Building scientific friendships: A reflection on the 21st annual meeting of the Northwest Student Chapter of the Society for Marine Mammalogy

By Dawn Barlow, M.Sc. student, Department of Fisheries and Wildlife, Geospatial Ecology of Marine Megafauna Lab

I recently had the opportunity to attend and present my research at the 21st meeting of the Northwest Student Chapter of the Society for Marine Mammalogy. This gathering represented a community of graduate and undergraduate students from the Pacific Northwest, networking and discussing their research on the biology of marine mammals. Dr. John Ford, whose name has become synonymous with killer whale research in the Pacific Northwest, delivered a compelling keynote speech on not only the history of his research, but also the history of the relationships he has built in the field and the people that have shaped the past five decades of killer whale research. This theme of cultivating scientific relationships was a thread that carried us through the weekend. Beautiful weather had us all smiling happily as we ate our lunches outside, musing about science in the sunshine. A philosopher’s café event facilitated roundtable discussions with experts in veterinary science, spatial statistics, management consulting, physiology, and marine pollution. Students were given the space to ask questions ranging from manuscript writing advice to the worth of our work in the current political climate (and write notes or doodle drawings on the paper-covered tables as we listened).

The oral and poster presentations were all very impressive. I learned that bowhead whales are likely feeding year-round in the Canadian Arctic, adjusting their dive depth to the vertical location of their copepod prey. I learned that the aerobic dive limit of stellar sea lions is more of a sliding scale rather than a switch as it is for Weddell seals. I learned that some harbor seals are estuary specialists, feeding on salmon smolt. And I learned about the importance of herring to Northeast Pacific marine mammals through an energy-based ecosystem model. I had the opportunity to present my research on the ecology of New Zealand blue whales to an audience outside of Oregon State University for the first time, and was pleased with how my presentation was received.

Aaron Purdy, MSc student with the University of British Columbia’s Marine Mammal Research Unit, moderates the first oral presentation session wearing the designated “fluke tuke”. I may have giggled at the Canadian word for beanie, but I have to admit, “fluke tuke” has a much better ring to it than “fluke beanie”!

But beyond the scientific research itself, I also learned that there is a strong community of motivated and passionate young scientists in the Pacific Northwest studying marine mammals. Our numbers may not be many and we may be scattered across several different universities and labs, but our work is compelling and valuable. At the end of the weekend, it felt like I was saying goodbye to new friends and future colleagues. And, I learned that the magnificent size of a blue whale never fails to impress and amaze, as all the conference attendees marveled over the blue whale skeleton housed in the Beaty Biodiversity Museum at the University of British Columbia.

Left to right: Michelle Fournet, Samara Haver, myself, and Niki Diogou representing Oregon State University at the student conference. Behind us is a blue whale skeleton, housed in the Beaty Biodiversity Museum on the University of British Columbia campus.

Many thanks to the graduate students from the University of British Columbia who organized such a successful event! At the end of the conference, it was decided that the next meeting of the Northwest Student Chapter will be hosted by the Oregon State University students here at Hatfield Marine Science Center in Newport. It is a year away, but I am already looking forward to seeing these newfound peers again and hearing how their research has progressed.

A happy student selfie at the end of a successful conference! We are looking forward to a reunion at Hatfield Marine Science Center next May!

GEMM Lab 2016: A Year in the Life

By Dawn Barlow, MSc Student, Department of Fisheries and Wildlife, Oregon State University

The year is rapidly coming to a close, and what a busy year it has been in the Geospatial Ecology of Marine Megafauna Lab! In 2016, our members have traveled to six continents for work (all seven if we can carry Rachael’s South African conference over from the end of 2015…), led field seasons in polar, temperate, and tropical waters, presented at international conferences, processed and analyzed data, and published results. Now winter finds us holed up in our offices in Newport, and various projects are ramping up and winding down. With all of the recent turmoil 2016 has brought, it is a nice to reflect on the good work that was accomplished over the last 12 months. In writing this, I am reminded of how grateful I am to work with this talented group of people!

The year started with a flurry of field activity from our southern hemisphere projects! Erin spent her second season on the Antarctic peninsula, where she contributed to the Palmer Station Long Term Ecological Research Project.

Erin collecting a crabeater seal scat sample.
Erin in action collecting a crabeater seal scat sample along the West Antarctic Peninsula.


Aerial image of the research vessel and a pair of blue whales during the 2016 New Zealand survey.
Aerial image of the research vessel and a pair of blue whales during the 2016 New Zealand survey.

The New Zealand blue whale project launched a comprehensive field effort in January and February, and it was a fruitful season to say the least. The team deployed hydrophones, collected tissue biopsy and fecal samples, and observed whales feeding, racing and nursing. The data collected by the blue whale team is currently being analyzed to aid in conservation efforts of these endangered animals living in the constant presence of the oil and gas industry.

Midway atoll is home to one of the largest albatross colony in the world, and Rachael visited during the winter breeding season. In addition to deploying tracking devices to study flight heights and potential conflict with wind energy development, she became acutely aware of the hazards facing these birds, including egg predation by mice and the consumption of plastic debris.

Laysan albatross equipped with a GPS data logger.
Laysan albatross equipped with a GPS data logger.
Fledgling from last year with a stomach full of plastic.
Fledgling from last year with a stomach full of plastic.

Early summertime brought red-legged kittiwakes to the remote Pribilof Islands in Alaska to nest, and Rachael met them there to study their physiology and behavior.

Rachael with a noosepole on St. George Island, Alaska
Rachael with a noosepole on St. George Island, Alaska
Solene with Dr. Claire Garrigue during fieldwork at the Chesterfield Reefs, New Caledonia.
Solene with Dr. Claire Garrigue during fieldwork at the Chesterfield Reefs, New Caledonia.

