Ecogenomics: answering complex questions of ecosystem composition for fisheries’ conservation
This week we acknolwedge International DNA and Genome Day (April 25th), first celebrated in 2003 by the National Human Genome Research Institute in the United States, to mark the 50th anniversary of the first journal publications on the double helix structure of DNA. It is a world-wide celebration to provide an opportunity to learn about the latest advances in genomic research and explore how those advances might impact society.
Today, the study of ecogenomics has evolved tremendously, providing an advanced scientific method that builds on fields ecology and evolution. Dr. Scott Pavey, one of the Canadian Rivers Institute’s (CRI) newest Science Directors, based at the University of New Brunswick Saint John (UNBSJ) is an emerging leader in the innovative field. He uses ‘big data’ supercomputers to scan entire genomes from individual animals and fish as well as environmental samples (water and soil). This allows him to investigate at high resolution both the species present in aquatic ecosystems as well as how populations are connected and locally adapted to their environments.
Dr. Scott Pavey in the CRI Genomics laboratory. The laboratory, based at the University of New Brunswick Saint John, is equipped with $1-M of the most modern wet-lab analytical infrastructure and supercomputers.
Canada has one-fifth of the worlds’ freshwater, and there still remain many complex questions about freshwater ecosystems. “The scientific methods we previously used to understand the ecological world are often very time intensive and do not easily scale-up to the enormous need,” says Dr. Pavey.
“As researchers, we can sample 10 lakes for fish species in a summer with a field crew, and we can sample 400 lakes for a water sample, analyze its environmental DNA and know their entire species composition,” he explains.
While ecogenomic methods can help answer more complex questions in a shorter period of time, it also allows scientists to draw conclusions about specific genes in species of interest and their relation to their environments. By analyzing DNA, Dr. Pavey is able to determine the exact gene that is responsible for a specific phenotypic adaptation that may be critical to a population’s survival.
Through his research on American Eel, in collaboration with Dr. Louis Bernatchez at Laval University, he was able to identify what genes were responsible for their survival in freshwater versus saltwater environments. Through the genetic analysis of the all-female eels in the Upper St. Lawrence River, he concluded that they have adaptive genetic traits that are unique to that rearing group as compared to groups in brackish or saltwater.
Knowing that a sub-population has unique genetic traits that enable them to adapt to their local environmental conditions gives decision makers important information that can inform changes or new regulations and policies to protect their habitats or migration routes.
“Now we know that the Upper St. Lawrence population is unique, it is even more critical for this population’s survival that we pass those maturing adult eels around dams so that they can go to the Sargasso Sea to spawn,” says Dr. Pavey.
These innovative research methods being forged by Dr. Pavey are helping to advise the management 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.
Since joining the CRI in 2015, Dr. Pavey has built strong research partnerships. In collaboration with CRI Science Director, Dr. Karen Kidd (UNBSJ), he is exploring new areas of discovery, such as describing the microbiome of aquatic insects that has never been done before. He also has an Atlantic Cod genomics project which is a collaboration with Dr. Sherrylynn Rowe at the Fisheries and Marine Institute of Memorial University of Newfoundland, and CRI Associate and Postdoctoral Fellow, Dr. Gregory Puncher (UNBSJ).
Dr. Pavey (top; photo credit: Greg Puncher) and his team of students and research associates (bottom; photo credit: Scott Pavey) conducting genetic analysis using state-of-the-art technologies in the CRI Genomics laboratory.
He does this technologically innovative work in the CRI Genomics Laboratory based at UNBSJ– the most advanced ecological genomics facility in New Brunswick. The laboratory has $1-M of the most modern infrastructure, both in wet-lab analytical equipment and supercomputers.
Because much of the research field combines biological methods and supercomputer programming, Dr. Pavey’s research is also leading the way in developing a next generation of scientists with unique and specialized skills. His 7 graduate and honours students, 2 research associates, and 1 technician are encouraged to learn computer-programming languages 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.
“Genomics is a rapidly growing field and with even more potential but there’s currently a shortage of people with those skills. My students learn a lot of modern skills that are in high demand and I think they’re really attracted to that,” says Dr. Pavey.
The ability to solve problems and answer questions of big proportion that only genetic analysis can answer is also enticing to academic, industry and government collaborators. Dr. Pavey and his team at CRI Genomics are the only regional researchers and facilities offering these customized services. They are currently working with the NB Museum, the Huntsman Marine Science Centre, Memorial University, Fisheries and Oceans Canada, University of Massachusetts and NovaEel, an aquaculture startup company in NS.