R Coding, Seed Germination, and Comparative Biology Labs

March 12, 2024

By Sarah VanRyswyk and Kylee Hanks

Recently in the RISEbio research stream, we have been working with R and Rstudio coding while also monitoring our seed germination experiment from Week Two. Within the next two weeks, we will also begin to plan our own experiment of choice.

Kylee working on R coding for the species Quercus suber.

Two weeks ago, we learned how to use R and Rstudio coding to calculate environmental niches for a species of our choice. R coding is a software that creates geographic maps to show data across an area. For example, we found soil pH levels for two species across the world. The species we chose to examine was the Quercus suber (cork oak tree) and the Dalea purpurea (purple prairie clover). Before going straight into R coding, we did background research on our species to get an idea of their native environment. Quercus suber is native to Europe and Northern Africa, but can also be commonly found in California currently. Dalea purpurea is native to grassland environments located mostly in the Western United States and Southern Canada. We did this research to know what area to analyze the most for the geographic data we were getting. By using areas the species is not native to, it could impact the accuracy of our results regarding topics like temperature zones it is most common in. From there, we began using the R coding software to create maps that could show us soil and temperature data. This process was difficult for us, as this was both of our first times coding. An area we struggled with was code constantly appearing red, meaning it was not working properly. A lot of these issues were resolved from reformatting the code or changing the way we spaced out the words. The maps ended up all working in the end, and we will use them in the future to apply them to a specific environmental niche. While R coding was hard to adjust to, we overcame the incorrect codes and got all of the geographic maps required for our species.

Sarah watering our planted wild lupine in the greenhouse.

A lab we have been working on since the first month of RISEbio is the seed germination lab. We chose two species, Lupinus perennis (wild lupine) and Campanula americana (tall bellower), to apply different germination codes to. We used C(30), which means germinate them for 30 days before planting, and the germination code H for our independent variable. We took half of each seed type and applied germination code H, which means scarifying the seeds. For scarification, we used sandpaper to rub off the outer seed coat. It was difficult to scarify the Campanula americana seeds because they are incredibly small, but we solved this by placing the seeds in between two pieces of sandpaper. So far, applying germination code H has benefited Lupinus perennis, but negatively impacted Campanula americana. Over the past week, we planted the germinated seeds from each group to see how they would grow in comparison to the control group. The results we have been seeing were what we had hypothesized, but we will continue to run the experiment to see further results.

A future experiment we will be doing is a comparative biology lab. We will be comparing a species to another species, or a species to their environment. Over the course of the next few weeks, we will begin to brainstorm and formulate an experiment to perform. As the research stream continues on, we will continue to monitor our germinated seeds and run a comparative biology experiment in the future. The hardest experiment we have done so far is the R coding because of the difficulties in finding errors, but we were able to overcome it with the help of our peer mentors and changing the spacing around. The other two experiments will take further time to find results, but we will continue working on them each week.

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