Student News

Learning Excursion: Cary Institute Fundamentals of Ecosystem Ecology Course 2017 by Morgan E. Peach

Every winter, the Cary Institute of Ecosystem Studies in Millbrook, NY offers a two-week intensive course in the Fundamentals of Ecosystem Ecology, led by the knowledgeable, accomplished, and approachable scientists of the Institute. The EEES program supported my enrollment in the class, which was an enriching and stimulating experience.

The course, of a slightly modified structure year to year, provided comprehensive exposure to both the fundamentals and cutting edge of ecosystem science. Topics, to name only a few, ranged from primary production, to urban ecology, disease ecology, and the new paradigm of conservation science. Each class meeting featured a Cary scientist, a leader in their field, that led lecture as well as facilitated discussion of pertinent primary literature. The course culminated with student group presentations of an NSF-style proposal defense, which was a valuable opportunity to develop grant-writing skills alongside practice at team-building scientific collaboration.

Beyond the classroom, the course experience provided opportunities to develop relationships with classmates from around the world as well as with Cary scientists. This was a rewarding aspect of the class, consisting of many substantive discussions that furthered my PhD research. All Cary scientists made themselves abundantly available to meet with students, and provided useful guidance, helping students to shape a promising career trajectory in the broad arena of ecosystem ecology.


I’d recommend this immersive learning experience to any and all students with interest in ecosystem science! Thanks to EEES for making it possible!

Last week several of us in the EEES community were lucky enough to attend the 1st meeting for the Network for Arthropods of the Tundra (NeAT) at the Aarhus Institute for Advanced Studies in Denmark.  NeAT is an academic network of Arctic and Antarctic researchers studying terrestrial and aquatic arthropods. Over 50 scientists from 10 countries were present to share recent research about their favorite study organisms including soil microfauna, invasive midges, and wolf spiders. A highlight of the meeting was keynote speaker Jane Uhd Jepsen’s talk about outbreaking geometrid caterpillars which periodically defoliate entire birch forests in Northern Europe(!).

From our Dartmouth group, we heard an exciting preview of Christine Urbanowitz’s new thesis chapter about Arctic pollinator networks, and an overview of Jess Trout-Haney’s dissertation research on cyanotoxins that transfer through aquatic and terrestrial food webs. Additionally, second year graduate student Melissa DeSiervo and Lauren Culler (PhD, Lecturer of Environmental Studies) presented exciting new research about population dynamics of Arctic mosquitoes. Overall the meeting was a blast, and we made dozens of new friends that we look forward to collaborating with on future projects.  We even got to sing a very special Danish Happy Birthday song to Christine!

Over 50 scientists were present at the 1st Network for Arthropods of the Tundra (NeAT) meeting in Aarhus, Denmark
Christine Urbanowitz explains her research on Arctic pollinator networks.
EEES graduate students Jess Trout-Haney, Christine Urbanowitz, Melissa DeSiervo and post-doc/lecturer Lauren Culler presented research at the first NeAT meeting

From EEES Student Andy Vacca:


Every year the Cary Institute, an independent environmental research institute located in Millbrook, NY, hosts a course titled Fundamentals of Ecosystem Ecology (FEE).  This course allows a small group of students from around the world the opportunity to learn from and interact with leading experts in the field of ecosystem science.  In fact, a number of researchers at the institution have played pivotal roles in defining this discipline and pushing the boundaries of knowledge regarding ecosystem structure and function.  Cary Institute researchers have substantial expertise in the following fields: freshwater health, infectious disease ecology, urban ecology, invasion ecology, climate change and biogeochemistry.

The 2016 FEE course was loosely organized around four major topic areas: energetics, biogeochemistry, frontiers in ecosystem ecology and professional development seminars.  Subject matter experts held either lecture-based or discussion-based sessions followed by an in depth discussion of related primary literature led by students in the class.  Major topics included primary and secondary productivity, decomposition pathways, an overview of biogeochemistry, coupled elemental cycling and nutrient cycles with the carbon, nitrogen and phosphorus cycles each having their own lecture.  We also explored cutting-edge topics in conservation, human ecological systems, coupled human-natural systems and urban ecology with Cary scientists who are leading the way in these fields.

One aspect of the class that was particularly enjoyable was the professional development sessions.  One of the session was devoted to a mock NSF proposal review panel, led by a Cary scientist and former NSF program officer.  This provided invaluable insight into the proposal review process and allowed students to ask questions regarding review and the organization of funding.

I would strongly recommend this course to other students in EEES.  The class covers a wide range of topics and allows students to solidify their fundamental knowledge and move into high level discussion of each subject area.  The opportunity to interact with leading scientists in ecosystem ecology in both a learning and professional development context was invaluable professionally and personally.