As the weather warmed for us in the northern hemisphere, Solene spent the austral winter with the humpback whales on their breeding grounds in New Caledonia. Her team traveled to the Chesterfield Reefs, where they collected tissue biopsy samples and photo-IDs, and recorded the whale’s songs. But Solene studies far more than just these whales! She is thoroughly examining every piece of environmental, physical, and oceanographic data she can get her hands on in an effort to build a thorough model of humpback whale distribution and habitat use.

A humpback whale in New Caledonia's South Lagoon.
A humpback whale in New Caledonia’s South Lagoon.

Summertime came to Oregon, and the gray whales returned to these coastal waters. Leigh, Leila, and Todd launched into fieldwork on the gray whale stress physiology project. The poop-scooping, drone-flying team has gotten a fair bit of press recently, follow this link to listen to more!

The overhead drone captures a pair of gray whales surfacing between kelp beds off Cape Blanco, Oregon, with the research vessel nearby. Take under NOAA/NMFS permit #16111 given to John Calambokidis.
The overhead drone captures a pair of gray whales surfacing between kelp beds off Cape Blanco, Oregon, with the research vessel nearby. Take under NOAA/NMFS permit #16111 given to John Calambokidis.

And while Leigh, Leila, and Todd followed the grays from the water, Florence and her team watched them from shore in Port Orford, tracking their movement and behavior. In an effort to gain a better understanding of the foraging ecology of these whales, Florence and crew also sampled their mysid prey from a trusty research kayak.

Florence and the summer 2016 gray whale field team.
Kelli Iddings sampling mysid near Port Orford.

With the influx of gray whales came an influx of new and visiting GEMM Lab members, as Florence’s team of interns joined for the summer season. I was lucky enough to join this group as the lab’s newest graduate student!

All summer 2016 GEMM Lab members.
All of the summer 2016 GEMM Lab members.

Our members have presented their work to audiences far and wide. This summer Leigh, Amanda, and Florence attended the International Marine Conservation Congress, and Amanda was awarded runner-up for the best student presentation award! Erin traveled to Malaysia for the Scientific Convention on Antarctic Research, and Rachael and Leigh presented at the International Albatross and Petrel Conference in Barcelona. With assistance from Florence and Amanda, Leigh led an offshore expedition on OSU’s research vessel R/V Oceanus to teach high school students and teachers about the marine environment.

Amanda with her award!
Amanda with her award!
Science Party musters in the dry lab for safety debrief aboard R/V Oceanus.
Science Party musters in the dry lab for safety debrief aboard R/V Oceanus.

Courtney fledged from the GEMM Lab nest before 2016 began, but the work she did while here was published in Marine Mammal Science this year. Congrats Courtney! And speaking of publications, additional congratulations to Solene for her publication in Marine Ecology Progress Series, Rachael for her four publications this year in PLOS ONE, Marine Ecology Progress Series, Marine Ornithology, and the Journal of Experimental Biology, and Leigh for her five publications this year in Polar Biology, Diversity and Distributions, Marine Ecology Progress Series, and Marine Mammal Science!

Wintertime in Newport has us tucked away indoors with our computers, cranking through analyses and writing, and dreaming about boats, islands, seabirds, and whales… Solene visited from the South Pacific this fall, and graced us with her presence and her coding expertise. It is a wonderful thing to have labmates to share ideas, frustrations, and accomplishments with.

No heat in the lab can't stop us from solving a coding problem together on a wintery evening!
Solving a coding problem together on a wintery evening.

As the year comes to a close, we have two newly-minted Masters of Science! Congratulations to Amanda and Erin on successfully defending their theses, and stay tuned for their upcoming publications!

Amanda's post-defense celebration!
Amanda’s post-defense celebration!
Erin's post-defense celebration!
Erin’s post-defense celebration!

We are looking forward to what 2017 brings for this team of marine megafauna enthusiasts. Happy holidays from the GEMM Lab!

Happy GEMM Lab members.
Happy GEMM Lab members, enjoying one another’s company and playing Evolution.

Challenges of fecal analyses (Round 1)

By Leila Lemos, Ph.D. Student, Department of Fisheries and Wildlife, OSU

Fieldwork is done for the year and lab analyses just started with some challenges. This is not unexpected since no previous hormonal analysis has been conducted with any gray whale tissue, and whale fecal sample analysis is a relatively new technique. So, I have been thinking, learning, consulting, and creating a methodology as I go along. I am grateful to the expert advice and help from many great collaborators:

  • Kathleen Hunt (Northern Arizona University, AZ, United States)
  • Shawn Larson (Seattle Aquarium, WA, United States)
  • Amy Green (Seattle Aquarium, WA, United States)
  • Rachel Ann Hauser-Davis (Fiocruz, RJ, Brazil)
  • Maziet Cheseby (Oregon State University, OR, United States)
  • Scott Klasek (Oregon State University, OR, United States)

I have learned that an important step before undertaking fecal a hormonal analysis is the desalting process of the samples since salts can interfere in hormonal determinations, leading to false results. In order to remove salt content, each sample was first filtered (Fig. 1A), to remove a majority of the salt water content (Fig. 1B) that is inevitably collected along with the fecal sample. Each sample was then re-suspended in ultra-pure water, to dilute the remaining salt content in a higher water volume (Fig. 1C).

Figure 1: Analytical processes: (A) Filtration of the samples; (B) Result from filtration; (C) Addition of pure water to the samples.
Figure 1: Analytical processes: (A) Filtration of the samples; (B) Result from filtration; (C) Addition of pure water to the samples.

After these steps were completed for each sample, the samples were centrifuged (Fig. 2A) to  precipitate the fecal matter and leave the lighter salt ions in the supernatant (the liquid lying above a solid residue; Fig. 2B). After finishing these two phases, the water was removed with aid of a plastic pippete (Fig. 2C), and I was left with only desalted fecal at the bottom of the tubes (Fig. 2D).

