Tag: genetics

A Gut Feeling: DNA Metabarcoding Gray Whale Diets

By Charles Nye, graduate student, OSU Department of Fisheries, Wildlife, & Conservation Sciences, Cetacean Conservation and Genomics Laboratory

Figure 1: An illustration (by me) of a feeding gray whale whose caudal end transitions into a DNA double helix.

Let’s consider how much stuff organisms shed daily. If you walk down a hallway, you’ll leave a microscopic trail of skin cells, evaporated sweat, and even more material if you so happen to sneeze or cough (as we’ve all learned). The residency of these bits and pieces in a given environment is on the order of days, give or take (Collins et al. 2018). These days, we can extract, amplify, and sequence DNA from leftover organismal material in environments (environmental DNA; eDNA), stomach contents (dietary DNA, dDNA), and other sources (Sousa et al. 2019; Chavez et al. 2021).

You might be familiar with genetic barcoding, where scientists are able to use documented and annotated pieces of a genome to identify a piece of DNA down to a species. Think of these as genetic fingerprints from a crime scene where all (described) species on Earth are prime suspects. With advancements in computing technology, we can barcode many species at the same time—a process known as metabarcoding. In short, you can now do an ecosystem-wide biodiversity survey without even needing to see your species of interest (Ficetola et al. 2008; Chavez et al. 2021).

(Before you ask: yes, people have tried sampling Loch Ness and came up with not a single strand of plesiosaur DNA (University of Otago, 2019).)

I received my crash course on metabarcoding when I was employed at the Monterey Bay Aquarium Research Institute (MBARI), right before grad school. There, I was employed to help refine eDNA survey field and laboratory methods (in addition to some cool robot stuff). Here at OSU, I use metabarcoding to research whale ecology, detection, and even a little bit of forensics  work. Cetacean species (or evidence thereof) I’ve worked on include North Atlantic right whales (Eubalaena glacialis), killer whales (Orcinus spp.), and gray whales (Eschrichtius robustus).

Long-time readers of the GEMM Lab Blog are probably quite knowledgeable about the summertime grays—the Pacific Coast Feeding Group (PCFG). All of us here at OSU’s Marine Mammal Institute (MMI) are keenly interested in understanding why these whales hang out in the Pacific Northwest during the summer months and what sets them apart from the rest of the Eastern North Pacific gray whale population. What interests me? Well, I want to double-check what they’re eating—genetically.

“What does my study species eat?” is a straightforward but underappreciated question. It’s also deceptively difficult to address. What if your species live somewhere remote or relatively inaccessible? You can imagine this is a common logistical issue for most research in marine sciences. How many observations do you need to make to account for seasonal or annual changes in prey availability? Do all individuals in your study population eat the same thing? I certainly like to mix and match my diet.

Gray whale foraging ecology has been studied comprehensively over the last several decades, including an in-depth stomach content evaluation by Mary Nerini in 1984 and GEMMer Lisa Hildebrand’s MSc research. PCFG whales seem to prefer shrimpy little creatures called mysids, along with Dungeness crab (Cancer magister) larvae, during their stay in the Pacific Northwest (PNW), most notably the mysid Neomysis rayii (Guerrero 1989; Hildebrand et al. 2021). Indeed, the average energetic values of common suspected prey species in PNW waters rival the caloric richness of Arctic amphipods (Hildebrand et al. 2021). However, despite our wealth of visual foraging observations, metabarcoding may add an additional layer of resolution. For example, the ocean sunfish (Mola mola) was believed to exclusively forage on gelatinous zooplankton, but a metabarcoding approach revealed a much higher diversity of prey items, including other bony fishes and arthropods (Sousa et al. 2016).

Given all this exposition, you may be wondering: “Charles—how do you intend on getting dDNA from gray whales? Are you going to cut them open?”

Figure 2: The battle station, a vacuum pump that I use to filter out all of the particulate matter from a gray whale dDNA sample. The filter is made of polycarbonate track etch material, which melts away in the DNA extraction process—quite handy, indeed!

