Stories from a whale’s life: how whale photo-identification is an essential part of the whale physiology toolkit

By Alejandro Fernandez Ajo, PhD student at the Department of Biology, Northern Arizona University, Visiting scientist in the GEMM Lab working on the gray whale physiology and ecology project  

Two years ago, in August 2018, I came to Newport and visited the Hatfield Marine Science Center for the first time with an NSF/RCN-founded laboratory exchange with the GEMM Lab and met Dr. Leigh Torres. My goals during this exchange where to learn about non-invasive fieldwork techniques for studying free-range whales while interacting, exchanging ideas, and networking with the GEMM Lab members; also, to discuss some projects and thoughts for future collaborations with Dr. Torres. During those two weeks in Newport, I had the opportunity to help with field work on the project “Evaluation of gray whale ecology and physiology in response to variable ambient ocean noise conditions”, which aims to evaluate the hormonal variability and health of the gray whales that forage along the Oregon coast in the context of multiple stressors. I would return during the summers of 2019 and 2020 as a visiting scientist and research assistant to work on this project. This year the experience has been a bit different in terms of interactions with the HMSC community due to COVID-19; however, we were able to successfully start the field season in time and now we are wrapping up our second month of surveys with many new and interesting data gathered, and many new, unforgettable memories to be treasured. Working with these animals is incredibly fascinating because there are so many things we don´t know about them, and the questions can become both overwhelming and exciting.

An essential part of this project, and arguably any research project done with cetaceans, is the identification of individuals. Hence, considerable effort is expended each year attempting to photograph every gray whale possible within our study region and to identify each whale we encounter. The GEMM Lab maintains a catalog of the gray whales that visit the Oregon coast, a sub-population known as the Pacific Coast Feeding Group (PCFG). This catalog currently consists of 173 individuals. which we frequently compare with a larger catalog of gray whales that includes 2060 individuals observed since 1977 (Cascadia Research Collective). These methods allow us to know who is who among the whales we encounter each day at sea.

The different species of cetaceans can be individually identified by markings on their bodies, very much like fingerprints in humans. Some features on these animals are unique and conserved through life. For example, Southern and Northern right whales are identified by the callosity patters in their heads (Picture 1), while humpback whales are mostly identified individually by the shape and the patterns of black and white pigmentation on the underside of their fluke (Picture 2). Gray whales have very mottled skin coloration, so we use a combination of markings and features to identify individuals: pigmentation patterns, scars, shape and pigmentation of their fluke, and sometimes the shape of their knuckles, which are a series of “humps” that gray whales have instead of a dorsal fin on their back. It might sound very difficult to do, and it can be a tedious task, however as you train your eye it becomes easier, and features that at first seemed undistinguishable become recognizable and unique (Picture 3). As a reward, it is such a joy to find a match and recognize old friends when they arrive from their long journeys in the vast ocean each year to the Oregon coast.

The callosity pattern of a southern right whale. Photo by Alejandro Fernández Ajó – Instituto de Conservación de Ballenas.
Three different humpback whales with notably different pigmentation patterns on their flukes. Photographs captured under NOAA/NMFS permit #21678.
The gray whale “Knife” we have observed frequently this summer off the Oregon coast. Can you see how the right pigmentation pattern identified looks like a knife? Photograph captured under NOAA/NMFS permit #21678.

As a result of our photo-identification efforts and the high site-fidelity of the whales we study, the large majority of the gray whales we observe here in Oregon are known individually. For many whales, we also have detailed sightings records that can span years and decades, that document calving history, lactation, appearance of scars indicative of injury or entanglement, minimum age, sex, habitat-use patterns, behaviors, etc. Holding such detailed information of individual whales provides incredible contributions to our understanding of the basic patterns in life history of whales, such as reproduction rates, calving intervals, age of first reproduction, etc. Moreover, when these life history events are linked with physiological sample collection large steps can be made in the development and validation of physiological methods. Many endocrine assays currently in use for whales are based on non-traditional sample types including feces, respiratory vapor, and baleen, which have been validated using the catalogs of well-known individuals to verify that measured hormones reflect patterns expected for various physiological states. For example, we can compare endocrine data of confirmed pregnant females, known mature males, and known-injured whales to learn how whale physiological responses are different during different life history events (e.g., Burgess et al. 2017, 2018, Corkeron et al. 2017, Hunt et al. 2006, 2016, 2018, Lysiak et al. 2018, Rolland et al. 2005).

Here in Oregon we are learning from the lives of the gray whales we study, and here I want to share with you two of their stories, one happy and one not-so-happy.

