Embracing Failures for Personal and Professional Growth 

By Autumn Lee, Mount Holyoke College rising senior, GEMM Lab REU Intern 2023

Hello! My name is Autumn Lee, and I am a GEMM lab REU student this summer being mentored by Allison Dawn and Dr. Leigh Torres! I am a rising senior at Mount Holyoke College studying Neuroscience and Behavior, focusing on coastal and marine science. It has been a pleasure working with the GEMM Lab this summer, and I have enjoyed learning more about the field of research before I graduate. 

As part of the research experience for undergraduates (REU) program, I am doing an independent project this summer in addition to our intense fieldwork for the TOPAZ project. I am working with the CamDo underwater video data that the GEMM Lab has collected since 2020. You can read Allison’s recent blog post to learn more about our CamDo underwater housings. Over the previous seasons, scuba divers have deployed our CamDo’s in our two study sites near Port Orford Titchener Cove and Mill Rocks on a weekly schedule of collection and redeployment. My project focuses on developing a methodology for examining the interactions between zooplankton prey and marine predators, and to quantify zooplankton density from the swarms seen on camera. Even though I hope my project’s success will contribute to the field, embarking on new method protocols always carries a risk of failure. Science tends to focus on successes; only in the footnotes do we hear about failures, wrong turns, and forgotten ideas. However, failure is how research advances; and with scientists who are brave enough to take that first step and humble enough to accept and reflect on failure.

Figure 1: Team prepping CamDo setup for deployment 

In the past, I have learned to troubleshoot computer software and lab equipment. However, there were already protocols in place, and my research contributions were part of another student’s pre-defined project. Unlike my previous research experience, for my REU project, I had to learn how to use unfamiliar software, set achievable goals, overcome obstacles, and devise a plan to accomplish them without relying on a team of peers. This is a project Allison and I have been working on together outside of field work, but we have not been without support. Both Victoria Hermanson, a Biological Science Aid with the Antarctic Ecosystem Research Division, and Suzie Winquist, a graduate student at the Marine Mammal Institute, have inspired and guided us through using VIAME for our research questions.

Taking that leap into uncharted waters, we chose to work with two software programs that were new to me called VIAME (Video and Image Analytics for the Marine Environment) and ImageJ. Our goal was to utilize VIAME so that it could distinguish between zooplankton or predators in our CamDo videos (from the hundreds of unannotated frames) and then use ImageJ to quantify the density of zooplankton in those identified frames. Although it has been exciting to use this software that uses Artificial Intelligence (AI) to track and detect prey and predator interactions in video footage, we have encountered many challenges along the way. Within 10 weeks, we had to learn this new software, train it to identify zooplankton and predators, and calculate density using classified frames that we would train. When tackling such an ambitious project in a limited time frame, we expected some setbacks, and through the advice of experienced professionals and the support of Allison (as well as a healthy dose of self-determination), we were able to gain success by breaking down the project into smaller tasks and using trial and error to fix any issues that arose.

Figure 2: Photo of Allison and myself working together to problem solve a VIAME error 

Although we have had some failures along the way, we have accomplished a lot, and I am eager to share some results with you. First, we developed and fine-tuned a workflow in VIAME to use AI to identify zooplankton prey and predators in our CamDo videos.

Figure 3:  Screenshot of VIAME program that illustrates how we trained a model to identify zooplankton prey (yellow boxes) and fish predators (blue box) in the CamDo videos. 

 In addition, we implemented a workflow in ImageJ (another software program designed to process and analyze scientific images) to quantify zooplankton density from frames identified by VIAME with zooplankton. Even though it took a lot of trial and error, our primary objectives were met, and we learned a great deal for future GEMM projects.

Figure 4: An example processed output image depicting how ImageJ  recognized bodies of zooplankton (black outlines) and counted individual zooplankton ( red dots). 

While working on my independent project, I learned that an ability to troubleshoot software and data processing can apply to tricky field work situations as well. For instance, when we lost a weighted cage attachment that protects our RBR concerto sensor, we needed a temporary solution until the divers recovered  our lost gear. So our team discussed a few different DIY options. After a frantic afternoon of trial and error, we ultimately decided on using a milk jug as a temporary cage. While it wasn’t the most glamorous solution, the GEMM lab is known to think outside the box as a fundamental part of both the fieldwork and research process. 

Figure 5: Photo of Allison testing out our RBR milk jug temporary setup 

I have found through this experience that sometimes it is more valuable to struggle and learn skills than to immediately succeed. I am hopeful that this lesson has prepared me for my future, and I couldn’t be more grateful. It has been an interesting summer for me as far as adapting to failures and embracing them. It was a difficult transition leaving my new friends at Hatfield in Newport where I spent my first 4 weeks and embracing an entirely different living dynamic here in Port Orford. With the field season and my research approaching its end, I realize how much I appreciate all the new people I have met here. Before this summer, I had not had many opportunities to interact with similar and enthusiastic marine scientists. Now I live and work with marine science mentors and peers in the field every day, which has been an invaluable experience, and I am grateful for the opportunity to learn from and interact with these inspiring people. It has been a meaningful summer, and I look forward to continuing to build relationships and learn from my failures during this next phase of my life. 

    Figure 6: Photo of Zoop Troop, from left to right Natalee, Autumn, Allison, Jonah, Aly 

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Accurate and Precise: Learning how to track a focal species

By Jonah Lewis, rising junior at Pacific High School, GEMM Lab Intern 2023

Hello, I’m Jonah Lewis, the other high school intern for the TOPAZ/JASPER Project. I am a rising junior for Pacific High School in Port Orford. I am interested in many things, including computer sciences, electrical sciences, different types of engineering, and lately, marine biology. At the end of February, my biology teacher, Hilary Johnson, was looking for high schoolers to join this internship and I decided that it could be a great experience for me. I applied, and somewhere in March, before I knew it, I was being interviewed by Allison Dawn, our Zoop Troop Sergeant, and Leigh Torres, the head of the operation. I was so nervous for my interview, and tried my best to do well. Then on March 31st, I saw the job offer email, and my family and I were overjoyed. Now that we are in our fourth week, I can say the people and the experiences have been amazing, but my favorite part of all has been the cliff site and the adrenaline rush of tracking a whale moving across the ocean.

Figure 1: Jonah smiles after fixing a whale using the theodolite. 

