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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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

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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).

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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


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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

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McLachlan Lab Takes Home 2nd Best Title Again!

Every year the McLachlan, Medvigy, and Rocha labs take on the Archie lab (+ friends) in bowling.  For the 6th straight year in a row, we are the 2nd best bowlers around!

We once again will display the DNA helix with pride until next year’s battle!

2018 2nd Best Bowling Champs

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Evolution Facilitates Colonization of Invasive Species – New Paper

New paper co-authored by Megan Vahsen from her master’s work has just come out in PNAS!

Szucs et al. 2017. Rapid adaptive evolution in novel environments acts as an architect of population range expansion. PNAS. 


Colonization and expansion into novel landscapes determine the distribution and abundance of species in our rapidly changing ecosystems worldwide. Colonization events are crucibles for rapid evolution, but it is not known whether evolutionary changes arise
mainly after successful colonization has occurred, or if evolution plays an immediate role, governing the growth and expansion speed of colonizing populations. There is evidence that spatial evolutionary processes can speed range expansion within a few generations because dispersal tendencies may evolve upwards at range edges. Additionally, rapid adaptation to a novel environment can increase population growth rates, which also promotes spread. However, the role of adaptive evolution and the relative contributions of spatial evolution and adaptation to expansion are unclear. Using a model system, red flour beetles (Tribolium castaneum), we either allowed or constrained evolution of populations colonizing a novel environment and measured population growth and spread. At the end of the experiment we assessed the fitness and dispersal tendency of individuals originating either from the core or edge of evolving populations or from nonevolving populations in a common garden. Within six generations, evolving populations grew three times larger and spread 46% faster than populations in which evolution was constrained. Increased size and expansion speed were strongly driven by adaptation, whereas spatial evolutionary processes acting on edge subpopulations contributed less. This experimental evidence demonstrates that rapid evolution drives both population growth and expansion speed and is thus crucial to consider for managing biological invasions and successfully introducing or reintroducing species for management and conservation.


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Field Trip to Maryland Marshes

Post by Erin Nguyen

The McLachlan team recently headed out into the field for some late season sampling. Jason, Megan, and two undergrads, Aleah and Erin, went to the Smithsonian Environmental Research Center (SERC) in Maryland to work with Pat Megonigal, Matt Kirwin and Nikki Brazzola.  The group’s goal was to obtain live samples of Schoenoplectus americanus as well as sediment cores. These efforts were the latest chapter of the lab’s ongoing project to study S. americanus’s changing genetic landscape in the Chesapeake Bay through space and time.

On the team’s first day out in the marshes, Jason and company took a boat to reach a number of promising sites. With an expanse of blue sky above and golden grasses and sedges below, it was a stunning morning for sampling.

Under the heat of a blazing sun, the team collected a staggering 12 sediment cores to be later sieved through in hopes of obtaining ancient scirpus seeds that can be germinated and compared to their modern descendants.

The day was long and the work was hard but the journey and people were fantastic! To top off a productive and exciting field trip, the team caught one last stunning sight before heading home to ND.

The McLachlan lab is happy to be back in the Bend, and working on exciting, new developments with the marsh project!


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New McLachlan Lab Publication! Genetic diversity in Eastern North America following Ice Age

Lumibao, C.Y., S.M. Hoban and J.S. McLachlan. 2017 Ice ages leave genetic diversity ‘hotspots’ in Europe but not in Eastern North America. Ecology Letters. doi:10.1111/ele.12853

In this paper the McLachlan lab studied the spatial pattern of genetic diversity of trees following glaciation  in Eastern North America compared to that of Europe.  While in Europe southern populations are more genetically diverse compared to northern populations, this is not the case in Eastern North America.

As noted in the paper: A common expectation in phylogeographic studies is that low latitude populations are reservoirs of genetic endemism due to long-term population isolation, and high latitude populations are genetically reduced due to post-glacial species migration (Taberlet et al. 1998). This expectation is largely based on European data, but has been assumed to be generally true across temperate forests (e.g. Roberts & Hamann 2015; Zinck & Rajora 2016). However, we did not find evidence that endemism across taxa was concentrated in southern latitudes in Eastern North America and we did not find reduced genetic diversity in northern latitudes in Eastern North America. (See figure 2 for example).

These findings have implications for genetic diversity in forests as they respond to future climate change.  Based on previous work conducted in Europe, there was concern that in Eastern North America the southern reservoirs of genetic diversity were at risk and that northern populations may lack the genetic diversity needed to withstand new environmental challenges. However, our results indicate that temperate trees in Eastern North America may not be as vulnerable to the genetic impacts of climate change  as European taxa.


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Welcome Back Students!

The undergrads who work in our lab are awesome!  Currently we have 10 students working on a diverse range of projects this semester.  There are students sieving and germinating seeds from cores taken from a marsh in Maryland. These seeds will help us assess how the sedge Schoenoplectus americanus, has evolved over the past 100 years in response to changes in CO2, temperature, salinity and flooding regimes.  We have students entering Public Land Survey data from the 1800s to help us recreate the composition, density, and biomass of historical forests of Indiana and Illinois.  Other students are working on a different tree project that involves counting tree rings from 100-200 year old trees in oak savannas compared to those in woodlands to examine the trees’ response to climate change through time.  This project also involves cutting up the tree rings to run isotope analyses to asses the water use efficiency of the trees throughout the trees’ lives and in the different conditions.  Finally, we have a student working on a project that will use the ecosystem model Linkages within the PEcAn tool to improve predictions of tree growth.

Our undergrads work hard, but they also have lots of fun and they make the lab fun!

Look at this huge old tree undergrads Emily Miller, Alec Helmke and Erin Nguyen found while taking the summer course at Notre Dame’s field station, UNDERC!
All 3 students have entered an extensive amount of historical Public Land Survey tree data for the lab. Even when students aren’t in the lab, they can’t get away from thinking about old trees.

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