Helena Kleiner’s Award Winning Poster

Helena’s poster for the 2021 Coastal and Estuarine Research Federation (CERF) Conference was awarded one of the Best Graduate Student Poster Awards. Click on the poster below to see it at full size.

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McLachlan Lab at ESA 2020

Jason McLachlan and Megan Vahsen both presented virtually at ESA 2020 this year.
Jason’s talk focused on the education initiatives for the Ecological Forecasting Initiative. You can see his abstract here and video here.


Megan’s talk highlighted how she incorporated results from our Blue Genes experiment from 2019 into a forecast predicting marsh accretion. You can see her abstract here and video here.


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McLachlan Lab Undergrad Brady Stiller Named 2020 Valedictorian

We are excited that Brady Stiller has been named the 2020 Valedictorian for the University of Notre Dame!  Brady joined the lab as a sophomore in 2017 working on the marsh project.  In addition to contributing to research during the academic year, Brady held a key role assisting McLachlan lab graduate student, Megan Vahsen, with her experiment at the Smithsonian Environmental Research Center during summer 2018.  In Summer 2019 Brady led the effort to cross Schoenoplectus americanus marsh plants in the lab at a large scale with great success creating 470 crosses that produced over 1700 seeds.  For his work in the lab and the Department of Biological Sciences, Brady also earned the Outstanding Biological Scientist Award.  Congratulations to Brady on these wonderful accomplishments!

Brady hand-pollinating an S. americanus flower

Brady helping at SERC in 2018. L: Setting up the experiment R: Measuring S. americanus plants

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2019 Blue Genes Harvest

Author: Megan Vahsen

In early October, several members of the McLachlan lab conducted a harvest of our mesocosm experiment at the Smithsonian Environmental Research Center (SERC) in Edgewater, MD. The experiment was a huge effort as a part of our ‘Blue Genes’ NSF grant (in collaboration with the Blum lab at the University of Tennessee Knoxville and the Megonigal lab at SERC) to investigate how intraspecific variation and evolution contribute to ecosystem-level processes. Previous experiments from our lab suggest that there is genetically-based variation in functional traits of a coastal marsh sedge (Schoenoplectus americanus) important to marsh accretion. Here, we investigated how genotype by environment interactions influenced phenotypic variation in a variety of functional traits. We exposed clones of 36 resurrected genotypes of S. americanus to a variety of environmental factors: elevated CO2, salinity, flooding, and interspecific competition. Resurrected genotypes were collected from varying depths of sediment cores across locations in the Chesapeake Bay.

We grew S. americanus genotype clones in PVC pots placed in ‘marsh organs’ (i.e. racks with positions that vary by elevation, Fig 1). We enclosed organs with open-air chambers which allowed us to manipulate atmospheric CO2. This experimental set-up was replicated at two sites: one at the Global Change Research Wetland (higher salinity) and one in a nearby creek (lower salinity, Fig 2). For some pots, S. americanus grew in the presence of an interspecific competitor, Spartina patens, a high marsh, less flood-tolerant species. In June 2019, we established plants in 670 PVC pots across 14 organs.

The harvest in October was a long week of hard work that resulted in a bounty of data to be analyzed! Megan Vahsen, Haley Kodak,  and Jason McLachlan from the McLachlan lab, Jenn Summers from UTK, and Helena Kleiner from SERC processed thousands of stems (Figs 3 &4). We were lucky to have over 10 volunteers outside of our team that helped with measuring and recording— it was a real team effort! For each PVC pot, we measured heights and widths of each stem, harvested aboveground biomass, and stored PVC pots in a freezer for processing of belowground biomass which will occur this fall and winter. Jenn and Haley also collected samples for RNA and epigenetic analysis, at harvest. This harvest data is just some of the interesting data we collected for this experiment. Over four field campaigns, Helena (SERC) took porometry measurements on a subset of plants to capture stomatal conductance. Tom Mozdzer (Bryn Mawr) took greenhouse gas flux measurements on a subset of pots and sampled soil for later microbial analysis. Finally, we took porewater samples from a subset of pots for nitrate concentration analysis that Helena is leading (Fig 5). From this experiment, we hope to have a broad picture of how intraspecific variation, evolution, and genotype by environment interactions influence ecosystem processes. 

Figure 1. View of experimental plants from the top of an open-air chamber. Pots are placed at different elevations to allow for different levels of flooding as tides move in and out of the creek. Photo credit: Helena Kleiner.

Figure 2. Drone-captured view of the newly built freshwater site. CO2 blowers and sensors were all run on solar power. Helena Kleiner (SERC) led the construction of the site. Photo credit: David Klinges.

Figure 3. Haley, Megan and Jenn measuring plants at the GCREW (high salinity) site. A small unicorn piñata was a good luck charm for the harvest. Photo credit: Helena Kleiner.