No. I’m going to extract DNA from their poop.

Well, actually, I’ve been doing that for the last two years. My lab (Cetacean Conservation and Genomics Laboratory, CCGL) and GEMM Lab have been collaborating to make lemonade out of, er…whale poop. An archive of gray whale fecal samples (with ongoing collections every field season) originally collected for hormone analyses presented itself with new life—the genomics kind. In addition to community-level data, we are also able to recover informative DNA from the gray whales, including sex ID from “depositing” individuals, though the recovery rate isn’t perfect.

Because the GEMM Lab/MMI can non-invasively collect multiple samples from the same individuals over time, dDNA metabarcoding is a great way to repeatedly evaluate the diets of the PCFG, just shy of being at the right place at the right time with a GoPro or drone to witness a feeding event.  While we can get stomach contents and even usable dDNA from a naturally deceased whale, those data may not be ideal. How representative a stranded whale is of the population is dependent on the cause of death; an emaciated or critically injured individual, for example, is a strong outlier.

Figure 3: Presence/absence of the top 10 most-common taxonomic Families observed in the PCFG gray whale dDNA dataset (n = 20, randomly selected). Filled-in dots indicate at least one genetic read associated with that Family, and empty dots indicate none. Note the prey taxa: mysids (Mysidae), krill (Euphausiidae), and olive snails (Olividae).

Here’s a snapshot of progress to date for this dDNA metabarcoding project. I pulled out twenty random samples from my much larger working dataset (n = 82) for illustrative purposes (and legibility). After some bioinformatic wizardry, we can use a presence/absence approach to get an empirical glimpse at what passes through a PCFG gray whale. While I am able to recover species-level information, using higher-level taxonomic rankings summarizes the dataset in a cleaner fashion (and also, not every identifiable sequence resolves to species).

The title of most commonly observed prey taxa belongs to our friends, the mysids (Mysidae). Surprisingly, crabs and amphipods are not as common in this dataset, instead losing to krill (Euphausiidae) and olive snails (Olividae). The latter has been found in association with gray whale foraging grounds but not documented in a prey study (Jenkinson 2001). We also get an appreciable amount of interference from non-prey taxa, most notably barnacles (Balanidae), with an honorable mention to hydrozoans (Clytiidae, Corynidae). While easy to dismiss as background environmental DNA, as gray whales do forage at the benthos, these taxa were physically present and identifiable in Nerini’s (1984) gray whale stomach content evaluation.

So—can we conclude that barnacles and hydrozoans are an important part of a gray whale’s diet, as much as mysids? From decades of previous observations, we might say…probably not. Gray whales are actively targeting patches of crabby, shrimpy zooplankton things, and even employ novel foraging strategies to do so (Newell & Cowles 2006; Torres et al. 2018). However, the sheer diversity of consumed species does present additional dimensionality to our understanding of gray whale ecology.

The whales are eating these ancillary organisms, whether they intend to or not, and this probably does influence population dynamics, recruitment, and succession in these nearshore benthic habitats. After all, the shallow pits that gray whales leave behind post-feeding provide a commensal trophic link with other predatory taxa, including seabirds and groundfish (Oliver & Slattery 1985). Perhaps the consumption of these collateral species affects gray whale energetics and reflects on their “performance”?

I hope to address all of this and more in some capacity with my published work and graduate chapters. I’m confident to declare that we can document diet composition of PCFG whales using dDNA metabarcoding, but what comes next is where one can get lost in the sea(weeds). How does the diet of individuals compare to one another? What about at differing time points? Age groups? How many calories are in a barnacle? No need to fret—this is where the fun begins!

References

Chavez F, Min M, Pitz K, Truelove N, Baker J, LaScala-Grunewald D, Blum M, Walz K,

Nye C, Djurhuus A, et al. 2021. Observing Life in the Sea Using Environmental

DNA Oceanog. 34(2):102–119. doi:10.5670/oceanog.2021.218.

