Saturday, April 7, 2018

Undergrad the Impaler

Editor's note (from Dan Bolnick): The following is a reflection written by Cole Thompson, who was an undergraduate at the University of Texas at Austin and worked in my lab from 2013 until his graduation in 2015. Cole is now a PhD student at the University of Texas. From his work in my lab, he produced a first-authored paper and was a co-author on two other papers.

I arrived on the University of Texas at Austin campus in August 2011 excited by the opportunities that college would provide me. I had chosen UT largely in part because of the excellent science departments. However, as sophomore I was still looking to find my place on campus. On a cool January day walking the halls of one of the building I had class in, I found a poster searching for students interested in doing biological field work in Canada. Excitedly, I sent my resume to Dr. Dan Bolnick. He shot me back an offer to meet him and discuss the summer work—an NSF funded project on the parallel evolution of three-spine stickleback in evolutionarily independent lake-stream pairs on Vancouver Island. At the meeting he offered me the summer position and I accepted, unaware of how great of an impact this would have on my life. 
As I learned later during my time in the lab and undergraduate studies, Vancouver Island is an ideal location for examining how parallel evolution has occurred. As most readers of this blog will know, stickleback colonized lakes and streams on Vancouver Island about ~12,000 years ago after the last ice age. The result is many replicate pairs of neighboring lake and stream populations.
Finally, the spring semester ended and we were slated for a May 21, 2013 departure, but I excitedly and mistakenly arrived for departure a day early. The next morning, arriving at the correct time I met Dr. Yoel Stuart, the postdoc running the parallel evolution project, as well as Dr. Travis Ingram, another post-doctoral researcher conducting field work on the assortative mating of stickleback on Vancouver Island. Our trip began with a four day drive from Texas to British Columbia, which showed the beautiful side of the western US, and as we approached British Columbia I disconnected from the grid and my excitement for the summer grew. Once we arrived at our cabin on Roberts Lake, the real work began--sorting through fish traps, labeling tubes for storage of fins and eggs, preparing tea bags to store fish, and learning the codes for assessing the habitat surrounding the trap as part of gathering the ecological data for each fish trap, and, most importantly, dealing with the constant rain. 
After a couple of days of preparing materials we went to the first site—Comida Lake. The process, which was to be repeated for 16 lake-stream pairs, began. After bushwhacking to the site, 50 traps to collect the fish were set, recording their GPS coordinates and marking the time placed in the water. Then the depth, trap habitat, and flow rate (if applicable) were measured while a couple members built a processing location where trapped fish could be sacrificed and then weighed, measured, and have their fin clips cut for DNA sequencing. After two hours, the traps were checked with the stickleback taken for processing. This was done until 80 fish had been collected. After all the fish had been collected, the four most productive traps were identified and samples of the substrate and zooplankton tows were taken at each of their location. Then we used a spectrophotometer to measure the amount of down- and side- welling light at water level and one and two meters below the surface. The first site proved that this summer was exactly what I had hoped, and as I stood in the 50 degree water in the pouring rain with my hands barely able to move I was thankful to be doing science.
After a week of working on lakes close to the base camp, we moved to the northern part of the island to begin collecting at a different watershed, heading out to Joe Lake on June 3rd, 2013. In the early afternoon, while transporting fish to the processing station, I impaled the bottom of my foot. A sharp branch edge sliced through the boots of my waders, my sock, and an inch into my foot. Surprised by this, I gingerly finished transporting the fish I was carrying and then calmly sat and irrigated the wound with sterile iodine solution. Luckily most members of the field team had been asked to take a weekend-long wilderness First Aid class before going to Canada, a time investment that paid off. . After initial first aid,  we headed to the Port McNeil hospital. The result of the injury was not so bad, just stitches and crutches. There goes my summer, I thought. 
Cole, after his injury
Fortunately not so. Dr. Ingram, with the assortative mating project, took me onto his project. His team needed a boater who would row around on a pontoon in support of snorkelers who were sampling nest sites. From the boat, I could transport fish and eggs and record environmental data more easily than the snorkelers. Luckily for me, I could row without applying too much pressure on my foot or risking getting it wet. I jumped at this opportunity to help the team’s data collection efforts, which were going to help understand if stickleback in each lake mated according to similarity in diet. This was done by checking the carbon and nitrogen isotope ratios from the eggs in the clutch; which served as a proxy for the female diet, against the isotope ratio in a muscle clip taken from the male stickleback defending the nest. I spent the rest of the summer field season passing the hours on the little pontoon inflatable rowboat taking in the beautiful Canadian landscape, which like the boating, continually took my breath away. 
From left to right: Yoel Stuart, Cole Thompson (the author), Andrew Doggett (a high school teacher), and Brian Lohman