Figure 2: Analytical processes: (A) Samples centrifugation; (B) Result from the centrifugation; (C, D) Results from separating water and sample.
Figure 2: Analytical processes: (A) Samples centrifugation; (B) Result from the centrifugation; (C, D) Results from separating water and sample.

The fecal samples were then frozen at -80°C (Fig. 3A & 3B) and then freeze-dried on a lyophilizer for 2 days to remove all remaining water content (Fig. 3C). Finally, I have what I need: desalted, dry fecal samples, ready for hormone analysis (Fig. 3D).

Figure 3: Analytical processes: (A) Freezing process of the samples; (B) Frozen samples ready to go to the lyophilizer; (C) Samples in the lyophilizer; (D) Final result of the lyophilizing process.
Figure 3: Analytical processes: (A) Freezing process of the samples; (B) Frozen samples ready to go to the lyophilizer; (C) Samples in the lyophilizer; (D) Final result of the lyophilizing process.

Writing this now, this process seems simple, but it was laborious, and took time to find the equipment needed at the right times. The end product is crucial to get a good final result, so my time investment (and my own increased stress level!) was worth it. This type of analysis is very new for marine mammals and our research lab is still in the learning the best methods. Along the way we were unsure of some decisions, some mistakes were made, and we were afraid of losing precious fecal material. But, this is the fun and challenge of working with a new species and new type of sample and, importantly, we have developed a working protocol that should make the process more efficient and reduce our stress levels next time around.

At the end of this sample preparation process, our 53 samples look great and are ready to be analyzed during my training at the Seattle Aquarium. We are also planning to analyze the water that was removed from the samples (Fig. 2D) to see if any hormone leached out from the poop into the water.

Results from this process will aid in future whale fecal hormone studies. Perhaps only the centrifugation step is needed and we can discard the water without losing hormone content. Or, perhaps we need to analyze both portions of the sample and sum the hormones found in each. We shall know the answer when we get our hormone metabolite results. Just another protocol to be worked out as I move ahead with the hormone analysis of these fecal samples. And through all these challenges I keep the end goal of this work in my mind: to learn about the reproductive and stress hormonal variation in gray whales and to link these variations to nutritional status and noise events. Onward!




Making a Splash

By: Cathryn Wood, Lawrence University ’17, summer REU in the GEMM Lab

Greetings from Port Orford! My name is Cathryn, and I am the fourth member of the GEMM Lab’s gray whale foraging ecology research team, which includes Florence, Kelli, and the other Catherine (don’t worry, I go by Cat). Nearly 5 weeks into field season, I am still completely amazed with my first West Coast experience and doing what I’ve always dreamt of: studying marine mammals. Coming from Michigan’s Upper Peninsula, this may seem slightly out of place, but my mom can attest; she read “Baby Beluga” to me every night when I was a toddler. Now a rising senior majoring in biology at Lawrence University, I’ve been focusing my coursework on aquatic and marine ecology to prepare for graduate school where I plan to specialize in marine science. Being part of this research is a very significant step for me into the field.

So how did I end up here, as part of this amazing project and dream, women-in-science team? I am interning through OSU’s Ocean Sciences REU program at the Hatfield Marine Science Center, where the GEMM Lab is located. REU stands for “Research Experience for Undergraduates ”, and is an NSF-funded research internship program found in numerous universities around the country. These internships allow undergrads to conduct independent research projects under the guidance of a faculty mentor at the program’s institution. I applied to several REUs this past winter, and was one of 12 undergrads accepted for the program at HMSC. Each of us is paired with different faculty members to work on various projects that cover a diverse range of topics in the marine sciences; everything from estuarine ecology, to bioacoustics. I was ecstatic to learn that I had been paired with Dr. Torres as my faculty mentor to work on Florence’s gray whale project, which had been my first choice during the application process.

My particular research this summer is going to complement Florence’s master’s thesis work by asking new questions regarding the foraging data. While her project focuses on the behavioral states of foraging whales, I will be looking at the whale tracks to see if there are patterns in their foraging behavior found at the individual level. Traditionally, ecological studies have accepted classical niche theory, treating all individuals within a population as ecological equivalents with the same niche width. Any variances present among individuals are often disregarded as having an insignificant consequence on the population dynamics as a whole, but this simplification can overlook the true complexity of that population . The presence of niche variation among conspecifics is known to occur in at least 93 species across a diverse array of taxa, so the concept of individual specialization, and how it can affect ecological processes is gaining recognition progressively in the field (Bolnick et al., 2003). My goal is to determine whether or not the gray whales in this study, and presumably others in the Pacific Coast Feeding Group (PCFG), exhibit individual specialization in their foraging strategies . There are many ways in which individuals can specialize in foraging, but I will be specifically determining if fine scale spatial patterns in the location of foraging bouts exists, regardless of time.

To address my question, I am using the whale tracking data from both 2015 and 2016, and learning to use some very important software in the spatial ecology world along the way through a method that Dr. Torres introduced to me. Starting in ArcGIS, I generate a kernel density layer of a raw track (Fig. 1 ), which describes the relative distribution of where the tracked whale spent time (Fig. 2 ). Next, using the isopleth function in the software Geospatial Modelling Environment, I generate a 50% density contour line that distinguishes where the whale spent at least 50% of its time during the track (Fig. 3 ). Under the assumption that foraging took place in these high density areas, we use these 50% contour lines to describe foraging bout locations. I now go back to ArcGIS to make centroids within each 50% line, which mark the exact foraging bout locations (Fig. 4 ).