Figure 4. Jason was a huge help shuffling pots back and forth from the marsh organs to processing tables. Photo credit: Helena Kleiner.

Figure 5. Porewater sippers in PVC pots.

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Science Conversations and Site Review with NSF Program Director

Classic SERC picture. Megan Vahsen, Pat Megonigal, Helena Kleiner, Liz Blood, Haley Kodak, Jason McLachlan (left to right).

On Tuesday, August 6, we had the opportunity to give Liz Blood, the DEB (Division of Environmental Biology) Program Director at NSF, a tour of our Blue Genes marsh experiment at the Smithsonian Environmental Research Center (SERC).  The day was set up to provide Liz a deeper understanding of our project and specifically our experiment this summer.  It was also an opportunity for us to get feedback from Liz about our project and the priorities of NSF and the DEB program. 

The day started with a tour of the GCREW and Freshwater sites where our experiment is taking place, a visit to the NEON tower (Liz had been a Macrosystems PI and Program Officer for NEON), and then presentations in the afternoon.  Our group included Jason McLachlan – PI at Notre Dame, Pat Megonigal – Associate Director for Research at SERC, Helena Kleiner – SERC Technician, and Haley Kodak and Megan Vahsen – Notre Dame Grad Students. Jenn Summer, Grad Student from the University of Tennessee Knoxville, was also able to call in to provide an overview of her work.

Showing Liz the Drake chambers that have been in use since 1987 at the Global Change Research Wetland (GCREW). The saltwater treatment for our Blue Genese experiment is located at GCREW.

Haley Kodak, Megan Vahsen, and Helena Kleiner (left to right) standing in front of the Freshwater location of our Blue Genes experiment. Helena led the effort to build all the infrastructure (boardwalk, chambers, solar panels, etc) at the Freshwater site.

In a nutshell, our experiment this summer is looking to answer these questions: 

  1. What are the phenotypic consequences of genetic change over time?
  2.  How does (1.) compare to genetic change over space?
  3.  Is there asynchrony in genetic change over time across locations? (ie. interaction between space and time; does the effect size in change over time vary across space?)
  4. How does the  environment influence all of this? (G x E interactions)

To answer these questions, we are using 670 plants germinated from modern (~15 years) and ancestral (~100 years) seeds collected from 5 different sites. The plants are exposed to two salinity levels at the brackish GRCREW site and the Freshwater site and to ambient and elevated carbon dioxide levels.

It was wonderful to be able to show off how we are pulling together ecological processes including plant physiology, community changes, ecosystem processes, and evolution.  It was equally wonderful to hear from Liz. As Jason said, “Liz is very wise. She sees the big picture in science.”  

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Jason McLachlan in the New York Times


Jason was quoted in today’s New York Times article highlighting different methods of handling the effect changing climate has on trees!

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McLachlan Lab at AGU 2018!

The McLachlan lab represented at AGU (American Geophysical Union) this year!  We had five lab members of the lab present.  There were four posters presented by graduate students, Kelly Heilman and Bethany Blakely, undergrad Marissa Kivi, and Jason. Graduate student, Ann Raiho gave a talk.  This is a nice overview of the type of research the McLachlan lab is conducting to examine forest dynamics through time.  Details of their posters and talk can be found below. Click on each image for a larger view of the posters and presentation.

Ann gave her talk on Thursday, December 13, 2018. Ann’s research uses state data assimilation with the forest gap model LINKAGES to examine forest carbon. Ann’s goal was to determine what specific factors attribute the most to the uncertainty in the model output.  She found that initial conditions and process variance are key sources of uncertainty.

Kelly, Marissa, Jason, and Bethany at the AGU poster session on Monday, December 10, 2018

Marissa’s research uses data assimilation and the forest gap model LINKAGES to investigate the oak-maple dynamics at Harvard Forest.  Analyses from the model and parameter data indicate that canopy structure and light are the primary factors limiting growth in oak-maple forests. 

Bethany examines how the forest transition in composition over the 19th and 20th centuries has affected the albedo, surface temp and transpiration of Midwest forests and assesses how well ecosystem models capture these changes.

Kelly studies how the increases in CO2 and climate change influence water use efficiency and growth of trees as seen through tree rings and ecosystem models. 

Jason’s poster feature changes in Midwest vegetation. In the 1800s the vegetation was distributed in a multiple stable state of discrete open oak assemblages and closed mesic forests which was promoted by positive feedbacks. Over the past 150 years, vegetation has transitioned to an intermediate unimodally distributed state which is now perpetuated via negative feedbacks. 

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Congratulations to senior Marissa Kivi!