Collins R, Wangensteen OS, O’Gorman EJ, Mariani S, Sims DW, Genner M. 2018. Persistence

of environmental DNA in marine systems. Comm Biol. 1(185).

https://doi.org/10.1038/s42003-018-0192-6

Ficetola GF, Miaud C, Pompanon F, Taberlet P. 2008. Species detection using

environmental DNA from water samples. Biol Lett. 4(4):423–425.

doi:10.1098/rsbl.2008.0118.

Hildebrand L, Bernard KS, Torres LG. 2021. Do Gray Whales Count Calories?

Comparing Energetic Values of Gray Whale Prey Across Two Different Feeding

Grounds in the Eastern North Pacific. Front Mar Sci. 8:683634.

doi:10.3389/fmars.2021.683634.

Jenkinson R. 2001. Gray whale (Eschrichtius robustus) prey availability and feeding ecology in

northern California, 1999-2000 [thesis]. California State Polytechnic University,

Humboldt. 81 p.

Newell CL, Cowles TJ. 2006. Unusual gray whale Eschrichtius robustus feeding in the summer

of 2005 off the central Oregon Coast. Geophys Res Lett. 33(22):L22S11.

doi:10.1029/2006GL027189.

Oliver JS, Slattery PN. 1985. Destruction and Opportunity on the Sea Floor: Effects of

Gray Whale Feeding. Ecology. 66(6):1965–1975. doi:10.2307/2937392.

Sousa LL, Silva SM, Xavier R. 2019. DNA metabarcoding in diet studies: Unveiling

ecological aspects in aquatic and terrestrial ecosystems. Environmental DNA.

1(3):199–214. doi:10.1002/edn3.27.

Sousa LL, Xavier R, Costa V, Humphries NE, Trueman C, Rosa R, Sims DW, Queiroz N.

2016. DNA barcoding identifies a cosmopolitan diet in the ocean sunfish. Sci

Rep. 6(1):28762. doi:10.1038/srep28762.

Torres LG, Nieukirk SL, Lemos L, Chandler TE. 2018. Drone Up! Quantifying Whale Behavior

From a New Perspective Improves Observational Capacity. Front Mar Sci. 5:319.

doi:10.3389/fmars.2018.00319.

University of Otago. 2019. First eDNA study of Loch Ness points to something fishy.

https://www.otago.ac.nz/news/news/otago717609.html. [accessed 2023 Apr 25]

“Do Dolphins Get Hives?”: The Skinny on Allergies in Cetaceans

By: Alexa Kownacki, Ph.D. Student, OSU Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab 

While sitting on my porch and watching the bees pollinate the blooming spring flowers, I intermittently pause to scratch the hives along my shoulders and chest. In the middle of my many Zoom calls, I mute myself and stop my video because a wave of pollen hits my face and I immediately have to sneeze. With this, I’m reminded: Welcome to prime allergy season in the Northern Hemisphere. As I was scratching my chronic idiopathic urticaria (hives caused by an overactive immune system), I asked myself “Do dolphins get hives?” I had no idea. I know most terrestrial mammals can and do—just yesterday, one of the horses in the nearby pasture was suffering from a flare of hives. But, what about aquatic and marine mammals? 

Springtime flowers blooming on the Central California Coast 2017. (Image Source: A. Kownacki)

As with most research on marine mammal health, knowledge is scare and is frequently limited to studies conducted on captive and stranded animals. Additionally, most of the current theories on allergic reactions in marine mammals are based on studies from terrestrial wildlife and humans. Because nearly all research on histamine pathways centers on terrestrial animals, I wanted to see what information exists the presence of skin allergies in marine mammals.  

Allergic reactions trigger a cascade within the body, beginning with the introduction of a foreign body, which for many people is pollen. The allergen binds to antibodies that are produced to fight potentially harmful substances. Once this allergen binds to different types of cells, including mast cells, chemicals like histamines are released. Histamines cause the production of mucus and constriction of blood vessels, and thus are the reason your eyes water, your nose runs, or you start coughing. 

