Most people would find working with fecal samples unappealing. However, with some investigative work, the DNA obtained from fecal samples can reveal very useful genetic information that can help with conservation efforts for endangered species. Here in the Genetics Division at the San Diego Zoo Institute for Conservation Research, we are taking part in a major collaborative effort with outside institutions, as well as our own Applied Animal Ecology Division, to study the genetic diversity and population structure of the Peninsular bighorn sheep in Baja California, Mexico. This subspecies is considered a Distinct Population Segment of desert bighorns Ovis canadensis nelsoni and is listed as federally endangered. Although there have been previous studies on various subspecies of bighorn sheep in the United States, not much is known about the populations in Baja California.
If our genetic study shows that there is connectivity between populations in northern Mexico and southern California, Peninsular bighorns in Baja may face some future challenges due to recent plans to expand the international border fence and to build wind farms in the Sierra Juárez ranges that are home to the sheep in our study. These structures could have negative impacts, causing fragmentation and preventing gene flow between populations. Understanding the levels of connectivity and the population structure prior to development projects will give us a baseline for assessing impacts on the bighorn migration during and after development.
We have completed the initial stages of our project, including establishing a protocol for sampling, DNA extraction, and genetic analysis of feces collected in the field. Obtaining any type of sample from Peninsular bighorns presents a challenge because of the rough terrain in the Sierra Juárez, paired with the elusive nature of bighorns. Using noninvasively collected biomaterial such as feces allows us to obtain samples for genetic analysis without the need to physically capture the animal. To date, we have collected around 200 tubes of fecal pellets in the field and have worked with authorities to bring them across the border.
After I receive the pellets, I perform a number of steps to obtain DNA, starting with “washing” the pellets several times to remove the sloughed epithelial cells present on their outer surface. We can then extract DNA from these cells for genetic analysis. Working with noninvasive samples can be challenging because of the lower quality and quantity of DNA obtained compared to using tissue or blood samples as sources of genetic material. However, months of running optimization tests have paid off, as we finally reached the point where we can identify individual Peninsular bighorn sheep using genetic markers called microsatellites.
To date, 200 fecal samples have been processed for DNA extraction, and out of the 107 fecal samples that passed the necessary quality index test for DNA analysis, I have identified 43 unique individuals. I intend on processing additional samples with the expectation of identifying even more individuals for the population structure analysis. Our hope is to generate data that will help us better understand the current population structure and connectivity of Peninsular bighorn sheep in Baja California so, in the future, we can properly measure how these animals respond to changes in their habitat caused by human development.
Asako Navarro is a research technician for the San Diego Zoo Institute for Conservation Research.