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2020 Update: common garden experiments

Since 1996, members of Team Echinacea have walked, crawled, and ~sometimes~ run next to rows of Echinacea angustifolia planted in common garden experiments. Although protocol varies depending on the experimental plot, every year team members record flowering phenology data, measuring data, and harvest the heads of the thousands of plants we have in common garden experiments.

Note that these experiments are not really gardens. “Common garden” refers to the experimental design. Most of our experimental plots are prairie restorations, a few are abandoned ag fields that are manged as grassland habitat. Some plots have multiple experiments within. The Echinacea Project currently has 10 established experimental plots:

exPts01-10. To avoid repetitiveness of reports on yearly phenology, measuring, and harvesting, this project status report will include updates on all experimental plots 1, 2, 4, 5, and 8. Reports for the others will be elsewhere: Amy Dykstra’s plot (exPt03), the hybrid plots (exPt06, exPt07, exPt09), and the West Central Area common garden (exPt10).

exPt01: Experimental plot 1 was first planted in 1996 (cleverly termed the 1996 cohort), and has been planted with nine other experiments in subsequent years, with the most recent planting being Amy Waananen’s inter-remnant crosses. It is the largest of the experimental plots, with over 10,000 planted positions; experiments in the plot include testing fitness differences between remnants (1996, 1997, 1999), quantifying effects of inbreeding (inb1inb2), and assessing quantitative genetic variation (qgen1). There are also a number of smaller experiments in it, including fitness of Hesperostipa sparteaaphid addition and exclusion, and pollen addition and exclusion. In 2020, we visited 4,340 of the original 10,622 planted and found 3,258 alive. Only 484 plants were classified as “flowering” in exPt01 this year. This is a drastic increase from the nearly 70 plants that flowered in summer 2019 – perhaps it is a testament to the benefits of controlled burning (we burned in spring 2020 but not in 2019). In summer 2020, we harvested ~815 total Echinacea heads in exPt01 (I have not finished the reconciliation process). In the fall, we added 484 staples to positions where plants were gone for three straight years, however, we ran out of staples, so 130 of these positions have “flaples” which are bent pin flags.

exPt02: Heritability of flowering time is the name of the game in exPt02. Planted in 2006, exPt02 was planted to assess heritability of flowering start date and duration in Echinacea. In summer 2020, we visited 2,010 positions of the 3,961 positions originally planted. We measured 1,638 living plants, of which 444 were flowering. In the fall, we harvested ~626 heads from exPt02. We do not have an exact number of heads harvested from exPt02 yet, as we have not had time to complete head reconciliation. Location: Hegg Lake WMA

exPt04: Experimental plot 4 was planted to gauge whether Echinacea from small remnant populations could be genetically rescued via an outcross to larger, more genetically diverse populations. Caroline Ridley and other members planted this plot in 2008. We did not measure exPt04 this year. Location: Hegg Lake WMA

exPt05: The only experimental plot planted at Staffanson Prairie Preserve (SPP), exPt05, was planted to compare progeny of maternal plants from burned and unburned sections of SPP. There were 2800 plants planted originally, but high mortality made it impractical to visit the plot row-by-row. Now, we and treat the plot like demography. We use our survey-grade GPS to find plants in exPt05 that have previously flowered and add more plants to the stake file if new plants in the plot flower. In 2020 we found 11 living plants, two of which were flowering! There was only one head to collect, since one of the flowering plants exhibited only vertical development (no head). Location: Staffanson Prairie Preserve

exPt08: Team Echinacea established quantitative genetics experiments to quantify additive genetic variance of fitness in Echinacea, with the idea that we can estimate evolutionary potential of study populations. The maternal parents of qGen2 and qGen3 are plants in the 1996, 1997, and 1999 cohorts. These plants were crossed with pollen from plants in remnants to produce seed for qGen2 and qGen3, which now inhabit exPt08. Originally, 12,813 seeds were sown in the common garden. Seeds from the same cross (shared maternal and paternal plants) were sown in meter-long segments between nails. A total of 3,253 seedlings were originally found, but only 562 plants were found alive in 2020. There were 5 flowering plants in 2020, and 5 heads. Note that there were an additional 2 heads collected from transplant plot.

