NOVEMBER 2021
Kyra's Blog
Kyra Bankhead, undergraduate student
1 November 2021
This has been an extremely busy month. I was able to turn in my NSF GRFP application after working on it for four months now. I wasn’t able to figure out the specifics of my methods, but my goal is to get the experience of going through the NSF process to learn from it and get feedback to increase my chances for next year when I will be applying for grad school. Additionally, if the NSF funds this year's proposal, I am not obliged to carry out this specific project, so I will have time to develop the methods further in the coming year. I am really passionate about the transmission of foraging specialization and am keen to collaborate with the Sarasota Dolphin Research Program. This way I can get everyone’s expertise and advice for developing my research project for graduate school. I hope as I advance to graduate school I can continue with these ideas and include everyone involved in collaboration as co-authors.
I have also been finishing up the draft of my manuscript for my project on the anthropogenic noise disturbance effects on Bellingham harbor seals. I also got in touch again with Wyatt Heimbichner about being a co-author on the manuscript. I still have to flush out the results and figure out what figures I want to use to best represent my research. I hope to get a final first draft done before the end of fall quarter so that Alejandro and I can start editing it and I can get it out to be reviewed by Wyatt. I am excited to start presenting and potentially publishing my research I’ve worked on for two years.
Until then,
Kyra Bankhead
Holland's Blog
Holland Conwell, undergraduate student
1 November 2021
As we drift into the rainy season, I’ve certainly had my hands full with classwork and work for this project! Last month's meeting helped illuminate the short-term path forward, eventually resulting in the decision to re-run some more plates. I began this month by helping Zoë double-check the sexing results for each plate, keeping a list of possible errors and plates that I believed should be re-run. We later met to discuss my notes and correct sexing errors in the dataset, and we ultimately decided upon a solid list of plates that should be re-run. While plates with half Y control failures and an odd case got a pass, plates with complete positive control failures, “false females”, and especially failed negative controls appeared to be the most concerning and thus were deemed the best candidates for being re-run.
In the meantime, while Zoë is re-running the troublesome plates, I’ve kept myself busy working on a graph of the sex ratios at each haul-out location from 2014 through 2018. This required me to brush up on my RStudio skills, and I’ve been enjoying putting it together! That said, I’ve certainly run into a couple of speed bumps along the way. Initially, I thought that I needed to convert the dataset from wide to long format, leading me to run into a million errors that turned out to be negligible. With some help along this wild goose chase, I was able to assemble a massive array of stacked bar charts organized into a facet grid. The figure organizes the information into columns by haul-out location and into rows by the year that each sample was collected (2014-2018). The x-axis depicts which month each sample was collected, while the y-axis displays the quantity of harbor seals at each site over time, with the sex data (male, female, unknown, and blank) plotted within each stacked bar chart. I just finished troubleshooting and making some adjustments to the axes in hopes that they might appear more readable, and overall, I’m pretty happy with the result! I think that using this time before I receive more sexing results to dust off my RStudio knowledge and learn more complex graphing skills should help me recreate this figure with updated results and jump into data analysis in the near future.
Zoë's Blog
Zoë Lewis, graduate student
1 November 2021
October was full of deadlines, in person tests (yikes!), more scat samples, and preliminary results from the DNA metabarcoding for this project! There have been so many moving pieces finally settling into place this month. As I told Alejandro last week in our one-on-one, I feel like all the hard work to set up this project to be on schedule and successful is paying off. After a year, I feel like I am finally able to organize and juggle all the aspects of this project and really dig into the research.
In the fisheries science class I am taking, I had my first in person test in over three years. Although slightly intimidating, I was excited to demonstrate my knowledge in a class I have been thoroughly enjoying. This class has contributed significantly to my understanding of Chinook salmon ecology. By using the correct language to describe Chinook salmon fish stocks, my thesis writing on salmon has drastically improved. Further, by practicing fisheries stock models and better understanding fish trophic dynamics has allowed me to critically think about my diet analysis within the full ecosystem framework.
Speaking of my thesis…. This month, I finally finished a first draft of my general introduction for initial revisions. After many conversations with Adrianne, Alejandro and Dietmar about the framework for this study, I was excited present an initial synthesis of this information. Although not perfect, I’m confident that this section will be a polished, critical component of my thesis by the time my defense rolls around. It feels good to meet the initial deadline and get started on the writing process.