Basic cartoon of an allergic reaction from exposure to the allergen to the reaction from the animal. (Image Source: Scientific Malaysian)

As you probably can tell just by looking at a marine mammal, they have thicker skin and fewer mucus membranes that humans, due to the fact that they live in the water. However, mast cells or mast cell-like cells have been described in most vertebrate lineages including mammals, birds, reptiles, amphibians, and bony fishes (Hellman et al. 2017, Reite and Evenson 2006). Mast cell-like cells have also been described in an early ancestor of the vertebrates, the tunicate, or sea squirt (Wong et al. 2014). Therefore, allergic-reaction cascades that may present as hives, red and itchy eyes or nose in humans, also exist in marine mammals, but perhaps cause different or less visible symptoms.  

Skin conditions in cetaceans are gathering interest within the marine mammal health community. Even our very own Dawn Barlow, Dr. Leigh Torres, and Acacia Pepper assessed the skin conditions in New Zealand blue whales in their recent publication. Most visible skin lesions or markings on cetaceans are caused by parasites, shark bits, fungal infections, and fishery or boat interactions (Leone et al. 2019, Sweeney and Ridgway 1985). However, there is very little scientific literature about allergic reactions in marine mammals, let alone cetaceans. That being said, I managed to find a few critical pieces of information supporting the theory that marine mammals do in fact have allergies that can produce dermal reactions similar to hives in humans.  

In one study, three captive bottlenose dolphins developed reddened skin, sloughing, macules, and wheals on their ventral surfaces (Monreal-Pawlowsky et al. 2017). The medical staff first noticed this atopic dermatitis in 2005 and observed the process escalate over the next decade. Small biopsy samples from the affected areas on the three dolphins coincided with the appearance of four pollens in the air within the geographic region: Betula, Pistacia, Celtis, and Fagus (Monreal-Pawlowsky et al. 2017). Topical prednisone treatments were applied to the affected areas at various dosages that slowly resolved the skin irritations. Researchers manufactured an allergy vaccine using a combination of the four pollens in hopes that it would prevent further seasonal outbreaks, but it was unsuccessful. In the coming years, the facility intends to adjust the dosages to create a successful vaccine.  

In the three top images, visible skin irritation including redness, macules, wheals, and sloughing are present. In the image below, the above animal was treated with methylprednisolone and the skin irritation subsides. (Monreal-Pawlowsky et al. 2017)

In addition to the above study, there is an unpublished case of suspected allergic reaction to another pollen that produces a pruritic reaction on the ventral areas of dolphins on a seasonal basis (Vicente Arribes, personal communication). Although there are only a few documented cases of environmentally-triggered allergic reactions that are visible on the dermal layer of cetaceans, I believe this evidence makes the case that some cetaceans suffer from allergies much like us. So, next time you’re enjoying the beautiful blooms and annoyingly scratch your eyes, know that you are not alone. 

Image Source: FurEver Family

Citations: 

Barlow DR, Pepper AL and Torres LG (2019) Skin Deep: An Assessment of New Zealand Blue Whale Skin Condition. Front. Mar. Sci. 6:757.doi: 10.3389/fmars.2019.00757 

Hellman LT, Akula S, Thorpe M and Fu Z (2017) Tracing the Origins of IgE, Mast Cells, and Allergies by Studies of Wild Animals. Front. Immunol. 8:1749. doi: 10.3389/fimmu.2017.01749 

Leone AB, Bonanno Ferraro G, Boitani L, Blasi MF. Skin marks in bottlenose dolphins (Tursiops truncatus) interacting with artisanal fishery in the central Mediterranean Sea. PLoS One. 2019;14(2):e0211767. Published 2019 Feb 5. doi:10.1371/journal.pone.0211767 

Monreal-Pawlowsky T, Fernández-Bellon H, Puigdemont A (2017) Suspected Allergic Reaction in Bottlenose Dolphins (Tursiops truncatus). J Vet Sci Ani Husb 5(1): 108. doi: 10.15744/2348-9790.5.108 

Reite OB, Evensen O. Inflammatory cells of teleostean fish: a review focusing on mast cells/eosinophilic granule cells and rodlet cells. Fish Shellfish Immunol (2006) 20:192–208. doi:10.1016/j.fsi.2005.01.012 

Sweeney, J. C., & Ridgway, S. H. (1975). Common diseases of small cetaceans. J. Am. Vet. Med. Assoc, 167(7), 533-540. 

