I have started work on analysis of my style shriveling data from the crosses between Echinacea pallida and Echinacea angustifolia. Attached is the R code I have so far.
July 2011 Archives
Here's the final dataset for my compatibility experiment. The experiment is officially ended today (I collected the last bit of data). The dataset contains GPS data (column name distBetween). I missed one plant while GPS-ing, so I used the hand-measured data (for flag #6 at Nessman's). I also corrected several errors in the datasheet.
We spent some time GPS-ing the plants, so we could get the exact distances between them. Here is a csv file with the gps data.
I have been working on analyzing all my data. I looked at plots of each of my individual sties, as well as all the data combined. The data are almost exactly opposite of what I expected.
Here's the script I've been exploring:
My days of research at the landfill are coming to an end! I'll be doing the last of my crosses there tomorrow and observing the results on Monday.
For the Coreopsis, I didn't end up with much data about style persistence. Each head has about four rows of styles and dries up soon after it finishes flowering. Since I've only been visiting the landfill every three days, I didn't get a chance to see what happened to most of the styles I pollinated before all the florets just turned black and fell off.
The good news is, I will be able to collected many of the flower heads I pollinated, so someone can assess their seed sets in the fall. (I was worried that when the florets fell off, they might have taken the seeds with them, but Stuart reassured me that the seeds are still there!)
I also have lots of data about Heliopsis style persistence. I'll upload it here once I have the data in from my last few pollen crosses.
This is my CSV file with information on my pollen crosses between Echinacea pallida and Echinacea angustifolia. It will be used in the analysis of that data.
Last week (well, 9 days ago), we headed north to the Crookston area to survey the Western Prairie Fringed Orchid (Platanthera praeclara).
Gretel is showing everyone what to look for on the plant here.
Katherine looks over the prairie
An ant dangles on a thread of spider silk, threatened by the dangerous milkweed
Here's what we were actually looking for; the WPFO itself. We found over 1000 plants, way more than last year. All in all, a good day.
Edited by cswitzer. 25 July 2011
See this example: http://blog.lib.umn.edu/wage0005/echinacea/2011/07/preliminary-analysis-for-calli.html
Characteristics of a good CSV file:
1. Use database format in Excel
2. Don't mix text, integer, or numeric fields (you may enter NA in a numeric field to signify missing data)
3. Remove spaces from excel cells
4. No punctuation in each column name
5. Don't start a column with a number
6. Column names should be in easily typable format -- use capitals at new words and use no spaces (called camelback format)
After enjoying the pig races out at the Grant County Fair yesterday, it was back to field work for me today. I biked out to the Hegg Lake Restoration area to discover that my Echinacea pallida site had experienced something that is now common for many prairie remnants - mowing.
Luckily I still have a decent number of crosses, and this just cuts the number I was planning on having a bit shorter. Tomorrow I will begin crosses to use up my remaining supply of Echinacea pallida pollen.
We accomplished a lot, even thought the weather was super hot! We even started at 7 am to try to beat the heat.
Monday, (July 18, 2011) was amazing in two different ways. The temperature was in the nineties, but the heat index was over 100 F. We worked in the morning, but by 10 am it was heating up. Because of the humidity, our clothes were soaked through by the end of the day. We measured plants in the common garden on Monday afternoon, and helped Katherine set up cages for her aphid experiments.
Tuesday and Wednesday, we decided not to work outside during the afternoon, so we did morning field work, and then spent time updating the website and computer work during the afternoon.
Here are a few photos of our projects.
5. Josh is helping other groups and helping with the main projects, because he's waiting for his Big Bluestem and Indian Grass to grow for his experiment (sorry, no photo).
8. Nicholas is just about to finish all his compatibility experiments between Echinacea angustifolia and Echinacea pallida. To do cross pollination experiments, he first paints the bracts that subtend the styles he will pollinate. Aqua is a easy color to recognize on the bracts.
On Thursday and Friday, we were able to do more fieldwork in the common garden, even in the afternoon (common garden measurements and phenology).
Here is the csv file to use for my compatibility of Echinacea in the remnants.
It's been a busy week for everybody. Plants are blooming, pollen is shedding, and everyone is dashing about madly to catch the field season before it passes us by. I have been running around like a chicken with its head cut off trying to get ready for my aphid addition/exclusion experiment. Everyone has been a wonderful help setting up cages in this sweltering heat. My goal for this week is to finish my first round of experimental treatments: exclusion on Thursday and addition on Friday. Before then, I need to finish setting up nets and teach everyone how to wrangle aphids. Here is a protocol I wrote up to assist the teaching process and the data sheets I mention in the protocol. These are works in progress, so any feedback is appreciated.
