Migrating to higher latitudes

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

On September 10th of 2015 I was catching an airplane to start a whole new phase of my life in Oregon, United States. Many thoughts, many doubts, many fears, many expectations, and one big dream that was about to come true: I was finally going to United States to work with whales.

I am from Rio de Janeiro, Brazil, a big city known for pretty beaches, tropical weather and restless nights. Thus, to arrive in a really small city on the countryside that usually rains for about six months a year was the opposite of what I was always used to. Trying to understand another language and culture differences was also not an easy step.

In addition, taking my first classes was a big challenge. It was hard to understand everything that was being said, but recording and listening to the classes afterwards definitely was what helped me the most. Also, my first meetings and discussions where I needed to explain my thoughts in another language was difficult, but when I look back and I can now see how much I have improved and it is gratifying to know that all of my efforts were worth it.

Feeling welcome was essential to start overcoming all of the difficulties. My advisor Leigh and my lab mates (Florence, Amanda, Rachael, Erin, Dawn and Courtney) always created a friendly atmosphere and I started being more confident over time. I also had amazing and understanding teachers who were patient and helped me along the way. My first roommates Jane and Angie, from US, and the students and teachers from Crossroads (an English group that I attend) made me practice English every day and I started feeling more comfortable about speaking (and also thinking) in English, and they became my “Oregon family” together with new friends I made from different nationalities. Also important were my family and friends back in Brazil that never stopped encouraging and supporting me.

Figure 1: GEMM-Lab, from left to right, starting at the top: Leigh Torres, me, Erin, Amanda, Dawn, Rachael, our interns from 2016 season (Catherine, Cat and Kelli), and Florence.


Figure 2: Practicing English at Crossroads.


The weather and seasons here are also very different from Brazil. We don’t have cold weather or snow, and we don’t see all of the changes that happen here from season to season. The first season I saw was the fall. Seeing all of the fall colors in the trees for the first time was magical and I can already say that fall is my favorite season here. The winter was a bit cruel for me, not because of the cold or eventually the snow, but because of the rain. There is a saying in my city that “people from Rio de Janeiro do not like gray days” and it is true: my mood changes with weather. However, I did travel a bit around Oregon during winter and got to enjoy the snow, and how fun is to slide in the snow, make snow angels and throw snowballs. The spring starts bringing sunny days after cold months and endless rain. Also all of the flowers around the Corvallis campus are so pretty and colorful. Finally the summer is hot, and in some days it can almost be as hot as Rio de Janeiro. However, I spend summer days in the coast, where the temperature is mild. For me, summer days are synonymous with fieldwork, since gray whales are migrating northbound and becoming resident along the Oregon coast to feed, and this is right when the fun begins!

Figure 3: Different seasons in Oregon: (A) Trees during the fall in Corvallis, (B) Winter in Crater Lake, (C) Spring at OSU campus: my office at Hovland Building, and (D) fieldwork in Port Orford during the summer.


I finally saw my first gray whale in July of 2016 and got to dive into all of the methodologies we wanted to apply in this project. I learned how to photograph whales for photo-identification, how to take important notes, how to collect fecal samples for hormonal analysis, and how to fly with a drone for the photogrammetry method.

Figure 4: Learning how to fly with a drone over gray whales.
Source: Florence Sullivan


I had to digest a lot of information while trying to equilibrate in the boat and to not get seasick. However, it was so pleasurable to see how my field skills were getting better over time and how close I was to the Pacific marine fauna.

During my master’s degree I worked on toxicology in dolphins, which means working with dead carcasses. I remember telling myself all of the time that I wanted to do something different for my PhD – that I would be involved in a project with live animals. I am very glad I could accomplish that goal. Gray whales, sea lions, seals and a variety of marine birds are just some examples of the great diversity the Pacific Ocean has to offer and I am totally amazed.

Figure 5: Great diversity of the Oregon coast. Source: GEMMLab (Leila Lemos, Leigh Torres and Florence Sullivan)

After months of fieldwork it was time to return to the land and start learning how to work with all of the data we collected. We have amazing collaborators working with us and I have had wonderful opportunities to learn from all of them about the different methods we are applying in our project.