Let´s start with the not-so-happy story so we can end with some brighter news. On June 24 this year, we encountered a whale near Cape Foulweather, which is a very tricky area to work as there are many rocks and shallow water that make the sea conditions very choppy even with low swell. We started documenting the sighting as usual, taking pictures of the left side, the right side and ideally also the fluke of the whale. As we approached this whale, we started noting that something was wrong with its fluke. With the challenging sea conditions, it was not easy to approach the whale and the whale was not exposing its fluke when diving. When we put our drone up to collect photogrammetry and behavior data we gained a much better perspective. This whale has a bad injury on it fluke (Picture 4.C). On the boat we started making conjectures about the cause of this terrible injury that had basically amputate most of its left fluke lobe. Once back on shore, we sorted out the photos and compared the field images captured during the day with the photo-ID catalog and we made a match. This whale is known in our catalog as “ROLLER SKATE”, is a female, and was first sighted in 2015, so she is at least 5 years old today.

The story unfolded when we reviewed Roller Skate’s sighting history. Interestingly we observed this same whale in the same location last September 2019. Unfortunately, it was a very brief encounter but enough for photo documentation of the whale and an interesting observation. Here I quote the field notes that Dr. Torres wrote from this sighting: “September 6th, 2019. Sighting 9: Scattered whales feeding and/or traveling across area to north of Cape Foulweather. One whale had recently chopped fluke; tried to re-find to get better photos but could not (looking at photos now, this whale is clearly entangled in line!). Ceiling too low for UAS [drone flight].” (Picture 4.B).

Progressive photos of Roller Skate’s fluke. In 2017, her fluke was healthy (A). In 2019, we observed her fluke with a line entanglement and “chewed up” (B). In 2020, we have observed the resulting wound and healing process (C). Photographs captured under NOAA/NMFS permit #21678.

Roller skate’s story is an example of how essential is to keep an ID catalog. After a close-up examination of the 2019 picture, we can clearly see a rope entanglement (Picture 4.B). Photos from previous years show how beautiful and healthy her fluke was before this event (Picture 4.A). This event is heart breaking to witness, but this whale could be considered lucky because she was able to shed the gear and survive this entanglement, at least in the short term. Additionally, we can learn from Roller Skate’s misfortune to help us understand what the consequences of such an injury (stressor) may be on the physiology of a whale. We have been eager to collect a fecal sample from Roller Skate to analyze how her hormone levels compare to non-injured whales. Fortunately, we got lucky a couple weeks ago and collected this sample, so now we need to get in the lab and analyze the samples. But more questions remain: Will this injury impact her ability to reproduce? If so, for how long? And at a larger scale, what are the population consequences of such events? If we can understand the magnitude of lethal and sublethal human caused impacts on individual whales and their populations from events such as entanglements, we can develop better methods to mitigate and limit such hazards for whales in their environments.

As I promised, there is also some good news to share. A very well-known PCFG whale, almost a celebrity I dear to say, is “Scarback”, or as we like to call her “Scarlett”. Scarlett is a female known since 1996, making her at least 24 years old, and she also has a very bad injury of unknown origin. Scarlett has a terrible scar on her back that is theorized to have been caused by an explosive harpoon, or maybe a bad ship-strike (Picture 5), but we really do not know. However, we do know she survived this injury and this year she brought a new calf into the population (Picture 6). This is the second calf we have documented from Scarlett, with her previous calf sighted during the 2016 field season and we call it “Brown”. Scarlett is an example of how resilient these amazing giants can be; however, it is likely that while she was recovering from this injury, she was unable to reproduce. How many calves from Scarlett did the PCFG population “lose” due to such a tragedy? We can´t know, but we are learning, and her story will also help us understand whale physiology as we will analyze her fecal hormones and body condition during pregnancy, lactation, and resting phases.

The scar on Scarlett’s back. This significant wound has an unknown origin. Photograph captured under NOAA/NMFS permit #21678.

Scarlett is a survivor. We need to recognize that we are sharing the ocean with different forms of life. We need to acknowledge their existence and understand how our use of the oceans is affecting them, and, more importantly, work toward improving their conditions. I hope that with our research we highlight and communicate how amazing are these animals, and how important are they for marine ecosystems. And ultimately, I hope our work helps minimize the impacts that affect other forms of ocean life that coexist with us, both above and below the surface.

The well-known gray whale “Scarlett” surfaces under her calf while it checks out the GEMM Lab field team. Photo by Alejandro Fernandez Ajo taken under NOAA/NMFS permit #21678.


Burgess, E., Hunt, K. E., Kraus, S. D. and Rolland, R. M. (2016). Get the most out of blow hormones: validation of sampling materials, field storage and extraction techniques for whale respiratory vapor samples. Conservation Physiology, 4, cow024.