Fig.1 Raw individual whale track.
Fig. 1 Raw individual whale track.
Fig. 2 Kernel Density map of whale track.
Fig. 2 Kernel Density map of whale track.
Fig. 3 50% isopleth contours of locations with highest foraging densities
Fig. 3 50% isopleth contours of locations with highest foraging densities
Fig. 4 Final centroids to signify foraging bouts
Fig. 4 Final centroids to signify foraging bouts

These centroids will be determined for every track by an individual whale, and then compared relative to foraging locations of all tracked whales to determine if the individual is foraging in different locations than the population. Then, the tracks of individuals who repeatedly visit the site at least three times will be compared with one another to determine if the repeat whales show spatial and/or temporal patterns in their foraging bout locations, and if specialization at a fine scale is occurring in this population. If you did not quite follow all those methods, no worries, it was a lot for me to take in at first too. I’ve finally gotten the hang of it though, and am grateful to now have these skills going into grad school.

Because I am interested in behavioral ecology and the concept of individuality in animal populations, I am extremely excited to see how this research plays out. Results could be very eye-opening into the fine scale foraging specialization of the PCFG sub-population because they already demonstrate diet specialization on mysid (as opposed to their counterparts in the Bering Sea who feed on benthic organisms) and large scale individual residency patterns along the Pacific Northwest (Newell, 2009; Calambokidis et al., 2012). Most significantly, understanding how individuals vary in their feeding strategies could have very important implications for future conservation measures for the whales, especially during this crucial foraging season where they replenish their energy reserves.  Management efforts geared for an “average population” of gray whales could ultimately be ineffective if in fact individuals vary from one another in their foraging strategies. Taking into account the ways in which variation occurs amongst individuals is therefore crucial knowledge for successful conservation approaches.

My project is unique from those of the other REUs because I am simultaneously in the midst of assisting in field season number two of Florence’s project. While most of the other interns are back at Hatfield spending their days in the lab and doing data analyses like a 9-5 job, I am with the team down in Port Orford for field season. This means we’re out doing research every dawn as weather allows. Though I may never have an early bird bone in my body, the sleepy mornings are totally worth it because ecology field work is my favorite part of research. To read more about our methods in the field, check out Florence’s post.

Since Catherine’s last update, we’ve had an eventful week. To our dismay, Downrigger Debacle 2.0 occurred. (To read about the first one, see Kelli’s post). This time it was not the line – our new line has been great. It was a little wire that connected the downrigger line to the pipe that the GoPro and TDR are connected to. It somehow snapped due to what I presume was stress from the currents.   Again, it was Catherine and I in the kayak, with a very successful morning on the water coming to a close when it happened. Again, I was in the bow, and she was in the stern deploying the equipment – very déjà vu. When she reeled in an equipment-less line, we at first didn’t know how to break it to Florence and Kelli who were up on the cliff that day. Eventually, Catherine radioed “Brace yourselves…” and we told them the bad news. Once again, they both were very level-headed, methodical, and un-blaming in the moments to follow. We put together the same rescue dive team as last time, and less than a week later, they set off on the mission using the GPS coordinates I had marked while in the kayak. Apparently, between the dredging taking place in the harbor and the phytoplankton bloom, visibility was only about 2 feet during the dive, but they still recovered the equipment, with nothing but baked goods and profuse thanks as payment. We are very grateful for another successful recovery, and are confident that our new attachment mechanism for the downrigger will not require a third rescue mission (Fig. 6-8). Losing the equipment twice now has taught us some very important things about field work. For one, no matter how sound you assume your equipment to be, it is necessary to inspect it for weak points frequently – especially when salt water and currents are in the picture. Perhaps even more importantly, we’ve gotten to practice our problem solving skills and see firsthand how necessary it is to act efficiently and calmly when something goes wrong. In ecological field research you have to be prepared for  anything.

Fig. 5 Original setup of GoPro and TDR.
Fig. 5 Original setup of GoPro and TDR.
Fig. 6 Photo taken after the wire that connected the pole to the downrigger line snapped.
Fig. 6 Photo taken after the wire that connected the pole to the downrigger line snapped.
Fig. 7 New mechanism for attaching the pole to the downrigger line.
Fig. 7 New mechanism for attaching the pole to the downrigger line.
Fig. 8 Equipment rescue team: Aaron Galloway and Taylor Eaton diving, Greg Ryder operating the boat, and Florence on board to direct the GPS location of where the equipment was lost.
Fig. 8 Equipment rescue team: Aaron Galloway and Taylor Eaton diving, Greg Ryder operating the boat, and Florence on board to direct the GPS location of where the equipment was lost.

In other news, unlike our slow-whale days during the first two weeks of the project, we have recently had whales to track nearly every day from the cliff! In fact, the same, small, most likely juvenile, whale pictured in Catherine’s last post has returned several times, and we’ve nicknamed her “Buttons” due to two distinguishing white spots on her tail peduncle near the fluke. Though we tend to refer to Buttons as “her”, we cannot actually tell what the sex is definitively…until now. Remember in Catherine’s post when she described how Buttons defecated a lot, and how our team if, given the opportunity, is supposed to collect the feces when we’re out in the kayak for Leila’s project?  Everything from hormone levels to reproductive status to, yes, sex, is held in that poop! Well, Miss (or Mr.) Buttons was in Tichenor Cove today, and to our delight, she performed well in the defecation department once again. Florence and I were on cliff duty tracking her and Kelli and Catherine were in Tichenor on the kayak when we first noticed the defecation.  I then radioed down to the kayak team to stop what they were doing and paddle quickly to go collect it before it sank (Fig. 9).  Even in these situations, it is important to stay beyond 100 yards of the animal, as required by the MMPA. Florence and I cheered them on and our ladies did indeed get the poop sample, without disturbing the whale (Fig. 10). It was a sight to behold.

Fig. 9 Kelli and Catherine on a mission.
Fig. 9 Kelli and Catherine on a mission.
Fig. 10 Kelli and Catherine collecting the feces.
Fig. 10 Kelli and Catherine collecting the feces.

