GEMM Lab – Geospatial Ecology of Marine Megafauna Laboratory

Are Most Whale Entanglements “Out of Sight, Out of Mind?”

By Lindsay Wickman, Postdoctoral Scholar, Oregon State University Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

Earlier this month, most of the GEMM Lab and I attended the 25th Biennial Conference on the Biology of Marine Mammals in Perth, Western Australia. This year’s theme, “Fishing for Change,” acknowledged that incidental entanglement in fishing gear is currently the most pervasive threat to marine mammals (e.g., Avila et al., 2018). While many presentations on the prevalence and impacts of entanglement on marine mammals were sobering, it was also inspiring to be surrounded by so many dedicated people working to address this urgent issue. For me, one of the most memorable anecdotes was an incredible whale disentanglement story shared by Paul Cottrell, a Marine Mammal Coordinator at the Department of Fisheries and Oceans Canada (DFO) in British Columbia.

An Incredible Story of Whale Disentanglement

During August 2024, DFO and a local NGO (Straitwatch) responded to a report of two humpback whales entangled in the same fishing gear near Quadra Island, B.C., Canada. Their photo-identification histories revealed that one whale had migrated from Hawaii, while the other had come from Mexico. Now tied together, the two whales’ fates became intertwined, forcing them to coordinate their movements. This situation obviously raised concerns about their welfare and survival, but I also had to silently wonder, “Did the two whales ever argue about where to migrate next? Would they choose Hawaii or Mexico?”

Thanks to the rescuers’ efforts, both whales were freed and able to make their own choice about where to spend the breeding season. As Paul explained, successfully disentangling one whale is challenging and dangerous, so freeing two was an impressive feat. After the rescue, a video showed the whales continuing to swim together synchronously, as if they did not realize they were no longer connected!

Most Entangled Whales are Out of Sight

The story above exemplifies a “confirmed” entanglement—these whales were seen dragging fishing gear and the event was reported by concerned citizens. However, most entanglement events are never witnessed, for several reasons.

When a whale becomes entangled in fishing gear, it rarely remains anchored in place. Instead, the whale often breaks part of the gear, dragging it behind as it swims. The likelihood of observing the entangled whale subsequently depends on both the chance of it being seen and the observer’s awareness and willingness to report the event (Robbins and Mattila, 2004).

*An entangled humpback whale drags gear off of San Diego, California. Credit: Keith Yip, taken under NOAA Permit #18786*.

Once entangled, many become a “dead whale swimming,” eventually succumbing to starvation and/or infections (Dolman and Moore, 2017). Many entanglements involve the mouth, severely impacting the whale’s ability to feed (Moore and van der Hoop, 2012). The additional drag imposed by entanglement is comparable to the energetic costs of migration or reproduction, causing a significant depletion in their energy reserves (van der Hoop et al. 2015). Serious injuries include amputations, hemorrhage, and infections (Cassoff et al., 2011).

Although some carcasses of entangled whales wash ashore, most are lost at sea and never recovered. For example, even with relatively intensive monitoring for North Atlantic right whale (NARW) carcasses, Pace et al. (2021) estimated that recovered carcasses represented just 36% of the total deaths. These recovered carcasses may also underestimate the toll of entanglement; entanglement accounted for 51% of mortality in the carcasses vs. 87% of serious injuries observed in living NARWs (Pace et al., 2021).

For whales that manage to dislodge the gear and survive, scars can provide clues to their past entanglement history. Injuries from the fishing lines can leave indentations where they cut through skin and blubber, and healed wounds often result in white pigmented scars that wrap around the body (especially the flukes and peduncle; e.g., Robbins and Matilla 2004). The widespread prevalence of these scars suggests that in many cases, whales can actually dislodge the gear on their own. For example, a study of entanglement scars on humpback whales in the Gulf of Maine revealed that 10% of adults and 30% of juveniles acquired new entanglement scars between 2009-2010. Without scarring analyses though, most of these entanglements would have been missed; just 7% of these individuals with entanglement-related scars were seen while entangled (Robbins 2012).

*A humpback whale fluke and peduncle showing scarring likely caused by a past entanglement. Credit: GEMM lab, taken under NOAA Permit # 27426 issued to MMI.*

Unfortunately, scars are not the only long-term consequence of non-lethal entanglement events. Previously entangled NARWs have lower survival rates than unaffected individuals (Robbins et al. 2015, Reed et al. 2024), and long-term stress responses can impact their future health and reproductive success (Pettis et al. 2004). It is tempting to assume that only severe entanglements affect future reproduction and survival, but a lack of extensive external injuries doesn’t necessarily mean that the impact of the entanglement event is more minor (Robbins and Matilla, 2004). For example, Reed et al. (2024) found that NARWs with entanglement injuries classified as minor were less likely to transition from a “non-breeder” to “breeder” status than those with severe injuries.

Tracking Unseen Entanglements: Project SLATE

Since reported entanglements and recovered carcasses reveal just a fraction of actual entanglements, researchers are continuing to innovate ways of documenting these “unseen” entanglement events.

As discussed in a previous blog post, photos of entanglement scars on the flukes and peduncles of humpback whales are being utilized in Project SLATE to detect trends in entanglement off the coast of Oregon, USA. Analyzing images of whales for signs of past entanglements is a meticulous process that may not seem as thrilling as responding to an actual disentanglement event. However, in areas with lower population densities, such as the Oregon coast, reported entanglements are undoubtedly an underestimate of the true number of events. Thus, tracking scarring rates can provide more comprehensive data on entanglement prevalence in Oregon than confirmed reports alone.

What to do if you see an entangled whale

If you happen to observe an entangled whale, please do not attempt to disentangle it yourself. Whale disentanglement is dangerous and complex, so best left to the experts! When well-meaning citizens attempt a disentanglement on their own, it can also result in an “incomplete disentanglement,” where some, but not all, gear is removed from the whale. Incomplete disentanglements just make it harder for responders to subsequently find and successfully rescue the whale.

Instead, report the entanglement by promptly calling:

Entanglement Reporting Hotline: 1-877-SOS-WHAL or 1-877-767-9425
or U.S. Coast Guard: VHF Ch. 16

Videos or photos showing the entangling gear is very helpful to trained responders, but remember to stay at least 100 yards from the whale, and beware of snagging your vessel in the lines. Visit NOAA Fisheries for more information.

*A NOAA-led team disentangle a humpback whale near Dutch Harbor, Alaska. Credit: Andy Dietrick/NOAA, taken under NOAA Permit #18786.*

References:

Avila, I.C., Kaschner, K., Dormann, C.F.. (2018). Current global risks to marine mammals: Taking stock of the threats. Biol. Conserv. 221, 44–58.

Cassoff, R.M., Moore, K.M., McLellan, W.A., Barco, S.G., Rotstein, D.S., Moore, M.J. (2011). Lethal entanglement in baleen whales. Dis. Aquat. Organ. 96, 175–185.

Dolman, Sarah J., and Michael J. Moore. (2024). Chapter 4: Welfare implications of cetacean bycatch and entanglements. In A. Butterworth (Ed.) Marine Mammal Welfare: Human Induced Change in the Marine Environment and Its Impacts on Marine Mammal Welfare (pp. 41-65).

Moore, M. J., and van der Hoop, J. M. (2012). The painful side of trap and fixed net fisheries: chronic entanglement of large whales. Journal of Marine Sciences, 2012.

Pace III, R. M., Williams, R., Kraus, S. D., Knowlton, A. R., & Pettis, H. M. (2021). Cryptic mortality of North Atlantic right whales. Conservation Science and Practice, 3(2), e346

Reed, J., New, L., Corkeron, P., Harcourt, R. (2024). Disentangling the influence of entanglement on recruitment in North Atlantic right whales. Proc. R. Soc. B Biol. Sci. 291.

Robbins, J., Mattila, D. (2004). Estimating humpback whale (Megaptera novaeangliae) entanglement rates on the basis of scar evidence. Rep. to Northeast Fish. Sci. Center, Natl. Mar. Fish. Serv. 43EANF030121 22p.

