Lodgepole pine linkage map reveals patterns of genomic clustering of locally adaptive loci

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dc.contributor.advisorYeaman, Samuel
dc.contributor.authorMcDonald, Tegan Krista
dc.contributor.committeememberRogers, Sean
dc.contributor.committeememberPossant, Jocelyn
dc.contributor.committeememberVamosi, Jana
dc.contributor.committeememberDe koning, Jason
dc.date2023-06
dc.date.accessioned2023-04-19T17:04:41Z
dc.date.available2023-04-19T17:04:41Z
dc.date.issued2023-03-17
dc.description.abstractAdaptation to heterogeneous local conditions is near ubiquitous throughout the tree of life. Climate adaption requires a complex system of trade-offs and multifaceted responses, and while the evolutionary theory is reasonably well developed and empirical evidence abundant, the genetic basis of local adaptation is poorly understood for complex traits outside of model organisms. Conifers demonstrate an immense capacity for local adaptation over a wide range of climatic and ecological conditions, and although they are ecologically and economically important, the size and complexities of conifer genomes have limited our ability to study the genetic basis of such adaptation as reference resources are scarce. Here, I have constructed a linkage map for lodgepole pine to examine the patterns of linkage disequilibrium and physical linkage amongst putative adaptive loci identified by Genotype-Environment Associations (GEAs) to 19 climate related variables. We find the high amounts of linkage disequilibrium (LD) observed amongst top-candidate genes are largely attributable to physical linkage, yet are generally distinct loci with some cases potentially indicative of neutral genetic hitchhikers. The context provided by the linkage map to signals of adaptation reveals an intriguing pattern of clustering of loci and reuse of genomic regions in response to distinct, but related, environment factors. These patterns suggest evolution of both clustered and diffuse architectures underlying climate adaptation in lodgepole pine.
dc.identifier.citationMcDonald, T. K. (2023). Lodgepole pine linkage map reveals patterns of genomic clustering of locally adaptive loci (Master's thesis, University of Calgary, Calgary, Canada). Retrieved from https://prism.ucalgary.ca.
dc.identifier.urihttps://prism.ucalgary.ca/handle/1880/116081
dc.identifier.urihttps://dx.doi.org/10.11575/PRISM/dspace/40927
dc.language.isoen
dc.publisher.facultyGraduate Studies
dc.publisher.institutionUniversity of Calgary
dc.rightsUniversity of Calgary graduate students retain copyright ownership and moral rights for their thesis. You may use this material in any way that is permitted by the Copyright Act or through licensing that has been assigned to the document. For uses that are not allowable under copyright legislation or licensing, you are required to seek permission.
dc.subjectEvolutionary Genetics
dc.subjectLocal Adaptation
dc.subjectForestry
dc.subjectLinkage Mapping
dc.subject.classificationGenetics
dc.subject.classificationBioinformatics
dc.titleLodgepole pine linkage map reveals patterns of genomic clustering of locally adaptive loci
dc.typemaster thesis
thesis.degree.disciplineBiological Sciences
thesis.degree.grantorUniversity of Calgary
thesis.degree.nameMaster of Science (MSc)
ucalgary.thesis.accesssetbystudentI do not require a thesis withhold – my thesis will have open access and can be viewed and downloaded publicly as soon as possible.
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