Tag: GoPro

How to apply my PhD?

By Leila Lemos, PhD candidate, Fisheries and Wildlife Department

Time has flown. It seems that it was like a month ago that I received the news that I was approved in a public notice from the Brazilian government to study abroad, and began the process of moving to Oregon. But actually almost three years have now passed, and I am starting to wrap up my PhD, since I need to defend it in a little bit more than a year.

Our team is now starting the third and last fieldwork season for my PhD project. I am also working on my study plan to determine the last classes I need to take, and our first manuscripts are ‘in press’ or ‘in prep’ for submission to journals. So, it’s time for me to think about what comes next.

I am from Rio de Janeiro, Brazil, and I am studying in the US through a Brazilian government program called Science Without Borders. This program aims to send students abroad to learn new techniques and to develop innovative projects. The projects needed to be original to be approved by the public notice. The main idea is to bring these students back to Brazil, after their PhD completion, to disseminate the acquired knowledge by applying the learned techniques.

My project includes a few novel aspects that allowed for funding by this program. The main focus of my thesis is to develop an endocrinology study of a cetacean species. This was (and still is) a critical field in Brazil, as reported by the “National Action Plan for the conservation of aquatic mammals: Small cetaceans” (2010). According to this Action Plan, cetacean hormonal analyses are rare and of high priority, but there are limited labs with the capacity to study cetacean endocrinology in Brazil. Other limiting factors are the associated analysis costs and a lack of human knowledge and skills. In addition to the hormonal analyses (Figure 1), I am also using other ‘new technologies’ in the project: drones (Figure 2; Video 1) and GoPros (Video 2).

Figure 1: Learning how to perform hormonal analysis at the Seattle Aquarium, WA.
Source: Angela Smith

 

Figure 2: Learning how to fly a drone in Newport, OR.
Source: Florence Sullivan

 

Video 1: Drone flights performed in Newport, OR, during fieldwork in 2016.

* Taken under NOAA/NMFS permit #16111 to John Calambokidis.

 

Video 2: Video of mysid swarms during a GoPro deployment conducted in Port Orford, OR, during fieldwork in 2016.

 

The importance of studying cetacean hormones includes a better understanding of their reproductive cycles (i.e., sex hormones such as progesterone, testosterone and estradiol) and their physiological stress response (i.e., cortisol) to possible threats (e.g., acoustic pollution, contaminants, lack of prey). In addition, through photographs and videos recorded by drones we can conduct photogrammetry analysis to monitoring cetacean body condition, and through GoPro recordings of the water column we can assess prey availability. Changes in both body condition and prey can help us explaining how and why hormone levels vary.

Through my PhD I have obtained skills in hormone analysis, photogrammetry and video prey assessment by studying the logistically accessible and non-threatened gray whale (Eschrichtius robustus). During method development, these features are important to increase sample size and demonstrate feasibility. But now that the methodologies have proven successful, we can start applying them to other species and regions, and under different circumstances, to improve conservation efforts of threatened populations.

Many cetacean species along the Brazilian coast are threatened, particularly from fishing gear and vessel interactions, chemical and noise pollution. By applying the methods we have developed in the GEMM Lab during my PhD to cetacean conservation issues in Brazil, we could enable a great expansion in knowledge across many fields (i.e., endocrinology, behavior, photogrammetry, diet). Additionally, these skills can promote safer work environments (for the scientist and for the object of study) and cheaper work processes. However, many countries, such as Brazil, do not have the infrastructure and access to technologies to conduct these same analyses, as in developed countries like the USA. These technologies, when sold in Brazil, have many taxes on the top of the product that they can become an extra hurdle, due to budget constraints. Thus, there is a need for researchers to adapt these skills and technologies, in the best manner possible, to the reality of the country.

Now that I am starting to think about ‘life after PhD’, I can see myself returning to my country to spread the knowledge, technologies and skills I have gained through these years at OSU to new research projects so that I am able to assist with conservation efforts for the ocean and marine fauna in Brazil.