Robbins, J. (2012). Scar-Based Inference Into Gulf of Maine Humpback Whale Entanglement : 2010. Report to the Northeast Fisheries Science Center National Marine Fisheries Service, EA133F09CN0253 Item 0003AB, Task 3.

van der Hoop JM, Corkeron P, Kenney J, Landry S, Morin D, Smith J, Moore MJ. (2015). Drag from fishing gear entangling North Atlantic right whales. Mar Mamm Sci 32(2):619–642.

From coast to coast: assessing impacts of human threats and climate change from dolphins to blue whales

By Nicole Principe, first-year PhD student, OSU Dept of Fisheries, Wildlife and Conservation Sciences, GEMM Lab

Humans rely on oceans and coastal ecosystems for a variety of resources, such as tourism and recreation, fishing and aquaculture, transport of goods, and resource extraction. However, each use is contributing to new and cumulative stressors that are impacting marine mammals. The health of marine mammal populations can often serve as indicators of overall environmental health. Therefore, studying the stressors they face can help provide insights into the broader impacts on marine ecosystems and determine if conservation or management measures are necessary. As a master’s student at the College of Charleston in South Carolina and subsequently the stranding and research technician with the Lowcountry Marine Mammal Network (LMMN), I saw first-hand how some of these stressors affect local marine mammal populations.

In my role as the stranding and research technician with LMMN, I led the response and recovery of all deceased marine mammals, mainly bottlenose dolphins (Tursiops erebennus), in South Carolina to determine cause of death and identify main sources of mortality. Threats to these cetaceans can be environmental or anthropogenic in origin. Carefully examining and sampling every individual during a necropsy was critical to determine the presence of infectious disease, the contaminant and microplastic load, and any sign human interaction. While deaths from environmental causes can be more challenging for humans to mitigate, direct threats from human activity can be lessened with conservation actions and increased education to the public. LMMN responds to several strandings of dolphins each year that are the result of entanglement or boat strike. South Carolina has one of the highest rates of crab pot entanglements. In some cases, the call came quick enough that a disentanglement was possible, but in others, we found the animal already deceased with rope and gear still attached. Hundreds, if not thousands, of commercial and recreational crab pots are deployed within South Carolina estuaries, yet there are currently no regulations in place to help mitigate the threat of entanglement.

*Images: Conducting a necropsy in the lab (left) and doing a preliminary examination in the field (right) on stranded bottlenose dolphins. Photo credit: Lowcountry Marine Mammal Network*

LMMN also conducts land and boat-based surveys to better understand strand feeding, which is a unique foraging strategy utilized by a small number of dolphins in South Carolina. When dolphins strand feed, they herd and trap fish up onto mudbanks or shorelines. The dolphins chase after the fish, briefly stranding themselves as they try to catch them. It is an incredible behavior to witness and because of this, it has become highly publicized as a tourist activity. There are areas where the public can walk right up as dolphins are attempting to hunt and many instances of people trying to touch, feed, or otherwise harass the dolphins have been reported. I also conducted a small study where I used drones to identify human interferences towards dolphins strand feeding and found that boaters and kayakers were often approaching the animals too closely, following them, or speeding through the inlet when animals were present. The write up on that project can be found here. High levels of human disturbance towards dolphins strand feeding could lead individuals to abandon otherwise suitable habitat, causing them to expend more energy to look for food elsewhere.

*Images: Bottlenose dolphins strand feeding (left) and an instance of a beachgoer illegally harassing dolphins while they hunt (right). Photo credit: Glen Cox & Lucy Grierson.*

To help mitigate threats to dolphins from entanglements, boat strikes, and illegal harassment, the LMMN team and I created an educational workshop called W.A.V.E., which stands for Wildlife Awareness and Viewing Etiquette. These half-day workshops are tailored to both recreational boaters/public and commercial tour operators and fishermen and cover topics ranging from the importance of marine mammals in our ecosystem, the Marine Mammal Protection Act, global and local threats, and ways we can view marine wildlife that reduce disturbance. It is my hope that with more education and awareness about how humans use our waterways and interact with wildlife in negative ways, it can lead to positive changes. For more information about LMMN’s W.A.V.E. Workshops, head to their website.

*Image: Successful W.A.V.E. Workshop with local eco-tour operators. Photo credit: Lowcountry Marine Mammal Network*

In addition to cumulative stressors from human interactions, I also began to contemplate the role of climate change as a threat to the lives of marine mammals during my master’s research on dolphin distribution within the Charleston Estuary System (CES). A main question I was investigating was if and why some dolphins travel into low salinity waters high in the estuarine system. Bottlenose dolphins have evolved in marine and estuarine environments where salinity levels are typically ~30 parts per thousand (ppt). While dolphins can withstand short durations of exposure to low salinity (defined as 15 ppt), prolonged exposure to freshwater can result in negative health consequences, such as sloughing of skin and ulcerative lesions, changes in pathophysiology, and eventual mortality (Ewing et al., 2017). Over the past 20 years, many intermittent dolphin sightings and strandings occurred in riverine areas of the CES where salinity levels were below 10 ppt. To better understand how and why dolphins use this risky habitat, I conducted drone surveys across the CES for a year. I did find dolphin groups traveling and feeding in low salinity waters, however, the encounters were only during months with warmer water temperatures (Principe et al., 2023). We hypothesize that environmental conditions during those months may lead to decreased prey availability in the lower, more suitable parts of the estuary, forcing dolphins to travel further up the rivers to access higher abundances of prey (especially mullet). Other studies in different regions have found similar results of dolphins traveling into low salinity water during warmer months potentially in response to prey (Mintzer and Fazioli, 2021; Takeshita et al., 2021).

*Images: Drone snapshot of six bottlenose dolphins traveling together (left) and a dolphin observed with skin lesions in low salinity habitat (right). Photo credit: Nicole Principe, NMFS Permit 21938*

These results lead to questions as to how prey and dolphin movements will shift under future climate change scenarios. Increasing warm water temperatures may lead to further shifts in prey distribution, potentially driving more estuarine dolphins to utilize upper riverine habitats to find food. Just since 2022, four dolphins were observed in freshwater habitat for several weeks. Two were eventually found and confirmed deceased and two went missing and are presumed deceased. If more dolphins use and remain in these low salinity habitats for extended periods, negative health consequences could lead to population impacts and signal a need for more conservation and management actions.

It is quickly becoming evident that climate change is threatening marine mammals, at both local and global scales. More research is needed to better understand how changing environmental conditions is impacting the availability and quality of prey and how large marine predators are shifting in response. For my PhD, I am working with the GEMM Lab on the SAPPHIRE (Synthesis of Acoustics, Physiology, Prey, and Habitat in a Rapidly changing Environment) project, where we are researching how changing ocean conditions affect the availability of krill, and blue whale behavior, health, and reproduction in New Zealand. The South Taranaki Bight (STB) region experiences a productive coastal upwelling system that supports enhanced primary productivity (Chiswell et al. 2017) and dense aggregations of prey (Bradford-Grieve et al., 1993). Pygmy blue whales (Balaenoptera musculus brevicauda) in this region are not known to migrate and instead use the STB region year-round for foraging and reproduction (Torres, 2013; Barlow et al., 2022). After a marine heatwave in the Tasman Sea in 2015-2016, there were less krill aggregations due to lessened upwelling (Barlow et al., 2020), which caused reduced foraging effort, and subsequently reduced reproductive activity by blue whales (Barlow et al. 2023). Continued field work and data analysis will help us to develop Species Health Models that will predict how these prey and predator populations will respond to future environmental change.

Overall, it is clear that human activity is leading to direct and indirect impacts on marine mammal populations at many different scales, from an individual human harassing a foraging dolphin to global climate change impacts on blue whale population dynamics. Ongoing research is essential in understanding these impacts better and thus inform development of effective conservation strategies to protect both marine mammals and the environment.

References

Barlow DR, Bernard KS, Escobar-Flores P, Palacios DM, Torres LG (2020) Links in the trophic chain: Modeling functional relationships between in situ oceanography, krill, and blue whale distribution under different oceanographic regimes. Mar Ecol Prog Ser 642:207–225.

Barlow DR, Klinck H, Ponirakis D, Branch TA, Torres LG (2023) Environmental conditions and marine heatwaves influence blue whale foraging and reproductive effort. Ecol Evol 13:e9770.

