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New year, new x-rays

Hello flog!

For those of you who read all of my flog posts (I know there’s a solid number of you out there!) you’ve probably figured out by now that I love posting about numbers. So what’s today’s number?

Why, it’s 1948 of course!

Now this is the point that you might furtively look at wikipedia and say “I don’t understand what 1948 has to do with Echinacea. Everyone already knows that 1948 was a leap year starting on Thursday of the Gregorian calendar, the 1948th year of the Common Era (CE) and Anno Domini (AD) designations, the 948th year of the 2nd millennium, the 48th year of the 20th century, and the 9th year of the 1940s decade.” To which I would say that we are dealing with the number 1948, not the year.

No, 1948 is the number of seed packets of echinacea we x-rayed at the garden this week: and it’s only Wednesday! Through the combined efforts of many volunteers we are making some headway into the daunting task of figuring out which achenes have seeds in them and which do not. Look for updates soon about these number for our pollen limitation heads!

Michael

p.s., here’s a small sampler of what the xrays look like

A look at our qGen_a xrays from 2013. There’s almost 900 images total in this folder (not nearly that many are shown here)

The Adventure Begins!

Hey hey hey! My name is Anna and I was a summer intern on the Echinacea Project in high school. Now, as a college freshman, I am currently exploring another side of the project at the Chicago Botanic Garden lab! For my two weeks in Chicago, I will be working on the soil component of Kristen Manion’s project. Her study considers numerous elements of native bees’ habitat in hopes to determine their nesting preferences.

Over the summer, soil samples from 8 sites were collected and each site had three different land uses: old field, native prairie, or restoration. In total there are 328 samples to be analyzed through the micropipette soil texture method! The micropipette method involves separating the soil into its clay and sand components and then calculating the percentage of sand, silt, and clay for each 2-gram sample. By the end, I am aiming to create two soil triangles and answer these questions :

  1. Does the soil type differ between bee presence/absence?
  2. Does the soil type differ between land use types (remnant and prairies and old fields)?

 

My other goal is to simply gain experience in a lab by being exposed to a variety of techniques through Kristen’s and the Echinacea Project’s methods. However, I also have a couple of personal goals… like eating deep dish pizza, taking my picture in front of the bean, figuring out public transportation, and did I mention deep dish pizza?!

My adventure here in Chicago is just beginning and I can’t wait! 

 

Cameo spent the fall with Team Echinacea!

This fall we had the wonderful opportunity to work with Cameo Chilcutt, a student of Northeastern Illinois University. Cameo spent the fall working in the lab and conducted her own growth chamber experiment with seeds from Selena’s summer REU project. Cameo was a great addition to the lab and asked some cool scientific questions about how water stress and maternal competitive environments affect germination in Lasthenia californica. Check out her final report posted below. We’ll miss having Cameo around but wish her luck in her future scientific endeavors!

Cameo Final Paper

 

Carleton Externs – Julie’s Final Update

Hello Flog!

This has been an exciting last week for the Carleton externs in the Echinacea lab! We had the incredible opportunity to not only analyze our collected data in R, but also to develop posters about our findings and present our results to the resident members of Team Echinacea. Tris’s project examined the effects of pollen limitation on future growth, survival, and fitness in Echinacea. Check out Tris’s flog entry for more! Meanwhile, Sarah and I determined that previous prairie burning and plant characteristics like flower head count may interact to differentially affect reproductive success in some Asteraceae. See Sarah’s post for the details!

It has been a pleasure working with the Echinacea Project over the past three weeks, and though this is our last day in the lab, I am excited to bring all that I have learned here with me into the future. Working up-close and personal with specimens as we carried them through data collection, analysis, and the presentation of results was a gratifying experience that introduced me to some of the joy of science. Thank you to Dr. Stuart Wagenius, Lea Richardson, and Michael LaScaleia for your mentorship and guidance! It was a pleasure to be a part of Team Echinacea.

Bye for now, Flog!

Julie

Carleton Externs – Sarah’s Final Update

Hello flog, one last time!

Today marks the end of my three weeks here on Team Echinacea, and I’m certainly sad to say goodbye! Nevertheless, it was exciting and rewarding to culminate this externship with a week of data analysis, poster creation, and presentation of findings to the team. While Tris chose to analyze data from Michael’s Echinacea pollen limitation experiment, Julie and I decided to delve into the worlds of Liatris aspera and Solidago speciosa, two other Asteraceae common to prairie ecosystems. Lea has been working with these species for her PhD project over the past few years, studying how timing and location of flowering influences reproductive success, so she was a great help as we commenced our analysis!