 

References:

PAN, 2010. Plano de ação nacional para a conservação dos mamíferos aquáticos: pequenos cetáceos / André Silva Barreto … [et al.]; organizadores Claudia Cavalcante Rocha-Campos, Ibsen de Gusmão Câmara, Dan Jacobs Pretto. – Brasília: Instituto Chico Mendes de Conservação da Biodiversidade, Icmbio, 132 p. Em: <http://www.icmbio.gov.br/portal/images/ stories/docs-plano-de-acao/pan-peqs-cetaceos/pan_pequenoscetaceos_web.pdf> Acessado em: 27 de Maio de 2015.

 

Dredging and low visibility doesn’t stop us! We paddle on.

By: Catherine Lo, Research Intern, Oregon State University ‘16

Hello everyone! My name is Catherine Lo and I am a recent graduate from Oregon State University with a Bachelor’s of Science in Biology with a focus in Marine Biology. It has been an incredible whirlwind leading up to this point: long nights studying for finals, completing my degree, and planning the next steps for my future. I am fortunate to be working as a summer research intern for the GEMM Lab under the supervision of Dr. Leigh Torres and Msc. student Florence Sullivan in their research on the foraging ecology of gray whales. I have dreamed of working with marine mammals, potentially as a research veterinarian and so, capturing this position has been a great opportunity to begin my career.

The days go slow, but the weeks go fast. It’s already week 4 of our field season and the team and I are definitely in the groove of our research. The alarm(s) goes off at 5:00 AM…okay maybe closer to 5:30 AM (oops!), getting dressed for either the kayak or cliff based work, scarfing down breakfast that is usually a diet consisting of toast and peanut butter, and then heading off to the beach to launch the kayak. But this week it was different. A dredging event in Port Orford coordinated by the US Army Corps of Engineers is now taking place right next to the port’s jetty near our study site (Figure 1). This is an important process to move the sediment built up during the year in order for ships to safely navigate in and out of the port. We knew this was going to happen at some point over the summer, and worried that it might impact our research methods and objectives, but at the same time it offers some new opportunities: the chance to see how our GoPro and mysid sampling methods in Tichenor Cove are impacted by the sediment flow from the dredging activities.

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Figure 1. View of the dredger from the cliff field site in Port Orford.

My teammate Kelli and I were stationed on the cliff during the first deposit of sediment after the dredge’s first night and morning’s worth of scooping sand. None of us knew where the actual deposit site would be so we kept a good eye on it. The ship headed past the jetty. Turned around and, as a concerned feeling mustered within our field team, it began lowering the platform holding the sand just 250 yards away from our primary study site in Tichenor Cove! At this point, we knew things were going to be different in our samples. Unfortunately along with the sediment stirring up from dredging, we think a phytoplankton bloom is occurring simultaneously. Our GoPro footage lately has been rather clouded making it difficult to identify any mysid relative to our past footage. You can compare Figure 2 to the GoPro image found in Figure 2 of a previous post. It is times like these that we learn how dynamic the ocean is, how human activity can alter the ocean ecosystem, and how to adapt to changes, whether these adaptations are within our reach or not. We are interested to see how our sample sites will change again over time as the dredging operation finishes and the phytoplankton bloom ends.

Figure 2. This GoPro image taken in Tichenor Cove illustrates exactly how murky our view of the water column is with the sediment dredging operation in close proximity.
Figure 2. This GoPro image taken in Tichenor Cove illustrates exactly how murky our view of the water column is with the sediment dredging operation in close proximity.

Aside from the current water clarity situation, we’ve also had some exciting moments! Given how few whales we’ve seen thus far and how the ones we have tracked are predominately hanging by Mill Rocks, which is ~1km east of Tichenor Cove, Dr. Leigh Torres—our head advisor—thought it would be a good idea to check out the mysid scene over there to see what the attraction was. So, we sent our kayak team over there to conduct a few GoPro drops and zooplankton net tows and figure out what is so enticing for the whales.