Burgess, E. A., Hunt, K. E., Kraus, S. D. and Rolland, R. M. (2018). Quantifying hormones in exhaled breath for physiological assessment of large whales at sea. Scientific Reports, 8, 10031.

Corkeron, P. J., Rolland, R. M., Hunt, K. E. and Kraus, S. D. (2017). A right whale PooTree: Fecal hormones and classification trees identify reproductive states in North Atlantic right whales (Eubalaena glacialis). Conservation Physiology, 5, cox006. DOI: 10.1093/conphys/cox006.

Hunt, K., Lysiak, N., Moore, M. and Rolland, R. (2017). Multi-year longitudinal profiles of cortisol and corticosterone recovered from baleen of North Atlantic right whales (Eubalaena glacialis). General and Comparative Endocrinology, 254, 50-59. DOI: 10.1016/j.ygcen.2017.09.009.

Hunt, K., Lysiak, N. S. J., Matthews, C. J. D., et al. (2018). Multi-year patterns in testosterone, cortisol and corticosterone in baleen from adult males of three whale species. Conservation Physiology, 6, coy049. DOI: 10.1093/conphys/coy049.

Hunt, K. E., Rolland, R. M., Kraus, S. D. and Wasser, S. K. (2006). Analysis of fecal glucocorticoids in the North Atlantic Right Whale (Eubalaena glacialis). General and Comparative Endocrinology, 148, 260-272.

Lysiak, N., Trumble, S., Knowlton, A. and Moore, M. (2018). Characterizing the duration and severity of fishing gear entanglement on a North Atlantic right whale (Eubalaena glacialis) using stable isotopes, steroid and thyroid hormones in baleen. Frontiers in Marine Science. DOI: 10.3389/fmars.2018.00168.

Rolland, R. M., Hunt, K. E., Kraus, S. D. and Wasser, S. K. (2005). Assessing reproductive status of right whales (Eubalaena glacialis) using fecal hormone metabolites. General and Comparative Endocrinology, 142, 308-317.

The teamwork of conservation science

Dr. Leigh Torres
PI, Geospatial Ecology of Marine Megafauna Lab, Marine Mammal Institute
Assistant Professor, Oregon Sea Grant, Department of Fisheries and Wildlife, Oregon State University

I have played on sports teams all my life – since I was four until present day. Mostly soccer teams, but a fair bit of Ultimate too. Teams are an interesting beast. They can be frustrating when communication breaks down, irritating when everyone is not on the same timeline, and disastrous if individuals do not complete their designated job. Yet, without the whole team we would never win. So, on top of the fun of competition, skill development, and exercise, playing on teams has always been part of the challenging and fulfilling process for me: everyone working toward the same goal – to win – by making the team fluid, complimentary, integrated, and ultimately successful.

I have come to learn that it is the same with conservation science.

A few of my teams through the ages, as player and coach. Some of my favorite people are on these teams, from 1981 to 2018.

Conservation efforts are often so complex, that it is practically impossible to achieve success alone. Forces driving the need for conservation typically include monetary needs/desires, social values, ecological processes, animal physiology, multi-jurisdictional policies, and human behavior. Each one of these forces alone is challenging to understand and takes expertise to comprehend the situation. Hence, building a well-functioning team is essential. Here’s a recent example from the GEMM Lab:

Since 2014 entanglements of blue, humpback and gray whales in fishing gear along the west coast of the USA have dramatically increased, particularly in Dungeness crab fishing gear. Many forces likely led to this increase, including increased whale population abundance, potential shifts in whale distributions, and changes in fishing fleet dynamics. While we cannot point a finger at one cause, many people and groups recognize that we cannot continue to let whales become entangled and killed at such high rates: whale populations would decline, fisheries would look bad in the public eye and potentially lose profits, whales have an intrinsic right to live in the ocean without being bycaught, and whales are an important part of the ecosystem that would deteriorate without them. In 2017, the Oregon Whale Entanglement Working Group was formed to bring stakeholders together that were concerned about this problem to discuss possible solutions and paths forward. I was lucky to be a part of this group, which also included members of the Dungeness crab fishery and commission, the Oregon Department of Fish and Wildlife (ODFW), other marine mammal scientists, and representatives of the American Cetacean Society, The Nature Conservancy, and a local marine gear supplier.

We met regularly over 2.5 years, and despite some hesitation at first about walking into a room of potentially disgruntled fishermen (I would be lying if I did not admit to this), after the first meeting I looked forward to every gathering. I learned an immense amount about the Dungeness crab fishery and how it operates, how ODFW manages the fishery and why, and what people do, don’t and need to know about whales in Oregon. Everyone agreed that reducing whale entanglements is needed, and a frequent approach discussed was to reduce risk by not setting gear where and when we expect whales to be. Yet, this idea flagged a very critical knowledge gap: We do not have a good understanding of whale distribution patterns in Oregon. Thus leading to the development of a highly collaborative research effort to describe whale distribution patterns in Oregon and identify areas of co-occurrence between whales and fishing effort to reduce the risk of entanglements. Sounds great, but a tough task to accomplish in a few short years. So, let me introduce the great team I am working with to make it all happen.

