By: Maggie O’Rourke-Liggett, GEMM lab summer intern, Oregon State University
Enjoy this short video showcasing the intern experience from the gray whale foraging ecology project this summer. Check back next week for a recap of our preliminary results.
By Quince Nye, GEMM Lab Summer Intern, Pacific High School Junior
I have spent a lot of my life surrounded by nature. I like to backpack, bike, dive, and kayak in these natural environments. I also have the luck of having parents who are always planning to take me on another adventure where I get to see nature and its inhabitants in ways most people don’t get to enjoy.
Through my backyard explorations, I have begun to realize that Port Orford has an amazing ecosystem in the coves and rivers that are very tied into our community. I’ve fished and swam in these rivers, gone on kayaking tours in these coves (with a great kayak company called South Coast Tours that we partner with), and I’ve seen the life that dwells in them.
Growing up in a school of less than 100 kids I have learned to never reject an opportunity to be a part of something bigger and learn from that experience. So when one of my close friends told me about an OSU project (a college I’m interested in attending) that needed interns to help collect data on gray whales, and kayak almost every day, I signed up without a doubt in my mind.
Fast forward a month, and I wake up at 5:20 am. I eat breakfast and get to the Port Orford Field Station. We make a plan for the operations of both the kayak team and cliff team. Today, I’m part of the cliff team, so I head up above the station to Fort Point. Florence and I set up the theodolite and computer at the lookout point and start taking half hour watch shifts searching the horizon for the spout of a gray whale. Sometimes you see one right away, but other times it feels like the whales are actively hiding from you. These are the times I wish Maggie was here with her endless supply of Disney soundtracks to help pass the hours.
A whale spouts out at Mill Rocks and starts heading across to the jetty. Hurray, its data collection time! I try to quickly move the cross-hairs of the theodolite onto the position of the whale using a set of knobs like those on an etch-a-sketch. As you may understand, it’s not an easy task at first but I manage to do it because I’ve been practicing for three weeks. I say “Mark!” cueing Florence to click a button in the program Pythagoras on the computer to record the whale’s position.
Meanwhile, Florence sees that the whale has two white spots where the fluke meets the knuckles. Those are identifying marks of the beloved whale, Buttons. This whale has been seen here since 2016 and is a fan favorite for our on-going research program. Florence gets just as excited every time and texts her eagerly awaiting interns of previous years all about the sighting. Of course Buttons is not the only whale to have identifying marks such as scars and pigmentation marks. This is why we make sure to get photos of the whales we spot, allowing us to do photo-ID analysis on them through comparison to our database of pictures from previous years.
So far I have gained skill after skill in this internship. I got CPR certified, took a kayak training class, learned how to use a theodolite, and have spent many educational (and frustrating) hours entering data in Excel. I joined the program because I was interested in all of these things. It surprised me that I was developing a relationship with the whales I’m researching. By the end of August I’m now sure that I will also know many of the whales by name. I will probably be much better at using an etch-a-sketch, and I will have had my first taste at what being a scientist is like. What I strive for, however, is to have the same look in my eyes that appears in Florence’s whenever a familiar whale decides to browse our kelp beds.
By Nathan Malamud, GEMM Lab summer intern, Pacific High School senior
I am someone who has lived in a small town for all his life. Pretty much everyone knows each other by their first name and my graduating class only has around 20 people. Everywhere you look you will find a farm, ranch, or cranberry bog (even our school has two bogs of their own!). Because of my small town life, I have a strong sense of community. However, I have also developed a curiosity about natural and global phenomena. I try to connect these two virtues by participating in scientific efforts that help my community. When I heard that the OSU Port Orford Field Station was offering internships, I knew right away that it would definitely be a great experience for me.
Port Orford, on Oregon’s southern coast, is a town that is closely tied to the ocean. So naturally, it’s important to understand and monitor our surroundings so that our town can thrive. Last year, my Marine Science class helped me further understand the complexity of the ocean. Our first semester taught us all about marine biology, zoology, and ecology. Our second semester immersed us into oceanography, ocean geology, and ocean chemistry. During the second semester, we also took trips to our town’s marine science center and to the marine reserve near Rocky Point. I loved this course and decided to try to expand my knowledge about the subject by going to the OSU Field Station.
As an intern, I am currently working with three teammates to understand the feeding behavior of gray whales – what places they like to eat zooplankton the most and why they like to eat there. This whale project helps our community by Port Orford enabling high school students to perform college-level scientific research and inquiry, as well as allowing us to learn valuable skills such as CPR, surveying using a theodolite, working with chemicals in a lab, and data processing.
This internship with OSU’s GEMM Lab has taught me many new skills and given me new experiences that I have never had before. Before this internship, I had never been in a kayak. Now, I go out on the water nearly every other day! When on the water, I always try to sharpen my navigating skills. I use a GPS to pinpoint the locations of our sampling stations, and I communicate to my partner where we need to go and how we will get there.
