Following Tracks: A Summer of Research in Quantitative Ecology

**GUEST POST** written by Irina Tolkova from the University of Washington.

R, a programming language and software for statistical analysis, gives me an error message.

I mull it over. Revise my code. Run it again.

Hey, look! Two error messages.

I’m Irina, and I’m working on summer research in quantitative ecology with Dr. Leigh Torres in the GEMM Lab. Ironically, as much as I’m interested in the environment and the life inhabiting it, my background is actually in applied math, and a bit in computer science.


(Also, my background is the sand dunes of Florence, OR, which are downright amazing.)

When I mention this in the context of marine research, I usually get a surprised look. But from firsthand experience, the mindsets and skills developed in those areas can actually be very useful for ecology. This is partly because both math and computer science develop a problem-solving approach that can apply to many interdisciplinary contexts, and partly because ecology itself is becoming increasingly influenced by technology.

Personally, I’m fascinated by the advancement in environmentally-oriented sensors and trackers, and admire the inventors’ cleverness in the way they extract useful information. I’ve heard about projects with unmanned ocean gliders that fly through the water, taking conductivity, temperature, depth measurements (Seaglider project by APL at the University of Washington), which can be used for oceanographic mapping. Arrays of hydrophones along the coast detect and recognize marine mammals through bioacoustics (OSU Animal Bioacoustics Lab), allowing for analysis of their population distributions and potentially movement. In the GEMM lab, I learned about light and small GPS loggers, which can be put on wildlife to learn about their movement, and even smaller lighter ones that determine the animal’s general position using the time of sunset and sunrise. Finally, scientists even made artificial nest mounds which hid a scale for recording the weight of breeding birds — looking at the data, I could see a distinctive sawtooth pattern, since the birds lost weight as they incubated the egg, and gained weight after coming home from a foraging trip…

On the whole, I’m really hopeful for the ecological opportunities opened up by technology. But the information coming in from sensors can be both a blessing and a curse, because — unlike manually collected data — the sample sizes tend to be massive. For statistical analysis, this is great! For actually working with the data… more difficult. For my project, this trade-off shows as R and Excel crash over the hundreds of thousands of points in my dataset… what dataset, you might ask? Albatross GPS tracking data.

In 2011, 2012, and 2013, a group of scientists (including Dr. Leigh!) tagged grey-headed albatrosses at Campbell Island, New Zealand, with small GPS loggers. This was done in the summer months, when the birds were breeding, so the GPS tracks represent the birds’ flights as they incubated and raised their chicks. A cool fact about albatrosses: they only raise one chick at a time! As a result, the survival of the population is very dependent on chick survival, which means that the health of the albatrosses during the breeding season, and in part their ability to find food, is critical for the population’s sustainability. So, my research question is: what environmental variables determine where these albatrosses choose to forage?

The project naturally breaks up into two main parts.

  • How can we quantify this “foraging effort” over a trajectory?
  • What is the statistical relationship between this “foraging effort metric” and environmental variables?

Luckily, R is pretty good for both data manipulation and statistical analysis, and that’s what I’m working on now. I’ve just about finished part (1), and will be moving on to part (2) in the coming week. For a start, here are some color-coded plots showing two different ways of measuring the “foraging value” over one GPS track:


Most of my time goes into writing code, and, of course, debugging. This might sound a bit dull, but the anticipation of new results, graphs, and questions is definitely worth it. Occasionally, that anticipation is met with a result or plot that I wasn’t quite expecting. For example, I was recently attempting to draw the predicted spatial distribution of an albatross population. I fixed some bugs. The code ran. A plot window opened up. And showed this:


I stared at my laptop for a moment, closed it, and got some hot tea from the lab’s electronic kettle, all the while wondering how R came up with this abstract art.

All in all, while I spend most of my time programming, my motivation comes from the wildlife I hope to work for. And as any other ecologist, I love being out there on the Oregon coast, with the sun, the rain, sand, waves, valleys and mountains, cliff swallows and grey whales, and the rest of our fantastic wild outdoors.



