Targeted search with eDNA for endangered, invasive species

By Will Ferguson, College of Arts & Sciences

turtle-headPULLMAN, Wash. – New technology at Washington State University could help save the world’s largest species of freshwater turtle from extinction.

The Yangtze giant softshell turtle weighs as much as an NFL lineman and once thrived in the lakes and rivers of Southeast Asia. Today, only four are known to be alive, and the lone male is infertile.

Yangtze giant softshell turtle.

Caren Goldberg, assistant professor at the WSU School of the Environment (SoE), is using environmental DNA (eDNA) to help conservationists search for Yangtze turtles that might be surviving in the wild. The technology detects telltale bits of genetic material that living creatures shed into their environment.

“Searching an entire country to find a single turtle is a monumental challenge for a few people on the ground,” Goldberg said. “Our hope is eDNA will enable us to confirm the presence of a turtle in a particular location, enabling conservationists to focus their search efforts and increase the likelihood of finding a living specimen.”

Tracking species near military bases

EDNA enables wildlife scientists to confirm the presence of an invasive or endangered species without the hassle of finding it. It is particularly useful for identifying the presence of fish and amphibians in aquatic environments.

“If you are looking for a cougar or some other large animal in a patch of trees, you can hear it and find other signs it is there,” Goldberg said. “But I can stand next to a wetland and wonder whether there is an endangered salamander there and not be able to tell for sure.”

Goldberg and WSU colleagues Alexander Fremier and Katherine Strickler received a grant from the U.S. Department of Defense in 2011 to bring eDNA from a proof of concept to a practical tool for species conservation. Their ongoing work – determining the presence of endangered species around military bases in Arizona, Washington and Florida – is some of the first to use eDNA in the field.

Technology less harmful to species sought

EDNA is relatively simple in application. A water sample is collected from a wetland, stream or river and put through a cellulose nitrate filter that separates out bits of creature DNA. In the lab, a quantitative PCR assay matches DNA from the sample to DNA of the particular organism researchers are looking for.

“We can learn a lot of things from a single sample,” Strickler said. “It tells us if the species in question is present at that particular place and time. We can also store the sample and use it years later to help determine when an invasive species was introduced to an area.”

Another advantage is that eDNA is minimally invasive. Researchers often rely on sampling methods like dip netting and bottom dredging to collect aquatic species for study. These methods can harm not only the environment but also the creatures being studied.

“An example of this is fairy shrimp in California’s vernal pools,” Strickler said. “The sampling methods used to get a positive ID on the shrimp will sometimes inadvertently kill them.”

One of the WSU researchers’ goals is to pin down how long eDNA lingers in a particular environment. Results of their work recently were published in a special edition of the journal Biological Conservation.

At work in western U.S., worldwide

Goldberg recently analyzed samples collected by Idaho Fish and Game biologists from lakes and wetlands in north Idaho. Her work showed the northern leopard frog has disappeared from several of its historic habitats.

In Washington’s Puget Sound, she is working with managers to track the spread of the invasive New Zealand mud snail.

The Federal Bureau of Land Management is working with the WSU eDNA lab and Goldberg’s graduate student, Matthew Smith, to look in eastern Oregon and Nevada for the Columbia spotted frog, a candidate for the federal endangered species list.

The WSU researchers also recently submitted a proposal to replace the invasive sampling methods used to survey fairy shrimp populations in California with eDNA analysis.

As for the Yangtze turtle, Goldberg’s eDNA assay hasn’t yet picked up any signs of the critically endangered reptile in new areas.

“We are working with the Turtle Survival Alliance in Vietnam to refine our eDNA methods,” she said. “If we are able to detect the turtle’s DNA in new areas, it will really improve the odds of finding one.”