The inbreeding 2 experiment was planted in exPt1 in 2006 to determine how genetic drift is differentially affecting average fitness of remnant populations. In 2005, team members crossed common garden plants from seven remnant populations. There are three cross types: inbred (crossed to a half-sib; I), within population (randomly chosen; W), and between population (B). Each year, team members assess flowering phenology and fitness of Echinacea in the inb2 common garden.
In 2019, the team searched for Echinacea at 508 positions of the original 1443 positions planted in inb2. In total, we found 351 living plants. Four plants flowered in 2019 but only three produced achenes. Since 2006, 163 Echinacea in inb2 have flowered; they have produced a total of 336 flowering heads.
This winter, Riley Thoen is working on analyzing data and drafting a manuscript for inb2. In these endeavors, he found a small discrepancy in inb2 data: not all plants that were planted in the inb2 plot have a complete pedigree. Therefore, only a subset of the total can be used for analysis. A total of 1136 plants with a complete pedigree were planted in inb2, and of those, 277 were found alive in 2019. All four plants that flowered in 2019 have known pedigrees. A total of 138 plants of known pedigree have flowered and they have produced 284 total heads since the plot was planted in 2006. Surprisingly, within-remnant crosses have the lowest survival of all cross types, at 20%. Inbred crosses have 24% survival and between-remnant crosses have 30% survival. Riley is starting to push data analysis forwards and will certainly post updates on the flog when more discoveries are made!
Data/material collected: flowering phenology on the flowering plants (available in the exPt1 phenology data frames in the cgData repo), measure data (cgData repo), and harvested heads (data available in hh.2019 in the echinaceaLab package; heads in ACE protocol at CBG).
Products:
Shaw, R. G., S. Wagenius and C. J. Geyer. 2015. The susceptibility of Echinacea angustifolia to a specialist aphid: eco-evolutionary perspective on genotypic variation and demographic consequences. Journal of Ecology 103: 809-818. PDF
Kittelson, P., S. Wagenius, R. Nielsen, S. Qazi, M. Howe, G. Kiefer, and R. G. Shaw. 2015. Leaf functional traits, herbivory, and genetic diversity in Echinacea: Implications for fragmented populations. Ecology 96: 1877–1886. PDF
Monitoring
reproductive fitness in the remnant populations is a staple of Team Echinacea’s
summer activities. Understanding the reproductive success of plants in remnant
populations provides insight to a vital demographic rate contributing to the
persistence (or decline) of remnant populations in fragmented environments.
In summer
2019, we harvested 40 seedheads to study patterns of reproductive fitness in 8
remnant Echinacea populations (ALF, EELR, KJ, NWLF, GC, NGC, SGC, NNWLF) (the
same populations used where I studied phenology and gene flow). I randomly selected 1/3 of
flowering heads at each remnant to harvest. In addition, I collected all seedheads
from especially small or isolated remnants (specifically, GC, KJ, and the
cluster of plants just north of EELR).
In early
January, I dissected the seedheads. I extracted the achenes by row so that I
will be able to observe temporal variation in seed set within heads. Ideally,
next I will x-ray the achenes and assess seed set by observing the proportion
of achenes that contain embryos. However, the x-ray machine at the Chicago
Botanic Garden is currently out of service, so instead I may need to weigh or
germinate the achenes to see if viable embryos are inside.
Extracting achenes by row, so that I know which achenes resulted from florets that flowered early (i.e., at the bottom of the seedhead) or late (i.e., at the top of the seedhead). Tedious but possible!
Start
year: 1996
Location: Roadsides,
railroad rights of way, and nature preserves in and around Solem Township, MN
You can
read more about reproductive fitness in remnants, as well as links to prior
flog entries mentioning the experiment, on the background page for this experiment.