Familiar Flukes and Faces

Greetings fellow marine enthusiasts! My name is Cricket, and I am one of the interns working on Florence’s Gray Whale project! I’m preparing to graduate from Oregon State University in a couple of months with a Bachelors of Science in Biology with the marine option. Before I graduate, I wanted to get some extra experience in the field this summer, which is how I ended up here with Florence, Justin, and Sarah, having surprisingly crazy whale adventures along the Oregon coast!

Panorama of Graveyard Point
Panorama of Graveyard Point

Today marks the end of our first week in Port Orford. We weren’t sure what we were going to get when we switched sites, though of course we had a few fears: No whales, low visibility, bad weather, etc. Depoe Bay had been good to us so far, and we were slightly worried about the transition. In actuality, Port Orford has been amazing!

Our sampling set-up on Graveyard point - above the port of Port Orford
Our sampling set-up on Graveyard point – above the port of Port Orford

Day one was foggy, and we only visited the site briefly to figure out a good location for the theodolite. One of our sites is located on a terrifyingly high cliff, but the view is stellar. We were only there for about an hour and we saw two whales, one of which came up into the cove just beneath us. In fact, one of our concerns with this site is that the whales actually get too close to view through the theodolite. What an unexpected problem to have!

Titchener Cove, Port Orford. Credit: Cricket Carine
Whale 63 Titchener Cove, Port Orford. Credit: Cricket Carine

From our vantage point, we can get some incredible photos of these whales. Photo identification is a breeze if the whale decides to come into the cove closest to us. We can watch them under the water, as opposed to in Depoe Bay where we could only really observe them when they surface.

Whale 59 Surfaces in Titchener Cove, Port Orford credit: Cricket Carine
Whale 59 Surfaces in Titchener Cove, Port Orford credit: Cricket Carine

We all get particularly excited when we see the same whale more than once. In Depoe Bay, we had at least four different whales appear on multiple days. We can verify this using the photos we manage to get of the whales, and comparing them between days.

For example, in Port Orford, we spotted a whale on the 20th with a particularly large white spot on the fluke. This spot made the whale easily identifiable, so we were able to get a good focal follow (because we could track this whale amongst other whales with confidence that we were tracking the same one the entire time), which in turn allowed us to create a track line of this whale’s dive patterns. This whale happened to be whale sixty (the 60th whale we’ve seen since the start of our data collection).

While this is a trackline of whale 82, photo ID confirms that 82,60, and 78 are all the same whale!
While this is a track-line of whale 82, photo ID confirms that 82, 60, and 78 are all the same whale! (The beginning of the track is labeled with the whale ID)

Then, days later, we spotted another whale. This was whale 78, and after a few surfaces, we realized this whale had the same white spot! We hesitantly referred to this whale as “sixty” but couldn’t be sure until we compared photos from the days before. And sure enough, it was!

Seen on July 24
Whale 82, Seen on July 24
Seen on July 20.
Whale 60, Seen on July 20.

I am particularly enthusiastic about our whale resights, and actively enjoy going through the photos and comparing each one to previous whales to try and identify individuals. It’s tedious, but rewarding when we can begin to learn individuals and identify them in the field. As a sort of rough guide to help us when scrounging through photo ID, I’ve put some of our good comparative photos into a google doc to use as reference. Here’s an example of some of the repeat whales we’ve seen:

Tomorrow will be day two at our second Port Orford site. Today was day one, and we managed to spot two whales, which is definitely promising. We hope we have as much luck finding and tracking whales there as we did on our cliffside!

Panorama from Humbug State Park survey site
Panorama from Humbug State Park survey site
Surveying our new Humbug site this morning
Surveying our new Humbug site this morning


Have a nice Gray!

Southern Sunshine Meets Oregon Wind: Interning with the GEMM Lab!