Barlow DR, Klinck H, Ponirakis D, Holt Colberg M, Torres LG (2022) Temporal occurrence of three blue whale populations in New Zealand waters from passive acoustic monitoring. J Mammal 104(1): 29–38.

Bradford-Grieve JM, Murdoch RC, Chapman BE (1993) Composition of macrozooplankton assemblages associated with the formation and decay of pulses within an upwelling plume in greater cook strait, New Zealand. New Zeal J Mar Freshw Res 27(1): 1–22.

Chiswell SM, Zeldis JR, Hadfield MG, Pinkerton MH (2017) Wind-driven upwelling and surface chlorophyll blooms in greater Cook Strait. New Zeal J Mar Fresw Res 51(4): 465–489.

Ewing RY, Mase-Guthrie B, McFee W, Townsend F, Manire CA, Walsh M,

Borkowski R, Bossart GD, Schaefer AM (2017). Evaluation of serum for pathophysiological effects of prolonged low salinity water exposure in displaced bottlenose dolphins (Tursiops truncatus). Front Vet Sci 4

Hornsby F, McDonald T, Balmer BC, Speakman T, Mullin K, Rosel P, Wells R, Telander A, Marcy P, Schwacke L (2017) Using salinity to identify common bottlenose dolphin habitat in Barataria Bay, Louisiana, USA. Endanger Species Res 33: 833–192.

Mintzer VJ, Fazioli KL (2021) Salinity and water temperature as predictors of bottlenose dolphin (Tursiops truncatus) encounter rates in upper Galveston Bay, Texas. Front Mar Sci 8

Principe N, McFee W, Levine N, Balmer B, Ballenger J (2023). Using Unoccupied Aerial Systems (UAS) to Determine the Distribution Patterns of Tamanend’s Bottlenose Dolphins (Tursiops erebennus) across Varying Salinities in Charleston, South Carolina. Drones 7(12): 10.3390/drones7120689.

Takeshita R, Balmer BC, Messina F, Zolman ES, Thomas L, Wells RS, Smith CR, Rowles TK, Schwacke LH (2021). High site-fidelity in common bottlenose dolphins despite low salinity exposure and associated indicators of compromised health. PLoS ONE, 16(9), e0258031.

Torres LG (2013) Evidence for an unrecognised blue whale foraging ground in New Zealand. New Zeal J Mar Freshw Res 47:235–248.

Hearing Gray: Diving into the Sonic World of the Gray Whale

By Natalie Nickells, visiting PhD Student, British Antarctic Survey

For the last three months, I’ve been lucky enough to be welcomed into the GEMM lab as a visiting PhD student to work on the acoustic data from hydrophones in CATS tags deployed on gray whales. This work has been a huge change for me! I’ve gone from studying Antarctic baleen whale foraging, the topic of my PhD, from a distance at my desk in Cambridge England, to studying PCFG gray whales in Newport- and finally being in the same country, state, and even county to the whales I am studying! Unlike my Antarctic research, where whale blows in the distance become tiny points in a sea of data, listening to the CATS tag data has allowed me to really connect with these animals on an emotional level, as I’ve spent days, weeks and months listening to the world as they hear it.

Humans are fundamentally visual creatures- we take in information through sight first, with hearing probably our second, or for some even third, sense in line. However, for marine mammals, the same cannot be said: their world is auditory first. This fact is an important realisation to get our heads around, highlighted beautifully by the phrase “the ears are the window to the soul of the whale” (Sonic Sea (2017)) or Tim Donaghy’s emotive statement that “a deaf whale is a dead whale”. High levels of ocean noise therefore have a huge impact on baleen whales. Imagine trying to do your groceries or find a friend while blindfolded or in a thick fog– you might struggle to access food or communicate with others, and your stress would certainly be high. To succeed, you would likely need to change your behaviour.

Behavioural changes in response to ocean noise are observed in baleen whales: for example, humpback whales change their foraging behaviour when ship noise increases (Blair et al., 2016), and gray whales have been shown to call more frequently and possibly more loudly in conditions of high ocean noise (Dahlheim & Castellote, 2016). However, even in the absence of notable behaviour change due to ocean noise, North Atlantic right whales may still be experiencing a stress response. When shipping traffic in the Bay of Fundy significantly decreased in the aftermath of 9/11, North Atlantic right whales in the area had decreased chronic stress levels (Rolland et al., 2012).

Previous work by the GEMM lab observed this stress response to ocean noise in gray whales. They found a correlation between high levels of glucocorticoid (a stress indicator) in male gray whale faeces with high vessel noise and vessel counts in the area. Vessel noise was measured using two static hydrophones off the Oregon coast, and it was assumed all animals in the area experienced the same noise (Lemos et al., 2022; Pirotta et al., 2023). However, a static hydrophone is an imperfect measure of the sound levels a mobile animal experiences, particularly as we might expect animals to change behaviour when disturbed (Sullivan & Torres, 2018). This previous work became the starting point for the question I have addressed during my time in the GEMM Lab: can we measure and characterise the sound levels an individual whale was exposed to? Enter CATS tags. These are suction-cup tags fitted with a host of sensors, which have been used by the GEMM lab since 2021 (see Image 1). So far, they have mostly been used for their accelerometry data (Colson et al. (in press), see also Kate’s blog post). However, the GEMM lab had the foresight to put hydrophones on these tags, and as a result I was welcomed into the lab by a bumper-crop of hydrophone data just waiting to be analysed!

*Image 1: A gray whale (“Slush”) being tagged with a CATS tag and Natalie (right) with the same tag.*

This tag data is particularly valuable, not only for its ability to follow the acoustic world of an individual whale, but also due to the whole suite of data that comes with the acoustics: essentially, the acoustic data comes with behavioural data. Or at least, it comes with data from which we can infer behaviour (Colson et al, in press)! Incorporating behaviour into passive acoustics work hugely strengthens its ecological usefulness (Oestreich et al., 2024). We can hear what an individual whale is hearing, and we can also infer what they were doing before, during, and after they heard or made that sound. Having behavioural data also means that we can ground-truth the sounds we hear. When hearing an interesting sound, I can go back to the video data and accelerometer data to check what the whale sees, what its body-position is doing (e.g., is it headstand foraging?) and the speed and direction of its travel. Context is key!

The importance of context was highlighted in my very first week here in the GEMM lab. I became very interested in a sound I could hear frequently when the whale would surface- a distorted bark-like noise, but the whale was surely too far offshore for any barking dog to be heard? And almost every time the whale surfaced? After a few days pondering, I shared my mystery with Leigh, who laughingly revealed that one of the whale-watching boats in this area has a ‘whale-alerting’ dog on board! Sometimes if it sounds like a dog… it’s a dog! Besides my slightly anticlimactic discovery of dogs barking, committing time to listening to the tags and hearing what the whales hear, has been a magical experience. My favourite hydrophone sound, that still gets me excited when I hear it, is the gray whale ‘bongo call’- or as it’s more formally known in the literature, M1 vocalisation (Guazzo et al., 2019). I’ll let you decide which name is more appropriate! I first heard this call when investigating a time on “Scarlett’s” tag when we knew her 14 year-old daughter “Pacman” had been close: about 15 minutes before “Pacman” appears on the video, Scarlett makes this call (you can play the clip below to listen). In “Lunita’s” tag, we even hear this call three times in a row!

Image 2: A ‘bongo call’ made by “Scarlett” when her daughter “Pacman” was nearby.

Relatively little research has been done on gray whale calls compared to other more studied species like humpbacks. Most of this research has taken place on gray whale migratory routes (Guazzo et al., 2019, 2017; Burnham et al. 2018) or in captivity (Fish et. al, 1974 ) so these tag recordings could be a valuable addition to a small sample from the foraging grounds (Clayton et al., 2023; Haver et al., 2023)- as well as being very personally exciting to hear!

We’ve also been able to use the tag hydrophone data to look at close calls with ships. As I was going through the data on “Scarlett’s” tag, I noticed a spike in vessel noise. Looking at the video from the same timestamp, I could see a small vessel passing directly over her as she surfaced. At the time this vessel passed over her, the tag was only 0.8 m under the surface of the water!