In summer
2019, I completed a second season of field work for a study monitoring pollen
movement between remnant populations. In summer 2018, I chose two focal areas,
the NW sites in the study area (populations: ALF, EELR, KJ, NWLF, GC, SGC, NGC,
KJ, NNWLF) and SW sites (populations: LC, NRRX, RRX, YOH, and two large populations
in between these sites). This summer, I limited the study to the NW sites. As
in 2018, I mapped and collected leaf tissue from all individuals in the study
areas and harvested seedheads from a subset of these individuals (see Reproductive Fitness in Remnants). In addition, I monitored the
flowering phenology of all of the flowering plants in these populations (see
Phenology in the Remnants).
Now, I am
working on extracting and genotyping the DNA from the leaf tissue samples and a
subset of the seeds I collected. This takes a long time! I will use the
microsatellite markers that Jennifer Ison developed in her dissertation to
match up the genotypes of the offspring (i.e., the seeds) with their most
likely father (i.e., the pollen source). To analyze patterns of gene flow, I
will assess how individuals’ location and timing of flowering influence their
reproductive success and distance of pollen movement.
In
addition, last summer we planted all of the seedlings from 2018 in the
experimental plot that John Van Kempen set up at West Central Area High School.
We will continue to monitor these seedlings to understand how pollen movement
distance (or the distance between parents) influences offspring fitness.
Here is the team after we planted nearly 298 seedlings in the experimental plot at WCA!
Start
year: 2018
Location: Roadsides, railroad rights of way, and nature preserves in and around
Solem Township, MN
Products: I presented a poster based on
the locations and flowering phenology of individuals from summer 2018 at the
International Pollinator Conference in Davis, CA this summer. The poster is
linked here: https://echinaceaproject.org/international-pollinator-conference/.
In 2019,
we collected data on the timing of flowering for 95 flowering plants (127
flowering heads) in 8 remnant populations, which ranged from 1 to 29 flowering heads.
The earliest bloomers (four plants at four different remnants) initiated
flowering on July 4. Plant 24050 in the aptly named remnant population North of
Northwest of Landfill was the latest bloomer, shedding its last anthers of
pollen on August 16. Township mowers had mowed over this plant earlier in the
season, which is perhaps why it took longer for it to sprout a new flowering
stem. Altogether, the flowering season was 43 days long. Peak flowering was on
July 19, when 105 heads were flowering.
This season
marked the 19th season of collecting phenology records in remnant populations! Though
we do not have data for all populations every year, Stuart monitored phenology
in all of our remnant populations in 1996 and in following years (2007, 2009,
2011-2019) students and interns studied phenology in particular populations. From
2014-2016, determining flowering phenology was a major focus of the summer
fieldwork, with Team Echinacea tracking phenology in all plants in all of our
remnant populations. The motivation behind this study is to understand how
timing of flowering affects the mating patterns and fitness of individuals in
natural populations.
Flowering
occurred much later this season than previous years, with peak flowering
falling a full 14 days later in the year than 2018, when flowering started on
June 20, and 10 days later than 2017. Of all the years that we data for flowering
phenology in the remnant populations in and around Solem Township, this season was
the second-latest, with only the 2013 season beginning later, on July 6.
However, this observation comes with the caveat that sampling effort varied
between years and some years focused on particular contexts, such as population
where a portion had experienced a spring burn (see Fire and Flowering at SPP). Many other plants and animals in
Minnesota seemed to have delayed phenology this spring and summer, perhaps a
result of an unusually wet and snowy spring.
Start
year: 1996
Location: Roadsides,
railroad rights of way, and nature preserves in and around Solem Township, MN
Overlaps
with: phenology in experimental plots, demography in the
remnants, gene flow in remnants, reproductive fitness in remnants
Data/materials
collected:We identify each plant with a numbered tag affixed to
the base and give each head a colored twist tie, so that each head has a unique
tag/twist-tie combination, or “head ID”, under which we store all phenology
data.We monitor the flowering status of all flowering plants in
the remnants, visiting at least once every three days (usually every two days)
until all heads were done flowering to obtain start and end dates of flowering.
We managed the data in the R project ‘aiisummer2019′ and added the records to
the database of previous years’ remnant phenology records, which is located
here: https://echinaceaproject.org/datasets/remnant-phen/.
