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.



Surveying Harbor Porpoises on the Oregon Coast!

Hello Gemm lab readers!

Spring has officially made it to the Oregon coast.  The smells of blooming flowers are lingering in the air at the Hatfield Marine Science Center (HMSC), the seagulls are hovering around our afternoon BBQ’s, the local whale watching tour boats are zipping through the jetty’s to catch sight of all the whales still hovering in the area, and my team and I are right behind them as the field season is upon us in full force!

My name is Amanda Holdman and I am a master’s student in the Oregon State University’s Department of Fisheries and Wildlife and Marine Mammal Institute. Our lab, the geospatial ecology of marine megafuana, or GEMM lab for short, focuseharbor-porpoises_569_600x450s on the ecology, behavior and conservation of marine megafauna including cetaceans, pinnipeds, seabirds, and sharks. My research in particular is centered around the cetacean species that inhabit Oregon’s near coastal waters. While the cetacean order includes over 80 species, 30 of which can be found in Oregon, I am specifically targeting the small and charismatic harbor porpoise! I am hoping to answer questions about seasonal and diel patterns, and the drivers of these patterns to create a better understanding of the porpoise community off the coast of Newport.

To accomplish this, I have been using a couple different survey methods! Over the last year or so I have been conducting marine mammal visual surveys with a crew of observers, binoculars, cameras and lifejackets.  We’ve been very fortunate to work alongside and partner up with a number of labs and projects taking place at HMSC — including Sarah Henkel’s Benthic Ecology Lab, Jay Peterson’s Zooplankton Ecology Project, and Rob Suryan’s Seabird Oceanography Lab — who’ve invited us to share their boat time and join in on cruises to spot marine mammals. We had some motivating cruises with last year’s field season (bow riding pacific white sided dolphins and a possible fin whale sighting!) but now that the summer season is around the corner, It’s time to recruit additional observers and get everyone up to date on their safety certifications (at sea safety, first aid, etc.)



While we currently have about 6-8 boat trips a month, I am not only just looking  for harbor porpoises, I’m also listening for them. To complement the visual surveys, I’ve added an acoustic component to my research, with the help of the Oregon State Research Collective for Applied Acoustics lab (ORCAA). This allows me to survey for harbor porpoises even under the worst sea conditions, when boat trips are unavailable. Odontocetes, such as the harbor porpoise use echolocation to navigate and forage and can be identified acoustically by their frequency range. While a full-depth analysis of last summer’s data hasn’t yet been accomplished, I was able to take a quick peek and MAN IT LOOKS GOOD! Both harbor porpoise and killer whale vocalizations were identified – you can check out the spectrogram below! This combination of using visual and acoustic surveys will help us answer when the porpoises are in our near waters, and where there primary hang-outs are!

Visual representation of an echolocation clicks emitted by a feeding harbor porpoise

But springtime isn’t just for fieldwork, it’s also for course work! This quarter, my lab mate Erin Picket and I have enrolled into Julia Jones “Arcaholics anonymous” class, an introductory spatial statistics and GIS course that helps us piece together all the hard work we’ve put towards data collection to look for trends of animal distributions across space and time. This is the first time for both of us that we  get to upgrade our excel spreadsheets into a visual representation of our data! There will be more updates to come soon on how our projects are unfolding, but if you can’t wait til then, feel free to follow along with our class website!