Plot management: To ensure that the common garden environment is as similar as possible to the prairie environment we must actively manage it. This management includes removing foreign species and supplementing with natives. One of our main management methods is through fire. We were unable to burn plots this fall however we hope to burn p8 and p1 this spring. We also collected seed to spread after burns including Schizachyrium scoparium, Bouteloua curtipendula, along with multiple species of Solidago and quite a few Asters.

Asclepias viridiflora in p1: In 2019, plugs of an uncommon prairie milkweed, Asclepias viridiflora, were planted in Experimental plot 1. The purpose of this experiment is to assess the survival and fitness of A. viridiflora. Assessing vitality will also provide a frame of reference for species conservation across modern prairies. In 2020 a protocol was developed to identify and measure A. viridiflora. These data are waiting to be entered and analyzed.

Hesperostipa demography:  In 2009 and 2010, porcupine grass (Hesperostipa spartea, a.k.a. “stipa”) was planted in experimental plot 1. In total, 4417 seeds were planted, 1 m apart from each other and all 10 cm north of Echinacea plants. Between 2010 and 2013, each position was checked, and the plant status recorded. Since 2014, we have searched for flowering plants. The data from this summer can be found here cgdata/summer2020/stipaSearch, these data have not been processed yet.

Inb1: The INB1 experiment investigates the relationship between inbreeding level and fitness in Echinacea angustifolia. Each plant in experiment INB1 originates from one of three cross types, depending on the relatedness of the parents: between maternal half siblings; between plants from the same remnant, but not sharing a maternal or paternal parent; and between individuals from different remnants. We continued to measure fitness and flowering phenology in these plants. In 2020, of the original 557 plants in INB1, 111 were still alive. Of the plants that were alive this year, 30 (27%) were flowering. This is up from the 4% that were flowering last year. All individuals were planted in 2001.

qgen: The qGen1 (quantitative genetics) experiment in p1 was designed to quantify the heritability of traits in Echinacea angustifolia. We are especially interested in Darwinian fitness. Could fitness be heritable? During the summer of 2002 we crossed plants from the 1996 & 1997 cohorts of exPt01. We harvested heads, dissected achenes, and germinated seeds over the winter. In the Spring of 2003 we planted the resulting 4468 seedlings (this great number gave rise to this experiment’s nickname “big batch”). In 2020 we assessed survival and fitness measures of the qGen1 plants. 1,642 plants in qGen1 were alive in 2020. Of those, 17% flowered in 2020. All were planted in 2003.

Stuart and John measure Echinacea plants in exPt02 under a gloomy sky

For more information on survival in common garden experiments, see this flog post about survival in common gardens.

Start year: Various, see individual listings above. First ever planting was 1996.

Location: Various, see above

Overlaps with: Pretty much everything we do.

Data/ materials collected: Measure data for all plots. All raw measure data available in cgData repository. Processed data should eventually be available in SQL database; ask GK for status of SQL database. GPS points were shot for the exPt09 flowering plant. Find the GPS jobs containing the exPt09 corners here: Dropbox/geospatialDataBackup2020/convertedASVandCSV2020/EXPT9_20200917_DARW.asv The stake file to find exPt5 plants is here: Dropbox/geospatialDataBackup2020/stakeFiles2020/exPt05stakeFile.csv Products: Many publications and independent projects.

Survival in common gardens

Last Friday, I was dispatched by Stuart to find the number of plants/ achenes planted in each experimental plot, along with the number alive as of a recent year (2017-2019, based on the plot). Although records of some plots were a bit harder to come across that others, I was able to compile data from each plot (besides p10 – planted 2019 – data coming soon). This would not have been possible without the help of Gretel, so thanks GK! I have attached a small datasheet with the survival data.

In the history of the Echinacea Project, the team has sown 31,888 Echinacea viable achenes in experimental plots. There were many more sown that likely did not have a seed. Team members found 3634 seedlings from these seeds, not including Amy D’s experimental plot 3 and remnant seedling refinds. The team has planted 18,869 Echinacea seedlings in experimental plots, not including p10 – planted at West Central Area HS in 2019. Finally, 7090 Echinacea are currently alive in the experimental plots!

Manuscript Submitted (Finally!)

Hi Flog!

