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.”  

Posted in Climate Change, Field Work, Lab Updates, Marsh | Comments Off on Science Conversations and Site Review with NSF Program Director

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!

Posted in Uncategorized | Comments Off on Jason McLachlan in the New York Times

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. 

Posted in Uncategorized | Comments Off on McLachlan Lab at AGU 2018!

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!



Posted in Uncategorized | Comments Off on Congratulations to senior Marissa Kivi!

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

Posted in Lab Updates, Marsh, PalEON | Comments Off on Summer Undergrad Research

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

Posted in Climate Change, Field Work, Lab Updates, Marsh | Comments Off on Welcome New Grad Student, Haley Kodak!

10th World Dendro Conference Re-cap

Post by Ann Raiho, Kelly Heilman, and Andria Dawson. This post is cross-listed on the PalEON website.

The 10th World Dendro Conference was held in Bhutan this summer! A Dendro Fieldweek was held the week prior to the conference where individuals learned about dendrochronology and reconstructing climate from tree rings, forest ecology and forest dynamics.  PalEON had 4 participants including two grad students from the McLachlan lab.  Below are the impressions and experiences from McLachlan members, Ann Raiho and Kelly Heilman and PalEONista, Andria Dawson.

Ann’s Impressions
Bhutan was an excellent destination for World Dendro for many reasons, mainly the country’s unique perspective on forest conservation. Bhutan is the only country in the world that could be considered carbon neutral or even carbon negative because of the amount of forest that the country preserves. Over 70% of Bhutan is forested and will remain so for the foreseeable future. The fourth king set in place a mandate that the country should always remain 70% forests. So many trees! Furthermore, Ed Cook and Paul Krusic have been working in Bhutan for over 25 years and have helped the Bhutanese establish a proliferate tree ring lab that has been in operation since 2001.

Bhutan is known as the Land of the Thunder Dragon. The Bhutan flag (right) shows an image of Druk, the Thunder Dragon

I attended the Dendro Fieldweek. Around 30 international and 20 Bhutanese students traveled 14 hours by bus to Bhumthang, Bhutan where there is a field station located next to the first queen’s palace.

Views from the Bus

The field week consisted of field work, tree ring analysis, and presentations of findings. There were groups working on dendroecology, dendrohydrology, and blue light intensity measurements. The dendroecology group was led by PalEONista, Neil Pederson!

Mounting and Measuring Tree Cores

Tree Cookies

We explored the relationship between fir and hemlock along an elevational gradient and found that fir growth may be more sensitive to increasing temperature. At the end of the week, everyone presented in their groups, my group’s presentation was about dendroecology and how you can incorporate disturbance history and biomass estimates to tell a story about the forest’s development.  I snuck some LINKAGES (forest gap model) runs in to show how ecosystem models can be used in conjunction with tree ring data to learn about limiting resources over successional time scales.  Our final night at the field station was spent dancing around a bonfire in traditional Bhutanese fashion (pinky’s locked together to form a circle) and singing karaoke.

Exploring the Forests of Bhutan

Kelly’s Impressions
A traditional Marchang ceremony opened the conference and kicked off a fun dendro-filled week.
The first section of talks discussed fusing both forest inventory analyses and dendrochronology methods and included awesome talks from two of our own PalEON members (Ann and Andria Dawson). Throughout the week, I learned about researchers around the world using dendrochronology to reconstruct volcanic events, to explore past human-environment interactions, and to better understand the impacts of earthquakes of forest disturbances. My favorite section was the encouragingly large dendroecology section (I’m biased), which discussed quantifying forest disturbances, the impacts of management and land-use on tree growth, and ultimately exploring how ecological variation might affect growth-climate relationships. I gave a talk in this section titled “Anthropogenic changes impact drought sensitivity across a savanna-forest biome boundary,” which highlighted results showing that both stand structure changes and increases in CO2boundary can impact drought sensitivity at the savanna-forest boundary.

To wrap up the conference, Soumaya Belmecheri gave a stellar Florence Hawley Diversity Lecture that blended both her research reconciling the differences observed between tree ring data and Eddy Flux data and an eloquent call for supporting greater diversity in dendrochronology. In between our packed conference schedule and before leaving Bhutan, we squeezed in some culture and exploration. My favorites were the traditional dancing at the conference banquet, venturing up to the massive Buddha, trekking up to Taktsang Buddhist monastery (aka “Tiger’s Nest”) with Andria, and eating all the spicy ema datshi and momos possible!