After having meticulously cleaned, counted, and classified innumerable Solidago and Liatris flowering heads, Julie and I wondered how the vast differences in head count between these two species may impact each plant’s fecundity (when Liatris plants generally have 10-20 heads, and many Solidago plants have hundreds or even thousands) . Further, knowing that human populations have largely suppressed the occurrence of natural fires in today’s prairies, we were also interested in analyzing the effects of prescribed burns on these common prairie species. We put these two questions together in our data analysis by forming a statistical interaction model–one in which the effect of fire would interact with the effect of flowering head count to influence reproductive success–and fitting it to our Liatris and Solidago data. Interestingly, we did not uncover the same results for these two closely-related plants! For Liatris, the interaction model was highly supported by our data: the head count of plants seemed to have more effect on seed set (a measure of fecundity) in plants that had not been recently burned than in plants that had been recently burned. Yet, for Solidago, this pattern was not present. Our findings suggest that prairie management strategies, of which prescribed burns are an integral part, should carefully consider the species composition of a prairie before burning, because different species may react to burn treatment in different ways. Check out our poster, attached here, for a more detailed analysis, as well as plots of our models!

Before I sign off, I want to send a huge ‘thank you’ to every member of Team Echinacea! This opportunity was incredibly influential for me–this was my first real research experience, and I learned so much about ecology, networking, career paths, data collection, statistics, and more. I had an amazing time, and I hope to see some team members again someday!

Thank you again,

Sarah

PDF version below:

Soliatris2018 Poster

Carleton Externs – Tris’s Final Update

Hi flog,

Wow! These last three weeks passed by super quickly! While the first two weeks were focused on seed cleaning, seed counting, and x-raying, we spent this past week on our independent projects. But that’s not to say this week was easy! In the past 5 days, I wrote exactly 900 lines of code in R to generate the figures and perform the analyses.

To get at how current pollen limitation affects Echinacea growth and future fitness, I performed analyses testing differences in plant traits between pollen exclusion, pollen addition, and open pollination treatments. I did not find evidence that pollination treatment affected either growth or fitness, which indicates that current pollen limitation will not benefit Echinacea in the future. This could be because Echinacea is not resource limited or because the cost of seed production is negligible.

Many thanks to the members of Team Echinacea who helped guide me through this process and made working in the lab such a pleasure!

 

Tris

Link to Poster

2018: A year for counting

Here at the Echinacea project, we like to count things. We like to count achenes, pollen, seeds from liatris and solidago, and really anything that will get us data. So, I am happy to give our (almost) full counting report from 2018.

This year, members of Team Echinacea counted over 717,000 achenes.

I, Personally, am wowed by this number,for not only does it mean that our team had to sit and click a computer screen 717,000 times, but it also means that we have roughly 1/3 that number of achenes sitting on the shelf right now! And that’s just from this year!

Thanks all for a great year of counting, and I hope we count even more next year!

Michael

The Tragic Saga of Echinacea Head CG2016 XD-9460

Here at the Echinacea Project, we have some pretty rigorous protocols to make sure that everything goes right. This applies doubly so when it comes to ACE — the process we use to make sure we count all of the achenes on every head (hence the acronym, Accurately Count Everything). The process starts when we harvest the head in Minnesota in August or September, and ends sometimes years later when we have classified the last xray, with rigidly defined steps in between. This process leads us to a data set that has a human error rate of less than 1%

This is a story about that <1%

In fact, I would argue that this is a story about the 1% of that <1%. A head that has not only 1 terminal error associated with it, but 3.

This is the story of CG2016 XD-9460.

My experience with this head, whom we’ll nickname XD, began when Tracie gave me a list of the necessary rescans for 2016. These are the heads that, for some reason, never had their achenes scanned. They can be particularly troublesome because usually their achenes are in 3 separate places as part of ACE protocol that normally comes after the scanning step. I had gotten XD’s achenes from 2 of the 3 locations, and went to look for its orange coin envelope — the envelope that contains most of its achenes.

It wasn’t in the first place I looked, where it should be.

It wasn’t in the second place, where it shouldn’t be.

Nor was it in the third, fourth, or fifth places I looked, where it definitely shouldn’t be.

