Tiny endangered shrimp may get big hand from environmental DNA testing

The San Diego fairy shrimp, a miniscule, puddle-dwelling crustacean that provides food for migrating birds, is nearing extinction as humans continue to encroach on its wetlands habitat. But a new approach to tracking the shrimp’s population numbers may give conservationists a boost in protecting the species, according to a UCLA study.

The fairy shrimp lives and breeds in vernal pools, puddles that appear after rains and dry up within a couple months. These pools are only about 6 inches deep and 10 to 30 feet long, yet they harbor a tremendous diversity of plants and animals, many of which provide a critical food resource that sustains waterfowl and other birds as they make their way across California.

As seasonal ecosystems, the pools are challenging to monitor and study. Complicating matters further, the endangered San Diego fairy shrimp is visually similar to a more common species of fairy shrimp and can only be distinguished microscopically by taxonomists who can identify tiny differences on the legs. And endangered shrimp must be killed to do so.

UCLA researchers have now found an effective new way of telling the species apart — one that saves time and money and does not require sacrificing endangered animals. All that’s needed is a few ounces of water from their habitat.

Known as environmental DNA, or eDNA, testing, the method uses genetic material that organisms shed throughout their habitats to identify species. In the case of the fairy shrimp, this  means they can be detected before there are adults present in vernal pools or even after they die off, expanding the time frame in which researchers can collect crucial data for conservation. The findings are published in the journal Conservation Genetics Resources.

The study, which was conducted entirely in Proctor Valley in San Diego County, makes a strong case for expanding the use of eDNA to manage and study fairy shrimp, said lead author Zack Gold, who carried out the research while a doctoral candidate at UCLA and is now a researcher at the University of Washington. The method could prove especially crucial as the fairy shrimp’s habitat continues to disappear.

“They were one of the first sets of vernal pool species to get listed as endangered,” Gold said. “They help protect these vernal pools. There are dozens of invertebrates, plants and amphibians in these pools, and none of them are doing really well. In Southern California, around 95% of our vernal pool wetlands are gone.”

Fairy shrimp, Gold notes, have an important place in the larger story of wildlife conservation. While large, charismatic species like panda bears and big cats get the lion’s share of attention, fairy shrimp and other invertebrates are just as important to healthy ecosystems. Their  disappearance could have a dramatic effect on the migratory birds that travel north from Central and South America to breed and that rely on these species as an important food source in a landscape where natural, freshwater pit stops are increasingly rare.

Paul Barber, a co-author of the study and a UCLA professor of ecology and evolutionary biology, said the research shows the practical value of eDNA, a relatively new technology that emerged a little over a decade ago.

“It saves time, it saves money and it’s better for these ecosystems and the preservation of fairy shrimp,” he said.