We were able to track Buttons for the remainder of our time on the cliff, and were extremely content with the day’s work as we packed all the gear up later in the afternoon. Right before we were about to leave, however, Buttons had one more big treat for us. As we looked to the harbor before starting the trek back to the truck, we paused briefly after noticing a large, white splash in the middle of the harbor, not far from the dock. We paused for a second and thought “No, it can’t be, was that —?” and then we see it again and unanimously yelled “BREACH!” Buttons breached about five times on her way back to Tichenor Cove from where she had been foraging in Mill Rocks. It is rare to see a gray whale breach, so this was really special. Florence managed to capture one of the breaches on video:

At first I thought a big ole humpback had arrived, but nope, it was our Buttons! I am in awe of this little whale, and am forever-grateful to be in the presence of these kinds of moments. She’s definitely made her splash here in Port Orford. I think our team has started to as well.


Bolnick, D. I., Svanback, R., Fordyce, J. A., Yang, L. H., Davis, J. M., Hulsey, C. D., & Forrister, M. L. (2003). Ecology of Individuals: Incidence and Implications of Individual Specialization. The American Naturalist, 161(1), 28.

Calambokidis, J., Laake, J. L., & Klimek, A. (2012). Updated analysis of abundance and population structure of seasonal gray whales in the Pacific Northwest, 1998-2010 (Vol. 2010).

Newell, C. (2009). Ecological Interrelationships Between Summer Resident Gray Whales (Eschrichtius robustus) and Their Prey, Mysid Shrimp (Holmesimysis sculpta and Neomysis rayi) along the Central Oregon Coast.








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.

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)!

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.

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.

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.


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

The Gray [Whale]s are back in town – Field season 2016 is getting started!

By Florence Sullivan – MSc Student, GEMM Lab

Hello Everyone, and welcome back for season two of our ever-expanding research project(s) about the gray whales of the Oregon coast!

Overall, our goal is document and describe the foraging behavior and ecology of the Pacific Coast Feeding Group of Gray Whales on the Oregon Coast. For a quick recap on the details of this project read these previous posts:

During this summer season, the newest iteration of team ro”buff”stus will be heading back down to Port Orford, Oregon to try to better understand the relationship between gray whales and their mysid prey. Half the team will once again use the theodolite from the top of Graveyard Point to track gray whales foraging in Tichenor Cove, the Port of Port Orford, and the kelp beds near Mill Rocks.  Meanwhile, the other half of the team will use the R/V Robustus (i.e. a tandem ocean kayak named after our study species – Eschrichtius robustus, the gray whale) to repeatedly deploy a GoPro camera at several sampling locations in Tichenor cove. We hope that by filming vertical profiles of the water column, we will be able to create an index of abundance for the mysid to describe their temporal and spatial distribution of their swarms.  We’re particularly interested in the differences between mysid swarm density before and after a whale forages in an area, and how whale behaviors might change based on the relative density of the available prey.

The GEMM lab's new research vessel being launched on her maiden voyage.
Ready to take the R/V Robustus out for her maiden voyage in Port Orford to test some of our new equipment. photo credit: Leigh Torres

In theory, asking these questions seems simple – get in the boat, drop the camera, compare images to the whale tracklines, get an answer!  In reality, this is not the case. A lot of preparatory work has been going on behind the scenes over the last six months. First, we had to decide what kind of camera to use, and decide what sort of weighted frame to build to get it to sink straight to the bottom. Then came the questions of deployment by hand versus using a downrigger,

Example A why it is a bad idea to try to sample during a diatom bloom.
Example A why it is a bad idea to try to sample during a diatom bloom – You can’t see anything but green.

what settings to use on the camera, how fast to send it down and bring it back up, what lens filters are needed (magenta) and other logistical concerns. (Huge thank you to our friends at ODFW Marine Reserves Program for the help and advice they provided on many of these subjects.) We spent some time in late May testing our deployment system, and quickly discovered that sampling during a diatom bloom is completely pointless because visibility is close to nil.

However, this week, we were able to test the camera in non-bloom conditions, and it works!  We were able to capture images of a few small mysid swarms very near the bottom of the water column, and we didn’t need external lights to do it. We were worried that adding extra lights would artificially attract mysid to the camera, and bias our measurements, as well as potentially disturbing the whale’s foraging behavior. (Its also a relief because diving lights are expensive, and would have been one more logistical thing that could go wrong. General advice: Always follow the KISS method when designing a project – keep it simple, ——!)


This image is taken at a depth of ~10 meters, with no color corrective filter on the lens
This image is taken at a depth of ~10 meters, with no color corrective filter on the lens – notice how blurry the mysid are.
This is empty water, in the mid water column
This is empty water, in the mid water column
More Mysid! This time with a Magenta filter on the lens to correct the colors for us.
Much clearer Mysid! This time with a magenta filter on the lens to correct the colors for us.

My advisor recently introduced me to the concept of the “7 Ps”; Proper Prior Planning Prevents Piss Poor Performance.  To our knowledge, we are the first group to try to use GoPro cameras to study the spatial and temporal patterns of zooplankton aggregations. With new technology comes new opportunities, but we have to be systematic and creative in how we use them. Trial and error is an integral part of developing new methods – to find the best technique, and so that our work can be replicated by others. Now that we know the GoPro/Kayak set-up is capable of capturing useable imagery, we need to develop a protocol for how to process and quantify the images, but that’s a work in progress and can wait for another blog post.   Proper planning also includes checking last year’s equipment to make sure everything is running smoothly, installing needed computer programs on the new field laptop, editing sampling protocols to reflect things that worked well last year, and expanding the troubleshooting appendixes so that we have a quick reference guide for when things go wrong in the field.  I am sure that we will run into more weird problems like last year’s “Chinese land whale”, but I also know that we would have many more difficulties if we had not been planning this field effort for the last several months.