In fact, it was no where I looked. After an upsettingly long and painfully fruitless searching process, I decided to check and see who had cleaned XD, and maybe that would give me a clue where the envelope was. To my surprise, I saw the label that should have been on XD’s orange envelope still on the master label sheet, and the words “head not here” written in the notes section by the volunteer assigned to clean it.

How then, did we have some achenes for XD if the head was never cleaned? How did we have achenes if the head was never here?

This is an insight into our ACE protocol. Even with our organization and attention to detail, things can go wrong in ways we could never predict. After I completed my detective work, here is what I believe happened to CG2016 XD-9460. This is the verbatim note I have left in our “missing scans” log. It is unusual for this log to contain more than 10 words about each head.

1:56 12/5/2018 MCL
XD-9460 has more than one error associated with it. This is my best guess as to what happened.

Error 1. On the day it was harvested, the harvester came to a plant that had two heads on the ground: XD-9460 and XM-9011. The harvester put both heads in the same bag and made a note of it. I believe that bag was labelled XM-9011

Error 2. When it came to cleaning, XM-9011 was cleaned normally, and no note of a second head was ever made. I believe only one head was selected from the bag (either 9460 or 9011), labelled as XM-9011, and processed, while the other was ignored.

Error 3. During randomizing 9460 was not skipped, despite having no seed packet associated with it There is a white envelope and clear baggie with achenes “from XD-9460” in it; however, seeing as that is not possible, they come from a completely unknown source.

So there you have it. A story that took up a few hours of my time, so I thank you for taking a few minutes of your time to read it. If you’re wondering what happened to the data from this head, it has been labelled as “lost in the field” and wont poorly influence our analyses (or torture our lab managers) anymore.

Have a good weekend!

Michael

Carleton Externs Update

Hi flog,

Things have really gotten going, here at Echinacea headquarters. Julie, Sarah, Lea, and I have been spending much of our time cleaning and counting Solidago, and we’ve made pretty good headway, each counting about 2-3 samples per hour. We’ve also made some preliminary observations about variability. We’ve found high variability between plants, but not within plants! For example, we’ve seen ranges of 3 to 372 heads per stalk, and anything from 7 to 24 achenes per head in different plants. But within a plant, achenes per head is relatively uniform, generally ranging by ~2 achenes, which should allow Lea to precisely estimate total number of achenes per plant.

In addition to the Solidago, we’ve been working on Liatris. We finished the most important part of estimating potential reproductive success: x-raying the achenes to see if they contain seeds. This process involves placing baggies filled with Liatris achenes over a reusable x-ray film, shooting x-rays through the achenes, and quickly feeding the film through a machine that digitizes the film and allows for online counting of full and empty achenes. From this, we can estimate proportion of achenes containing seeds, multiply this proportion by number of achenes, and thus estimate reproductive potential of the plant. Because my project doesn’t involve seed set, Julie will be doing all the counting for Liatris (Fig. 1) while Sarah will handle counting for Solidago x-rays.

Until next time,

Tris

Fig. 1. Julie diligently counts full and empty Liatris achenes while Lea continues to count Solidago heads.

Carleton Externs Update

Hi Flog!

With half of our externship now past, some exciting things are happening in the lab! Yesterday, Sarah, Tris, and I had the opportunity to talk with Stuart, Michael, and Lea about some of the research questions and hypotheses we’ve started to form while working so closely with the specimens over the past week and a half. Stuart offered several suggestions about how to formulate these questions so that they are testable with the kinds of data we have, while also advising us about the statistical approaches we could take to assess our hypotheses. As we gather together the last crucial pieces of data, we’ll have the opportunity to try answering some of these questions. If all goes well, we will be rounding out our experience working with Team Echinacea by the end of next week with our own independent projects and analyses of the data.

In the meantime, we have been continuing our final steps of data collection. Despite our earlier trials and tribulations holding our breath while individually counting hundreds of seeds the size of sand grains, our new Solidago counting procedure seems to be a success! With a more efficient system in place, we hope to finish counting seeds by the start of next week. All that remains after that is x-raying and classifying the x-rays from all of our samples of Echinacea, Liatris, and Solidago before we can gather together all of our data into frames. As we learn more and more from our mentors about how to manipulate data sets in RStudio, I can’t wait to start assessing regressions and comparing models soon!

Excited for the number crunching,

Julie

 

Tris and Sarah demonstrating our new and improved Solidago counting procedure