A flowering curve (created here using the R package mateable) summarizes the flowering phenology data that we collected in 2019, indicating the number of individuals flowering on a given day and the flowering period for all individuals over the course of the season.
We shot
GPS points at all of the plants we monitored. Soon, we will align the locations
of plants this year with previously recorded locations and given a unique
identifier (‘AKA’). We will link this year’s phenology and survey records via
the headID to AKA table.
We
harvested a random sample of 1/3 of the flowering heads from each remnants in
August and September, plus an X additional heads from populations that were highly
isolated, for a total of X harvested seedheads. These are currently stored at
the University of Minnesota. This winter, I will assess the relationship
between phenology and reproductive fitness by x-raying all of the seeds we collected.
In addition, I will determine the paternity (i.e., pollen source) for a sample
of seeds by matching the seed genotype to the potential pollen donors. Doing so
will shed light on how phenology influences pollen movement and gene flow
patterns.
You can
find more information about phenology in the remnants and links to previous
flog posts regarding this experiment at the background
page for the experiment.
Products: I presented a poster based on the
locations and flowering phenology of individuals from summer 2018 at the
International Pollinator Conference in Davis, CA this summer. The poster is
linked here: https://echinaceaproject.org/international-pollinator-conference/.
Small remnant Echinacea populations may suffer from
inbreeding depression. To assess whether gene flow (in the form of pollen) from
another population could “rescue” these populations from inbreeding depression,
we hand pollinated Echinacea from six different prairie remnants with pollen
from a large prairie remnant (Staffanson Prairie) and from a relatively small
population that we call “Northwest Landfill.” We also performed
within-population crosses as a control. Amy Dykstra planted achenes (seeds)
that resulted from these crosses in an experimental plot at Hegg Lake WMA.
Plants in the crossing plots were originally found as seedlings like this one
We sowed a total of 15,491 achenes in 2008. 449 of these
achenes germinated and emerged as seedlings. Each summer we census the
surviving plants and measure them. This summer we found 48 surviving plants.
None of these plants has flowered, but we think some of them are close! The
largest plant we measured had 4 leaves, the longest of which was 35 cm.
You can read more about the interpopulation crosses, as well as links to prior flog entries mentioning the experiment, on the background page for this experiment.
Start year: 2008
Location: Hegg
Lake WMA
Data collected: Plant
fitness measurements (plant status, number of rosettes, number of leaves, and
length of longest leaf), and notes about herbivory. Contact Amy Dykstra to
access this data.
Products: Dykstra, A. B. 2013. Seedling recruitment in fragmented populations of Echinacea angustifolia. Ph.D. Dissertation. University of Minnesota. PDF
To see how ploidy varies in Echinacea species in our study site, in fall 2019, wecollected and dried tissue from E. pallida, E. angustifolia, and E. purpurea. We also collected tissue from potential hybrids and known hybrids. We brought the dried tissue back to the Chicago Botanic Garden, where we plan to analyze ploidy using a flow cytometer, a device that can be used to find relative genome size.
The flow cytometer used to assess relative genome size. Although it just looks like a box, it is truly a powerful machine.
Example of dried Echinacea tissue… We thought it might be a hybrid when we visited it in the field!
Unfortunately, preparing samples for the flow cytometer is difficult, so we are going to first optimize our Echinacea tissue preparation protocol using live tissue. To do this, we withdrew accessions of E. angustifolia, E. pallida, and E. purpurea from Millennium Seed Bank at the CBG. For E. pallida, we took seed from collections throughout its range to see if its ploidy varies with latitude. We are currently germinating this live tissue to use for ploidy analysis with Elif. We are very excited to see what we find – any finding will help expand genomic knowledge for the genus Echinacea!
Start year: 2019
Location: Hegg Lake WMA, various prairie remnants and
restorations, hybrid experimental plots
Data/ materials collected:Dried tissue from
plants throughout the study area; samples are currently held at Chicago Botanic
Garden, in a small box in the glass cupboard to the right upon entering room 159,
the Population Biology Lab. Updates will be posted when genome data is
available.