Planning our sampling pattern in Tichenor Cove
Planning our sampling pattern in Tichenor Cove.

Team Ro”buff”stus is from all over the place this year – we will have members from Oregon, North Carolina and Michigan – and we are all meeting for the first time this week.  The next two weeks are going to be a whirlwind of introductions, team bonding, and learning how to communicate effectively while using the theodolite, our various computer programs, GoPro, Kayak, and more!  We will keep the blog updated with our progress, and each team member will post at least once over the course of the summer. Wish us luck as we watch for whales, and feel free to join in the fun on pretty much any cliff-side in Oregon (as long as you’ve got a kelp bed nearby, chances are you’ll see them!)

How can we reconstruct life-history pathways of whales?

By Leila Lemos, Ph.D. Student, Department of Fisheries and Wildlife, OSU


Have you ever heard of statistical modeling? What about Hierarchical Bayes Models?

Hard words, I know…

Modeling is when known data (previously collected) is analyzed using sophisticated computer algorithms to look for patterns in these data. Models can be very useful for filling in data gaps where and when no sampling occurred. Hierarchical Bayes model is a type of statistical model that hierarchically integrates the observed data to estimate parameters. This type of model can analyze long-term data from individual animals to predict into data gaps and inform us about population dynamics.

When studying wild animals we often only collect data from brief and random encounters. Therefore, many researchers struggle with the reconstruction of possible pathways that could connect different sightings of wild animals to determine where, when and how the animal was doing in between sightings.

For instance, consider an animal that was observed in healthy condition at one sighting but in a subsequent sighting it was in poor health. How can we estimate what happened to this animal between sightings? Can we estimate where, when and how health deteriorated?

This is where the modeling comes in! It is a powerful tool used by many researchers to fill in gaps in our scientific knowledge using data that we do have. We use these ‘known data’ to estimate patterns and determine probabilities. The hierarchical Bayes model is a type of modeling that can be used to estimate the probability of pathways between known events. Schick et al. (2013) used hierarchical Bayes models to estimate the many factors that impact whale health and survivorship including distribution and movement patterns, true health condition of the individual and survival rates.

Modeling is very advantageous when studying aquatic animals like dolphins and whales that are very hard to spot since they spend a higher proportion of their lives submerged than above water. Also, sea conditions can hamper visual detection.

Schick et al. (2013) analyzed decades of data from photo-identifications of North Atlantic right whale resightings along the east coast of North America. They assessed different information from these pictures including body condition, infestation of cyamids, presence of fishing gear entanglements, rake marks and skin condition. The authors also used information of age and calving of the individuals. A model using these data was constructed and a more complete scenario of health and movement patterns of individuals and the populations were estimated. Survival rates of each individual were also estimated using this model. This is an example of a well-informed model and is important to notice that a model is only as good as the data you put into the model.

Using this model, Schick et al. documented variations in annual spatial distribution patterns between sexes (Fig. 1). For example, females arrive earlier to the BOF region than males, and have greater estimated transitions to SEUS region at the end of the year. It is also possible to see that there is a lack of information for the region MIDA, characterizing another advantage of modeling since it can highlight areas where effort should be increased.

Figure 1: Movement transition estimates from North to South regions in the western Atlantic Ocean for male and female right whales over the course of a year. Size of the circles in each region at each month corresponds to the actual number of right whales observed. Lines connecting regions indicate probability of transition. Magnitude of probability is depicted by line thickness. (NRTH: North region; BOF: Bay of Fundy; JL: Jeffreys Ledge; GOM: Gulf of Maine; RB: Roseway Basin; NE: Northeast; GSC: Great South Channel; MIDA: Mid-Atlantic; and SEUS: Southeastern US). Source: Figures 5 and 6 from Schick et al. 2013.
Figure 1: Movement transition estimates from North to South regions in the western Atlantic Ocean for male and female right whales over the course of a year. Size of the circles in each region at each month corresponds to the actual number of right whales observed. Lines connecting regions indicate probability of transition. Magnitude of probability is depicted by line thickness.
(NRTH: North region; BOF: Bay of Fundy; JL: Jeffreys Ledge; GOM: Gulf of Maine; RB: Roseway Basin; NE: Northeast; GSC: Great South Channel; MIDA: Mid-Atlantic; and SEUS: Southeastern US).
Source: Figures 5 and 6 from Schick et al. 2013.


When the model is applied to individual whales, the authors were able to estimate survival and health rates across the whale’s life-span (Fig. 2). Whale #1077 was a rarely seen adult male, with a sparse sighting history over 25 years. The last sighting of this whale was in 2004 when its health status was poor due to a poor body condition. According with his condition in the last sighting, the model predicted a high decrease in his health over time and since the whale was not seen for more than six years, so was presumed dead, following the standards set by the North Atlantic Right Whale Consortium.

Figure 2: Health time series for whale #1077. Time series of health observations for body condition, cyamids, entanglements, rake marks and skin condition (circles), estimates with uncertainty of health (thick line and dashed lines) and estimates of survivals (height rectangle at bottom). Photographic observations are color and size coded by class (three categories for body condition: green is good, orange is fair and purple is poor; and two categories for skin condition: green is good and orange is poor). Source: Figure 11 from Schick et al. 2013.
Figure 2: Health time series for whale #1077. Time series of health observations for body condition, cyamids, entanglements, rake marks and skin condition (circles), estimates with uncertainty of health (thick line and dashed lines) and estimates of survivals (height rectangle at bottom). Photographic observations are color and size coded by class (three categories for body condition: green is good, orange is fair and purple is poor; and two categories for skin condition: green is good and orange is poor).
Source: Figure 11 from Schick et al. 2013.


