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Washington State University
CAS Connect February 2015

New tech to help stop extinctions

The Yangtze giant soft shell turtle weighs as much as a NFL lineman and once thrived in the lakes and rivers of Southeast Asia. It is now struggling for survival: only four individuals are known to be alive and the lone male is infertile.

Environmental scientists at WSU are developing a new technology that could help save the Yangtze, the world’s largest species of freshwater turtle, from extinction.

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

“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.”

Game-changing technology

Environmental DNA 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 where they can be difficult to locate.

Katherine Strickler collects a water sample in Florida to analyze for eDNA of reticulated flatwoods salamanders.
Katherine Strickler collects a water sample in Florida to analyze for eDNA of reticulated flatwoods salamanders.

“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 spent years wading through temperate forests and wetlands, looking for frogs and salamanders under rocks and in knee-deep mud, prior to the advent of eDNA.

“I was really excited when the first paper demonstrating that aquatic eDNA could be used to find vertebrates was published in 2008,” she said. “I was finishing my PhD work at the time and remember thinking this has a huge amount of potential if we can make it work.” 

Goldberg, SoE assistant professor Alexander Fremier and researcher 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 DoD work, determining the presence of endangered species around military bases in Arizona, Washington, and Florida, are three of the first projects using eDNA in the field.

More focused conservation

Caren Goldberg collects a water sample in Arizona to analyze for eDNA of Chiricahua leopard frogs.
Caren Goldberg collects a water sample in Arizona to analyze for eDNA of Chiricahua leopard frogs.

Environmental DNA is relatively simple in application. Water is collected from a wetland, stream, or river and put through a cellulose nitrate filter that separates out bits of creature DNA. The sample DNA is then taken to a lab where researchers use a quantitative polymerase chain reaction (PCR) assay to match it with DNA of known organisms.

“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 of eDNA is it 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.”

Environmental DNA is proving to be a valuable tool to identify the presence of both invasive and endangered species, but it has some limitations. It cannot, for instance, determine the exact number of a species, the relation of males to females in a population, or the age of individuals.

“Environmental DNA is not going to replace conservation fieldwork,” Goldberg said. “On the contrary, our hope is that eDNA will help field researchers perform more targeted and prioritized research.”

One of the WSU researchers’ current 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.

A growing body of work

Goldberg is using eDNA analysis to perform species surveys in the Northwest and elsewhere across the United States. She 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 its traditional range. In Washington’s Puget Sound, Goldberg is working with managers to track the spread of the invasive New Zealand mudsnail.

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 giant soft shell turtle, Goldberg’s eDNA assay hasn’t picked up any signs of the critically endangered reptile in new areas yet.

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