Once we are there, it is my job to keep the boat close to the station location so that my partner can get accurate samples. This part is a very tricky task, because not only do I have to pay attention to the GPS to make sure we are within 10 meters of the spot, but I also have to pay attention to my surroundings. I have to look at the ocean, and figure out what direction the waves are coming from. I have to watch how external forces, like wind and currents, can cause the boat to drift far from station, and I have to correct drifting with gentle paddle strokes. This is hard, especially since the kayak is so light and easy to get pushed around by the wind. However, despite the difficulty, I have learned that it is crucial not to panic. Frustration only makes things worse. The key is to maintain a harmonic balance of concentration and zen.
I have also learned that when collecting data in the field, it’s important to observe and document as much as possible. When we are in the kayak, we have 12 stations that we try to visit every day (as long as the weather cooperates). At each station, we first use a secchi disk to test the water clarity, then lower the GoPro to film the water column and see where the zooplankton are. Sometimes we catch other interesting things on the video too, such as siphonophores (my personal favorites are jellies and salps) and rockfish.
Next we tow a zooplankton net through the water, and let it collect zooplankton of all shapes and sizes, from tiny mysids to skeleton shrimp. Then we proceed to the next station and repeat the process. We have to remember to label everything, and tell the GoPro camera what station we’re at so we can sort all the information correctly when we get back to the field station. At the end of the day, we log our data into a computer, and preserve half our plankton samples with ethanol, so that we can identify the species present. The other half gets frozen for caloric content analysis by our collaborator Dr. Kim Bernard to help us understand how much zooplankton a whale needs to eat to meet its energy needs each day.
By repeating this entire process every day, we are able to look at daily changes, which also helps us to better understand why whales spend time in certain areas and not others. Be sure to check out my teammate Maggie’s blog post about some of the tools and technologies we use to track the whales!
This whale project has been, and definitely still is, a great experience for me! I have learned a lot and have worked with some amazing people. I believe that I am learning many valuable skills, and that the skills I learn will allow me to help my community.
Guest writer: Maggie O’Rourke-Liggett, GEMM Lab summer intern, Oregon State University,
One of the biggest obstacles an undergraduate can face is fulfilling the degree requirement of completing an internship or research opportunity. With almost every university and degree program requiring it for graduation and many employers requiring prior experience, the amount of pressure and competition is intense.
After being rejected from the internships I applied for earlier in the year, I heard about Dr. Leigh Torres’s research with the Geospatial Ecology of Marine Megafauna (GEMM) Lab . I decided to email her and ask if she had any open positions. Fast-forward a few weeks and I am collaborating with Florence Sullivan, a recent masters graduate from OSU, on the logistics of my Gray Whale Foraging Behavior internship with the GEMM Lab.
During my time with the GEMM Lab team, I have been assisting with photo identification analysis of gray whales (Eschrichtius robustus), using a theodolite and Pythagoras computer program to track their movements, collecting samples of the zooplankton they eat, and recording other oceanographic data with our time-depth recorder. This project is hoping to identify the drivers of gray whale fine-scale foraging behavior. For instance: Why do gray whales spend more time in some areas than others? Does the type or density of prey affect their behavior? Do the whales use static features like kelp beds to help find their food? As a senior currently studying oceanography, who desires to study whale behavior in the future, this internship is like finding a gold mine.
Ever since day one at Hatfield Marine Science Center, I’ve been working with people who share the same passions for marine mammals as me. Spending hours upon hours sorting thousands of pictures may seem like a painful, tedious job, but knowing my work helps others to update existing identification catalogs makes it worthwhile. Plus, who wouldn’t want to look at whales all day?! After a while, you start to recognize specific individuals based on their various pigment configurations and scars. Once you can recognize individuals, it makes the sorting go by faster and helps with recognizing individual whales in the wild faster. It’s always exciting to sort through the photos and observe from the cliff or kayak and recognize a whale from the photo identification work.
After Florence taught me how to set up and operate the theodolite, a survey tool used to track a whale’s movements, we taught a class to undergrads on how to use it. I’ll never get over how people’s faces lit up when we discussed how the instrument works and its role in the overall mission.
These past two weeks at OSU’s Port Orford Field Station have been like living on a little slice of heaven. My days are filled with clear views of the coast and the sound of waves crashing serve as a backdrop on my home for the month, the bed-and-breakfast turned field station. Each morning, the sun fills my room as I gather my gear for the day and help my teammates load the truck. We spend long days on the water collecting zooplankton samples and GoPro video or on the cliff recording whale behavior through the theodolite. To anyone searching for an internship and feeling burnt out from completing application after application, don’t give up. You’ll find your slice of heaven too.
