Understanding what a species eats – and how that changes over time – not only gives us a window into the lives of wild animals, but also gives us the power to be responsible stewards of their ecosystems.
Genetic metabarcoding is changing the way we look at diet and foraging ecology in whales. With each new sample, we gain new insight into the feeding behavior of these enigmatic species. Learn more about how the Whale And Dolphin Ecology Lab (WADE), led by SAFS Assistant Professor Amy Van Cise, is using genetic metabarcoding to understand and conserve southern resident killer whales in the Salish Sea.
Killer whales are the only natural predator of baleen whales – those that have “baleen” in their mouths to sieve their plankton diet from the water. More solitary than toothed whales, baleen whales face predatory attacks from killer whales, especially mother and calf pairs. When attacked, some species fight back, while others choose flight. But whale species also produce loud underwater songs…what stops killer whales from homing in on their calls and attacking them?
In new acoustic research conducted by Trevor Branch, a Professor in the University of Washington School of Aquatic and Fishery Sciences, he found that some baleen whale species call at such deep frequencies that they’re completely undetectable by killer whales—who cannot hear sounds below 100 Hz. These tend to be the whale species that flee in the face of attack. Meanwhile, their high-frequency singing brethren who fight back when attacked, also tend to be slower-moving and more maneuverable. The deep singers are in the flight club and include blue, fin, sei, Bryde’s and minke whales, while the fight club includes right, bowhead, gray and humpback whales. Branch’s research was published in Marine Mammal Science on Jan 31. 2025.
P. Markovic, CETREC, Western Australia
Killer whales charging next to a blue whale calf with visible killer whale toothmarks like a rake and missing chunks of flesh. Location: Bremer Bay, Western Australia.
The fight or flight hypothesis is not new, but research into acoustics is shedding new insights into the behavioral, morphometric, and ecological adaptations of baleen whales. Could this so-called acoustic crypsis, where whales that call at such deep frequencies that they are acoustically invisible to killer whales, have developed as a defense mechanism from attack?
Killer whales are found in every one of the world’s oceans, and their prey ranges from small fish to the largest whales on Earth. The fight species of baleen whales usually migrate and calve closer to the coast in shallow water, a haven of sorts which provides easier defense against killer whale attacks—especially for group defense in aggregations. Combined with their slow-swimming and more navigable bodies, their communication with other whales is often at higher frequencies easily heard by killer whales—above 1500 Hz. In contrast, flight species have streamlined and slender bodies adapted for speed, and typically disperse across wider open ocean regions for mating and calving, where they are able to flee in all directions.
These behaviors also have implications for feeding and mating. Denser congregations in shallow coastal areas leaves less food for fight species, in comparison to the open ocean favored by flight species. However, the opposite is true for finding a mate—it’s easier when you’re all in a similar location, versus spread out over long distances. Where do acoustics fit into this picture?
Singing is a fundamental part of mate attraction and selection for whales. Males of the flight species sing in a way that maximizes the number of females that hear them, producing simple and repeated songs to attract a potential mate, and singing over prolonged periods to allow females to track them down. “But these super loud songs could expose them and their mates to killer whale attack. And this is where acoustic crypsis comes in: singing at low frequencies that are impossible, or very difficult, for killer whales to hear,” Branch said.
J. Daw, CETREC, Western Australia
After a killer whale pod kills a blue whale calf, one dives into the mouth of the blue whale to feast on its tongue. Location: Bremer Bay, Western Australia.
Branch conducted a review of aquarium experiments on killer whale hearing ranges, reviewed the source frequency and source level of populations of all baleen whales, and combined these with knowledge of how sounds move through the ocean, to predict which whale populations can be easily heard by killer whales. It turns out that flight species generally can’t be heard more than 1 km away by killer whales, unlike the calls of fight species.
The research shows that under the sea there is a sound landscape governed by fear, with some whale species choosing to sing their songs to their prospective Valentines at deep levels to avoid attacks; while other whale species compete to sing the most varied and interesting songs, and fight back when attacked. The fight vs. flight differences appear to drive all aspects of the lives of baleen whales, from where they are found, to their communication, to where and when they breed and feed.
Branch said: “It just never occurred to me that some whales sing low to avoid killer whales, but the more I looked at this, the more I realized that every aspect of their behavior is influenced by the fear of predation.”
Alongside two student researchers from her lab, SAFS Assistant Professor Amy Van Cise has been out on the Puget Sound for a few days conducting killer whale research. Working with a team comprised of UW students, Wild Orca, and San Diego Zoo Wildlife Alliance, they’re assisted in locating fecal samples from the whales by Wild Orca’s poop-sniffing dog, Eba.
Eba, the poop-sniffing Wild Orca dog.
