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Project Assistantship Second Check-in: Further Data Exploration

An R file of my exploratory work into experiment 7 can be found here: https://www.dropbox.com/scl/fi/j9gnnsokwv17226lj06uj/expt07exploration.R?rlkey=aklc2gvs82q781s4juf2xk9j5&dl=0

The goal of this second data exploration was to determine the number of plants living in 2023 in each cross type and their plant status (e.g. basal, flowering, etc).

Additionally, we wanted to know how many plants flowered each year given their cross types.

Project Assistantship First Check-in: Data Exploration

An R file on my initial exploration of the various data files that make up experiment 7 can be found here: https://www.dropbox.com/scl/fi/j9gnnsokwv17226lj06uj/expt07exploration.R?rlkey=aklc2gvs82q781s4juf2xk9j5&dl=0

The goal of this initial data exploration was to determine questions and hypotheses that I will be exploring with aster models. To do this it is important to see what groundwork has been laid. Nicholas Goldsmith is the one who laid most of the groundwork on analysis for this project and it can be found here: https://conservancy.umn.edu/handle/11299/252544

Initial question: How does pedigree effect reproductive effort (i.e. flowering)?

This is of interest because 61 plants in experiment 7 have flowered since 2018 (this may not be 61 unique flowering plants but instead 61 unique instances of flowering across those years [2018 – 2023]).

Parasite Placements in P1 (exPt01)

Attached is a csv containing the coordinates for parasitic plantings in exPt01. ID is a unique ID to a Row x Position combination, Row is the row in exPt01 (starts at row 13 and increases by 5), Position is the position in exPt01 (starts at 861.85 and increases by 5), Treatment is what was placed there (seeds, Comandra, Pedicularis, or C + P which is Comandra and Pedicularis), siteOne is where the first plant planted came from and siteTwo is where Pedicularis came from if Comandra and Pedicularis were both planted.

Experimental plot ten Pedicularis planting

To experimentally test hypotheses about how much Pedicularis canadensis, a native hemiparasite, affects the demographic rates (survival, growth, and reproduction) of other species, we planted plugs of P. canadensis in the center of a circle (with a radius of 20 cm) that contains 8 species. These eight common native prairie plant species are Echinacea angustifolia, Liatris ligulistylis, Solidago speciosa, Dalea purpurea, Pediomelum argophyllum, Sporobolus heterolepis, Koeleria macrantha, and Hesperostipa spartea. For all but Echinacea, seed was collected last year from local sources. Echinacea is the focal species of other experiments and had been planted previously. Echinacea plants served as a reference point when establishing our circles and were always directly west of P.canadensis. Circles are planted in 6 rows that were randomly selected from within the existing experimental plot 10. Rows 315, 436, 443, 643, 656, and 785 were selected. Rows contain 11 circles each, starting at 1m and going to 11m, evenly distributed 1m apart.

All circles were planted on July 29th, 2021.Plants were planted as plugs. Plugs were grown by Chicago Botanic Garden production staff before being transported to Minnesota and transplanted. Pedicularis served as the treatment and had 3 factor levels (0, 1, or 2 Pedicularis plants). Treatments were randomly assigned to circles and Pedicularis were planted in the center of each circle between August 9th and 13th, 2021. Plants in the circles were measured between August 16th and 20th, 2021.Traits measured were size and reproductive status.

Start year: 2021

Location: Grant County, Minnesota; exPt 10

Overlaps with: Experimental plot management,

Experimental plot one parasite planting update

Over the last two years I designed and planted an experiment in an already established prairie restoration (exPt01) to test hypotheses about the effects of parasite inclusion in restorations. This experimental planting of hemiparasites has three factors (Comandra umbellata, Pedicularis canadensis, and soil plugs), each with two levels (presence or absence), but three factor-level combinations are impossible because the presence of parasites is confounded with presence of soil. This translates to me having 216 row x position combinations in which I randomly assigned Comandra umbellata, Pedicularis canadensis, and soil plugs. However, roots trap soil and therefore soil is always carried in with parasites, the two treatments are confounded and so we used soil transplants to account for this.