Yesterday we went on a trip to the Crookston area to help Gretel with her White Fringed Orchid search. Here are pictures for your viewing pleasure :)
We quickly headed back to the cars for safety, and watched the awesome storm while eating lunch. Fortunately the storm passed over quickly, and soon the skies were clear again.
We went back to work in another section of the prairie for the rest of the afternoon.
After that we drove back to Douglas County. Stopped at Fertile, MN for ice cream but sadly they were closed on Saturdays. Also found out that Cafe 116, the dinner place in Fergus Falls we were going to, closes at 6pm on Saturdays. So we had a pretty sumptuous dinner at Don Pablos, a quirky Mexican restaurant in Fergus Falls :)
Reached Hjelm House around 9 or 10pm. That was a long but fun day! :D
This past week a lot more Echinacea started flowering, which meant we had plenty to do. We located all the Echinacea plants in the Common Garden that will flower this year. There were so many! They seemed to be particularly abundant in the 99 garden.
We also completed some more aphid surveys for Katherine's project, continued work on the New Media Initiative, and set insect traps for Greg's project. I really enjoyed taking a quick peek at some of the insects that Greg's traps caught. I don't have tons of experience with insects, so I don't know what genus any of them are yet, but some of them looked pretty nifty. I'm looking forward to finding out more about them.
My own independent project is coming along as well. I've been spending quite a bit of time this week working at the dump! For those of you who aren't familiar with the prairie remnants we're studying, I should clarify that I'm not actually working in a garbage heap. There are some little hills that haven't been used for agriculture because they are within the landfill's property, but they're not really close to all the trash either. As a result, they are covered in beautiful native prairie species! (And when the wind's coming from the right direction, it doesn't even smell bad!) Two of the species I'm studying grow there, Coreopsis palmata
and Heliopsis helianthoides.
I've started doing pollen crosses, with mixed results. On the Heliopsis, it looks like styles shrivel after receiving outcross pollen (suggesting they have been successfully fertilized), but not after receiving self pollen. I had a harder time seeing what happened to the styles on the Coreopsis I crossed because when I went back to check on them two days later, some of the flower heads had started falling apart. (As Amber Rae put it, "The Coreopsis are losing their heads!") Stuart says that this is unusual though, so hopefully the heads I use for crosses this coming week won't fall apart and I'll be able to get some clearer results.
Uff da! I believe the first round of Dichanthelium seed collection is done. Thanks to Gretel and everyone who helped. And for all the times you waited for me after 5pm.
Collected seeds from 158 plants from 5 sites - Jul 7 Hegg Lake south of parking lot, Jul 8 near Hegg Lake PHEN plot, Jul 9 Hegg Lake field trip area, Jul 11 (yesterday) Loeffler's Corner (west) and Staffanson's (old field).
112 plants had spreading/expanded panicles (not sure what's the correct term) and 47 were not spreading/erect.
Here's the maternal lines data from the plants I sampled, if you're interested:
I'm planning to return to some of these plants a week (or perhaps a little earlier/later, depending on scheduling) after I first collected the seeds. Hopefully there's still some seeds left on the culms for me to harvest!
July 14 update: It is actually 158 plants, not 159. Sorry for the arithmetic error! :P
A quick list of flowering plants I noticed while assessing phenology in Jennifer's experimental plot at Hegg Lake WMA on 10 July. I list only plants observed in the plot. Asclepias speciosa is flowering just outside the SE corner of the plot.
F = flowering
X = done flowering/in fruit
N = not yet
Heliopsis helianthoides F
Amorpha canescens N
Coreopsis palmata F
Rosa arkansana F
Anemone cylindrica X
Asclepias syriaca F
Amphicarpea bracteata F
Morning glory sp F
Cirsium arvense F
Lathyrus venosus XF (almost all done flowering)
Galium boreale F
Psoralea argophylla F
Medicago sativa F
Linum sulcatum F
Carduus acanthoides F
Red field clover F
Yellow fl lactucid F
Potentiall arguta F
Dichanthelium leibergii XF
No Phlox pilosa in the plot!
We found 147 flowering plants in Jennifer's Phenology Experiment during a thorough, but not exhaustive, search on Friday. Most of these plants have buds only and will start shedding pollen later. I posted a map of locations of all plants to flower this year.
Jennifer planted this experiment to investigate heritability of flowering timing (phenology) in spring 2006.
Last year eight plants flowered and about 2700 plants were alive. Read about measuring last year.
Assuming that almost all of those plants are still alive and that we didn't find all the flowering plants, then about 6% of surviving plants will flower this year (>147/2700).
For kicks, I made maps of the paths of data enterers. We usually worked in pairs and used one person's PDA to enter data. Here are the paths...
Josh D's visor, Amber E's, Nicholas G's visor, Gretel K's visor, Lee R's visor, Callin S's, Stuart W's visor, Maria W's visor, Amber Z's visor. For the record Katherine M's visor had only one record and we didn't use Karen T's visor.