Theodolite is an important aspect of this research project. This instrument was invented by Leonard Digges back in the 1550’s and is a highly accurate instrument for mapping, engineering, etc. Read here to learn more about the theodolite’s component parts, written by last year’s intern Nichola Gregory, a previous JASPER intern. In Port Orford, we use it for tracking where a gray whale blows and surfaces! Setting up the theodolite can be a challenge for newcomers, but as you repeatedly put this device together, and then take it down, you understand and can troubleshoot better and faster than the previous time. It took me and the team some practice to be able to get all three ways it needs to level just right, or else the instrument decides to throw a fit. For example, when the theodolite isn’t exactly leveled right, or maybe the batteries are low, or the cord just isn’t plugged in all the way, it will just beep at you, trying to say there is an error. After the theodolite is properly leveled, you connect it to the computer that runs our software program called Pythagoras.

Not only does the physical setup require care, but “fixing” a whale requires technique. Here, we are trained to be both accurate and precise when following our focal species. To be accurate, we would need to position the theodolite scope so that the whale is close to the crosshairs. To be precise, we need to fix the whale in the same location on the theodolite crosshairs consistently. Our team has learned how to be both accurate and precise.

Figure 2: Accurate and precise diagram using the crosshairs of a theodolite as reference, diagram by A. Dawn.

Being on cliff team can get tedious, even when you are not using the theodolite to fix a whale. Staring at the waves and the horizon can feel like an eternity, especially when gray whales aren’t active in our study area. Yet, during this time we have to be “on effort”. Being on effort is making sure you scan the horizon consistently, both you and a partner are constantly looking at our study sites. All this is best represented by our team manager Allison: On the cliff with her, she is always looking at the ocean, paying attention to both sites, and for at least the first hour or longer, she will not sit down. 

Figure 3: Kelp bed behind the jetty while a whale flukes in the background.

After we collect all of our data from kayak and cliff each day, we head down to the dry lab and get prepared to download and transfer our data to a hard drive known as “Tharp”. I learned that Marie Tharp was a woman in the 20th century, who mapped the ocean floors, which helps scientists even now. (The GEMM Lab names each hard drive after famous scientists; it helps to track the many hard drives.) When I use the hard drive, I think about her and about how I also helped collect data for mapping features in our marine study site. During the first week of data collection, Allison and I looked through the theodolite scope, found obvious kelp patches on the surface of the water, and fixed many times around the edges, making a complete polygon around the kelp beds. 

Figure 4: Team bonding at the Prehistoric Gardens in Port Orford

This internship for the past four weeks has been an amazing experience. In addition to our fieldwork, I’ve been able to participate and connect with many other interns and professionals here at the Field Station. I have also enjoyed connecting with visitors from all different areas who come by and ask what research we’re doing on the cliff.  At the field station I have fun hanging with the guys at the house as well, where we play sports in our downtime and cook together. I also learn about what projects they are doing, from urchin culling to sea otter research, it all fascinates me. I have helped POSS (Port Orford Sustainable Seafood) with bagging fish, washing dishes, and in return they provide samples of the amazing food they make. I am overjoyed about what I have learned and the people I have met during this experience, and am so thankful to be a part of the ninth year of this project.

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Diving into new experiences

By Natalee Webster, Oregon State University rising senior, GEMM Lab Intern 2023

When I was younger, I was terrified of the water, sobbing on a rock across the river, afraid to be immersed in the unknown. Flash-forward to the present and I have one more year left to finish my undergraduate degree in Biology at Oregon State University with a focus in Marine Biology. I was a little hesitant about choosing a more focused degree since I wasn’t sure what aspect of sciences piqued my interest more. However my curiosity for the ocean grew as I took the PADI Open Water scuba class through school. After earning my certification, I discovered I loved being in the water, and seeing the habitats I read about firsthand. I quickly took my Advanced Scuba and worked my way up to Divemaster, and ultimately AAUS Scientific diving. This new certification provided me with skills for a career in marine biology, performing tasks and taking surveys underwater. Through the diving community at OSU, I met Allison Dawn, our graduate student leader of the TOPAZ/JASPER project studying gray whale foraging ecology. Through meeting her I was informed about this project and decided to apply. Now, as I write, we are working on week three of this project, and I could not be happier with my decision. This internship has already taught me so much about the hard work and logistics that goes into studying the behaviors of large marine mammals in the field, as well as what it is like to closely work with a team to accomplish our goals.

Figure 1. Port of Port Orford at dawn.

Each morning we wake up before the sun with a new set of goals, with a variety of tasks ahead that certainly keeps you on your toes. Long-time readers will know of our kayak and cliff methods, but another aspect of this project is our CamDo underwater cameras. These are cameras that we place in Mill Rocks and Tichenor Cove, our two sampling sites, for a week at a time for longer term footage. In order to deploy these cameras we utilize scuba equipment to properly place them in a location. When the week is up, we go to recover the cameras to gather the data, replace SD card and batteries, and reset them for another week of underwater video footage. 

Although CamDo deployment is not a required part of this internship, I have been able to use my scientific diving certification to assist this project on the dives. I appreciate the opportunity to take apply skills to assist the project from a different perspective. Before my first week here I had never dove off the Oregon coast from a boat, so this task was daunting, as I was still getting to know everyone around the field station, and get a sense of my environment.

Figure 2. Photo of Natalee geared up for a dive in Mill Rocks. 

Our very first dive at Mill Rocks was intimidating but exciting. Allison and I got up before dawn to prepare the cameras and get to the dive boat the Black Pearl. Allison is our dive tender, handling equipment and logistics, and we worked alongside two other divers — Caroline Rice, an intern with ORKA here at the Port Orford field station, and Kevin Buch, our dive leader and the dive safety officer and scientific diving professor at OSU. Once we rolled off the boat and started our descent I began to feel more in my element as the green waters surrounded us. As we continued further and further to the ocean floor, I realized that visibility was turning from a green you could see rays of sunlight through, into a dark black — barely visible further than five inches from my face. We were able to position the camera lander as needed, but we could not secure the camera because of those black-out conditions. While I waited in the waters for direction on the dive, I put my face as close to the rock as the tides would let me and I saw a purple urchin underwater for the first time, and let me tell you, in the dark waters it was eerie. We finally surfaced and got on the boat to venture off to Tichenor Cove in an attempt to deploy the other CAMDO. Here, I realized that despite the best preparation, scientists need to remain adaptable and determined in the face of challenging ocean conditions.  