While conducting this sampling work at Mill Rocks, I and my teammate were lucky enough to encounter a gray whale foraging. And believe me, we were going “off-the-walls” as soon as we heard from the cliff team and saw a blow as the whale surfaced nearby. It was one of those “best time of my life” moments where my dreams of kayaking this close to a whale came true. We fumbled around for our waterproof camera to get clear shots of its lateral flanks for photo identification while also trying to contain our excitement to a more decent level, and at the same time we had to make sure we were not in the whale’s path. There it was; surface after surface, we admired the immense size and beauty of a wild animal before our eyes. The worst part of it was when our camera battery died not long after taking a few pictures, but in a way it gave us a chance to really appreciate the existence of these animals. Note to self during research: always check your batteries are fully charged before heading out!

It baffles me how so often people walk along beaches or drive by without knowing an animal as incredible as this whale is just outside of the shoreline. Every time I’m inside pulling out time stamps or doing photo identification, I always think, “I wonder if there’s a whale in Tichenor Cove or at Mill Rocks right now…Yeah, there probably is one”. Alas, the data management work needs to be done and there’s always the next day for an opportunity of a sighting.

For a few days, our kayak team wasn’t able to work due to a small craft advisory. If you’ve ever been to Port Orford, you’d understand the severity of how windy it gets here. Ranging between 15 knots to 25 knots as early as 7am, so it gets rather difficult to maintain position at each of our sampling stations in our kayak. Fortunately our cliff team was able to set out. We were lucky to see a small whale foraging inside Tichenor Cove and later move onto Mill Rocks. This little one was giving us quite a show! Almost every time it came to the surface, defecation was observed shortly after. As unpleasant as feces might be, it can actually provide an abundance of information about a specific whale including sex, reproductive status, hormone levels, and much more. While doing our research, we are always keeping an eye out for signs of defecation in order to collect samples for another lab member’s PhD work. Here you can check out more information about Leila’s research. Figure 3 depicts a great image of defecation captured by our cliff team.

Figure 3. Gray whale defecating as it dives into the water in Tichenor Cove.
Figure 3. Gray whale defecating as it dives into the water in Tichenor Cove.
Figure 4. Gray whale swimming in Tichenor Cove taken by fellow intern Cathryn Wood.
Figure 4. Gray whale swimming in Tichenor Cove taken by fellow intern Cathryn Wood.

In addition to helping out Leila’s work, we recently began a collaboration with Aaron Galloway from The Oregon Institute of Marine Biology (OIMB). Aaron and his post-doc are looking at the fatty acid composition of mysid as an approach to eventually infer the diet of an aquatic animal. Check out his website which is linked to his name to learn more about the basis of his approach! While we collect mysid samples for them, in return they give us substantial information about the energy content of the mysid. This information on the energetic content of mysid will help the GEMM Lab answer questions about how much mysid gray whales need to eat.

Oregon State University and University of Oregon have a long-standing, intense rivalry. However, as an Alumna from Oregon State, I am amazed and thrilled to see how these two institutions can come together and collaborate. I mean, we’re all here for the same thing. Science, right? It creates the opportunity to apply integrative research by taking advantage of various expertise and resources. If we have those chances to reach out to others, why not make the most of it? In the end, sound science is what really matters, not rooting for the ducks or beavers.

My marine science background is based on my experiences looking at tidepools and hopping around on rocks to understand how vast intertidal communities range from invertebrates to algae. These experiences were an incredible part of my life, but now I look at the ocean unsure of what animals or environmental situations I might encounter. That’s what makes it so attractive. Don’t get me wrong. The intertidal will always hold a special place in my heart, but the endless possibilities of being a part of this marine mammal research team is priceless. I have learned so much about myself including my strengths and weaknesses. Living in Port Orford, which is a small coastal town with just a little over 1,000 people gives you a new perspective. The community has been very welcoming and I have appreciated how so much interest is placed on the kind of work we do. As I eat my nightly bowl of ice cream, I think about how, from here on out, the good and the bad can only bring a lifetime of skills and memories.

Figure 5. Me being extremely happy to be out on the kayak on a beautiful morning.
Figure 5. Me being extremely happy to be out on the kayak on a beautiful morning.

 

 

 

 

 

 

From the highs to the lows, that’s just how it blows!