Wong GW, Zhuo L, Kimata K, Lam BK, Satoh N, Stevens RL. Ancient originof mast cells. Biochem Biophys Res Commun (2014) 451:314–8. doi:10.1016/j.bbrc.2014.07.124 

A Weekend of Inspiration in Marine Science: NWSSMM and Dr. Sylvia Earle!

By Karen Lohman, Masters Student in Wildlife Science, Cetacean Conservation and Genomics Lab, Oregon State University

My name is Karen Lohman, and I’m a first-year student in Dr. Scott Baker’s Cetacean Conservation and Genomics Lab at OSU. Dr. Leigh Torres is serving on my committee and has asked me to contribute to the GEMM lab blog from time to time. For my master’s project, I’ll be applying population genetics and genomics techniques to better understand the degree of population mixing and breeding ground assignment of feeding humpback whales in the eastern North Pacific. In other words, I’ll be trying to determine where the humpback whales off the U.S. West Coast are migrating from, and at what frequency.

Earlier this month I joined the GEMM lab members in attending the Northwest Student Society of Marine Mammalogy Conference in Seattle. The GEMM lab members and I made the trip up to the University of Washington to present our work to our peers from across the Pacific Northwest. All five GEMM lab graduate students, plus GEMM lab intern Acacia Pepper, and myself gave talks presenting our research to our peers. I was able to present preliminary results on the population structure of feeding humpback whales across shared feeding habitat by multiple breeding groups in the eastern North Pacific using mitochondria DNA haplotype frequencies. In the end GEMM lab’s Dawn Barlow took home the “Best Oral Presentation” prize. Way to go Dawn!

A few of the GEMM lab members and me presenting our research at the NWSSMM conference in May 2019 at the University of Washington.

While conferences have a strong networking component, this one feels unique.  It is a chance to network with our peers, who are working through the same challenges in graduate school and will hopefully be our future research collaborators in marine mammal research when we finish our degrees. It’s also one of the few groups of people that understand the challenges of studying marine mammals. Not every day is full of dolphins and rainbows; for me, it’s mostly labwork or writing code to overcome small and/or patchy sample size problems.

All of the CCGL and GEMM Lab members excited to hear Dr. Sylvia Earle’s presentation at Portland State University in May 2019 (from L to R: Karen L., Lisa H., Alexa K., Leila L., Dawn B., and Dom K.) . Photo Source: Alexa Kownacki

On the way back from Seattle we stopped to hear the one and only Dr. Sylvia Earle, talk in Portland. With 27 honorary doctorates and over 200 publications, Dr. Sylvia Earle is a legend in marine science. Hearing a distinguished marine researcher talk about her journey in research and to present such an inspiring message of ocean advocacy was a great way to end our weekend away from normal grad school responsibilities. While the entirety of her talk was moving, one of her final comments really stood out. Near the end of her talk she called the audience to action by saying “Look at your abilities and have confidence that you can and must make a difference. Do whatever you’ve got.” As a first-year graduate student trying to figure out my path forward in research and conservation, I couldn’t think of better advice to end the weekend on.

 

Inter- and Transdisciplinary Sea Otter Research

By Dominique Kone, Masters Student, Marine Resource Management

As the human population continues to grow, so does our impact on marine environments. In many cases, these problems – such as microplastics, vessel noise, or depleted fisheries – are far too grand for any one person to tackle on their own and it takes a team effort to find adequate solutions. Experts within a single field (e.g. ecology, economics, genetics) have been collaborating to tackle these issues for decades, but there is an increasing interest and recognition of the importance in working with others outside one’s own discipline.