By: Catherine Lo, Research Intern, Oregon State University ‘16
Hello everyone! My name is Catherine Lo and I am a recent graduate from Oregon State University with a Bachelor’s of Science in Biology with a focus in Marine Biology. It has been an incredible whirlwind leading up to this point: long nights studying for finals, completing my degree, and planning the next steps for my future. I am fortunate to be working as a summer research intern for the GEMM Lab under the supervision of Dr. Leigh Torres and Msc. student Florence Sullivan in their research on the foraging ecology of gray whales. I have dreamed of working with marine mammals, potentially as a research veterinarian and so, capturing this position has been a great opportunity to begin my career.
The days go slow, but the weeks go fast. It’s already week 4 of our field season and the team and I are definitely in the groove of our research. The alarm(s) goes off at 5:00 AM…okay maybe closer to 5:30 AM (oops!), getting dressed for either the kayak or cliff based work, scarfing down breakfast that is usually a diet consisting of toast and peanut butter, and then heading off to the beach to launch the kayak. But this week it was different. A dredging event in Port Orford coordinated by the US Army Corps of Engineers is now taking place right next to the port’s jetty near our study site (Figure 1). This is an important process to move the sediment built up during the year in order for ships to safely navigate in and out of the port. We knew this was going to happen at some point over the summer, and worried that it might impact our research methods and objectives, but at the same time it offers some new opportunities: the chance to see how our GoPro and mysid sampling methods in Tichenor Cove are impacted by the sediment flow from the dredging activities.
My teammate Kelli and I were stationed on the cliff during the first deposit of sediment after the dredge’s first night and morning’s worth of scooping sand. None of us knew where the actual deposit site would be so we kept a good eye on it. The ship headed past the jetty. Turned around and, as a concerned feeling mustered within our field team, it began lowering the platform holding the sand just 250 yards away from our primary study site in Tichenor Cove! At this point, we knew things were going to be different in our samples. Unfortunately along with the sediment stirring up from dredging, we think a phytoplankton bloom is occurring simultaneously. Our GoPro footage lately has been rather clouded making it difficult to identify any mysid relative to our past footage. You can compare Figure 2 to the GoPro image found in Figure 2 of a previous post. It is times like these that we learn how dynamic the ocean is, how human activity can alter the ocean ecosystem, and how to adapt to changes, whether these adaptations are within our reach or not. We are interested to see how our sample sites will change again over time as the dredging operation finishes and the phytoplankton bloom ends.
Aside from the current water clarity situation, we’ve also had some exciting moments! Given how few whales we’ve seen thus far and how the ones we have tracked are predominately hanging by Mill Rocks, which is ~1km east of Tichenor Cove, Dr. Leigh Torres—our head advisor—thought it would be a good idea to check out the mysid scene over there to see what the attraction was. So, we sent our kayak team over there to conduct a few GoPro drops and zooplankton net tows and figure out what is so enticing for the whales.
While conducting this sampling work at Mill Rocks, I and my teammate were lucky enough to encounter a gray whale foraging. And believe me, we were going “off-the-walls” as soon as we heard from the cliff team and saw a blow as the whale surfaced nearby. It was one of those “best time of my life” moments where my dreams of kayaking this close to a whale came true. We fumbled around for our waterproof camera to get clear shots of its lateral flanks for photo identification while also trying to contain our excitement to a more decent level, and at the same time we had to make sure we were not in the whale’s path. There it was; surface after surface, we admired the immense size and beauty of a wild animal before our eyes. The worst part of it was when our camera battery died not long after taking a few pictures, but in a way it gave us a chance to really appreciate the existence of these animals. Note to self during research: always check your batteries are fully charged before heading out!
It baffles me how so often people walk along beaches or drive by without knowing an animal as incredible as this whale is just outside of the shoreline. Every time I’m inside pulling out time stamps or doing photo identification, I always think, “I wonder if there’s a whale in Tichenor Cove or at Mill Rocks right now…Yeah, there probably is one”. Alas, the data management work needs to be done and there’s always the next day for an opportunity of a sighting.
For a few days, our kayak team wasn’t able to work due to a small craft advisory. If you’ve ever been to Port Orford, you’d understand the severity of how windy it gets here. Ranging between 15 knots to 25 knots as early as 7am, so it gets rather difficult to maintain position at each of our sampling stations in our kayak. Fortunately our cliff team was able to set out. We were lucky to see a small whale foraging inside Tichenor Cove and later move onto Mill Rocks. This little one was giving us quite a show! Almost every time it came to the surface, defecation was observed shortly after. As unpleasant as feces might be, it can actually provide an abundance of information about a specific whale including sex, reproductive status, hormone levels, and much more. While doing our research, we are always keeping an eye out for signs of defecation in order to collect samples for another lab member’s PhD work. Here you can check out more information about Leila’s research. Figure 3 depicts a great image of defecation captured by our cliff team.
