Kyra Bankhead, undergraduate student
1 August 2020
I am finally starting observations! The virus may have a big effect on my research as not as many people are going out to the waterfront. I’m starting to notice that the Semiahmoo Marina has as much or more human activity as the Bellingham Bay Waterfront. I may think about comparing my data to that of Wyatt’s but this would carry a lot of confounding variables, like the fact that Wyatt was only able to get data from one season. To do this, I will also have to make sure all of our methods were the same, which I believe won’t be a problem as we talked about his methods before I started my project.
Another concern with COVID is the constant transfer of equipment between my volunteers. I have had to pick up the noise meter after each observation and clean it before giving it to the next volunteer which has been difficult given that I work full-time. Luckily my volunteers have agreed to come to my apartment where I have left the equipment outside my door in order to keep a no-contact research project going. It is going great right now as I simply ask my roommate to leave the noise meter outside when I am at work.
Early in the month the windshield on the noise meter got lost by one of my volunteers (I don’t blame her because the windshield was very loose). Peter Thut has ordered a new one and for the meantime observations will continue. To fix this error I will take multiple readings with and without the windshield and find the average difference to apply to the readings taken without the windshield.
The Semiahmoo Marina has still not emailed me back about special access so I will most likely have to stick with my current observation spot. Counting pups compared to adults will be nearly impossible in this area so I will just try my best and most likely add them all up in analyzing my data. Additionally, I am extremely far away from the area that the seals will be picking up noise and I am instead in the noisiest area where visitors pass by. I will have to account for this somehow as it may affect the correlation of noise to haul outs at the Marina.
In awesome news, I got my scuba diving license! I went diving at Mukilteo to get certified and it was the best experience of my life. I got to see flounders, rockfish, moon snails, crabs and a wolf eel! I am hoping that I can use this skill for research in the future and dive with marine mammals.
Kyra before diving in Mukilteo. Photo by J. Garman.
Grace Freeman, graduate student
1 August 2020
I must admit that I had to go back and reread last month’s post to remember what’s happened since then. With the consistently beautiful weather and the work from home routine, time has become even more fluid than in the spring. That said, I’m still making progress on my research and have a few updates from the past month to pass along:
After wrapping up the first round of photo ID at the end of June, I spent the first few weeks of July going through the unidentified photos again. In the end, I was able to find IDs for all but about 200 of the 14,825 photos we currently have. I picked up the process with 159 individuals identified and as I progressed, that number quickly grew. In the end, I had a database of 212 individuals who have visited Whatcom Creek since 2011. After wrapping up the IDs, I went back through each folder in the database in an attempt to match them together and reduce that number a bit. I found a few duplicates likely stemming from the fact that many people have been involved with the ID process over the years and sometimes the same individual was given two IDs. I also found a few matches! For example, the folder for ID0014 contained only photos of the left side of the face while ID0018 contained only the right. Using timestamps and photos from the front, I was able to match the two together to create one complete image. Those were the most exciting discoveries and brought the number of individual IDs down while increasing the number of complete IDs. In the end, I removed 35 IDs from the database leaving us with 177 mostly complete profiles of individual seals at Whatcom Creek!
From that point, I was able to go through the timestamps for each photo to compile a dataset of visitation by each individual. I now know how many individuals were at the creek each day and who those individuals were. Analysis of these data will allow me to see if there are ‘rogue individuals’ under the traditional definition (those who appear at the creek more often than others). Spoiler alert: just by looking at the spreadsheet I can tell that there are! I also received some hatchery data from Alejandro yesterday that will allow me to map seal numbers and ID against the salmon run numbers by day and species.
So now what? Well, that’s a great question. Now I’m working through the behavioral observations to see if I can match hunting success recordings to an ID from a photo with the corresponding timestamp. With 294 days of observation and issues with watch/camera time discrepancies, this is proving more difficult than I anticipated. The goal now is to work through these observations in hopes of finding a year or two for which I can confidently match behaviors to IDs. This may not allow me to run the robust analysis I planned, but I’m hoping a small set of data will still provide some idea of the trends in behavior taking place at the creek. Stay tuned for updates on that in August!
Speaking of updates, last month I promised an update on the course I was teaching in July. Just a few days after that post, however, the class was cancelled due to low enrollment. It was extremely disappointing after all the work I put into curriculum development, but it’s also understandable. Fingers crossed the course can run normally next summer!