Amy Van Cise, with student researchers Sofia Kaiaua and Mollie Ball, were aboard the Wild Orca boat with Research Director Dr. Deborah Giles, who is also a Resident Scientist at Friday Harbor Laboratories, where she teaches Marine Mammals of the Salish Sea in the Spring. Recent UW Marine Biology and Oceanography graduate, Aisha Rashid, was also present, now working for Wild Orca. They were joined by Hendrik Nollens from the San Diego Zoo Wildlife Alliance, and Eba’s handler, Jim Rappold.
NOAA research permit #26288 (Wild Orca)
The research team is collecting fecal samples from Southern Resident killer whales.
To collect samples, Wild Orca drives slowly about 500-1000m downwind of the killer whales (preferably behind them), waiting for Eba to catch a scent. Once she does, one of her trainers (either Giles or Jim Rappold) works with Eba to have her direct the boat to the sample location, where the team then scoops it out of the water and carefully spins it down, pours off the excess sea water, and stores it in a conical tube on ice until they can get it in a freezer.
Hendrik Nollens (San Diego Zoo Wildlife Alliance) holds one of the samples collected during the trip.
From a single sample, the collaborative research team can get hormones (to tell things like pregnancy, stress, or nutritional stress), genetics (to ID the whale, determine diet composition, and/or look a gut microbiome and parasites), and also look at toxins/contaminants.
NOAA Research Permit #26288 (Wild Orca)
A single fecal sample can reveal a wealth of information about a killer whale.
The trip has also been used to collect content to develop an outreach video based on the diet research underway at the WADE lab and how it fits into the broader conservation goals for Southern Resident killer whales. For the video, Mollie and Sofia interviewed Dr. Michael Weiss, who is the Research Director of the Center for Whale Research, and Jay Julius, the former Chairman of the Lummi Nation, full time fisherman and father, and the Founder and President of Se’Si’Le.
The research team aboard the Wild Orca boat.
UW student researchers in the WADE lab interview Dr. Michael Weiss, Research Director of the Center for Whale Research.
All photos of killer whales are taken under NOAA research permit #26288 to Wild Orca
Over the last two decades, there has been huge growth in the availability of different ‘omics methods used to study marine mammals. From elusive beaked whales and near extinct vaquitas to more common dolphins and sea lions, understanding the ecology, evolution, and health of marine mammal populations around the globe is critical for conservation efforts. A new paper published in Marine Mammal Science, involving 19 scientists from around the globe, has laid out best practices for collecting and preserving marine mammal biological samples in the ‘omics era.
The branches of science known informally as omics are various disciplines in biology whose names end in the suffix -omics, such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics.
Marine mammal scientists are working on different species, in different locations, and asking different questions, using tissue samples collected from wild marine mammals. Those tissue samples give scientists access to vast amounts of information, allowing them to answer questions ranging from a population’s recent foraging habits, health status, or contaminant load to its deeper evolutionary history or its resilience in the face of climate change. They provide scientists, and us, a window into the secret lives of these elusive animals and hints about how we can be better stewards of their ecosystems, but they come at a price – literally.
NOAA (permit # 21348)
NOAA scientists collect data near a pod of Bigg’s killer whales.
Most marine mammals live far from shore, and spend the majority of their lives underwater. To collect tissue samples from these animals, large teams of scientists will venture out onto the ocean for months at a time. Many marine mammal species have huge home ranges, such as the 9,000 mile migration range of humpback whales; simply finding them is a monumental task. Adding to the challenge, collecting samples from marine mammals is inherently invasive and scientists work under strict permits to minimize both the number of times samples need to be taken, and the impact on the animal during collection.
Arial Brewer (permit # 21348)
Jeff Hogan (Killer Whale Tales/NOAA) presents a freshly collected fecal sample from a Southern Resident killer whale.
Phillip Morin from NOAA Southwest Fisheries Science Center, who has been working in genetics for over 35 years, understands all too well the difficulty in getting quality samples for genomics. “A good illustration is the sample used for the vaquita reference genome, which is one of only two live-cell samples ever obtained from this species. The vaquita, a member of the porpoise family, is the most endangered marine mammal in the world,” he shared. “A conservation project in 2017 took two years of extensive planning with over 90 experts from nine countries, and 11 days at sea, to try to capture vaquita for captive management. As part of that project, we worked to get the appropriate samples collected, transported quickly to the cell culture lab across the international border, and cultured to preserve live cells for DNA and RNA extraction.”