In addition to helping out Leila’s work, we recently began a collaboration with Aaron Galloway from The Oregon Institute of Marine Biology (OIMB). Aaron and his post-doc are looking at the fatty acid composition of mysid as an approach to eventually infer the diet of an aquatic animal. Check out his website which is linked to his name to learn more about the basis of his approach! While we collect mysid samples for them, in return they give us substantial information about the energy content of the mysid. This information on the energetic content of mysid will help the GEMM Lab answer questions about how much mysid gray whales need to eat.
Oregon State University and University of Oregon have a long-standing, intense rivalry. However, as an Alumna from Oregon State, I am amazed and thrilled to see how these two institutions can come together and collaborate. I mean, we’re all here for the same thing. Science, right? It creates the opportunity to apply integrative research by taking advantage of various expertise and resources. If we have those chances to reach out to others, why not make the most of it? In the end, sound science is what really matters, not rooting for the ducks or beavers.
My marine science background is based on my experiences looking at tidepools and hopping around on rocks to understand how vast intertidal communities range from invertebrates to algae. These experiences were an incredible part of my life, but now I look at the ocean unsure of what animals or environmental situations I might encounter. That’s what makes it so attractive. Don’t get me wrong. The intertidal will always hold a special place in my heart, but the endless possibilities of being a part of this marine mammal research team is priceless. I have learned so much about myself including my strengths and weaknesses. Living in Port Orford, which is a small coastal town with just a little over 1,000 people gives you a new perspective. The community has been very welcoming and I have appreciated how so much interest is placed on the kind of work we do. As I eat my nightly bowl of ice cream, I think about how, from here on out, the good and the bad can only bring a lifetime of skills and memories.
By: Kelli Iddings, MSc Student, Duke University, Nicholas School of the Environment
The excitement is palpable as I wait in anticipation. But finally, “Blow!” I shout as I notice the lingering spray of seawater expelled from a gray whale as it surfaces to breathe. The team and I scurry about the field site taking our places and getting ready to track the whale’s movements. “Gray whale- Traveling- Group 1- Mark!” I exclaim mustering enough self-control to ignore the urge to drop everything and stand in complete awe of what in my mind is nothing short of a miracle. I’ve spotted a gray whale searching and foraging for food! As a student of the Master of Environmental Management program at Duke University, I am collaborating on a project in Port Orford, Oregon where my team and I are working to gain a better understanding of the interactions between the Pacific Coast Feeding Group (PCFG) gray whales and their prey. Check out this blog post written earlier by my teammate Florence to learn more about the methods of the project and what motivated us to take a closer look at the foraging behavior of this species.
Understanding the dynamics of gray whale foraging within ecosystems where they are feeding is essential to paint a more comprehensive picture of gray whale health and ecology—often with the intent to protect and conserve them. A lot of our recent effort has been focused on developing and testing methods that will allow us to answer the questions that we are asking. For example, what species of prey are the PCFG whales feeding on in Port Orford? Based on the results of a previous study (Newell and Cowles 2006) that was conducted in Depoe Bay, Oregon, and a lot of great knowledge from the local fisheries and the Port Orford community, we hypothesized that the whales were feeding on a small, shrimp-like crustacean in the order Mysida. Given the results of our videos, and the abundance of mysid, it looks like we are right (Fig. 1)!
![DSCF0776[3]](http://blogs.oregonstate.edu/gemmlab/files/2016/07/DSCF07763-e1468372770128.jpg)
Once we know what the gray whales are eating, and why, we ask follow up questions like how is the distribution of mysid changing across space and time, if at all? Are there patterns? If so, are the patterns influencing the feeding behavior and movement of the whales? For the most part, we are having success characterizing the relative abundances of mysid. No conclusions can be made yet, but there are a few trends that we are noticing. For instance, it seems that the mysid are, as we hypothesized, very dense and abundant around the rocky shoreline where there are kelp beds. Could these characteristics be predictors of critical habitat that whales seek as foraging grounds? Is it the presence of kelp that mysid prefer? Or maybe it’s the rocky substrate itself? Distance to shore? Time and data analysis will tell. We have also noticed that mysid seem to prefer to hang out closer to the bottom of the water column. Last, but certainly not least, we are already noticing differences in the sizes and life stages of the mysid over the short span of one week at our research site! We are excited to explore these patterns further.