Click here for full view of Marissa’s FURF Poster

Marissa Kivi is an Applied and Computational Mathematics and Statistics senior. She joined the McLachlan lab as a freshman in the fall of 2015 and began by entering tree information from the 1800s for our PalEON project.  In the fall of 2017, Marissa took on more responsibility since then has been working in collaboration with Ann Raiho to develop an ensemble-based state data assimilation analysis at Harvard Forest via the LINKAGES forest-gap model. This data assimilation analysis be applied to other sites in the northeast in the upcoming months.  On October 25, Marissa presented a poster of her work at Notre Dame’s College of Science Fall Undergraduate Research Fair (FURF) and she will present her work this December at the American Geophysical Union (AGU) meeting in Washington, D.C.

In October, Marissa traveled to Boston and Harvard Forest to meet with PalEON collaborators to discuss her data-assimilation project.
L to R: Ann and Marissa at the top of the flux tower at Harvard Forest; forest fun; meeting up with Mike Dietze at Boston University; getting ready to present to collaborators at Harvard Forest.

In addition to the outstanding work Marissa has done with her research, she is also an amazing boxer participating in Notre Dame’s Baraka Bouts since her Freshman year.  This year Marissa was the President of Baraka Bouts, an athletics club that is committed to service and education and raising funds for the Holy Cross Missions in East Africa.

In her 4 years of participating in Baraka Bouts, Marissa “the Minnesota Monster” has only lost 1 match.  Marissa was once again the champ in the 2018 Finals round.

You can see Marissa’s match which starts at time 1:35 in the video. She is the competitor in Gold. We are proud of Marissa’s work in the lab and in the ring!



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Summer Undergrad Research

Next week is the start of a new semester at Notre Dame.  Before we start back up we want to highlight the outstanding work two undergrads did this summer. 

Aidan Draper and Luke Onken conducted research in the McLachlan lab this summer.  Aidan is rising senior Computer Science and Statistics student at Elon University and was supported through a DISC-REU Fellowship from Notre Dame.  Luke will be junior Biology student at Notre Dame and was supported by an ND College of Science Summer Research Fellowship.  Throughout the summer they worked on a vegetation mapping project for our Marsh project and a fire reconstruction modeling effort for PalEON. 

More details about each project can be found in the videos and posters below.

Marsh Work

Charcoal Work

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Welcome New Grad Student, Haley Kodak!

The McLachlan lab is thrilled to welcome Haley Kodak as the newest graduate student member!

Haley graduated from Armstrong State University of Savannah, Georgia with a Bachelor of Science in Biology. During undergrad she took part in plant genomics research in an REU at UC Berkeley where she studied plant development with Dr. Sarah Hake by experimenting with mutant forms of Maize in efforts to determine the genes responsible for certain aspects of development. Following this experience, she partook in ecological epigenetics research at Armstrong State University with Dr. Aaron Schrey where she investigated the variation in DNA methylation patterns in house sparrow populations. Haley joined the lab this June and has jumped right in on our NSF-funded project that examines the evolutionary dimensions of coastal marsh responses to environmental change.

Haley began a project that will investigate the phenotypic diversity of Schoenoplectus americanus in populations across the Chesapeake Bay at the Smithsonian Environmental Research Center (SERC). With the help of undergraduate Luke Onken and graduate student Megan Vahsen, she was able to collect over 100 plant samples from 10 different populations across 4 marshes at the SERC in Edgewater, MD. The populations varied in community composition, elevation, and location. The samples were shipped back to Notre Dame and were propagated in the greenhouse. 

Top Left: View of experimental CO2 and heat chambers at Kirkpatrick Marsh. Top Right: Haley and Luke surrounded by towering sedges. Bottom Left: Haley at Sellman Island. Bottom Right: Patch of Spartina within S. americanus populations at Kirkpatrick Marsh.

Of her first week in the field, Haley says, “It was a lot more physical work than I imagined, and of course we chose the hottest week to collect the plants. But I had such a great time visiting SERC and getting to see the Chesapeake Bay for the first time. It reminded me of the marshes back home in Savannah, GA. I was able to learn a lot on the trip and getting to see the beautiful marsh every morning and work up close with this sedge for the first time was itself a reward, despite having to stop from time to time ring sweat from our waders! I am already looking forward to the next visit and getting to walk among the tall sedges again.” 

Just this week Haley moved the plants to ND LEEF to start a common garden experiment where weekly measurements of height and width will be recorded throughout the remainder of the summer. Data on these measurements will be analyzed for differences in phenotypes that may be attributed to community type, elevation, and location. Haley is interested in whether these differences are detectable from plants collected across a relatively small spatial scale at SERC, and if elevation and community type are contributors to the variation in plant traits across SERC marshes.  

This project is supported through a fellowship from ND LEEF and from the NSF grant 1655702.

Top Left: S. americanus were propagated in the greenhouse before being transplanted to a common garden experiment at ND LEEF (Top Right and Bottom).

In conjuction with her ND LEEF fellowship Haley also got the opportunity to present her work to students from Bowman Creek Academy

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