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Lois counted her 800,000th achene today

Lois Jackim, citizen scientist working on Team Echinacea since 2009, counted her 800,000th Echinacea achene this morning around 9:30 AM. Scientists from the Chicago Botanic Garden and Northwestern University were present as Lois was presented with a giant check thanking her for her dedication to plant science and conservation. Lois wore her “Achene Queen” crown, which she earned in 2015 after surpassing the half-million mark. Lois was not aware she was so close to the 800,000 milestone.

Counting fruits, also known as achenes in Echinacea, is a critical activity for scientists measuring reproductive fitness of plants. The Echinacea Project conducts experiments to assess environmental and genetic factors that influence plant fitness. Echinacea Project research contributes to basic ecological and evolutionary science in addition to informing conservation of perennial plants and prairies.

Other citizen scientists present this morning were cleaning and preparing seedheads and making digital images for counting. Each year the Echinacea project harvests heads from experimental plots and volunteer citizen scientists at the Chicago Botanic Garden count all achenes from each head. Citizen scientists also x-ray samples of achenes from each head to count how many of the achenes were pollinated.

Team Echinacea celebrates Lois counting 800,000 achenes

Stuart presents Lois with a giant check to thank her for counting over 800,000 achenes.

Winter update

Hi Flog! It’s me, Amy!

This winter we’ve been working on ‘demap’, a project to coordinate 20+ years of demography and spatial data from remnant populations of Echinacea in Solem Township. When we are done we will have a great long-term dataset of over 3000 individuals in 27 remnant populations. We can use that information to answer all kinds of questions about flowering dynamics in natural populations, population growth, and the consequences of disturbances such as habitat fragmentation and fire! In particular, this January we focused our efforts on answering questions about the demographic consequences of fire. Does fire’s stimulation of flowering contribute to increased population growth over the long term? Do reproductive benefits of fire outweigh potential survival costs?  We’re not sure, but we hope to find out by analyzing four populations– a large population that had one fire event, a large population that has not been burned in the past 20 years, a small population that burned once, and a small population that has not burned in the past 20 years. We’ll combine our demography data about flowering and survival with other information, such as the seedling recruitment and remnant seed set data, to project population growth.

Will was here to help out with the project in the first two weeks of January. We got a lot done with demap and made meaningful progress on other big questions such as “Is kale overrated?” and “What does overrated mean statistically?”. We also made big strides in terms of professional development by studying business mogul DJ Khaled’s keys to success. Stay tuned for updates!

Sincerely,

Amy

 

Demap is a team effort! In this shot, we are helping Will find a plant on the computer.

 

 

Farewell Flog Post

Hey Flog readers, Sam here.

After a quarter of hard work, all of the achenes from my thirty-two flowerheads have been counted, x-rayed, and classified! I am looking forward to analyzing the data next quarter in R through a class Stuart teaches at Northwestern. It’s been quite a journey learning about both the nitty-gritty of going from flower head to data sheet and the conservation biology through which we contextualize our data. Special thanks to Stuart for giving me the opportunity to intern for the Echinacea project, to Amy and Scott for being wonderful, helpful mentors, and to everyone else in the lab for your amazing company and support. If anyone reading this would like to know more about what it is like to intern for the Echinacea Project, feel free to e-mail me at Samuelhamilton2017@u.northwestern.edu.

Best,
Sam

“She doesn’t even go here.”

We’re done! Yesterday Emma and I finished up our poster with mere minutes to spare and some timely help from Stuart (the man knows concise language). I thought of about five other tests that we should run (to characterize interactions between explanatory variables, etc) while wrapping up our last section, but defeated the urge. We’re both very proud of the poster and the work we did these past three weeks.

Thanks to everyone in the Echinacea Project for your guidance, help, and companionship! This externship has been an awesome experience and has definitely helped us to grow as scientists.

Here’s a link to our final poster:

Kropp_Stewart_Poster

Our Not-So-Tiny Problem

After two grueling days and one exceptionally grueling one (during which we had to solve an issue with our tinies–what even is a confounding variable??), we’ve finally finished analyzing our data.

