Very nice article on using environmental DNA (eDNA) to study invasive species just came out in The Scientist. They feature our work just published in Diversity and Distributions on using eDNA to track the invasive freshwater diatom Didymo (aka, rock snot) in Maryland and Pennsylvania streams.
Didymosphenia geminata in West Branch Pine Creek, PA. Photo credit: Matt Shank
Lots of good news to report from an active spring 2017 semester. Some highlights:
We inaugurated the first of what we hope to be many annual lab ski trips this winter! A beautiful sunny day and snow in abundance as we gathered at Trapp Family Lodge, near Stowe. For many, it was their first time on skis...
After getting geared up, we skied about 4km mostly uphill up to the Cabin, where we stopped for a picnic lunch, and a snowball fight. The trip back down was fast and exciting, and full of bumps and turns. We then went to nurse our wounds at the Bluestone in Waterbury afterwards. Soooo fun -- see you next year!
We had a great (but busy!) Fall 2016 semester. Here are some updates on what's been happening:
OK, so it's been a little while since our last blog post. We've been busy! A lot has happened in the interim, so here are some of the highlights:
At the end of July, Karl, Phil, and Steve traveled to the Agroforestry Development Centre at Indian Head, Saskatchewan to phenotype the second balsam poplar common garden experiment. The ADC is operated by Agriculture and Agri-Food Canada (AAFC), and our colleague there Raju Soolanayakanahally has been a key collaborator on our poplar research. We were joined there by Andy Gougherty, a PhD student from Matt Fitzpatrick's lab at UMCES who is working on spatial modeling for the poplar project, as well as Garth Inouye from the ADC, who has been overseeing much of the garden phenology data collection and general maintenance.
What followed was a week of hard work -- early mornings to capture the best window for gas exchange measurements, followed by late afternoons in the lab processing leaves for imaging, SLA, isotopes, and stomatal densities. We got it all done, in no small way thanks to Garth's keen knowledge of the garden and the plot layout. We also squeezed in some grilling time in the parking lot of our lodging, and enjoyed some great sunsets behind the iconic Indian Head grain elevators. After the phenotyping was complete, Karl headed to Idaho for some fossil hunting, while Phil, Andy, and Steve took a side trip to Grasslands National Park. It was a nice way to toast the successful completion of our phenotyping push for summer 2015!
Brittany Verrico has joined the lab this summer as a new graduate student! Brittany has already hit the ground running, and has been getting her feet wet working on phenotyping in the poplar common garden, as well as pairing up with Madie to collect tissue samples for DNA analysis from poplar across northern New England and red spruce from the elevation transects in the Green Mountains. We're excited to have her here -- welcome, Brittany!
Karl and Vikram returned from the recent New Phytologist Forest Tree Genomics Symposium, and Karl has summarized his experience in this blog post. Enjoy!
Vikram and I just returned from the 35th New Phytologist symposium on the genomes of forest trees held at Arnold Arboretum of Harvard University. It was an amazing experience for me as a young scientist and first year graduate student. The people were great, the talks revealed the complexity of tree genomics, the facilities at the Arboretum were fantastic, and the living collections of the Arboretum were truly inspiring. The stories we learned about the collections from Peter del Tredici put into context the thousands of untold stories of genome evolution waiting to be discovered.
I was fortunate enough to receive funding from the New Phytologist Trust and the University of Vermont to attend the meeting and to present the work of my Lab. The meeting was my first introduction to the tree genomics community. Hearing talks from Carl Douglas (“Microevolution in Populus trichocarpa driven by introgression.”), Nathalie Isabel (“Journey into the genome of white spruce: achievements, lessons and challenges for the future.”), Steve DiFazio (“Comparative and ecological genomics in the Salicaceae.”), Ian MacLachlan (“The effects of selective breeding on adaptive phenotypic traits in the interior spruce (Picea engelmannii x P. glauca) of western Canada.”) allowed me to put my work on local adaptation to climate in Populus balsamifera into context. As a first year working on a very collaborative project, I’ve had my nose to the ground (or computer screen really) searching for a path through the suckers to find a view point where I can really understand what I’m doing, why I’m doing it, and what the limitations of my tools and viewpoint (i.e. experimental design) are.
From the volume of questions Carl and I received about population structure influencing the outcomes of association tests, I have a new appreciation for the importance of understanding one’s tools, and asking questions that eliminate potential confounding variables, even if your tools should account for spurious effects in the data. In other words, simplify. One comment I received over and over was to subset my data so that non-random allele frequencies differences due to demography are negligible and environmental differences between populations are clear. Said differently, take a small view of your question in order to get a clear view. Thanks to all of those who visited my poster (e.g. Richard Buggs) and commented after my talk for that bit of clarity!
The talks about association genetics, genome evolution, paleobotany, and cell wall synthesis demonstrated the broad and interconnected nature of tree genomic inquiry. It was really amazing to see connections between experimental tree physiology, association genetics and paleobotany! I want to stress the contribution that paleobotany and morphology/anatomy provide to put our findings into a physical, polarized context.
Tree genomics presents complex challenges (even more complex than what I thought going in!) and many of these challenges are not quite within our reach to solve. Verifying candidate genes identified in association genetics was a problem that many raised, but few offered easy solutions to.
In all, the conference gave me a great introduction to the tree genomics community. It was a great event and very well organized. Can’t wait to implement some of the knowledge I gained from the conference in my own work!
Here is a list of the papers that were referenced during talks and caught my eye.
This past week was spent working hard in our VT poplar common garden. We've been phenotyping for a suite of ecophysiological traits to understand quantitative genetic variation in how trees have adapted to different climates, and how this translates into a difference in performance when genotypes are transferred to a novel climate. All of this data will feed into our database to be merged with our GBS SNP genotypes for genome-wide association mapping.
For now though, we are happy to celebrate the finishing of phenotyping in the VT garden, and enjoy each other's good company at Steve's house for a lab BBQ. The desserts were particularly delicious and restorative. We'll need it, as we head to Indian Head to phenotype garden #2 in the weeks ahead!
High elevation forests have been key places to study the effects of environmental change. In a new project funded by a USDA-HATCH grant, we are studying the landscape genomics of red spruce across an elevation gradient in the Green Mountains to understand genetic variability for cold hardiness and tolerance to winter injury, and how this is affected by gene flow between low and high elevation stands. This work builds upon a long-term dataset of forest community monitoring on Camel's Hump mountain, which has shown a retreat of the spruce-fir ecosystem upslope to higher elevations (Beckage et al. 2008). Early this June, we were out at Camel's Hump with Tim Perkins and crew re-sampling forest tree composition along an elevational transect in plots first established by Thomas Siccama 50 years ago! Enjoy the pics...