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2019 Update: Gene Flow in Remnants

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

Overlaps with: Reproductive Fitness in RemnantsPhenology in the Remnants

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: http://echinaceaproject.org/international-pollinator-conference/.

2018 Update: Gene Flow in Remnants

In summer 2018, I began a project to look at pollen movement within and among the remnant populations. To do this, I chose two focal areas, the NW sites in the study area (populations: ALF, EELR, KJ, NWLF, GC, SGC, NGC, KJ, NNWLF) and the SW sites (populations: LC, NRRX, RRX, YOH, and two large populations in between these sites). 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). I am currently extracting the DNA from the leaf tissue samples and a subset of the seeds I collected, and 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).

An Echinacea that has had today’s load of pollen fully removed by pollinators

Start year: 2018

Location: Remnant prairies in central Minnesota

Overlaps with: Reproductive Fitness in Remnants, Phenology in the Remnants

Products: Check back with the flog for preliminary results and annual reports.

Team members who worked on this project include: Amy Waananen

 

2019 Update: Flowering Phenology in Remnants

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: http://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: http://echinaceaproject.org/international-pollinator-conference/.

Fire, flowering phenology, and fitness of Liatris and Solidago

Here are the code and data for the manuscript:

“Flowering phenology responds to fire and influences reproductive success “

CODE: R script completeAsterphenAnalysis.R replicates the data analysis and produces Figures 2 and 3. The R script reads the csv file below. Figure 1 in the manuscript is a conceptual figure generated using Adobe Illustrator. 

This analysis was generated using R version 3.5.1

Required R packages:

FNN: Alina Beygelzimer, Sham Kakadet, John Langford, Sunil Arya, David Mount and Shengqiao Li (2013). FNN: Fast Nearest Neighbor Search Algorithms and Applications. R package version 1.1. https://CRAN.R-project.org/package=FNN

ggpubr: Alboukadel Kassambara (2019). ggpubr: ‘ggplot2’ Based Publication Ready Plots. R package version 0.2.1.
https://CRAN.R-project.org/package=ggpubr

lubridate: Garrett Grolemund, Hadley Wickham (2011). Dates and Times Made Easy with lubridate. Journal of Statistical Software,
40(3), 1-25. URL http://www.jstatsoft.org/v40/i03/.

mateable: Stuart Wagenius, Danny Hanson and Amy Waananen (2016). mateable: Tools to Assess Mating Potential in Space and Time.
R package version 0.3.1. https://CRAN.R-project.org/package=mateable

tidy verse: Hadley Wickham (2017). tidyverse: Easily Install and Load the ‘Tidyverse’. R package version 1.2.1.
https://CRAN.R-project.org/package=tidyverse

DATA: The ascii comma-separated-values file solLiaPhenCtNew.csv, contains phenological and reproductive measures for burned and unburned Liatris aspera and Solidago speciosa from 2016-2018.

Fields include:

uniqueID: unique identifier for each row, generated from a combination of plantID and year that observations were conducted (character)

plantID: unique name for each individual plant in the dataset, plants may be associated with multiple rows of data if they were observed in multiple years (character)

year: year the observations were taken (numeric)

flagNo: flag number is the field identifier for each individual, not a unique identifier for each row of data (numeric)

unit: west or east, indicates the placement of each individual plant in either the east or west management unit of the preserve. Burns were conducted on the west in 2016 and east in 2018 (character)

startDate: day of year that an individual plant first released pollen and was receptive to pollination (date)

doneDate: first day of year that an individual plant was done releasing pollen and no longer receptive to pollination (date)

hdInflCt: count of flowering heads per individual plant (Liatris) or count of flowering stems (Solidago) (numeric)

full: count of full achenes from x-ray images of a random sample of achenes from each individual plant (numeric)

empty: count of empty achenes from x-ray images of a random sample of achenes from each individual plant (numeric)

species: either Solidago or Liatris (character)

 

ESA Poster: Synchrony of flowering phenology within clusters depends on the spatial scale at which clusters are defined

