Current Research Blogs
Kyra Bankhead, undergraduate student
1 July 2020
My name is Kyra Bankhead and I am the new project lead for the Whatcom Waterfront Seal Observation Project. I am a Biology major and have been on the project for over a year and am thrilled to take on my own research project: The effect of anthropocentric noise disturbance on haul-out patterns of harbor seals.
While doing observations throughout the year, I have become extremely interested in the interactions as well as habituation of harbor seals with humans. I have had more than a quarter to come up with questions to investigate these interactions and have finally decided to look into anthropocentric noise pollution. After reading the past project lead research posters, I became most interested in Wyatt Heimbichner’s poster and wanted to change to looking at underwater noise pollution. After much consideration, I have decided in order to be able to start conducting research in the summer I would need a lot more time to research underwater acoustics as well as find a possible measurement of underwater effects on harbor seals. With this in mind, I decided to stick with in-air noise pollution as haul-outs can be measured in relevance to ambient noise.
I am hoping to receive a grant for this project as I work full-time at my job in the summer and would love to take some time off to focus on my project. Additionally, with the money I could hire students to take observations at the Semiahmoo Marina, a place with a lot less human disturbance than the Bellingham Bay Waterfront. I visited the Marina for the first time and have found that the observation spot is extremely far away from the seal haul-out spot and even with binoculars it is hard to take an accurate count of the seals. Because of this, I have emailed the Semiahmoo Marina office to ask if I can have access to the docks. Luckily, for the meantime, there are a certain number of seals that come close to the current observation spot, like this mom and seal pup:
Harbor seals in Semiahmoo. Photo by K. Bankhead.
Working along COVID-19 has been a struggle to say the least. I am trying to start research for the summer but have had to reschedule multiple times to limit exposure to all my volunteers. I am having to manage a group of people which is allowing me to work on my communication skills. I have still not been able to go into the lab and grab the equipment I need for my volunteers and I to start observing, but since the research has been approved, I will hopefully be able to start observing soon.
Grace Freeman, graduate student
1 July 2020
I’ve waited ‘til the last day of the month to write this because I wanted to finish the task and share some exciting news: I’ve completed the first round of photo ID! That means I have put my eyes of each of the 14,825 photos at least once. It’s a huge accomplishment and one that I never thought I would reach this early in the summer. I will still have to run through at least one more round, but this first benchmark is big! To date, I have IDed 31 new individuals bringing our total to 190 individuals. I have also found several IDs that were overlapped or opposite sides of an individual’s face. Those are probably the most exciting discoveries since I can then form a full understanding of what the individual looks like from the front, left, and right. In addition, there are several individuals I’ve learned to ID just by sight, and I’m already starting to get an idea of some of the trends that might exist within the data. It will be interesting to see what comes out when I run statistical analysis later this summer or in the fall.
Aside from my work on photo ID, June has been a busy month of curriculum development. Over the winter, I was offered a position to teach with College Quest through the biology department and Western. This program allows high school students to take a class at Western for one week over the summer while earning college credit. The course I was hired to teach is called Biol 194: Local Marine Habitats. Basically, it was going to be a weeklong fieldtrip with daily visits to different habitats near Western including Padilla Bay mudflats, tidepools at Larabee State Park, a boat trip at Shannon Point Marine Center and others. Given my extensive experience as a camp counselor, environmental educator, and backpacking guide, I figured I was ready for the challenge, and I looked forward to returning to my routes of trip leading and working with high schoolers. Then March happened, and all that changed! The course will still be happening, but it’s going to be completely virtual. This means that I’ve been working hard to develop an entirely new curriculum that will allow my students to engage digitally with the environment and gather preliminary ecological data – perhaps through simulation - they can use for a project proposal to be delivered at the end of the week. It’s a huge change from the original plan and has meant that I’m re-writing the syllabus and developing a new course nearly from scratch. It’s a challenge for sure, but as I spend more and more hours sorting through materials, I’m gaining confidence in my ability to pull this off! There are so many incredible resources online, and I’m excited to pull them all together to create a course for my students that is both educational and interactive. The course will take place in late July, so I’ll be able to fill you in on how it went with next month’s blog.
Bobbie Buzzell, graduate student
1 July 2020
I am very pleased to announce the scat sorting benchmark was met earlier this month and all remaining samples with fish bones have been mailed to the fish expert. It was a long 6-month journey of sorting to get to this point. As I briefly described in the last blog entry, one of my goals this month was to find crayfish to serve as reference specimens for the invertebrate ID. I was able to catch a couple of signal crayfish (Pacifastacus leniusculus) from a lake here in Bellingham. These crayfish are truly “lobsterettes”, a term I encountered while researching where to find these freshwater crustaceans. They can reach as large as 8 inches! I can also confirm they are mighty tasty.