Figure 3. A screenshot of CAMDO footage showing fish swimming in the water column.

As we prepared for the next dive and began our descent, I silently wondered what I had gotten myself into. I hoped that not all dives off the Oregon Coast were as dark. While slowly descending into Tichenor Cove, I was pleasantly surprised to see that the waters were beautiful in contrast to the darkness of Mill Rocks. Tichenor seemed to be a safe haven in comparison to Mill Rocks; rather than the strong current pushing me along the rocks and urchins, I was able to calmly swim through the rocks and look at the many sea stars, nudibranch, anemones, and different hues of purple urchins living along them. 

Figure 4. Photos taken from GoPro of Tichenor Cove environment, showing rockfish, urchins, and an anemone. 

More recently, we recovered the camera for data processing. While comparing the footage between the two locations, I have learned the ocean is incredibly variable. From clear blue waters where you can clearly see juvenile and adult fish swimming in the water column, compared to nothing but murky brown and black waters. This variability inspired me to think more deeply about what the gray whales see while they forage for food. Dr. Leigh Torres visited our team and I was able to discuss our dives and inquire about the methods these whales use in order to eat. My basic knowledge of whale anatomy tells me that they have eyes; however, I was curious if they used eyesight to locate zooplankton and other food. Leigh informed me that these whales have whiskers! This was an exciting discovery for me, I googled it later and found that gray whales and many other baleen whales have hair follicles, called vibrissae (watch this NOAA video to learn more!), around their rostrum and mouth they use as tactile sensors. Leigh Torres has hypothesized a “sense-of-scale” that illustrates an interchange of sensory modalities such as vision, audition, chemoreception, magnetoreception and somatosensory perception that allows whales to track and capture of prey (Torres 2017). Research in this sensory field continues to grow to better understand how marine mammals  capture and track prey at various scales.

Figure 5. Image of a gray whale, the spot markings along its jaw and rostrum are hair follicles known as vibrissae. (2016)

Seeing these small segments of their habitat myself while underwater has given me much more respect for how these gray whales are able to forage in such a challenging and changing environment. My teammate Autumn is currently working on quantifying the zooplankton abundance recorded in the footage taken through CAMDO, so stay tuned on the Port Orford blogs to hear more about their project!

Figure 6. Photo of Aly, Natalee, and Autumn before kayak training. Honorable mention to the bucket hats. 

The opportunity to participate in this year’s Gray Whale Foraging Ecology project is something I will not take for granted and will appreciate greatly for years. It has given me the opportunity to grow my knowledge about the marine environment that I have been fascinated with, as well as given me skills and training in methods of field research. I  even got to apply my hard-earned underwater skills and conduct my first official scientific dives! I have been able to interact with the long-time locals of Port Orford, whether it be a fisherman sharing their orca encounter tales to retired photographers that chase the whales along the shore. The field station houses many projects focusing on different aspects of the Oregon coast from sea urchins and kelp to river otters along the shores and to outreach programs within the community. When everyone is settling back into the field station after their long day of work, it is great to be gathered in the kitchen and hear about the progress we’ve made and the experiences we’ve had. I look forward to the remaining three weeks I have in Port Orford with this community and my team! Wish us luck as we prepare to deploy the next round of CamDo cameras next week.

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Torres, L.G. (2017), A sense of scale: Foraging cetaceans’ use of scale-dependent multimodal sensory systems. Mar Mam Sci, 33: 1170-1193. https://doi.org/10.1111/mms.12426

What pushes whales north in the Baja. (2016). iTravel Cabo. Retrieved August 7, 2023, fromhttp://www.itravel-cabo.com/news/cabo-news/what-pushes-whales-north-in-the-baja.

How to be a Zooper Trooper: Getting Comfy with the Uncomfortable

By Aly Covey, Marshfield High School student, GEMM Lab Intern 2023

Hello, everyone! My name is Aly Covey and I am a rising senior, one of two high school interns part of the  TOPAZ/JASPER project this summer. I have the pleasure of introducing the team name for this year. We came up with our name not too long after meeting each other last week, when our team member Autumn started calling the zooplankton samples we collected  “zoop soup”, which then led us to call our team the “zoop troop” (because it rhymes!). We had some other contenders for names, but none of them felt just right. I think this is because Zoop Troop has begun to mean more to us than just the convenient rhyme. We’ve all heard the phrase “being a trooper”, which describes someone who overcomes their struggles and we certainly have embodied that in each task, where we have demonstrated resilience in the face of specific challenges and pushing forward despite discomfort both mentally and physically.

Figure 1: Logo for this year’s team name, created by Autumn Lee.

As a team, we have bonded over this quality of resiliency, and quickly became close during our first week. We go on routine sunset beach walks where we look at interesting sand fleas, baby shrimp, and bring back pocket-fulls of shells and beach glass. As well as our group meals that always lead to fun conversation and a warm, family, feel. Personally, I have enjoyed getting to know everyone on the team and seeing their unique skills. Since the first day, Jonah has constantly been trying to help cook and clean for Zoop Troop whenever he can. Natalee and I have bonded over our daily need to find time for a quick cat nap. We usually find Autumn working on her individual research project in the kitchen. And of course, Allison has earned the name of “Whale Mom” because of her dedication to taking care of the team’s needs outside of the daily training and being the best mentor to all of us. 

Over the last two weeks of training, I learned all the new technology and protocols the team needs to successfully use the gear for our research. Allison has been such a huge help teaching us the in’s and out’s of everything while still letting us make mistakes and allowing us to learn from them. So far, I feel confident in all the things I have learned. That said, I still wonder what it will feel like out in the field without a supervisor helping when something goes wrong. Allison has given us a few “non-data collecting” days to feel out the scene without her there and so far I, and whoever I’m working with that day, seem to be feeling fairly satisfied in our skill level, and it has been a nice opportunity to help each other when needed. 

Figure 2: Team prepping CamDo for deployment underwater

For me, it has been uncomfortable allowing myself to fail at certain tasks and having to restart from the beginning to get it right the next time. Patience is such an important skill needed for the work we do everyday. It’s very exciting to feel myself slowly start enjoying the idea of “trial and error” as I lean into all the new information we have absorbed these past few weeks. 

