Four hundred million lines of text: that’s how much data is in a single gene-sequencing file when Scott Pavey’s team receives it. If you wanted to scan it manually, and generously assume it would take one second per line to look at, it would take you 12 and a half years of reading around the clock to get through it all.
Fortunately, Dr. Pavey is backed up by $1 million in infrastructure, making his lab at the University of New Brunswick the most sophisticated of its kind in the province.
The Canadian Rivers Institute genomics lab at UNB’s Saint John campus is dedicated to advancing the relatively new science of ecogenomics. Ecogenomics is, broadly speaking, the science of harvesting DNA from individuals or the environment and using it to better understand its inhabitants.
As people across the globe recognize World Oceans Day on June 8 and citizens in this country mark Canadian Rivers Day on June 11, we take a look inside the lab and the cutting-edge science happening there thanks to Dr. Pavey and his team.
DNA analysis has been used for decades, but individual projects were fairly limited in scope due to technological limitations. Modern computing and sequencing technology has changed the scale completely.
“Until about 2008, you could only look at a handful of genes at a time, 10 or 20,” says Dr. Pavey, a science director with the Canadian Rivers Institute who is based at UNB’s Saint John campus. “Starting in 2008, you could suddenly look at thousands, or tens of thousands, simultaneously. Not only could you talk about the broad patterns of how populations are connected, you could also make statements about what genes are adaptive in those populations.”
One of the areas in which Dr. Pavey is applying this new tech is the cod fishery. The research – undertaken in collaboration with Dr. Gregory Puncher, a UNB postdoctoral scholar at the genomics lab, and Memorial University researcher Dr. Sherrylynn Rowe – comes as cod stocks today are at historically low levels. In order to manage them correctly, we need to understand them better.
“We have samples from the three major spawning grounds in the northern cod stock that famously crashed,” says Dr. Pavey, who holds a Canada Research Chair in Aquatic Molecular Ecology and Ecological Genomics at UNB. “If there are genetic differences among those three groups, then you want to manage them as three separate units. But if there are no genetic differences and they’re all mixing around, then you want to manage them as one single unit.”
The innovative research methods being forged by Dr. Pavey are helping to the inform the management of economically important commercial fisheries of Atlantic cod, striped bass, Atlantic bluefin tuna and American eel – all listed as varying levels of concern in the Canadian Species at Risk Act. Dr. Pavey and his team are working closely with Fisheries and Oceans Canada to ensure that species’ critical genetic considerations are incorporated into the development of species recovery plans.
Another important application of ecogenomics is species identification in aquatic systems. In the Atlantic, thousands of species are shedding cells into the water along with uncountable single-celled organisms. A given sample can contain DNA from any number of species. And depending on where you look in the sequence, much of the genetic code is identical even among distantly related species.
Dr. Pavey and his team are able to use something called DNA barcoding to sort through this noise and figure out whose DNA is whose. Using a database of DNA sequences known to be unique to particular species, they can check found DNA against known types and quickly identify samples.
“The scientific methods we previously used to understand the ecological world were very time intensive and do not scale up easily,” says Dr. Pavey. “As researchers, we can sample 10 lakes for fish species in a summer with a field crew or we can sample 400 lakes for a water sample, analyze its environmental DNA and know their entire species composition.”
Dr. Pavey’s research is also leading the way in developing a next generation of scientists with unique and specialized skills. His students, research associates and technician are encouraged to learn computer programming in order to work with the large raw data files. He is increasingly supervising students in joint biology and computer science academic programs. This interdisciplinary research, along with the chance to work and train in an advanced ecology-based genomics laboratory, entices students to his research.
Maintaining the health of ocean ecosystems is about more than saving a particular industry, or even a particular species. Dr. Pavey points out that we tend to forget how much raw economic value our environment provides.
“Humans get trillions of dollars of free ecosystem services that pollinate crops, provide nutrients to soils, provide clean water,” he says. “Being able to monitor biodiversity quickly and on a large scale protects the services that humans need to survive on this planet.”
Photo: Dr. Scott Pavey, right, works with Larissa Roehl at his lab on the UNB Saint John campus. Dr. Pavey, science director for the Canadian Rivers Institute, runs the $1 million genomics lab, which performs large-scale genetic analyses. (Rob Blanchard/UNB Photo)
Media contact: Colin Hodd