Figure 6: Learning the hormonal analysis technique at the Seattle Aquarium.


Thus, after one year and a half in Oregon I can already say that I feel home. The experience as an international student is not easy, but that’s what makes it such a valuable and gratifying experience. It has been a great journey, and I hope to continue to see improvements over time and keep learning throughout this amazing project studying gray whales.


“Marching for Science” takes many forms

By Florence Sullivan, MSc student, Oregon State University.

Earth day is a worldwide event celebrated annually on April 22, and is typically observed with beach, park, or neighborhood clean ups, and outreach events sponsored by environmental groups.  Last year, environmentalists rejoiced when 195 nations signed the Paris Agreement – to “strengthen global response to the threat of climate change by keeping global temperature rise below 2 degrees C”.

GEMM Lab member Dawn Barlow helps carry the banner for the Newport, OR March for Science which over 600 people attended. photo credit: Maryann Bozza

This year, the enviro-political mood is more somber. Emotions in the GEMM Lab swing between anger and dismay to cautious optimism and hope. The anger comes from threatened budget cuts, the dismissal of climate science, and the restructuring of government agencies, while we find hope at the outpouring of support from our local communities, and the energy building behind the March for Science movement.

The Newport March for Science. photo credit: Maryann Bozza

What is perhaps most striking about the movement is how celebratory it feels. Instead of marching against something, we are marching FOR science, in all its myriad forms. With clever signs and chants like “The oceans are rising, and so are we”, “Science, not Silence”, and “We’re nerds, we’re wet, we’re really quite upset” (it rained on a lot of marches on Saturday) echoing around the globe, Saturday’s Marches for Science were a cathartic release of energy, a celebration of like-minded people.

Our competition room for NOSB 2017! Game officials are in the front of the picture, competitors at the first two desks, and parents, coaches and supporters in the back.

While millions of enthusiastic people were marching through the streets, I “Ran for Science” at the 20th annual National Ocean Science Bowl (NOSB) – delivering question sheets and scores between competitors and graders as 25 teams competed for the title of national champion! Over the course of the competition, teams of four high school students compete through rounds of buzzer-style multiple choice questions, worksheet style team challenge questions, and the Scientific Expert Briefing, a mock congressional hearing where students present science recommendations on a piece of legislation.  The challenges are unified with a yearly theme, which in 2017 was Blue Energy: powering the planet with our ocean.  Watching the students (representing 33 states!) compete is exciting and inspiring, because they obviously know the material, and are passionate about the subject matter.  Even more encouraging though, is realizing that not all of them plan to look for jobs as research scientists. Some express interest in the arts, some in policy, or teaching or engineering. This competition is not just about fostering the next generation of leading marine scientists, but rather about creating an ocean-literate, and scientifically-literate populace.  So, congratulations to Santa Monica High School, who took home the national title for the first time this year! Would you like to test your knowledge against some of the questions they faced? Try your luck here!

Santa Monica competes in the final round

The GEMM Lab also recently participated in the Hatfield Marine Science Center’s Marine Science Day.  It’s an annual open house where the community is invited to come tour labs, meet scientists, get behind the scenes, and learn about all the exciting research going on.  For us as researchers, it’s a great day to practice explaining our work and its relevance to many different groups, from school children to parents and grandparents, from artists to fishermen to teachers, fellow researchers, and many others.  This year the event attracted over 2,000 people, and the GEMM Lab was proud to be a part of this uniquely interactive day.  Outreach events like this help us feel connected to our community and the excitement present in all the questions field during this event reassure us that the public still cares about the work that we do.

Lab members Florence, Leila, and Dawn (L to R) answer questions from the public.

Our science is interdisciplinary, and we recognize the strength of multiple complimentary avenues of action to affect change.  If you are looking to get involved, consider taking a look at these groups:

500 Women Scientists: “working to promote a diverse and inclusive scientific community that brings progressive science-based solutions to local and global challenges.” Read their take on the March for Science.

314Action: starting from Pi (3.14), their mission is “to (1) strengthen communication among the STEM community, the public and our elected officials, (2) Educate and advocate for and defend the integrity of science and its use, (3) Provide a voice for the STEM community on social issues, (4) Promote the responsible use of data driven fact based approaches in public policy and (5) Increase public engagement with the STEM Community through media.”

