Skip to content

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.