Finally, after a year of searching, I got my hands on Steller sea lion and California sea lion known sex scat samples! A huge thanks to the Vancouver Aquarium and The Marine Mammal Center for collecting these samples the many hurdles presented by the impacts of the COVID pandemic. Yes, I know I said I was “done with scats” Next week, Maddie and I will begin working on extracting and validating these samples using out Harbor seal probes.
This week, I also met with Sarah Brown to better understand the DNA metabarcoding process, and get the first glimpses of my data! It is so cool to see the product of all our work, even in the initial phases. Sarah spent almost two hours walking me through the data analysis, I am so lucky to the incredible collaborators I have had the privilege of working with throughout the past year. We had lots of fun digging through the known species DNA sequences and testing our scientific naming knowledge. Although the diet proportions are incomplete, I now have a better conceptual understanding of these data and I’m able to play around with data visualization and analysis.
I have my work cut out for me, but meeting these initial goals and seeing these data begin to emerge has continued to inspire me… For now, I’ll keep writing, understanding my data analysis and completing the sex-determination analysis for my project. Overall, things are going well and I’m so lucky to feel on track despite the many challenges of this year.
Kathleen's Blog
Kathleen McKeegan, graduate student
1 November 2021
It has been a busy month at Whatcom Creek! Between photo processing, data wrangling, and observations, this lab has kept me very busy! Unfortunately, I did not accomplish all of the goals I had set for the month of October. That said, I have made great strides in the project so far and I am very proud of the work Kate and I have accomplished.
As a status update, Kate is currently processing the 2021 photos as they come in from the observations. I am working on inputting the 2019 and 2020 data into a usable format. Due to the nature of this project, the data is a little messy and distributed in different formats across several excel sheets. Zoë and I spent a few hours talking through the data and developing a format that will enable me to test my hypotheses. Essentially, I am breaking down each observation into seal occurrence counts, AKA how many minutes each seal observed with or without a fish per sample period (observation). These occurrence counts can then be associated with TAST status, as well as other potential predictors like tide or month, etc. The only downside is that it takes a while to transfer our data from cropped and IDed photos to the datasheet, especially because I am using this as an opportunity to confirm 2019 IDs based on the catalog updates I made this summer. The process is slow but worth the time because the data will be trustworthy. Once that is completed, I can begin data analysis and actually get some results!
Outside of photo processing and IDing, things are going well. Our lab participated in an outreach opportunity for Fall Family Weekend and will be presenting to the Bellingham Technology College hatchery students sometime this quarter. I also finished a first draft of my thesis introduction! It’s rough but a great first step! My goals for this next month are to finish data wrangling, begin data analysis, and submit a couple abstracts for various conferences.
Kate's Blog
Kate Clayton, undergraduate student
1 November 2021
October has been a very busy month! Between training new students, conducting observations, processing 2021 data, and taking classes it has been hard to keep up. I know this month will only add more to my plate, but I am hoping after November, things will die down a bit.
Kathleen and I have trained all but one of our students on how to conduct observations. Everyone now has several observations under their belt, so they should feel comfortable and confident when the creek gets busy this month. Entering November, we are ramping up our observation schedule to about five observations per week.
The season has started to pick up and we have already seen a lot of our returning seals as well as a few new individuals despite it being in the early stages of the salmon run. Kathleen and I have noticed that we seem to be seeing more individuals than usual (compared to past Octobers). This is especially interesting because the hatchery escapement reports seem to be similar to previous years. Due to these anecdotal observances, we are expecting a busier than usual season as we enter November (Chum run).
Kyra kindly gave us an extra pair of binoculars this last week to help us ID seals while we are in the field. This will continue to help speed up the data entry process, so we are very grateful for the binocs!
Kathleen has been entering all the data from 2019 and 2020 and I am in charge of processing the photos as they come in for 2021. We have changed our photo process a bit to include the 2021 season in our data. This year I am sorting the photos into folders based on ID as they come in. In the Winter and the Spring, we will have students crop and name these photos, but for now, we can enter the data based on the ID, date, and time that each individual was seen at the creek.
Besides our final folders of un-IDable photos and a bit of double checking that we are slowly working through, we are done with the 2020 season. Kathleen is doing an amazing job managing our data and beginning the stats process! She has just finished the 2019 data and will begin working on the 2020 data as we complete our final steps.
I also need to finalize our process on photo cropping in our new format. I am hoping to get this up and running in the next couple weeks. I have most of the details sorted out, with just a few technicalities I need to finalize.
Hopefully in the next couple of months we will have some preliminary results on the effectiveness of TAST on the Whatcom creek Harbor seal population.