A study published today in Marine Mammal Science, co-led by Deborah Giles of Wild Orca and Sarah Teman of the SeaDoc Society, a program of the UC Davis School of Veterinary Medicine, looked at more than 60 years of recorded interactions between Southern Resident killer whales and porpoises in the Salish Sea to better understand why they exhibit this behavior.

Southern Resident killer whales are an endangered population, numbering only 75 individuals. Their survival is intimately tied to the fortunes of Chinook salmon — also an endangered species. Without enough Chinook salmon, these whales are in danger of extinction.

“I am frequently asked, why don’t the Southern Residents just eat seals or porpoises instead?” said Giles. “It’s because fish-eating killer whales have a completely different ecology and culture from orcas that eat marine mammals — even though the two populations live in the same waters. So we must conclude that their interactions with porpoises serve a different purpose, but this purpose has only been speculation until now.”

Three plausible explanations

While scientists have recorded instances of Southern Resident killer whales engaging in porpoise harassment as early as 1962, reasons for this behavior have long remained a mystery. Giles, Teman, and a team of collaborators analyzed 78 documented incidents of porpoise harassment from 1962 to 2020. The study suggests three plausible explanations:

• Social play: Porpoise harassment may be a form of social play for killer whales. Like many intelligent species, these whales sometimes engage in playful activities to bond, communicate, or simply enjoy themselves. This behavior might benefit group coordination and teamwork.
• Hunting practice: Another hypothesis suggests that porpoise harassment might hone their salmon-hunting skills. Southern Resident killer whales could view porpoises as moving targets to practice their hunting techniques, even if they do not intend to consume them.
• Mismothering behavior: This theory suggests that the whales may be attempting to provide care for porpoises they perceive as weaker or ill-a manifestation of their natural inclination to assist others in their group. Females have been witnessed carrying their deceased calves and have been seen similarly carrying porpoises.

“Mismothering behavior — also known as ‘displaced epimeletic behavior’ to scientists — might be due to their limited opportunities to care for young,” Giles explained. “Our research has shown that due to malnutrition, nearly 70% of Southern Resident killer whale pregnancies have resulted in miscarriages or calves that died right away after birth.”

Salmon specialists

Despite these intriguing insights, Giles, Teman, and their collaborators acknowledge that the exact reason behind porpoise harassment may never be fully understood. What is clear, however, is that porpoises are not a part of the Southern Resident killer whale diet. Southern Resident killer whale diets are highly specialized for salmon, making the idea of eating porpoises highly unlikely.

“Killer whales are incredibly complex and intelligent animals. We found that porpoise-harassing behavior has been passed on through generations and across social groupings. It’s an amazing example of killer whale culture,” Teman says. “Still, we don’t expect the Southern Resident killer whales to start eating porpoises. The culture of eating salmon is deeply ingrained in Southern Resident society. These whales need healthy salmon populations to survive.”

This research underscores the importance of conserving salmon populations in the Salish Sea and throughout the whales’ entire range. Maintaining an adequate supply of salmon is vital for the survival and well-being of Southern Resident killer whales and the overall health of the Salish Sea ecosystem.

Affinity for play

This study comes at a time when a separate population of killer whales on the Iberian Peninsula has drawn international headlines for interacting with, and on three occasions, sinking boats off the coast of Portugal and Spain. Ultimately, the Southern Resident killer whales and the Iberian Peninsula orcas are two different populations with distinct cultures. One thing the two might have in common is their affinity for play behavior.

The study was funded by Wild Orca and SeaDoc Society. Additional partners include the University of Exeter, Fisheries and Oceans Canada, Orca Behavior Institute, National Oceanic and Atmospheric Administration, Cascadia Research, The Whale Museum, Center for Whale Research, Ocean Research College Academy (ORCA) at Everett Community College, Bay Cetology, North Gulf Oceanic Society, George Mason University, and Marine-Med.

Today, the last remaining stocks of Atlantic walrus are more at danger than ever, due to a combination of Arctic warming and a long history of devastating human exploitation. Rising global temperatures are significantly impacting Arctic marine ecosystems and their inhabitants. However, little is known about exactly how this combination of stress factors will impact Arctic species.

Now, researchers have examined how walrus coped with past cycles of climate change. Using breakthroughs in ancient genomics, the team was able to extract, sequence and interpret ancient genetic information contained in teeth and bone that survive well in the Arctic’s frozen archaeological sites. These DNA results were integrated with modern genetic samples, enabling them to reconstruct how the genetic diversity of Atlantic walrus had changed under earlier cycles of global warming.

“We found that Arctic warming has led to a surprisingly high genetic separation of local walrus stocks. Because they have very specific habitat requirements such as how they feed, for example, this has led to the rapid spreading, isolation and in many cases extinction of walrus stocks,” says Peter Jordan, Professor of Archaeology at Lund University.