The biggest thing we’re learning out here, however, is the absolute necessity for patience, ingenuity, adaptability, and perseverance in science. You heard that right, as with most things, I am learning more from our failures, than I am from our successes. For starters, understanding mysid abundance and distribution is great in and of itself, but we cannot draw any conclusions about how those factors are affecting whales if the whales don’t come! We were very fortunate to see whales while training on our instruments in Newport, north of our current study site. We saw whales foraging, whales searching, mother/calf pairs, and even whales breaching! Since we’ve been in Port Orford, we have seen only three whales, thrown in among the long hours of womanpower (#WomenInScience) we have been putting in! We are now learning the realities of ecological science that >gasp< fieldwork can be boring! Nevertheless, we trust that the whales will hear our calls (Yes, our literal whale calls. Like I said, it can get boring up on the cliff) and head on over to give the cliff team in Port Orford some great data—and excitement!
Then, there is the technology. Oh, the joys of technology. You see I’ve never considered myself a “techie.” Honestly, I didn’t even know what a hard drive was until some embarrassing time in the not-so-distant past. And now, here I am working on a project that is using novel, technology rich approaches to study what I am most passionate about. Oh, the irony. Alas, I have been putting on my big girl britches, saddling up, and taking the whale by the fluke. Days are spent syncing a GoPro, Time-Depth Recorder (TDR), GPS, associated software, and our trusty rugged laptop, all the while navigating across multiple hard drives, transferring and organizing massive amounts of data, reviewing and editing video footage, and trouble shooting all of it when something, inevitably, crashes, gets lost, or some other form of small tragedy associated with data management. Sounds fun, right? Nonetheless, within the chaos and despair, I realize that technology is my friend, not my foe. Technology allows us to collect more data than ever before, giving us the ability to see trends that we could not have seen otherwise, and expending much less physical effort doing so. Additionally, technology offers many alternatives to other invasive and potentially destructive methods of data collection. The truth is if you’re not technologically savvy in science these days, you can expect to fall behind. I am grateful to have an incredible team of support and such an exciting project to soften the blow. Below (Fig. 3) is a picture of myself embracing my new friend technology.
Last but not least, there are those moments that can best be explained by the Norwegian sentiment “Uff da!” I was introduced to the expression while dining at The Crazy Norwegian, known famously for having the best fish and chips along the entire west coast and located dangerously close to the field station. The expression dates back to the 19th century, and is used readily to concisely convey feelings of surprise, astonishment, exhaustion, and sometimes dismay. This past week, the team was witness to all of these feelings at once as our GoPro, TDR, and data fell swiftly to the bottom of the 42-degree waters of Tichenor cove after the line snapped during deployment. Uff da!!! With our dive contact out of town, red tape limiting our options, the holiday weekend looming ahead, and the dreadful thought of losing our equipment on a very tight budget, the team banded together to draft a plan. And what a beautiful plan it was! The communities of Port Orford, Oregon State University, and the University of Oregon’s Institute of Marine Biology came together in a successful attempt to retrieve the equipment. We offer much gratitude to Greg Ryder, our retrieval boat operator, OSU dive safety operator Kevin Buch, and our divers, Aaron Galloway and Taylor Eaton! After lying on the bottom of the cove for almost three days, the divers retrieved our equipment within 20 minutes of the dive – thanks to the quick and mindful action of our kayak team to mark a waypoint on the GPS at the time of the equipment loss. Please enjoy this shot (Fig. 4) of Aaron and Taylor surfacing with the gear as much as we do!
The moral of the story is that science isn’t easy, but it’s worth it. It takes hard work, long hours, frustration, commitment, collaboration, and preparedness. But moments come along when your team sits around a dining room table, exhausted from waking and paddling at 5 am that morning, and continues to drive forward. You creatively brainstorm, running on the fumes of the passion and love for the ocean and creatures within it that brought everyone together in the first place; each person growing in his or her own right. Questions are answered, conclusions are drawn, and you go to bed at the end of it all with a smile on your face, anxiously anticipating the little miracles that the next day’s light will bring.
References
Newell, C. and T.J. Cowles. (2006). Unusual gray whale Eschrichtius robustus feeding in the summer of 2005 off the central Oregon Coast. Geophysical Research Letters, 33:10.1029/2006GL027189
By Florence Sullivan – MSc Student, GEMM Lab
Hello Everyone, and welcome back for season two of our ever-expanding research project(s) about the gray whales of the Oregon coast!
Overall, our goal is document and describe the foraging behavior and ecology of the Pacific Coast Feeding Group of Gray Whales on the Oregon Coast. For a quick recap on the details of this project read these previous posts:
During this summer season, the newest iteration of team ro”buff”stus will be heading back down to Port Orford, Oregon to try to better understand the relationship between gray whales and their mysid prey. Half the team will once again use the theodolite from the top of Graveyard Point to track gray whales foraging in Tichenor Cove, the Port of Port Orford, and the kelp beds near Mill Rocks. Meanwhile, the other half of the team will use the R/V Robustus (i.e. a tandem ocean kayak named after our study species – Eschrichtius robustus, the gray whale) to repeatedly deploy a GoPro camera at several sampling locations in Tichenor cove. We hope that by filming vertical profiles of the water column, we will be able to create an index of abundance for the mysid to describe their temporal and spatial distribution of their swarms. We’re particularly interested in the differences between mysid swarm density before and after a whale forages in an area, and how whale behaviors might change based on the relative density of the available prey.