From DeSilva Lab scholar Ellie McNutt:

I took the course Geometric Morphometrics in R hosted by Transmitting Science. GM is an analysis tool based in the programing language R, which allows the user to use 2D or 3D landmark data of an object to quantify shape differences between objects, for example the bones of different species. The course took place in Hostalets de Pierola, which is a small town outside of Barcelona. This course was both an enjoyable and beneficial experience. The course participants were diverse both in the geographic distribution of their home countries and the interests that they were hoping to apply geometric morphometrics (GM). The course is intense and immersive, with participants spending eight hours a day for 5 days learning various ways to apply geometric morphometrics to data. Topics included a basic introduction to R, how to import both 2D and 3D landmark data from multiple sources, how to use R itself to generate landmark data, and how to use multiple R packages to run different types of GM analysis (e.g., elliptical Fourier transform and generalized Procrustes analysis). Participants were encouraged to bring their own data sets, which allowed me to generate the backbone of the code needed for my own experiments while building on the expertise of the course instructor, Dr. Julien Claude.

GM will be a critical component of my dissertation allowing me to make, and statistically quantify, potentially novel differences between different species of primate calcanei. Learning GM in R was ideal for several reasons. First, R allows for much faster and easier handling of large sample sizes compared to other GM programs. Second, the versatility of the program’s coding lets users easily compare subsets of species and landmark data out of the total dataset, which makes it ideal for working with fragmentary fossils. Third, R is a free, open source software which is frequently updated, making it an ideal platform to learn new methodologies. Forth, this course presented an opportunity for me to improve my own understanding of and competence coding in R, which is an extremely useful statistical tool. A working knowledge of both R and GM are valuable skills that improve my CV and marketability when I begin to search for a job.

From the Calsbeek Lab's own Deb Goedert:

I received the EEES course award to attend the High Throughput Sequencing of Non-model Organisms course offered at Nord University in Bodo, Norway. High throughput sequencing (HTS) is any genomic sequencing method that generates a large number of sequenced base pairs, such as next or third generation DNA sequencing. These methods are the state of the art in evolutionary biology, allowing researchers to answer innumerable difficult questions in studies of genomics of adaptation. Due to many developments in the technology, these methods are becoming more financially accessible to researchers, so much that HTS is expected to substitute the more traditional methods for identification of SNPs and microsatellites. This is particularly relevant for non-model organisms, like the wood frogs, since the knowledge of their genome is much deficient. Therefore, understanding and developing the required skills for HTS techniques was a great and invaluable opportunity for my development as an evolutionary biologist.

The Nord University campus in Bodo has a strong research group in the area of genomics, focusing on both the development of new methods and in the use of these methods to test hypotheses in evolutionary biology. I had the opportunity to interact with amazing researchers, lab technicians, post-docs and grad students, developing a network and support group that were essential to get me up to speed during the course - since I was the only student not coming from a “DNA lab” - but that will also be of exceptional value when I need to work on my PhD data.

Over the course of 11 days (May 31st to June 10th, 2016), we had lectures, lab practical and bioinformatics sections. In the lectures, we covered the theoretical foundations of the methods, had invited talks about research using all the different methods we talked about, talks about the technology we were using in the lab section of the course (Ion Torrent sequencer and Illumina), and we were asked to give two presentations: the first being about our own projects, and the second about a paper using the methods we were interested in. During the lab section, we were able to sequence our own samples, preparing them to go into the sequencer ourselves, which included everything from DNA extraction, DNA quantification, fragment size analyses, library preparation (i.e. adding barcode and adapters to the DNA fragments for future identification of fragments), PCR, and fragment size selection. Once the sequencing was finished, we moved on to the bioinformatics practices. We were able to look at our own data set and learn basic tools for big data analyses, which allowed us to check the quality of our sequence, trim low quality reads as well as barcodes and adapters, etc. Finally, we were able to, at least partially, map our sequences. For the wood frog data I obtained, I was able to partially match some of the resultant sequences to mitochondrial DNA sequences of wood frogs published in BLAST, as well as a few important and highly conserved oncogenes from other species of frogs - not too bad for a frog without a reference genome!

DNA fragment distribution of wood frog obtained from the sample
DNA fragment distribution of wood frog obtained from the sample

Most importantly, difficulties that I will face during the analyses for my PhD project became evident during this course, and I was able to discuss possibilities of techniques that will most likely allow me to succeed considering specificities of my project and organism of study, as well as expected budget. This experience was, to me, one of the most incredible experiences I have had in a course, considering how much I was able to learn in such a short period of time: from a clueless field biologist with no experience in the area, to someone having a pretty decent idea of what I need to do for my project - what a journey! I cannot thank enough the organizers, invited speakers and lab technicians for how much effort and dedication they put into it. I am very thankful for the opportunity to participate in this course, due to the course award I received, and I hope other students can have an opportunity like that too.

HTS of non-model organisms 2016 course participants and faculty wait for the sequencer to run in big style.
HTS of non-model organisms 2016 course participants and faculty wait for the sequencer to run in big style.