Because of all of these challenges, each tissue sample could represent an investment of tens of thousands of dollars. Caring for those samples and preserving them in a way that will allow them to be used by many generations of future scientists, and with many generations of emerging techniques, is a priority that is always at the forefront of a marine mammal scientists’ mind. “For some populations or species, decades of sampling effort have resulted in only 10s of samples, highlighting how critical it is to figure out the best collection and preservation techniques,” says Amy Van Cise, Assistant Professor at the University of Washington School of Aquatic and Fishery Sciences (SAFS).
NOAA (permit # 21348)
NOAA scientists collect a fecal sample from the water using a pole net.
What are some of the best practices for collecting and preserving marine mammal samples that research teams have gone through such effort to collect? This is the overarching question bringing together a team spanning 11 different institutions, including Van Cise, with the goal of creating a unifying set of guidelines that will ensure these samples can be shared among labs, analyzed with a variety of new and emerging technologies, and used for years to come. “What’s impressive about this study is that it brings together scientists examining different types of questions,” shared Amy Apprill from Woods Hole Oceanographic Institution (WHOI). Apprill’s particular focus is on microbiome analysis, which sheds insight into the health of marine mammals as a result of changing oceans and human impact.
Microbiome analysis is a great example of an emerging technology that’s revolutionizing how we study marine mammal health. Unlike humans, it’s difficult to assess the health of wild animals, and nearly impossible when those animals live in the ocean. “Wherever you are in the world, a doctor can sample and test your blood and those results are understandable and comparable around the globe,” Apprill said. Marine mammals don’t schedule regular doctor’s appointments, but emerging ‘omics technologies are making it possible to determine whether an individual is sick or healthy using tissue samples. Apprill is one of the scientists at the forefront of the effort to characterize the microbiomes of healthy and diseased individuals. “As we obtain samples from different animal health states, we’re gaining valuable data that builds a type of health metric,” Apprill said. This type of work can only be successful if researchers can examine samples collected by many scientists around the world. Similar to the way hospitals have standardized the way they test for diseases and assess human health, Apprill said that, “as scientists in marine mammal research, we need a similar system of guidelines, best practices, and protocols to follow, so that our samples have the maximum use.”
Kim Parsons (NOAA/ NMFS/ NWFSC) processes cetacean tissue biopsies in a makeshift lab onboard a survey vessel in Southeast Alaska.
Images courtesy of NOAA Fisheries, Marine Mammal Laboratory.
The gold standard for sample preservation is collecting it quickly from the animal, either when alive or recently dead before the cells start degrading, and freezing it to -80°C or colder immediately. However if this isn’t possible in the field, then what is the best alternative? The answer depends on the anticipated research needs, availability and transportability of preservatives, and time until samples reach a permanent storage site. While there is no single solution for all situations, some methods provide broader preservation characteristics, allow international transport, and/or greater stability prior to freezing.
“In science, there are a thousand ways you could conduct each step,” Apprill shared. “But you don’t want to spend valuable time, effort, and resources figuring out those steps if someone else already has the best method and protocol laid out.”
Arial Brewer (permit # 21348)
NOAA scientists approach a pod of Southern Resident killer whales for data collection.
The ways we can use ‘omics techniques are rapidly expanding every year, adding another layer of importance to the need for high-quality, well-preserved samples. “Just like forensics held on to human samples from crime scenes while the world was waiting for DNA capabilities to expand, marine mammal science works the same way. As technological advancement expands really quickly, it’s imperative to preserve samples in a way that the wealth of information contained in them can be uncovered in the future,” Morin said.
A new article, titled “Conservation challenges of predator recovery”, has been accepted for publication into Conservation Letters: A journal for the Society for Conservation Biology. This article is a result of the collaboration of SAFS post-doc Kristin Marshall, SMEA Professor Ryan Kelly, NOAA scientist and SAFS affiliate faculty Eric Ward, and NOAA scientists Jameal Samhouri and Adrian Stier.
Abstract
Predators are critical components of ecosystems. Globally, conservation efforts have targeted depleted populations of top predators for legal protection, and in many cases, this protection has helped their recoveries. Where the recovery of individual species is the goal, these efforts can be seen as largely successful. From an ecosystem perspective, however, predator recovery can introduce significant new conservation and legal challenges. We highlight three types of conflicts created by a single-species focus: (1) recovering predator populations that increase competition with humans for the same prey, (2) new tradeoffs that emerge when protected predators consume protected prey, and (3) multiple predator populations that compete for the same limited prey. We use two food webs with parallel conservation challenges, the Northeast Pacific Ocean and the Greater Yellowstone ecosystem, to demonstrate legal/policy conflicts and the policy levers that exist to ameliorate conflicts. In some cases, scientific uncertainty about the ecological interaction hinders progress towards resolving conflicts. In others, available policy options are insufficient. In all cases, management decisions must be made in the face of an unknown future. We suggest a framework that incorporates multispecies science, policy tools, and tradeoff analyses into management.