To catch crayfish, I baited a minnow trap with a can of cat food and set the trap in the evening. I simply tossed the trap out where it was submerged beneath several feet of water along the bank. I tied it off to a nearby shrub and left it overnight. When I returned the next morning, I pulled it in and found a single crayfish of about 4 inches (sport fishing regulations mandate crayfish length of 3 ¼ inches for retention). The bait was still quite smelly, so I decided to reset the trap and check it again the next morning. Pulling in the trap a second time (a 24-hour soak) I found a slightly larger crayfish of about 4 ½ inches, but it weighed almost twice as much as the first.
Washington Department of Fish and Wildlife suggests humane euthanasia of crayfish by either submersing them in a slurry of ice water or using a knife to puncture between the eyes. I tried both methods, but I would argue the cold slurry is a surer way of humane euthanasia. To prepare them as reference specimens, I first boiled a small pot of water with salt and a bay leaf (I was planning to eat the tails after all) and let the crayfish boil for 3-5 minutes, much like you would do with shrimp.
After turning bright red, I removed the crayfish and ran them under cold water. I used a knife to split open the undersides of the tail and removed the meat. The larger of the two crayfish had sizeable claws, so I cracked those open to extract that meat and avoided damaging the most characteristic part of the claws. Having the shell broken up a little bit is actually more helpful to use as a reference since that is how I will to ID the fragments leftover in the scats. I retained all the hard parts of the shell, cleaning out the remaining innards under a running tap. I placed the shells on aluminum foil and left them in my oven at 200 degrees Fahrenheit for a couple of hours to completely dry.
With my reference specimens and ID guides in hand, I have begun the next step of the invertebrate ID which will also require a great deal of time and patience, but the benefit of pre-sorting samples has granted me a better understanding of what kind of prey to expect in the samples beforehand. While I’ve only just completed my first of hundreds of samples, I was able to confirm the first green crab observation. Although I didn’t find any claws and can’t confirm which of the crab legs belong to it, the green crab rostrum was very distinctive among the other Dungeness crab fragments. I was able to match the green crab rostrum up with two other fragments containing spines (much like a jigsaw puzzle) and compare them to intact green crab specimens. This is really promising as I continue the ID, and I look forward to hopefully confirming green crab observations as I move forward.
Jonathan Blubaugh, graduate student
1 July 2020
Classes are over and all grades have been submitted. It feels weird to be “done” with all my coursework and being a TA but still have the final stretch of my thesis to complete. This quarter was difficult with remote classes and adjusting to being stuck inside my apartment for weeks. And now that classes are over, I’m stuck inside with only my thesis to finish. Early this month, I sent my committee the first full draft of my thesis and have received some very good feedback. I’m aiming for an August defense which means a final version of my thesis by the beginning of August, if not earlier. This is complicated by having to move out of my apartment in July which is a lot of work and planning plus the cross-country drive to Virginia to stay with my parents. I am confident I can find time to work on my thesis, but it definitely won’t be easy. The job hunt for post-thesis life is going well and I have an interview 4 days after moving back to Virginia in July. The interview is extra motivation to finish my thesis because they only hire people with master’s degrees for this position. The final stretch feels the hardest, but I know it’ll be worth it in the end.
Nathan Guilford, graduate student
2 July 2020
In the midst of a global pandemic, this month marked the end of a unique spring quarter, and the completion of my coursework. Now, all that is left is to complete my thesis and defend. I am currently working on thesis revisions with my advisors, and I am hoping to defend in late summer/early fall. Ultimately, my project has tied up quite nicely, and it looks like scat samples may represent a promising resource for studies of individual specialization (or other phenomena) in wild seal populations. After enrichment for eukaryotic DNA, an average of 35% of my sequence reads mapped to the harbor seal reference genome, which is higher than I was expecting (and higher than the method developer’s result of ~28%). I was then able to construct confident genotypes from scat samples, that successfully identified known resampled individuals robustly, even when factoring in close relatives like siblings or parents. In addition, prey sequences were identifiable in the samples, and on average, ~20% of reads mapped to prey reference genomes. Interestingly, sample type seemed to make a difference in the performance of samples, as homogenized scat slurries had higher percentages of seal DNA (average 42%) while scat surface swabs had much lower percentages (average 23%). Conversely, swabs contained higher proportions of prey reads (average 53%), while slurries had much lower (average 5%). I think future work should look into these apparent disparities between sample types and further test their performance in various molecular analyses, as different types may suit different investigations. However, I believe this will further prove the efficacy of non-invasive methods such as scat analyses in expanding our toolkit to investigate protected and/or inaccessible species such as marine mammals. Hopefully soon I will finish my thesis and defend, when you can read more about my project and what I found. Until then, I will continue to stay at home, work, and begin the ever-wonderful job hunt