The Power of ‘Environmental DNA’ For Monitoring Whales

Where ever endangered orcas swim, they leave behind traces of their DNA that can reveal their passage to scientists as long as two hours later

by GrrlScientist for Forbes | @GrrlScientist

A pod of wild killer whales, also known as orcas (Orcinus orca), swims in the Puget Sound, also known as the Salish Sea. (Seattle in the background.)
(Credit: Candice Emmons / NOAA / Public domain)

As they swim through the Puget Sound, wild killer whales, also known as orcas, Orcinus orca, leave traces of their DNA in their wake. This “environmental DNA” or “eDNA” can reveal their passage for as long as two hours after they’ve moved on, reports a team of scientists in a recent study (ref).

“It’s been well-established that you can follow a whale and capture some of its fecal plume before it dissipates,” said lead author, Scott Baker, head of the Cetacean Conservation and Genomics Laboratory and associate director of the Marine Mammal Institute at Oregon State University, in email.

In addition to poop, eDNA can be isolated from a variety of sources, including skin cells in air exhaled from a whale’s blowhole, and skin shed in the water as they swim.

“Whales slough a lot of skin,” Professor Baker pointed out.

These biological samples are shed or excreted during normal activities and can be easily collected from the environment, concentrated into smaller sample sizes, and diagnostic regions of DNA can then be amplified and analyzed.

Representation of oil emulsion technique used in digital droplet PCR.

Currently, most genetic samples from wild whales, dolphins and porpoises are collected in the field using a biopsy dart — a method that is challenging for humans and disturbing for the subjects. For this reason, Professor Baker and his collaborators have been adapting an innovative and non-invasive technique, droplet digital PCR (ddPCR) technology, specifically for detecting and identifying cetacean species from eDNA found in seawater. ddPCR is a method for amplifying specific regions of DNA in very tiny reaction quantities (nanoliter sizes) by encapsulating the entire reaction within oil droplets. These reactions are so small that a typical 20 μL PCR sample — a volume that is similar to a raindrop — can be divided into 20,000 ddPCR droplets.

After adapting the method for their purposes, Professor Baker and his collaborators conducted a series of proof-of-concept tests for using ddPCR on eDNA collected during 25 encounters with wild orcas near the San Juan Islands, located in the Puget Sound (the Salish Sea). This is where the “southern resident” pod of orcas are typically found. Water samples were collected at 15 minute intervals for up to 2 hours after the orcas’ passage, concentrated into smaller quantities, and PCR amplified. Of these samples, 68% yielded usable eDNA.

“On a couple of occasions, we drifted up to five kilometers, so there was a lot of water movement — and we still got eDNA,” Professor Baker said.

Oregon State University researchers used environmental DNA filtered from seawater, to detect the passage of endangered killer whales (Orcinus orca), in Puget Sound.
(Credit: Candice Emmons / NOAA / Public domain)

Although eDNA tends to be too fragmented to provide specific information about whales, such as individual identities or their sex, further development of the methodology could change that.

“Technology is improving rapidly, so it may be a matter of time,” Professor Baker said. “And, of course, expense — especially for research in the open ocean.”

This methodology shows promise that it can be adapted to detecting the presence of other whale species, particularly rare or “cryptic” species. One such group of whales are the enigmatic and poorly-known beaked whales that Professor Baker and his collaborators are ultimately developing this methodology for.

“There are 23 species of beaked whale and some of them have never been seen alive. They have only been identified through skeletal remains. And four of those species were identified in the last decade, so there may be more out there.”

Surrounded by onlookers, university researchers conduct an autopsy on a female beaked whale, probably a Gray’s beaked whale (Mesoplodon grayi), beached on Sunset Beach, Port Waikato, New Zealand. Another beached whale lies in front.
Avenue / GNU Free Documentation License.)

Beaked whales, which are named for their distinctively long toothy “beaks”, are classified into the taxonomic family, Ziphiidae. (Read more about one species of beaked whale.)

“We think the beaked whales are a priority because of the difficulty of conventional sampling,” Professor Baker elaborated.

Beaked whales live in open ocean, where they are difficult to locate and impractical to sample using the traditional biopsy method. Adapting this eDNA method to detecting and tracking beaked whales would be comparatively easy: it would only require one person to collect water samples, filter them down to small sample sizes and bring them back to the lab for analysis.

“If this method works in the open ocean, which we still have to test, it will be a powerful tool,” Professor Baker said.

Environmental DNA has many other uses. For example, conservation biologists are already exploring the usefulness of eDNA for tracking and monitoring endangered shark species (ref), and are using their findings to improve conservation strategies.

Analysis of eDNA is an innovative and promising tool that could help us better understand and conserve marine biodiversity — “especially when our ‘conventional’ sampling methods are challenged, e.g., the beaked whales,” Professor Baker said.


C. Scott Baker, Debbie Steel, Sharon Nieukirk, and Holger Klinck (2018). Environmental DNA (eDNA) From the Wake of the Whales: Droplet Digital PCR for Detection and Species Identification, Frontiers in Marine Science, 9(4):968–980 | doi:10.3389/fmars.2018.0013

Also cited:

Germain Boussarie, Judith Bakker, Owen S. Wangensteen, Stefano Mariani, Lucas Bonnin, Jean-Baptiste Juhel, Jeremy J. Kiszka, Michel Kulbicki, Stephanie Manel, William D. Robbins, Laurent Vigliola, and David Mouillot (2018). Environmental DNA illuminates the dark diversity of sharks, Science Advances, 4(5):eaap9661 | doi:10.1126/sciadv.aap9661

More whale science stories:

GrrlScientist. “Meet the songbirds of the Arctic Sea: The bowhead whales”, Forbes, 6 April 2018. (Medium link).

GrrlScientist. “Extinction Looms for North Atlantic Right Whales”, Forbes, 29 March 2018. (Medium link.)

GrrlScientist. “‘Talking’ Orca Learns To Mimic Human Speech”, Forbes, 31 January 2018. (Medium link.)

GrrlScientist. “Ancient Whales Could Hear Like Hippos And Camels, Fossils Show”, Forbes, 8 June 2017. (Medium link.)

GrrlScientist. “In every whale’s earwax is a record of its lifetime exposure to pollutants”, The Guardian, 17 September 2013. (Medium link.)

GrrlScientist. “First ever sighting of world’s rarest whale on New Zealand coast”, The Guardian, 6 November 2012. (Medium link.)

Originally published at Forbes on 18 May 2018.