Studying a cryptic marine mammal species by eDNA

- By Lauren Jacobsen, D.V.M. December 6, 2017
The R/V Reuben Lasker in port at Ford Island, Honolulu

In the words of The Who, I am reminded of a catchy tune: “Who are you? Who, who, who, who?” As we search for the identity of a mysterious beaked whale, I just can’t help but find this to be the most fitting theme song for my expedition to the central Pacific Ocean. In mid-October, I had the exciting opportunity to participate in the Hawaiian Islands Cetacean Assessment and Ecosystem Survey (HICEAS) aboard NOAA’s R/V Reuben Lasker. This was a special opportunity, not only because it was my first pelagic research cruise, but I also had the chance to participate in a study using environmental DNA (eDNA) to learn more about a cryptic marine mammal species.

I spent a total of 25 days at sea, but the entire HICEAS effort will span a total of 187 days aboard two NOAA ships: the R/V Oscar Elton Sette and the R/V Reuben Lasker. The HICEAS expedition was a huge collaborative effort to study whales, dolphins, seabirds, and the ecosystem of the Pacific Ocean around the Main and Northwest Hawaiian Islands. Both ships made multiple trips, or ‘legs’ to cover the entire Island territory; my involvement was on leg 3 of 4 on the R/V Reuben Lasker. We departed from Oahu and traveled west along different transect lines on the north side of the Northwest Hawaiian Islands out to Midway Island. We circumnavigated Midway, and then returned to Oahu by way of the south side of the Island chain. Plans to cross the International Date Line were thwarted by rough seas, which you can see in the photo. In general, HICEAS (oops, I mean high seas) were a common theme for the trip; we averaged 6-10 foot seas and 25 knot winds for the entire leg.

Sunrise over Midway Island
High seas on the HICEAS
Lauren deploying a sonobuoy aboard the R/V Reuben Lasker

Despite the lack of cooperation from Mother Nature, we managed to see a lot of wildlife! I learned so much about sea birds! I saw 5 different types of boobies, tons of Bonin petrels, wedge-tailed shearwaters, plovers, white terns, and black-footed albatross. In my opinion, observing bird behavior was one of the most interesting parts of the trip. On one occasion, I witnessed a fascinating kleptoparasitic duet. Two Bonin petrels harassed a storm petrel to give up its meal. When the first thief stole the fish, the second Bonin petrel harassed the first one to give up the loot. I’m glad that I have better friends than that! We saw several large groups of sperm whales, most of which were cow-calf nurseries. We also saw several Fraser’s dolphins swimming in multiple chorus lines, Blainville’s beaked whales, pygmy sperm whales, false killer whales, pilot whales, and humpback whales. I found it particularly interesting to monitor the acoustics equipment used on this trip. We towed an acoustics array, which detected high frequency sounds, deployed sonobuoys in the evenings to study low frequency calls, and operated an echosounder to monitor fish, squid, and crustacean populations. Tracking minke whale “boings,” dolphin whistles in real time, and clicks from the elusive ‘Cross Seamount beaked whale’ were highlights for me.

Laboratory set up of filtering equipment

My primary duty on leg 3 of the R/V Reuben Lasker was to participate in a project to study the mysterious ‘Cross Seamount beaked whale.’ At Cross Seamount, which is located approximately 150 nautical miles south of Oahu, unique beaked whale vocalizations have been recorded but they have yet to be associated with a known species. Of the approximately 75 different whale, dolphin, and porpoise species that make click-type noises (echolocation), scientists have taxonomically narrowed this animal down to 1 of 4 types of beaked whales. The animal’s true identity has yet to be determined, so it has been affectionately referred to as the ‘Cross Seamount beaked whale.’ Since beaked whales are generally difficult to see (even in low sea states) and these calls occur primarily at night, sighting data are scarce. Extracting eDNA from seawater offers an opportunity to collect biologic information from the animal generating these calls.

Lauren and (hopefully) some beaked whale DNA

In efforts to identify the cryptic ‘Cross Seamount beaked whale,’ we collected water samples at several depths in places where positive acoustic detections were made. Water samples were collected at the surface and at a range of depths (0–1,000 meters deep) with a CTD (conductivity-temperature-depth) unit, which is an oceanographic instrument used to track ocean currents. Water was then frozen and filtered through a polycarbonate filter to concentrate the DNA. In total, we collected over 170 liters of water at different sites and depths, all of which were filtered during my trip. Once the seawater was reduced on the round filter paper, the paper was folded and spiraled into an ice cream cone-like shape, and placed into a microtube. A preservative called Longmire’s solution was added for storage and later transport. After docking, the samples will be sent to the Cetacean Conservation and Genomics Lab at Oregon State University to be analyzed by Dr. Scott Baker and his team to investigate the genetic material in these samples. Check out DNA Surveillance to learn more.These methods have been successful for identifying other marine mammal species, so stay tuned to see what we will find! “Who are you,” beaked whale? “Who, who, who, who?”

If you are interested in following the remaining cruise or looking through all the exciting things that have happened on the HICEAS efforts, click here.

Acknowledgements: Lauren’s trip was funded by the Office of Naval Research and made possible by the collaborative efforts of Pacific Island Fisheries Science Center (PIFSC), Southwest Fisheries Science Center (SWFSC), Cornell University, and Oregon State University.