She should run: “A movement working to create a culture that inspires women and girls to aspire towards public leadership. We believe that women of all backgrounds should have an equal shot at elected leadership and that our country will benefit from having a government with varied perspectives and experiences.” https://peoplesclimate.org/

And finally, The March for Science is finishing up it’s week of action, culminating in the People’s Climate March on April 29.

How will you carry the cause of science forward?


How Unmanned Aircraft Systems (UAS, aka “drones”) are being applied in conservation research

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


Unmanned Aircraft Systems (UAS), also known as “drones”, have been increasingly used in many diverse areas. Concerning field research, the use of drones has brought about reduced errors, increased safety and survey efforts, among other benefits, as described in a previous blog post of mine.

Several study groups around the world have been applying this new technology to a great variety of research applications, aiding in the conservation of certain areas and their respective fauna and flora. Examples of these studies include forest monitoring and tree cover analyses, .

Using drones for forest monitoring and tree cover analyses allows for many applications, such as biodiversity and tree height monitoring, forest classification and inventory, and plant disease and detection. The Ugalla Primate Project, for example, performed an interesting study on tree coverage mapping in western Tanzania (Figure 1).

Figure 1: Tree coverage analyses in Tanzania.
Source: Conservation Drones, 2016.


The access to this data (not possible before from the ground) and the acquired knowledge on tree density and structure were important to better understand how wild primates exploit a mosaic landscape. Here is a video about this project:


Forest restoration activities can also be monitored by drones. Rainforests around the world have been depleted through deforestation, partly to open up space for agriculture. To meet conservation goals, large areas are being restored to rainforests today (Elsevier 2015). It is important to monitor the success of the forest regeneration and to ensure that the inspected area is being replenished with the right vegetation. Since inspection events can be costly, labor intensive and time consuming, drones can facilitate these procedures, making the monitoring process more feasible.

Zahawi et al. (2015) conducted an interesting study in Costa Rica, being able to keep up with the success of the forest regeneration. They were also able to spot many fruit-eating birds important for forest regeneration (eg. mountain thrush, black guan and sooty-capped bush tanager). Researchers concluded that the automation of the process lead to equally accurate results.

Drones can also be used to inspect areas for illegal logging and habitat destruction. Conservationists have struggled to identify illegal activities, and the use of drones can accelerate the identification process of these activities and help to monitor their spread and ensure that they do not intersect with protected areas.

The Amazon Basin Conservation Association Los Amigos conservancy concession (LACC) has been monitoring 145,000 hectars of the local conservation area. Illegal gold mining and logging activities were identified (Figure 2) and drones have aided in tracking the spread of these activities and the progress of reforestation efforts.

Figure 2: Identification of illegal activities in the Amazon Basin.
Source: NPR, 2015.


Another remarkable project was held in Mexico, in one of the most important sites for monarch butterflies in the country: the Monarch Butterfly Biosphere Reserve. Around 10 hectars of vital trees were cut down in the reserve during 2013-2015, and a great decrease of the monarch population was perceived. The reserve did not allow researchers to enter in the area for inspection due to safety concerns. Therefore, drones were used and were able to reveal the illegal logging activity (Figure 3).

Figure 3: Identification of illegal logging at the Monarch Butterfly Biosphere Reserve, Mexico.
Source: Take Part, 2016.


Regarding the use of drones for mapping vulnerable areas, this new technology can be used to map potential exposed areas to avoid catastrophes. Concerning responses to fires or other natural disasters, drones can fly immediately, while planes and helicopters require a certain time. The drone material also allows for operating successfully under challenging conditions such as rain, snow and high temperatures, as in the case of fires. Data can be assessed in real time, with no need to have firefighters or other personnel at a dangerous location anymore. Drones can now fulfill this role. Examples of drone applications in this regard are the detection, monitoring and support for catastrophes such as landslides, tsunamis, ship collisions, volcanic eruptions, nuclear accidents, fire scenes, flooding, storms and hurricanes, and rescue of people and wildlife at risk. In addition, the use of a thermal image camera can better assist in rescue operations.

