The Mission

The CRI Genomics leverages state-of- the-art genomics techniques to address basic and applied questions in conservation, fisheries management, evolution and ecology. This research is used to conserve biodiversity, make aquaculture more sustainable and improve management of fisheries.

The Team

 

Scott A. Pavey, PhD, Canada Research Chair

Born in The United States of America, Scott has devoted years of hard work to stand where he is today.  Intrigued with science at a young age, Scott attended Colorado State University, CO, USA, where he received a BSc in Wildlife Biology. After acquiring his diploma, Scott attended University of Alaska Anchorage, AK, USA, to obtain a MSc in Biological Sciences. Hoping to continue his education, Scott went to Simon Fraser University in Burnaby, BC, Canada to earn his PhD in Biological Sciences. Fresh out of his studies, Scott traveled to Québec, Canada where he became a Postdoctoral Fellow at Université Laval. Today, Scott works at the University of New Brunswick, Saint John, NB, Canada as a Research Chair and an Associate Professor.

Scott is broadly interested in ecology, evolution, and conservation. More specifically, he uses high-resolution genomic tools to understand how populations of fishes are connected, uses environmental DNA to identify and quantify abundance of species, understand the physiology of local adaptation, and determine the ecological role of genetic elements. Scott is the head of CRI Genomics, a state-of-the-art research lab at the Canadian Rivers Institute, University of New Brunswick Saint John.

Papers that Scott has published or co-wrote can be found here.

 

Nathalie M. LeBlanc, PhD, Post-Doctoral Fellow 

Fascinated by genetics from a young age, Nathalie began her research career as an undergrad at Acadia University in the picturesque Annapolis Valley, Nova Scotia, where she graduated with a second major in Computer Science and an honours in Biology, studying population genetics of Purple Sandpipers. She then stayed at Acadia to continue the research she had begun as an honours student and graduated with a Masters degree in Biology in 2015. Nathalie originally came to UNB in 2016 as a PhD student studying population structure of Striped Bass and text-mining possibilities in ecological genomics.

As a Post-Doctoral Fellow, Nathalie will be taking a look at the thousands of SNPs she found during her PhD work and carefully selecting a small subset of the most highly informative. She will use these to optimize a fast and efficient method of identifying the source population of Striped Bass that winter across the eastern coast of North America, called GT-Seq. With this protocol, she will be able to genotype thousands of Striped Bass sent in by researchers and managers of Striped Bass across North America. Using a combination of genetic data and acoustic telemetry, Striped Bass researchers hope to fine-tune their understanding of Striped Bass movements throughout the year, and track them as those movements change in response to climate change.

The papers that Nathalie has published or co-wrote can be found here.

 

Faith Penny, PhD Candidate

Faith began in the Pavey lab after completing her MSc at UNB with Dr. James Kieffer, during which she studied the physiology of shortnose sturgeon. She previously worked as the lab’s technician, creating lab operating procedures, setting up equipment and helping out where needed. For her doctoral studies, she will be exploring the evolution and molecular ecology of genes facilitating euryhalinity and temperature in striped bass though various field and laboratory studies. Her project will include collection of wild juvenile striped bass from various local and international populations of varying temperatures and salinities. These fish will be used to quantify changes and interactions of gene expression, physiology and whole-animal biology.

The papers that Faith wrote or co-wrote can be found here.

 

Shawn Kroetsch, PhD Candidate

Shawn joined the Pavey Lab after completing his BSc in General Biology at UNBSJ. He then completed his MSc in Biology at UNBSJ under the co-supervision of Drs. Scott Pavey and Karen Kidd, in which he studied how taxonomy, diet, and several ecological factors impact the composition and diversity of the aquatic invertebrate gut microbiota. Shawn’s doctoral studies will build upon this previous work; he will be further exploring the impacts of diet on aquatic invertebrate gut microbiota and will be evaluating the impacts of an additional abiotic factor – salinity. His project will involve the collection and dissection of aquatic invertebrates from various locations along the Saint John River. These invertebrates will be used not only in assessing the composition and diversity of the gut microbiota, but also in studying the gene expression of these complex bacterial communities using metatranscriptomic analyses.

The papers that Shawn wrote or co-wrote can be found here.

 

Melissa Morrison, MSc Candidate

Melissa received her BSc in Biochemistry and Molecular Biology at the University of Northern British Columbia, completing her Honours research on lodgepole pine population genetics following mountain pine beetle devastation. Melissa’s interest in molecular ecology guided the continuation of her studies into the budding field of environmental DNA (eDNA) as a non-invasive monitoring method. Her current research will evaluate the complex relationships among eDNA and environmental conditions to assess how well eDNA can predict Atlantic Salmon population abundance in Fundy National Park, New Brunswick.

