Browsing by Author "LeBlanc, Nathalie M."

Now showing 1 - 2 of 2
  • Thumbnail Image
    Item
    Developing genomic resources using striped bass (Morone saxatilis): genetic structure, associations, and text-mining
    (University of New Brunswick, 2021) LeBlanc, Nathalie M.; Pavey, Scott
    The advent of next-generation sequencing technologies has revolutionized the field of molecular ecology, facilitating increasingly fine-scale detection of genetic differences among populations and adaptationally significant mutations. In this thesis, I use genomics to advance solve longstanding mysteries of Striped Bass genetics and lay the groundwork for future studies. In the first chapter, I characterize a group of Striped Bass that were thought to be extirpated in the Saint John River, but likely survive as a remnant population. In the second chapter, I investigate connectivity and relatedness of Striped Bass populations more widely across their native range on the North American Atlantic Coast. I found that Gulf of St. Lawrence, Shubenacadie River, and Saint John River populations were all very distinct from each other and from US populations. US Striped Bass, however, could be separated into three major regions: Hudson River-Kennebec River, Chesapeake Bay-Delaware River, and Roanoke River-Cape Fear River. Demonstrating that this work is useful for management, my SNP loci were able to assign 99% of Striped Bass to these six regions, the first time Roanoke River Striped Bass have been reliably distinguished from Chesapeake Bay bass. Additionally, the presence of apparent US-origin Striped Bass on the northeastern coast of Nova Scotia raises important questions about movement patterns of Striped Bass in this area and highlights the importance of further study. In the third chapter, I used computer modelling simulations to assess the performance of four recent techniques used to find associations between phenotypes and genotypes. I found that Random Forest algorithm with population correction performed similarly to a recent, complex model implemented in confounder adjusted multiple testing. Finally, in chapter four I created 9 novel tools and used them to create an automated text-mining pipeline that can scan full-text articles and extract sentences that contain associations between genes and ecological variables. This pipeline is the first step toward improving genome annotations of non-model organisms such as Striped Bass. Together, these four chapters lay important groundwork for future genomic research both for Striped Bass and other ecologically important species.
  • Thumbnail Image
    Item
    Genomic population structure of Striped Bass (Morone saxatilis) from the Gulf of St. Lawrence to Cape Fear River
    (Wiley Open Access, 2020-07-14) LeBlanc, Nathalie M.; Gahagan, Benjamin I.; Andrews, Samuel N.; Avery, Trevor S.; Puncher, Gregory N.; Reading, Benjamin J.; Buhariwalla, Colin F.; Curry, R. Allen; Whiteley, Andrew R.; Pavey, Scott A.
    Striped Bass, Morone saxatilis (Walbaum, 1792), is an anadromous fish species that supports fisheries throughout North America and is native to the North American Atlantic Coast. Due to long coastal migrations that span multiple jurisdictions, a detailed understanding of population genomics is required to untangle demographic patterns, understand local adaptation, and characterize population movements. This study used 1,256 single nucleotide polymorphism (SNP) loci to investigate genetic structure of 477 Striped Bass sampled from 15 locations spanning the North American Atlantic coast from the Gulf of St. Lawrence, Canada, to the Cape Fear River, United States. We found striking differences in neutral divergence among Canadian sites, which were isolated from each other and US populations, compared with US populations that were much less isolated. Our SNP dataset was able to assign 99% of Striped Bass back to six reporting groups, a 39% improvement over previous genetic markers. Using this method, we found (a) evidence of admixture within Saint John River, indicating that migrants from the United States and from Shubenacadie River occasionally spawn in the Saint John River; (b) Striped Bass collected in the Mira River, Cape Breton, Canada, were found to be of both Miramichi River and US origin; (c) juveniles in the newly restored Kennebec River population had small and nonsignificant differences from the Hudson River; and (d) tributaries within the Chesapeake Bay showed a mixture of homogeny and small differences among each other. This study introduces new hypotheses about the dynamic zoogeography of Striped Bass at its northern range and has important implications for the local and international management of this species.