Researchers from the Universidad Politécnica de Madrid (UPM) are developing a system to detect forest fires by using a color index (Cruz et al. 2016). This index is based on vegetation classification techniques that have been adapted to detect different tonalities for flames and smoke (Figure 4). This new technique would result in more cost-effective outcomes than conventional systems (eg. helicopters, satellites) and in reaching inaccessible locations.

Figure 4: Fire detection with Forest Fire Detection Index (FFDI) in different scenes.
Source: UPM, 2016.


Marine debris detection by drones is another great functionality. The right localization and the extent of the problem can be detected through drone footage, and action plans for clean-ups can be developed.

A research conducted by the Duke University Marine Lab has been detecting marine debris on beaches around the world. They indicate that marine debris impacts water quality, and harms wildlife (eg. whales, sea birds, seals and sea turtles) that might confuse floating plastic with food. You can read a bit more about their research and its importance for conservation ends here.

Drones are also being extensively used for wildlife monitoring. Through drone footage, researchers around the world have been able to detect and map wildlife and habitat use, estimate densities and evaluate population status, detect rare behaviors, combat poaching, among others. One of the main benefits of using a drone instead of using helicopters or airplanes, or having researchers in the area, is the lower disturbance it may cause on wildlife.

A research team from Monash University is using drones for seabird monitoring in remote islands in northwestern Australia (Figure 5). After some tests, researchers were able to detect which altitude (~75 meters) the drone would not cause any disturbances to the birds. Results achieved by projects like this should be used in the future for approaching the species safely.

Figure 5: Photograph taken by a drone of a crested tern colony on a remote island in Australia.
Source: Conservation Drones, 2014.


Drones are also being used to combat elephant and rhino poaching in Africa. They are being implemented to predict, trace, track and catch suspects of poaching. The aim is to reduce the number of animals being killed for the detusking and dehorning practices and the illegal trade. You can read more about this theme here. The drone application on combating one of these illegal practices is also shown here in this video.

As if the innovation of this device alone was not enough, drones are also being used to load other tools. A good example is the collection of whale breath samples by attaching Petri dishes or sterile sponges in the basal part of the drones.

The collection of lung samples allows many health-monitoring applications, such as the analysis of virus and bacteria loads, DNA, hormones, and the detection of environmental toxins in their organisms. This non-invasive physiological tool, known as “Snotbot”, allows sampling collection without approaching closely the individuals and with minimal or no disturbance of the animals. The following video better describes about this amazing project:

It is inspiring to look at all of these wonderful applications of drones in conservation research. Our GEMM Lab team is already applying this great tool in the field and is hoping to support the conservation of wildlife.




Conservation Drones. 2014. Conservation Drones for Seabird Monitoring. Available at: https://conservationdrones.org/2014/05/05/conservation-drones-for-seabird-monitoring/

Conservation Drones. 2016. Tree cover analyses in Tanzania in collaboration with Envirodrone. Available at: https://conservationdrones.org/2016/09/17/tree-cover-analyses-in-tanzania-in-collaboration-with-envirodrone/

Cruz H, Eckert M, Meneses J and Martínez JF. 2016. Efficient Forest Fire Detection Index for Application in Unmanned Aerial Systems (UASs). Sensors 16(893):1-16.

Elsevier. 2015. Drones Could Make Forest Conservation Monitoring Significantly Cheaper: new study published in the Biological Conservation wins Elsevier’s Atlas award for September 2015. Available at: https://www.elsevier.com/about/press-releases/research-and-journals/drones-could-make-forest-conservation-monitoring significantly-cheaper

NPR. 2015. Eyes In The Sky: Foam Drones Keep Watch On Rain Forest Trees. Available at: http://www.npr.org/sections/goatsandsoda/2015/05/19/398765759/eyes-in-the-sky-styrofoam-drones-keep-watch-on-rainforest-trees

Take Part. 2016. Drones Uncover Illegal Logging in Critical Monarch Butterfly Reserve. Available at: http://www.takepart.com/article/2016/06/22/drones-uncover-illegal-logging-monarch-butterfly-habitat

UPM. 2016. New automatic forest fire detection system by using surveillance drones. Available at: http://www.upm.es/internacional/UPM/UPM_Channel/News/dc52fff26abf7510VgnVCM10000009c7648aRCRD

Zahawi RA, Dandois JP, Holl KD, Nadwodny D, Reid JL and Ellis EC. 2015. Using lightweight unmanned aerial vehicles to monitor tropical forest recovery. Biological Conservation 186:287–295.