Last week, I attended ESA for the first time and presented a poster on a project I’ve been working on for the past few months: how the synchrony of flowering phenology within clusters of Echinacea depends on the connection distance used to define those clusters. I presented on Tuesday, August 7, 2018 in PS 18: Habitat Structure, Fragmentation, Connectivity from 4:30-6:30, board #92 (just feet away from Will’s poster). My main results are that clusters of Echinacea defined by a small connection distance tend to have lower synchrony on average than clusters defined by larger connection distances. Clusters defined by smaller connection distances also have more variation in synchrony. In terms of a bee’s perspective, this could mean that bees with smaller foraging distances are experiencing more synchronous clusters of Echinacea as they travel from one plant to the next. However, the experience from one small bee to the next is variable. Larger bees with larger foraging distances might be experiencing clusters that are more asynchronous, so as they travel from one Echinacea to the next, plant flowering times might not be overlapping as much.

There was an almost continuous flux of people coming by, and even though I was nervous at first, these couple of hours were probably my favorite part of the conference. Even if some of the listeners didn’t ask me specific questions at the end, just describing my project over and over made me realize what parts I wanted to continue thinking about and working on. I had scientists come by that I recognized from talks I had seen, Team Echinacea alumni interested in what we are doing now, and people I didn’t know that just came because of the title! It was all really exciting and I have a page of notes with questions and ideas to think about as I move forward with this project.

The conference as a whole was a really great experience for me, because I could start to see how both this specific project and my general interests fit in with the rest of the ecology world. It helped me to start to define the questions I want to ask as I think about grad school and the future.

Tracie and her poster at ESA 2018 🙂

Stay posted for more updates on this clusters project!

Link to PDF of Tracie’s ESA poster

 

Big Event: shooing bees AWAY from flowers

The team hard at work shooing pollinators

Yup you read right, today we shooed the bees from the Echinacea. Now you may be asking why would a group of scientists trying to save native bee populations tried to stop bees from pollinating flowers. Well, it’s a reasonable question. Since plants can’t move, it is difficult for them to find a mate, therefore, they have evolved to use bees to do the moving part for them. The different types of bees can have differing effects on the plant’s fitness (not how big its muscles are but how many offspring it has) and those effects are exactly what we are trying to determine with this experiment. Many plants have both male and female parts. Female being how many seeds are being made and male being how many seeds a plant helps make. This raises the question of: how good are different types of bees at distributing pollen from a plant? In order to do this, we need to have plants that are only pollinated by one type of bee. Once we have plants only pollinated by one type of bee we can track where this pollen goes using genetic work. This is where the shooing comes in, to have plants only pollinated by one type of bee we needed to shoo away the other types.

So today the entire team (except Kristen – she was busy working with bees 🙁 ) went out to P2 and worked on the male fitness project. This shooing event has been dubbed the “Big Event.” Today was the first Big Event of five(?) to come, and it was quite successful. We observed around 200 pollinators, the majority of the bees that we saw fit into the category of “small black bee” not to be confused with “medium black bees”, we also saw a fair number of Andrena which are impressive due to the great amount of pollen that each bee carries.

John holding a male Megachile

We saw some Augochlorellas, and Agapostomons – both of which are neat because they are green! My favorite of the day was a male Megachile which I have never seen before. They are very distinct with hairs on their front legs. This mere two and half hours of observations show you the high level of diversity of different bee species at one of our study sites! Can’t wait for the next Big Event titled Big Event 2: Electric Boogaloo and all of the bees that will be found then!

Gretel and Stuart examining a bee

A female Megachile on a echinacea(notice how she caries pollen on her abdomen)

See ya’ next time flog!

Mia

2017 update: Flowering phenology in experimental plots

This year, the number of flowering plants in our main experimental plot (exPt1) dropped in half compared to last year. This might be due to the lack of a burn in the prior fall or spring. Plot 2 (exPt2) had about the same number of heads in ’16 & ’17.

