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

McDonald, Tegan Krista

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

dc.contributor.advisor	Yeaman, Samuel
dc.contributor.author	McDonald, Tegan Krista
dc.contributor.committeemember	Rogers, Sean
dc.contributor.committeemember	Possant, Jocelyn
dc.contributor.committeemember	Vamosi, Jana
dc.contributor.committeemember	De koning, Jason
dc.date	2023-06
dc.date.accessioned	2023-04-19T17:04:41Z
dc.date.available	2023-04-19T17:04:41Z
dc.date.issued	2023-03-17
dc.description.abstract	Adaptation 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.citation	McDonald, 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.uri	https://prism.ucalgary.ca/handle/1880/116081
dc.identifier.uri	https://dx.doi.org/10.11575/PRISM/dspace/40927
dc.language.iso	en
dc.publisher.faculty	Graduate Studies
dc.publisher.institution	University of Calgary
dc.rights	University 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.subject	Evolutionary Genetics
dc.subject	Local Adaptation
dc.subject	Forestry
dc.subject	Linkage Mapping
dc.subject.classification	Genetics
dc.subject.classification	Bioinformatics
dc.title	Lodgepole pine linkage map reveals patterns of genomic clustering of locally adaptive loci
dc.type	master thesis
thesis.degree.discipline	Biological Sciences
thesis.degree.grantor	University of Calgary
thesis.degree.name	Master of Science (MSc)
ucalgary.thesis.accesssetbystudent	I do not require a thesis withhold – my thesis will have open access and can be viewed and downloaded publicly as soon as possible.