Our models fit, and our p-values are significant (sometimes), but the best takeaway from this week is definitely what we’ve learned about statistics and R. Prior to this Emma had never seen R before and I had only a rudimentary knowledge, but yesterday we wrote some code and solved a few problems without even consulting the internet! A HUGE shout-out to Stuart, Scott, and Amy for teaching us about generalized linear models, backwards step-wise regression, logistic transformations and all of the R syntax we didn’t know we needed, and for being patient with our sometimes-constant questions. I indubitably feel like I understand much more than I did coming into this week.

Stay tuned for our poster, which will include all the juicy juicy results that Emma and I have been slaving over. How has time passed this quickly?

Mikaela

R we going to suRvive R?

At the end of last week Mikaela and I officially finished data collection and entry. With a few hours left until the weekend, we came up with a handy dandy poster that can be used in the future when randomizing achenes. A similar guide existed for volunteers, but it had actual achenes glued to it and most had fallen off. We picked through the achenes we had sorted and put together pictures detailing the differences between informatives and uninformatives.

acheneidentificationposter

This week we started statistical analysis using R. Our hypotheses are currently being put to the test! With our limited stats and R knowledge, our progress is slow, but we’re getting the hang of things. Hopefully by the end of this week we’ll have some conclusive results; stay tuned!

 

 

PS: Here’s a link to the pdf of our poster acheneidentificationposter

We Slowed Down

Classifying x-rays stopped being fun very quickly today. Emma and I had divided the slides randomly and were each doing half, and I finished mine first so I decided to classify a handful of hers and see how the numbers matched up. They didn’t. Around 50% of the slides I recounted had new numbers. All of the discrepancies were because achenes were in between being full and partial or partial and empty (partial achenes were fertilized, but the embryo either did not develop normally or was destroyed). Together we went back to go over the discrepancies, and we came up with a few rules to make things clearer in the future. We were already working with a few rules that Danny had set out for defining partials:

  1. The embryo is fragmented
  2. The embryo has concave (curved inward) or irregular edges
  3. The width of the embryo is less than half the width of the achene at its widest pointThis was a good start, but we still found plenty of ambiguous achenes. Our new definitions for “partial” are:
  4. Both the top and bottom of the embryo is rounded, and there is plenty of space not filled within the achene. Looking for space along the sides of the achene can help identify this one.

    xray-rounded-ends

    (71top)

  5. A strong, bright line inside an achene indicates a partial achene, whether it curves or not. Make sure this is distinct from the edges of the achene.

    (59bot)

    (59bot)

  6. If the achene is bright, but not as bright as regular full achenes, the achene is partial (this can be described as cloudiness).

 

We also came up with a few hints (learned the hard way):

  • Be careful of florets–they can show up as brightly as embryos, but don’t count them! The florets at top left of this image are almost as bright as the embryos bottom-right, and could be mistaken for partial achenes.

    the florets at top left are almost as bright as the embryos bottom-right, and could be mistaken for partial achenes. (93top)

    (93top)

  • If a bright spot has no outline of an achene around it and no band near it, and it isn’t a recognizable shape, assume it is chaff and let it alone.
    • The “band” is the little bright line at the top of x-rayed achenes.
  • When there is less contrast in an image and the brightness of embryos is hard to see, look at the bands at the tops of each achene. These are usually about as bright as embryos, so you can set a standard by that shade.
  • xray-contrast (70bot)

It is also worth noting that we decided to count achenes as full when the embryos don’t fill the entire outline: a space between the embryo and the achene is definitely permissible, and even smaller embryos count when they still maintain the proper shape (flat/convex top, pointed bottom) and aren’t smaller than half the width of the achene.

 

It was a long day of checking and rechecking classifications, but we’re finally happy with our counts. Now we’re working on a poster to help recruits learn the difference between informative and uninformative achenes, and Amy is helping us compile data. We’re officially out of the collection phase!