Challenges of fecal hormone analyses (Round 2): finally in Seattle!

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

In a previous blog of mine, you could read about the challenges I have been facing while I am learning to analyze the hormone content in fecal samples of gray whales (Eschrichtius robustus). New challenges appeared along the way over the last month, while I was doing my training at the Seattle Aquarium (Fig. 1).

Figure 1: View of the Seattle Aquarium.


My training lasted a week and I am truly grateful to the energy and time our collaborators Shawn Larson (research coordinator), Amy Green and Angela Smith (laboratory technicians) contributed. They accompanied me throughout my training to ensure I would be able to conduct hormonal analysis in the future, and to handle possible problems along the way.

The first step was weighing all of the fecal samples (Fig. 2A). Subsequently, the samples were transferred to appropriate glass tubes (Figs. 2B & 2C) for the next laboratorial step.

Figure 2: Analytical processes: (A) Sample weighing; (B) Transference of the sample to a glass tube; (C) Result from the performed steps.


The second conducted step was the hormone extraction. The extraction began with the addition of an organic solvent, called methanol (CH3OH), to the sample tubes (Fig. 3A & 3B). Hormones leach out from the samples and dissolve in the methanol, due to their affinity for this polar solvent.

Tubes were then placed on a plate shaker (Fig. 3C) for 30 minutes, which is used to mix the substances, in order extract the hormones from the fecal samples. The next step was to place the tubes in a centrifuge (Fig. 3D) for 20 minutes. The centrifuge uses the sedimentation principle, causing denser substances or particles to settle to the bottom of the tube, while the less dense substances rise to the top.

Figure 3: Analytical processes: (A) Methanol addition; (B) Sample + methanol; (C) Plate shaker; (D) Centrifuge.


After this process, the two different densities were separated: the high-density particles of the feces were in the bottom of the tube, while the methanol containing the extracted hormones was at the top. The top phase (methanol + hormones) was then pipetted into a different tube (Fig. 4A). The solvent was then evaporated, by using an air dryer apparatus (Fig. 4B), with only the hormones remaining in the tube.

The third performed step was dilution. A specific amount of water, measured in correlation with sample weight and to the amount of the methanol mixed with each sample, was added to each tube (Fig. 4C). Since the hormones were concentrated in the methanol, the readings would exceed the measurement limits of the equipment (plate reader). Thus, in order to prepare the extracts for the immunoassays, different dilutions were made.

Figure 4: Analytical processes: (A) Methanol transference; (B) Methanol drying; (C) Water addition.


The fourth and final step was to finally conduct the assays. Each assay kit is specific to the hormone to be analyzed with specified instructions for each kit. Since we were analyzing four different hormones (cortisol, testosterone, progesterone, and triiodothyronine – T3) we followed four different processes accordingly.

First, a table was filled with the identification numbers of the samples to be analyzed in that specific kit (Fig. 5A). The kit (Fig. 5B) includes the plate reader and several solutions that are used in the process to prepare standard curves, to initiate or stop chemical reactions, among other functions.

A standard curve, also known as calibration curve, is a common procedure in laboratory analysis for determining the concentration of an element in an unknown sample. The concentration of the element is determined by comparison with a set of standard samples of known concentration.

The plate contains several wells (Fig. 5C & 5D), which are filled with the samples and/or these other solutions. When the plate is ready, (Fig.5D) it is carried to the microplate reader that measures the intensity of the color of each of the wells. The intensity of the color is inversely proportional to the concentration of the hormone in both the standards and the samples.

Figure 5: (A) Filling the assay table with the samples to be analyzed; (B) Assay kit to be used; (C) Preparation of the plate; (D) Plate ready to be read.


Since this is the first fecal hormone analysis being performed in gray whales, a validation process of the method is required. Two different tests (parallelism and accuracy) were performed with a pool of three different samples. Parallelism tests that the assay is measuring the antigen (hormone) of interest and also identifies the most appropriate dilution factor to be used for the samples. Accuracy tests that the assay measurement of hormone concentration corresponds to the true concentration of the sample (Brown et al. 2005).