In exPt1, we kept track of approximately 72 heads. The peak date was July 19th. The first head started flowering on July 2nd and the last head finished up on August 21st. In contrast, we kept track of 1076 heads in exPt2, about 140 more than last year! The peak date for these Echinacea was a bit earlier, July 13th. exPt2 heads also started and ended earlier (June 22 – August 19).

We harvested the heads at the end of the field season and brought them back to the lab, where we will count fruits (achenes) and assess seed set.

Flowering schedules for 2017 in exPt1 and exPt2. Black dots indicate the number of flowering heads on each date. Gray horizontal line segments represent the duration of each head’s flowering and are ordered by start date. The solid vertical line indicates peak flowering, while the dashed lines indicate the dates when 25% and 75% of heads had begun flowering, respectively. Note the difference in y-axes between the two plots. Click to enlarge!

Start year: 2005

Location: Experimental Plots 1 and 2

Overlaps with: Heritability of flowering time, common garden experiment, phenology in the remnants

Physical specimens: Harvested heads from both experimental plots are in the lab at CBG. The ACE protocol for these heads will begin soon.

Data collected: We visit all plants with flowering heads every 2-3 days starting before they flower 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 our long-term dataset. The figures above were generated using package mateable in R. If you want to make figures like this one, download package mateable from CRAN!

You can find more information about phenology in experimental plots and links to previous flog posts regarding this experiment at the background page for the experiment.

 

 

2016 update: Flowering phenology in experimental plots

Every year we keep track of flowering phenology in our main experimental plots, exPt1 and exPt2. Fewer plants than usual flowered in exPt1 in 2016: 149 plants (179 heads) flowered between June 24th and August 7th. The population’s mean start date of flowering was July 5th and the mean end date was July 18th. Peak flowering in 2016 was on July 10th, when 143 heads were in flower. For comparison, peak flowering in 2015 was on July 27th, when there were nearly 10x as many heads flowering as on this year’s peak. The earlier phenology and low numbers of flowering we observed this year relative to 2015 is likely due at least in part to the plot burn schedule (2015 was a burn year and 2016 was a non-burn year), but there were still many fewer flowering plants than any season, burn or non-burn, in the past 10 years.

We kept track of 934 flowering heads in ExPt2, where 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. ExPt2 was designed to study the heritability of  phenology—you can read more about progress of that experiment in the upcoming 2016 heritability of phenology project status update.

At the end of the season we harvested the heads and brought them back to the lab, where we will count fruits (achenes) and assess seed set.

expt1and2floweringschedule

ExPt1 and Expt2 flowering schedules from 2016. Dots represent the number of flowering heads on each date. Horizontal line segments represent the duration of each heads flowering and are ordered by start date. The solid vertical line indicates peak flowering, while the dashed lines indicate the dates when 25% and 75% of heads had begun flowering, respectively. Click to enlarge!

Start year: 2005

Location: Experimental Plots 1 and 2

Overlaps with: Heritability of flowering time, common garden experiment, phenology in the remnants

Physical specimens: We harvested 177 heads from exPt1 and 870 from exPt2. Attentive readers may note that we harvested about 64 fewer heads than we tracked for phenology. That’s because before we could harvest many seedheads at exPt2, rodents chewed through their stems and ate some fruits (achenes). We recovered most of the heads that were grazed from the ground and made estimates of number of fruits lost due to herbivory, but we couldn’t find some heads. Arg. We brought the harvest back to the lab, where we will count fruits and assess seed set.

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. The figure above was generated using package mateable in R. If you want to make figures like this one, download package mateable from CRAN!

You can find more information about phenology in experimental plots and links to previous flog posts regarding this experiment at the background page for the experiment.

 

 

Ridley’s next generation rescue

Description: In 2008 Caroline Ridley established an experiment to investigate next generation effects of genetic rescue on plant fitness. We are comparing fitness (recruitment and survival) of seeds collected from plants in the INB1 experiment in exPt 1. All of the maternal plants in INB1 were open-pollinated and in one of three groups: 1. individuals with parents from a single large remnant population, 2. individuals with parents from a small remnant population (non-rescued), and 3. individuals with parents from a large and small remnant (rescued). Eri and NWLF served as “small” remnant populations, while Lf and SPP were the “large” remnants. Rescued individuals were offspring of crosses using Eri × SPP, Eri × Lf, NWLF × SPP and NWLF × Lf.

