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Grad student blog

By Madi Gamble

The University of Washington hosts short courses on a range of subjects each year through its Summer Institutes program. The course I attended, “Mixed Models for Quantitative Genetics,” is part of the Summer Institute for Statistics and Genetics. The course was two and a half days long and covered a staggering amount of material in that time. The course was taught by Bruce Walsh (University of Arizona), one of the authors of a classic textbook on quantitative genetics, and Guilherme Rosa (University of Wisconsin), who specializes in the biostatistics behind plant and animal breeding.

We began with a review of vectors and matrices and how to use them to store multi-dimensional information. We then reviewed matrix algebra, discussed eigenvalues and eigenvectors as characteristics of matrix geometry and dimensionality, how to express systems of equations in matrix form, and then on to general linear models, generalized linear models, and finally the uses of fixed and random effects in linear mixed models.

Throughout, the course was fast paced but welcoming of questions and discussion. I really appreciated that the instructors encouraged us to ask questions and never expressed surprise or disappointment at more basic questions (that said, one instructor did refer to the second edition of his book as “the new testament” – whether he was referring to its length or its perceived impact on the world was unclear).

While I learned a lot about the mathematics behind linear models, I wish that we had spent less time on the math and more on the applications of those models. For example, I would have liked more concrete examples relative to biology when discussing the use of certain models, and more practice using the models to analyze data with tangible variables.

Perhaps the best part of the course was the people I met, who I will certainly remain in touch with as I use mixed effect models in my research. The participants in the course ranged from mathematicians, to statisticians, to biologists working with humans, livestock, crops, and other plants and animals. The diverse perspectives of the students in the course helped to make the material more accessible to everyone. I would highly recommend this course and others that are part of the Summer Institutes at UW to other students!

Did you know New Hampshire has no native earthworms? 

After glaciers receded from this part of the country at the beginning of the Holocene, the land was scoured and effectively soil-free. This habitat was unwelcoming to soil-dwelling earthworms, which cannot migrate far without human intervention. . .

Enter explorers! After Europeans arrived in North America, earthworms hitching a ride on their ships were able to colonize New England. These days, earthworms are still moving around New Hampshire with the help of humans--as fishing bait, in soil on the wheels of logging equipment, and more.

So how does the introduction of earthworms into forests across New Hampshire affect soil properties? This is the question our students in Ecology lab here at Dartmouth are going to investigate! But before we set them loose, we decided to see for ourselves just how many earthworms live at the local forest across from the Dartmouth Organic Farm...  

It takes a team to successfully search for worms

Sure enough, we found a fair few! We identified at least five species.

Worms in our collection bucket after they were counted and identified

Nightcrawlers are great for catching fish...and teaching assistants!

Our trip was a roaring success--worms galore, beautiful fall weather, and great enthusiasm for introducing our Ecology students to this interesting study system!

Posted by Ashley

This June, Fiona and I got the chance to travel to Colorado State University and learn about all aspects of soil ecology from the awesome researchers in the CSU Natural Resource Ecology Lab in Fort Collins, CO. We were excited to learn all about the different dimensions of soil ecology that might be important to our research, but that we don’t usually think much about.

Using a hammer corer to collect surface soil from a montane pine forest impacted by wildfire and mountain pine beetle

We learned about techniques for sampling soil and felt a little bit jealous of the lack of rocks in the forest and grassland soils of Colorado.

We also learned about the various invertebrates that live in soil, their functions, and how to quantify their abundance in space and time.

Ashley with former lab-mate Melanie Taylor investigating the soil invertebrates of a grassland soil sample

We noticed dramatic differences in the soil from Colorado compared to New England, and we’re feeling quite proud of our beautiful soil horizons in the northeast!

A soil profile from a shortgrass steppe in Colorado


We also had some time to travel around the region, and we stopped for a bit to camp in beautiful Wyoming.

At the end of the trip, we rounded off the Colorado experience with a quick hike up to Emmaline Lake near the CSU Mountain Campus. We saw some beautiful landscapes and looked a little closer and the plant and fungal communities we were hiking past.

Emmaline Lake, a glacial lake near the border of Rocky Mountain National Park
A lovely waterfall on the way up to the lake
Cirque Meadow on the way back down from the lake (after the morning fog had cleared).

We had such a great time in Colorado, and now that we’re back home, it’s time to apply our new knowledge to our research questions!


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.