This validation process only needs to be done once. Once good parallelism and accuracy results are obtained, and we have identified the correct dilution factor and approximate concentration of the samples, the samples are ready to be analyzed. Below you can see examples of a good parallelism test (parallel displacement; Fig. 6) and bad parallelism tests (Fig. 7) that indicate no displacement, low concentration or non-parallel displacement; and a good accuracy test (Fig. 8).

Figure 6: Example of a good parallelism test. The dark blue line indicates the standard curve; the pink line indicates a good parallelism test, showing a parallel displacement; and the ratios in black indicate the dilution factors.
Source: Brown et al. (2005)


Figure 7: Examples of bad parallelism tests. The dark blue line indicates the standard curve; the light blue line is an example of no displacement; the pink line is an example of low concentration of the sample; and the green line is an example of non-parallel displacement.
Source: Brown et al. (2005)


Figure 8: Example of a good accuracy test while analyzing hormone levels of pregnanediol glucuronide (Pdg) in elephant urine. The graph shows good linearity (R2 of 0.9986) and would allow for accurate concentration calculations.
Source: Brown et al. (2005)


After the validation tests returned reliable results, the samples were also analyzed. However, many complications were encountered during the assay preparations and important lessons were learned that I know will allow this work to proceed more smoothly and quickly in the future. For instance, I now know to try to buy assay kits of the same brand, and to be extremely careful while reading the manual of the process to be performed with the assay kit. With practice over the coming years, my goal is to master these assay preparations.

Now, the next step will be to analyze all of the results obtained in these analyses and start linking the multiple variables we have from each individual, such as age, sex and body condition. The results of this analysis will lead to a better understanding of how reproductive and stress hormones vary in gray whales, and also link these hormone variations to nutritional status and noise events, one of my PhD research goals.


Cited Literature:

Brown J, Walker S and Steinman K. 2005. Endocrine manual for reproductive assessment of domestic and non-domestic species. Smithsonian’s National Zoological Park, Conservation and Research Center, Virginia 1-69.

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!




The five senses of fieldwork

By Leila Lemos, PhD student


This summer was full of emotions for me: I finally started my first fieldwork season after almost a year of classes and saw my first gray whale (love at first sight!).

During the fieldwork we use a small research vessel (we call it “Red Rocket”) along the Oregon coast to collect data for my PhD project. We are collecting gray whale fecal samples to analyze hormone variations; acoustic data to assess ambient noise changes at different locations and also variations before, during and after events like the “Halibut opener”; GoPro recordings to evaluate prey availability; photographs in order to identify each individual whale and assess body and skin condition; and video recordings through UAS (aka “drone”) flights, so we can measure the whales and classify them as skinny/fat, calf/juvenile/adult and pregnant/non-pregnant.

However, in order to collect all of these data, we need to first find the whales. This is when we use our first sense: vision. We are always looking at the horizon searching for a blow to come up and once we see it, we safely approach the animal and start watching the individual’s behavior and taking photographs.

If the animal is surfacing regularly to allow a successful drone overflight, we stay with the whale and launch the UAS in order to collect photogrammetry and behavior data.

Each team member performs different functions on the boat, as seen in the figure below.

Figure 1: UAS image showing each team members’ functions in the boat at the moment just after the UAS launch.
Figure 1: UAS image showing each team members’ functions in the boat at the moment just after the UAS launch.


While one member pilots the boat, another operates the UAS. Another team member is responsible for taking photos of the whales so we can match individuals with the UAS videos. And the last team member puts the calibration board of known length in the water, so that we can later calculate the exact size of each pixel at various UAS altitudes, which allows us to accurately measure whale lengths. Team members also alternate between these and other functions.

Sometimes we put the UAS in the air and no whales are at the surface, or we can’t find any. These animals only stay at the surface for a short period of time, so working with whales can be really challenging. UAS batteries only last for 15-20 minutes and we need to make the most of that time as we can. All of the members need to help the UAS pilot in finding whales, and that is when, besides vision, we need to use hearing too. The sound of the whale’s respiration (blow) can be very loud, especially when whales are closer. Once we find the whale, we give the location to the UAS pilot: “whale at 2 o’clock at 30 meters from the boat!” and the pilot finds the whale for an overflight.