In June, I went out and assessed the realized design of my experimental planting of hemiparasites. I assessed presence or absence of Comandra umbellata and Pedicularis canadensis at each of my 216 row x position combinations. I found only one Comandra but I found 30/72 or 42% of all Pedicularis.

In late August through early September, I planted 1 plug of Liatris ligulistylis and one plug of Solidago speciosa at each of my 216 locations.  These plants were then measured. I added these plugs to serve as response variables to my three-factored experiment.

Last year, at all 216 locations I distributed seeds from 32 native plant species. In September, I went out and assessed seedlings present. I recorded the number and photographed the seedling to identify later in the laboratory.

In late October I intend to harvest 216 strips (0.1m x 1.0m) of dried biomass (1/6th of the dried biomass) from my 216 locations as I have also done in the last 2 years.

Start year: 2019

Location: Douglas County, Minnesota; exPt 1

Overlaps with: Experimental plot management, Hesperostipa common garden experiment

Materials collected: 216 .1 x 1m strips of dried biomass are stored at the Chicago Botanic Garden.

Demcirc – Entry # 1

Stuart and Drake on November 24th, 2020 discussed how Drake should go about entering the data he collected on his circles, apply named “Drake’s circles for the possible intedended purposes of burning with fire and planting with parasites” or “demcirc” for short.

Drake went to the following sites and set up 10 randomly placed (to the best of his ability using his cellphone, laptop, and paper maps) circles: South of Golf Course, East Riley/Riley (10 total across both), Woody’s, Leuffler’s Corner East, Leuffler’s Corner West, Hill across from Leuffler’s Corner West, RRX, NRRX, In front of the Tower Rd Tower, Nice Island, The hill just east of Unity Drive on Hwy 27, Around Landfill North, Around Landfill South, Sap, TH, NNWLF, and KJs.

Additionally 30 circles each at: Aan, Eelr, Landfill, AgalinisRRX (NW Corner of Roland Lake RD and Hwy 55), and all-around Wennersborg Rd SW & HWY 55.

Each circle had a radius of ~0.4m and I recorded every species present within the circle and I recorded whether they were flowering (or had flowered at some point that year) or not.

Experimental plot one parasite planting (pipp)

Throughout the summer, I designed and collected materials to establish an experiment in experimental plot 1 to study parasites and their impact on the community of host plants they live in. Parasitic plants are plants which absorb nutrients from neighboring plants. Parasitism is an important part of nutrient cycling in many ecosystems and parasite scientists hypothesize it to be an important part of prairie ecosystem maintenance.

This experiment has three factors, each with two levels (presence or absence), but three factor-level combinations are impossible, because the presence of parasites is confounded with presence of soil. Which translates to me having 216 row x position combinations in which I randomly assigned Comandra umbellata, Pedicularis canadensis, and soil plugs. However, because roots trap soil and therefore soil is always carried in with parasites, the two are confounded and so we used soil transplants to account for this.  

Additionally, in all 216 of my “pipp places” I distributed seeds from 32 native plant species: Achillea millefolium (5 seeds), Allium stellatum (3), Anemone patens (3), Astragalus canadensis (1), Bromus kalmii (5), Calylophus serrulatus (3), Carex brevior (3), Carex gravida (1), Dalea purpurea (5), Delphinium carolinianum (2), Elymus canadensis (1), Elymus trachycaulus (5), Geum trifolium (2), Grindelia squarrosa (2), Heuchera richardsonii (2), Koeleria macrantha (5), Liatris aspera (3), Lilium philadelphicum (3), Mirabalis nyctaginea (1), Monarda fitulosa (3), Muhlenbergia cuspidata (1), Oenothera biennis (3), Oxytropis lambertii (2), Pediomelum argophyllum (1), Scrophularia lanceolata (2), Sisyrinchium campestre (2), Solidago nemoralis (3), Sporobolus heterolepis (3), Viola pedatifida (1), Zigadenus elegans (2), Zizia aptera (5).

I developed this experiment to address questions about the impact native parasitic plants have on plant community members. In late October I harvested biomass from my pipp places to understand how species diversity and abundance change after planting parasites.