While I may know a few things about whales and spatial ecology, I don’t know too much about fisheries in Oregon. My collaboration with folks at ODFW, particularly Kelly Corbett and Troy Buell, has enabled this project to develop and go forward, and ultimately will lead to success. These partners provide feedback about how and where the fishery operates so I know where and when to collect data, and importantly they will provide the information on fishing effort in Oregon waters to relate to our generated maps of whale distribution. This spatial comparison will produce what is needed by managers and fishermen to make informed and effective decisions about where to fish, and not to fish, so that we reduce whale entanglement risk while still harvesting successfully to ensure the health and sustainability of our coastal economies.

So, how can we collect standardized data on whale distribution in Oregon waters without breaking the bank? I tossed this question around for a long time, and then I looked up to the sky and wondered what that US Coast Guard (USCG) helicopter was flying around for all the time. I reached out to the USCG to enquire, and proposed that we have an observer fly in the helicopter with them along a set trackline during their training flights. Turns out the USCG Sector North Bend and Columbia River were eager to work with us and support our research. They have turned out to be truly excellent partners in this work. We had some kinks to work out at the beginning – lots of acronyms, protocols, and logistics for both sides to figure out – but everyone has been supportive and pleasant to work with. The pilots and crew are interested in our work and it is a joy to hear their questions and see them learn about the marine ecosystem. And our knowledge of helicopter navigation and USCG duties has grown astronomically.

On the left is a plot of the four tracklines we survey for whales each month for two years aboard a US Coast Guard helicopter. On the right are some photos of us in action with our Coast Guard partners.

Despite significant cost savings to the project through our partnership with the USCG, we still need funds to support time, gear and more. And full credit to the Oregon Dungeness Crab Commission for recognizing the value and need for this project to support their industry, and stepping up to fund the first year of this project. Without their trust and support the project may not have got off the ground. With this support in our back pocket and proof of our capability, ODFW and I teamed up to approach the National Oceanographic and Atmospheric and Administration (NOAA) for funds to support the remaining years of the project. We found success through the NOAA Fisheries Endangered Species Act Section 6 Program, and we are now working toward providing the information needed to protect endangered and threatened whales in Oregon waters.

Despite our cost-effective and solid approach to data collection on whale occurrence, we cannot be everywhere all the time looking for whales. So we have also teamed up with Amanda Gladics at Oregon Sea Grant to help us with an important outreach and citizen science component of the project. With Amanda we have developed brochures and videos to inform mariners of all kinds about the project, objectives, and need for them to play a part. We are encouraging everyone to use the Whale Alert app to record their opportunistic sightings of whales in Oregon waters. These data will help us build and test our predictive models of whale distribution. Through this partnership we continue important conversations with fishermen from many fisheries about their concerns, where they are seeing whales, and what needs to be done to solve this complex conservation challenge.  

Of course I cannot collect, process, analyze, and interpret all this data on my own. I do not have the skills or capacity for that. My partner in the sky is Craig Hayslip, a Faculty Research Assistant in the Marine Mammal Institute. Craig has immense field experience collecting data on whales and is the primary observer on the survey flights. Together we have navigated the USCG world and developed methods to collect our data effectively and efficiently (all within a tiny space flying over the ocean). In a few months we will be ¾ of the way through our data collection phase, which means data analysis will take over. For this phase I am bringing back a GEMM Lab star, Solene Derville, who recently completed her PhD. As the post-doc on the project, Solene will take the lead on the species distribution modeling and fisheries overlap analysis. I am looking forward to partnering with Solene again to compile multiple data sources on whales and oceanography in Oregon to produce reliable and accurate predictions of whale occurrence and entanglement risk. Finally I want to acknowledge our great partners at the Cascadia Research Collective (Olympia, WA) and the Cetacean Conservation and Genomics Lab (OSU, Marine Mammal Institute) who help facilitate our data collection, and conduct the whale photo-identification or genetic analyses to determine population assignment.  

As you can see, even this one, smallish, conservation research project takes a diverse team of partners to proceed and ensure success. On this team, my position is sometimes a player, coach, or manager, but I am always grateful for these amazing collaborations and opportunities to learn. I am confident in our success and will report back on our accomplishments as we wrap up this important and exciting conservation science project.   

A fin whale observed off the Oregon coast during one of our surveys aboard a US Coast Guard helicopter.