Image 3: A close encounter between a small vessel and “Scarlett”, shown both on the video from the CATS tag (top) and the spectrogram (bottom). The close call is outlined in a yellow box, when a greater intensity of noise occurred as illustrated by the brighter colour intensity compared to the white box (quieter vessel noise). Brighter colours denote a louder volume. The red boxes show surfacing noise- this can essentially be ignored when interpreting the echogram for our purposes.

Sometimes vessels may be more distant, but possibly equally harmful: we have seen vessel noise from larger and presumably more distant vessels dominate the soundscape in some of the tag data. Remembering that to a whale, the sonic world is as important as the visual world is to us, this elevated background noise from ships could have major consequences. So, the first step is to try to quantify the gray whales’ exposure to this vessel noise. I’ve been running some systematic sampling on the tag data to try to quantify background noise levels, and how this changes depending on the time of day: do individual whales experience the same daily spikes in ocean noise that were detected on the static hydrophones, at around 6am and noon due to vessel traffic (Haver et al., 2023)? If not, are they taking evasive action to avoid these spikes? These are just some of the questions that these CATS tags can help us answer, although ideally we need longer acoustic data recordings to capture day and night data, as well as potentially improving the hydrophones on the CATS tags themselves to minimise the impacts of tag interference and random noise.

When explaining to the public what it is to be a PhD student, I often refer to myself as a ‘scientist in training’, or to young children, a ‘baby scientist’. As I look toward my departure from the GEMM lab, I hope to have developed into at least a scientific toddler, having gained the ability to walk through reams of acoustic data with (relative) independence. More than that, I’m excited to take home a refreshed sense of curiosity about what drives marine mammals to behave as they do, an openness to collaboration and new approaches, and a large dose of ‘American emotion’! Let’s hope my British colleagues can handle it!

My heartfelt thanks to all those who welcomed me so warmly at the GEMM lab and Oregon State University, particularly my mentors Leigh Torres and Samara Haver.

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Bibliography

Sonic Sea (2017) Directed by Michelle Dougherty [Film] Distributed by the Natural Resources Defense Council.

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Pirotta, E., Fernandez Ajó, A., Bierlich, K.C., Bird, C.N., Buck, C.L., Haver, S.M., Haxel, J.H., Hildebrand, L., Hunt, K.E., Lemos, L.S., New, L. & Torres, L.G. (2023) Assessing variation in faecal glucocorticoid concentrations in gray whales exposed to anthropogenic stressors S. Cooke (ed.). Conservation Physiology. 11 (1), coad082. doi:10.1093/conphys/coad082.

Rolland, R.M., Parks, S.E., Hunt, K.E., Castellote, M., Corkeron, P.J., Nowacek, D.P., Wasser, S.K. & Kraus, S.D. (2012) Evidence that ship noise increases stress in right whales. Proceedings of the Royal Society B: Biological Sciences. 279 (1737), 2363–2368. doi:10.1098/rspb.2011.2429.

Sullivan, F.A. & Torres, L.G. (2018) Assessment of vessel disturbance to gray whales to inform sustainable ecotourism. The Journal of Wildlife Management. 82 (5), 896–905. doi:10.1002/jwmg.21462.

Toward an enhanced understanding of large whale ecology: a standardized protocol to quantify hormones in whale blubber

Dr. Alejandro A. Fernández Ajó, Postdoctoral Scholar, Marine Mammal Institute – OSU Department of Fisheries, Wildlife, & Conservation Sciences, Geospatial Ecology of Marine Megafauna (GEMM) Lab.

Whales are exposed to an increasing number of human-induced stressors—ranging from pollution and bycatch to the impacts of climate change on prey quality and distribution. Understanding how these factors affect whale health is critical for their conservation. The use of alternative approaches (i.e., alternative to blood samples) for gathering physiological information on large whales using a variety of non-lethal and non to minimally invasive sample matrices (i.e., blubber biopsies, blow, and fecal samples) provides a window into their endocrine state, allowing researchers to assess how these animals respond to both short-term and long-term stressors, and assess their reproductive and nutritional status. However, a lack of standardized protocols might hinder the comparability of results across studies, making it difficult to draw broad conclusions about the health and reproductive parameters of different whale populations.

Dr. Logan Pallin and I organized a lab exchange, funded by The Company of Biologists, to start a new collaboration aimed at bridging this gap by validating and standardizing methods for endocrine assessments in whale blubber. This is not just a technical exercise; it is a foundational step towards building equity and capacity in laboratories worldwide to conduct reliable and comparable endocrine assessments, enhancing the opportunities for multi-lab collaborations. Through this exchange, we aim to consolidate a standardized approach that will yield consistent results between laboratories, enabling better comparisons across different large whale populations. Hosted by the University of California Santa Cruz Biotelemetry and Behavioral Ecology Lab (UCSC-BTBEL Lab) under the mentorship of Dr. Logan Pallin, this experience is instrumental in advancing my research on large whale ecology and conservation.

Dr. Logan Pallin and Alejandro Fernandez Ajó conducting hormone extractions from gray whale blubber samples (left). Preparing a microtiter assay plate for hormone quantification in blubber (right).

During this exchange at the BBE Lab, I had the privilege of working closely with Dr. Logan Pallin, whose expertise in large whale endocrinology (particularly analyzing blubber biopsies) has been instrumental in shaping modern approaches to whale research. The lab’s cutting-edge equipment and Logan’s extensive experience with hormone extraction and quantification methods provided an ideal setting for refining our protocols. Our work focused on the extraction and quantification of progesterone from gray whale blubber samples provided by the Oregon State University Marine Mammal Stranding Network, part of MMI. These large blubber sections allow for repeated sub-sampling to ensure that the selected immunoassays reliably detect and measure the hormones of interest, while also assessing potential sources of variability when applying a standardized protocol. We initially focused our tests and validations on progesterone, as it is the precursor of all major steroid hormones and serves as an indicator of reproductive state in females.

A fieldwork day off Monterrey Bay, California with Dr. Logan Pallin, and PhD candidate Haley Robb. Blubber. Blubber biopsies can be obtained from free swimming whales with minimally invasive methods. From each sample we can derive multiple information about the reproductive status, genetics and overall health of the individuals.

The broader impact of our work
The successful validation and standardization of these protocols represents a significant advancement in whale conservation physiology. Once these methods are established, we plan to acquire funds to apply them to a larger collection of blubber samples. We hope to expand our work to include other species and regions, building a broader network of researchers dedicated to studying large whales in a rapidly changing world, and to assess hormone profiles in relation to factors like reproductive success, body condition, and exposure to stressors such as vessel traffic and environmental changes.

During our fieldwork in Monterey Bay, we had fascinating encounters with Minke whales (Balaenoptera acutorostrata, top left), a large group of Risso’s dolphins (Grampus griseus, bottom left), playful Humpbacks (Megaptera novaeangliae, top right), and a Blue whale (Balaenoptera musculus, no photo).

As I conclude this lab exchange, I am filled with excitement for the future. The knowledge and skills gained during this experience will undoubtedly shape the next phase of my research, allowing me to contribute more effectively to the conservation of these incredible animals. I look forward to applying these standardized methods to ongoing and future projects, and to continuing this fruitful collaboration with the BBE Lab. This journey has reinforced the importance of collaboration, standardization, and innovation in the field of conservation physiology. By working together, we can better understand the complex lives of large whales and take meaningful steps towards their protection in an increasingly challenging environment.

Acknowledgments: This exchange was made possible by the support of The Company of Biologists Traveling Fellowship Grant. I would like to thank Dr. Ari Friedlaender (BBE Lab PI) for facilitating this exchange, and Dr. Leigh Torres (GEMM Lab PI) and Dr. Lisa Balance (MMI director) for their support in helping me expand my collaboration network and skillsets. Special thanks to PhD student Haley Robb for her assistance in the laboratory and fieldwork, and a heartfelt thank you to Dr. Logan Pallin for generously sharing his knowledge and time.

