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Genomics of Dendroctonus ponderosae (Coleoptera: Curculionidae) in Alberta

  • Author / Creator
    Trevoy, Stephen Andrew Lane
  • Rapid advances in sequencing technologies and analysis methods have greatly increased our understanding of genomic architecture in non-model organisms. The mountain pine beetle (MPB; Dendroctonus ponderosae) is a non-model organism that has received intensive genomic study and is of great economic interest in western Canada. I apply next-generation sequencing (NGS) technologies to create a library of single nucleotide polymorphism (SNP) markers, and use the markers to address basic questions concerning population structure in MPB. Then, using the same dataset, I amend standard filtering and analysis techniques for population genomics data to ask questions about genomic architecture and functional genetics. By combined use of linkage network and principal components analysis (PCA), I find new SNP markers for determining sex, and describe a novel method for finding putative islands of genomic divergence that I apply to the major Canadian populations of MPB. Finally, I validate the chromosomal contiguity of these islands of genomic divergence by generating two linkage maps for male- and female-associate sets of MPB SNPs, which I developed using a colony of lab-bred F2 sibling crosses. Both linkage analysis and the viability of experimental crosses suggest the existence of incipient speciation between populations of MPB within their Canadian range. The results described here also contribute to a reassessment of the value of cohorts of loci in tight linkage disequilibrium that have previously been viewed as unusable for population genomics studies.

  • Subjects / Keywords
  • Graduation date
    Spring 2019
  • Type of Item
    Thesis
  • Degree
    Master of Science
  • DOI
    https://doi.org/10.7939/r3-qkdv-fw33
  • License
    Permission is hereby granted to the University of Alberta Libraries to reproduce single copies of this thesis and to lend or sell such copies for private, scholarly or scientific research purposes only. Where the thesis is converted to, or otherwise made available in digital form, the University of Alberta will advise potential users of the thesis of these terms. The author reserves all other publication and other rights in association with the copyright in the thesis and, except as herein before provided, neither the thesis nor any substantial portion thereof may be printed or otherwise reproduced in any material form whatsoever without the author's prior written permission.