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Using Our (Green) Thumbs for Typin’

Trevor here! And for, sadly, what is the last time. I can’t believe time flew by so fast! Alas, Nina and I began writing our research papers as we near the end of our externship experience. Our  “mini-papers” will be available on the flog and our broken down into four sections: introduction, methodology, results, and discussion. Make sure to check them out! Nina’s will be about diversity of plant species and its affect on Echinacea seed-set, while mine will concern how the burning of certain sides of a field-site affect the seed-set Liatris and Solidago species. Nina and I also had our “dissertation defense” sessions with Stuart, which both were very enjoyable and left us with lots of answers, but also plenty of questions to consider as we move forward as both students and researchers.

We also got to attend Dr. Kelly Ksiazek Mikenas public dissertation defense discussing her research on green roofs in both Chicago and Germany. In fact, the green roof pictured above is quite famous and is located on top of Chicago’s very own City Hall! Her talk was extremely enlightening and taught me a lot about promoting biodiversity in an urban setting. She defended the use of prairie species on green roofs in cities. She also had a wonderful array of snacks and her resume was quite inspiring and left me lots to think about when it comes to my future.

Thanks for everything Team Echinacea,

Trevor

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.

2017 update: Ridley’s next generation rescue

geneticRescueSlideIn 2017 Stuart and Lea relocated and measured 19 individuals of the 381 seedlings originally found. These plants had 1-4 leaves; the longest leaf was 32 cm. It should be interesting to see which individuals are hanging on!

Caroline Ridley established this experiment to compare fitness (recruitment and survival) of seeds originating from individuals with parents from three different backgrounds: 1. both from a large remnant population, 2. both from a small remnant population (not rescued), and 3. one from a large population and one from a small population (genetically rescued). Caroline sowed achenes in an experimental plot at Hegg Lake WMA and marked seedlings with colored toothpicks in May 2009.

Start year: 2008

Site: exPt 4 at Hegg Lake WMA

Overlaps with: crossing experiments qGen1, qGen2, qGen3 & recruitment experiment; INB1

You can find more information about Ridley’s next generation rescue and links to previous flog posts regarding this experiment at the background page for this experiment.

“R” We There Yet?

Hey! Trevor here! Today, Nina and I continued our work on the R platform, aggregating data and creating figures to be included in our final reports, which (spoiler alert!), will be available on the Flog starting Friday! So if you’re interested in checking out our work, feel free to look at those to get a sense of our projects.

Nina calculated the percent of invasive species for each of her plots using data from the United States Department of Agriculture (USDA) website. She used these percentages to create various graphs to attempt to predict the success of echinacea based on the number of invasive species. However, she found that this was not an effective way of predicting echinacea success. Aside from these quantitative activities, Nina also worked on “beautifying” her graphs, which includes adding R-squared and p values. Look at the red graph to the left, isn’t it beautiful?!

 

I finished up my work on the top/middle/bottom data and progressed onto the seed counts and cleaning data from the Liatris and Solidago species, which meant that I learned how to merge two different “csv” files together; a challenge, but a challenge I accepted. Afterwards, I worked through some obstacles to effectively calculate the mean seed-set for the East and West sides for the Staffenson site.  East had a higher mean seed set at 0.34, compared to west’s 0.20. In the realm of ecology, that’s a big difference! Currently, I am working on calculating the p value for these findings; it’s a process.

Nina and I hope to finish up working in R tomorrow (we’re almost there!) and begin writing our papers.

Until next time,

Trevor 🙂

“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!

2017 Update: Echinacea hybrids — exPt 9

This summer, we measured open-pollinated hybrid Echinacea plants in experimental plot 9 at Hegg Lake. The table below shows the number of plants found alive during each search since the experiment started in 2014. Of the surviving plants in 2017, 90% had fewer than 3 leaves, the mean length of the longest basal leaf was 25 cm, and only six plants had more than one basal rosette. This year we searched for plants once then rechecked every position where we didn’t find a plant during our first search. No plants flowered this year.

Year / Event Number Alive % Original remaining % Of previous year
Planting (2014) 746 100
2014 638 85.5 85.5
2015 521 69.8 81.7
2016 493 66.1 94.6
2017 401 53.8 81.3

This experiment comparing the fitness of Echinacea hybrids with pure-bred E. angustifolia and E. pallida will give insight into the possible consequences of non-native E. pallida being planted in restorations in Minnesota, where E. angustifolia is the only native Echinacea.