Brought to you by PhD student Rebecca Finger:

As temperatures start to drop and the colors change, graduate students are returning from near and far field sites to fill EEES laboratories with samples and specimens. For me, the spring and summer brought me to western Greenland, along with fellow EEES graduate students Melissa DeSiervo, Christine Urbanowicz, and Jessica Trout-Haney, where I spent over 7 weeks tracking the progression of the short Arctic summer. I am particularly interested in modelling the phenology of plant systems and biogeochemical cycles to better understand potential changes occurring as the climate warms. Some of the questions I am asking include: How do soil characteristics relate to plant traits? As temperatures warm, are growing seasons lengthening promoting more plant production or are soils becoming drier and limiting plant growth? How is Greenland different than other parts of the Arctic?

Sitting at our campsite, I am launching 75 temperature loggers in order to track soil and ambient air temperatures as the Arctic transition from spring to summer (Photo credit: Melissa DeSiervo).
Sitting at our campsite, I am launching 75 temperature loggers in order to track soil and ambient air temperatures as the Arctic transition from spring to summer (Photo credit: Melissa DeSiervo).

Currently I am sifting through over 200 soil cores and thousands of shrub leaf samples that were collected from May-July in order to better understand plant-soil linkages in the tundra of Greenland. But before I can answer any questions, samples must be sieved, sorted, extracted, ground, and analyzed. It is going to take quite a long time, but luckily I have all fall and winter to transition a freezer full of samples into spreadsheets full of data. Perhaps that is just one of the hidden perks of being an ecologist; each season brings about its own tasks and challenges. Well that, and we sure do get to do a lot of cool science that matters in some truly special places.

Here I am installing temperature loggers and site markers for one of my study sites (Photo credit: Melissa DeSiervo).
Here I am installing temperature loggers and site markers for one of my study sites (Photo credit: Melissa DeSiervo).

After a record warm winter in New England, spring has arrived early and many EEES grad students are beginning local fieldwork. Here are just a few examples of local projects going on in Spring 2016.



Second year graduate student Debora Goedert collects wood frogs from a small pond in Mink Brook with a little help from field assistant Banjo the dog. Deb is an evolutionary biologist interested in variation in morphology and behavior between individuals and populations, and how traits may vary across life stages (pre and post metamorphosis). Deb brings these frogs back to the lab in the LSC to take measurements, photographs, and record their jumping performance.



Second year graduate student Andy Vacca and first year graduate student Animakshi Bhushan collect dragonfly larvae from a freshwater stream in nearby Lyme, NH. Again, Banjo the dog provides valuable field assistance! Andy is an environmental toxicologist, interested in how mercury, a trace metal contaminant, moves through aquatic and terrestrial foodwebs. He plans on rearing these dragonfly larvae in the lab and beginning some experimental trials with them this spring.



After a mostly snow-free winter, we welcome a little bit of winter weather in April! First year graduate student Ashley Lang examines an Ash tree near Concord, NH with damage from an invasive insect, the Emerald Ash Borer (EAB).  Ashley is interested in the ecosystem level consequences of insect pests on forest nutrient cycling and belowground microbial and invertebrate communities.

giraffegrass_smallBy Michael Butler Brown

The mathematical inequality statement is seemingly simple: (16 feet of giraffe) > (4 feet of grass).  Under this premise, it’s easy to imagine that locating groups of giraffe in the open grassy savannas might be a relatively straightforward task…but occasionally giraffe behaviour trumps rudimentary mathematical representations. It was mid-afternoon during  the second day of our seasonal giraffe surveys of Murchison Falls National Park and as we bounced along the dusty game track, we saw what appeared to be a lone giraffe standing in an area of open savanna. I pulled my Nikon Monarch binoculars to my eyes and as I glassed the apparently solo adult female, several other giraffes in repose gracefully lifted their heads above the swards to reveal a group of Rothschild’s giraffe in what – moments before- appeared to be a silent sea of grass.

The Rothschild’s giraffe (Giraffa camelopardalis rothschildi) is among the most endangered of the giraffe subspecies, with fewer than 2,000 individuals scattered across isolated populations in Kenya and Uganda. The largest population, found in Murchison Falls National Park in Uganda, has recently exhibited some very interesting trends. Following a period of civil unrest in the region that ended nearly two decades ago, the giraffe population in Murchison Falls National Park has grown remarkably and now contains roughly two-thirds of all known wild Rothschild’s giraffe. These population-level trends run contrary to the many of the other giraffe populations throughout Africa, which data suggest have declined dramatically over the same timeframe.

Dartmouth College, The Giraffe Conservation Foundation and the Uganda Wildlife Authority are working together to understand the factors that might contribute to these population dynamics. Like Grevy’s zebra, giraffe have unique coat patterns that almost act as a name tag and allow us to track unique individuals over space and time. With digital photographs and pattern recognition software, we can accurately assess survival and reproduction as well as map out changing spatial distribution over time. Combining these methods with other giraffe movement studies, we hope to better understand the complex relationships that giraffe have with this fascinating ecosystem, examining how changes in ecological interactions can influence individual giraffe behaviour and giraffe population dynamics. ​