 

By: Kelli Iddings, MSc Student, Duke University, Nicholas School of the Environment

The excitement is palpable as I wait in anticipation. But finally, “Blow!” I shout as I notice the lingering spray of seawater expelled from a gray whale as it surfaces to breathe. The team and I scurry about the field site taking our places and getting ready to track the whale’s movements. “Gray whale- Traveling- Group 1- Mark!” I exclaim mustering enough self-control to ignore the urge to drop everything and stand in complete awe of what in my mind is nothing short of a miracle. I’ve spotted a gray whale searching and foraging for food! As a student of the Master of Environmental Management program at Duke University, I am collaborating on a project in Port Orford, Oregon where my team and I are working to gain a better understanding of the interactions between the Pacific Coast Feeding Group (PCFG) gray whales and their prey. Check out this blog post written earlier by my teammate Florence to learn more about the methods of the project and what motivated us to take a closer look at the foraging behavior of this species.

Understanding the dynamics of gray whale foraging within ecosystems where they are feeding is essential to paint a more comprehensive picture of gray whale health and ecology—often with the intent to protect and conserve them. A lot of our recent effort has been focused on developing and testing methods that will allow us to answer the questions that we are asking. For example, what species of prey are the PCFG whales feeding on in Port Orford? Based on the results of a previous study (Newell and Cowles 2006) that was conducted in Depoe Bay, Oregon, and a lot of great knowledge from the local fisheries and the Port Orford community, we hypothesized that the whales were feeding on a small, shrimp-like crustacean in the order Mysida. Given the results of our videos, and the abundance of mysid, it looks like we are right (Fig. 1)!

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Figure 1: Mysids, only 5-25mm in length, collected in Tichenor Cove using a downrigger to lower a weighted plankton net into the water column from our kayak.
Mysids are not typically the primary food source of gray whales. In their feeding grounds in the Bering and Chukchi Seas near Alaska, the whales feed on benthic amphipods on the ocean floor by sucking up sediment and water and pushing it through baleen plates that trap the food as the water and sediment is filtered out. However, gray whales demonstrate flexible feeding strategies and are considered opportunistic feeders, meaning they are not obligate feeders on one prey item like krill-dependent blue whales. In Oregon, mysid congregate in dense swarms by the billions, which we hypothesize, makes it energetically worthwhile for the massive 13-15m gray whales to hang around and feed! Figure 2 illustrates a mysid swarm of this kind in Tichenor Cove.

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Figure 2: Image captured using a Hero 4 Black GoPro. Rocky Substrate is visible in lower portion of image and a clear swarm of mysid is aggregated around this area.

Once we know what the gray whales are eating, and why, we ask follow up questions like how is the distribution of mysid changing across space and time, if at all? Are there patterns? If so, are the patterns influencing the feeding behavior and movement of the whales? For the most part, we are having success characterizing the relative abundances of mysid. No conclusions can be made yet, but there are a few trends that we are noticing. For instance, it seems that the mysid are, as we hypothesized, very dense and abundant around the rocky shoreline where there are kelp beds. Could these characteristics be predictors of critical habitat that whales seek as foraging grounds? Is it the presence of kelp that mysid prefer? Or maybe it’s the rocky substrate itself? Distance to shore? Time and data analysis will tell. We have also noticed that mysid seem to prefer to hang out closer to the bottom of the water column. Last, but certainly not least, we are already noticing differences in the sizes and life stages of the mysid over the short span of one week at our research site! We are excited to explore these patterns further.

The biggest thing we’re learning out here, however, is the absolute necessity for patience, ingenuity, adaptability, and perseverance in science. You heard that right, as with most things, I am learning more from our failures, than I am from our successes.  For starters, understanding mysid abundance and distribution is great in and of itself, but we cannot draw any conclusions about how those factors are affecting whales if the whales don’t come! We were very fortunate to see whales while training on our instruments in Newport, north of our current study site. We saw whales foraging, whales searching, mother/calf pairs, and even whales breaching! Since we’ve been in Port Orford, we have seen only three whales, thrown in among the long hours of womanpower (#WomenInScience) we have been putting in! We are now learning the realities of ecological science that >gasp< fieldwork can be boring! Nevertheless, we trust that the whales will hear our calls (Yes, our literal whale calls. Like I said, it can get boring up on the cliff) and head on over to give the cliff team in Port Orford some great data—and excitement!

