Nathan Guilford, graduate student
1 May 2020
This month I received the sequence data from my second run, and it does in fact look like we roughly doubled our depth, which I am hoping will allow me to not only screen for prey at a finer scale, but also capture more rare SNPs and alleles in the seal reads, strengthening my relatedness measures. Since this second run was only a subset of 7 out of the original 13 samples, I am now deciding if I will only use these new reads, or combine both runs, to include all 13 samples in the final set. While this would create coverage disparities between samples, this may give better allele frequency estimations and help me capture rare alleles. Therefore, I am looking at both avenues and will compare the results. I have not yet looked at the proportion of prey reads in this new run, however the proportion of reads that mapped to the seal genome are roughly similar to the proportions from the first run. This makes me think that we will see similar results in the prey, however, since this run will have many more reads, I am hoping it gives us better mapping resolution.
Bobbie Buzzell, graduate student
1 May 2020
It’s been a weird month amidst the pandemic. With the shelter in place order still in effect I have been working from home sorting scat samples and continuing my preliminary analysis. While it has been difficult not seeing my cohort, friends, and family, I keep reminding myself of how fortunate I am to be able to continue my work from home. I know not everyone can say the same.
I’ve continued to make progress with sorting samples and am now a little over 200 samples away from completing the sorting benchmark of my project. Progress also continues with my funding paperwork. It’s been quite a learning curve negotiating the processes of contracts, grants, and administration.
I received word this month that my project has been awarded some additional funding through CREOi (Conservation Research and Education Opportunities International). This is great news, because I can now have all of the scat samples identified by the fish expert, Bill. While this puts a little more pressure on me to get all the scats sorted by the end of June (which is more than feasible at this point), I am extremely fortunate to have a very robust sample size.
Last week I had a revelation about my mystery crustacean that has now haunted the blog for a couple months. I had been so caught up in try to identify this crustacean as a marine specimen that I neglected to check into freshwater species. Sure enough, the very characteristic rostrum I had found belongs to a crayfish. At this time, I’m not certain of the species, but I have learned there are currently four known species of crayfish in the Pacific Northwest, two of which are invasive. If I am able to key these out to species, it will be interesting to find out if any of them fall into the invasive category.
Grace Freeman, graduate student
1 May 2020
Another blog, another month gone too quickly. Since we last talked, remarkably little has changed. I am still working from home, still sheltering in place, and still trucking along through the quarter. I am still feeling extremely fortunate to have the opportunity to work from home and continue making progress on my project. I’ve been working my way through photo ID, and after being stuck on November 27, 2016 for the better part of two months (I guess that was a busy day at the creek!), I’ve progressed my way into 2018. IDing certainly has its ups and downs. Some days I can identify nearly every individual simply by sight as there are a few seals at the creek I’ve come to recognize. Other times, I sit at the computer and scroll through the database for hours without being able to ID a single photo. I’m reassured by the fact that I will have the entire summer devoted to just this, and I’m motivated to finish the photo work by August at the latest.
In the meantime, when I’m not working through thousands of seal photos, I’m making plans to take more! Actually, I’m recruiting undergraduates to work in the lab next year and do it for me. While this time of quarantine has certainly thrown a wrench into our usual data collection and our plans to interview candidates, Delaney and I are hoping to find some eager help to join our team in the fall. If classes remain remote and campus is closed in the fall, it might mean getting creative during the November salmon run as this is when the bulk of our work is done. Future Grace will have to troubleshoot that situation if things come to it.
My fingers crossed that it doesn’t!
See you in June. Take care!
Delaney Adams, undergraduate student
1 May 2020
Progress for the month has been pretty slow, as the start of classes online has been a significant challenge for me. I finally feel like I am getting into more of a routine, and that has felt really good! Grace, my wonderful graduate student, and I, have spent a large portion of time trying to figure out how we can make sure that we have consistency with the data we are both using, and unfortunately, that meant taking one step forward and two steps backward. We have decided to go back through the data and make sure that the column that asks whether a new fish is caught during that surfacing event or not is completely consistent, since the original input was based on the judgement of the person entering data into the computer.
Most of the month has been spent working on that in addition to shaping up my draft for my project. That has gone relatively smoothly so far, and the fact that it will be due in a little bit over a month has really started to sink in for me. I’m looking forward to starting with a little bit of analysis with the data that we’ve finished sorting through this next month. I’m definitely starting to miss being out on the water for observations, but enjoying perusing though old photos in the meantime. That’ll have to do for the time being.
Jonathan Blubaugh, graduate student
1 May 2020
April has been a challenging month as I transition into working from home full-time. This has had its own issues with my focus and productivity, but overall has been going well. I’ve been trying to make progress on my thesis and have almost a full draft of the whole thing. There will probably be a lot of organization and fine touches, but the general writing and ideas are solidified.
Teaching has been an interesting endeavor. Online teaching is a totally different beast than in-person and the physiology instructor has been amazing helpful. She totally redesigned the lab and is recording the lab activity lectures for the students. I’ve only had to wrangle the weekly quizzes and grading students’ assignments, though I probably spend 10 hours a week grading. The students have been more proactive about asking questions and I am looking forward to the rest of the quarter.
Hopefully in May, we will be able to use this good spring weather for some hiking and camping if our restrictions lift. I’m a little tired of the white walls of my apartment.