It’s not surprising that most collaborative efforts are between experts from the same field. It’s easier to converse with those with similar vocabulary, we often enjoy learning from our peers, and our thought-processes and problem-solving skills are typically very similar. However, as issues become more complex and stretch across disciplines, the need for interdisciplinary collaboration becomes more and more imperative. As a graduate student studying marine resource management, I’ve learned the great value in conducting interdisciplinary work. Yet, I still have much to learn if I want to continue to help find solutions to the many complex marine issues. Therefore, over the next year, I’ve committed to joining a interdisciplinary team of graduate students, as part of an NSF-funded fellowship program at Oregon State University (OSU), to further investigate a potential sea otter reintroduction to Oregon. Here, I provide a brief overview of the program and my team’s goals for the coming year.

Source: Hakai Magazine.

The fellowship program emphasizes both interdisciplinary and transdisciplinary approaches, so before I explain the program, it’s important to first understand these terms. In short, interdisciplinarity typically relates to experts from different fields analyzing, synthesizing, and coordinating their work as a whole (Choi & Pak 2006). Another way to think about this, in more practical terms, is if two or more experts share information and learn from one another; each expert can then individually apply that information or lessons-learned to their own line of work. In contrast, transdisciplinary work is slightly more collaborative, where experts work more hand-in-hand to develop a product or solution that transcends their disciplines’ traditional boundaries. The experts essentially create a product that would not have been possible working in isolation. In practice, the product(s) that stems from inter- and transdisciplinary work – if they truly are inter- or transdisciplinary by definition – is potentially very different.

Source: Dr. Shoshanah Jacobs.

With an increasing interest in interdisciplinary work, the National Science Foundation (NSF) developed the National Research Traineeship (NRT) program to encourage select universities to develop and implement innovative and transformative models for training graduate students in STEM disciplines. After soliciting proposals, the NSF awarded OSU one of these NRT projects to support OSU’s Risk and Uncertainty Quantification in Marine Science NRT Program. OSU’s NRT program was born out of the recognition that much of the complexity of marine issues is largely due to the uncertainty of natural and human systems. Therefore, the primary purpose of this program is to train the next generation of natural resource scientists and managers to be better equipped to study and manage complex marine systems, especially under extreme uncertainty and potential risk.

Source: Oregon State University.

This NRT program trains graduate students in three core concept areas: coupled natural human systems, big data, and risk and uncertainty analyses and communications. To learn these core concepts, students fulfil a minor that includes coursework in statistical inference, uncertainty quantification, risk analyses, earth system science, and social systems. In addition to the minor, students also conduct collaborative research in small (3-5 students) cross-disciplinary teams to address specific issues in marine resource management. Within each team, students come from different disciplines and fields, and must learn to work together to produce a transdisciplinary research product. Throughout the year, each team will develop a set of research questions to address their issue at hand, conduct research which links all their fields, and produce a transdisciplinary report summarizing the process they undertook and the end product. Most students who are accepted into the NRT program are awarded one-year fellowships, funded by the NSF.

At the start of this academic year, I was awarded one of these NRT fellowships to address the many issues and implications of a potential sea otter reintroduction to Oregon. Over the next year, I will be working with two other OSU graduate students with backgrounds in genetics and social sciences. Our task is to not only investigate the ecological implications – which I am currently doing for my own thesis – but we are to expand this investigation to also address many of the genetic, political, and social factors, as well. While each of us is capable of addressing one of these factors individually, the real test will be in finding linkages between each of our disciplines to make this project truly transdisciplinary.

Structure and vision of OSU’s NRT program. Source: Oregon State University.

Since our project started, we have worked to better understand each another’s expertise, interests, and the general need for a transdisciplinary project of this sort. After acquiring this base understanding, we spent a considerable amount of time developing research questions and potential methods for addressing our issue. Throughout this process, it’s already become apparent that each of us is starting to learn important teamwork and collaboration skills, including effective communication and explanation of complicated concepts, active listening, critical thinking, and constructive feedback.  While these skills are imperative for our research over the next year, they are also life-long skills that we’ll continue to use in our careers beyond graduate school.