Some short hikes brought us to amazing views! Left: views from the large Buddha temple in Thimphu. Middle: Buddha Dordenma statue. Right: A large prayer wheel on the way up to Taktsang monastery near Paro. Look closely at the prayer wheel and you’ll see one of the friendly dogs that accompanied us on our hikes and always found the best napping places!

Hiking to Taktsang Monastery (Tiger’s Nest) with Andria. Taktsang monastery is located on a cliffside around 10,000 ft elevation. We enjoyed the pine forests, prayer flags, and views of the valley on the way up!

Andria’s Impressions
Bhutan has undergone a wave of modernization over the last 40 years. They are now at a point in time where they have the infrastructure to conduct and disseminate scientific research. Ed and Paul have been working in collaboration with Bhutanese colleagues for some time; however, there is still a lot to learn about the forests of Bhutan (and how they fit into our global perspective of the biosphere). Our Bhutanese colleagues at the conferences continued to emphasize their commitment to collaboration with international colleagues.

I want to thank the people of the Kingdom of Bhutan for welcoming us. Their generosity and profound appreciation for the environment and all living things has had a profound impact on my perspective of life and humanity. Bhutan, you are far away (from North America) but never forgotten.

Left: PalEON Pals, Middle: Traditional Dancers at the Closing Banquet. We all joined later!, Right: A Good Reminder To Go Home With

Posted in Lab Updates, PalEON, Tree Rings | Comments Off on 10th World Dendro Conference Re-cap

Intraspecific S. americanus Variation & Diversity Summer Experiment

Post by McLachlan lab undergraduate, Brady Stiller

During these first two weeks of the summer, I joined Megan Vahsen (PhD student in the McLachlan lab) in the scenic marshes of the Chesapeake Bay to help set up an experiment that she has been planning these past few months. After much time the past semester acquiring sediment cores from various locations in these marshes, and sieving and germinating seeds of the marsh sedge, Schoenoplectus americanus, from this sediment, we seek to understand the role of intraspecific variation and diversity in predicting S. americanus productivity. Much as interspecific (i.e. between species) variation can explain the productivity of communities, intraspecific variation within the species S. americanus may influence its productivity at the population-level. The presence of many diverse genotypes of S. americanus sieved from a single layer of a sediment core suggests that this intraspecific diversity may confer an ecological advantage to S. americanus. An example of this advantage would be resource partitioning, in which different S. americanus genotypes occupy particular niches (e.g. genotype C might have deeper roots than B), allowing for more efficient resource acquisition by the species. Further, changes in genetic structure over time (i.e. from ancestral to modern populations) could reflect adaptive evolution in response to a changing climate.

Jason (left) and Brady (right) showing perseverance in transporting and assembling experimental plots in field conditions.

To better understand these mechanisms, we selected seven ancestral genotypes (from deep in the sediment core) and seven modern genotypes (near the top of the sediment core) to grow in either homogeneous (monoculture) or diverse (polyculture) plots, with replicates of each of the following categories:

  1. Monocultures: for each genotype, 4 plants of the same genotype were grown in the same pot
  2. Ancestral polycultures: 4 plants of different ancestral genotypes
  3. Modern polycultures: 4 plants of different modern genotypes
  4. Ancestral-modern polycultures: 2 plants of different ancestral genotype and 2 plants of different modern genotypes

The plants were grown in peat contained in 60cm-long PVC pots, which were suspended in 4 wooden frames in the water, allowing for the plants to experience natural tidal fluctuations. Over the course of the summer growing season, stem counts and heights will be measured to track productivity. After termination of the experiment, aboveground and belowground biomass will be obtained from weighing stems, and roots and rhizomes, respectively.

Experimental populations of Schoenoplectus americanus in PVC pots. Each population is composed of four plants from one genotype, or a variety of genotypes which were germinated and cloned in the Notre Dame greenhouse.

Given the possible advantages of intraspecific diversity, we predict that polycultures will show greater productivity than monocultures. Additionally, given the change in environmental conditions over the past several decades, modern genotypes may show greater productivity if the species has strongly evolved to adapt to current conditions.

These past two weeks have constituted my first authentic fieldwork experience, and the realizations I have come to were expected but perhaps not to the degree I thought. The plan seemed simple: we are going to suspend some wooden frames in the water, put some peat in PVC pipes, drop these into the frames, and plant some plants… what could go wrong? It took only a few hours out in the marsh to realize that hauling over 96 PVC pipes, 40-lb bags of peat, and heavy wooden frames would take hours. 

An unusually high tide results in the team rethinking how to best secure PVC pots in frames.

