CRI Genomics

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.

Larissa Roehl, MSc, Laboratory Manager

After completing a BSc at Brandon University, Larissa’s interest in marine life led her to Saint John to pursue a second BSc in Marine Biology at UNBSJ. She joined the Pavey Lab to complete her MSc, spearheading the lab’s research in environmental DNA (eDNA). Larissa was the first at UNBSJ to use eDNA to detect an endangered aquatic species, wood turtle, and continues to aid in assay development and project management as the Pavey Lab Genomics Manager.

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.

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.

Jagger Watters-Gray, PhD 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 National 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. 

Silas Jones, MSc Candidate

Jake Reicker, MSc Candidate

Jake was first introduced to the Pavey Lab in 2021 as a laboratory technician, after completing his Bachelor of Science in Biology and Environmental Science (co-op option) at Acadia University. His honours thesis, supervised by Dr. Allison Walker, focused on identifying lignicolous marine fungi, specifically those with biodegradation potential, from Bay of Fundy intertidal mudflats.

Now an MSc student in the Pavey Lab, Jake is working closely with the Mactaquac Aquatic Ecosystem Study (MAES) to determine the movement/distribution of several key species – Atlantic salmon (Salmo salar), American shad (Alosa sapidissima), Alewife and Blueback herring (Alosa pseudoharengus and Alosa aestivalis, respectively; collectively known as River herring), Largemouth bass (Micropterus salmoides), and American eel (Anguilla rostrata) – upstream of the Mactaquac Generating Station (MGS). The facility is relied on for a large portion of New Brunswick’s energy consumption, but current passage options for anadromous species have proven ineffective. Jake will be using environmental DNA (eDNA) sampling methods to inform MAES and the MGS on upstream habitat distribution and how it relates to existing fish passage questions.

Laken Devost, MSc Candidate

Marijune Lina Tiamzon , MSc Candidate

Josh Bacon-Qaunaq, Intern

Suroush Bastani, Lab Technician

Alumni

Gregory N. Puncher, PhD, Post-Doctoral Fellow 

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

Faith Penny, PhD

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.

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

Melissa K. Morrison, MSc

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.

Co-supervised by Drs. Scott Pavey and Anaïs Lacoursière-Roussel (Fisheries and Oceans Canada), Melissa’s master’s research explored the complex relationships among eDNA and environmental conditions measure juvenile Atlantic Salmon population abundance using shed eDNA in Fundy National Park, New Brunswick.  She is continuing her research on the optimal eDNA detection period for key coastal Species At Risk and Aquatic Invasive Species along the eastern coast of Canada.

Rina Guxholli, MSc

Cody Bourque, BSc Honours

Josee-Lea Bastarache, BSc Honours

Nadine Nzirorera, BSc Honours

Alyson Hasson, BSc Honours

Jillian Fraser, BSc Honours

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.