As I begin data collection for my thesis project to examine gray whale health along the Oregon coast in relation to ocean noise and inter-annual variability, I am considering how to apply a similar modeling approach to enhance our understanding of what influences individual gray whale health and also connect pathways between our resightings.

The marine environment is constantly changing, across space and over time. Therefore, distinguishing what contributes most significantly to whale stress levels can be very challenging. However, through a model we may be able to decipher the contributions of several factors to individual stress among the many parameters we are monitoring: ocean noise, prey availability, environmental patterns, season, sex, age, geographic area, reproductive status and body condition.

Marine ecology is a complex world, and sometimes complex models are needed to help us to find patterns in our data! Once estimates of these ecological processes are created and different hypotheses are explored, information can then be provided to conservation and environmental management to aid decision making, such as defining thresholds of ambient ocean noise levels in the vicinity of baleen whales.


Bibliographic Reference:

Schick RS, Kraus SD, Rolland RM, Knowlton AR, Hamilton PK, Pettis HM, Kenney RD and Clark JS. 2013. Using Hierarchical Bayes to Understand Movement, Health, and Survival in the Endangered North Atlantic Right Whale. PLOS ONE 8(6):e64166.

Grad School Headaches

By Florence Sullivan, MSc student GEMM lab

Over the past few months I have been slowly (and I do mean SLOWLY – I don’t believe I’ve struggled this much with learning a new skill in a long, long time) learning how to work in “R”.  For those unfamiliar with why a simple letter might cause me so much trouble, R is a programming language and free software environment suitable for statistical computing and graphing.

My goal lately has been to interpolate my whale tracklines (i.e. smooth out the gaps where we missed a whale’s surfacing by inserting artificial locations).  In order to do this I needed to know (1) How long does a gap between fixes need to be to identify a missed surfacing? (2) How many artificial points should be used to fill a given gap?

The best way to answer these queries was to look at a distribution of all of the time steps between fixes.  I started by importing my dataset – the latitude and longitude, date, time, and unique whale identifier for each point (over 5000 of them) we recorded last summer. I converted the locations into x & y coordinates, adjusted the date and time stamp into the proper format, and used the package adehabitatLT  to calculate the difference in times between each fix.  A package known as ggplot2 was useful for creating exploratory histograms – but my data was incredibly skewed (Fig 1)! It appeared that the majority of our fixes happened less than a minute apart from each other. When you recall that gray whales typically take 3-4 short breathes at the surface between dives, this starts to make a lot of sense, but we had anticipated a bimodal distribution with two peaks: one for the quick surfacings, and one for the surfacings between 4-5 minutes dives. Where was this second peak?

Histogram of the difference in time (in seconds) between whale fixes.
Fig. 1.  Histogram of the difference in time (in seconds on x-axis) between whale fixes.

Sometimes, calculating the logarithm of one of your axes can help tease out more patterns in your data  – particularly in a heavily skewed distribution like Fig. 1. When I logged the time interval data, our expected bimodal distribution pattern became evident (Fig. 2). And, when I back-calculate from the center of the two peaks we see that the first peak occurs at less than 20 seconds (e^2.5 = 18 secs) representing the short, shallow blow intervals, or interventilation dives, and that the second peak of dives spans ~2.5 minutes to  ~5 minutes (e^4.9 = 134 secs, e^5.7 = 298 secs). Reassuringly, these dive intervals are in agreement with the findings of Stelle et al. (2008) who described the mean interval between blows as 15.4 ± 4.73 seconds, and overall dives ranging from 8 seconds to 11 minutes.

Fig. 2. Histogram of the log of time difference between whale fixes.
Fig. 2. Histogram of the log of time difference between whale fixes.

So, now that we know what the typical dive patterns in this dataset are, the trick was to write a code that would look through each trackline, and identify gaps of greater than 5 minutes.  Then, the code calculates how many artificial points to create to fill the gap, and where to put them.

Fig. 3. A check in my code to make sure the artificial points are being plotted correctly. The blue points are the originals, and the red ones are new.
Fig. 3. A check in my code to make sure the artificial points are being plotted correctly. The blue points are the originals, and the red ones are new.

One of the most frustrating parts of this adventure for me has been understanding the syntax of the R language.  I know what calculations or comparisons I want to make with my dataset, but translating my thoughts into syntax for the computer to understand has not been easy.  With error messages such as:

Error in match.names(clabs, names(xi)) :

  names do not match previous names

Solution:  I had to go line by line and verify that every single variable name matched, but turned out it was a capital letter in the wrong place throwing the error!

Error in as.POSIXct.default(time1) :

  do not know how to convert ‘time1’ to class “POSIXct”

Solution: a weird case where the data was in the correct time format, but not being recognized, so I had to re-import the dataset as a different file format.

Error in data.frame(Whale.ID = Whale.ID, Site = Site, Latitude = Latitude,  :   arguments imply differing number of rows: 0, 2, 1

Solution: HELP! Yet to be solved….

Is it any wonder that when a friend asks how I am doing, my answer is “R is kicking my butt!”?

Science is a collaborative effort, where we build on the work of researchers who came before us. Rachael, a wonderful post-doc in the GEMM Lab, had already tackled this time-based interpolation problem earlier in the year working with albatross tracks. She graciously allowed me to build on her previous R code and tweak it for my own purposes. Two weeks ago, I was proud because I thought I had the code working – all that I needed to do was adjust the time interval we were looking for, and I could be off to the rest of my analysis!  However, this weekend, the code has decided it doesn’t work with any interval except 6 minutes, and I am lost.

Many of the difficulties encountered when coding can be fixed by judicious use of google, stackoverflow, and the CRAN repository.

But sometimes, when you’ve been staring at the problem for hours, what you really need is a little praise for trying your best. So, if you are an R user, go download this package: praise, load the library, and type praise() into your console. You won’t regret it (See Fig. 4).

Screenshot (74)
Fig. 4. A little compliment goes a long way to solving a headache.