Although it is frustrating at times, I believe the team does a great job of creating a fun environment for each other while still being able to slow down and take in all the small details needed for each new task Allison teaches us. This experience has shown me that in order to persevere, you need to get comfortable with the uncomfortable.

Figure 3: Aly and Natalee learning kayak sampling skills

While completing tasks on my own, I am vigilant to catch errors and run over each protocol in my head multiple times before going out into the field. For example, our theodolite is a very important but delicate piece of equipment we use on the cliff to track and fix on the whales we see out in the water. It is incredibly tedious to set up Theota (our nickname for the theodolite) in a sufficient amount of time without messing up the leveling, cords, or measuring needed to properly run the program. During training, we get up to the cliff around 8am and are able to take as much time as we need to correctly level, connect the telescope to the computer, and reach each fix point without feeling rushed. However, during a “real” workday, we are up on the cliff as early as 6am, held to a standard of having all our gear fully charged and ready to go for the day, as well as being able to efficiently set everything up and ready to watch the whales and be the safety watch for kayak team. The first few times I put up Theota, I got very annoyed with having trouble leveling out everything, but after my 4th or 5th set up, I was feeling very confident in my ability and also being able to quickly move from one place to another to fix on something out in the water. 

Figure 3:  Aly fixing on a whale through the theodolite  

Like cliff site tasks, on-the-water protocols call for adaptability when things get rough; and the kayak is, in my opinion, more rigorous in protocol requirements, with much more room for error than the cliff work. This is likely because of the many types of gear we use while sampling from the kayak: we conduct visibility measurements, RBR Concerto and GoPro deployments, zooplankton net sampling — all while navigating in tricky ocean conditions. During our training, Allison took us out in the morning and taught us each how to properly navigate with the GPS and use all the sampling equipment like a pro. While it was a nice opportunity to double check everything with her, I knew going out without her wouldn’t be so easy. My first morning without Allison’s support, I had to redo multiple stations but was able to correct myself and learn from my mistakes. 

It is incredibly tiresome, but so rewarding to go out in the field early in the morning and come back to the lab in the afternoon with a tote full of new zooplankton samples or pictures of high-quality whale flukes to show everyone. The protocols in the lab are extensive, but the team has done a great job of taking tasks into their own hands and finishing processing data on their own accord.

Figure 4:  Zoop Troop on a beach walk 

So far, this internship has been an incredible opportunity for me, not just in my career but also in my personal life. I have learned so much from my team, everyone staying in the field station, and all the amazing people that I’ve had the pleasure to meet in the community. It has been so intriguing to learn about another small town in my home state of Oregon and compare all the similarities and differences from my home, Coos Bay. I’m so excited for what is to come in these next 4 weeks of research and for the team to keep you all informed. Having another summer to learn about the Pacific Ocean and solidify my love for marine life is such an endearing opportunity and I’m very grateful. I’m most excited for the first day I am able to complete all 12 sampling stations with ease. I believe my skills will continue to improve and I don’t expect any day to be dull working on this project. 

Zoop Troop team member, Aly, signing off!

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Updates from the 2023 Port Orford Gray Whale Foraging Ecology Project (team name TBD!)

Allison Dawn, Master’s student, OSU Department of Fisheries, Wildlife and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

Greetings from the South Coast Outpost, aka the Port Orford Field Station! Long-time GEMM lab blog readers will know that by this time of the year, our TOPAZ and JASPER projects are fully underway. We have officially entered our 9th consecutive year of these two integrated projects, which provides experiential learning internships to high school and undergraduate students while conducting long-term monitoring of gray whale foraging ecology in our small study region.

Much like last year, the Port Orford Field Station is at full capacity, with our team of five plus six other NSF REU, MSI, and Sea Grant interns. The research efforts here span a wide-range of subjects, including the long-standing ORKA kelp-urchin monitoring projects, river otter predation, science communication initiatives with the Redfish Rocks Marine Reserve, and more. This diversity in subject matter makes for excellent discussion during our communal dinners, and keeps the field station’s labs bustling with a variety of samples, gear, and equipment being transported in-and-out on a daily basis. Needless to say, it is a thriving environment for young scientists who are passionate about the community and ecosystems of the southern Oregon Coast. 

This is my third year participating in the project, and my second time as the solo graduate team leader. After having defended my master’s thesis this past June, I have been so excited to return to this incredible study site and share what I have learned about the system here with a new group of interns. I will write about my thesis work in a separate blog soon, but for now, I’d like to introduce you to the excellent group of motivated students that are on the team this year!

Figure 1: Autumn draws a pyramid while learning the equation for estimating zooplankton patch density, as provided in Hermanson, 2019.

First up, we have Autumn Lee.  Autumn is one of the GEMM Lab’s three REU students and together we are diligently working to automate the detection of zooplankton and predator occurrence from our in situ underwater cameras using the program VIAME. We hope to describe the predator-prey dynamics in Port Orford and a new, calculated metric for zooplankton patch density. Autumn moved to Mount Holyoke College, MA after celebrating their high school graduation with a drive-through commencement in Spring 2020. Despite the challenging start to undergrad due to COVID, Autumn is now a rising senior with a major in Neuroscience and Behavior with a certificate in Coastal Marine Sciences. Initially Autumn wanted to be a neurosurgeon or do veterinary medicine, but has always loved the ocean. After taking a few marine science classes back home, they decided to apply for our REU project in hopes of gaining their first marine science fieldwork experience. Autumn is excited to connect with like-minded students, the community, and volunteer with Port Orford Sustainable Seafood with the goal of consuming as much fresh, local seafood as possible in these six weeks.

Figure 2: Natalee beams after having captured two separate whales on camera for the first time.

Next on our team is Natalee Webster! Natalee is originally from St. Helens, OR and has her associates degree from Portland Community College. Natalee was on a nursing track but slowly accumulated environmental and marine biology classes that led her to obtain her first SCUBA diving certification. After this, she was hooked and decided to major in biology with a focus in marine biology. Now, Natalee has earned both her dive master and AAUS scientific dive certifications, and has already helped us deploy our underwater in situ cameras. Like Autumn, Natalee is excited to get involved with the community, meet other interns, and get her first scientific fieldwork experience. In addition to her water sport skills, she is already quite a natural at taking photos from the cliff site.

Figure 3: Aly enjoying a sunny morning on the cliff site with our high-powered binoculars.