In theory, asking these questions seems simple – get in the boat, drop the camera, compare images to the whale tracklines, get an answer! In reality, this is not the case. A lot of preparatory work has been going on behind the scenes over the last six months. First, we had to decide what kind of camera to use, and decide what sort of weighted frame to build to get it to sink straight to the bottom. Then came the questions of deployment by hand versus using a downrigger,
what settings to use on the camera, how fast to send it down and bring it back up, what lens filters are needed (magenta) and other logistical concerns. (Huge thank you to our friends at ODFW Marine Reserves Program for the help and advice they provided on many of these subjects.) We spent some time in late May testing our deployment system, and quickly discovered that sampling during a diatom bloom is completely pointless because visibility is close to nil.
However, this week, we were able to test the camera in non-bloom conditions, and it works! We were able to capture images of a few small mysid swarms very near the bottom of the water column, and we didn’t need external lights to do it. We were worried that adding extra lights would artificially attract mysid to the camera, and bias our measurements, as well as potentially disturbing the whale’s foraging behavior. (Its also a relief because diving lights are expensive, and would have been one more logistical thing that could go wrong. General advice: Always follow the KISS method when designing a project – keep it simple, ——!)
My advisor recently introduced me to the concept of the “7 Ps”; Proper Prior Planning Prevents Piss Poor Performance. To our knowledge, we are the first group to try to use GoPro cameras to study the spatial and temporal patterns of zooplankton aggregations. With new technology comes new opportunities, but we have to be systematic and creative in how we use them. Trial and error is an integral part of developing new methods – to find the best technique, and so that our work can be replicated by others. Now that we know the GoPro/Kayak set-up is capable of capturing useable imagery, we need to develop a protocol for how to process and quantify the images, but that’s a work in progress and can wait for another blog post. Proper planning also includes checking last year’s equipment to make sure everything is running smoothly, installing needed computer programs on the new field laptop, editing sampling protocols to reflect things that worked well last year, and expanding the troubleshooting appendixes so that we have a quick reference guide for when things go wrong in the field. I am sure that we will run into more weird problems like last year’s “Chinese land whale”, but I also know that we would have many more difficulties if we had not been planning this field effort for the last several months.
Team Ro”buff”stus is from all over the place this year – we will have members from Oregon, North Carolina and Michigan – and we are all meeting for the first time this week. The next two weeks are going to be a whirlwind of introductions, team bonding, and learning how to communicate effectively while using the theodolite, our various computer programs, GoPro, Kayak, and more! We will keep the blog updated with our progress, and each team member will post at least once over the course of the summer. Wish us luck as we watch for whales, and feel free to join in the fun on pretty much any cliff-side in Oregon (as long as you’ve got a kelp bed nearby, chances are you’ll see them!)
By Florence Sullivan, MSc student GEMM lab
Over the past few months I have been slowly (and I do mean SLOWLY – I don’t believe I’ve struggled this much with learning a new skill in a long, long time) learning how to work in “R”. For those unfamiliar with why a simple letter might cause me so much trouble, R is a programming language and free software environment suitable for statistical computing and graphing.
My goal lately has been to interpolate my whale tracklines (i.e. smooth out the gaps where we missed a whale’s surfacing by inserting artificial locations). In order to do this I needed to know (1) How long does a gap between fixes need to be to identify a missed surfacing? (2) How many artificial points should be used to fill a given gap?
The best way to answer these queries was to look at a distribution of all of the time steps between fixes. I started by importing my dataset – the latitude and longitude, date, time, and unique whale identifier for each point (over 5000 of them) we recorded last summer. I converted the locations into x & y coordinates, adjusted the date and time stamp into the proper format, and used the package adehabitatLT to calculate the difference in times between each fix. A package known as ggplot2 was useful for creating exploratory histograms – but my data was incredibly skewed (Fig 1)! It appeared that the majority of our fixes happened less than a minute apart from each other. When you recall that gray whales typically take 3-4 short breathes at the surface between dives, this starts to make a lot of sense, but we had anticipated a bimodal distribution with two peaks: one for the quick surfacings, and one for the surfacings between 4-5 minutes dives. Where was this second peak?