This experiment was designed to study how well adapted Echinacea populations are to their local environments. Amy collected achenes from Echinacea populations in western South Dakota, central South Dakota, and Minnesota, and then sowed seeds from all three sources into experimental plots near each collection site. You can read more about the experiment and see a map of the seed source sites on the background page for this experiment.
This summer, during our annual census of the experimental plots, we found 67 living Echinacea plants in the western South Dakota plot, including 9 flowering plants. We found 116 living plants, including one flowering plant in the Minnesota plot. This was the first flowering plant in the Minnesota plot! (We abandoned the central SD plot after it was inadvertently sprayed in 2009, killing all the Echinacea). For more details and graphs, please read this brief report.
First flowering plant in the MN local adaptation plot!
Start year: 2008
Location: Grand River National Grassland (Western South
Dakota), Samuel H. Ordway Prairie (Central South Dakota), Staffanson Prairie
Preserve (West Central Minnesota), and Hegg Lake WMA (West Central Minnesota).
Data/ materials collected: Plant fitness measurements
(plant status, number of rosettes, number of leaves, and length of longest
leaf), heads from all flowering plants
Products: Dykstra,
A. B. 2013. Seedling recruitment in fragmented populations of Echinacea angustifolia. Ph.D.
Dissertation. University of Minnesota. PDF
This field season the team continued the seedling
recruitment experiment begun in 2007. The original goal of the project was to
determine the rates of establishment and growth of seedlings in remnant
populations of Echinacea angustifolia.
From 2007 to 2013, plants which had flowered in the preceding year were visited
in the spring to find any resulting seedlings. Each fall since then the team
visits the plants, re-finds the seedlings and measures the living offspring.
In 2019 Team Echinacea visited 69 focal maternal plants in
12 prairie remnants to determine the survival and growth of their offspring.
The team searched for 128 of the original 955 seedlings and found 87 of them
(10 fewer than were found in 2018.) However, the team also re-found 27 seedlings
which could not be located in 2018. None of the original seedlings flowered
this year.
In addition to the annual seedling search, in 2019 the team
began working on a project to relate the fitness and mating scene of maternal
plants to their offspring. In late October 2019, Erin and Riley staked to the
locations of 451 maternal plants included in the original experiment which now
have “inactive” circles with no living seedlings. They visited these maternal
plants because they were not included in demo in 2018 or 2019, and their goal
was to determine the status of every original maternal plant. Since then, a
group of Team Echinacea alums and current members has begun working to prepare
the data for analysis in 2020 with the goal of submitting a manuscript in the
spring.
The first day of searching occurred at East Elk Lake Road, where 13 of the original maternal plants still have living offspring.
Sites with seedling searches East Elk Lake Road, East Riley, East of Town Hall, KJ’s, Loeffler’s Corner, Landfill, Nessman, Northwest of Landfill, Riley, Steven’s Approach, South of Golf Course, Staffanson Prairie
Data/materials collected: The EchinaceaSeedlings repository holds the data for this experiment. Lea Richardson restructured the repo in December 2019 to facilitate collaboration on the new project.
Notes on the project and master datasheet scans are at ~Dropbox\remData\115_trackSeedlings\slingRefindsFall2019
Data specific to the new 2019 project, including maps and
datasheets used to refind the inactive circle maternal plants, is at ~Dropbox\slingProject2019
Team members involved
with the 2019 project: Lea Richardson, Erin Eichenberger, Riley Thoen,
Drake Mullett, Amy Waananen, Scott Nordstrom, Will Reed, Amy Dykstra, Gretel
Kiefer , Stuart Wagenius
Products: Amy Dykstra used seedling survival data from 2010 and 2011 to model population growth rates as a part of her dissertation.
You can read more about seedling establishment, as well as links to prior flog entries mentioning the experiment, on the background page for this experiment.
Poor weather conditions delayed demo this year but did not
dampen our spirits! In 2019 Team Echinacea added 4031 visor records to demo and
1431 GPS points to surv. The largest effort this summer occurred at Aanenson
where eight team members took demo records on over 200 flowering plants. We
found flowering plants at Northwest of Landfill with tags from 1995 in situ, meaning the plants were at
least several years older than most of the team. We also found non-angustifolia
Echinacea invading prairie remnants Dog and Yellow Orchid Hill.
