Drought and habitat fragmentation over the past 30 years have caused a sudden and severe loss in genetic diversity for a rare species called the Coachella Valley fringe-toed lizard (Uma inornata), according to new research.

This small, burrowing lizard evolved among the windblown desert dunes of Riverside County in southern California. It’s uniquely adapted for this habitat, with specialized nostrils that allow it to breathe through the sand while digging for plants and insects to eat. Unfortunately most of the lizard’s previous habitats have long-since been lost to development or agriculture and the species is now mostly restricted to the Coachella Valley National Wildlife Refuge, which was founded in 1985 to protect the species.

Researchers from the U.S. Geological Survey (USGS) and other institutions took at a look at some of the last lizards living within the refuge and compared their genetics of specimens collected in 1996 and 2008. They found that one population, living in a portion of the refuge called the Whitewater Preserve, had experienced a 7.5 percent drop in allelic richness, a measure of genetic diversity. This means they have a lower genetic diversity than other species in their genus, not to mention other lizard species.

“It’s statistically significant, but whether it’s biologically significant will require further investigation,” says Amy Vandergast, a USGS research geneticist and the lead author of a paper in the journal Diversity and Distributions. Other species with similarly low genetic diversity have experienced birth defects, increased susceptibility to disease, low birth rates and similar threatening side effects.

Vandergast says the lizards probably had a history of population booms and busts, where environmental factors have caused certain sub-populations to disappear for a time. Extirpated habitats would then be recolonized by new lizards when populations grew again. That dispersal is no longer possible because populations are now so low and geographically isolated from each other.

Development has done more than just isolate the lizards. It also limits the amount of new sand that can contribute to the dunes each year. Conservation efforts in the refuge often focus on replenishing the dunes, as well as other attempts to protect the habitat.

It may be time to add long-term genetic testing into those existing conservation and management efforts. “Given the instability and fluctuations these populations experience, repeated genetic sampling may be useful in determining whether they’ll continue on a trajectory of further differentiation and loss of diversity over time,” Vandergast says. “Assessing to the extent possible whether there are links between loss of diversity and inbreeding effects, and ultimately to population viability, are important next steps.”