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The Beginning of the End

By Rachel Kaplan, PhD candidate, Oregon State University College of Earth, Ocean, and Atmospheric Sciences and Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

I moved to Corvallis exactly four years ago, in the deep, dark midst of the Covid pandemic, and during the added chaos of the 2020 Labor Day Fires, some of the worst in Oregon’s history. I vividly remember attending our virtual lab meeting sitting on the floor surrounded by boxes, while my labmates told me their own stories (many, surprisingly!) of moving during natural disasters. At the time, beginning graduate school represented so many big changes in my life: I had quit my job, sold my furniture, and moved across the country, hoping to explore an area of research that had been calling to me for years, and to gain a new skillset and confidence.

*Highlight: A very pandemic cruise. My first day of marine mammal fieldwork in 2021, at sea with (now Dr.) Dawn Barlow.*

Now, I’m starting the fifth year of my PhD, thinking about all that has happened and all that is to come. Graduate school is full of milestones to mark time and progress: I’ve taken the courses required for my program, sat for a written exam to test my broad knowledge of oceanography, and written a dissertation proposal. Earlier this year, I spent two months buried in the literature on oceanography, krill, and whale ecology in preparation for my oral qualifying exam. I’ve stared at the water for dozens of hours watching for whales off the Oregon coast, and experienced polar night studying winter krill in Antarctica. I’ve conquered my fear of learning to code, and felt constant, profound gratitude for the amazing people I get to work with.

The last four years have been incredibly busy and active, but now more than ever, it feels like the time to really do. I can see the analytical steps ahead for my final two dissertation chapters more clearly than I’ve been able to see either of the other two chapters that have come before. One of my favorite parts of the process of research is discussing analytical decisions with my labmates and supervisors, and experiencing how their brains work. Much of our work hinges on modeling relationships between animals and their environment. A model, most fundamentally, is a reduced-scale representation of a system. As I’ve learned to use statistical models to understand relationships between krill and whales, I have simultaneously been building a mental model of the Northern California Current (NCC) ecosystem and the ecological relationships within it. Just as I have long admired in my supervisors and labmates, I can now feel my own mind becoming more playful as I think about this ocean environment, the whales and krill that make a living in the NCC, and the best way to approach studying them analytically.

*Highlight: Working on my dissertation proposal during a friend’s 2022 wedding celebration in Utah.*

Graduate school demands that you learn and work to constantly exceed your own bounds, and pushing to that extent for years is often stressful and even existentially threatening. However, this process is also beautiful. I have spent the last four years growing in the ways that I’ve long wanted to, and reveled in feeling my mind learn to play. I wouldn’t give up a moment of the time I’ve spent in the field, the relationships I’ve built with my labmates, or the confidence I’ve developed along the way.

As I look ahead to this next, final, year of graduate school, I hope to use what I’ve learned every day – and not just about how to conduct research, but about myself. I want to always remember that krill, whales, and the ocean ecosystem are incredible, and that it is a privilege to study them. I hope to work calmly and intentionally, and to continue appreciating this process of research and growth.

*Highlight: My first in-person oral presentation, at the 2024 ICES-PICES International Zooplankton Production Symposium in Hobart, Tasmania.*

The Theme of the Year is Learning New Things!

By Hali Peterson, rising freshman, Western Oregon University

Hello, my name is Hali Peterson and I am a rising freshman in college. Last summer (2023) I was given the opportunity to be a paid high school intern for the OSU Marine Mammal Institute’s very own GEMM Lab (Geospatial Ecology of Marine Megafauna Laboratory) based at the Hatfield Marine Science Center in Newport, Oregon. My time working in the GEMM Lab has been supported by the Oregon Coast STEM Hub. I started my internship in June 2023 and I was one of the two GEMM Lab summer interns. However, my internship did not end when summer did, as I continued to work throughout the school year and even into this summer.

**Figure 1:** Leaving work late and accompanied with a beautiful view of the Newport bridge over Yaquina Bay.

June 29, 2023 to September 20, 2024 (1 year, 2 months, and 21 days if anyone is curious) – what did I do and what did I learn during this time…

Initially, I was tasked with helping the GRANITE project (Gray whale Response to Ambient Noise Informed by Technology and Ecology) by processing drone footage of Pacific Coast Feeding Group (PCFG) gray whales and identifying their zooplankton prey. I started off my internship under the mentorship of KC Bierlich and Lisa Hildebrand and I dove into looking at zooplankton underneath a microscope and watching whales in drone footage, both gathered by the GEMM Lab field team.

KC taught me how to process drone footage, measure whales and calibration boards, test an artificial intelligence model, as well as write a protocol of the drone processing methods that I had worked on. These tasks were a big responsibility as the measurements need to be accurate and precise so that they can be used to effectively assess the body condition of gray whales, which provides crucial insights into population health.

**Figure 2:** My favorite drone video of moms and calves meeting up for a playdate!

Under Lisa’s mentorship I learned how to identify and process zooplankton prey samples, process underwater GoPro videos, as well as identify and analyze kelp patches from satellite images. Within these tasks, I honed my expertise in zooplankton and habitat analysis and the results of my work will contribute to a deeper understanding of gray whale feeding habits along the Oregon coast.

**Figure 3:** My favorite zooplankton to see, a juvenile crab larva.

As my main mentors, KC and Lisa taught me so much about the world of science and research. All of these detail-oriented and multi-layered tasks helped me improve some of the skills I already had before I started the internship as well as gift me with skills I didn’t previously possess. For example, I learned how to collaborate and work with a team, pay attention to detail, double and even triple check everything for quality work, problem solve, and learn to ask questions.

However, as my time in the GEMM Lab extended beyond the summer of 2023, so did my tasks. Later on I received another mentor, Clara Bird. Under Clara I learned how to identify whales from drone footage recorded in Baja, Mexico (an area that is specifically known as the breeding lagoons where the gray whales go in the winter), as well as use the Newport, Oregon drone footage and CATS (Customized Animal Tracking Solution) tag data to measure inhalation duration and bubble blast occurrences. These experiences furthered my knowledge and yet again I learned something new, a common theme throughout my time in the GEMM Lab.

Just a few months ago, the GEMM Lab hired Laura Flores Hernandez as a new high school student summer intern, and under the guidance of both Lisa Hildebrand and Leigh Torres, I was given the opportunity to develop my own mentoring skills. I used the skills I had obtained over the past year to teach someone else how to do the tasks I once was new to. I taught Laura how to identify zooplankton, process drone footage, and measure calibration boards. Stepping into that mentor role helped me reflect on my own learning and experiences. I had to go back and figure out how I did things, where I struggled, and how I overcame those struggles. Not an easy task but one I was glad to be presented with.

**Figure 4:** Matthew Vaughan (chief scientist on the trip) and me (right) looking at a box core sample.

During my time here I was also invited to join a STEM (Science, Technology, Engineering, Mathematics) cruise led by Oregon Sea Grant with fellow high school students. On this science cruise I got to help look at box core samples (a tool used to collect large amounts of sediment off of the ocean floor). Equipped with my previous knowledge on zooplankton identification, I was able to help the chief scientist on the trip to explain to other high school students what we were seeing in the samples. This trip helped me grow my teamwork and identification skills, as well as experience what it is like to collect data while on a moving ship.

**Figure 5:** Sea Kayaking through the fjord with the Girls on Icy Fjords team of 2024.

Another amazing opportunity I was selected for was to join the 2024 Girls on Icy Fjords team. This program, in association with OSU, was designed to empower young women in STEM in the backcountry of Alaska. With a team of 3 amazing instructors and 8 girls (all from different parts of the United States of America) we camped in the backcountry for 8 days, learning about glaciers and fjords, surviving in the backcountry, sea kayaking, and working as a team. I would highly recommend any young woman interested in science, art, or just an amazing experience to check out Inspiring Girls Expeditions.

**Bonus Image:** This is Jeff the Moyebi Shrimp and I love him.

All in all this will be a job that I will not soon forget; interning in the GEMM Lab has been both a learning opportunity as well as a challenge. My internship wasn’t without its challenges, from a computer that seemed determined to shut down whenever I made progress, to endless hours spent staring at a green screen, waiting to count a fish that might eventually swim by. Though the job had its ups and downs, I am so glad I was given this opportunity and was kept on in the lab for as long as I was. In just a few weeks, I will start my Bachelors of Aquarium Science at Western Oregon University and I’m both excited and nervous. I know that without a doubt the skills I learned during this internship will come in handy as I continue my education and pursue a career in the future.