Until the end of August,
Bobbie Buzzell, graduate student
1 August 2020
This month has been very productive for my project. It’s comforting to continue meeting benchmarks I had previously set for myself last year, as I know I am still very fortunate in my situation compared to other graduate students. I am pretty much working under the microscope for 30+ hours each week. Each sample varies in the amount of time it takes to adequately identify the hard remains. Samples with very little material could take as little as a couple minutes, while samples with several ounces of material can take upwards of an hour to work through completely.
When I begin ID, my first task is to separate out any unique fragments that provide insight into the specimen: legs, spines, carapace sections, mouthparts, etc.… One fragment does not necessarily allow for direct evidence of the species, but rather several different types of fragments that help provide a more complete picture. Size, texture, shape, and even color (to some degree) can help distinguish remains of two different species in a single sample. After examining enough fragments, it becomes easier to identify even the most minute differences between seemingly similar pieces.
The familiarity I’ve built with the ID has been crucial to picking out green crab remnants. While I wasn’t able to always see green crab remains during the cleaning and even the sorting, I now have an eye for what to look for in samples with even the sparsest of material. Using reference specimens has also been key. I could not continue identifying the crustaceans to the genus or species level if it were not for having these references on hand. I have nearly completed the 2019 samples from the lower Wa’atch, and I can confidently say there is a small handful of samples with evidence of green crab. These preliminary findings are very promising to understanding a natural check and balance to the green crab propagation in Makah Bay.
Sophie Carlson, undergraduate student
1 August 2020
Hi everyone! My name’s Sophie, this is my FIRST BLOG EVER on the site. After spending a year as a general member of the harbor seal foraging project, I have taken the lead on my own research project under the guidance of Dietmar Schwarz and Alejandro! I am studying the diet preferences of male and female harbor seals in the Salish Sea.
My job when I’m in lab is to determine the sex of harbor seals by analyzing extracted DNA from scat with qPCR. The technique I use basically allows me to see if the DNA contains only X chromosomes or both X and Y chromosomes so I can make educated predictions about the sex of each seal. The scat samples were collected from many locations throughout the Salish Sea as far back as 2012 and have already been analyzed for diet contents based on bone and shell pieces. Ultimately, the idea is to analyze any correlations between seal sex and diet preference. A similar, smaller study was carried out by our lab in 2018 -- look for the paper in the “Publications” tab on this site! The first authors are Schwarz, D. and Spitzer, S. -- they found some interesting connections and have more thorough explanations of the methods involved in this study.
I’ve only been analyzing the new DNA for a little over a week now thanks to all the setbacks brought by COVID-19. The process itself is relatively simple but tedious and time-consuming. Right now, my main focus is on improving my pipetting skills to get more consistent results; I don’t want to have to rerun plates for fear of methodological error in failed samples. Hopefully practice makes perfect!
Wish me luck,
Nathan Guilford, graduate student
1 August 2020
With July as my last month in Bellingham, I have been trying to enjoy the summer weather while continuing to work on creating the final draft of my thesis and search for jobs back down in Seattle. I am hoping that I can land a role in some sort of genomics research and have found a few cool opportunities I am actively pursuing. While things are pretty crazy in this day and age, it’s nice to see that at least some research organizations are still hiring! I have also found that the work I have done for my thesis has taught me skills and techniques that I can use to strengthen my candidacy when applying for jobs, and that has been a very exciting and rewarding feeling while interviewing at various institutions. The methods involved in my thesis, most notably the application of NGS methods and analysis of NGS data, have taught me that I am passionate about the technologies we have access to for a wide range of genetic investigations, and I would love to continue expanding this skill set in my career.
As I said, I am working with my advisors on creating a solid draft of my thesis, which will then be passed on to my committee. Due to COVID-19 and our world right now, my timeline has been pushed back, however I am hoping to have my defense scheduled in the early fall. This should give me plenty of time to make sure my committee is happy with the project and defend my thesis successfully! Until then, my life is pretty much editing and interviewing!
Jonathan Blubaugh, graduate student
2 August 2020
As of the end of this month, I am officially back in Virginia. It took a week of packing and a week of driving to make it out of my apartment in Bellingham. I’ve been settling back into life during my two-week mandatory quarantine. My thesis has been coming along slowly but steadily. I am trying to address and least one feedback comment per day which usually leads to me doing 3 or 4 comments and some general editing. The editing and writing process has definitely been my least favorite part of getting my Master’s degree but also where I am feeling the most improvement. Hopefully August is a little less crazy and I can dedicate more time to my thesis.