Aly is a rising senior at Marshfield High School in Coos Bay, Oregon where her favorite subject is science. In particular, her favorite class is AP environmental where she first learned how to read dissolved oxygen graphs and was fascinated by how this metric can describe water quality for public health considerations. As of now, Aly is considering several colleges, including Oregon State University, with aspirations to major in marine science. Interestingly enough, she used to be afraid of the water. Despite this fear, and being the intrepid person she is, Aly taught herself how to surf during COVID and has since found a new-found respect for the ocean — so much so that she is now ready to make marine conservation her career. Aly is excited for our kayak training session next week and is ready to get in the water to start collecting zooplankton samples. Aly has had a consistently positive attitude during training week, even when learning the most tedious tasks, and can always make our team laugh. 

Figure 4: Jonah poses near Port Orford Sustainable Seafood while listening to the Junket audio tour of the town. 

Jonah is a junior at Pacific High School here in Port Orford where his favorite classes are math and woodshop, and he also loves to get involved in sports such as track and field, soccer, and basketball. As a freshman, Jonah took a 3-D printing class which affirmed his desire to learn more engineering techniques. While considering a summer job, Jonah was excited to watch our recruitment presentation and learn that he could use specialized equipment for marine science applications. He is now considering Oregon State University and Oregon Institute of Technology for his undergraduate career. Jonah has been a quick learner with excellent attention to detail, and is also an excellent cook — which myself and the others are grateful for. He is excited to spend more time on the cliff and wants to perfect his theodolite techniques to track whale movements.

Figure 5: First team photo! We were all very excited and grateful to have been greeted by two whales on our first day together.

In just this first week, we have deployed underwater cameras, tracked multiple whales in one day from the cliff, obtained Basic Life Safety/CPR certifications, and practiced kayak sampling methods from the dock. Next week, we have our kayak safety training, and will have many more days of practicing the cliff and kayak methods before we jump into official data sampling days. I know the team is just as excited as I am for the rest of the season, especially because of this increase in whale activity. It is heartening to see so many whales after our low occurrence year in 2021. Stay tuned for more updates, including what we decide for this year’s team name!

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Whale Filled Summer in the GEMM Lab

By Cristy Milliken, Thomas More University, GEMM Lab REU Intern

It’s summertime in the GEMM Lab, meaning many visiting students, interns, and technicians working in the lab (12 additional people to be precise!). This influx of new faces in the lab means blog posts by some new people, including me, Cristy Milliken, as I am an NSF REU intern. I am a rising junior at Thomas More University where I am majoring in Biology along with obtaining a double minor in marine biology and environmental science. Prior to this internship I knew little about humpback whales aside from them being baleen whales and large mammals. Safe to say, I know much more about humpbacks after researching them for the SLATE project. SLATE stands for Scar-based Long-term Assessment of Trends in whale Entanglements. The project utilizes photos of humpback whales that have been collected from 2005 to 2023 to develop and refine methods of analyzing scaring rates. These methods of scar analysis will be used to determine the effectiveness of fishing regulations in Oregon. The SLATE project started recently (February 2023) and thus the current stage of the project is focused on analyzing many individual photographs of humpback whales captured in Oregon waters to determine the presence or absence of an entanglement scar.

Finding evidence of a scar on a whale is tricky, and we have encountered a few issues while developing our methodology.  There is no universal method to analyze the scarring rate in whales, yet we are building off the methods created and utilized by Annabelle Wall and Jooke Robbins (Wall et al., 2019; Robbins., 2012). Robbins first developed the method of scar analysis using images of humpback whales in the Gulf of Maine. Wall refined the methods by creating set categories that classified every sighting of each  individual to determine the likelihood of being entangled in the past. The image scoring methods have some flaws, and the descriptions can be vague, leaving more questions than answers. One specific issue we faced was how best to define when an image is of the dorsal or perpendicular side of a whale’s tailstock because there were photos that were a mix of both body parts as seen in Figure 1. In the end, we chose to classify photos that did not show a clear view of both insertion points of the fluke into the tailstock as a perpendicular tailstock. It is important to make this distinction because the view of a whale’s body part can show very different markings that could change our perspective of the whale’s possible entanglement history. We also have to assess the quality of each image because the quality can hide or show details that could influence our ability to access the whale’s history. The quality of the photos range from being very good to being illegible, which can make scoring a bit difficult. Aside from these issues, I have been making progress and I have been enjoying the work that I am doing knowing could help researchers in the future. This area of research is something that I could possibly pursue in the future because I enjoy working in an area helping with conservation efforts.

Figure 1: Perpendicular tail fluke of a humpback whale. Photo taken by Jenn Tackaberry; Copyright Cascadia Research Collective.

In addition to my research project, I am also expanding my personal connections and boundaries.  I have started to feel more comfortable here in Newport, although I do miss my family. Everyone in the GEMM lab, as well as in the MMI in general, was very welcoming and kind so that made things easier to settle in. I have also been learning about other projects occurring since everyone has been showing off all the amazing videos and data being collected.  

It’s hard to believe that it’s already been four weeks since I’ve arrived in Oregon. Had anyone told me that after my freshman year of college I would spend an entire summer in Oregon studying humpback whales scarring I would have never believed them and called them crazy. I’ve spent the majority of my life in Ohio thinking that it’d be impossible to study marine biology. But yet I was offered the opportunity to work in the GEMM lab and I will always be thankful for the opportunity.

Confidence has always been a struggle for me, but I wanted to challenge my insecurities, so I put myself out there in my application. Doing so opened up this opportunity and it makes me glad that I took the chance. Internships are a great way to build up confidence while gaining research experience, especially this one. I have met many amazing and kind people here and it has created an amazing atmosphere here at the Hatfield Marine Science Center. So, this is my message to everyone: take the chance and reach out because the opportunity could be an arm’s length away.


  1. Robbins, J. (2012). Scar-based Inference Into Gulf of Maine Humpback Whale Entanglement: 2010.
  2. Wall, A. (2019). Temporal and spatial patterns of scarred humpback whales (Megaptera novaeangliae) off the U.S. West Coast. Master thesis, Macquarie University, Sydney, Australia.

Roger Payne: A life dedicated to whale conservation

By Dr. Alejandro A. Fernández Ajó, Postdoctoral Scholar, Marine Mammal Institute – OSU Department of Fisheries, Wildlife, & Conservation Sciences, Geospatial Ecology of Marine Megafauna (GEMM) Lab.