I just wanted to give you all a quick update on the heritability of flowering time project I have been working on (for a long time)! We collected data on the phenology of the plants at experimental plot 2 during the summers of 2015 and 2016 and the phenotypes of those individuals to the phenotypes of their parents in 2005. Jennifer Ison began this project as a part of her dissertation in 2006 and I was lucky enough to pick it up when the individuals in experimental plot 2 really began to flower.

Since we collected data in ’15/’16 we have been working on analyses to determine the amount of variation in flowering time that is heritable. We found that there is substantial heritability for both onset of flowering and duration of flowering. Both of these traits are critical in describing the synchrony of an individual compared to the population and for determining the number of mating opportunities an individual will have in a season.

Today we submitted the manuscript that describes these results to Evolution. Drafting this manuscript has been an excellent learning opportunity for me and I have been lucky to work with some amazing scientists and writers. Thank you to my co-authors: Jennifer Ison, Stuart Wagenius, Frank Shaw, and Ruth Shaw.

2017 update: Heritability of flowering time

In 2017, we monitored the start and end dates of flowering for the 676 flowering plants (1116 heads) in experimental Plot 2. The first head started shedding pollen on June 26 and the latest bloomer ended flowering on August 19. Peak flowering was on July 13th. Note that these dates are subject to change as this is preliminary data that has not been fully cleaned and analyzed.

To examine the role flowering phenology plays in the reproduction of Echinacea angustifolia, Jennifer Ison planted this plot in 2006 with 3961 individuals selected for extreme (early or late) flowering timing, or phenology. Using the phenological data collected this summer, we will explore how flowering phenology influences reproductive fitness and estimate the heritability of flowering time in Echinacea angustifolia.

One of the earlier flowering plants at exP2 this summer, a plant with 5 heads at Row 2 Position 1.

Start year: 2006

Location: Experimental Plot 2, Hegg Lake WMA

Overlaps with: phenology in experimental plots, phenology in the remnants

Physical specimens: We harvested approximately 1081 heads from exPt 2 (preliminary inventory). Some of these heads had a major loss of achenes, either due to the early flowering time that we were not expecting or windy and rainy weather that dispersed the achenes quickly. We brought the harvested heads back to the lab, where we will count fruits and assess seed set for each head.

Data collected: We visited all plants with flowering heads every two days (three days after weekends) until they are done flowering to record start and end dates of flowering for all heads. We will manage phenology data in R and add it to the full dataset.

Products: Will estimated heritability of flowering time using data from 2015 and presented his findings last summer at ESA (see his poster). He is continuing this work by assessing how heritability estimates differ between years in burn and non-burn years, now including 2016.

You can find more information about the heritability of flowering time and links to previous flog posts at the background page for the experiment.

2016 update: Heritability of Flowering Time

To examine the role flowering phenology plays in the reproduction of Echinacea angustifolia, Jennifer Ison planted experimental plot 2 (exPt 2) in 2006 with 3961 individuals selected for extreme (early or late) flowering timing, or phenology. In 2016, we monitored the start and end dates of flowering for the 570 flowering plants (933 heads) in the plot. The first head started shedding pollen on June 22 and the latest bloomer ended flowering on August 8th. Peak flowering was on July 7th, when 810 heads were flowering. Using the phenological data collected this summer, we will explore how flowering phenology influences reproductive fitness and estimate the heritability of flowering time in Echinacea angustifolia.

Tracking phenology for 900+ heads in exPt2 was a big job. Here, three teams assess phenology on a nice day at exPt 2.

Start year: 2006

Location: Experimental Plot 2, Hegg Lake WMA

Overlaps with: phenology in experimental plots, phenology in the remnants

Physical specimen: We harvested 870 heads from exPt 2. We were unable to harvest some heads which had been grazed by rodents. We brought the harvest back to the lab, where we will count fruits and assess seed set. Jennifer previously collected tissue samples from all individuals in the plot and plans to use these to genotype all of the individuals that flowered in 2016 this year and determine their parentage in exPt 1.

Data collected: We visit all plants with flowering heads every three days until they are done flowering to record start and end dates of flowering for all heads. We managed phenology data in R and added it to the full dataset.

Products: Will estimated heritability of flowering time using the data from 2015 and presented his findings this summer at ESA (see his poster here). He is continuing this work by assessing how heritability estimates differ between two years. He is comparing flowering in 2015 (a burn year) and 2016 (a non-burn year).