Sometimes, calculating the logarithm of one of your axes can help tease out more patterns in your data – particularly in a heavily skewed distribution like Fig. 1. When I logged the time interval data, our expected bimodal distribution pattern became evident (Fig. 2). And, when I back-calculate from the center of the two peaks we see that the first peak occurs at less than 20 seconds (e^2.5 = 18 secs) representing the short, shallow blow intervals, or interventilation dives, and that the second peak of dives spans ~2.5 minutes to ~5 minutes (e^4.9 = 134 secs, e^5.7 = 298 secs). Reassuringly, these dive intervals are in agreement with the findings of Stelle et al. (2008) who described the mean interval between blows as 15.4 ± 4.73 seconds, and overall dives ranging from 8 seconds to 11 minutes.
So, now that we know what the typical dive patterns in this dataset are, the trick was to write a code that would look through each trackline, and identify gaps of greater than 5 minutes. Then, the code calculates how many artificial points to create to fill the gap, and where to put them.
One of the most frustrating parts of this adventure for me has been understanding the syntax of the R language. I know what calculations or comparisons I want to make with my dataset, but translating my thoughts into syntax for the computer to understand has not been easy. With error messages such as:
Error in match.names(clabs, names(xi)) :
names do not match previous names
Solution: I had to go line by line and verify that every single variable name matched, but turned out it was a capital letter in the wrong place throwing the error!
Error in as.POSIXct.default(time1) :
do not know how to convert ‘time1’ to class “POSIXct”
Solution: a weird case where the data was in the correct time format, but not being recognized, so I had to re-import the dataset as a different file format.
Error in data.frame(Whale.ID = Whale.ID, Site = Site, Latitude = Latitude, : arguments imply differing number of rows: 0, 2, 1
Solution: HELP! Yet to be solved….
Is it any wonder that when a friend asks how I am doing, my answer is “R is kicking my butt!”?
Science is a collaborative effort, where we build on the work of researchers who came before us. Rachael, a wonderful post-doc in the GEMM Lab, had already tackled this time-based interpolation problem earlier in the year working with albatross tracks. She graciously allowed me to build on her previous R code and tweak it for my own purposes. Two weeks ago, I was proud because I thought I had the code working – all that I needed to do was adjust the time interval we were looking for, and I could be off to the rest of my analysis! However, this weekend, the code has decided it doesn’t work with any interval except 6 minutes, and I am lost.
Many of the difficulties encountered when coding can be fixed by judicious use of google, stackoverflow, and the CRAN repository.
But sometimes, when you’ve been staring at the problem for hours, what you really need is a little praise for trying your best. So, if you are an R user, go download this package: praise, load the library, and type praise() into your console. You won’t regret it (See Fig. 4).
Thank you to Rachael who created the code in the first place, thanks to Solene who helped me trouble shoot, thanks to Amanda for moral support. Go GEMM Lab!
Why do pirates have a hard time learning the alphabet? It’s not because they love aaaR so much, it’s because they get stuck at “c”!
Stelle, L. L., W. M. Megill, and M. R. Kinzel. 2008. Activity budget and diving behavior of gray whales (Eschrichtius robustus) in feeding grounds off coastal British Columbia. Marine mammal science 24:462-478.
By Florence Sullivan, MSc. Student, GEMM Lab
Happy Spring everyone! You may be wondering where the gray whale updates have been all winter – and while I haven’t migrated south to Baja California with them, I have spent many hours in the GEMM Lab processing data, and categorizing photos.
You may recall that one of my base questions for this project is:
Do individual whales have different foraging strategies?
In order to answer this question, we must be able to tell individual gray whales apart. Scientists have many methods for recognizing individuals of different species using tags and bands, taking biopsy samples for DNA analysis, and more. But the method we’re using for this project is perhaps the simplest: Photo-Identification, which relies on the unique markings on individual animals, like fingerprints. All you need is a camera and rather a lot of patience.
Bottlenose dolphins were some of the first cetaceans to be documented by photo-identification. Individuals are identified by knicks and notches in their fins. Humpback whales are comparatively easy to identify – the bold black and white patterns on the underside of their frequently displayed flukes are compared. Orcas, one of the most beloved species of cetaceans, are recognized thanks to their saddle patches – again, unique to each individual. Did you know that the coloration and shape of those patches is actually indicative of the different ecotypes of Orca around the world? Check out this beautiful poster by Uko Gorter to see!
Gray whale photo identification is a bit more subtle since these whales don’t have dorsal fins and do not show the undersides of their fluke regularly. Because gray whales can have very different patterns on either side of their body, it is also important to get photos of both their right and left sides, as well as the fluke, to be sure of recognizing an individual if it comes around again. When taking photos of a gray whale, it’s a good idea to include the dorsal hump, where the knuckles start as it dives, as an easy indicator of which side of the body you are looking at when you’re trying to match photos. Some clues that I often use when identifying an individual include the placement of barnacles, and patterns of pigmentation and scars. You can see that patience and a talent for pattern recognition come in handy for this sort of work.