Then, there is the technology. Oh, the joys of technology. You see I’ve never considered myself a “techie.” Honestly, I didn’t even know what a hard drive was until some embarrassing time in the not-so-distant past. And now, here I am working on a project that is using novel, technology rich approaches to study what I am most passionate about. Oh, the irony. Alas, I have been putting on my big girl britches, saddling up, and taking the whale by the fluke. Days are spent syncing a GoPro, Time-Depth Recorder (TDR), GPS, associated software, and our trusty rugged laptop, all the while navigating across multiple hard drives, transferring and organizing massive amounts of data, reviewing and editing video footage, and trouble shooting all of it when something, inevitably, crashes, gets lost, or some other form of small tragedy associated with data management. Sounds fun, right? Nonetheless, within the chaos and despair, I realize that technology is my friend, not my foe. Technology allows us to collect more data than ever before, giving us the ability to see trends that we could not have seen otherwise, and expending much less physical effort doing so. Additionally, technology offers many alternatives to other invasive and potentially destructive methods of data collection. The truth is if you’re not technologically savvy in science these days, you can expect to fall behind. I am grateful to have an incredible team of support and such an exciting project to soften the blow. Below (Fig. 3) is a picture of myself embracing my new friend technology.

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Figure 3: Retrieving the GoPro, and some tag-a-long kelp, from the water after a successful deployment in Tichenor Cove.

Last but not least, there are those moments that can best be explained by the Norwegian sentiment “Uff da!” I was introduced to the expression while dining at The Crazy Norwegian, known famously for having the best fish and chips along the entire west coast and located dangerously close to the field station. The expression dates back to the 19th century, and is used readily to concisely convey feelings of surprise, astonishment, exhaustion, and sometimes dismay. This past week, the team was witness to all of these feelings at once as our GoPro, TDR, and data fell swiftly to the bottom of the 42-degree waters of Tichenor cove after the line snapped during deployment. Uff da!!! With our dive contact out of town, red tape limiting our options, the holiday weekend looming ahead, and the dreadful thought of losing our equipment on a very tight budget, the team banded together to draft a plan. And what a beautiful plan it was! The communities of Port Orford, Oregon State University, and the University of Oregon’s Institute of Marine Biology came together in a successful attempt to retrieve the equipment. We offer much gratitude to Greg Ryder, our retrieval boat operator, OSU dive safety operator Kevin Buch, and our divers, Aaron Galloway and Taylor Eaton! After lying on the bottom of the cove for almost three days, the divers retrieved our equipment within 20 minutes of the dive – thanks to the quick and mindful action of our kayak team to mark a waypoint on the GPS at the time of the equipment loss. Please enjoy this shot (Fig. 4) of Aaron and Taylor surfacing with the gear as much as we do!

Figure 4: Aaron Galloway and Taylor Eaton surface with our lost piece of equipment after a successful dive retrieval mission.
Figure 4: Aaron Galloway and Taylor Eaton surface with our lost piece of equipment after a successful dive retrieval mission.

The moral of the story is that science isn’t easy, but it’s worth it. It takes hard work, long hours, frustration, commitment, collaboration, and preparedness. But moments come along when your team sits around a dining room table, exhausted from waking and paddling at 5 am that morning, and continues to drive forward. You creatively brainstorm, running on the fumes of the passion and love for the ocean and creatures within it that brought everyone together in the first place; each person growing in his or her own right. Questions are answered, conclusions are drawn, and you go to bed at the end of it all with a smile on your face, anxiously anticipating the little miracles that the next day’s light will bring.

References

Newell, C. and T.J. Cowles. (2006). Unusual gray whale Eschrichtius robustus feeding in the summer of 2005 off the central Oregon Coast. Geophysical Research Letters, 33:10.1029/2006GL027189