MARCH 2020
Helen's Blog
Helen Krueger, undergraduate student
1 March 2020
I am narrowing down on my last quarter at Western, which means that it is crunch time to complete my project. Since the last blog posting, at the end of January, I have finished preparing my bacteria samples for SEM, and began to get some really interesting images back! I’ve included on of my early images from the harbor seal haul-outs.
Fig. 1- SEM image of a seawater bacteria sample at 11.5
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In terms of analysis, I have completed a survey of the bacteria growth morphology of all my samples (seawater, control haul-outs and haul-outs) and categorized their form and margin. The purpose of this survey is purely to look at proportional differences between sample types. I have also been playing with the image processing software ImageJ to help quickly process my SEM images. Right now, I am simply looking for the area of randomly selected bacteria in each image by: Area =L*W*pi for a generic area of an oval. However, I am also looking into thresholding to hopefully use the software to get more precise areas of every bacteria in the view field. All of this, and a finished poster product, will hopefully be done by the end of dead week! The deadline is set, and my work is cut out for me.
Additionally, I am excited to announce that I got my first post-college job! In early April I will be surveying marbled murrelets in Oregon for four months! I am looking forward to the security of a full time job and the adventure of exploring backcountry Oregon to monitor this species.
Bobbie's Blog
Bobie Buzzell, graduate student
1 March 2020
We are well into winter quarter now, but there is little to really update about the sorting process. My assistants and I have been powering away at getting samples sorted, and although we are still a little behind the original goal, I anticipate things will speed up here as the end of this quarter nears and spring quarter begins. I have also been refining my thesis proposal for approval over the course of this quarter. With my proposal under my belt, I can begin fine tuning the sorting process and devote more time to sorting samples.
One of the benefits of sorting through samples prior to the ID is being able to take a glimpse at what’s to come in terms of the different prey taxa. I have been trying to identify a couple of different reoccurring specimens in the scats, shuffling through all the literature and guides I can to identify the mystery fragments. There is one crustacean, which I am sure to be a shrimp, that pops up frequently in the Tsoo-Yess scats. With several of these shrimps co-occurs hard, white mushroom-shaped pieces. I will most likely need to send the hard fragments to Bill to have a look at and verify they aren’t fish bones of some sort, but since they often occur with the crustacean it’s difficult to truly tell if it’s either. I am also planning a trip to Neah Bay during spring break to gather more reference specimens. This may help me solve which shrimp species is continuing to occur in the scats.
Nathan's Blog
Nathan Guilford, graduate student
1 March 2020
After exploring the preliminary data from my first sequencing run, my committee and I decided that it would be worthwhile to proceed with a second run for the same scat samples. It was difficult to identify a large number of SNPs while also maximizing the number of SNPs present across all samples. Most of the SNPs identified were only in 3 or fewer samples (out of 13), and this would make any pairwise genotype comparisons of samples very weak, if not impossible. Unsurprisingly, it appears scat may not actually be the leading source of seal DNA for NGS methods! However, it does look like it is feasible with some troubleshooting (which is exciting for both my project and other non-invasive studies)!
Therefore, we have decided to 1) reduce the number of samples sequenced from 13 to 8, and 2) commission either 1/2 or 3/4 of a sequencing lane (rather than the original 1/4). These changes will give us significantly deeper sequencing, hopefully returning more reads per sample, allowing us to identify more SNPs that we will be able to capture in the majority of the samples. Then we can construct more thorough genotypes for each sample and make stronger comparisons. We selected the best performing samples out of the original 13 for this second run, which we based on the percent of reads that ended up mapping to our seal reference genome, as well as the number of SNP loci recovered per sample.
Depending on funding, we are also planning a third sequencing run, using tissue samples collected by the San Juan Co. Marine Mammal Stranding Network. This will provide us with genomic information and loci from high-quality DNA, that we can employ as needed depending on the project’s results. I believe that these new runs will strengthen the project immensely, and I am very anxious to see how these new results will compare (even if it may push back my timeline slightly)!