Once delivering all these materials down a long boardwalk, we immediately had to address key questions, involving everything from physics to common sense, which would determine the success or disaster of our experiment: “How high in the water will the frame sit?” and “do PVC pots float?” The former of these questions was answered fairly easily through collaboration with scientists at the Smithsonian Environmental Research Center facility, the latter by a heart-breaking observation one morning that many of our pots, which we had spent hours filling with peat, were floating upside-down in the water. Thankfully, we didn’t lose any pots which we had needed, and the experiment is currently underway.

This account of the fieldwork would not be complete without sharing our experience with nature. Although a rainy first week made the set-up a little wet and quite muddy, the sunny week ahead allowed us to appreciate the serene paradise of the marshes, which was only interrupted by the occasional deer fly attack, rat snake swimming between our experiment, or giant carp splashing for a reason still unknown to me.

Overall, even though the experiment might have looked different from what I had originally imagined, our flexibility and perseverance allowed us to set up an exciting experiment which we hope will yield notable results at the end of the summer.

A snake sharing the experimental workspace (left). Excited to be completely finished with the experimental set-up in late May (right).

Posted in Climate Change, Field Work, Lab Updates, Marsh | Comments Off on Intraspecific S. americanus Variation & Diversity Summer Experiment

Undergraduate Research: S. americanus flowers, fertilization and crosses

Post by Mairead Willis, Senior Neuroscience and Behavior Major; Mairead was out of town during the poster session. She describes her work this past year here.

This year I got the chance to follow in the footsteps of Gregor Mendel. The McLachlan lab is working on a series of experiments with Schoenoplectus americanus. and wanted to know if it was possible to cross different individuals, or for them to fertilize themselves. Armed with Google, a greenhouse, a paper that a fellow student found (thanks, Erin!), and lots of help from everyone who works in the lab, I set out on a nine-month journey to make some baby plants.


Figure 1. S. americanus flower

The first thing I had to do was watch the flowers. I learned that the stigmata emerge before the anthers. I also learned that if the stigmata aren’t pollinated, the spikelet will sometimes extend to give the flower another shot at reproduction; the photo above shows a flower doing just that. Armed with that knowledge, I sheathed each new flower with a pollen bag, tied the bottom with string, and used a paintbrush to apply pollen from some flowers to the stigma of others. Then, I waited.

Figure 2. S. americanus seeds (see brown disks at the base of the flower)

In the first week of December, just before I was supposed to go home for winter break, eureka (was that a proper use of eureka?)! Fully formed seeds began to drop from the flowers I had pollinated, as well as some I hadn’t. The brown disks at the base of the flower in Figure 2 above are seeds. I left for break, thrilled and wondering how, exactly, one would germinate S. americanus seeds.

When I returned for the spring semester, I tried out one scientific method, one home-gardening technique, and one method proposed by grad student Megan to put the seeds in a state of mock dormancy for six weeks. At last, just before spring break, I was able to plant my seeds with help from Brady, who taught me how to set up a germination trial.

Figure 3. Germination! The white arrow points to the tiny green germinated plant.

When I returned from break, I couldn’t believe my eyes! You can’t really see them in Figure 3 above, but inside my germination pots were the cutest, sweetest little seedlings I ever did see. Do I anthropomorphize them? Absolutely.

Figure 4. Grown-up plant

Today was my last day in the lab, and I transferred the plants, still tiny, to grown-up pots in the greenhouse (Figure 4). This has been by far one of the most exciting and rewarding projects I’ve gotten to work on during my time in college, and I can’t thank Jason and Jody enough for letting me do it. To whoever has this job after me: Have fun and treat those plants right.


All my best,

Mairéad Willis

Class of 2018


Posted in Uncategorized | Comments Off on Undergraduate Research: S. americanus flowers, fertilization and crosses

Undergraduate Research: 2018 COS-JAM Posters

Today was the College of Science – Joint Annual Meeting (COS-JAM).  Undergrads across Notre Dame came together to share the results of their research projects from the past year with the rest of the University.

This year we had 3 students who presented posters:

Clare Buntrock, Sophomore Biology Major

The Effects of Increasing Atmospheric CO2 Levels on Tree Growth and Carbon Isotope Uptake


Erin Nguyen, Senior Biology Major

(Update 5-9-18: Erin was one of six students to win a best poster presentation prize)

Through time and space: mapping Schoenoplectus americanus population change in the salt marshes of the Chesapeake Bay


Aleah Appling, Junior Environmental Science Major

Inquiry-Based Laboratory Course: Current Status and Future Improvement

Posted in Climate Change, Lab Updates, Marsh, Tree Rings | Comments Off on Undergraduate Research: 2018 COS-JAM Posters