The last Ice Age peaked between about 27,000 and 19,000 years ago. At this time the Arctic was buried under kilometers of glacial ice sheets, and so marine mammals were pushed southwards to areas of ice floes and more open water. Walrus survived in some areas of the Atlantic located further to the south, and as soon as climates warmed again, the ice edge retreated and walrus populations pushed quickly northwards again. This combination of warming and climate-driven dispersal led to local walrus populations becoming more genetically differentiated.

In addition, during the last thousand years, human hunting and commercial exploitation has led to numerous local extinction events. These include the expansion of Norse settlers into Iceland and the North Atlantic in pursuit of walrus ivory, which was a valuable trade good, and in more recent times, with industrial scale culling of walrus populations.

Currently, the genetic diversity of walrus stocks is a fragment of what existed earlier, making them even more vulnerable to pressures such as accelerating ice loss, disturbance by Arctic shipping, resource extraction and mass tourism, according to the researchers.

“As Arctic sea ice retreats, the depleted walrus stocks will disperse further into smaller and more isolated pockets, where the genetic isolation and reduced connectivity makes them ever more vulnerable to other stressors such as Arctic shipping, resource extraction and large-scale tourism,” says Peter Jordan.

“Our results underscore the urgency of rethinking conservation goals for species in rapidly changing Arctic marine environments,” he concludes.

Rice University scientists have described in detail the three-dimensional structure of one of the smallest known CRISPR-Cas13 systems used to shred or modify RNA and employed their findings to further engineer the tool to improve its precision. According to a study published in Nature Communications, the molecule works differently than other proteins in the same family.

“There are different types of CRISPR systems, and the one our research was focused on for this study is called CRISPR-Cas13bt3,” said Yang Gao, an assistant professor of biosciences and Cancer Prevention and Research Institute of Texas Scholar who helped lead the study. “The unique thing about it is that it is very small. Usually, these types of molecules contain roughly 1200 amino acids, while this one only has about 700, so that’s already an advantage.”

A diminutive size is a plus as it allows for better access and delivery to target-editing sites, Yang Gao said.

Unlike CRISPR systems associated with the Cas9 protein — which generally targets DNA — Cas13-associated systems target RNA, the intermediary “instruction manual” that translates the genetic information encoded in DNA into a blueprint for assembling proteins.

Researchers hope these RNA-targeting systems can be used to fight viruses, which generally encode their genetic information using RNA rather than DNA.

“My lab is a structural biology lab,” Yang Gao said. “What we are trying to understand is how this system works. So part of our goal here was to be able to see it in three-dimensional space and create a model that would help us explain its mechanism.”

The researchers used a cryo-electron microscope to map the structure of the CRISPR system, placing the molecule on a thin layer of ice and shooting a beam of electrons through it to generate data that was then processed into a detailed, three-dimensional model. The results took them by surprise.

“We found this system deploys a mechanism that’s different from that of other proteins in the Cas13 family,” Yang Gao said. “Other proteins in this family have two domains that are initially separated and, after the system is activated, they come together — kind of like the arms of a scissor — and perform a cut.

“This system is totally different: The scissor is already there, but it needs to hook onto the RNA strand at the right target site. To do this, it uses a binding element on these two unique loops that connect the different parts of the protein together.”

Xiangyu Deng, a postdoctoral research associate in the Yang Gao lab, said it was “really challenging to determine the structure of the protein and RNA complex.”

“We had to do a lot of troubleshooting to make the protein and RNA complex more stable, so we could map it,” Deng said.

Once the team figured out how the system works, researchers in the lab of chemical and biomolecular engineer Xue Sherry Gao stepped in to tweak the system in order to increase its precision by testing its activity and specificity in living cells.

“We found that in cell cultures these systems were able to hone in on a target much easier,” said Sherry Gao, the Ted N. Law Assistant Professor of Chemical and Biomolecular Engineering. “What is really remarkable about this work is that the detailed structural biology insights enabled a rational determination of the engineering efforts needed to improve the tool’s specificity while still maintaining high on-target RNA editing activity.”

Emmanuel Osikpa, a research assistant in the Xue Gao lab, performed cellular assays that confirmed the engineered Cas13bt3 targeted a designated RNA motif with high fidelity.

“I was able to show that this engineered Cas13bt3 performed better than the original system,” Osikpa said. “Xiangyu’s comprehensive study of the structure highlights the advantage that a targeted, structurally guided approach has over large and costly random mutagenesis screening.”

The research was supported by the Welch Foundation (C-2033-20200401, C-1952), the Cancer Prevention and Research Institute of Texas (RR190046), the National Science Foundation (2031242) and the Rice startup fund.