The team does demo at everyone’s favorite site: East Riley! Also known as Whose Loc Is It Anyway? Where the status is “Can’t find” and the GPS points don’t matter.
This year we performed demo and surv at 32 prairie remnants
and 10 additional sites with angustifolia populations. For our smaller sites we
visit every mature plant (ones which have flowered before.) At the larger sites
we measure a subsample of the mature population. At every site we also perform
flowering demo, where we visit plants which flowered for the first time or were
not included in the subsample. We record the status of each plant we visit, its
neighbors and the number of heads it produced. All flowering plants are tagged
and shot in surv, and in the coming months we will use demap to reconcile the
2019 demo and surv records with each other as well as those from previous years
to construct our spatial dataset of reproductive fitness in the tallgrass
prairies of our study area.
Total Demo Bill Thom’s Gate, Common Garden, Dog, East of Town Hall, Golf Course, Hegg Lake, Martinson’s Approach, Nessman, North of Golf Course, REL, RHE, RHP, RHS, RHX, RKE, RKW, Randt, Railroad Crossing Douglas County, South of Golf Course, Sign, Town Hall, Tower, Transplant Plot, West of Aanenson, Woody’s, Yellow Orchid Hill
Annual Sample Aanenson, Around Landfill, East Elk Lake Road, East Riley, KJ’s, Krusmark’s , Loeffler’s Corner, Landfill, North of Railroad Crossing, Norwest of Landfill and North of Northwest of Landfill (lumped,) On 27, Riley, Railroad Crossing, Steven’s Approach, Staffanson Prairie
In addition to the annual collection of data, this year Erin
began developing a study to investigate whether flowering return interval and
isolation by distance are correlated in Echinacea.
Start year: 1995
Location: Unbroken (never tilled) remnant prairies in Douglas County, MN, located along roadsides, nature preserves, railroad right-of-ways and privately-owned land.
Data: Access the most recent copies of allDemoDemo.RData and allSurv.RData at ~Dropbox\demapSupplements\demapInputFiles. Demap accepts these files and the demap team will clean and reconcile them in the demap repository. ~Dropbox\geospatialDataBackup2019 houses the raw GPS jobs while the aiisummer2019 repo houses the raw demo records.
Data related to
the flowering isolation study can be found in the floiso repository (contact
Erin Eichenberger for access) and in the folder ~Dropbox\floweringIsolation2019
Products: Amy Dykstra’s dissertation included matrix projection modeling using demographic data
Project “demap” merges phenological, spatial and demographic data for remnant plants
You can read more about the demographic census in the remnants, as well as links to prior flog entries mentioning the experiment, on the background page for this experiment.
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 common garden, 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. The Echinacea Project currently has 10 established experimental plots: exPts1-10. Due to the repetitiveness of yearly phenology, measuring, and harvesting, this project status report will include updates on all common garden experiments except for Amy Dykstra’s plot (exPt3), qgen2qgen3 (exPt8), and the West Central Area common garden (exPt10).
exPt1: Experimental plot 1 was first planted in 1996 (cleverly termed the 1996 cohort), and has been planted numerous times in subsequent years, with the most recent planting being inbreeding 2. 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) effects of inbreeding (inb1, inb2), and quantitative genetics experiments (qgen1). There are also a number of smaller experiments in it, including fitness of Hesperostipa spartea, aphid addition/exclusion, and pollen addition/exclusion. In 2019, we visited 4392 of the original 10,622 planted and found 3486 alive. Only 70 plants were classified as “flowering” in exPt1 this year. This is a drastic change from the nearly 1000 plants that flowered in summer 2018 – perhaps it is a testament to the benefits of controlled burning (we burned in spring 2018 but not in 2019). In summer 2019, we harvested 52 total Echinacea heads in exPt1. In the fall, we added 789 staples to positions where plants were gone for three straight years – this was desperately needed because no staples were added to positions with dead plants after 2018.