Thank you to all my mentors, anyone who answered one of the many questions I had, and to the friends I made along the way!

Expand your rolodex and meet some more IndividuWhales!

In case you aren’t already aware, I want to remind you of a website called IndividuWhale we created about Pacific Coast Feeding Group (PCFG) gray whales we study as part of our GRANITE project. IndividuWhale features stories of some of the Oregon coast’s most iconic gray whales, as well as information about how we study them, stressors they experience in our waters, and even a game to test your gray whale identification skills. We also provide details about where to best spot gray whales along our coast and the different behaviors you might see gray whales displaying at different times of the year. Since launching the website in late 2021, we have made small tweaks and updates along the way, but now, after about 2.5 years, the time has come for a major content update as we are introducing you to three new individuals and their stories! Head over to IndividuWhale.com to check out the updates or continue reading for a preview of the content…

Lunita

Even though “Lunita” is only two years old (as of 2024), they (sex currently unknown!) have quickly become a star of our dataset and hearts. We documented Lunita as a calf with their mother “Luna” (hence the name Lunita, which means little Luna/moon) in 2022. We observed the mom-calf pair in our study area for almost two weeks during which it seemed like Lunita was a very attentive calf, always staying close to Luna and appearing to benthic feed alongside their mom. As is often the case when we document mom–calf pairs, we wonder whether we will see the calf again and how it will fair in an environment increasingly impacted by human activities. Much to our delight, we were reunited with Lunita later in the same summer when we saw them feeding independently, indicating that they had successfully weaned. We were even more delighted when we were reunited with Lunita again many times during the summer of 2023 as Lunita spent almost the entire feeding season along the central Oregon coast. This is yet another example, much like “Cheetah” and “Pacman,” of successful internal recruitment of calves born to PCFG females into the PCFG sub-population.

Lunita’s high site fidelity to our study area in 2023 meant that she was an excellent candidate for the suction-cup tagging we have been conducting in the last few years. During suction-cup tagging, we attach a device (or tag) via suction cups to a whale’s back. The tag contains a number of different sensors, including an accelerometer (to measure speed), a gyroscope (to measure direction), and a magnetometer (to measure magnetic field), as well as a high-definition video camera and hydrophone (or underwater microphone). These tags typically stay on for a maximum of 24 hours before they pop off the whale leaving no harm to the whale. Upon retrieval, we can recreate the whale’s dive path and see the environment and conditions that the whale experienced over several hours. We sometimes refer to tagging as giving the gray whales some temporary jewelry because the tags are a very flashy, bright orange color. From the video from Lunita’s tag shows how they soared through kelp forests feeding on mysids for many, many hours. Check out their profile here: https://www.individuwhale.com/whales/lunita/

Burned

There are many ways to assess the health of a whale. In our lab, we calculate body condition from drone images to determine how fat or skinny a whale is, examine different hormones from their poop, and assess growth rates via length measurements from drone images. Another health assessment metric that we explore in the lab is the skin and scarring on the individuals that we see in our central Oregon study area. By conducting a skin and scarring analysis, we can identify scarring patterns and lesions that may indicate interactions with human activities and track the progression of skin diseases that will help us understand the prevalence and impacts of pathogens on whales. One skin condition that we are particularly interested in tracking appears as a thick white or gray layer that can mask a gray whale’s natural pigmentation. An example of a whale that has experienced this skin condition is “Burned.”

Burned is a female who is at least 9 years old (as of 2024), as she was first documented in the PCFG range in 2015. We saw Burned for the first time in 2016. At the time, we noticed small, isolated, gray patches of the skin condition on both sides of Burned’s body. Throughout the years as we have continued to resight Burned, we noticed the skin condition spreading progressively across her body. We saw the skin condition at its maximum extent in 2022 when, at first glance, Burned was hardly recognizable. Luckily, we can identify gray whales using more than just their pigmentation patterns (learn more on our whale identification page). Interestingly, when we saw Burned in June 2024, it appeared that the skin condition completely disappeared! Burned is just one example of whales with this skin condition, leaving us with many questions about its origin and impact on the whales: What causes the skin condition (viral, fungal, bacterial?); How it is transmitted (via air or contact?); Is it harmful to the whale (weakened immune system?). Our research is aimed at addressing these questions to make this skin condition a little less mysterious. Check out her profile here: https://www.individuwhale.com/whales/burned/

Heart

“Heart,” who is also known as “Ginger,” is a very well known and popular whale in the Depoe Bay region. Heart is a female who is particularly famous for being a “tall fluker,” meaning that when she dives, she arches her tail fluke high in the air before it glides elegantly into the water. Heart was first documented as a calf in 2010, which means that she is 14 years old (as of 2024). At 14 years of age, we would expect for Heart to have had at least one, if not more, calves by now, as it is believed that gray whales reach sexual maturity at age 8 or 9. However, Heart has never been documented with a calf. Why?

While we cannot know for sure, we have a theory that it might be linked to her body length. Recent work in our lab has explored how growth of PCFG whales has changed over time. Using measurements of whales from our drone data, we investigated how the asymptotic length (i.e. the final length reached once an individual stops growing) for the PCFG whales has changed since the 1980s. Shockingly, we found that starting in the year 2000 the asymptotic length of PCFG whales has declined at an average rate of 0.05–0.12 meters per year. Over time, this means that a whale born in 2020 is expected to reach an adult body length that is 13% shorter than a gray whale born prior to 2000. In Heart’s case specifically, when we last measured her length at 13 years old, she was 10.65 meters long. If she had been born prior to 2000, then she would be 12.04 meters long by now at the age of 13. That’s a whole 1.5 meters (or almost 5 feet) shorter!

You might be wondering how Heart’s length links back to her ability to have a calf. It takes a lot of energy to be pregnant and support the fetus, so by being smaller, Heart may not be able to store and allocate enough energy towards reproduction. Many of the whales we commonly see are shorter than expected based on their age (including “Zorro”), so we are monitoring the number and frequency of calves in the PCFG to see how this decline in length may impact the population. Check our her profile here: https://www.individuwhale.com/whales/heart/

Be sure to head over to IndividuWhale.com to explore all of the whale profiles and lots of other information that we have provided there about PCFG gray whales and how we study them here in Oregon waters!

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Reflecting on a solitary journey surrounded by an incredible team

Clara Bird, PhD Candidate, OSU Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

Graduate school is an odd phase of life, at least in my experience. You spend years hyperfocused on a project, learning countless new skills – and the journey is completely unique to you. Unlike high school or undergrad, you are on your own timeline. While you may have peers on similar timelines, at the end of day your major deadlines and milestone dates are your own. This has struck me throughout my time in grad school, and I’ve been thinking about it a lot lately as I approach my biggest, and final milestone – defending my PhD!

I defend in just about two months, and to be honest, it’s very odd approaching a milestone like this alone. In high school and college, you count down to the end together. The feelings of anticipation, stress, excitement, and anticipatory grief that can accompany the lead-up to graduation are typically shared. This time, as I’m in an intense final push to the end while processing these emotions, most of the people around me are on their own unique timeline. At times grad school can feel quite lonely, but this journey would have been impossible without an incredible community of people.

A central contradiction of being a grad student is that your research is your own, but you need a variety of communities to successfully complete it. Your community of formal advisors, including your advisor and committee members, guide you along the way and provide feedback. Professors help you fill specific knowledge and skill gaps, while lab mates provide invaluable peer mentorship. Finally, fellow grad students share the experience and can celebrate and commiserate with you. I’ve also had the incredible fortune of having the community of the GRANITE team, and I’ve recently been reflecting on how special the experience has been.

To briefly recap, GRANITE stands for Gray whale Response to Ambient Noise Informed by Technology and Ecology (read this blog to learn more). This project is one of the GEMM lab’s long-running gray whale projects focused on studying gray whale behavior, physiology, and health to understand how whales respond to ocean noise. Given the many questions under this project, it takes a team of researchers to accomplish our goals. I have learned so much from being on the team. While we spend most of the year working on our own components, we have annual meetings that are always a highlight of the year. Our team is made up of ecologists, physiologists, and statisticians with backgrounds across a range of taxa and methodologies. These meetings are an incredible time to watch, and participate in, scientific collaboration in action. I have learned so much from watching experts critically think about questions and draw inspiration from their knowledge bases. It’s been a multi-year masterclass and a critically important piece of my PhD.