For Lee, I found that there is a good deal of Heli. heli at Aanenson - most bloomed the center head but not the sides.
For all, there wasn't much Ech blooming at RRX, LC, RI, or YOH as I remember in years past.
For whomever is interested, west of YOH and not IN Douglas county but there is a good deal of Rudbeckia? - I was moving pretty fast and didn't stop to look close - just a lot of yellow flowers!
I don't know if matches up to the BOB MAHONEY RESTORATION, but its there to be seen.
Hi everyone, Maria here again. Today was a particularly happening day in my opinion. Everyone had something to do. Amber E. is back from Alaska with Ruth! Karen arrived from Evanston in the afternoon!
In the morning those of us who hadn't finished our Stipa searches in the common garden finished that! (So Stipa is done! - we scaled back though and only searched for the 2011(?) cohort). After that Gretel, Ruth, Amber E and I put Position/Row signs in the common garden and made the signs face East/Westwards so now it's so much easier to read the signs while you are walking in the common garden. Then we got started on looking at the phenology of Echinacea in the common garden. We systematically walked through each row, looking out for flowering Echinacea with emerged anthers and pollen, twist-tying the heads and recording them in our visors. Josh joined us when he finished his Stipa searches. We found quite a few flowering heads - bet there'll be more soon.
While we were looking for flowering Echinacea, we saw Stuart, Callin, Amber Z and Nicholas crowded around 'Joe' - the pet name given to the prominently flowering Echinacea at row 28, position 860. As described by Callin in the previous post, they were practicing bract-painting for their independent projects on Joe.
When we finished looking at all the rows, it was time for lunch and short presentations of our projects. It was good to hear about everyone's projects and talk about my own projects and get feedback. After lunch, we got started on our independent projects or worked on the New Media Initiative.
Gretel and I headed to Hegg Lake to look for Dichanthelium (Panic Grass) seeds for my second project. This summer I will be collecting seeds from Dichanthelium plants from different remnants, including Hegg Lake and Loettler's Corner (I might not have spelt that right - sorry). My plan is to collect seeds from 30 individuals from each "site", as there are several places at Hegg Lake that seem to have a lot of Dichanthelium. After collecting the seeds, I will be bringing them back to Chicago Botanic Garden and do more work on them in the fall/later.
Click here for the
Google doc of my summer project proposals
I am super super indebted/thankful/grateful for Gretel. Without her guidance, I'd probably be in a big mess/not knowing what to do/still be at Hegg Lake as this is my first time doing independent field work.
When we reached the place at Hegg Lake (it was near the road, area with ditch, south of the parking lot), a lot fo the Dichanthelium seeds had already fallen off the culms. It was quite disheartening. We walked a little north and found a patch of Dichanthelium with most of their seeds intact, then we laid out the tape measure for 20m in a roughly north-south direction (I kept thinking it was 2m while Gretel patiently corrected me ^^;;). Initial plan was to do every plant within arm's length from transect, or every other plant if population was dense. However, that was not quite possible given the circumstances. After Gretel and I collected seed from the first plant and did all the measurements, she continued measuring/collecting while I picked ~30 plants near the transect (more than my arm's length) that had at least one culm with 8 or more seeds to collect from and flagged them with a blank flag. I started measuring/collecting after I finished flagging. Around 4pm, Lee called - reinforcements were coming! Ruth and Lee arrived with Karen and they helped us finished the rest of the plants (by that time Gretel had completed 17 plants (!!) and I was on my 6th plant). It turned out that we had 31 flags so 31 envelopes with data and samples! We also collected some "random" samples - ie seeds from various random plants away from transect. Finished around 5pm - thanks to Gretel, Lee, Ruth and Karen! Really excited to get the first 30 done!
Take a look at the simple data entry for today's collection for more technical details if you're interested. I might also do the seed count for today's samples just to see how many seeds we can get from 30 plants using the '8 or more' rule. (I just need to be rreally careful not to lose any seed >.<)
We left 11 flags (labelled with sample number) at the site that we will return to later to collect more seeds from.
Now that I have more experience, I'll definitely be more systematic+efficient about it.
Notes to self for tomorrow/next time:
- "just-in-case" extras (extra equipment, envelopes, pens, sharpies, flags) do come in handy! Meter sticks are probably more efficient than tape measures. More flags would be good. Maybe use a different color for "done" or for extras.
- Extra samples are good too. Maybe do 32 plants per site?
- Bring a plastic bag/something to put a plant specimen in - I need to get a sample of the other Dichanthelium species ("hairy leaved") to press and identify.
- Equipment list would be useful esp when I have more than 5 things to remember.
Lesson of the Day: Having an experienced person around and helpers is always always always helpful! =D
Thanks again to Gretel and everyone who helped!