Start year: 2019

Location: Douglas County, Minnesota; exPt 1

Overlaps with: Experimental plot management, Hesperostipa common garden experiment

Materials collected: 216 .1 x 1m strips of dried biomass are stored at the Chicago Botanic Garden.

Data collected: Find data related to this project including the planting scheme in the cgdata repository in ~cgdata\summer2019\Hemiparasites (note/the key for HemiparaMap: C. umbellata = Blue, P. canadensis = Red, C + P = Purple, Soil plugs = Brown, Just seeds = Green).

2019 Update: Native Parasitic Plant Seed Collection and Planting

Throughout the summer, I designed and collected materials to establish an experiment in experimental plot 1 to study parasites and their impact on the community of host plants they live in. Parasitic plants are plants which absorb nutrients from neighboring plants. Parasitism is an important part of nutrient cycling in many ecosystems and parasite scientists hypothesize it to be an important part of prairie ecosystem maintenance.

This summer I collected seeds from five parasitic plant species which are native to the prairie. I also collected the seeds of over 100 species that can be commonly found in Douglas County, Minnesota and I have begun experimental germination of them and will continue to do so in the future. I developed a plan to plant Comandra and Pedicularis throughout exPt 1 and establish communities of 40 host species around them to address questions about the impact native parasitic plants have on plant community members. In late October I harvested biomass from the proposed parasite planting locations to understand the species diversity and abundance present before planting.

Start year: 2019

Location: Douglas County, Minnesota; exPt 1

Overlaps with: Experimental plot management, Hesperostipa common garden experiment

Materials collected: Parasitic plant seeds (Cuscuta glomerata:18,000 across 6 individuals in 4 locations; Agalinis aspera: ~8,000 across 81 individuals in 3 locations; Agalinis tenuifolia: ~4,500 across 41 individuals in 1 location; Pedicularis canadensis: ~14,000 from 1 location; and Comandra umbellata: ~1,800 from 3 locations) and host plant seeds (500+ seeds per host species, numbering approximately 100 species). Seeds are stored at the Chicago Botanic Garden.

Additionally, 216 .1 x 1m strips of dried biomass are stored at the Chicago Botanic Garden.

Data collected: Find data related to this project including the proposed planting scheme in the cgdata repository in ~cgdata\summer2019\Hemiparasites

A peek into the life of a graduate student

This week I spent my free time exploring the wet prairies of Douglas County, MN.

This is a picture of a small piece of wet prairie. Notice the high level of biodiversity! How many different species can you see? If you look closely, you’ll notice small pink flowers (it also helps if you zoom in). Those small pink flowers are the flowers of Agalinis tenuifolia which is the species I studied in my Master’s and is a parasitic plant that feeds off the roots of nearby plants!

Today I headed back to Chicago for my Master’s defense which is on Tuesday.

I met my new roommate Nigel.
I have to drop off all my seeds at the Chicago Botanic Garden this week. I have used over 1500 coin envelopes on seed collections!

I need to get back to working on a grant, but first I want to show the world the first meme I ever made.

And take a moment also to appreciate that sometimes things just line up.

Weekend Update

Hello, flog followers! It has been a while since I last posted a flog and this one is coming in a little late, but better late than never, right?

This weekend some of the crew went to the Minnesota State Fair!

The gang splurged on lots of unhealthy fair food that was delicious. We collectively got: pickle dog, peach strawberry smoothie, root beer, pickle on a stick (pictured above with Erin), french onion monkey bread, deep-fried cheese curds, nachos with cheese, sweet potato tacos, and probably more!
We saw horses and remembered how frighteningly tall they are…
We saw chickens, pigeons, and turkeys. We collectively agreed that this was the most perfect chicken on display.
I found a melancholic beauty in these star-crossed lovers’ plight. If only it were meant to be…
These were the most classic sheep we agreed. Their wool was so soft. Alpaca wool is also remarkably soft. When I have an extra $130 I think I might splurge for an alpaca wool sweater.
We eventually took a break and lounged in the shade. What a beautiful group of human beings. 😭 😭 😭 (These are crying emojis if they are too hard to see).

We had a wonderful time and many of us were totally exhausted afterward.