On Saturday, June 10, Dr. Roger Payne passed away. Throughout his remarkable life, he made impactful contributions to the study, understanding, and conservation of whales. His passion, research, and advocacy efforts played a pivotal role in reshaping public perception, and thus promoting the conservation of these giants, profoundly influencing generations of researchers in the field of conservation biology, including myself.

Roger in Patagonia where here found his love for Southern Right Whales. Credit: Mariano Sironi.

Roger in Patagonia where here found his love for Southern Right Whales. Credit: Dr. Mariano Sironi / ICB.

In 1970, Roger and his first wife Katy Paine began the Southern Right Whale (SRW) Research Program in Patagonia, Argentina, which in 1996 was continued by the Whale Conservation Institute of Argentina (the ICB) , becoming the longest continually running research program on a great whale (based on known individuals) in existence. In this study, Dr. Payne recognized that individual whales can be identified by the unique marks on their heads, establishing an important milestone for photo-ID, a technique that forms the bedrock of whale science.

I am proud to say that I am part of his legacy, as a member of the ICB. With the SRW program, I continued advancing research on SRW through my doctoral dissertation by advancing methods in conservation physiology (see blog post) to understand the underlaying mechanisms affecting young whales’ mortality in Patagonia (see blog post ).

Probably, one of the most remarkable contributions of Dr. Payne to the field and to whale conservation was his groundbreaking discovery of the humpback whale song. In the mid-20th century, the world’s whale populations were intensively killed by commercial whalers, threatening their extinction. In the late 1960s, Payne and his collaborators unveiled the melodic symphonies of humpback whales, marking the start of modern whale biology and catalyzing the global conservationist movement “Save the Whales”. These haunting songs connected humans with these enigmatic animals in an emotional manner, raising public opinion and support for whale conservation that ultimately led to the global moratorium on commercial whaling in 1982.

Listen to this story on NPR featuring Roger Payne’s LP, ‘Songs of the Humpback Whale,’ released in 1970, which played a pivotal role in sparking the global environmental movement “Save the Whales”, helping whale populations on the brink of extinction. Photo: Ocean Alliance.

While he continued to believe that science provides essential information about the necessary changes needed to protect whales, Dr. Payne strongly believe in that the paths to accelerate these changes often involve a combination of activism and creative arts.

…All of the great movements in human history have been based not on data but on emotion and passion, and a dream of a better society and a better life. For unless people connect emotionally with a problem they won’t connect with the numbers and the data that describe its dimensions…

“…It seems highly likely that the changes we so desperately need will only come by invoking emotions, and that is something that poets, musicians, writers, playwrights, sculptors, painters, dancers, composers—in fact, creative people of every stripe do well, but that scientists do at their peril. For the real challenge here is to get the world to fall so deeply in love with Nature that we will no longer tolerate the destruction of creation, and will risk our careers and our lives to save all plankton, mosses, ferns, trees, flowers, jellyfish, crinoids, nautiloids, crabs, bees, butterflies, beetles, squid, fishes, frogs, turtles, birds, and mammals—in other words, we will fight to save all of the non-human “Other”…”

From the “Final Voyage

Roger Payne’s influence and legacy continue to inspire generations of scientists and conservationists. His work expanded our understanding of whales, deepened our empathy for these creatures, and paved the way for international collaborations aimed at protecting marine life and preserving our oceans. Today, there are many of us who, inspired by Roger, dedicate our lives to research, environmental education, and conservation. And following Roger’s teachings, we constantly ask questions to seek answers that allow us to continue learning about whales in a changing world.

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The Way Forward is the End

By Morgan O’Rourke-Liggett, M.S., Oregon State University, Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

It is the end.

I graduated with a Master’s degree.

This journey began 10 years ago when I visited colleges as a high school junior.

Begin with the end in mind. 

I knew I would major in science as an undergrad and focus on something more specific as a graduate student. Studying whales required a background in marine biology, which led to my undergraduate degree in oceanography with strong emphasis in fisheries and wildlife, policy, and ecology. My master’s degree was built on that and added specific skills in data collection, management, and analysis.

The last time I wrote a blog, I was sharing the details of the data management and intricacies of my master’s project. Part of what made that project so successful was knowing the end goal: we wanted to know the area surveyed based on visibility and a visual representation of it. This knowledge aided in the development of matrices for environmental conditions, assigning integer variables to text survey notes, and determining what toolboxes and packages would be the most appropriate for analysis.

As a visual learner, I like to sketch out what I am doing or draw it on a whiteboard in a concept board. This approach is something I have always done and was further reinforced as a necessary step in my programming classes early on in my master’s education. My professors would assign a problem that could be solved in programming by making a function or script of code. We were taught to write out what our end goals were and what inputs were available for the problem. From there, filling in what steps were needed would be added. That was a critical step that made writing many difficult Python and R for loops and functions easier to build.

This skill and mentality of “beginning with the end” in mind can also be useful in preparation for data collection. There are eleven common data types that are described with examples in Table 1. Understanding what data type is being collected could save several hours of data management and wrangling during the data analysis phase. From my experience in data analytics, some models yield more accurate results if the character data is manipulated to behave like an integer in R. Additionally, certain packages and toolboxes in R and GIS are only useful for certain data types.

Data TypeDefinitionExample
Integer (int)Numeric data without fractions-707, 0, 707
Floating point (float) or DoubleNumeric data with fractions707.07, 0.7, 707.00
Character (char)Single letter, digit, space, punctuation mark, symbola, !
String (str or text) or ComplexSequence of characters, digits, or symbolsHello, +1-999-666-3333
Boolean (bool) or LogicalTrue or false values0 (false), 1 (true)
Enumerated type (enum)Small set of predefined values that can be text or numericalrock (0), jezz (1)
ArrayList with a number of elements in a specific orderrock (0), jazz (1), blues (2), pop (3)
DataDate in YYYY-MM-DD fomat2021-09-28
TimeTime in hh:mm:ss format or a time interval between two events12:00:59
DatetimeStores a value of both YYYY-MM-DD hh:mm:ss2021-09-28
TimestampNumber of seconds that have elapsed since midnight, 1st January 1970 in UTC1632855600
Table 1. Table of the eleven most common data types with a short definition and an example of the data type. Table inspired by (Choudhury 2022).