As I’ve stated previously, learning to be an effective collaborator is extremely important to me. Getting the opportunity to work interdisciplinarily is what attracted me to my thesis, the marine resource management program, and the NRT program. By choosing to take my graduate education down this path, I’ve been fortunate to obtain important skills in collaboration, as well as work on a project that allows me to tackle real-world issues and creatively develop scientifically-based solutions. I have high hopes for this NRT project, and I’m excited to continue to conduct meaningful and targeted research over the next year with my new team.

2018-19 OSU NRT Cohort. Source: Oregon State University.

References:

Choi, B. C., and A. W. Pak. Multidisciplinarity, interdisciplinarity and transdisciplinarity in health research, service, education and policy: 1. Definitions, objectives, and evidence of effectiveness. Clinical and Investigative Medicine. 29(6): 351-64.

Biopsy sampling blue whales in New Zealand

By: Callum Lilley

Senior Ranger, Marine – Department of Conservation, Taranaki, New Zealand

During the end of January, I had the privilege to be part of the research team studying blue whales in the South Taranaki Bight, New Zealand.  My role, along with assisting with visual survey, was to obtain biopsy samples from whales using a Paxarm modified veterinary rifle.   This device fires a plastic dart fitted with a sterilized metal tip that takes a small skin and blubber sample for genetic and stable isotope analysis. This process is very carefully managed following procedures to ensure that the whales are not put under any undue stress.  Biopsy sampling provides a gold mine of genetic and dietary information to help us understand the dynamics of this whale population.

Although firing a dart at a creature that is considerably larger than a city bus sounds reasonably easy, it is rarely the case.  The first challenge is to find whales within a large expanse of ocean.  The team then needs to photograph the side of each animal and take note of any distinctive features so that each individual is only sampled once.  Sometimes other work will be undertaken (such as collecting fecal samples, or deploying a drifting hydrophone or unmanned aerial system/drone).  Finally the team will attempt to get close enough to the whales, while taking care not to unduly disturb them, to get a biopsy sample.  Wind, vessel movement, glare, the length of time whales spend underwater and the small target they sometimes present above the water are further challenges.

The video below shows a successful biopsy attempt.  It is a well-coordinated team effort that relies on great communication. You can hear observer Todd Chandler direct the skipper of the vessel Ikatere into position while keeping me (the biopsy sampler) informed as to which whale is surfacing and where.  From the vantage point of the flying bridge, Todd can see the whales’ position and movement (my view is limited from the lower deck).  Todd points out where the whale is surfacing and it momentarily presents a target.  This was the second sample from the two racing whales previously discussed by Dr. Torres, so it will be interesting to see their relationship to one-another.

The ideal angle to approach a whale to take a biopsy sample is from behind at a 45 degree angle, as this causes the least disturbance.  The following video was taken from an unmanned aerial system.  It shows the vessel Ikatere approaching from the whale’s left flank. Department of Conservation (DOC) biodiversity ranger Mike Ogle is on the bow of the vessel and fires a biopsy dart at the whale.  After the biopsy is taken the vessel maneuvers to collect the dart/sample from the water while the whale continues to travel.

In addition to blue whale samples, the DOC permit issued to Oregon State University also allowed for opportunistic sampling of other whales.  The following video was taken during an encounter with a large pod of pilot whales.  The video shows how the lightweight dart bounces off the animal and floats in the water.  Care is taken to communicate its location to the skipper who positions the vessel so it can be retrieved with a net.

Once samples have been retrieved they are handled very carefully to prevent contamination.  The sample is split, with some preserved for genetic analysis and the rest for stable isotope analysis.  Analysis of genetic samples provides information on sex, abundance (through genetic capture-recapture, which is calculated by analyzing the proportion of individuals repeatedly sampled over subsequent seasons), and relationships to other blue whale populations.  Stable isotope analysis provides information on diet.  Also, a portion of all samples will be stored for potential future opportunities such as hormone and fatty acid analysis. It blows me away how much information can be gleaned from these tiny samples!