The GRANITE team during our first in person meeting

These annual meetings have also served as markers of the passage of time. It’s been fascinating to observe how our discussions, questions, and ideas have evolved as the project progressed. In the early years, our presentations shared proposed research and our conversations focused on working out how on earth we were going to tackle the big questions we were posing. In parallel, it was so helpful to work out how I was going to accomplish my proposed PhD questions as part of this larger group effort. During the middle years, it was fun to hear progress updates and to learn from watching others go through their process too. In grad school, it’s easy to feel like your setbacks and stumbles are failures that reflect your own incompetence, but working alongside and learning from these scientists has helped remind me that setbacks and stumbles are just part of the process. Now, in the final phase, as results abound, it feels extra exciting to celebrate with this team that has watched the work, and me grow, from the beginning.

The GRANITE team taking a beach walk after our second in person meeting.

We just wrapped up our last team meeting of the GRANITE project, and this year provided a learning experience in a phase of science that isn’t often emphasized in grad school. For graduate students, our work tends to end when we graduate. While we certainly think about follow-up questions to our studies, we rarely get the opportunity to follow through. In our final exams, we are often asked to think of next steps outside the constraints of funding or practicality, as a critical thinking exercise. But it’s a different skillset to dream up follow-up questions, and to then assess which of those questions are feasible and could come together to form a proposal. This last meeting felt like a cool full-story moment. From our earliest meetings determining how to answer our new questions, to now deciding what the next new questions are, I have learned countless lessons from watching this team operate.

The GRANITE team after our third in person meeting.

There are a few overarching lessons I’ll take with me. First and foremost, the value of patience and kindness. As a young scientist stumbling up the learning curve of many skills all at once, I am so grateful for the patience and kindness I’ve been shown. Second, to keep an open mind and to draw inspiration from anything and everything. Studying whales is hard, and we often need to take ideas from studies on other animals. Which brings me to my third takeaway, to collaborate with scientists from a wide range of backgrounds who can combine their knowledges bases with yours, to generate better research questions and approaches to answering them.

I am so grateful to have worked with this team during my final sprint to the finish. Despite the pressure of the end nearing, I’m enjoying moments to reflect and be grateful. I am grateful for my teachers and peers and friends. And I can’t wait to share this project with everyone.

P.S. Interested in tuning into my defense seminar? Keep an eye on the GEMM lab Instagram (@gemm_lab) for the details and zoom link.

New publication reveals gray whale habitat use patterns over three decades in the Northern California Current

By Dr. Dawn Barlow, Postdoctoral Scholar, OSU Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

The EMERALD project (Examining Marine mammal Ecology through Regional Assessment of Long-term Data) has reached a milestone with a recent publication detailing our findings on long-term gray whale distribution, abundance, and habitat use patterns (Barlow et al. 2024). The study is made possible by an incredible dataset. Every May-July since 1992, a team of observers surveyed the coastline between the Columbia River at the border between Oregon and Washington and San Francisco Bay, California for marbled murrelets, a seabird species of conservation concern. They drive a small vessel along pre-determined tracklines, and record observations of seabirds and marine mammals—not just marbled murrelets—and fortunately for us, that means there is a record of annual gray whale distribution and abundance patterns that spans over three decades.

The Crescent Coastal Research team collecting survey data. We are incredibly grateful to Craig Strong and the many folks who collected these valuable observations over the years!

We analyzed these valuable data using density surface modeling to better understand what drives gray whale distribution and abundance, what their habitat preferences are, and whether and how these occurrence patterns have changed over time. I am excited to share a few of our findings here!

Long-term, stable hotspots

The survey data revealed three main areas with consistently high gray whale density: the central Oregon Coast off Newport, Cape Blanco off Oregon’s south coast, and the mouth of the Klamath River in northern California. Despite fluctuations in how many whales were observed over the years, these areas have remained predicable hotspots for gray whales during their summer feeding season.

(A) Mean gray whale encounter rate (whales/kilometers surveyed) summarized by year, across all latitudes. (B) Mean gray whale encounter rate summarized by 1° latitude bin, across all years. White indicates times and locations with no survey effort. (C) Mean gray whale encounter rate summarized by year and 1° latitude bin. (D) Map of the study area, with region boundaries shown by the dashed lines, and major placenames denoted. Figure and caption reproduced from Barlow et al. 2024.

Key regional differences

Major features like prominent capes divide the California Current into different regions with distinct oceanographic characteristics. We found that gray whales showed different habitat preferences in the different regions. In the northern part of our study area between the Columbia River and Cape Blanco, we found that rocky bottom substrate was strongly related to areas of higher gray whale abundance, despite being far less available than soft, sandy bottom habitat. In the region between Cape Blanco and Cape Mendocino, gray whales were more abundant in areas south of prominent capes and in closer proximity to river estuaries.

Coastal upwelling and relaxation are key

Coastal upwelling—the process by which winds in the spring and summer push surface water offshore that is then replaced by cold, nutrient-rich water that is brought into the sunlight and drives an abundance of marine life—is a critically important influence in the oceanography, ecology, and biodiversity of our study region. But relaxation of those upwelling winds is also important for coastal species, as relaxation events allow the upwelled nutrients to be retained in the nearshore waters and enhance and aggregate local productivity and prey. We found that gray whale abundance was highest when there was a combination of both upwelling and relaxation events—a critical balance of “enough but not too much”—that seems to be optimal for gray whale feeding opportunities in nearshore waters.

You are what, where, and how you eat

Gray whales are incredibly flexible predators and have a wide range of prey items they are known to feed on. We found that throughout our study range, gray whales have different habitat preferences. As they spend their summers here to feed, these habitat preferences are linked to their foraging preferences. Off the central Oregon Coast, gray whales are known to feed on zooplankton that aggregate around rocky reefs and kelp forests (Hildebrand et al. 2022, 2024).

A gray whale surfaces in a patch of kelp, foraging around a rocky reef. UAS image credit: GEMM Lab.

Further south, in the region between Cape Blanco and Cape Mendocino that encompassed the long-term hotspot of gray whale sightings off the Klamath River, our models revealed different habitat preferences. In the soft-bottom habitat off the Klamath River, gray whales are known to do more benthic feeding, whereby they scoop up the seafloor and filter out the invertebrates in the sediment such as amphipods and cumaceans (Mallonée 1991, Jenkinson 2001).

A gray whale surfaces with a mouth full of muddy sediment, filtering out the invertebrate prey. UAS image credit: GEMM Lab.

These differences in regional habitat preferences and preferred prey likely relate to larger-scale phenomena as well. Indeed, when we looked at how gray whale abundance in different regions related to widespread warm or cool phases in the North Pacific Ocean, the responses differed by region. This aspect of the study indicates that what gray whales eat and where they forage influences how they respond to shifting environmental conditions and prey availability.

Conservation of an iconic nearshore predator

The unique mosaic of habitat characteristics throughout the Northern California Current summer feeding range of gray whales provides them the opportunity to gain the energetic stores they need to survive, reproduce, and migrate. Thus, the reliability of these resources has led them to return to these stable foraging hotspots year after year. Under climate change, one potential impact on upwelling systems is shifts in the intensity and location of upwelling (Bograd et al. 2023); in the Northern California Current, this could mean reduced relaxation events that we found are crucial for gray whales feeding in this habitat. Furthermore, these whales overlap with human activities such as vessel disturbance, entanglement and vessel strike risk, and ocean noise throughout the foraging season, and have to bear the consequences of these anthropogenic stressors (Sullivan & Torres 2018, Lemos et al. 2022, Pirotta et al. 2023) as they also navigate changing environmental conditions. Our study highlights the value of long-term monitoring to better understand present ecological patterns in the context of the past, which can be used to inform conservation management decisions for the future.

For more details, we invite you to read the full, open access publication here: https://www.nature.com/articles/s41598-024-59552-z

References

Barlow DR, Strong CS, Torres LG (2024) Three decades of nearshore surveys reveal long-term patterns in gray whale habitat use, distribution, and abundance in the Northern California Current. Sci Rep 14:9352.