**GUEST POST**written by Cheyenne Coleman of Savannah State University

My first journey to the west coast, was spent on a six hour flight to Portland, Oregon in anticipation of my upcoming summer internship with the Geospatial Ecology and Marine Megafuana lab (GEMM Lab) at the Hatfield Marine Science Center (HMSC). I had never before been to the west coast, but luckily for me I did not have to make this long journey alone; my friend, Kamiliya Daniels, was also doing an internship at HMSC. After a long bus ride to Corvallis, Kamiliya and I, were warmly greeted by one of my GEMM lab members, Amanda Holdman. With her, was honorary GEMM lab member and Amanda’s dog, Boiler, who spent the greater part of the drive to Newport sleeping on my lap while I spent the drive asking Amanda several series of questions,

“Are there bears in these woods?”

“What do the dorms look like? How do I get around town? I hear it’s a small town, is there at least a Walmart?”

But without any answer to my curiosity, all of these questions were left with one reply:

“I’ll let you see for yourself.”

And then just as Amanda proposed, I did exactly that.

My name is Cheyenne and I am from Savannah State University in Georgia interning with LMRCSC (Living Marine Resources Cooperative Science Center) in Newport, Oregon. My expectations of the Oregon coast and the reality was vastly different than what I had pictured. I imagined the entire West Coast would match a California summer; Sunny and hot.

But on the contrary, upon arrival to Newport, I learned, it doesn’t. It is windy and chilly and hardly ever above 70 degrees. Thinking an Oregon summer would match a California summer, in my suitcase I possessed only three small sweaters and an abundant supply of shorts and tank tops. Needless, to say I was quickly off to buy an Oregon Coast sweatshirt that would double as warmth and a souvenir. Upon first entering Newport, I was mostly shocked at how small the town felt, and I noticed every structure was made of wood, and coming from Georgia this was strange to me. In Georgia, everything is made of bricks and cement. The dorms on first glance reminded me of summer camp for adults: slightly dated with bunk bed sleeping arrangements. Yikes!

However, my worries that come along with moving to a new place, were quickly diminished when I was welcomed to the GEMM lab; Florence greeted with a warm cup of tea, I was introduced to everyone who worked at HMSC, and even given my very own desk in the GEMM lab. After a day of transitions, and a much needed good night’s rest, I was introduced to my project on California Sea Lions (Zalophus californianus).

If you’ve been following along with all of the latest posts from GEMM lab students, you might think the lives of spatial ecologists revolve around glamorous fieldwork. We’ve got Amanda eavesdropping on porpoises, Florence surveying for foraging gray whales, and Leigh playing hide and seek with seabirds down in Yachats. I, however, am admittedly not spending my summer in the field this year and am learning that there is more to being a scientist than picturesque moments with charismatic study species in beautiful locations.

Prior to entering the GEMM lab, I had limited experience in computing and data analysis and spent my prior summer’s doing fieldwork on invertebrates, usually bagging sediment and collecting water samples. This internship was a new and unique opportunity for me to learn the next step of the scientific process. While I had always wondered, “What happens after data collection?” I was not given the experience to find out.  I quickly learned, that this includes a lot of sorting, categorizing, and modeling, all of which are very time consuming.

By using satellite tracking information of California sea lions collected by the Oregon Department of Fish and Wildlife (ODFW) from 2005 and 2007, I am able to measure movements and habitat use of California sea lions. By analyzing their routes between their initial and final locations, we can study their distributions patterns.

To some people, sitting at a computer doing analysis may not seem as glamorous as working in the field. Some people might question why someone would chose to spend their career in front of a computer screen. But my internship this summer, really showed me the value of having experience working at all stages of the scientific process. Seeing all of my efforts in processing, sorting, and categorizing come together to create an end result really enhanced my love for science. By connecting the questions to the answers, and making contributions to the scientific community, I feel rewarded for my hard work.

My internship has come to an end, and given my initial hesitations, I’ve grown accustomed to Newport and the GEMM lab. I enjoy sitting at my desk running through a wild assortment of data and hearing the wonderful ding of the teapot. In the last days of my internship, I was able to escape my computer screen to assist Florence in data collection on beautiful gray whale surveys. Last Thursday, a lab meeting was held and my lab mates and I were able to update each other on our research. We shared ideas on how to enhance everyone’s project, and who might be able to answer questions we were struggling with in our own data sets. As my internship comes to a close, I have gained more knowledge and real life skill then I would ever hope to gain just through courses at Savannah State. I learned new software programs like R Statistical Package and sharpened my own skills in ArcGIS. I gained the experience of collaborating with a lab, and understanding how powerful working with your peers and colleagues can be. Gaining this much experience has, without a doubt, given me an edge in the competitive field I will enter after graduation. I have made connections, hopefully life long, with the nicest people; I know that in the future, which ever path I may choose, I’ll always be a part of the GEMM lab.