Beginning with the end in mind allows more clarity and strategies to be efficient and achieve your goal. It develops a better understanding of why each stage of data collection and analysis is important; why each stage in a career is important. It provides a road map for what will, undoubtedly, be an incredible learning experience.


Choudhury, A. 2022. What are Data Types and Why are They Important. https://amplitude.com/blog/data-types#datetime

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“May the Force be with you” – or how to be a good mentor?

By Solène Derville, Postdoc, OSU Department of Fisheries, Wildlife, and Conservation Science, Geospatial Ecology of Marine Megafauna Lab

This year, for the 15th consecutive summer, the Hatfield Marine Science Center (HMSC) will be hosting undergraduate interns as part of the NSF-funded Research Experiences for Undergraduate (REU) program. The GEMM Lab will provide research experiences to no less than three REU interns for a 10-week period starting mid-June. Along with Leigh, Dawn, and Allison, I will be a daily “mentor” to one of these students; a role that the HMSC REU program takes very seriously.

I used quotation marks here because although I have been supervising/helping/engaging/leading teams and students for many years, I only really learned this new word, “mentoring”, after moving to the US. In my native language, French, the word “mentor” exists and has the same meaning as in English (i.e. a person who gives a younger or less experienced person help and advice over a period of time, especially at work or school; Cambridge Dictionary). However, the verb derived from this noun – “mentoring” – does not exist in French and the word we use instead sounds more like “supervising”. Actually, an advisor to a trainee or intern is often called “maître de stage”, literally meaning “internship master”, which conveys a pretty different message from the title mentor…

Why does that semantic nuance matter? Well, I believe that the words we use are an extension of the way we see the world. Fact is, although I have been an advisor to several students before, I had never received any formal mentoring training up to today and I never put that much thought into what mentoring meant to me. Well, I certainly did not see myself being anyone’s Master! So, what is the difference between mentoring and supervising?

A quick google search gave me a hint… supervision is very much task-oriented, it’s about overseeing a person’s activities and providing instructions and recommendations to ensure that the task is successfully completed. That’s all good and well, but mentoring adds an additional layer of care for the person’s long-term development, in an approach that strives to be more holistic. That approach may seem obvious to many academics today, but unfortunately things don’t always happen that way. Many of us could cite several cases where we have observed students being used as additional work force without much attention given to their wellbeing, learning, and personal development. Who has never seen a real-life professor like that of Phd Comics (Illustration below)? On top of that, mentoring styles, and the academic system as a whole, have long shaped the new generations of scientists to resemble their senior mentors, hence perpetuating inequity in education and a lack of diversity in research carriers.

PhD Comics is probably one of the most hilarious yet highly accurate depictions of the flaws of academic mentoring. Comic reproduced from “Piled Higher and Deeper” by Jorge Cham, www.phdcomics.com.

I discovered that there are a lot of great resources out there to help early-career scientists navigate the waters of mentorship (e.g., Center for Improved Mentored Experiences in Research, OSU guidance for DEI learning). I also really appreciated the fact that the HMSC REU program director, Itchung Cheung, would take the time to meet all future mentors ahead of time, and make sure that they had the tools and resources to be good mentors. He made it clear that a student has many mentoring needs (e.g., role models, emotional support, access to opportunities, professional development…) and that it is not possible for one person to fill all these shoes. As PhD student Rachel Kaplan pointed out “It takes a village to raise a PhD student”! That being said, there are a couple simple rules that everyone should agree on before taking on interns or new students. I will not list all these best practices here but some of main take-away messages for me were the importance of planning, having clear expectations while staying flexible, encouraging interns to take an active role in setting goals and providing critical feedback, and fostering a welcoming environment in which the student can feel a sense of belonging.

Along those lines, I would like to end on a more personal note. Although I never received formal mentorship training, I do believe that I learned some of these skills in the most traditional way;  that is by learning by example. And (hopefully!) this process did not turn too badly because I was lucky to have great mentors to look up to. Among other qualities, my mentors always made me feel like I belonged, like what I had to say mattered. Reflecting upon my years as a graduate student, I now realize that this feeling is one of the things that allowed me to love research, with all its setbacks and challenges. My mentors always made me feel like I was among their priorities, whether it be by returning manuscript edits in time or listening to me present all of my latest analysis outputs and coding tribulations. Holistic mentoring is a bit of a jargony word, and although I am still learning the theories underlying that approach, I know that if that’s what I experienced as a mentee, then that’s what I will try to do as a mentor!

To learn more about research experiences for undergraduate at Oregon State University, check out this link.

Individual Specialization Part 3: How do individual characteristics relate to individual specialization?

Clara Bird, PhD Candidate, OSU Department of Fisheries, Wildlife, and Conservation Sciences, Geospatial Ecology of Marine Megafauna Lab

While I did not mean to start a mini-blog series on individual specialization, here I am with my third blog about individual specialization in as many years. Looking back, these blogs are actually a lovely documentation of my own journey of learning about individual specialization and I hope you’re enjoying being along for the ride.

So, what have we learned so far? In my first blog I described the concept of individual specialization, why it matters, and presented some case studies. In my second blog I discussed the roles of competition and learning as drivers of individual specialization. Let’s review: Individual specialization is when individuals within a population only use a subset of the resources that the full population uses, but different individuals use different subsets. This is important to quantify for two reasons: (1) it affects how we think about conserving and managing a population (Bolnick et al., 2003), and (2) it can affect the relationships between the population and the other species in its community (Bolnick et al., 2011). Common drivers of specialization are competition and learning. Competition can lead to specialization because it reduces the availability of a resource, driving individuals to switch resource use (Pianka, 1974). Learning can also lead to specialization through ‘one-to-one’ learning, where one individual learns from one demonstrator (Sheppard et al., 2018). This individual tends to then use, and eventually teach, that specialized technique.

While understanding these drivers is important, the question of why specific individuals employ specific specializations remains. If learning is not the driver of specialization, then how do individuals end up using their specific subset. Is it random? Or are there underlying patterns? The common sources of variation are related to sex, age, or size (and often these three can be inter-connected) (Dall et al., 2012). 

