations that founded the captive breeding program may have lasting impacts on the species.

Endangered species are susceptible to loss of genetic diversity and the accumulation of harmful genetic variants (so-called genetic load), a process of genomic erosion that leads to decreased survival and reproduction and further exacerbates the risk of extinction to small populations. The adverse effects of high genetic load in small populations can be alleviated by interbreeding with outside populations, a strategy called genetic rescue.

The conditions under which genetic rescue are likely to succeed or fail, however, are not well understood, and PPM can provide some important insights.

A Model for Genetic Rescue

Breakthroughs in genomic sequencing now allow us to measure genetic load along with the classic genetic hallmarks of population health, and incorporate this information into the way we manage and conserve species.

To this end, we have begun a project to sequence the genomes of most of the captive population and a subset of wild PPM (a sample which comprises most of the PPM gene pool), to follow trends in genetic load under a genetic rescue scenario. A wealth of physiological, reproductive and behavioral observations carefully collected over more than five generations of captive breeding allow us to measure the impact of genetic factors on survival and reproduction in PPM, and better understand the fate of harmful genetic load, beneficial genetic diversity, and the factors that determine the outcome of genetic rescue.

The ability to monitor PPM in the wild and in captivity and study traits associated to reproduction and survival make PPM an excellent model for understanding genetic load and genetic rescue of small populations. This information will not only directly inform management and reintroduction of PPM back into the wild, but also provides more universal insights into conservation strategies in other critically endangered species.