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Nina’s Externship Report

Hello, Nina here! These past few months, I was an extern with the Echinacea project, looking specifically at data collected last summer about Echinacea success and surrounding plant diversity. My findings are summarized in the report that I’ve attached here.

Externship Experiences: An Exit Poll

Nina here! Today was Trevor and I’s last day of our externship, which was bittersweet. Although I’m very excited to sleep in past 6:30, I’m definitely going to miss our mentors, Tracy, Lea, and Stuart, as well as all of the volunteers and the whole Botanic Garden community that we briefly got to know during our time here. Trevor and I mostly continued working on our papers, but we also gave short presentations of our projects to the lab to practice presenting. We also had closing interviews regarding our experiences and our thoughts on the externship. Trevor and I have both really enjoyed our time with the¬†Echinacea¬†project, and we hope that you will stay tuned for our final papers, which will be coming very soon (either this weekend or on Monday).

Thanks for everything,

Nina ūüôā

Developing achene eye for statistics

Nina here! Today, Trevor and I continued analyzing the data that we collected during the first two weeks of our externship. We both kept working in R, perfecting our papers, and analyzing our results.

Trevor found the confidence intervals for mean seed-set for Liatris and was very excited to see that the two intervals didn’t overlap, strengthening his confidence in his previous findings. Next, he aggregated and merged¬†Solidago¬†data before repeating the analysis he did for¬†Liatris¬†on the¬†Solidago¬†data, but with very different results. It seems as if¬†Solidago¬†was not effected by the burn that occurred in the site (as you can see from the photo on the left), but stay tuned for more updates!

Meanwhile, I looked the diversity function within R’s ‘vegan’ package to use Shannon’s and Simpson’s Diversity Indices on my plant community from each plot. I plotted seed-set, fecundity, and achene count against each index and found the highest correlation when looking at achene count. Next, I calculated species richness as well as the Shannon’s and Simpson’s Diversity Indices including only flowering plants. More updates to follow! After finishing up my actual analysis, I got back to working on my paper (which you can see a preview of on the right) and started thinking about which portions of my results and which graphs I might want to include in my paper.

“There’s nowhere up but here!”: Externship Week 3

Nina here! To start off the third week of our externship, Trevor and I got back to work in R. We started making our own scripts to try to visualize our data and understand our results. I found a strong correlation between seed-set and fecundity and a correlation between seed-set and achene count (although the R squared value was small). I downloaded a database of plants of Minnesota from the USDA database that included information on whether or not the plants were native, threatened, or endangered as well as their fire tolerance and growth habit. I merged this database with the diversity data collected in the field in order to provide more data about each species. Next, I tried to calculate the percent of invasive and nonnative species for each plot. Meanwhile, Trevor calculated the means for the numbers of achenes in the top, middle, and bottom samples and determined whether or not there was statistical significance between pairwise comparisons of the findings. Next, he looked at confidence intervals for his findings. We both continued our work on our papers, writing up our methods sections specifically. As Trevor meant to say, there’s nowhere to go from here but up!

R We Ready For Analysis?

Nina here! Today, Trevor and I downloaded R and RStudio and started familiarizing ourselves with R by using the tutorial package ‘swirl’ and completing several of the lessons about the basic building blocks, vectors, matrices, data frames, logic, functions, and much more! Thanks in part to Trevor’s donut holes and Tracy and Lea’s support, we powered through and completed the swirl tutorials. Next, I got started with looking at my own data by reading in some of the csv data files into R and trying to get started on viewing them and writing a script to determine species richness. Also, just for fun, here’s a¬†counting timelapse¬†from a couple days ago of an evaluating empty, partially empty, and full achenes!

 

Cleaning, Randomizing, Counting, X-raying: Externship Day 7

Nina here! Trevor and I were hard at work today, getting our achenes ready to be X-rayed and counted. I finished randomizing achenes in preparation for X-raying them later, and started counting the achenes in each of my samples. Trevor finished cleaning his achenes, placed them all on X-ray sheets, and X-rayed all his samples. Now he has to count which of the achenes in each of his samples were full and which do not havean embryo. An image of one of his X-ray sheets is below.

Trevor Ate an Achene: Echinacea Externship Day 5

Nina here! Today, Trevor continued cleaning his¬†Solidago¬†heads, which have very small and delicate achenes. However, because his achenes are so small and fluffy, they tend to fly everywhere, including onto the bread that Trevor was eating! He cleaned 28 heads today, which was very impressive. Meanwhile, I finished re-checking my¬†Echinacea¬†heads for any stray achenes that were stubbornly clinging to the heads and proceeded to scanning the achenes for counting. While I was re-checking, I found quite a few miscellaneous bees and spiders, some of which are pictured below. Also, a picture of one of my scans below – for this site, the achenes needed to be separated according the the location that they came from on the head, so ‘top,’ ‘mid,’ ‘bot,’ and ‘other’ achenes were segregated. Next week, I hope to start randomizing my samples for X-raying and counting the scans that I took. Trevor hopes to finish counting and move on to X-raying next week as well.

We also had a lab meeting today to discuss a draft of a paper on Echinacea pollination, specifically analyzing the number of pollinators over the course of the season as well as type of pollinator and quality of pollination. The paper had some interesting (and confusing!) results, so it was nice to discuss the draft with others from the lab and look at the feedback that the draft received from reviewers.

 

Cleaning heads

Hey, this is Nina! Today at the Chicago Botanic Garden, Trevor and I continued cleaning¬†Echinacea, Liatris,¬†and¬†Solidago¬†heads. We learned a new technique to clean seed heads today, which involves sorting the achenes based on the location on the head. For my¬†Echinacea¬†heads, I separated 30 achenes from the top of each head and 30 from the bottom of each head (not including any ray achenes present at the bottom of the head). Here’s a¬†timelapse of me cleaning one of the heads. I got some help today when Marisol, a lovely intern from Lake Forest College, helped me clean some of my¬†Echinacea¬†heads. Trevor separated achenes based on location on and counted the number present on each head. From preliminary data, Trevor thinks there is a lot of variation from plant to plant, but no trend between numbers of achenes based on location on the stem. Tomorrow, I hope to finish cleaning my seed heads and move on to scanning!

Meet Nina!

Hello, my name is Nina Denne and I am currently a freshman at Carleton College. I will be working as an extern at the Chicago Botanic Garden for the next 3 weeks, specifically looking at the relationship between reproductive fitness of¬†Echinacea¬†and the diversity of the surrounding habitat. For now, I’m mostly cleaning Echinacea¬†heads and then I will be counting the achenes and X-raying achenes to determine whether they are viable.¬†I’m very excited to be back at the Botanic Garden after having conducted a germination experiment with two species of¬†Echinacea in high school.¬†

Poster Version of Echinacea Seed Head Website

Hello! The poster version of the webpage displaying parts of an Echinacea seedhead is now available online, in pdf form. The poster displays the parts of an Echinacea seed head and the types of chaff that might be found while cleaning a seedhead, with many pictures. The link can be found here: http://echinaceaproject.org/wp-content/uploads/2015/12/Echinacea-Seed-Head-poster-pdf.pdf.