Individual differences related to the sex of the individuals are called sexual dimorphisms. Physical and ecological differences between the sexes are common throughout nature (peacocks for example) and these differences can lead to different specializations. Northern elephant seals provide a fascinating example (Kienle et al., 2022). Northern elephant seal males are the distinctly larger sex as they engage in competitionfor females. Because of their larger body size and energy expenditure during competition, they have much higher energetic requirements than females during the breeding season, meaning that they need to consume more prey. This elevated requirement has led to a difference in foraging behaviors. Males forage near the continental shelf where there is more prey while females forage further offshore in the open ocean. However, the tradeoff of feeding on the continental shelf is an increased predation risk due to overlap with predator habitat, and indeed Kienle et al. found that the mortality rate for foraging trips was 5-6 times higher for males than females. So, while males need to take the risk of foraging in an area with higher predator presence to meet their energetic demands, females can forage in a safer habitat with less prey because their energetic requirements are lower. This study presents an excellent example of how sexual dimorphism can cause individual specialization and the subsequent consequences.

An illustration depicting a male (background) and female (foreground) northern elephant seal. source: https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/northern-elephant-seal. Illustration by Pieter Folken.

Individual specializations attributed to differences between distinct morphs are called resource polymorphisms. A morph is the physical appearance of an individual; distinct morphs are when there are clearly different kinds of morphs within a population. Morphs can range from color polymorphism (ex. lizards of different colors within the same species) to differences in skull shape and size. A study on the European eel found that differences in skull morphology were related to different foraging strategies (Cucherousset et al., 2011).  Eels with larger head widths consumed larger prey types. Interestingly, they found that eels on either end of the head width spectrum (i.e., very narrow or very wide) were more successful (i.e., in better body condition) than eels with intermediate head widths. They suggest that this difference in nutrition success is because the intermediate head width eels were less efficient foragers than eels at the extremes. In this example we see that morphology is related to the ability to feed on a prey type and has consequences for individual health.

Figure 2. from Cucherousset et al., 2011. Small-bodied eels with narrower (a) and broader (b) heads and large-bodied eels with narrower (c) and broader (d) heads. TL (Total Length) and HW (Head Width):TL are shown for each individual

Individual differences related to changes in size, shape, and behavior that occur as an individual grows are called ontogenetic shifts. As you have experienced yourself, there are many changes that occur as an individual grows, and these changes can mean that different age classes have different specializations. Gustafsson (1988) found an ontogenetic shift in where coal tits (a species of bird) fed within a pine tree. Younger birds were more generalists but tended to feed on the outer sections of the tree, while adults foraged on the more profitable, central portion of the tree. He attributes this difference to dominance of adults over juveniles. Gustafsson also found that the larger individuals within each age class also tended to feed closer to the center of the tree. This within age class difference is attributed to a larger body size being better suited for feeding closer to the center of the tree, while smaller body sizes are better suited for hovering and foraging on the outside. Interestingly, this study occurred over multiple years, and Gustafsson documented several juvenile individuals that shifted foraging behavior when they became adults. 

Photo of a coal tit. Source: https://ebird.org/species/coatit2

These sources of behavioral variation are important to account for because ultimately phenotypic variation can affect not only a population’s niche, but its population size, distribution, evolutionary potential, and vulnerability to environmental change (Wennersten & Forsman, 2012). And it’s important to determine which source(s) of variation are at play to inform best population management practices. Different behaviors between sexes versus age classes have different implications for the population, making it necessary to not only assess if there are differences but also to try and understand their drivers.

This behavioral variability relative to morphs is something that is of particular interest to me, and it is the focus of my first chapter. We’ve documented that the PCFG gray whales in our study region employ a variety of foraging tactics, and I want to know if there is specialization in tactic use and if we can find an underlying source of the variation. I can’t wait to share results with you in the next installment of this individual specialization journey. Stay tuned!

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Bolnick, D. I., Amarasekare, P., Araújo, M. S., Bürger, R., Levine, J. M., Novak, M., Rudolf, V. H. W., Schreiber, S. J., Urban, M. C., & Vasseur, D. A. (2011). Why intraspecific trait variation matters in community ecology. Trends in Ecology & Evolution26(4), 183–192. https://doi.org/10.1016/j.tree.2011.01.009

Bolnick, D. I., Svanbäck, R., Fordyce, J. A., Yang, L. H., Davis, J. M., Hulsey, C. D., & Forister, M. L. (2003). The ecology of individuals: Incidence and implications of individual specialization. American Naturalist161(1), 1–28. https://doi.org/10.1086/343878

Cucherousset, J., Acou, A., Blanchet, S., Britton, J. R., Beaumont, W. R. C., & Gozlan, R. E. (2011). Fitness consequences of individual specialisation in resource use and trophic morphology in European eels. Oecologia167(1), 75–84. https://doi.org/10.1007/s00442-011-1974-4

Dall, S. R. X., Bell, A. M., Bolnick, D. I., & Ratnieks, F. L. W. (2012). An evolutionary ecology of individual differences. Ecology Letters15(10), 1189–1198. https://doi.org/10.1111/j.1461-0248.2012.01846.x

De Meyer, J., Belpaire, C., Boeckx, P., Bervoets, L., Covaci, A., Malarvannan, G., De Kegel, B., & Adriaens, D. (2018). Head shape disparity impacts pollutant accumulation in European eel. Environmental Pollution240, 378–386. https://doi.org/10.1016/j.envpol.2018.04.128

Gustafsson, L. (1988). Foraging behaviour of individual coal tits, Parus ater, in relation to their age, sex and morphology. Animal Behaviour36(3), 696–704. https://doi.org/10.1016/S0003-3472(88)80152-0

Kienle, S. S., Friedlaender, A. S., Crocker, D. E., Mehta, R. S., & Costa, D. P. (2022). Trade-offs between foraging reward and mortality risk drive sex-specific foraging strategies in sexually dimorphic northern elephant seals. Royal Society Open Science9(1), 210522. https://doi.org/10.1098/rsos.210522

Pianka, E. R. (1974). Niche Overlap and Diffuse Competition71(5), 2141–2145.

Sheppard, C. E., Inger, R., McDonald, R. A., Barker, S., Jackson, A. L., Thompson, F. J., Vitikainen, E. I. K., Cant, M. A., & Marshall, H. H. (2018). Intragroup competition predicts individual foraging specialisation in a group-living mammal. Ecology Letters21(5), 665–673. https://doi.org/10.1111/ele.12933

Wennersten, L., & Forsman, A. (2012). Population-level consequences of polymorphism, plasticity and randomized phenotype switching: A review of predictions. Biological Reviews87(3), 756–767. https://doi.org/10.1111/j.1469-185X.2012.00231.x