Thank you to Rachael who created the code in the first place, thanks to Solene who helped me trouble shoot, thanks to Amanda for moral support. Go GEMM Lab!

Why do pirates have a hard time learning the alphabet?  It’s not because they love aaaR so much, it’s because they get stuck at “c”!

Stelle, L. L., W. M. Megill, and M. R. Kinzel. 2008. Activity budget and diving behavior of gray whales (Eschrichtius robustus) in feeding grounds off coastal British Columbia. Marine mammal science 24:462-478.

Does ocean noise stress-out whales?

By Leila Lemos, Ph.D. Student, Department of Fisheries and Wildlife, OSU


We’ve all been stressed. You might be stressed right now. Deadlines, demands, criticism, bills, relationships. It all adds up and can boil over: Chronic stress is linked with poor health, and also increased risk of illness (like cancer; Glaser et al. 2005, Godbout and Glaser 2006).

Biologically, stress manifests itself in vertebrate animals as variable levels of hormones, particularly the hormone cortisol. This academic term I am taking a class at OSU called “vertebrate endocrinology” where I am learning the different types of secretions and organs involved and the mechanisms of hormone action: how secretion, transport and signaling happen. These issues are important for my research because I will be examining stress levels in gray whales.

It may seem strange to study how stressed out a whale is, but there are reasons to believe that the long-term health of animals, including whales, is significantly related to their stress-hormone levels (Jepson et al. 2003, Cox et al. 2006, Wright et al. 2007, Rolland et al. 2012).

So what could be stressing out whales? Probably lots of things including food availability, predators and mating. However, we are mostly interested in describing how much added stress human activities in the oceans are causing, particularly from increased ocean noise. Ambient ocean noise levels have increased considerably over the last decades: according to IUCN, the increase was about 3 dB per decade over the past 60 years and now it seems to be increasing from 3 to 5 dB per decade (Simard and Spadone 2012).

Baleen whales communicate through low-frequency signals, reaching between 20 and 200 Hz and large ships generate noise in the same frequency band, which can mask whale vocalizations and potentially add stress (Rolland et al. 2012), especially in areas with high anthropogenic activities such as big ports, where an intense traffic occurs.

To get a sense of how noisy oceans can disrupt the acoustic lives of whales, the Monterey Institute has created an excellent interactive website where it is possible to listen to the whales’ vocalization and add other sources of sounds, like ship traffic, to compare the difference in noise levels.

We still do not understand the population level consequences of this increased ocean noise on whales, however it has been demonstrated that whales respond behaviorally to increased noise, including changes in vocalization rates and habitat displacement (Morton and Symonds 2002, Nowacek et al. 2007, Weilgart 2007, Rolland et al. 2012). In order to understand how acoustic disturbance may influence marine mammal populations, the population consequences of acoustic disturbance model (PCAD) was developed by the US National Academies of Sciences (National Resource Council 2005; We believe that examining stress levels in whales can provide a useful link between ocean noise and population-level impacts.

One previous study convincingly demonstrated the impacts of ocean noise on whale stress hormones due to the chance experiment caused by the shut-down of all air and vessel traffic during the days following September 11, 2001. Rolland et al. (2012) collected acoustic samples from the Bay of Fundy, Canada, and fecal samples from north Atlantic right whales in the area before and after September 11th over five years. The results found a 6 dB decrease in ocean noise (Figure 1) in the area after this date and an associated decrease in glucocorticoids (GC) metabolite (stress) levels in the whales (Figure 2 – highlighted in red).

Spectrum of the noise in different days along the Bay of Fundy, Canada. Source: Rolland et al. (2012)
Figure 1: Spectrum of the noise in different days along the Bay of Fundy, Canada.
Source: Rolland et al. (2012)


Figure 2
Figure 2: (a) Levels of fecal glucocorticoids metabolites (ng g -1) in North Atlantic right whales before (gray) and after (white) 11 September; (b) Yearly difference in median fecal GC levels. Source: Rolland et al. (2012)


For my PhD research we are attempting to assess how multiple, confounding factors contribute to stress levels in individual whales: prey availability, body condition, location, ocean noise, sex and sexual maturity. My advisor, Dr. Leigh Torres, developed a conceptual pathway diagram that illustrates potential scenarios caused by dichotomous levels of three major ecological components and their hypothesized influence on whale stress levels (Figure 3).


Figure 3
Figure 3: Conceptual pathway diagram of the hypothesized stress response of whales based on high or low levels of the three contributing ecological factors on stress that will be measured (developed by L. Torres).


From this diagram we can generate different hypotheses for our research to test. Distinct levels (high or low) of noise, prey availability, and health condition can lead to varied responses in the amplitude and duration of stress. We will measure prey availability through GoPro camera drops, hormone levels through fecal sample collection, and body condition through photogrammetry measurements of aerial images captured through an Unmanned Aerial System (aka drone).

Watch a video clip filmed via a UAS of a gray whale defecation event, and the field team collecting the sample for analysis.

Our study species is the gray whale, a non endangered species that regularly visits the Oregon coast during summer and fall months to feed, allowing accessibility to whales and repeatability of sighting individual animals. This ability to resight individual whales within and between years is important so that we can evaluate natural stress variability, thus allowing us to identify ‘stressful events’ and potential causes.

Overall, the main aim of my PhD research is to better understand how gray whale hormone levels vary across individual, time, body condition, location, and ambient noise environments. We may then be able to scale-up our results to better understand the population level impacts of elevated ocean noise on reproduction, distribution and abundance of whales.

We plan to study the correlation between stress levels in whales and ocean noise over many years to compile a robust database that allows us to identify how animals may be impacted physiologically at short- and long- term scales. These results will inform environmental management decisions regarding thresholds of ambient ocean noise levels in order to limit harm posed to baleen whales.


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