Caroline sowed achenes in an experimental plot at Hegg Lake WMA. The plot (exPt 4) has 3 blocks, each with 2 rows. Sets of achenes (East & West) were sowed in 50-cm segments within the rows. Caroline searched for and marked seedlings with colored toothpicks in May 2009. Team Echinacea assessed late season survival in August 2009. Since then we have annually assessed survival and growth of these plants. When an individual flowers we will measure reproductive fitness!

Start year: 2008

seedling search

C. Ridley searches for seedlings in nextGenRescue

Location: exPt 4 at Hegg Lake WMA

Products: Long-term dataset for Aster analysis

Overlaps with: crossing experiments qGen1, qGen2, qGen3 & recruitment experiment; INB1

Link to flog posts: Read updates about this experiment written by members of Team Echinacea.

flowering in 2011

Flowering of Echinacea angustifolia in almost all prairie remnants was down this year. Overall, approximately half as many plants flowered this year as last. Two areas distinctly bucked the trend: flowering was high at Hegg Lake WMA, which was burned this spring, and at our main experimental plot, which was burned this spring. Burning really encourages flowering!

We finished our first round of mapping all flowering plants in nearby remnants and a summary of the raw dataset is shown below. Each line lists the name of a site and the count of demo records and survey records at the site–also the difference in counts. We call our visits to remnants to find and refind plants “demography,” or demo for short. We call mapping the plants surveying because we used to use a survey station. Now we use a survey-grade RTK GPS (a Topcon GRS-1).

      site demo surv diff
1        x    1    0    1
2       aa  131  103   28
3      alf   79   52   27
4      btg    8    3    5
5       cg   20    5   15
6      dog    4    2    2
7     eelr   60   44   16
8      eri  153  122   31
9      eth    9    3    6
10      gc    7    1    6
11      kj   61   44   17
12    krus   69   21   48
13      lc    0    0    0
14     lce   58   45   13
15     lcw   48   31   17
16      lf    0    0    0
17     lfe   77  117  -40
18     lfw   65    0   65
19     lih    2    0    2
20    mapp    5    3    2
21    ness    7    3    4
22     ngc   28   12   16
23   nnwlf   20    7   13
24    nrrx   42   27   15
25    nwlf   27   10   17
26    on27   71   85  -14
27      ri  241  210   31
28     rlr    0    0    0
29    rndt   10    2    8
30     rrx   70   51   19
31   rrxdc    4    0    4
32     sap   80   38   42
33     sgc   10    4    6
34    sign    0    0    0
35     spp  126   78   48
36      th   19   12    7
37   tower   10    3    7
38 unknown    8    0    8
39     waa   10    6    4
40    wood   33   21   12
41     yoh   23    8   15

Notice that most sites have more demo records than survey records. This is because each data recorder enters an empty record at the beginning and end of demoing a site. Also, in certain circumstances we do demo on non-flowering plants.

Something strange is going on with the on27 site. I think someone may have entered the incorrect site name when doing demo. Also, lf looks strange, but is easily explained: lf is divided into two hills (lfe and lfw). We distinguished the two when doing demo, but not when surveying. Our next field activity is to verify the demo and survey dataset and make sure everything makes sense. Being people, we sometimes make mistakes in data entry. Because we know we make mistakes, we generate two separate datasets of flowering records (demo and surv) and compare them. When records don’t match, we go back and check.

We assess survival and reproduction of Echinacea plants in remnants to understand the population dynamics of these remnant populations. We want to know if the populations are growing, holding their own, or shrinking. To figure this out will take a few years because plants live a long time. Estimating a population’s growth trajectory based on just a couple of years of flowering records probably won’t be that informative.