A Week-Full of Whales

Hello and greetings from the sort of sunny Oregon Coast! Sarah reporting in to offer an update on Florence’s Gray Whale study now that we’re about ten days into sampling. If you’re new to our blog you can read up on the preliminary field season right here.

This little gray was incredibly frustrating to follow due to its irregular surfacing and tiny spouts that were hard to see. We affectionately named it Ninja.
This little savior came through on the day all our technology failed and cheered us up with his rainbow spouts.  Thankfully, he’s a repeat visitor and though we may have missed him on the 14th, we were able to get a good focal follow on him today.

Before I get to the project though, let me introduce myself a bit further. As I said, my name’s Sarah – one of the three interns on our whale surveying team. I got my Bachelor of Science in Oceanography at the University of Washington a few years back and have since worked as a lab tech at UW’s Friday Harbor Labs and as an Americorps volunteer serving as a teacher’s aide. Eventually I plan to become a science teacher, but thought a little more field work this summer would be a nice break after two years of service.

Cricket and Justin pondering the challenges of whale watching.
Cricket and Justin pondering the challenges of whale watching.

Thus, I moved to Newport last week just in time to catch the first day of our main surveying season. And what a season it’s been. We’ve tracked 48 whales since I’ve arrived, averaging about six a day. Of course, those aren’t all 48 different whales. If we lose sight of a whale for longer than 20 minutes, we assume it has left our study area and pronounce it lost, and unless we can identify the next sighting as the same whale based on markings (which we’re getting pretty good at), we give it a new number to keep track. We also give whales we’ve already seen new numbers when we see them on a different day.

Table for two: these whales caused some confusion among the team as they began to forage together before we could tell the difference between the two.
Table for two: these whales caused some confusion among the team as they began to forage together before we could tell the difference between the two.

You might be wondering how we can tell gray whales apart when they’re mostly, well, gray and underwater. And the short answer is we have a pretty difficult time doing so at first sight. Gray whales aren’t like orcas, whose saddle patch just behind the dorsal fin serves as a fingerprint, nor are they humpbacks, whose patterned flukes are cataloged for easy matching. Gray whales have more of a dorsal hump than a fin, followed by five or six ridges we call knuckles. They aren’t famous for showing their flukes above water either, so unless you get several views of a particular whale’s sides, dorsal, and, if you’re lucky, fluke, it’s hard to have a positive ID for the whale. The good news is, that part of our sampling equipment is a camera with a massive zoom lens, so we can take photos of most of the whales we track with the theodolite (see the previous post to learn about theodolites). From those photos (at least 400 a day) we can look at scars from barnacles and killer whales, pigmentation spots that are part of the whales’ coloring, and parasites like barnacles and amphipods to recognize whales we’ve seen before. Eventually we’ll send all the photos we take to the Cascadia Research Group in Olympia, Washington, that keeps a database of all identified gray whales.

Sitting on a clifftop photographing whales might sound more like a vacation than science, so here's some (very peliminary) data of one whale. This is Mitosis on three different days. The first day is red, second is yellow, and the third is green.
Sitting on a clifftop photographing whales might sound more like a vacation than science, so here’s some (very peliminary) data of one whale. This is Mitosis on three different days. The first day is red, second is yellow, and the third is green.

Anyways, thanks for keeping with me to the bottom of the page. It’s been a fun first week-or-so and I’m excited to be heading to our second study site in Port Orford tomorrow after surveying. We’ll be there for 15 days, so next time you hear from us, we’ll be a bit further down the coast.

Yes, we named a whale after cell replication, because look at those overlapping spots!
Yes, we named a whale after cell replication, because look at those overlapping spots!

Best Fishes!