I wrote this up last week, but neglected to post it on the flog. Here is a detailed protocol for the 2011 recruitment searches. See Wagenius et al. 2011* for a description of the seedling recruitment study.
*Wagenius, S., A.B. Dykstra, C.E. Ridley, and R.G. Shaw. 2011. Seedling recruitment in the long-lived perennial, Echinacea angustifolia: A 10-year experiment. Restoration Ecology.
The flog is back and running! All the links should be working and all pages formatted nicely now!
The credit goes to John, my friend from home, who has been troubleshooting and coming up with the solutions to the problems.....super super indebted to him :)
But the flog team is not totally done yet...now that our Twitter account is up, we'll need to add a Twitter button on the flog. We'll also continue to sort entries into categories. Also note the new description of the field log (credits to Lee)!
Comments on the flog are most welcome!
Team Echinacea got a lot done this past week. On Monday we finished seedling searches, and on Wednesday we finished recruitment surveys. We've also made a lot of progress with the New Media Initiative: We now have a Facebook page and a Twitter account.
Then on Thursday, we started stipa searches. We looked in the Common Garden experimental plot for stipa that were planted as seed in the past two years. This means we were looking through bunches of grass to find this one specific kind of grass, which posed quite a challenge. As Stuart put it, it's like looking for a needle in a needlestack. But we persevered! We found quite a few stipa plants, and will continue searching this week.
We also began aphid searching, as Katherine mentioned. I was glad that I didn't find too many aphid infestations on our lovely Echinacea plants. It was a very satisfying way to end the work week.
Over the weekend, we had a 4th of July potluck-picnic celebration at Elk Lake. The food was all so delicious! And a construction team directed by Per made a formidable sandcastle fortress. Below are some pictures that Maria took. Happy (belated) 4th everyone!
Here are google doc links to the most up-to-date proposals by Callin, Amber, and Maria
After checking at Hegg Lake again, it appears there are enough Echinacea pallida plants to be able to do reciprocal crosses. I have attached my updated proposal.
Long story. This morning, I managed to put on a Facebook like button, a search box, and a link to the Echinacea website under the Links heading; but later discovered that the Categories links and RSS feed links were not working properly (led to xml files rather than html files), but the Archives and Monthly Archives were fine. Not sure whether this was due to the addition of the Facebook like button or the search box or accidental changes to the rest of the script or due to older changes. Josh backed up the templates and then returned the templates to default settings, but the categories still weren't working. I also discovered that the formatting for the Monthly Archive pages were lost, and couldn't figure out how to restore the backup templates. To at least salvage the main page of the flog, I decided to switch to a new style (hence the change in the appearance of the flog), re-added the Facebook like button and search box and clustermap. But rest assured that the content of the flog has not been changed, just that the formatting/appearance may not look so nice right now.
So sorry for the mess-up T_T At this point, I'm not sure what else I can do. Josh suggested posting on the support forum, so I just did that. Hopefully I will be able to get some help from the forum. If anyone reading this has any idea, please do not hesitate to comment. Any help is greatly appreciated!
p/s Are people okay with the current layout? Or is the original layout better? Thanks
Today we surveyed a patch of the common garden for aphid infestation. I chose my survey area based on observations I made Wednesday morning, during my initial search for aphids. I wanted my square to include at least one heavily-infested plant with ant domatia (dirt structures that ants build to cultivate aphids). Otherwise my choice of positions and rows was random.
Here is a description of today's survey. This weekend I will go over the data and make a map of aphid infestation. Because it's still early in the season for aphids, I hope to repeat this survey one or more times this summer to look for spatial and temporal patterns of infestation. Thank you to the Echinacea team members for your diligent data gathering.
I'm happy to say the survey went smoothly. Everyone seemed to have an easy time recognizing aphid life stages and ant domatia. My only goof-up was accidentally assigning the same row to two people, leaving us one row short, but thankfully we caught it in time to finish up before a thunderstorm hit. Next time I will be more careful about my row assignments.
I would like to repeat this survey several times throughout the summer--maybe once every two weeks. Here are some thoughts I have based on my observations in the common garden:
1. We have observed that plants with heavy infestations early in the season tend to have wrinkly, stunted leaves--possibly due to aphid overwintering. I suspect that these plants may serve as aphid source populations that spread to surrounding host plants. It will be interesting to see whether aphid infestation is more prevalent among plants nearby heavy aphid infestations (i.e. plants with all three aphid life stages, wrinkly leaves, and ant domatia).
2. I noticed that on plants with small infestations, ants seemed to be carrying away gravid females. Perhaps ants play a role in mitigating population-wide aphid infestation by concentrating aphids on a few heavily-infested plants. This survey won't tell me much about the role of ants, but I am curious to see whether some plants lose their aphids throughout the season.
Thanks again everyone for helping me gather my first data set!