While we were in the field, it was important for my team to quickly find reference features to make sure we were always tracking the same whale. If you stopped by to visit our field station, you may have heard use saying things like “68 has white on both fluke-tips”, “70 has a propeller scar on the left side”, “the barnacles on 54’s head looks like a polyp”, or “27 has a smiley face in front of the first knuckle left side.” Sometimes, if a trait was particularly obvious, and the whale visited our field station more than once, we would give them a name to help us remember them. These notes were often (but to my frustration, not always!) recorded in our field notebook, and have come in handy this winter as I have systematically gone through the 8000+ photos we took last summer, identifying each individual, and noting whenever one was a repeat visitor. With these individuals labeled, I can now assess their level of behavioral and distribution consistency within and between study sites, and over the course of the summer.
Why don’t you try your luck? How many individuals are in this photoset? How many repeats? If I tell you that my team named some of these whales Mitosis, Smiley, Ninja and Keyboard can you figure out which ones they are?
Keep scrolling for the answer key ( I don’t want to spoil it too easily!)
Answers:
There are 7 whales in this photoset. Smiley and Keyboard both have repeat shots for you to find, and Smiley even shows off both left and right sides.
Hello everyone,
Florence here with an update about the final numbers from this summer’s gray whale field season.
For folks just hearing about the project, my team of interns and I spent the summer alternating between study sites at Depoe Bay and Port Orford to conduct fine-scale focal follows of gray whales foraging in near-shore Oregon waters using a theodolite. That is to say, we gathered 10,186 ‘marks’ or ‘locations’ where whales came to the surface, and by connecting the dots, we are able to create tracklines and analyze their movement patterns. The idea is to document and describe gray whale foraging behavior in order to answer the questions: Are there patterns in how the whales use the space? Is there a relationship between foraging success and proximity to kelp beds? Do behaviors vary between individuals, location, or over time during the season?
While at our study sites, we often received questions about vessel disturbance on the whale’s behavior. Over the course of the summer, we saw whales completely ignore boats, approach boats, and actively avoid boats. Therefore, we documented these vessel interactions in order to ask questions such as: Does vessel disturbance alter behavior? How close is too close? Does the potential for vessel disturbance vary depending on (1) size of motor, (2) speed of approach, (3) type of vessel, i.e. kayak, fishing boat, tour boat, (4) the number of vessels already in the area, (5) amount of time a vessel has been following a whale, (6) time of season, (7) the presence of a calf or other whales? The end goal, once the data have been analyzed, is to bring our results to local vessel operators (commercial and recreational) and work together to write reasonable, effective, and scientifically informed guidelines for vessel operations in the presence of gray whales.
And now, the numbers you’ve all been waiting for, here is the tally of our data collection this summer:
| Boiler Bay | Graveyard Point | Humbug Mountain | |
| Whales total | 80 | 73 | 28 |
| Boats total | 307 | 105 | 7 |
| Total survey time (HH:MM:SS) | 122:22:41 | 72:49:17 | 50:22:35 |
| Total survey time with whales (HH:MM:SS) | 64:47:54 | 80:39:57 | 22:59:00 |
| Total Marks | 4744 | 4334 | 1108 |
Table 1. Summary of survey effort for gray whale foraging ecology field season summer 2015
So, what does this all mean? Well, the unsatisfying answer is of course: we don’t know yet. However, it is my job to find out! I will spend the fall and winter processing data, writing and running behavioral models, communicating my successes and frustrations, and finally presenting my results to the community.
The human eye is well adapted to pick out patterns. Test yourself – what trends can you see in these images? Are there areas that the whales seem to prefer over other areas? In the Port Orford images with Keyboard & our kelp patches, does our theory of a relationship between whale presence and kelp patches seem valid?
This field season would not have been possible without the help of some truly excellent people. Thank you Cricket and Justin and Sarah for making up the core of Team Ro”buff”stus. It was a pleasure working with you this summer. Thank you to guest observers and photographers Era, Steven, Diana, Cory, Kelly, Shea and Brittany for filling in when we needed extra help! Thank you to our support network down in Port Orford: Tom, Tyson and the team at the Port Orford Field Station – we appreciate the housing and warm welcome, and to Jim and Karen Auborn and the Port of Port Orford for allowing us access to such a fantastic viewing location. Thank you to Oregon State Parks for allowing us access to the field sites at Boiler Bay and Humbug. Finally, thank you to Depoe Bay Pirate Coffee Company for keeping us warm and caffeinated on many foggy, cold early mornings. This work was funded by the William and Francis McNeil Fellowship Award, the Wild Rivers Coast Alliance, and the American Cetacean Society: Oregon Chapter.
Fair winds,
Florence