 

Silas Jones, MSc Candidate

 

Jagger Watters-Gray, MSc Candidate

Jagger’s research interests include aquatic molecular ecology and conservation, which led him to join the CRI Genomics Lab as a laboratory technician and honours student studying the genetic population structure of Brown Trout and Rainbow Trout in New Brunswick. For his doctoral studies and as part of a project known as GEN-FISH, he will be focusing on developing and validating environmental DNA (eDNA) tools for monitoring the occurrence and distribution of several Canadian freshwater fishes. Additionally, Jagger will be characterizing the use of environmental microsatellite DNA for population abundance monitoring of Atlantic Salmon based on eDNA samples. 

 

Rina Guxholli, MSc Candidate

Rina began in the Pavey lab after completing her Bachelor of Science in Biology at the University of Windsor with Dr. Trevor Pitcher, studying abiotic factors affecting environmental DNA detection using Redside dace. 
 
Her MSc project is focused on developing species-specific environmental DNA (eDNA) quantitative PCR assays for New Brunswick’s freshwater fish. Using the mitochondrial Cytochrome B gene as a marker, assays will be developed to detect species found in New Brunswick’s freshwater ecosystems. This research is being done in partnership with GEN-FISH, a national project focused on monitoring and conserving Canada’s freshwater fishes. The development of specific eDNA assays will be applied on a Canada wide scale after their development in New Brunswick. The development of these eDNA assays will help industries, government agencies and educational institutions to more accurately and efficiently monitor occurrence and distribution of Canadian freshwater fishes that are of environmental, economic and cultural importance.

 

Larissa Roehl, MSc, Laboratory Manager

 

 

 

Jake Reicker, BSc (Hons), Genomics Technician

Jake joined the Pavey Lab this year after earning his BSc in biology and environmental science from Acadia University in 2019. Supervised by Dr. Allison Walker, he studied the biodegradation capabilities of some marine fungi and worked to characterize their abundance in the Bay of Fundy intertidal mudflats. Jake’s interest in the rapidly growing field of environmental DNA (eDNA) research led him to take a genomics technician position in the Pavey Lab in order to gain valuable experience in molecular biology, and he plans to begin pursuing his MSc in this or a similar field of biological research in the near future.

Alumni

Gregory Neils Puncher, PhD – Post-Doctoral Fellow – Marine Biology

Originally from Ontario, Greg developed a deep curiousity in the marine environment and a passion for conservation at an early age. He attended the University of Guelph and received an Honours degree in Marine and Freshwater Biology. Greg was fortunate to receive Erasmus mundus funding for graduate studies in Europe where he completed a master’s degree in Marine Biodiversity and Conservation (EMBC) at the Universities of the Algarve (Portugal) and Oviedo (Spain) and a doctoral degree in Marine Ecosystem Health and Conservation at the Universities of Bologna (Italy) and Ghent (Belgium).

Greg’s research focuses on the development of genetic tools for the improvement of fisheries management and the analysis of adaptive responses to the many challenges of the Anthropocene. He argues that the future of life on earth is dependent on the health of the world’s oceans and fish populations are an integral part of that system. The multi-disciplinary research inherent to fisheries science allows Greg the opportunity to explore many of his interests, including ecology, economics, sociology, politics and anthropology. Currently, his research subjects are the Atlantic cod, striped bass and Atlantic Bluefin tuna.

The papers that Greg has published or co-wrote can be found here

 

Howard Huynh, PhD, Post-Doctoral Fellow

 

Bethany Reinhart, MSc

Bethany’s research interests center around anthropogenic impacts in aquatic ecosystems. Particularly, her focus is on the accumulation of metals in biota in marine, freshwater and estuarine environments. Past research involved measuring trace metals in sandshrimp from a potentially contaminated sewage site as well as reference sites.

 

Ty Gormley, MSc

Project: Comparing genetic variation among Atlantic Cod (Gadus morhua) off Newfoundland and Labrador following the stock collapse

Cody Bourque, BSc Honours

Josee-Lea Bastarache, BSc Honours

Nadine Nzirorera, BSc Honours

Alyson Hasson, BSc Honours

The Lab

CRI Genomics is equipped to perform the DNA isolation and Next Generation Sequencing (NGS) library preparation (both pre-sequencing activities), as well as bioinformatics (post-sequencing step). The types of current projects in the lab include: genotype-by-sequencing (GBS) to determine the genetic basis of study phenotypes; identification of unique adaptations in local fish species; sequencing barcode regions to identify species for microbiomes or insect community identification, environmental DNA (uses small tissues and cells suspended in the water to identify species in a lake or river), and finally, targeted resequencing of candidate genes of many individuals simultaneously. Feature pieces of equipment include a dedicated server with 2 TB of RAM, pipetting robot, automated cassette size selection, several means to asses DNA quantity and quality, and a sonicator.

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