Always tired,

Mikaela

Over the Hill (We Can’t Slow Down)

Whew! This week has been BUSY–and it’s only Wednesday! Here’s a run-down of our milestones:

Monday: FINISHED CLEANING SEED HEADS. For good. For ever. Cleaning is definitely the most time consuming step of our process, and having it over with is a dream. We also learned how to x-ray our seeds, and my feelings on it are pretty confused. On the one hand, radiation is scary; on the other, using x-rays for botany is pretty darn cool. On the third hand, there is a lot of waiting involved in the process. All in all, definitely glad I learned how to do it.

Tuesday: We finished scanning on Tuesday morning (all 110 scans!) so we’re feeling pretty good going into the rest of the week. In the afternoon we got a start on randomizing and met with a PhD student here, Jessa. She was really cool–we talked about grad school, biology and our names, which are all fun and interesting things to talk about (note that neither Emma nor I have gotten started on thinking about grad school yet–it’s only fun to talk about for now).

Wednesday: We finished randomizing! And then we finished assembling! And then we finished x-raying!! Then we did some data entry…and then we finished counting! Because we already processed 2/3 of our samples last week, this final pull has been a breeze. (Which Scott and Amy are blown away by. Apparently we’re pretty quick!)

My head is whirling a bit from everything we’ve accomplished this week, but we still have a lot to do. Our next steps will be:

  1. Finish classifying the x-rayed seeds (we got a start on this today and I love it; it could make a pretty good video game)
  2. Compile our data for analysis
  3. Analysis!

We’ve decided to focus our analysis on the uninformatives. Are smaller seed heads more likely to have tiny uninformatives? Are seed heads from dense populations more likely than isolated heads to have larval holes in their achenes? These and many questions are waiting to be answered…I’d better get back on that!

 

Mikaela

These yellow coin envelopes contain the products of cleaning: achenes sorted into top, middle, and bottom for each seed head.

These yellow coin envelopes contain the products of cleaning: achenes sorted into top, middle, and bottom for each seed head. The pink and blue cards at the front of each box show our progress.

These white coin envelopes contain the products of randomization: the uninformative achenes from each yellow envelope. The informative achenes are in the clear baggies in the next image!

These white coin envelopes contain the products of randomization: the uninformative achenes from each yellow envelope. The informative achenes are in the clear baggies in the next image!

Sheets prepared for x-ray. Each of the little baggies contains informative achenes from either the top, middle or bottom of a seed head.

Sheets prepared for x-ray. Each of the little baggies contains informative achenes from either the top, middle or bottom of a seed head.

One week’s progress

As of this afternoon Mikaela and I have cleaned, scanned, and randomized 72 out of the 110 seed heads from the regular remnant populations. Two-thirds of the way done! We just learned how to count the scanned achenes and will get started on that and xraying soon. Hopefully we can be totally done with cleaning, scanning, randomizing, counting, and xraying the remaining third of the seed heads by the end of next week.

We’ve learned so much this past week and have met a lot of cool people. Today we sat in on a lab meeting where we got to see what the draft process is like for scientific papers. I thought it was really interesting; I’ve read a lot of published studies for different classes, but it always seemed like an out-of-reach process. Seeing a bit of the development up close and meeting the people involved made it seem not so distant after all.

In other news, all of our larvae have passed on to a better place. It seems the petri dish full of yummy food (old achenes) wasn’t enough to keep them going. Without their further development, the identity of the larvae may remain a mystery forever…

 

Caught in the Act!

This morning I was devastated to find that our larva had died overnight–as we said in the previous post, we were hoping to raise them, and I had also become a little attached. My grief didn’t last very long, though, because I found two larva wreaking havoc in my second head of the day! Emma and I quickly repopulated our petri dish with wriggly pink bugs.

When a seed head has a larva, we can expect a good number of the achenes to have holes burrowed in their sides. Today, we finally caught a larva in the act! This little guy was found with the front half of its body inside an achene. It’s good to have conclusive evidence for what precisely is going on around these seeds…

Other exciting updates: we’ve officially passed the half-way point on cleaning our 110 seed heads. At closing, we’re working on #61. Woo for progress!

Ta ta for now,

Mikaela

The perpetrator themself

The perpetrator  (image quality fuzzy to better convey shadiness)