You can find more information about our experiment the heritability of flowering time and links to previous flog posts regarding this experiment at the background page for the experiment.

Project status update 2015: Heritability of phenology in experimental plot 2

For his REU research project, Will is investigating heritability of flowering phenology in experimental plot 2 (p2), which was planted in 2006 with 3961 individuals selected for extreme (early or late) flowering phenology. This summer Will and Team Echinacea monitored the phenology of all 646 flowering plants (1216 individual heads) in p2, as well as the phenology of their parents in p1. Flowering in p2 began on the 4th of July and ended on August 26th. The peak day of flowering was July 27th when 1018 heads were flowering. The average duration of flowering for a head was 12.1 days. It was a huge year for flowering in p2 with nearly 5 times more heads than 2014 and over 16 times more than 2013. Will is comparing the flowering schedules of the p2 plants with the 2005 phenology records of their parents. As the plants in p2 mature, and perhaps flower more frequently, we will continue to gather data on family lines of Echinacea to discern the genetic component of their flowering phenology.

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Many flags indicate many flowering plants in experimental plot 2

Start year: 2006

Location: Experimental plot 2 (Hegg Lake WMA)

Overlaps with: phenology in experimental plots

Products: The 2015 phenology records from p2 will be added to the existing multi-year ExPt2 phenology dataset. Will is using tools from the R package echPhenology  developed by Team Echinacea to analyze and produce visualizations of the flowering schedule observed in p2. He plans to present his findings at a conference in spring or summer 2016.

2015 flowering schedule of all heads in p2: First day of flowering was July 4th, peak was July 27th, and the last day was August 26th.

 

 

Read previous posts about this experiment.

 

 

Project status update: Fitness and phenological extremes in experimental plot 2

2014-07-23 18.43.40

To examine the role flowering phenology plays in the reproduction of Echinacea angustifolia, Jennifer Ison planted experimental plot 2 (P2) in 2006 with 3961 individuals selected for extreme (early or late) flowering phenology. In 2014, we measured traits for all 2123 living plants and monitored the daily phenology of 247 flowering heads. Echinacea flowering began on July 2 in P2 and continued through August 24. Using the phenological and trait data collected this summer, we will explore how flowering phenology influences reproductive fitness and estimate the heritability of flowering time in Echinacea angustifolia.

Read previous posts about this experiment.

Start year: 2006

Location: experimental plot 2 (Hegg Lake WMA)

Overlaps with: pollinator efficiency

Flowering in Jennifer’s Phenology Experiment

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.

c2Phenology2011initial.png Click on thumbnail to see a larger map.

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.

Plants measured in the PHEN plot at Hegg Lake

We finished measuring plants in Jennifer’s Phenology plot at Hegg Lake WMA this Friday.

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We measured many plants.

We measured about 2700 plants. Eight plants flowered this year. We visited another 1300 locations where we couldn’t find a plant (mostly because they had died). Here’s a map of the plot with the status of each location (click to see a bigger version)…
monitorPHEN2010.png

In addition to Echinacea angustifolia, we saw some good prairie plants in the plot, including lead plant (Amorpha canescens), yellow lady-slipper (Cypripedium calceolus), prairie rose (Rosa arkansana), Missouri goldenrod (Solidago missouriensis), silver leaf scurf pea (Psoralea argophylla), and many others.

It was a big job, but we were quite efficient. We laid out 50m tapes on every other row to help guide us. Four of us went out on Wednesday to flag positions 1 and 50 for all rows. That took ~2h. We started flagging positions 10, 20, but that was unnecessary. On Thursday we all went out and measured from 2-4 pm. On Friday we did two shifts: 10 -12 and 2:30 -5.

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We were happy to be done.

On the way out we removed a weed that we had noticed the day before–spotted knapweed. We were careful not to touch it because it can be a skin irritant. I’d never seen this plant in the study area before.

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Heading home.

What a great way to end the week. It was Katie and Laura’s last day. They are heading back to the Chicago Botanic Garden to prepare their posters and talks.

measure plants in the PHEN plot at Hegg Lake

This afternoon we are going to measure plants in Jennifer’s Phenology plot at Hegg Lake WMA. Here is a script that makes a datasheet that assigns us rows to measure. The order is approximately 1 – 80, but they are slightly mixed up (just to keep us on our toes): measurePHENatHeggLakeRows.r