The opposite – too many whales around – can also happen. While we are observing one individual or searching for it in one direction, we may hear a blow from another whale right behind us, and that’s the signal for us to look for other individuals too.

But now you might be asking yourself: “ok, I agree with vision and hearing, but what about the other three senses? Smell? Taste? Touch?” Believe it or not, this happens. Sometimes whales surface pretty close to the boat and blow. If the wind is in our direction – ARGHHHH – we smell it and even taste it (after the first time you learn to close your mouth!). Not a smell I recommend.

Fecal samples are responsible for the 5th sense: touch!

Once we identify that the whale pooped, we approach the fecal plume in order to collect as much fecal matter as possible (Fig.2).

Figure 2: A: the poop is identified; B: the boat approaches the feces that are floating at the surface (~30 seconds); C: one of the team members remains at the bow of the boat to indicate where the feces are; D: another team member collects it with a fine-mesh net. Filmed under NOAA/NMFS permit #16111 to John Calambokidis).
Figure 2: A: the poop is identified; B: the boat approaches the feces that are floating at the surface (~30 seconds); C: one of the team members remains at the bow of the boat to indicate where the feces are; D: another team member collects it with a fine-mesh net. Filmed under NOAA/NMFS permit #16111 to John Calambokidis).


After collecting the poop we transfer all of it from the net to a small jar that we then keep cool in an ice chest until we arrive back at the lab and put it in the freezer. So, how do we transfer the poop to the jar? By touching it! We put the jar inside the net and transfer each poop spot to the jar with the help of water pressure from a squeeze bottle full of ambient salt water.

Figure 3: Two gray whale individuals swimming around kelp forests. Filmed under NOAA/NMFS permit #16111 to John Calambokidis).
Figure 3: Two gray whale individuals swimming around kelp forests. Filmed under NOAA/NMFS permit #16111 to John Calambokidis).


That’s how we use our senses to study the whales, and we also use an underwater sensory system (a GoPro) to see what the whales were feeding on.

GoPro video of mysid swarms that we recorded near feeding gray whales in Port Orford in August 2016:

Our fieldwork is wrapping up this week, and I can already say that it has been a success. The challenging Oregon weather allowed us to work on 25 days: 6 days in Port Orford and 19 days in the Newport and Depoe Bay region, totaling 141 hours and 50 minutes of effort. We saw 195 whales during 97 different sightings and collected 49 fecal samples. We also performed 67 UAS flights, 34 drifter deployments (to collect acoustic data), and 34 GoPro deployments.

It is incredible to see how much data we obtained! Now starts the second part of the challenge: how to put all of this data together and find the results. My next steps are:

– photo-identification analysis;

– body and skin condition scoring of individuals;

– photogrammetry analysis;

– analysis of the GoPro videos to characterize prey;

– hormone analysis laboratory training in November at the Seattle Aquarium


For now, enjoy some pictures and a video we collected during the fieldwork this summer. It was hard to choose my favorite pictures from 11,061 photos and a video from 13 hours and 29 minutes of recording, but I finally did! Enjoy!

Figure 4: Gray whale breaching in Port Orford on August 27th. (Photo by Leila Lemos; Taken under NOAA/NMFS permit #16111 to John Calambokidis).
Figure 4: Gray whale breaching in Port Orford on August 27th. (Photo by Leila Lemos; Taken under NOAA/NMFS permit #16111 to John Calambokidis).


Figure 5: Rainbow formation through sunlight refraction on the water droplets of a gray whale individual's blow in Newport on September 15th. (Photo by Leila Lemos; Taken under NOAA/NMFS permit #16111 to John Calambokidis).
Figure 5: Rainbow formation through sunlight refraction on the water droplets of a gray whale individual’s blow in Newport on September 15th. (Photo by Leila Lemos; Taken under NOAA/NMFS permit #16111 to John Calambokidis).


Likely gray whale nursing behavior (Taken under NOAA/NMFS permit #16111 to John Calambokidis):