Grace's Blog
Grace Freeman, graduate student
1 March 2020
As always, it seems like the month has flown by. I’ve certainly settled into life in Washington, and I’m loving this early feeling of spring. I can go running in a t-shirt and appreciate the flowers blooming along the trail! Back home it’s still the depth of winter, and there’s probably no an end in sight for another 2-3 months. I don’t think we’ll be getting any May snowstorms out here!
February has been a month full of the usual TAing, classes, and photo ID, but there’s one thing that’s finally been crossed off my to-do list. I submitted the final draft of my proposal to my committee this week!! When I started writing in July, I was still working as an environmental educator and trip leader in Wisconsin and the Upper Peninsula of Michigan. I had only ever seen one harbor seal in the wild and I’d never even been to Bellingham. Six months later, a whole lot has changed! I feel so much more comfortable in the project, and I’m confident in the direction I will take to answer the questions I’ve proposed. I know there is a lot more work ahead of me but having reached one milestone feels pretty darn good for now.
Now that I finally have that direction nailed down, I’m proud to share the summary of my proposed work. Here’s hoping my committee approves when we meet at the end of the quarter!
“High-level predators have the capacity to shape entire ecosystems, and thus require informed approaches for management. One strategy for the management of predators is the culling or removal of individuals thought to prey on endangered populations in efforts to reduce predation pressures. Typically, individuals are removed based on their proximity to an endangered population assuming that all predators impact the prey population equally. However, evidence suggests that some individuals consume a disproportionately large amount of prey relative to others of their species. These predators are known as rogue individuals, and their removal may have a similarly large impact on reducing predation on endangered species. The harbor seal (Phoca vitulina) is an abundant marine predator with significant impacts on Pacific salmon (Oncorhynchus spp.), a species of conservation concern. Salmonids are listed as threatened under the Endangered Species Act and are a shared resource with orca whales (Orcinus orca) and humans. The recovery of seal populations under the Marine Mammal Protection Act coupled with this competition for limited salmonid resources has led to a complicated management regime. My research will use photographic identification and nine years of data regarding foraging success to identify rogue individuals in Whatcom Creek, Bellingham, WA. These individuals will be classified based on variability in both visitation rate and foraging success - a strategy that has not been employed before. Refining the current model and definition used in management of rogue individuals can inform not only management policies for seals and salmon, but also for the fisheries that rely on the Salish Sea.”
Jonathan's Blog
Jonathan Blubaugh, graduate student
1 March 2020
I am excited to be writing my thesis now. I’ve been working on the Introduction and Methods so they can get to my committee next week and have started my Results already. I think writing out the Results is going to help me tremendously in deciding what I want to include as my analysis. I’ve been stuck in analysis limbo since every way to visualize or look at differences has turned up something new or interesting. I’m hoping getting all my ideas on paper, or computer, will help me organize and prioritize for the question I am asking.
My thesis partner from the Writing Studio on campus has been extremely helpful. Even just as an accountability buddy for making sure I have some writing to share each week. Also helpful in setting realistic goals for each week, not just saying “Oh yeah, I’ll just have the whole methods done”, but having like the outline done, then filling in one section at a time. I would whole heartedly recommend all graduate students to at least meet with them once. I also found it was a lot lower pressure and I can bring rough writing to them and get good usable feedback.
I’m looking forward to Finals Week and spring break as ways to get ahead on some writing since I won’t have any teaching to do.
Where’s the pause button on time?
Delaney Adams, undergraduate student
1 March 2020
This last month has been a blur. I found it zooming by before I even realized it was February. With some extra stresses added on this month, every minute of my time has been occupied. This came as a bit of surprise for me since I tried to plan a less intense quarter for myself this quarter. Fortunately, I have been able to take a few moments during observations this month to take a breath and enjoy the presence of the playful seals in the creek. Although it’s been a crazy one for me so far, winter quarter can be particularly slow for some, especially the seals who don’t frequent the creek as often in the winter months. This means the lab assistants and I have had more time in the lab, working on cropping, photo identification, and for me, separating independent surfacing events for my project. For each day of data, I have been going through and separating each separate surfacing event that occurs during an observation, and this has not been an easy task. For each year, there is a huge range in observations that show seal activity. So far I have made it through 2011-2014 data, and I am looking forward to digging deeper into some of the more recent data, especially for the observations I have been around for starting in 2017.