Bograd SJ, Jacox MG, Hazen EL, Lovecchio E, Montes I, Pozo Buil M, Shannon LJ, Sydeman WJ, Rykaczewski RR (2023) Climate Change Impacts on Eastern Boundary Upwelling Systems. Ann Rev Mar Sci 15:1–26.

Hildebrand L, Derville S, Hildebrand I, Torres LG (2024) Exploring indirect effects of a classic trophic cascade between urchins and kelp on zooplankton and whales. Sci Rep 14.

Hildebrand L, Sullivan FA, Orben RA, Derville S, Torres LG (2022) Trade-offs in prey quantity and quality in gray whale foraging. Mar Ecol Prog Ser 695:189–201.

Jenkinson RS (2001) Gray whale (Eschrichtius robustus) prey availability and feeding ecology in Northern California, 1999-2000. Humboldt State University

Lemos L, Haxel J, Olsen A, Burnett JD, Smith A, Chandler TE, Nieukirk SL, Larson SE, Hunt KE, Torres LG (2022) Effects of vessel traffic and ocean noise on gray whale stress hormones. Sci Rep 12:1–13.

Mallonée JS (1991) Behaviour of gray whales (Eschrichtius robustus) summering off the northern California coast, from Patrick’s Point to Crescent City. Can J Zool 69:681–690.

Pirotta E, Fernandez Ajó A, Bierlich KC, Bird CN, Buck CL, Haver SM, Haxel JH, Hildebrand L, Hunt KE, Lemos LS, New L, Torres LG (2023) Assessing variation in faecal glucocorticoid concentrations in gray whales exposed to anthropogenic stressors. Conserv Physiol 11:coad082.

Sullivan FA, Torres LG (2018) Assessment of vessel disturbance to gray whales to inform sustainable ecotourism. J Wildl Manage 82:896–905.

Measure faster! New tools for automatically obtaining body length and body condition of whales from drone videos

Dr. KC Bierlich, Postdoctoral Scholar, OSU Department of Fisheries, Wildlife, & Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

Monitoring the body length and body condition of animals can help provide important information on the health status of individuals and their populations, and can even serve as early warning signs if a population is adapting to habitat changes or is at risk of collapse (Cerini et al., 2023). As discussed in previous blogs, drone-based photogrammetry provides a method for non-invasively collecting important size measurements of whales, such as for detecting differences in body condition and length between populations, and even diagnosing pregnancy. Thus, using drones to collect measurement data on the growth, body condition, and pregnancy rates of whales can help expedite population health assessments to elicit conservation and management actions.

However, it takes a long time to manually measure whales filmed in drone imagery. For every video collected, an analyst must carefully watch each video and manually select frames with whales in good positions for measuring (flat and straight at the surface). Once frames are selected, each image must then be ranked and filtered for quality before finally measuring using a photogrammetry software, such as MorphoMetriX. This entire manual processing pipeline ultimately delays results, which hinders the ability to rapidly assess population health. If only there was a way to automate this process of obtaining measurements…

Well now there is! Recently, a collaboration between researchers from the GEMM Lab, CODEX, and OSU’s Department of Engineering and Computer Science published a manuscript introducing automated methods for obtaining body length and body condition measurements (Bierlich et al., 2024). The manuscript describes two user-friendly models: 1) “DeteX”, which automatically detects whales in drone videos to output frames for measuring and 2) “XtraX”, which automatically extracts body length and body condition measurements from input frames (Figure 1). We found that using DeteX and XtraX produces measurements just as good as manual measurement (Coefficient of Variation < 5%), while substantially reducing the processing time by almost 90%. This increased efficiency not only saves hours (weeks!) of manual processing time, but enables more rapid assessments of populations’ health.

Future steps for DeteX and XtraX are to adapt the models so that measurements can be extracted from multiple whales in a single frame, which could be particularly useful for analyzing images containing mothers with their calf. We also look forward to adapting DeteX and XtraX to accommodate more species. While DeteX and XtraX was trained using only gray whale imagery, we were pleased to see that these models performed well when trialing on imagery of a blue whale (Figure 2). These results are encouraging because it shows that the models can be adapted to accommodate other species with different body shapes, such as belugas or beaked whales, with the inclusion of more training data.

We are excited to share these methods with the drone community and the rest of this blog walks through the features and steps for running DeteX and XtraX to make them even easier to use.

Figure 1. Overview of DeteX and XtraX for automatically obtaining body length and body condition measurements from drone-based videos.

Figure 2. Example comparing manual (MorphoMetriX) vs. automated (XtraX) measurements of a blue whale.

DeteX and XtraX walkthrough

Both DeteX and XtraX are web-based applications designed to be intuitive and user-friendly. Instructions to install and run DeteX and XtraX are available on the CODEX website. Once DeteX is launched, the default web-browser automatically opens the application where the user is asked to select 1) the folder containing the drone-based videos to analyze and 2) the folder to save output frames (Figure 3). Then, the user can select ‘start’ to begin. The default for DeteX is set to analyze the entire video from start to finish at one frame per second; if recording a video at 30 frames per second, the last (or 30^th) frame is processed for each second in the video. There is also a “finetune” version of DeteX that offers users much more control, where they can change these default settings (Figure 4). For example, users can change the defaults to increase the number of frames processed per second (i.e., 10 instead of 1), to target a specific region in the video rather than the entire video, and adjust the “detection model threshold” to change the threshold of confidence the model has for detecting a whale. These specific features for enhanced control may be particularly helpful when there is a specific surfacing sequence that a user wants to have more flexibility in selecting specific frames for measuring.

Figure 3. A screenshot of the DeteX web-based application interface.

Figure 4. The DeteX “finetune” version provides more control for users to change the default settings to target a specific region in the video (here between 3 min 00 sec and 3 min 05 sec), change the number of frames per second to process (now 10 per second), and the detection threshold, or level of confidence for identifying a whale in the video (now a higher threshold at 0.9 instead of the default at 0.8).

Once output frames are generated by DeteX, the user can select which frames to input into XtraX to measure. Once XtraX is launched, the default web-browser automatically opens the application where the user is asked to select 1) the folder containing the frames to measure and 2) the folder to save the output measurements. If the input frames were generated using DeteX, the barometric altitude is automatically extracted from the file name (note, that altitudes collected from a LiDAR altimeter can be joined in the XtraX output .csv file to then calculate measurements using this altitude). The image width (pixels) is automatically extracted from the input frame metadata. Users can then input specific camera parameters, such as sensor width (mm) and the focal length of the camera (mm), the launch height of the drone (i.e., if launching from hand when on a boat), and the region along the body to measure body condition (Figure 5). This region along the body is called the Head-Tail range and is identified as the area where most lipid storage takes place to estimate body condition. To run, the user selects “start”. XtraX then will output a .png file of each frame showing the keypoints (used for the body length measurement) and the shaded region (used for the body condition estimate) along the body to help visual results so users can filter for quality (Figure 6). XtraX also outputs a single .csv containing all the measurements (in meters and pixels) with their associated metadata.

Figure 5. User interface for XtraX. The user specifies a folder containing the images to measure and a folder to save the outputs measurements, and then can enter in camera specifications, the launch height of the drone (to be added to the barometer altitude) and the range of body widths to include in the body condition measurement (in the case, 0.2 and 0.7 correspond to body region between widths 20% and 70% of the total length, respectively).

Figure 6. Example output from XtraX showing (red) keypoints along the body to measure body length and the (green) shaded region used for body condition.

We hope this walkthrough is helpful for researchers interested in using and adapting these tools for their projects. There is also a video tutorial available online. Happy (faster) measuring!

References

Bierlich, K. C., Karki, S., Bird, C. N., Fern, A., & Torres, L. G. (2024). Automated body length and body condition measurements of whales from drone videos for rapid assessment of population health. Marine Mammal Science, e13137. https://doi.org/10.1111/mms.13137

Cerini, F., Childs, D. Z., & Clements, C. F. (2023). A predictive timeline of wildlife population collapse. Nature Ecology & Evolution, 7(3), 320–331. https://doi.org/10.1038/s41559-023-01985-2

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