Measuring at Hegg Lake

Start year: 2014

Location: Hegg Lake Wildlife Management Area — experimental plot 9

Overlapping experiments: Echinacea hybrids — experimental plot 6Echinacea hybrids — experimental plot 7

Data collected: Rosette number, length of all leaves, herbivory for each plant collected electronically and exported to CGData. Recheck information for plants not found was also collected electronically and stored in CGData.

You can find out more information about experimental plot 9 and flog posts mentioning the experiment on the background page for the experiment.

Friday: A Day of Holiday

Trevor here! Today, Nina and I finished our work in “R” and diverged paths. I recounted Solidago to ensure that my initial counts were accurate. Nina began aggregating her data in “R” and created five extremely beautiful and effective graphs to display her data efficiently. Then, we progressed to the lab meeting, stuffing our faces with salami, cheese, and crackers as we learned about different management methods used with western prairie fringe orchids in Northwest Minnesota. Whilst attempting to answer questions, it seems as if these meetings yield more questions then answers as the intense discussion amongst fellow researchers brings up perspectives not previously contemplated, providing opportunities for future research. Stuffing our faces at lab meeting progressed into stuffing our faces at the holiday party as we joined everyone in the festivities. Highlights include chocolate covered strawberries, mac and cheese, and meatballs. Nina and I, on the recommendation of Leslie and Marty, then proceeded to walk off our meal with a stroll through the garden, visiting the amazing green houses in the Regenstein center. It’s super surreal to be inside a tropical-esque greenhouse in the middle of December! Ending our Friday, we began researching and writing the background information for our future research papers and are excited to continue our writing next week.

2017 Update: Echinacea hybrids — exPt 7

This summer, we measured hybrid Echinacea plants in experimental plot 7 at Hegg Lake. 159 of the original 294 planted seedlings (54%) were found this year. We searched 243 of the 294 positions where plants were originally planted (the other 51 positions were not searched because plants have not been found for at least three years in a row). The table below shows the fate of plants in 2017 summarized by cross-type — the first name in the cross type is the maternal species, and the second name is the paternal species (e.g., ‘ang x pal’ is angustifolia mother and pallida father).

Status 2017 ang x ang ang x pal pal x ang pal x pal
not found 53 10 33 35
found 21 18 52 72

Flowering Echinacea angustifolia.

Start year: Crossing in 2012, Planting in 2013

Location: Hegg Lake Wildlife Management Area – Experimental Plot 7

Overlaps with: Echinacea hybrids: ex Pt 6; Echinacea hybrids: ex Pt 9

Data collected: Rosette number, length of all leaves, herbivory for each plant collected electronically and exported to CGData. Recheck information for plants not found was also collected electronically and stored in CGData.

Products: Taylor Harris’s 2015 poster demonstrating fitness benefits of pallida parenthood.

You can find more information and links to previous flog entries involving experimental plot 7 on the background page for the experiment.

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!

 

Hypotheses, Predictions, and Fecundity. Oh my!

Hi! Trevor here, reporting on today’s events. Today I finished up my counting and classification of my achenes for both the Liatris and Solidago species. Better yet, Nina also finished her counting of the Echinacea species. Oh my! With our data collection finished, we are moving up the “corporate ladder,” and had our workday filled with enlightening meetings. We began by meeting with Jessa, a lovely 5th year Northwestern grad student. She told us everything from her educational background to her potential future jobs (including the possibility of teaching at the undergraduate level or possibly government work?!). She also explained the realities of being both accepted and working in a graduate environment, specifically at the Chicago Botanic Garden, which was a narrative we had not heard before. After brainstorming potential inquiries and hypotheses that emerged through our research, Nina and I also had a meeting with Stuart, Lea, and Tracie to discuss analyzing these hypotheses.

As you can see, we were hard at work (I was taking in the picture, but I promise I was there!). The meeting left us with lots of questions answered, but also lots of other questions to ponder was we begin our data analysis with two preliminary hypotheses we came up with. Tomorrow begins the start of “R.”
Wish us luck!