exPt2: Heritability of flowering time is the name of the game in exPt2. Planted in 2006, exPt2 was planted to assess if flowering start date and duration was heritable in Echinacea. In summer 2019, we visited 2050 positions of the 3961 positions originally planted. We measured 1802 living plants, of which 654 were flowering. In the fall, we harvested ~1100 heads from exPt2. We do not have an exact number of heads harvested from exPt2 yet, as we have not had time to complete head reconciliation. Location: Hegg Lake WMA
Stuart explains Echinacea capitulum morphology to Shea in one of the experimental plots.
exPt4: Experimental plot 4 was planted to determine if Echinacea from small remnant populations could be genetically rescued via an outcross to larger, more genetically diverse populations. Caroline Ridley and other members of Team Echinacea sowed 3584 achenes at Hegg Lake WMA in 2008, and we have assessed survival and basal plant characters every year since. Survival in exPt4 is incredibly low. We only visited 21 plants in 2019 and only 7 were alive. No plants have flowered in this plot yet. Location: Hegg Lake WMA
exPt5: The only experimental plot planted at Staffanson Prairie Preserve (SPP), exPt5, was planted in an attempt to compare progeny of maternal plants from burned and unburned sections of SPP. There were 2800 plants planted originally, but high mortality made it impossible to visit the plot row-by-row. Now, we and treat the plot like demography. We use a GPS to find plants in exPt5 that have previously flowered and add more plants to the stake file if new plants in the plot flower. In 2019, we visited 10 plants in the plot, all of which were alive! There were no plants flowering in exPt5 in 2019, though. Location: Staffanson Prairie Preserve
exPt6: Experimental plot 6 was the first E. angustifolia x E. pallida hybrid plot planted by Team Echinacea. A total of 66 Echinacea hybrids were originally planted; all have E. angustifolia dams and E. pallida sires. In 2019, we visited 40 positions and found 28 living plants. No plants have flowered in this plot yet. As of January 2020, all exPt6 measure data through summer 2019 is uploaded to the SQL database. Location: near exPt8
exPt7: Planted in 2013, experimental plot 7 was the second E. pallida x E. angustifolia plot. It contains conspecific crosses of each species as well as reciprocal hybrids. There were 294 plants planted. Out of the 205 plants we visited in 2019, we found 161 plants still alive and basal; there were no flowering plants this year. For some context, survival of pure E. angustifolia crosses was lower than all other cross types. As of January 2020, all exPt7 measure data through summer 2019 is uploaded to the SQL database. Location: Hegg Lake WMA
exPt9: Experimental plot 9 is another hybrid plot, but unlike the other two hybrid plots, we do not have a perfect pedigree of the plants. That is because E. angustifolia and E. pallida maternal plants used to generate seedlings for exPt9 were open-pollinated. We need to do paternity analysis to find the true hybrid nature of these crosses (assuming there are any hybrids). There were originally 745 seedlings planted in exPt9, and in 2019 we visited 510 positions. It was one of the harder plots to measure because over half of the positions did not have a plant and we do not use staples at Hegg Lake WMA. We found 308 living plants in 2019, one of which was flowering! We know the flowering plant has an E. pallida mother, but we are still unsure of the paternity of the flowering plant. When we know, we will post an update. As of January 2020, all exPt9 measure data through summer 2019 is uploaded to the SQL database. Location: Hegg Lake WMA
Summer 2019 measures exPt9… so many “Can’t Finds!”
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 exPt9 flowering plant, as well as for all surviving
plants in exPt4. Find the GPS jobs containing the exPt4 and exPt9 points in
~Dropbox\geospatialDataBackup2019, saved in three formats in
temporaryDarwBackups2019, convertedXML2019 and convertedASVandCSV2019. The job
name is SURV_20191002_DARW and the points have names that distinguish them by
the experimental plot. The stake file to find exPt5 plants is here: ~Dropbox\geospatialDataBackup2019\stakeFiles2019\exPtFiles\exPt05stakeFile.csv
Products: Many publications and independent projects.