Once the field season ended I continued working in the lab performing DNA extractions and morphometric analysis on the specimens collected on Vancouver Island until the end of the summer. During this time I became awed by being part of the scientific process. I was doing science. Not only had I helped collect specimens, but now I was generating data for analysis and I wanted to find out what the data said. To do that, I began volunteering in the lab after my summer contract ended.  I sorted through benthic samples, took pictures of the fish we collected, used these pictures to measure differences in morphological traits, dissected out gill rakers and gut contents, examined gut contents for parasites, and transcribed ecological data. I couldn’t get enough. I wanted to learn how the environment and evolution has shaped these fish. As we sorted through the data, our preliminary data from the pictures of the fish showed that some lake stream pairs are evolving in a parallel fashion but this could be entirely antiparallel to other lake stream pairs, showing that there is clustering in directionality, but no steadfast uniformly parallel direction of evolution that holds across all watersheds. Dr. Yoel Stuart worked tirelessly on this project, and with help from Dr. Bolnick, formalized his findings on parallel evolution in the lake and stream in a Nature Evolution and Ecology in May 2017 titled Contrasting effects of environment and genetics generate a continuum of parallel evolution, showing that the environment dictated the direction of evolution, but genetics dictated the extent to which evolution occurred. My field and lab work earned me co-authorship on this paper.
Invigorated by my experiences in the lab thus far, I wanted to work in the lab again the following summer and with help from Dr. Bolnick and Dr. Stuart, was awarded an undergraduate research fellowship and an NSF-funded REU (Research Experience for Undergraduates) fellowship for summer 2014 to work on my own independent project in the Bolnick Lab. This project, examining the parallel evolution of jaw morphology and biomechanical values such as suction index, would be an extension of the work I had helped with the previous summer. For this project, I would excise the jaws of fish I had previously processed and take pictures of the jaw to calculate different metrics related to jaw function. With this I got to further embody the scientific process---creating hypotheses and synthesizing the results into a manuscript in addition to data collection, processing, and analysis I helped with the year before.

I worked, and worked, and worked on this project from summer 2014 until the November 2017 Evolution publication titled Many‐to‐one form‐to‐function mapping weakens parallel morphological evolution(Thompson et al 2017 Evolution). The results from my data collection and functional calculations showed that there is increasingly weak parallel evolution for biomechanical systems in which there are a greater number of morphological combinations that can generate the same functional output. That is, systems that are one-to-one in form and function are more parallel to each other than systems that are many-to-one in form and function, as there are multiple solutions that generate the same value.  I also collaborated with a fellow undergraduate Newaz Ahmed documenting the not-so-parallel evolution of brain morphology in these stickleback (Ahmed et al 2017 Ecology and Evolution).
During this 3 year process, with lots of help from Dr. Bolnick and Dr. Yoel Stuart, I did things I never thought I could do, or would do, like using R, a statistical software, to test our data, and help write a formal manuscript for publication; which, even with lots of encouragement and help, sometimes felt like an impossible task. Even so, in parallel to this project, I filled my life with lab-related things. I helped assist two other major projects in the lab, made life-long friends in the lab, found a quiet study place in the lab, met my wife across the hall from the lab, and learned about evolution, immunology, statistics, and countless other subjects while in the lab. In short, I spent the rest of my time in undergrad in “my place” at UT: Dr. Bolnick’s lab. 
Cole and Lauren got married last summer!
And now, almost 5 years since my first trip, I am thankful for the opportunity to go to Canada, do field work, and be a part of the scientific process—which to this day, has been the most influential experience of my life. 

Papers cited (blue names indicate undergraduate or K-12 STEM teacher co-authors:
Ahmed, N., Thompson, C D.I. Bolnick, Y. Stuart. 2017 Brain morphology of the threespine stickleback (Gasterosteus aculeatus) varies inconsistently with respect to habitat complexity: A test of the Clever Foraging Hypothesis.Ecology and Evolution7: 3372-3380.
Stuart, Y.E., T. Veen, C. Thompson, T. Tasneem, N. Ahmed, R. Izen, B. Doggett, D. Hanson, B. Lohman, K. Peichel, A.P. Hendry, and D.I. Bolnick.2017. Contrastingeffects of environment and genetics generate a predictable continuum of parallel evolution. Nature Ecology & Evolution. 1, 0158.  

This final part of the post is a video. Cole liked to video himself when he was on the pontoon rowboat and no snorkeler needed himself. He would babble about nothing in particular. We found a bunch of these kinds of videos on our GoPro cameras after the field season. And he probably never thought these would resurface to embarrass him. Little did he know.

There are more where this came from...

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Undergrad the Impaler

Editor's note (from Dan Bolnick): The following is a reflection written by Cole Thompson, who was an undergraduate at the University of...